Viruses

2024

Jump to: 2023, 2022, 2021

10 pages, 221 KiB

Open AccessEditorial

Editorial for SARS-CoV-2 and COVID-19 Topical Collection

by Luis Martinez-Sobrido and Fernando Almazán

Viruses 2024, 16(3), 356; https://doi.org/10.3390/v16030356 - 25 Feb 2024

Viewed by 1199

Abstract

A previously unknown coronavirus, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), was isolated in Wuhan, China in December 2019, from a patient with a respiratory disease linked to potential contact with wild animals [...] Full article

20 pages, 2311 KiB

Open AccessReview

Evolution of the SARS-CoV-2 Omicron Variants: Genetic Impact on Viral Fitness

by Wenhao Liu, Zehong Huang, Jin Xiao, Yangtao Wu, Ningshao Xia and Quan Yuan

Viruses 2024, 16(2), 184; https://doi.org/10.3390/v16020184 - 25 Jan 2024

Cited by 9 | Viewed by 3531

Abstract

Over the last three years, the pandemic of COVID-19 has had a significant impact on people’s lives and the global economy. The incessant emergence of variant strains has compounded the challenges associated with the management of COVID-19. As the predominant variant from late [...] Read more.

Over the last three years, the pandemic of COVID-19 has had a significant impact on people’s lives and the global economy. The incessant emergence of variant strains has compounded the challenges associated with the management of COVID-19. As the predominant variant from late 2021 to the present, Omicron and its sublineages, through continuous evolution, have demonstrated iterative viral fitness. The comprehensive elucidation of the biological implications that catalyzed this evolution remains incomplete. In accordance with extant research evidence, we provide a comprehensive review of subvariants of Omicron, delineating alterations in immune evasion, cellular infectivity, and the cross-species transmission potential. This review seeks to clarify the underpinnings of biology within the evolution of SARS-CoV-2, thereby providing a foundation for strategic considerations in the post-pandemic era of COVID-19. Full article

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19 pages, 2173 KiB

Open AccessArticle

Incidence and Severity of COVID-19 in Relation to Anti-Receptor-Binding Domain IgG Antibody Level after COVID-19 Vaccination in Kidney Transplant Recipients

by A. Lianne Messchendorp, Jan-Stephan F. Sanders, Alferso C. Abrahams, Frederike J. Bemelman, Pim Bouwmans, René M. A. van den Dorpel, Luuk B. Hilbrands, Céline Imhof, Marlies E. J. Reinders, Theo Rispens, Maurice Steenhuis, Marc A. G. J. ten Dam, Priya Vart, Aiko P. J. de Vries, Marc H. Hemmelder, Ron T. Gansevoort and RECOVAC Investigators

Viruses 2024, 16(1), 114; https://doi.org/10.3390/v16010114 - 12 Jan 2024

Cited by 1 | Viewed by 1533

Abstract

Kidney transplant recipients (KTRs) elicit an impaired immune response after COVID-19 vaccination; however, the exact clinical impact remains unclear. We therefore analyse the relationship between antibody levels after vaccination and the risk of COVID-19 in a large cohort of KTRs. All KTRs living [...] Read more.

Kidney transplant recipients (KTRs) elicit an impaired immune response after COVID-19 vaccination; however, the exact clinical impact remains unclear. We therefore analyse the relationship between antibody levels after vaccination and the risk of COVID-19 in a large cohort of KTRs. All KTRs living in the Netherlands were invited to send a blood sample 28 days after their second COVID-19 vaccination for measurement of their IgG antibodies against the receptor-binding domain of the SARS-CoV-2 spike protein (anti-RBD IgG). Information on COVID-19 was collected from the moment the blood sample was obtained until 6 months thereafter. Multivariable Cox and logistic regression analyses were performed to analyse which factors affected the occurrence and severity (i.e., hospitalization and/or death) of COVID-19. In total, 12,159 KTRs were approached, of whom 2885 were included in the analyses. Among those, 1578 (54.7%) became seropositive (i.e., anti-RBD IgG level >50 BAU/mL). Seropositivity was associated with a lower risk for COVID-19, also after adjusting for multiple confounders, including socio-economic status and adherence to COVID-19 restrictions (HR 0.37 (0.19–0.47), p = 0.005). When studied on a continuous scale, we observed a log-linear relationship between antibody level and the risk for COVID-19 (HR 0.52 (0.31–0.89), p = 0.02). Similar results were found for COVID-19 severity. In conclusion, antibody level after COVID-19 vaccination is associated in a log-linear manner with the occurrence and severity of COVID-19 in KTRs. This implies that if future vaccinations are indicated, the aim should be to reach for as high an antibody level as possible and not only seropositivity to protect this vulnerable patient group from disease. Full article

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13 pages, 698 KiB

Open AccessArticle

Performance Analysis of Serodiagnostic Tests to Characterize the Incline and Decline of the Individual Humoral Immune Response in COVID-19 Patients: Impact on Diagnostic Management

by Ronald von Possel, Babett Menge, Christina Deschermeier, Carlos Fritzsche, Christoph Hemmer, Hilte Geerdes-Fenge, Micha Loebermann, Anette Schulz, Erik Lattwein, Katja Steinhagen, Ralf Tönnies, Reiner Ahrendt and Petra Emmerich

Viruses 2024, 16(1), 91; https://doi.org/10.3390/v16010091 - 6 Jan 2024

Cited by 2 | Viewed by 1476

Abstract

Serodiagnostic tests for antibody detection to estimate the immunoprotective status regarding SARS-CoV-2 support diagnostic management. This study aimed to investigate the performance of serological assays for COVID-19 and elaborate on test-specific characteristics. Sequential samples (n = 636) of four panels (acute COVID-19, [...] Read more.

Serodiagnostic tests for antibody detection to estimate the immunoprotective status regarding SARS-CoV-2 support diagnostic management. This study aimed to investigate the performance of serological assays for COVID-19 and elaborate on test-specific characteristics. Sequential samples (n = 636) of four panels (acute COVID-19, convalescent COVID-19 (partly vaccinated post-infection), pre-pandemic, and cross-reactive) were tested for IgG by indirect immunofluorescence test (IIFT) and EUROIMMUN EUROLINE Anti-SARS-CoV-2 Profile (IgG). Neutralizing antibodies were determined by a virus neutralization test (VNT) and two surrogate neutralization tests (sVNT, GenScript cPass, and EUROIMMUN SARS-CoV-2 NeutraLISA). Analysis of the acute and convalescent panels revealed high positive (78.3% and 91.6%) and negative (91.6%) agreement between IIFT and Profile IgG. The sVNTs revealed differences in their positive (cPass: 89.4% and 97.0%, NeutraLISA: 71.5% and 72.1%) and negative agreement with VNT (cPass: 92.3% and 50.0%, NeutraLISA: 95.1% and 92.5%) at a diagnostic specificity of 100% for all tests. The cPass showed higher inhibition rates than NeutraLISA at VNT titers below 1:640. Cross-reactivities were only found by cPass (57.1%). Serodiagnostic tests, which showed substantial agreement and fast runtime, could provide alternatives for cell-based assays. The findings of this study suggest that careful interpretation of serodiagnostic results obtained at different times after SARS-CoV-2 antigen exposure is crucial to support decision-making in diagnostic management. Full article

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2023

Jump to: 2024, 2022, 2021

12 pages, 4361 KiB

Open AccessArticle

Differential Outcomes of Infection by Wild-Type SARS-CoV-2 and the B.1.617.2 and B.1.1.529 Variants of Concern in K18-hACE2 Transgenic Mice

by Yicheng He, Jill Henley, Philip Sell and Lucio Comai

Viruses 2024, 16(1), 60; https://doi.org/10.3390/v16010060 - 29 Dec 2023

Viewed by 1388

Abstract

Background: SARS-CoV-2 is a respiratory virus with neurological complications including the loss of smell and taste, headache, and confusion that can persist for months or longer. Severe neuronal cell damage has also been reported in some cases. The objective of this study was [...] Read more.

Background: SARS-CoV-2 is a respiratory virus with neurological complications including the loss of smell and taste, headache, and confusion that can persist for months or longer. Severe neuronal cell damage has also been reported in some cases. The objective of this study was to compare the infectivity of the wild-type virus, Delta (B.1.617.2) and Omicron (B.1.1.529) variants in transgenic mice that express the human angiotensin-converting enzyme 2 (hACE2) receptor under the control of the keratin 18 promoter (K18) and characterize the progression of infection and inflammatory response in the lungs, brain, medulla oblongata, and olfactory bulbs of these animals. We hypothesized that wild type, Delta and Omicron differentially infect K18-hACE2 mice, thereby inducing distinct cellular responses. Methods: K18-hACE2 female mice were intranasally infected with wild-type, Delta, or Omicron variants and euthanized either at 3 days post-infection (dpi) or at the humane endpoint. None of the animals infected with the Omicron variant reached the humane endpoint and were euthanized at day 8 dpi. Virological and immunological analyses were performed in the lungs, brains, medulla oblongata and olfactory bulbs isolated from infected mice. Results: At 3 dpi, mice infected with wild type and Delta displayed significantly higher levels of viral RNA in the lungs than mice infected with Omicron, while in the brain, Delta and Omicron resulted in higher levels of viral RNA than with the wild type. Viral RNA was also detected in the medulla oblongata of mice infected by all these virus strains. At this time point, the mice infected with wild type and Delta displayed a marked upregulation of many inflammatory markers in the lungs. On the other hand, the upregulation of inflammatory markers was observed only in the brains of mice infected with Delta and Omicron. At the humane endpoint, we observed a significant increase in the levels of viral RNA in the lungs and brains of mice infected with wild type and Delta, which was accompanied by the elevated expression of many inflammatory markers. In contrast, mice which survived infection with the Omicron variant showed high levels of viral RNA and the upregulation of cytokine and chemokine expression only in the lungs at 8 dpi, suggesting that infection and inflammatory response by this variant is attenuated in the brain. Reduced RNA levels and the downregulation of inflammatory markers was also observed in the medulla oblongata and olfactory bulbs of mice infected with Omicron at 8 dpi as compared with mice infected with wild-type and Delta at the humane end point. Collectively, these data demonstrate that wild-type, Delta, and Omicron SARS-CoV-2 induce distinct levels of infection and inflammatory responses in K18-hACE2 mice. Notably, sustained brain infection accompanied by the upregulation of inflammatory markers is a critical outcome in mice infected with wild type and Delta but not Omicron. Full article

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24 pages, 10772 KiB

Open AccessArticle

Cross-Reactivity of Human, Wild Boar, and Farm Animal Sera from Pre- and Post-Pandemic Periods with Alpha- and Βeta-Coronaviruses (CoV), including SARS-CoV-2

by Marcel Hulst, Arie Kant, José Harders-Westerveen, Markus Hoffmann, Yajing Xie, Charlotte Laheij, Jean-Luc Murk and Wim H. M. Van der Poel

Viruses 2024, 16(1), 34; https://doi.org/10.3390/v16010034 - 23 Dec 2023

Cited by 1 | Viewed by 1666

Abstract

Panels of pre- and post-pandemic farm animals, wild boar and human sera, including human sera able to neutralize SARS-CoV-2 in vitro, were tested in serological tests to determine their cross-reactivity with β- and α-CoV originating from farm animals. Sera were tested in neutralization [...] Read more.

Panels of pre- and post-pandemic farm animals, wild boar and human sera, including human sera able to neutralize SARS-CoV-2 in vitro, were tested in serological tests to determine their cross-reactivity with β- and α-CoV originating from farm animals. Sera were tested in neutralization assays with high ascending concentrations (up to 1 × 10⁴ TCID₅₀ units/well) of β-CoV Bovine coronavirus (BCV), SARS-CoV-2, and porcine α-CoV-transmissible gastroenteritis virus (TGEV). In addition, sera were tested for immunostaining of cells infected with β-CoV porcine hemagglutinating encephalomyelitis (PHEV). Testing revealed a significantly higher percentage of BCV neutralization (78%) for sera of humans that had experienced a SARS-CoV-2 infection (SARS-CoV-2 convalescent sera) than was observed for human pre-pandemic sera (37%). Also, 46% of these human SARS-CoV-2 convalescent sera neutralized the highest concentration of BCV (5 × 10³ TCID₅₀/well) tested, whereas only 9.6% of the pre-pandemic sera did. Largely similar percentages were observed for staining of PHEV-infected cells by these panels of human sera. Furthermore, post-pandemic sera collected from wild boars living near a densely populated area in The Netherlands also showed a higher percentage (43%) and stronger BCV neutralization than was observed for pre-pandemic sera from this area (21%) and for pre- (28%) and post-pandemic (20%) sera collected from wild boars living in a nature reserve park with limited access for the public. High percentages of BCV neutralization were observed for pre- and post-pandemic sera of cows (100%), pigs (up to 45%), sheep (36%) and rabbits (60%). However, this cross-neutralization was restricted to sera collected from specific herds or farms. TGEV was neutralized only by sera of pigs (68%) and a few wild boar sera (4.6%). None of the BCV and PHEV cross-reacting human pre-pandemic, wild boar and farm animal sera effectively neutralized SARS-CoV-2 in vitro. Preexisting antibodies in human sera effectively neutralized the animal β-CoV BCV in vitro. This cross-neutralization was boosted after humans had experienced a SARS-CoV-2 infection, indicating that SARS-CoV-2 activated a “memory” antibody response against structurally related epitopes expressed on the surface of a broad range of heterologous CoV, including β-CoV isolated from farm animals. Further research is needed to elucidate if a symptomless infection or environmental exposure to SARS-CoV-2 or another β-CoV also triggers such a “memory” antibody response in wild boars and other free-living animals. Full article

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16 pages, 4890 KiB

Open AccessArticle

Chemoprophylactic Assessment of Combined Intranasal SARS-CoV-2 Polymerase and Exonuclease Inhibition in Syrian Golden Hamsters

by Eduardo Gallardo-Toledo, Megan Neary, Joanne Sharp, Joanne Herriott, Edyta Kijak, Chloe Bramwell, Paul Curley, Usman Arshad, Henry Pertinez, Rajith K. R. Rajoli, Anthony Valentijn, Helen Cox, Lee Tatham, Anja Kipar, James P. Stewart and Andrew Owen

Viruses 2023, 15(11), 2161; https://doi.org/10.3390/v15112161 - 27 Oct 2023

Viewed by 1442

Abstract

Pibrentasvir (PIB) has been demonstrated to block exonuclease activity of the SARS-CoV-2 polymerase, protecting favipiravir (FVP) and remdesivir (RDV) from post-incorporation excision and eliciting antiviral synergy in vitro. The present study investigated the chemoprophylactic efficacy of PIB, FVP, RDV, FVP with PIB, or [...] Read more.

Pibrentasvir (PIB) has been demonstrated to block exonuclease activity of the SARS-CoV-2 polymerase, protecting favipiravir (FVP) and remdesivir (RDV) from post-incorporation excision and eliciting antiviral synergy in vitro. The present study investigated the chemoprophylactic efficacy of PIB, FVP, RDV, FVP with PIB, or RDV with PIB dosed intranasally twice a day, using a Syrian golden hamster contact transmission model. Compared to the saline control, viral RNA levels were significantly lower in throat swabs in FVP (day 7), RDV (day 3, 5, 7), and RDV+PIB (day 3, 5) treatment groups. Similarly, findings were evident for nasal turbinate after PIB and RDV treatment, and lungs after PIB, FVP, and FVP+PIB treatment at day 7. Lung viral RNA levels after RDV and RDV+PIB treatment were only detectable in two animals per group, but the overall difference was not statistically significant. In situ examination of the lungs confirmed SARS-CoV-2 infection in all animals, except for one in each of the RDV and RDV+PIB treatment groups, which tested negative in all virus detection approaches. Overall, prevention of transmission was observed in most animals treated with RDV, while other agents reduced the viral load following contact transmission. No benefit of combining FVP or RDV with PIB was observed. Full article

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35 pages, 9912 KiB

Open AccessArticle

Exploring Conformational Landscapes and Cryptic Binding Pockets in Distinct Functional States of the SARS-CoV-2 Omicron BA.1 and BA.2 Trimers: Mutation-Induced Modulation of Protein Dynamics and Network-Guided Prediction of Variant-Specific Allosteric Binding Sites

by Gennady Verkhivker, Mohammed Alshahrani and Grace Gupta

Viruses 2023, 15(10), 2009; https://doi.org/10.3390/v15102009 - 27 Sep 2023

Cited by 4 | Viewed by 1681

Abstract

A significant body of experimental structures of SARS-CoV-2 spike trimers for the BA.1 and BA.2 variants revealed a considerable plasticity of the spike protein and the emergence of druggable binding pockets. Understanding the interplay of conformational dynamics changes induced by the Omicron variants [...] Read more.

A significant body of experimental structures of SARS-CoV-2 spike trimers for the BA.1 and BA.2 variants revealed a considerable plasticity of the spike protein and the emergence of druggable binding pockets. Understanding the interplay of conformational dynamics changes induced by the Omicron variants and the identification of cryptic dynamic binding pockets in the S protein is of paramount importance as exploring broad-spectrum antiviral agents to combat the emerging variants is imperative. In the current study, we explore conformational landscapes and characterize the universe of binding pockets in multiple open and closed functional spike states of the BA.1 and BA.2 Omicron variants. By using a combination of atomistic simulations, a dynamics network analysis, and an allostery-guided network screening of binding pockets in the conformational ensembles of the BA.1 and BA.2 spike conformations, we identified all experimentally known allosteric sites and discovered significant variant-specific differences in the distribution of binding sites in the BA.1 and BA.2 trimers. This study provided a structural characterization of the predicted cryptic pockets and captured the experimentally known allosteric sites, revealing the critical role of conformational plasticity in modulating the distribution and cross-talk between functional binding sites. We found that mutational and dynamic changes in the BA.1 variant can induce the remodeling and stabilization of a known druggable pocket in the N-terminal domain, while this pocket is drastically altered and may no longer be available for ligand binding in the BA.2 variant. Our results predicted the experimentally known allosteric site in the receptor-binding domain that remains stable and ranks as the most favorable site in the conformational ensembles of the BA.2 variant but could become fragmented and less probable in BA.1 conformations. We also uncovered several cryptic pockets formed at the inter-domain and inter-protomer interface, including functional regions of the S2 subunit and stem helix region, which are consistent with the known role of pocket residues in modulating conformational transitions and antibody recognition. The results of this study are particularly significant for understanding the dynamic and network features of the universe of available binding pockets in spike proteins, as well as the effects of the Omicron-variant-specific modulation of preferential druggable pockets. The exploration of predicted druggable sites can present a new and previously underappreciated opportunity for therapeutic interventions for Omicron variants through the conformation-selective and variant-specific targeting of functional sites involved in allosteric changes. Full article

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17 pages, 3498 KiB

Open AccessArticle

Substitutions in SARS-CoV-2 Mpro Selected by Protease Inhibitor Boceprevir Confer Resistance to Nirmatrelvir

by Karen Anbro Gammeltoft, Yuyong Zhou, Line Abildgaard Ryberg, Long V. Pham, Alekxander Binderup, Carlos Rene Duarte Hernandez, Anna Offersgaard, Ulrik Fahnøe, Günther Herbert Johannes Peters, Santseharay Ramirez, Jens Bukh and Judith Margarete Gottwein

Viruses 2023, 15(9), 1970; https://doi.org/10.3390/v15091970 - 21 Sep 2023

Cited by 8 | Viewed by 2010

Abstract

Nirmatrelvir, which targets the SARS-CoV-2 main protease (Mpro), is the first-in-line drug for prevention and treatment of severe COVID-19, and additional Mpro inhibitors are in development. However, the risk of resistance development threatens the future efficacy of such direct-acting antivirals. To gain knowledge [...] Read more.

Nirmatrelvir, which targets the SARS-CoV-2 main protease (Mpro), is the first-in-line drug for prevention and treatment of severe COVID-19, and additional Mpro inhibitors are in development. However, the risk of resistance development threatens the future efficacy of such direct-acting antivirals. To gain knowledge on viral correlates of resistance to Mpro inhibitors, we selected resistant SARS-CoV-2 under treatment with the nirmatrelvir-related protease inhibitor boceprevir. SARS-CoV-2 selected during five escape experiments in VeroE6 cells showed cross-resistance to nirmatrelvir with up to 7.3-fold increased half-maximal effective concentration compared to original SARS-CoV-2, determined in concentration–response experiments. Sequence analysis revealed that escape viruses harbored Mpro substitutions L50F and A173V. For reverse genetic studies, these substitutions were introduced into a cell-culture-infectious SARS-CoV-2 clone. Infectivity titration and analysis of genetic stability of cell-culture-derived engineered SARS-CoV-2 mutants showed that L50F rescued the fitness cost conferred by A173V. In the concentration–response experiments, A173V was the main driver of resistance to boceprevir and nirmatrelvir. Structural analysis of Mpro suggested that A173V can cause resistance by making boceprevir and nirmatrelvir binding less favorable. This study contributes to a comprehensive overview of the resistance profile of the first-in-line COVID-19 treatment nirmatrelvir and can thus inform population monitoring and contribute to pandemic preparedness. Full article

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25 pages, 2975 KiB

Open AccessArticle

Characterizing Risk Factors for Hospitalization and Clinical Characteristics in a Cohort of COVID-19 Patients Enrolled in the GENCOV Study

by Gregory Morgan, Selina Casalino, Sunakshi Chowdhary, Erika Frangione, Chun Yiu Jordan Fung, Simona Haller, Elisa Lapadula, Mackenzie Scott, Dawit Wolday, Juliet Young, Saranya Arnoldo, Navneet Aujla, Erin Bearss, Alexandra Binnie, Yvonne Bombard, Bjug Borgundvaag, Laurent Briollais, Marc Dagher, Luke Devine, Hanna Faghfoury, Steven M. Friedman, Anne-Claude Gingras, Lee W. Goneau, Zeeshan Khan, Tony Mazzulli, Shelley L. McLeod, Romina Nomigolzar, Abdul Noor, Trevor J. Pugh, David Richardson, Harpreet Kaur Satnam Singh, Jared Simpson, Seth Stern, Lisa Strug, Ahmed Taher, Jordan Lerner-Ellis and Jennifer Taher Show full author list Hide full author list

Viruses 2023, 15(8), 1764; https://doi.org/10.3390/v15081764 - 18 Aug 2023

Cited by 1 | Viewed by 2203

Abstract

The GENCOV study aims to identify patient factors which affect COVID-19 severity and outcomes. Here, we aimed to evaluate patient characteristics, acute symptoms and their persistence, and associations with hospitalization. Participants were recruited at hospital sites across the Greater Toronto Area in Ontario, [...] Read more.

The GENCOV study aims to identify patient factors which affect COVID-19 severity and outcomes. Here, we aimed to evaluate patient characteristics, acute symptoms and their persistence, and associations with hospitalization. Participants were recruited at hospital sites across the Greater Toronto Area in Ontario, Canada. Patient-reported demographics, medical history, and COVID-19 symptoms and complications were collected through an intake survey. Regression analyses were performed to identify associations with outcomes including hospitalization and COVID-19 symptoms. In total, 966 responses were obtained from 1106 eligible participants (87% response rate) between November 2020 and May 2022. Increasing continuous age (aOR: 1.05 [95%CI: 1.01–1.08]) and BMI (aOR: 1.17 [95%CI: 1.10–1.24]), non-White/European ethnicity (aOR: 2.72 [95%CI: 1.22–6.05]), hypertension (aOR: 2.78 [95%CI: 1.22–6.34]), and infection by viral variants (aOR: 5.43 [95%CI: 1.45–20.34]) were identified as risk factors for hospitalization. Several symptoms including shortness of breath and fever were found to be more common among inpatients and tended to persist for longer durations following acute illness. Sex, age, ethnicity, BMI, vaccination status, viral strain, and underlying health conditions were associated with developing and having persistent symptoms. By improving our understanding of risk factors for severe COVID-19, our findings may guide COVID-19 patient management strategies by enabling more efficient clinical decision making. Full article

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14 pages, 1648 KiB

Open AccessArticle

Analysis of SARS-CoV-2 Population Genetics from Samples Associated with Huanan Market and Early Cases Identifies Substitutions Associated with Future Variants of Concern

by Xiaofeng Dong and Julian A. Hiscox

Viruses 2023, 15(8), 1728; https://doi.org/10.3390/v15081728 - 12 Aug 2023

Cited by 1 | Viewed by 1321

Abstract

SARS-CoV-2 began spreading through human-to-human transmission first within China and then worldwide, with increasing sequence diversity associated with time and the further spread of the virus. The spillover events in the Huanan market were associated with two lineages of SARS-CoV-2 (lineages A and [...] Read more.

SARS-CoV-2 began spreading through human-to-human transmission first within China and then worldwide, with increasing sequence diversity associated with time and the further spread of the virus. The spillover events in the Huanan market were associated with two lineages of SARS-CoV-2 (lineages A and B). Infecting virus populations and those in infected individuals consist of a dominant genomic sequence and minor genomic variants; these latter populations can indicate sites on the genome that may be subject to mutational changes—either neutral or advantageous sites and those that act as a reservoir for future dominant variants—when placed under selection pressure. The earliest deposited sequences with human infections associated with the Huanan market shared very close homology with each other and were all lineage B. However, there were minor genomic variants present in each sample that encompassed synonymous and non-synonymous changes. Fusion sequences characteristic of defective RNA were identified that could potentially link transmission chains between individuals. Although all the individuals appeared to have lineage B as the dominant sequence, nucleotides associated with lineage A could be found at very low frequencies. Several substitutions (but not deletions) associated with much later variants of concern (VoCs) were already present as minor genomic variants. This suggests that low-frequency substitutions at the start of a pandemic could be a reservoir of future dominant variants and/or provide information on potential sites within the genome associated with future plasticity. Full article

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12 pages, 1151 KiB

Open AccessBrief Report

Genomic and Temporal Analysis of Deletions Correlated to qRT-PCR Dropout in N Gene in Alpha, Delta and Omicron Variants

by Giulia Gatti, Martina Brandolini, Andrea Mancini, Francesca Taddei, Silvia Zannoli, Giorgio Dirani, Martina Manera, Valentina Arfilli, Agnese Denicolò, Anna Marzucco, Maria Sofia Montanari, Irene Zaghi, Massimiliano Guerra, Rita Tennina, Maria Michela Marino, Laura Grumiro, Monica Cricca and Vittorio Sambri

Viruses 2023, 15(8), 1630; https://doi.org/10.3390/v15081630 - 26 Jul 2023

Cited by 1 | Viewed by 1214

Abstract

Since the first SARS-CoV-2 outbreak, mutations such as single nucleotide polymorphisms (SNPs) and insertion/deletions (INDELs) have changed and characterized the viral genome sequence, structure and protein folding leading to the onset of new variants. The presence of those alterations challenges not only the [...] Read more.

Since the first SARS-CoV-2 outbreak, mutations such as single nucleotide polymorphisms (SNPs) and insertion/deletions (INDELs) have changed and characterized the viral genome sequence, structure and protein folding leading to the onset of new variants. The presence of those alterations challenges not only the clinical field but also the diagnostic demand due to failures in gene detection or incompleteness of polymerase chain reaction (PCR) results. In particular, the analysis of understudied genes such as N and the investigation through whole-genome next generation sequencing (WG-NGS) of regions more prone to mutate can help in the identification of new or reacquired mutations, with the aim of designing robust and long-lasting primers. In 48 samples of SARS-CoV-2 (including Alpha, Delta and Omicron variants), a lack of N gene amplification was observed in the genomes analyzed through WG-NGS. Three gene regions were detected hosting the highest number of SNPs and INDELs. In several cases, the latter can interfere deeply with both the sensitivity of diagnostic methodologies and the final protein folding. The monitoring over time of the viral evolution and the reacquisition among different variants of the same mutations or different alterations within the same genomic positions can be relevant to avoid unnecessary consumption of resources. Full article

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20 pages, 4537 KiB

Open AccessArticle

Complement Activation-Independent Attenuation of SARS-CoV-2 Infection by C1q and C4b-Binding Protein

by Nazar Beirag, Praveen M. Varghese, Martin Mayora Neto, Ahmad Al Aiyan, Haseeb A. Khan, Moneeb Qablan, Mohamed H. Shamji, Robert B. Sim, Nigel Temperton and Uday Kishore

Viruses 2023, 15(6), 1269; https://doi.org/10.3390/v15061269 - 29 May 2023

Cited by 5 | Viewed by 3046

Abstract

The complement system is a key component of the innate immune response to viruses and proinflammatory events. Exaggerated complement activation has been attributed to the induction of a cytokine storm in severe SARS-CoV-2 infection. However, there is also an argument for the protective [...] Read more.

The complement system is a key component of the innate immune response to viruses and proinflammatory events. Exaggerated complement activation has been attributed to the induction of a cytokine storm in severe SARS-CoV-2 infection. However, there is also an argument for the protective role of complement proteins, given their local synthesis or activation at the site of viral infection. This study investigated the complement activation-independent role of C1q and C4b-binding protein (C4BP) against SARS-CoV-2 infection. The interactions of C1q, its recombinant globular heads, and C4BP with the SARS-CoV-2 spike and receptor binding domain (RBD) were examined using direct ELISA. In addition, RT-qPCR was used to evaluate the modulatory effect of these complement proteins on the SARS-CoV-2-mediated immune response. Cell binding and luciferase-based viral entry assays were utilised to assess the effects of C1q, its recombinant globular heads, and C4BP on SARS-CoV-2 cell entry. C1q and C4BP bound directly to SARS-CoV-2 pseudotype particles via the RBD domain of the spike protein. C1q via its globular heads and C4BP were found to reduce binding as well as viral transduction of SARS-CoV-2 spike protein expressing lentiviral pseudotypes into transfected A549 cells expressing human ACE2 and TMPRSS2. Furthermore, the treatment of the SARS-CoV-2 spike, envelope, nucleoprotein, and membrane protein expressing alphaviral pseudotypes with C1q, its recombinant globular heads, or C4BP triggered a reduction in mRNA levels of proinflammatory cytokines and chemokines such as IL-1β, IL-8, IL-6, TNF-α, IFN-α, and RANTES (as well as NF-κB) in A549 cells expressing human ACE2 and TMPRSS2. In addition, C1q and C4BP treatment also reduced SARS-CoV-2 pseudotype infection-mediated NF-κB activation in A549 cells expressing human ACE2 and TMPRSS2. C1q and C4BP are synthesised primarily by hepatocytes; however, they are also produced by macrophages, and alveolar type II cells, respectively, locally at the pulmonary site. These findings support the notion that the locally produced C1q and C4BP can be protective against SARS-CoV-2 infection in a complement activation-independent manner, offering immune resistance by inhibiting virus binding to target host cells and attenuating the infection-associated inflammatory response. Full article

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36 pages, 7847 KiB

Open AccessArticle

Balancing Functional Tradeoffs between Protein Stability and ACE2 Binding in the SARS-CoV-2 Omicron BA.2, BA.2.75 and XBB Lineages: Dynamics-Based Network Models Reveal Epistatic Effects Modulating Compensatory Dynamic and Energetic Changes

by Gennady Verkhivker, Mohammed Alshahrani and Grace Gupta

Viruses 2023, 15(5), 1143; https://doi.org/10.3390/v15051143 - 10 May 2023

Cited by 11 | Viewed by 2502

Abstract

Evolutionary and functional studies suggested that the emergence of the Omicron variants can be determined by multiple fitness trade-offs including the immune escape, binding affinity for ACE2, conformational plasticity, protein stability and allosteric modulation. In this study, we systematically characterize conformational dynamics, structural [...] Read more.

Evolutionary and functional studies suggested that the emergence of the Omicron variants can be determined by multiple fitness trade-offs including the immune escape, binding affinity for ACE2, conformational plasticity, protein stability and allosteric modulation. In this study, we systematically characterize conformational dynamics, structural stability and binding affinities of the SARS-CoV-2 Spike Omicron complexes with the host receptor ACE2 for BA.2, BA.2.75, XBB.1 and XBB.1.5 variants. We combined multiscale molecular simulations and dynamic analysis of allosteric interactions together with the ensemble-based mutational scanning of the protein residues and network modeling of epistatic interactions. This multifaceted computational study characterized molecular mechanisms and identified energetic hotspots that can mediate the predicted increased stability and the enhanced binding affinity of the BA.2.75 and XBB.1.5 complexes. The results suggested a mechanism driven by the stability hotspots and a spatially localized group of the Omicron binding affinity centers, while allowing for functionally beneficial neutral Omicron mutations in other binding interface positions. A network-based community model for the analysis of epistatic contributions in the Omicron complexes is proposed revealing the key role of the binding hotspots R498 and Y501 in mediating community-based epistatic couplings with other Omicron sites and allowing for compensatory dynamics and binding energetic changes. The results also showed that mutations in the convergent evolutionary hotspot F486 can modulate not only local interactions but also rewire the global network of local communities in this region allowing the F486P mutation to restore both the stability and binding affinity of the XBB.1.5 variant which may explain the growth advantages over the XBB.1 variant. The results of this study are consistent with a broad range of functional studies rationalizing functional roles of the Omicron mutation sites that form a coordinated network of hotspots enabling a balance of multiple fitness tradeoffs and shaping up a complex functional landscape of virus transmissibility. Full article

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19 pages, 833 KiB

Open AccessArticle

Intra-Host Co-Existing Strains of SARS-CoV-2 Reference Genome Uncovered by Exhaustive Computational Search

by Xinhui Cai, Tian Lan, Pengyao Ping, Brian Oliver and Jinyan Li

Viruses 2023, 15(5), 1065; https://doi.org/10.3390/v15051065 - 26 Apr 2023

Viewed by 2078

Abstract

The COVID-19 pandemic caused by SARS-CoV-2 has had a severe impact on people worldwide. The reference genome of the virus has been widely used as a template for designing mRNA vaccines to combat the disease. In this study, we present a computational method [...] Read more.

The COVID-19 pandemic caused by SARS-CoV-2 has had a severe impact on people worldwide. The reference genome of the virus has been widely used as a template for designing mRNA vaccines to combat the disease. In this study, we present a computational method aimed at identifying co-existing intra-host strains of the virus from RNA-sequencing data of short reads that were used to assemble the original reference genome. Our method consisted of five key steps: extraction of relevant reads, error correction for the reads, identification of within-host diversity, phylogenetic study, and protein binding affinity analysis. Our study revealed that multiple strains of SARS-CoV-2 can coexist in both the viral sample used to produce the reference sequence and a wastewater sample from California. Additionally, our workflow demonstrated its capability to identify within-host diversity in foot-and-mouth disease virus (FMDV). Through our research, we were able to shed light on the binding affinity and phylogenetic relationships of these strains with the published SARS-CoV-2 reference genome, SARS-CoV, variants of concern (VOC) of SARS-CoV-2, and some closely related coronaviruses. These insights have important implications for future research efforts aimed at identifying within-host diversity, understanding the evolution and spread of these viruses, as well as the development of effective treatments and vaccines against them. Full article

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10 pages, 1659 KiB

Open AccessCommunication

Liposomal Lactoferrin Exerts Antiviral Activity against HCoV-229E and SARS-CoV-2 Pseudoviruses In Vitro

by Sabina Andreu, Inés Ripa, Raquel Bello-Morales and José Antonio López-Guerrero

Viruses 2023, 15(4), 972; https://doi.org/10.3390/v15040972 - 15 Apr 2023

Cited by 8 | Viewed by 3123

Abstract

A limited number of effective therapies are currently available to treat human coronavirus SARS-CoV-2 and other human coronaviruses, which are responsible for nearly a third of global cases of the common cold. The possibility of new emerging coronaviruses demands powerful new antiviral strategies. [...] Read more.

A limited number of effective therapies are currently available to treat human coronavirus SARS-CoV-2 and other human coronaviruses, which are responsible for nearly a third of global cases of the common cold. The possibility of new emerging coronaviruses demands powerful new antiviral strategies. Lactoferrin is a well-known protein that possesses anti-inflammatory and immunomodulatory activities, and it has previously shown antiviral activity against several viruses, including SARS-CoV-2. To increase this antiviral activity, here we present bovine liposomal lactoferrin. Liposomal encapsulation of the compound was proven to increase permeability, bioavailability, and time release. In the present work, we compare the antiviral activity of free and liposomal bovine lactoferrin against HCoV229E and SARS-CoV-2 in vitro and in human primary bronchial epithelial cells, and we demonstrated that the liposomal form exerts a more potent antiviral activity than its free form at non-cytotoxic doses. Full article

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38 pages, 2072 KiB

Open AccessReview

Hyperinflammatory Response in COVID-19: A Systematic Review

by Marcos Jessé Abrahão Silva, Layana Rufino Ribeiro, Maria Isabel Montoril Gouveia, Beatriz dos Reis Marcelino, Carolynne Silva dos Santos, Karla Valéria Batista Lima and Luana Nepomuceno Gondim Costa Lima

Viruses 2023, 15(2), 553; https://doi.org/10.3390/v15020553 - 16 Feb 2023

Cited by 45 | Viewed by 4115

Abstract

COVID-19 is a multisystemic disease caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). The immunopathogenic conditions of the hyperinflammatory response that cause systemic inflammation are extremely linked to its severity. This research sought to review the immunopathological elements that contribute to [...] Read more.

COVID-19 is a multisystemic disease caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). The immunopathogenic conditions of the hyperinflammatory response that cause systemic inflammation are extremely linked to its severity. This research sought to review the immunopathological elements that contribute to its progression. This is a systematic review using the PUBMED, LILACS, MEDLINE, and SCIELO databases using articles between May 2020 and July 2022 with the following search terms in conjunction with “AND”: “SARS-CoV-2”; “COVID-19”; “ARDS” and “Cytokine Storm”. The quality appraisal and risk of bias were assessed by the JBI checklists and the Cochrane Collaboration’s RoB 2.0 and ROBINS-I tools, respectively, and the risk of bias for in vitro studies by a pre-defined standard in the literature. The search resulted in 39 articles. The main actors in this response denote SARS-CoV-2 Spike proteins, cellular proteases, leukocytes, cytokines, and proteolytic cascades. The “cytokine storm” itself brings several complications to the host through cytokines such as IL-6 and chemokines (such as CCL2), which influence tissue inflammation through apoptosis and pyroptosis. The hyperinflammatory response causes several unfavorable outcomes in patients, and systemic inflammation caused largely by the dysregulation of the immune response should be controlled for their recovery. Full article

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18 pages, 4299 KiB

Open AccessArticle

SARS-CoV-2 Omicron Subvariants Balance Host Cell Membrane, Receptor, and Antibody Docking via an Overlapping Target Site

by Michael Overduin, Rakesh K. Bhat and Troy A. Kervin

Viruses 2023, 15(2), 447; https://doi.org/10.3390/v15020447 - 6 Feb 2023

Cited by 2 | Viewed by 2478

Abstract

Variants of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) are emerging rapidly and offer surfaces that are optimized for recognition of host cell membranes while also evading antibodies arising from vaccinations and previous infections. Host cell infection is a multi-step process in which [...] Read more.

Variants of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) are emerging rapidly and offer surfaces that are optimized for recognition of host cell membranes while also evading antibodies arising from vaccinations and previous infections. Host cell infection is a multi-step process in which spike heads engage lipid bilayers and one or more angiotensin-converting enzyme 2 (ACE-2) receptors. Here, the membrane binding surfaces of Omicron subvariants are compared using cryo-electron microscopy (cEM) structures of spike trimers from BA.2, BA.2.12.1, BA.2.13, BA.2.75, BA.3, BA.4, and BA.5 viruses. Despite significant differences around mutated sites, they all maintain strong membrane binding propensities that first appeared in BA.1. Both their closed and open states retain elevated membrane docking capacities, although the presence of more closed than open states diminishes opportunities to bind receptors while enhancing membrane engagement. The electrostatic dipoles are generally conserved. However, the BA.2.75 spike dipole is compromised, and its ACE-2 affinity is increased, and BA.3 exhibits the opposite pattern. We propose that balancing the functional imperatives of a stable, readily cleavable spike that engages both lipid bilayers and receptors while avoiding host defenses underlies betacoronavirus evolution. This provides predictive criteria for rationalizing future pandemic waves and COVID-19 transmissibility while illuminating critical sites and strategies for simultaneously combating multiple variants. Full article

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11 pages, 582 KiB

Open AccessBrief Report

Association between SARS-CoV-2 Viral Load and Patient Symptoms and Clinical Outcomes Using Droplet Digital PCR

by Elizabeth Hastie, Harold Amogan, David Looney and Sanjay R. Mehta

Viruses 2023, 15(2), 446; https://doi.org/10.3390/v15020446 - 5 Feb 2023

Cited by 7 | Viewed by 2185

Abstract

The association between nasopharyngeal (NP) SARS-CoV-2 viral loads and clinical outcomes remains debated. Here, we examined the factors that might predict the NP viral load and the role of the viral load as a predictor of clinical outcomes. A convenience sample of 955 [...] Read more.

The association between nasopharyngeal (NP) SARS-CoV-2 viral loads and clinical outcomes remains debated. Here, we examined the factors that might predict the NP viral load and the role of the viral load as a predictor of clinical outcomes. A convenience sample of 955 positive remnant NP swab eluent samples collected during routine care between 18 November 2020 and 26 September 2021 was cataloged and a chart review was performed. For non-duplicate samples with available demographic and clinical data (i.e., non-employees), an aliquot of eluent was sent for a droplet digital PCR quantification of the SARS-CoV-2 viral load. Univariate and multivariate analyses were performed to identify the clinical predictors of NP viral loads and the predictors of COVID-19-related clinical outcomes. Samples and data from 698 individuals were included in the final analysis. The sample cohort had a mean age of 50 years (range: 19–91); 86.6% were male and 76.3% were unvaccinated. The NP viral load was higher in people with respiratory symptoms (p = 0.0004) and fevers (p = 0.0006). In the predictive models for the clinical outcomes, the NP viral load approached a significance as a predictor for in-hospital mortality. In conclusion, the NP viral load did not appear to be a strong predictor of moderate-to-severe disease in the pre-Delta and Delta phases of the pandemic, but was predictive of symptomatic diseases and approached a significance for in-hospital mortality, providing support to the thesis that early viral control prevents the progression of disease. Full article

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16 pages, 3534 KiB

Open AccessArticle

Anti-Entry Activity of Natural Flavonoids against SARS-CoV-2 by Targeting Spike RBD

by Jie-Ru Meng, Jiazheng Liu, Lu Fu, Tong Shu, Lingzhi Yang, Xueji Zhang, Zhi-Hong Jiang and Li-Ping Bai

Viruses 2023, 15(1), 160; https://doi.org/10.3390/v15010160 - 4 Jan 2023

Cited by 13 | Viewed by 2793

Abstract

COVID-19 is still a global public health concern, and the SARS-CoV-2 mutations require more effective antiviral agents. In this study, the antiviral entry activity of thirty-one flavonoids was systematically evaluated by a SARS-CoV-2 pseudovirus model. Twenty-four flavonoids exhibited antiviral entry activity with IC [...] Read more.

COVID-19 is still a global public health concern, and the SARS-CoV-2 mutations require more effective antiviral agents. In this study, the antiviral entry activity of thirty-one flavonoids was systematically evaluated by a SARS-CoV-2 pseudovirus model. Twenty-four flavonoids exhibited antiviral entry activity with IC₅₀ values ranging from 10.27 to 172.63 µM and SI values ranging from 2.33 to 48.69. The structure–activity relationship of these flavonoids as SARS-CoV-2 entry inhibitors was comprehensively summarized. A subsequent biolayer interferometry assay indicated that flavonoids bind to viral spike RBD to block viral interaction with ACE2 receptor, and a molecular docking study also revealed that flavonols could bind to Pocket 3, the non-mutant regions of SARS-CoV-2 variants, suggesting that flavonols might be also active against virus variants. These natural flavonoids showed very low cytotoxic effects on human normal cell lines. Our findings suggested that natural flavonoids might be potential antiviral entry agents against SARS-CoV-2 via inactivating the viral spike. It is hoped that our study will provide some encouraging evidence for the use of natural flavonoids as disinfectants to prevent viral infections. Full article

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13 pages, 544 KiB

Open AccessArticle

Variability in the Clinical Course of COVID-19 in a Retrospective Analysis of a Large Real-World Database

by Robert Flisiak, Piotr Rzymski, Dorota Zarębska-Michaluk, Przemysław Ciechanowski, Krystyna Dobrowolska, Magdalena Rogalska, Jerzy Jaroszewicz, Anna Szymanek-Pasternak, Marta Rorat, Dorota Kozielewicz, Justyna Kowalska, Ewa Dutkiewicz, Katarzyna Sikorska and Anna Moniuszko-Malinowska

Viruses 2023, 15(1), 149; https://doi.org/10.3390/v15010149 - 3 Jan 2023

Cited by 31 | Viewed by 3693

Abstract

The COVID-19 pandemic proceeds in waves, with variable characteristics of the clinical picture resulting from the evolution of the SARS-CoV-2 virus. This study aimed to compare the epidemiological characteristics, symptomatology, and outcomes of the disease in patients hospitalized for COVID-19 during periods of [...] Read more.

The COVID-19 pandemic proceeds in waves, with variable characteristics of the clinical picture resulting from the evolution of the SARS-CoV-2 virus. This study aimed to compare the epidemiological characteristics, symptomatology, and outcomes of the disease in patients hospitalized for COVID-19 during periods of different variants dominance. Comparing the periods of dominance of variants preceding the Delta variant, the Delta period was characterized by a higher share of hospitalized females, less frequent comorbidities among patients, and a different age distribution. The lowest need for oxygen therapy and mechanical ventilation was observed under Omicron dominance. The triad of classic COVID-19 symptoms, cough, fever, dyspnoea, and fatigue, were most prevalent during the Delta period, and significantly less common under the Omicron dominance. During the Omicron period, nearly twice as many patients as in the previous periods could be discharged from the hospital within 7 days; the overall 28-day mortality was significantly lower compared to that of the Delta period. It also did not differ between periods that were dominated by the BA.1 and BA.2 subvariants. The study indicates that the Omicron SARS-CoV-2 variant that dominated between January and June 2022 caused a disease which resembled the common cold, and was caused by seasonal alpha and beta-coronaviruses with a low pathogenicity for humans. However, one should note that this effect may not only have been related to biological features of the Omicron lineage, but may additionally have been driven by the increased levels of immunization through natural infections and vaccinations, for which we could not account for due to a lack of sufficient data. Full article

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2022

Jump to: 2024, 2023, 2021

10 pages, 3046 KiB

Open AccessArticle

A Cross-Sectional Comparative Characterization of Hematological Changes in Patients with COVID-19 Infection, Non-COVID Influenza-like Illnesses and Healthy Controls

by Mansi Kala, Sohaib Ahmad, Meghali Dhebane, Kunal Das, Manish Raturi, Meghna Tyagi and Anuradha Kusum

Viruses 2023, 15(1), 134; https://doi.org/10.3390/v15010134 - 31 Dec 2022

Cited by 6 | Viewed by 1984

Abstract

Introduction: Studies have documented the role of the “neutrophil-to-lymphocyte ratio” (NLR) in influenza virus infection. In addition, morphometric parameters derived from automated analyzers on the volume, scatter and conductivity of monocytes, neutrophils and lymphocytes in many viral etiologies have helped with their early [...] Read more.

Introduction: Studies have documented the role of the “neutrophil-to-lymphocyte ratio” (NLR) in influenza virus infection. In addition, morphometric parameters derived from automated analyzers on the volume, scatter and conductivity of monocytes, neutrophils and lymphocytes in many viral etiologies have helped with their early differentiation. With this background, we aimed to characterize the hematological changes of coronavirus-positive cases and also compare them with the healthy controls and patients affected by non-COVID Influenza-like illnesses so that early isolation could be considered. Material and Methods: This was a cross-sectional analytical study carried out in the years 2020–2022. All cases with COVID-19 and non-COVID-19 Influenza-like illnesses and healthy controls above 18 years were included. Cases were diagnosed according to the WHO guidelines. All samples were processed on a Unicel DxH 800 (Beckman Coulter, California, USA) automated hematology analyzer. The demographic, clinical and regular hematological parameters along with additional parameters such as volume, conductivity and scatter (VCS) of the three groups were compared. Results: The 169 COVID-19 cases were in the moderate to severe category. Compared with 140 healthy controls, the majority of the routine hematological values including the NLR (neutrophil-to-lymphocyte ratio) and PLR (platelet-to-lymphocyte ratio) showed statistically significant differences. A cutoff of an absolute neutrophil count of 4350 cell/cumm was found to have a sensitivity of 76% and specificity of 70% in differentiating moderate and severe COVID-19 cases from healthy controls. COVID-19 and the non-COVID-19 Influenza-like illnesses were similar statistically in all parameters except the PLR, mean neutrophilic and monocytic volume, scatter parameters in neutrophils, axial light loss in monocytes and NLR. Interestingly, there was a trend of higher mean volumes and scatter in neutrophils and monocytes in COVID-19 cases as compared to non-COVID-19 Influenza-like illnesses. Conclusion: We demonstrated morphological changes in neutrophils, monocytes and lymphocytes in COVID-19 infection and also non-COVID-19 Influenza-like illnesses with the help of VCS parameters. A cutoff for the absolute neutrophils count was able to differentiate COVID-19 infection requiring hospitalization from healthy controls and eosinopenia was a characteristic finding in cases with COVID-19 infection. Full article

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12 pages, 3720 KiB

Open AccessArticle

Predicting the Trajectory of Replacements of SARS-CoV-2 Variants Using Relative Reproduction Numbers

by Chayada Piantham and Kimihito Ito

Viruses 2022, 14(11), 2556; https://doi.org/10.3390/v14112556 - 18 Nov 2022

Cited by 2 | Viewed by 1362

Abstract

New variants of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) with high effective reproduction numbers are continuously being selected by natural selection. To establish effective control measures for new variants, it is crucial to know their transmissibility and replacement trajectory in advance. [...] Read more.

New variants of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) with high effective reproduction numbers are continuously being selected by natural selection. To establish effective control measures for new variants, it is crucial to know their transmissibility and replacement trajectory in advance. In this paper, we conduct retrospective prediction tests for the variant replacement from Alpha to Delta in England, using the relative reproduction numbers of Delta with respect to Alpha estimated from partial observations. We found that once Delta’s relative frequency reached 0.15, the date when the relative frequency of Delta would reach 0.90 was predicted with maximum absolute prediction errors of three days. This means that the time course of the variant replacement could be accurately predicted from early observations. Together with the estimated relative reproduction number of a new variant with respect to old variants, the predicted replacement timing will be crucial information for planning control strategies against the new variant. Full article

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12 pages, 495 KiB

Open AccessReview

ACE2-Independent Alternative Receptors for SARS-CoV-2

by Suhyeon Lim, Monica Zhang and Theresa L. Chang

Viruses 2022, 14(11), 2535; https://doi.org/10.3390/v14112535 - 16 Nov 2022

Cited by 51 | Viewed by 4904

Abstract

Severe acute respiratory syndrome-related coronavirus (SARS-CoV-2), the causative agent of coronavirus disease 2019 (COVID-19), is highly contagious and remains a major public health challenge despite the availability of effective vaccines. SARS-CoV-2 enters cells through the binding of its spike receptor-binding domain (RBD) to [...] Read more.

Severe acute respiratory syndrome-related coronavirus (SARS-CoV-2), the causative agent of coronavirus disease 2019 (COVID-19), is highly contagious and remains a major public health challenge despite the availability of effective vaccines. SARS-CoV-2 enters cells through the binding of its spike receptor-binding domain (RBD) to the human angiotensin-converting enzyme 2 (ACE2) receptor in concert with accessory receptors/molecules that facilitate viral attachment, internalization, and fusion. Although ACE2 plays a critical role in SARS-CoV-2 replication, its expression profiles are not completely associated with infection patterns, immune responses, and clinical manifestations. Additionally, SARS-CoV-2 infects cells that lack ACE2, and the infection is resistant to monoclonal antibodies against spike RBD in vitro, indicating that some human cells possess ACE2-independent alternative receptors, which can mediate SARS-CoV-2 entry. Here, we discuss these alternative receptors and their interactions with SARS-CoV-2 components for ACE2-independent viral entry. These receptors include CD147, AXL, CD209L/L-SIGN/CLEC4M, CD209/DC-SIGN/CLEC4L, CLEC4G/LSECtin, ASGR1/CLEC4H1, LDLRAD3, TMEM30A, and KREMEN1. Most of these receptors are known to be involved in the entry of other viruses and to modulate cellular functions and immune responses. The SARS-CoV-2 omicron variant exhibits altered cell tropism and an associated change in the cell entry pathway, indicating that emerging variants may use alternative receptors to escape the immune pressure against ACE2-dependent viral entry provided by vaccination against RBD. Understanding the role of ACE2-independent alternative receptors in SARS-CoV-2 viral entry and pathogenesis may provide avenues for the prevention of infection by SARS-CoV-2 variants and for the treatment of COVID-19. Full article

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12 pages, 1245 KiB

Open AccessArticle

Effect of Previous COVID-19 Vaccination on Humoral Immunity 3 Months after SARS-CoV-2 Omicron Infection and Booster Effect of a Fourth COVID-19 Vaccination 2 Months after SARS-CoV-2 Omicron Infection

by Jinsoo Kim, Hyeonji Seo, Han-Wool Kim, Dongbum Kim, Hyung-Joo Kwon and Yong-Kyun Kim

Viruses 2022, 14(11), 2458; https://doi.org/10.3390/v14112458 - 6 Nov 2022

Cited by 10 | Viewed by 2403

Abstract

In this study, we aimed to determine the effect of COVID-19 vaccination on 3-month immune response and durability after natural infection by the Omicron variant and to assess the immune response to a fourth dose of COVID-19 vaccination in patients with prior natural [...] Read more.

In this study, we aimed to determine the effect of COVID-19 vaccination on 3-month immune response and durability after natural infection by the Omicron variant and to assess the immune response to a fourth dose of COVID-19 vaccination in patients with prior natural infection with the Omicron variant. Overall, 86 patients aged ≥60 years with different vaccination histories and 39 health care workers (HCWs) vaccinated thrice before Omicron infection were enrolled. The sVNT50 titer was significantly lower in patients with incomplete vaccination before SARS-CoV-2 infection with the S clade (p < 0.001), Delta variant (p < 0.001), or Omicron variant (p = 0.003) than in those vaccinated thrice. The sVNT results against the Omicron variant did not differ significantly in patients aged ≥60 years (p = 0.49) and HCWs (p = 0.17), regardless of the recipient receiving the fourth dose 2 months after COVID-19. Incomplete COVID-19 vaccination before Omicron infection for individuals aged ≥60 years conferred limited protection against homologous and heterologous virus strains, whereas two or three doses of the vaccine provided cross-variant humoral immunity against Omicron infection for at least 3 months. However, a fourth dose 2 months after Omicron infection did not enhance immunity against the homologous strain. A future strategy using the bivalent Omicron-containing booster vaccine with appropriate timing will be crucial. Full article

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11 pages, 1743 KiB

Open AccessArticle

Expression of SARS-Cov-2 Entry Factors in Patients with Chronic Hepatitis

by Chiara Rosso, Cristina Demelas, Greta Agostini, Maria Lorena Abate, Marta Vernero, Gian Paolo Caviglia, Daphne D’Amato, Angelo Armandi, Marta Tapparo, Marta Guariglia, Giulia Troshina, Alessandro Massano, Antonella Olivero, Aurora Nicolosi, Antonella Zannetti, Rinaldo Pellicano, Alessia Ciancio, Giorgio Maria Saracco, Davide Giuseppe Ribaldone, Elisabetta Bugianesi and Sharmila Fagoonee Show full author list Hide full author list

Viruses 2022, 14(11), 2397; https://doi.org/10.3390/v14112397 - 29 Oct 2022

Cited by 2 | Viewed by 2368

Abstract

Chronic hepatitis (CH) of dysmetabolic or viral etiology has been associated with poor prognosis in patients who experienced the severe acute respiratory coronavirus virus-2 (SARS-Cov-2) infection. We aimed to explore the impact of SARS-Cov-2 infection on disease severity in a group of patients [...] Read more.

Chronic hepatitis (CH) of dysmetabolic or viral etiology has been associated with poor prognosis in patients who experienced the severe acute respiratory coronavirus virus-2 (SARS-Cov-2) infection. We aimed to explore the impact of SARS-Cov-2 infection on disease severity in a group of patients with CH. Forty-two patients with CH of different etiology were enrolled (median age, 56 years; male gender, 59%). ACE2 and TMPRSS2 were measured in plasma samples of all patients by ELISA and in the liver tissue of a subgroup of 15 patients by Western blot. Overall, 13 patients (31%) experienced SARS-Cov-2 infection: 2/15 (15%) had CHB, 5/12 (39%) had CHC, and 6/15 (46%) had non-alcoholic fatty liver disease (NAFLD). Compared to viral CH patients, NAFLD subjects showed higher circulating ACE2 levels (p = 0.0019). Similarly, hepatic expression of ACE2 was higher in subjects who underwent SARS-Cov-2 infection compared to the counterpart, (3.24 ± 1.49 vs. 1.49 ± 1.32, p = 0.032). Conversely, hepatic TMPRSS2 was significantly lower in patients who experienced symptomatic COVID-19 disease compared to asymptomatic patients (p = 0.0038). Further studies are necessary to understand the impact of COVID-19 in patients with pre-existing liver diseases. Full article

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16 pages, 2404 KiB

Open AccessArticle

Evolutionary Pattern Comparisons of the SARS-CoV-2 Delta Variant in Countries/Regions with High and Low Vaccine Coverage

by Jiahao Zhang, Linqian Fan, Hanli Xu, Yuanhui Fu, Xianglei Peng, Yanpeng Zheng, Jiemei Yu and Jinsheng He

Viruses 2022, 14(10), 2296; https://doi.org/10.3390/v14102296 - 19 Oct 2022

Cited by 4 | Viewed by 2151

Abstract

It has been argued that vaccine-breakthrough infections of SARS-CoV-2 would likely accelerate the emergence of novel variants with immune evasion. This study explored the evolutionary patterns of the Delta variant in countries/regions with relatively high and low vaccine coverage based on large-scale sequences. [...] Read more.

It has been argued that vaccine-breakthrough infections of SARS-CoV-2 would likely accelerate the emergence of novel variants with immune evasion. This study explored the evolutionary patterns of the Delta variant in countries/regions with relatively high and low vaccine coverage based on large-scale sequences. Our results showed that (i) the sequences were grouped into two clusters (L and R); the R cluster was dominant, its proportion increased over time and was higher in the high-vaccine-coverage areas; (ii) genetic diversities in the countries/regions with low vaccine coverage were higher than those in the ones with high vaccine coverage; (iii) unique mutations and co-mutations were detected in different countries/regions; in particular, common co-mutations were exhibited in highly occurring frequencies in the areas with high vaccine coverage and presented in increasing frequencies over time in the areas with low vaccine coverage; (iv) five sites on the S protein were under strong positive selection in different countries/regions, with three in non-C to U sites (I95T, G142D and T950N), and the occurring frequencies of I95T in high vaccine coverage areas were higher, while G142D and T950N were potentially immune-pressure-selected sites; and (v) mutation at the N⁶-methyladenosine site 4 on ORF7a (C27527T, P45L) was detected and might be caused by immune pressure. Our study suggested that certain variation differences existed between countries/regions with high and low vaccine coverage, but they were not likely caused by host immune pressure. We inferred that no extra immune pressures on SARS-CoV-2 were generated with high vaccine coverage, and we suggest promoting and strengthening the uptake of the COVID-19 vaccine worldwide, especially in less developed areas. Full article

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8 pages, 247 KiB

Open AccessCommunication

Molnupiravir When Used Alone Seems to Be Safe and Effective as Outpatient COVID-19 Therapy for Hemodialyzed Patients and Kidney Transplant Recipients

by Paweł Poznański, Hanna Augustyniak-Bartosik, Anna Magiera-Żak, Karolina Skalec, Katarzyna Jakuszko, Oktawia Mazanowska, Dariusz Janczak, Magdalena Krajewska and Dorota Kamińska

Viruses 2022, 14(10), 2224; https://doi.org/10.3390/v14102224 - 9 Oct 2022

Cited by 21 | Viewed by 3511

Abstract

Background: Molnupiravir demonstrated an in vitro antiviral activity against positive-sense RNA viruses, including SARS-CoV-2. The study aimed to present the results of outpatient molnupiravir use in kidney transplant recipients and hemodialysis patients during the first months of 2022 in Poland. Methods: The retrospective [...] Read more.

Background: Molnupiravir demonstrated an in vitro antiviral activity against positive-sense RNA viruses, including SARS-CoV-2. The study aimed to present the results of outpatient molnupiravir use in kidney transplant recipients and hemodialysis patients during the first months of 2022 in Poland. Methods: The retrospective observational cohort study at one kidney transplant center included 36 patients diagnosed with COVID-19 with an automated nucleic acid amplification test on nasopharyngeal swab specimens. All patients received molnupiravir for home-based therapy at a dose of 800 mg every 12 h orally for 5 days. Both kidney transplant recipients (n = 16) and hemodialysis patients (n = 20) presented a lot of comorbidities with a Charlson comorbidity index of 4.1 and 5.1, respectively. Results: Patients presented with fever, cough, and weakness followed by muscle and joint pain. Five kidney transplant recipients experienced acute kidney injury with a rise in serum creatinine level from 0.4 to 1.9 mg/dL. No serious side effects of molnupiravir therapy or interactions with immunosuppressive medications were observed. Symptoms of COVID-19 improved rapidly or resolved within 24–48 h of starting treatment. Conclusion: The study suggests the safety and efficacy of molnupiravir therapy alone early after the onset of SARS-CoV-2 infection, but further investigations should be performed to confirm our preliminary results. To the best of the authors’ knowledge, it is the first published report on molnupiravir use in end-stage kidney disease (ESKD) patients on hemodialysis and the third concerning kidney transplant recipients. Full article

26 pages, 5839 KiB

Open AccessArticle

Model-Based Analysis of SARS-CoV-2 Infections, Hospitalization and Outcome in Germany, the Federal States and Districts

by Christiane Dings, Katharina Martha Götz, Katharina Och, Iryna Sihinevich, Quirin Werthner, Sigrun Smola, Marc Bliem, Felix Mahfoud, Thomas Volk, Sascha Kreuer, Jürgen Rissland, Dominik Selzer and Thorsten Lehr

Viruses 2022, 14(10), 2114; https://doi.org/10.3390/v14102114 - 24 Sep 2022

Cited by 7 | Viewed by 2357

Abstract

The coronavirus disease 2019 (COVID-19) pandemic challenged many national health care systems, with hospitals reaching capacity limits of intensive care units (ICU). Thus, the estimation of acute local burden of ICUs is critical for appropriate management of health care resources. In this work, [...] Read more.

The coronavirus disease 2019 (COVID-19) pandemic challenged many national health care systems, with hospitals reaching capacity limits of intensive care units (ICU). Thus, the estimation of acute local burden of ICUs is critical for appropriate management of health care resources. In this work, we applied non-linear mixed effects modeling to develop an epidemiological SARS-CoV-2 infection model for Germany, with its 16 federal states and 400 districts, that describes infections as well as COVID-19 inpatients, ICU patients with and without mechanical ventilation, recoveries, and fatalities during the first two waves of the pandemic until April 2021. Based on model analyses, covariates influencing the relation between infections and outcomes were explored. Non-pharmaceutical interventions imposed by governments were found to have a major impact on the spreading of SARS-CoV-2. Patient age and sex, the spread of variant B.1.1.7, and the testing strategy (number of tests performed weekly, rate of positive tests) affected the severity and outcome of recorded cases and could reduce the observed unexplained variability between the states. Modeling could reasonably link the discrepancies between fine-grained model simulations of the 400 German districts and the reported number of available ICU beds to coarse-grained COVID-19 patient distribution patterns within German regions. Full article

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7 pages, 848 KiB

Open AccessBrief Report

Burden of Pediatric SARS-CoV-2 Hospitalizations during the Omicron Wave in Germany

by Maren Doenhardt, Christin Gano, Anna-Lisa Sorg, Natalie Diffloth, Tobias Tenenbaum, Rüdiger von Kries, Reinhard Berner and Jakob P. Armann

Viruses 2022, 14(10), 2102; https://doi.org/10.3390/v14102102 - 22 Sep 2022

Cited by 10 | Viewed by 2355

Abstract

(1) Background: When the Omicron variant of SARS-CoV-2 first emerged in Germany in January 2022, data on related disease severity among children and adolescents were not yet available. Given Omicron’s high transmissibility, the ability to assess its impact on admission and hospitalization rates [...] Read more.

(1) Background: When the Omicron variant of SARS-CoV-2 first emerged in Germany in January 2022, data on related disease severity among children and adolescents were not yet available. Given Omicron’s high transmissibility, the ability to assess its impact on admission and hospitalization rates in children’s hospitals is critical for the purpose of understanding the scope of its burden on the German healthcare system. (2) Methods: From 24 January 2022 to 31 July 2022, SARS-CoV-2 cases admitted to German pediatric hospitals were monitored via a national, clinician-led reporting system (CLRS) established by the German Society for Pediatric Infectious Diseases (DGPI). Cases treated on general wards and intensive care units, as well as patient age and the need for respiratory support, were recorded. (3) Results: From January to July 2022, a median of 1.7 cases (range 0.4–3) per reporting pediatric hospital per day was hospitalized in general wards, whereas a median of 0.1 cases (range 0–0.4 cases) was admitted to intensive care units. Of all hospitalized patients, 4.2% received respiratory support. (4) Conclusions: Despite the high incidence rates documented in connection with the Omicron variant in early 2022, the number of pediatric hospital admissions, and especially the number of cases with the need for intensive care treatment and respiratory support due to symptomatic SARS-CoV-2 infection, remained relatively low. Higher Omicron incidence rates had only a modest impact on SARS-CoV-2-related admissions and hospitalization in German children’s hospitals. Full article

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14 pages, 1688 KiB

Open AccessArticle

Genomic and Epidemiological Features of COVID-19 in the Novosibirsk Region during the Beginning of the Pandemic

by Natalia Palyanova, Ivan Sobolev, Alexander Alekseev, Alexandra Glushenko, Evgeniya Kazachkova, Alexander Markhaev, Yulia Kononova, Marina Gulyaeva, Lubov Adamenko, Olga Kurskaya, Yuhai Bi, Yuhua Xin, Kirill Sharshov and Alexander Shestopalov

Viruses 2022, 14(9), 2036; https://doi.org/10.3390/v14092036 - 14 Sep 2022

Cited by 2 | Viewed by 2060

Abstract

In this retrospective, single-center study, we conducted an analysis of 13,699 samples from different individuals obtained from the Federal Research Center of Fundamental and Translational Medicine, from 1 April to 30 May 2020 in Novosibirsk region (population 2.8 million people). We identified 6.49% [...] Read more.

In this retrospective, single-center study, we conducted an analysis of 13,699 samples from different individuals obtained from the Federal Research Center of Fundamental and Translational Medicine, from 1 April to 30 May 2020 in Novosibirsk region (population 2.8 million people). We identified 6.49% positive for SARS-CoV-2 cases out of the total number of diagnostic tests, and 42% of them were from asymptomatic people. We also detected two asymptomatic people, who had no confirmed contact with patients with COVID-19. The highest percentage of positive samples was observed in the 80+ group (16.3%), while among the children and adults it did not exceed 8%. Among all the people tested, 2423 came from a total of 80 different destinations and only 27 of them were positive for SARS-CoV-2. Out of all the positive samples, 15 were taken for SARS-CoV-2 sequencing. According to the analysis of the genome sequences, the SARS-CoV-2 variants isolated in the Novosibirsk region at the beginning of the pandemic belonged to three phylogenetic lineages according to the Pangolin classification: B.1, B.1.1, and B.1.1.129. All Novosibirsk isolates contained the D614G substitution in the Spike protein, two isolates werecharacterized by an additional M153T mutation, and one isolate wascharacterized by the L5F mutation. Full article

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12 pages, 775 KiB

Open AccessArticle

Epstein–Barr Virus and Human Herpesvirus-6 Reactivation in Acute COVID-19 Patients

by Bailey Brooks, Christina Tancredi, Yufeng Song, Alemu Tekewe Mogus, Meei-Li W. Huang, Haiying Zhu, Tuan L. Phan, Harrison Zhu, Alexandra Kadl, Judith Woodfolk, Keith R. Jerome and Steven L. Zeichner

Viruses 2022, 14(9), 1872; https://doi.org/10.3390/v14091872 - 25 Aug 2022

Cited by 25 | Viewed by 4379

Abstract

Beyond their pulmonary disease, many COVID-19 patients experience a complex constellation of characteristics, including hyperinflammatory responses, autoimmune disorders, and coagulopathies. However, the pathogenesis of these aspects of COVID-19 is obscure. More than 90% of people are latently infected with the lymphotropic herpesviruses Epstein–Barr [...] Read more.

Beyond their pulmonary disease, many COVID-19 patients experience a complex constellation of characteristics, including hyperinflammatory responses, autoimmune disorders, and coagulopathies. However, the pathogenesis of these aspects of COVID-19 is obscure. More than 90% of people are latently infected with the lymphotropic herpesviruses Epstein–Barr Virus (EBV) and/or Human Herpesvirus-6 (HHV-6). Some of the inflammatory features of COVID-19 resemble clinical syndromes seen during EBV and HHV-6 infection, and these latent viruses can be reactivated by inflammatory mediators. We hypothesized that EBV and HHV-6 reactivation might be a common feature of early COVID-19, particularly in patients with more inflammation. We tested for EBV and HHV-6 reactivation in 67 patients acutely hospitalized with COVID-19 using previously validated quantitative PCR assays on the plasma. In our cohort, we found that 15/67 (22.4%) patients had detectable EBV and 3/67 (4.5%) had detectable HHV-6. This frequency of activation is somewhat more than the frequency reported for some healthy cohorts, such as blood donors and other healthy control cohorts. There was no association between EBV or HHV-6 and markers indicative of more inflammatory disease. We conclude that EBV and HHV-6 activation at about day 7 of hospitalization occurred in a modest fraction of our cohort of COVID-19 patients and was not associated with high levels of inflammation. In the modest fraction of patients, EBV and HHV-6 reactivation could contribute to some features of acute disease and pre-disposition to post-acute sequelae in a subset of patients. Full article

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15 pages, 626 KiB

Open AccessArticle

Results of a European-Wide External Quality Assessment (EQA) Scheme for Serological Detection of Anti-SARS-CoV-2 (CoVimm)—Pitfalls of Routine Application

by Maximilian Kittel, Romy Eichner, Sihem Aida, Anna Bode, Volker Ast, Anja Kessler, Michael Neumaier, Roman Wölfel and Verena Haselmann

Viruses 2022, 14(8), 1662; https://doi.org/10.3390/v14081662 - 28 Jul 2022

Cited by 4 | Viewed by 2253

Abstract

Background: During the last two years, a variety of assays for the serological detection of antibodies to the new SARS-CoV-2 virus have been launched and used as part of standard care in many laboratories. The pace with which these tests have been introduced [...] Read more.

Background: During the last two years, a variety of assays for the serological detection of antibodies to the new SARS-CoV-2 virus have been launched and used as part of standard care in many laboratories. The pace with which these tests have been introduced into routine care emphasizes the importance of quality measures for analytical methods, particularly with regard to the implications of results for clinical and epidemiologic decisions. Accuracy, reliability and comparability of analytical test results are thus essential, and here external quality assessment (EQA) is the most important quality assurance tool. It allows us to achieve harmonization of test methods as a prerequisite for a high standard of performance for laboratory and analytical techniques and their interpretation. Methods: This EQA scheme consisted of pre-characterized clinical biospecimens dedicated to the analysis of anti-SARS-CoV-2 IgG total antibodies and differentiation into spike protein-specific IgG antibodies against SARS-CoV-2 (anti-S-SARS-CoV-2) and nucleocapsid-specific IgG antibodies against SARS-CoV-2 (anti-N-SARS-CoV-2). Results: A total of 239 laboratories across Europe participated in this scheme, called CoVimm. In detail, 536 results for anti-SARS-CoV-2 IgG, 431 results for anti-S-SARS-CoV-2 IgG, and 200 results for anti-N-SARS-CoV-2 IgG were reported. Based on the pre-defined thresholds, the success rates for the determination of anti-S-SARS-CoV-2 IgG and anti-N-SARS-CoV-2 IgG were 96% and 90%, respectively. Interestingly, only 64% of the participating laboratories successfully passed the EQA scheme for the determination of total anti-SARS-CoV-2 IgG. Conclusions: This EQA revealed serious concerns regarding the reliability and appropriate use of anti-SARS-CoV-2 antibody assays in routine care. In addition to the wide heterogeneity of different assays used by participating laboratories, a lack of standardization and harmonization is also evident. This is of particular importance for reliable and clinically meaningful interpretation of test results. Full article

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15 pages, 2164 KiB

Open AccessCase Report

The Role of Lebanon in the COVID-19 Butterfly Effect: The B.1.398 Example

by Dalal Nour, Rayane Rafei, Alessandra P. Lamarca, Luiz G. P. de Almeida, Marwan Osman, Mohamad Bachar Ismail, Hassan Mallat, Atika Berry, Gwendolyne Burfin, Quentin Semanas, Laurence Josset, Hamad Hassan, Fouad Dabboussi, Bruno Lina, Philippe Colson, Ana Tereza R. Vasconcelos and Monzer Hamze

Viruses 2022, 14(8), 1640; https://doi.org/10.3390/v14081640 - 27 Jul 2022

Cited by 7 | Viewed by 2505

Abstract

In the present study, we provide a retrospective genomic surveillance of the SARS-CoV-2 pandemic in Lebanon; we newly sequence the viral genomes of 200 nasopharyngeal samples collected between July 2020 and February 2021 from patients in different regions of Lebanon and from travelers [...] Read more.

In the present study, we provide a retrospective genomic surveillance of the SARS-CoV-2 pandemic in Lebanon; we newly sequence the viral genomes of 200 nasopharyngeal samples collected between July 2020 and February 2021 from patients in different regions of Lebanon and from travelers crossing the Lebanese–Syrian border, and we also analyze the Lebanese genomic dataset available at GISAID. Our results show that SARS-CoV-2 infections in Lebanon during this period were shaped by the turnovers of four dominant SARS-CoV-2 lineages, with B.1.398 being the first to thoroughly dominate. Lebanon acted as a dispersal center of B.1.398 to other countries, with intercontinental transmissions being more common than within-continent. Within the country, the district of Tripoli, which was the source of 43% of the total B.1.398 sequences in our study, was identified as being an important source of dispersal in the country. In conclusion, our findings exemplify the butterfly effect, by which a lineage that emerges in a small area can be spread around the world, and highlight the potential role of developing countries in the emergence of new variants. Full article

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20 pages, 8691 KiB

Open AccessArticle

Network Pharmacology and Molecular Docking Elucidate the Underlying Pharmacological Mechanisms of the Herb Houttuynia cordata in Treating Pneumonia Caused by SARS-CoV-2

by Junying Liu, Shouli Yuan, Yao Yao, Jinfan Wang, Gaia Scalabrino, Shibo Jiang and Helen Sheridan

Viruses 2022, 14(7), 1588; https://doi.org/10.3390/v14071588 - 21 Jul 2022

Cited by 10 | Viewed by 4157

Abstract

Used in Asian countries, including China, Japan, and Thailand, Houttuynia cordata Thumb (H. cordata; Saururaceae, HC) is a traditional herbal medicine that possesses favorable antiviral properties. As a potent folk therapy used to treat pulmonary infections, further research is required to [...] Read more.

Used in Asian countries, including China, Japan, and Thailand, Houttuynia cordata Thumb (H. cordata; Saururaceae, HC) is a traditional herbal medicine that possesses favorable antiviral properties. As a potent folk therapy used to treat pulmonary infections, further research is required to fully elucidate the mechanisms of its pharmacological activities and explore its therapeutic potential for treating pneumonia caused by SARS-CoV-2. This study explores the pharmacological mechanism of HC on pneumonia using a network pharmacological approach combined with reprocessing expression profiling by high-throughput sequencing to demonstrate the therapeutic mechanisms of HC for treating pneumonia at a systemic level. The integration of these analyses suggested that target factors are involved in four signaling pathways, including PI3K-Akt, Jak-STAT, MAPK, and NF-kB. Molecular docking and molecular dynamics simulation were applied to verify these results, indicating a stable combination between four metabolites (Afzelin, Apigenin, Kaempferol, Quercetin) and six targets (DPP4, ELANE, HSP90AA1, IL6, MAPK1, SERPINE1). These natural metabolites have also been reported to bind with ACE2 and 3CLpro of SARS-CoV-2, respectively. The data suggest that HC exerts collective therapeutic effects against pneumonia caused by SARS-CoV-2 and provides a theoretical basis for further study of the active drug-like ingredients and mechanism of HC in treating pneumonia. Full article

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16 pages, 1850 KiB

Open AccessArticle

Predictive Models of within- and between-Species SARS-CoV-2 Transmissibility

by Ricardo Soares, Cristina P. Vieira and Jorge Vieira

Viruses 2022, 14(7), 1565; https://doi.org/10.3390/v14071565 - 19 Jul 2022

Cited by 1 | Viewed by 2373

Abstract

Viruses from the Coronaviridae family have been reported to infect a large range of hosts, including humans. The latest human-infecting coronavirus, SARS-CoV-2, turned into a pandemic and subtypes with different transmissibility have appeared since then. The SARS-CoV-2 Spike (S) protein interacts with the [...] Read more.

Viruses from the Coronaviridae family have been reported to infect a large range of hosts, including humans. The latest human-infecting coronavirus, SARS-CoV-2, turned into a pandemic and subtypes with different transmissibility have appeared since then. The SARS-CoV-2 Spike (S) protein interacts with the angiotensin-converting enzyme 2 (ACE2) host receptor, and thus, in silico models, based on the structural features of the SARS-CoV-2 S protein–ACE2 receptor complex, as well as ACE2 amino acid patterns, may be used to predict the within- and between-species transmissibility of SARS-CoV-2 subtypes. Here, it is shown that at the beginning of the pandemic, the SARS-CoV-2 S protein was, as expected for a virus that just jumped the species barrier, ill-adapted to the human ACE2 receptor, and that the replacement of one SARS-CoV-2 variant by another is partially due to a better fitting of the S protein–human ACE2 complex. Moreover, it is shown that mutations that are predicted to lead to a better fit have increased in the population due to positive selection. It is also shown that the number of ACE2-interfacing residues is positively correlated with the transmissibility rate of SARS-CoV-2 variants. Finally, it is shown that the number of species that are susceptible to infection by SARS-CoV-2, and that could be a reservoir for this virus, is likely higher than previously thought. Full article

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10 pages, 1164 KiB

Open AccessArticle

Description of a One-Year Succession of Variants of Interest and Concern of SARS-CoV-2 in Venezuela

by Rossana C. Jaspe, Carmen L. Loureiro, Yoneira Sulbaran, Zoila C. Moros, Pierina D’Angelo, Mariana Hidalgo, Lieska Rodríguez, Víctor Alarcón, Marwan Aguilar, Doneyla Sánchez, Jesús Ramírez, Domingo J. Garzaro, José Luis Zambrano, Ferdinando Liprandi, Héctor R. Rangel and Flor H. Pujol

Viruses 2022, 14(7), 1378; https://doi.org/10.3390/v14071378 - 24 Jun 2022

Cited by 8 | Viewed by 2298

Abstract

Some of the lineages of SARS-CoV-2, the new coronavirus responsible for COVID-19, exhibit higher transmissibility or partial resistance to antibody-mediated neutralization and were designated by WHO as Variants of Interests (VOIs) or Concern (VOCs). The aim of this study was to monitor the [...] Read more.

Some of the lineages of SARS-CoV-2, the new coronavirus responsible for COVID-19, exhibit higher transmissibility or partial resistance to antibody-mediated neutralization and were designated by WHO as Variants of Interests (VOIs) or Concern (VOCs). The aim of this study was to monitor the dissemination of VOIs and VOCs in Venezuela from March 2021 to February 2022. A 614 nt genomic fragment was sequenced for the detection of some relevant mutations of these variants. Their presence was confirmed by complete genome sequencing, with a correlation higher than 99% between both methodologies. After the introduction of the Gamma VOC since the beginning of the year 2021, the variants Alpha VOC and Lambda VOI were detected as early as March 2021, at a very low frequency. In contrast, the Mu VOI, detected in May 2021, was able to circulate throughout the country. After the detection of the Delta VOC in June 2021, it became the predominant circulating variant. With the arrival of the Omicron VOC in December, this variant was able to displace the Delta one in less than one month. Full article

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14 pages, 2970 KiB

Open AccessArticle

A Newly Engineered A549 Cell Line Expressing ACE2 and TMPRSS2 Is Highly Permissive to SARS-CoV-2, Including the Delta and Omicron Variants

by Ching-Wen Chang, Krishna Mohan Parsi, Mohan Somasundaran, Emma Vanderleeden, Ping Liu, John Cruz, Alyssa Cousineau, Robert W. Finberg and Evelyn A. Kurt-Jones

Viruses 2022, 14(7), 1369; https://doi.org/10.3390/v14071369 - 23 Jun 2022

Cited by 24 | Viewed by 5335

Abstract

New variants of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) continue to emerge, causing surges, breakthrough infections, and devastating losses—underscoring the importance of identifying SARS-CoV-2 antivirals. A simple, accessible human cell culture model permissive to SARS-CoV-2 variants is critical for identifying and assessing [...] Read more.

New variants of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) continue to emerge, causing surges, breakthrough infections, and devastating losses—underscoring the importance of identifying SARS-CoV-2 antivirals. A simple, accessible human cell culture model permissive to SARS-CoV-2 variants is critical for identifying and assessing antivirals in a high-throughput manner. Although human alveolar A549 cells are a valuable model for studying respiratory virus infections, they lack two essential host factors for SARS-CoV-2 infection: angiotensin-converting enzyme 2 (ACE2) and transmembrane serine protease 2 (TMPRSS2). SARS-CoV-2 uses the ACE2 receptor for viral entry and TMPRSS2 to prime the SARS-CoV-2 spike protein, both of which are negligibly expressed in A549 cells. Here, we report the generation of a suitable human cell line for SARS-CoV-2 studies by transducing human ACE2 and TMPRSS2 into A549 cells. We show that subclones highly expressing ACE2 and TMPRSS2 (“ACE2plus” and the subclone “ACE2plusC3”) are susceptible to infection with SARS-CoV-2, including the delta and omicron variants. These subclones express more ACE2 and TMPRSS2 transcripts than existing commercial A549 cells engineered to express ACE2 and TMPRSS2. Additionally, the antiviral drugs EIDD-1931, remdesivir, nirmatrelvir, and nelfinavir strongly inhibit SARS-CoV-2 variants in our infection model. Our data show that ACE2plusC3 cells are highly permissive to SARS-CoV-2 infection and can be used to identify anti-SARS-CoV-2 drugs. Full article

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21 pages, 1889 KiB

Open AccessArticle

Time Trend in SARS-CoV-2 Seropositivity, Surveillance Detection- and Infection Fatality Ratio until Spring 2021 in the Tirschenreuth County—Results from a Population-Based Longitudinal Study in Germany

by Sebastian Einhauser, David Peterhoff, Stephanie Beileke, Felix Günther, Hans-Helmut Niller, Philipp Steininger, Antje Knöll, Klaus Korn, Melanie Berr, Anja Schütz, Simon Wiegrebe, Klaus J. Stark, André Gessner, Ralph Burkhardt, Michael Kabesch, Holger Schedl, Helmut Küchenhoff, Annette B. Pfahlberg, Iris M. Heid, Olaf Gefeller, Klaus Überla and Ralf Wagner Show full author list Hide full author list

Viruses 2022, 14(6), 1168; https://doi.org/10.3390/v14061168 - 27 May 2022

Cited by 5 | Viewed by 3170

Abstract

Herein, we provide results from a prospective population-based longitudinal follow-up (FU) SARS-CoV-2 serosurveillance study in Tirschenreuth, the county which was hit hardest in Germany in spring 2020 and early 2021. Of 4203 individuals aged 14 years or older enrolled at baseline (BL, June [...] Read more.

Herein, we provide results from a prospective population-based longitudinal follow-up (FU) SARS-CoV-2 serosurveillance study in Tirschenreuth, the county which was hit hardest in Germany in spring 2020 and early 2021. Of 4203 individuals aged 14 years or older enrolled at baseline (BL, June 2020), 3546 participated at FU1 (November 2020) and 3391 at FU2 (April 2021). Key metrics comprising standardized seroprevalence, surveillance detection ratio (SDR), infection fatality ratio (IFR) and success of the vaccination campaign were derived using the Roche N- and S-Elecsys anti-SARS-CoV-2 test together with a self-administered questionnaire. N-seropositivity at BL was 9.2% (1st wave). While we observed a low new seropositivity between BL and FU1 (0.9%), the combined 2nd and 3rd wave accounted for 6.1% new N-seropositives between FU1 and FU2 (ever seropositives at FU2: 15.4%). The SDR decreased from 5.4 (BL) to 1.1 (FU2) highlighting the success of massively increased testing in the population. The IFR based on a combination of serology and registration data resulted in 3.3% between November 2020 and April 2021 compared to 2.3% until June 2020. Although IFRs were consistently higher at FU2 compared to BL across age-groups, highest among individuals aged 70+ (18.3% versus 10.7%, respectively), observed differences were within statistical uncertainty bounds. While municipalities with senior care homes showed a higher IFR at BL (3.0% with senior care home vs. 0.7% w/o), this effect diminished at FU2 (3.4% vs. 2.9%). In April 2021 (FU2), vaccination rate in the elderly was high (>77.4%, age-group 80+). Full article

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13 pages, 1382 KiB

Open AccessArticle

Impaired Vagal Activity in Long-COVID-19 Patients

by Domenico Acanfora, Maria Nolano, Chiara Acanfora, Camillo Colella, Vincenzo Provitera, Giuseppe Caporaso, Gabriele Rosario Rodolico, Alessandro Santo Bortone, Gennaro Galasso and Gerardo Casucci

Viruses 2022, 14(5), 1035; https://doi.org/10.3390/v14051035 - 13 May 2022

Cited by 30 | Viewed by 5802

Abstract

Long-COVID-19 refers to the signs and symptoms that continue or develop after the “acute COVID-19” phase. These patients have an increased risk of multiorgan dysfunction, readmission, and mortality. In Long-COVID-19 patients, it is possible to detect a persistent increase in D-Dimer, NT-ProBNP, and [...] Read more.

Long-COVID-19 refers to the signs and symptoms that continue or develop after the “acute COVID-19” phase. These patients have an increased risk of multiorgan dysfunction, readmission, and mortality. In Long-COVID-19 patients, it is possible to detect a persistent increase in D-Dimer, NT-ProBNP, and autonomic nervous system dysfunction. To verify the dysautonomia hypothesis in Long-COVID-19 patients, we studied heart rate variability using 12-lead 24-h ECG monitoring in 30 Long-COVID-19 patients and 20 No-COVID patients. Power spectral analysis of heart rate variability was lower in Long-COVID-19 patients both for total power (7.46 ± 0.5 vs. 8.08 ± 0.6; p < 0.0001; Cohens-d = 1.12) and for the VLF (6.84 ± 0.8 vs. 7.66 ± 0.6; p < 0.0001; Cohens-d = 1.16) and HF (4.65 ± 0.9 vs. 5.33 ± 0.9; p = 0.015; Cohens-d = 0.76) components. The LF/HF ratio was significantly higher in Long-COVID-19 patients (1.46 ± 0.27 vs. 1.23 ± 0.13; p = 0.001; Cohens-d = 1.09). On multivariable analysis, Long-COVID-19 is significantly correlated with D-dimer (standardized β-coefficient = 0.259), NT-ProBNP (standardized β-coefficient = 0.281), HF component of spectral analysis (standardized β-coefficient = 0.696), and LF/HF ratio (standardized β-coefficient = 0.820). Dysautonomia may explain the persistent symptoms in Long COVID-19 patients. The persistence of a procoagulative state and an elevated myocardial strain could explain vagal impairment in these patients. In Long-COVID-19 patients, impaired vagal activity, persistent increases of NT-ProBNP, and a prothrombotic state require careful monitoring and appropriate intervention. Full article

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15 pages, 907 KiB

Open AccessArticle

Efficacy of the Sentinox Spray in Reducing Viral Load in Mild COVID-19 and Its Virucidal Activity against Other Respiratory Viruses: Results of a Randomized Controlled Trial and an In Vitro Study

by Donatella Panatto, Andrea Orsi, Bianca Bruzzone, Valentina Ricucci, Guido Fedele, Giorgio Reiner, Nadia Giarratana, Alexander Domnich, Giancarlo Icardi and STX Study Group

Viruses 2022, 14(5), 1033; https://doi.org/10.3390/v14051033 - 12 May 2022

Cited by 4 | Viewed by 6101

Abstract

Sentinox (STX) is an acid-oxidizing solution containing hypochlorous acid in spray whose virucidal activity against SARS-CoV-2 has been demonstrated. In this paper, results of a randomized controlled trial (RCT) on the efficacy of STX in reducing viral load in mild COVID-19 patients (NCT04909996) [...] Read more.

Sentinox (STX) is an acid-oxidizing solution containing hypochlorous acid in spray whose virucidal activity against SARS-CoV-2 has been demonstrated. In this paper, results of a randomized controlled trial (RCT) on the efficacy of STX in reducing viral load in mild COVID-19 patients (NCT04909996) and a complementary in vitro study on its activity against different respiratory viruses are reported. In the RCT, 57 patients were randomized (1:1:1) to receive STX three (STX-3) or five (STX-5) times/day plus standard therapy or standard therapy only (controls). Compared with controls, the log₁₀ load reduction in groups STX-3 and STX-5 was 1.02 (p = 0.14) and 0.18 (p = 0.80), respectively. These results were likely driven by outliers with extreme baseline viral loads. When considering subjects with baseline cycle threshold values of 20–30, STX-3 showed a significant (p = 0.016) 2.01 log₁₀ reduction. The proportion of subjects that turned negative by the end of treatment (day 5) was significantly higher in the STX-3 group than in controls, suggesting a shorter virus clearance time. STX was safe and well-tolerated. In the in vitro study, ≥99.9% reduction in titers against common respiratory viruses was observed. STX is a safe device with large virucidal spectrum and may reduce viral loads in mild COVID-19 patients. Full article

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8 pages, 796 KiB

Open AccessArticle

Detection of SARS-CoV-2 Nucleocapsid, Spike, and Neutralizing Antibodies in Vaccinated Japanese

by Rie Midorikawa, Moriyuki Nakama, Hiroshi Furukawa, Shomi Oka, Takashi Higuchi, Hideaki Nagai, Nobuhiro Nagai and Shigeto Tohma

Viruses 2022, 14(5), 965; https://doi.org/10.3390/v14050965 - 5 May 2022

Cited by 5 | Viewed by 2432

Abstract

Serological detection of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) nucleocapsid (N), spike (S), and neutralizing antibodies (Abs) is commonly undertaken to evaluate the efficacy of vaccination. However, the relative efficiency of different SARS-CoV-2 Ab detection systems has not been extensively investigated. Here, [...] Read more.

Serological detection of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) nucleocapsid (N), spike (S), and neutralizing antibodies (Abs) is commonly undertaken to evaluate the efficacy of vaccination. However, the relative efficiency of different SARS-CoV-2 Ab detection systems has not been extensively investigated. Here, we evaluated serological test systems in vaccinated Japanese. SARS-CoV-2 N, S, and neutralizing Abs in sera of 375 healthy subjects a mean 253 days after vaccination were assessed. The sensitivity of Elecsys Anti-SARS-CoV-2 S (Roche S) and Anti-SARS-CoV-2 S IgG (Fujirebio S) was 100% and 98.9%, respectively, with a specificity of 100% for both. The sensitivity of Anti-SARS-CoV-2 neutralizing Ab (MBL Neu) was 2.7%, and the specificity was 100%. Fujirebio S correlated with Roche S (rho = 0.9182, p = 3.97 × 10⁻¹⁵²). Fujirebio S (rho = 0.1295, p = 0.0121) and Roche S (rho = 0.1232, p = 0.0170) correlated weakly with MBL Neu. However, Roche S did correlate with MBL Neu in patients with COVID-19 (rho = 0.8299, p = 1.01 × 10⁻¹²) and in healthy subjects more recently after vaccination (mean of 90 days, rho = 0.5306, p = 0.0003). Thus, the Fujirebio S and Roche S results were very similar, but neither correlated with neutralizing antibody titers by MBL Neu at a later time after vaccination. Full article

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14 pages, 1762 KiB

Open AccessArticle

SARS-CoV-2 Variants in Paraguay: Detection and Surveillance with an Economical and Scalable Molecular Protocol

by Magaly Martinez, Phuong-Vi Nguyen, Maxwell Su, Fátima Cardozo, Adriana Valenzuela, Laura Franco, María Eugenia Galeano, Leticia Elizabeth Rojas, Chyntia Carolina Díaz Acosta, Jonás Fernández, Joel Ortiz, Florencia del Puerto, Laura Mendoza, Eva Nara, Alejandra Rojas and Jesse J. Waggoner

Viruses 2022, 14(5), 873; https://doi.org/10.3390/v14050873 - 22 Apr 2022

Cited by 10 | Viewed by 3429

Abstract

SARS-CoV-2 variant detection relies on resource-intensive whole-genome sequencing methods. We sought to develop a scalable protocol for variant detection and surveillance in Paraguay, pairing rRT-PCR for spike mutations with Nanopore sequencing. A total of 201 acute-phase nasopharyngeal samples were included. Samples were positive [...] Read more.

SARS-CoV-2 variant detection relies on resource-intensive whole-genome sequencing methods. We sought to develop a scalable protocol for variant detection and surveillance in Paraguay, pairing rRT-PCR for spike mutations with Nanopore sequencing. A total of 201 acute-phase nasopharyngeal samples were included. Samples were positive for the SARS-CoV-2 N2 target and tested with the Spike SNP assay to detect mutations associated with the following variants: alpha (501Y), beta/gamma (417variant/484K/501Y), delta (452R/478K), and lambda (452Q/490S). Spike SNP calls were confirmed using amplicon (Sanger) sequencing and whole-genome (Nanopore) sequencing on a subset of samples with confirmed variant lineages. Samples had a mean N2 Ct of 20.8 (SD 5.6); 198/201 samples (98.5%) tested positive in the Spike SNP assay. The most common genotype was 417variant/484K/501Y, detected in 102/198 samples (51.5%), which was consistent with the P.1 lineage (gamma variant) in Paraguay. No mutations (K417 only) were found in 64/198 (32.3%), and K417/484K was identified in 22/198 (11.1%), consistent with P.2 (zeta). Seven samples (3.5%) tested positive for 452R without 478K, and one sample with genotype K417/501Y was confirmed as B.1.1.7 (alpha). The results were confirmed using Sanger sequencing in 181/181 samples, and variant calls were consistent with Nanopore sequencing in 29/29 samples. The Spike SNP assay could improve population-level surveillance for mutations associated with SARS-CoV-2 variants and inform the judicious use of sequencing resources. Full article

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18 pages, 1806 KiB

Open AccessArticle

Early and Longitudinal Humoral Response to the SARS-CoV-2 mRNA BNT162b2 Vaccine in Healthcare Workers: Significance of BMI, Adipose Tissue and Muscle Mass on Long-Lasting Post-Vaccinal Immunity

by Marlena Golec, Martyna Fronczek, Joanna Zembala-John, Martyna Chrapiec, Adam Konka, Karolina Wystyrk, Hanna Botor, Zenon Brzoza, Sławomir Kasperczyk and Rafał Jakub Bułdak

Viruses 2022, 14(5), 868; https://doi.org/10.3390/v14050868 - 22 Apr 2022

Cited by 7 | Viewed by 3154

Abstract

Background: This study aimed to investigate the early and longitudinal humoral response in Healthcare Workers (HCWs) after two doses of the BNT162b2 vaccine and to assess the association between metabolic and anthropometric parameters and the humoral response after vaccination. Methods: The study included [...] Read more.

Background: This study aimed to investigate the early and longitudinal humoral response in Healthcare Workers (HCWs) after two doses of the BNT162b2 vaccine and to assess the association between metabolic and anthropometric parameters and the humoral response after vaccination. Methods: The study included 243 fully vaccinated HCWs: 25.50% previously infected with SARS-CoV-2 (with prior history of COVID-19—PH) and 74.40%—uninfected, seronegative before the first vaccination (with no prior history of COVID-19—NPH). IgG antibodies were measured, and sera were collected: prior to the vaccination, 21 days after the first dose, and 14 days and 8 months after the second dose. Results: 21 days after the first dose, 90.95% of individuals were seropositive; 14 days after the second dose, persistent immunity was observed in 99.18% HCWs, 8 months after complete vaccination—in 61.73%. Statistical analysis revealed that HCWs with PH had a greater chance of maintaining a humoral response beyond eight months after vaccination. Increased muscle mass, decreased fat mass, and younger age may positively affect long-term immunity. Smokers have a reduced chance of developing immunity compared to non-smokers. Conclusions: Fully vaccinated HCWs with PH are more likely to be seropositive than fully inoculated volunteers with NPH. Full article

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14 pages, 2345 KiB

Open AccessArticle

Delta Variant of SARS-CoV-2 Replacement in Brazil: A National Epidemiologic Surveillance Program

by Joice P. Silva, Aline B. de Lima, Luige B. Alvim, Frederico S. V. Malta, Cristiane P. T. B. Mendonça, Paula L. C. Fonseca, Filipe R. R. Moreira, Daniel C. Queiroz, Jorge G. G. Ferreira, Alessandro C. S. Ferreira, Renan P. Souza, Renato S. Aguiar and Danielle A. G. Zauli

Viruses 2022, 14(5), 847; https://doi.org/10.3390/v14050847 - 20 Apr 2022

Cited by 14 | Viewed by 4491

Abstract

Coronavirus disease 2019 (COVID-19) pandemic has caused immeasurable impacts on the health and socioeconomic system. The real-time identification and characterization of new Variants of Concern (VOCs) are critical to comprehend its emergence and spread worldwide. In this sense, we carried out a national [...] Read more.

Coronavirus disease 2019 (COVID-19) pandemic has caused immeasurable impacts on the health and socioeconomic system. The real-time identification and characterization of new Variants of Concern (VOCs) are critical to comprehend its emergence and spread worldwide. In this sense, we carried out a national epidemiological surveillance program in Brazil from April to October 2021. Genotyping by reverse transcription-quantitative polymerase chain reaction (RT-qPCR) and sequencing were performed to monitor the dynamics and dissemination of VOCs in samples from 15 federative units. Delta VOC was first detected on June 2021 and took sixteen weeks to replace Gamma. To assess the transmissibility potential of Gamma and Delta VOCs, we studied the dynamics of RT-qPCR cycle threshold (Ct) score in the dominance period of each variant. The data suggest that Delta VOC has a higher transmission rate than Gamma VOC. We also compared relevant symptom patterns in individuals infected with both VOCs. The Delta-infected subjects were less likely to have low oxygen saturation or fatigue, altered results on chest computed tomography, and a propensity for altered X-rays. Altogether, we described the replacement of Gamma by Delta, Delta enhanced transmissibility, and differences in symptom presentation. Full article

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16 pages, 1640 KiB

Open AccessArticle

Investigations on SARS-CoV-2 Susceptibility of Domestic and Wild Animals Using Primary Cell Culture Models Derived from the Upper and Lower Respiratory Tract

by Iris Färber, Johannes Krüger, Cheila Rocha, Federico Armando, Maren von Köckritz-Blickwede, Stefan Pöhlmann, Armin Braun, Wolfgang Baumgärtner, Sandra Runft and Nadine Krüger

Viruses 2022, 14(4), 828; https://doi.org/10.3390/v14040828 - 16 Apr 2022

Cited by 10 | Viewed by 3415

Abstract

Several animal species are susceptible to SARS-CoV-2 infection, as documented by case reports and serological and in vivo infection studies. However, the susceptibility of many animal species remains unknown. Furthermore, the expression patterns of SARS-CoV-2 entry factors, such as the receptor angiotensin-converting enzyme [...] Read more.

Several animal species are susceptible to SARS-CoV-2 infection, as documented by case reports and serological and in vivo infection studies. However, the susceptibility of many animal species remains unknown. Furthermore, the expression patterns of SARS-CoV-2 entry factors, such as the receptor angiotensin-converting enzyme 2 (ACE2), as well as transmembrane protease serine subtype 2 (TMPRSS2) and cathepsin L (CTSL), cellular proteases involved in SARS-CoV-2 spike protein activation, are largely unexplored in most species. Here, we generated primary cell cultures from the respiratory tract of domestic and wildlife animals to assess their susceptibility to SARS-CoV-2 infection. Additionally, the presence of ACE2, TMPRSS2 and CTSL within respiratory tract compartments was investigated in a range of animals, some with unknown susceptibility to SARS-CoV-2. Productive viral replication was observed in the nasal mucosa explants and precision-cut lung slices from dogs and hamsters, whereas culture models from ferrets and multiple ungulate species were non-permissive to infection. Overall, whereas TMPRSS2 and CTSL were equally expressed in the respiratory tract, the expression levels of ACE2 were more variable, suggesting that a restricted availability of ACE2 may contribute to reduced susceptibility. Summarized, the experimental infection of primary respiratory tract cell cultures, as well as an analysis of entry-factor distribution, enable screening for SARS-CoV-2 animal reservoirs. Full article

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18 pages, 3934 KiB

Open AccessArticle

Genome Profiling of SARS-CoV-2 in Indonesia, ASEAN and the Neighbouring East Asian Countries: Features, Challenges and Achievements

by Inswasti Cahyani, Eko W. Putro, Asep M. Ridwanuloh, Satrio Wibowo, Hariyatun Hariyatun, Gita Syahputra, Gilang Akbariani, Ahmad R. Utomo, Mohammad Ilyas, Matthew Loose, Wien Kusharyoto and Susanti Susanti

Viruses 2022, 14(4), 778; https://doi.org/10.3390/v14040778 - 8 Apr 2022

Cited by 16 | Viewed by 3674

Abstract

Whole-genome sequencing (WGS) has played a significant role in understanding the epidemiology and biology of SARS-CoV-2 virus. Here, we investigate the use of SARS-CoV-2 WGS in Southeast and East Asian countries as a genomic surveillance during the COVID-19 pandemic. Nottingham–Indonesia Collaboration for Clinical [...] Read more.

Whole-genome sequencing (WGS) has played a significant role in understanding the epidemiology and biology of SARS-CoV-2 virus. Here, we investigate the use of SARS-CoV-2 WGS in Southeast and East Asian countries as a genomic surveillance during the COVID-19 pandemic. Nottingham–Indonesia Collaboration for Clinical Research and Training (NICCRAT) initiative has facilitated collaboration between the University of Nottingham and a team in the Research Center for Biotechnology, National Research and Innovation Agency (BRIN), to carry out a small number of SARS-CoV-2 WGS in Indonesia using Oxford Nanopore Technology (ONT). Analyses of SARS- CoV-2 genomes deposited on GISAID reveal the importance of clinical and demographic metadata collection and the importance of open access and data sharing. Lineage and phylogenetic analyses of two periods defined by the Delta variant outbreak reveal that: (1) B.1.466.2 variants were the most predominant in Indonesia before the Delta variant outbreak, having a unique spike gene mutation N439K at more than 98% frequency, (2) Delta variants AY.23 sub-lineage took over after June 2021, and (3) the highest rate of virus transmissions between Indonesia and other countries was through interactions with Singapore and Japan, two neighbouring countries with a high degree of access and travels to and from Indonesia. Full article

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9 pages, 4995 KiB

Open AccessArticle

Avidity of IgG to SARS-CoV-2 RBD as a Prognostic Factor for the Severity of COVID-19 Reinfection

by Victor Manuylov, Olga Burgasova, Olga Borisova, Svetlana Smetanina, Daria Vasina, Igor Grigoriev, Alexandra Kudryashova, Maria Semashko, Bogdan Cherepovich, Olga Kharchenko, Denis Kleymenov, Elena Mazunina, Artem Tkachuk and Vladimir Gushchin

Viruses 2022, 14(3), 617; https://doi.org/10.3390/v14030617 - 16 Mar 2022

Cited by 14 | Viewed by 2960

Abstract

The avidity index (AI) of IgG to the RBD of SARS-CoV-2 was determined for 71 patients with a mild (outpatient) course of COVID-19, including 39 primarily and 36 secondarily reinfected, and 92 patients with a severe (hospital) course of COVID-19, including 82 primarily [...] Read more.

The avidity index (AI) of IgG to the RBD of SARS-CoV-2 was determined for 71 patients with a mild (outpatient) course of COVID-19, including 39 primarily and 36 secondarily reinfected, and 92 patients with a severe (hospital) course of COVID-19, including 82 primarily and 10 secondarily infected. The AI was shown to correlate with the severity of repeated disease. In the group of outpatients with a mild course, the reinfected patients had significantly higher median AIs than those with primary infections (82.3% vs. 37.1%, p < 0.0001). At the same time, in patients with a severe course of COVID-19, reinfected patients still had low-avidity antibodies (median AI of 28.4% vs. 25% in the primarily infected, difference not significant, p > 0.05). This suggests that the presence of low-avidity IgG to RBD during reinfection is a negative prognostic factor, in which a patient’s risk of developing COVID-19 in a severe form is significantly increased. Thus, patients with IgG of low avidity (AI ≤ 40%) had an 89 ± 20.5% chance of a severe course of recurrent COVID-19, whereas the detection of high-avidity antibodies (AI ≥ 50%) gave a probability of 94 ± 7.9% for a mild course of recurrent disease (p < 0.05). Full article

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10 pages, 1380 KiB

Open AccessCase Report

Multiorgan and Vascular Tropism of SARS-CoV-2

by Cédric Hartard, Ahlam Chaqroun, Nicla Settembre, Guillaume Gauchotte, Benjamin Lefevre, Elodie Marchand, Charles Mazeaud, Duc Trung Nguyen, Laurent Martrille, Isabelle Koscinski, Sergueï Malikov and Evelyne Schvoerer

Viruses 2022, 14(3), 515; https://doi.org/10.3390/v14030515 - 3 Mar 2022

Cited by 11 | Viewed by 2589

Abstract

Although the respiratory tract is the main target of SARS-CoV-2, other tissues and organs are permissive to the infection. In this report, we investigated this wide-spectrum tropism by studying the SARS-CoV-2 genetic intra-host variability in multiple tissues. The virological and histological investigation of [...] Read more.

Although the respiratory tract is the main target of SARS-CoV-2, other tissues and organs are permissive to the infection. In this report, we investigated this wide-spectrum tropism by studying the SARS-CoV-2 genetic intra-host variability in multiple tissues. The virological and histological investigation of multiple specimens from a post-mortem COVID-19 patient was performed. SARS-CoV-2 genome was detected in several tissues, including the lower respiratory system, cardio-vascular biopsies, stomach, pancreas, adrenal gland, mediastinal ganglion and testicles. Subgenomic RNA transcripts were also detected, in favor of an active viral replication, especially in testicles. Ultra-deep sequencing allowed us to highlight several SARS-CoV-2 mutations according to tissue distribution. More specifically, mutations of the spike protein, i.e., V341A (18.3%), E654 (44%) and H655R (30.8%), were detected in the inferior vena cava. SARS-CoV-2 variability can contribute to heterogeneous distributions of viral quasispecies, which may affect the COVID-19 pathogeny. Full article

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10 pages, 1828 KiB

Open AccessArticle

Effect of Different Adjuvants on Immune Responses Elicited by Protein-Based Subunit Vaccines against SARS-CoV-2 and Its Delta Variant

by Naru Zhang, Qianting Ji, Zezhong Liu, Kaiming Tang, Yubin Xie, Kangchen Li, Jie Zhou, Sisi Li, Haotian Shang, Zecan Shi, Tianyu Zheng, Jiawei Yao, Lu Lu, Shuofeng Yuan and Shibo Jiang

Viruses 2022, 14(3), 501; https://doi.org/10.3390/v14030501 - 28 Feb 2022

Cited by 20 | Viewed by 3832

Abstract

The global pandemic of coronavirus disease 2019 (COVID-19) caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has become more serious because of the continuous emergence of variants of concern (VOC), thus calling for the development of broad-spectrum vaccines with greater efficacy. Adjuvants [...] Read more.

The global pandemic of coronavirus disease 2019 (COVID-19) caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has become more serious because of the continuous emergence of variants of concern (VOC), thus calling for the development of broad-spectrum vaccines with greater efficacy. Adjuvants play important roles in enhancing the immunogenicity of protein-based subunit vaccines. In this study, we compared the effect of three adjuvants, including aluminum, nanoparticle manganese and MF59, on the immunogenicity of three protein-based COVID-19 vaccine candidates, including RBD-Fc, RBD and S-trimer. We found that the nanoparticle manganese adjuvant elicited the highest titers of SARS-CoV-2 RBD-specific IgG, IgG1 and IgG2a, as well as neutralizing antibodies against infection by pseudotyped SARS-CoV-2 and its Delta variant. What is more, the nanoparticle manganese adjuvant effectively reduced the viral load of the authentic SARS-CoV-2 and Delta variant in the cell culture supernatants. These results suggest that nanoparticle manganese, known to facilitate cGAS-STING activation, is an optimal adjuvant for protein-based COVID-19 subunit vaccines. Full article

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11 pages, 271 KiB

Open AccessPerspective

A Perspective on the Roles of Adjuvants in Developing Highly Potent COVID-19 Vaccines

by Naru Zhang, Kangchen Li, Zezhong Liu, Kutty Selva Nandakumar and Shibo Jiang

Viruses 2022, 14(2), 387; https://doi.org/10.3390/v14020387 - 14 Feb 2022

Cited by 21 | Viewed by 3589

Abstract

Several countries have made unremitting efforts to develop an optimal vaccine in the fight against coronavirus disease 2019 (COVID-19) caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). With the increasing occurrence of SARS-CoV-2 variants, current vaccines show decreased neutralizing activities, especially towards [...] Read more.

Several countries have made unremitting efforts to develop an optimal vaccine in the fight against coronavirus disease 2019 (COVID-19) caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). With the increasing occurrence of SARS-CoV-2 variants, current vaccines show decreased neutralizing activities, especially towards the Omicron variant. In this context, adding appropriate adjuvants to COVID-19 vaccines can substantially reduce the number of required doses and improve efficacy or cross-neutralizing protection. We mainly focus on research progress and achievements associated with adjuvanted COVID-19 subunit and inactivated vaccines. We further compare the advantages and disadvantages of different adjuvant formulations in order to provide a scientific reference for designing an effective strategy for future vaccine development. Full article

6 pages, 957 KiB

Open AccessCommunication

Steep Decline in Binding Capability of SARS-CoV-2 Omicron Variant (B.1.1.529) RBD to the Antibodies in Early COVID-19 Convalescent Sera and Inactivated Vaccine Sera

by Wenhao Zhou, Ping He, Junhua Li, Huan Liu, Mengjuan Shi, Junping Yu and Hongping Wei

Viruses 2022, 14(2), 335; https://doi.org/10.3390/v14020335 - 7 Feb 2022

Cited by 12 | Viewed by 2955

Abstract

A new SARS-CoV-2 variant B.1.1.529 was named by the WHO as Omicron and classified as a Variant of Concern (VOC) on 26 November 2021. Because this variant has more than 50 mutations, including 30 mutations on the spike, it has generated a lot [...] Read more.

A new SARS-CoV-2 variant B.1.1.529 was named by the WHO as Omicron and classified as a Variant of Concern (VOC) on 26 November 2021. Because this variant has more than 50 mutations, including 30 mutations on the spike, it has generated a lot of concerns on the potential impacts of the VOC on COVID-19. Here through ELISA assays using the recombinant RBD proteins with sequences the same to that of SARS-CoV-2 WIV04 (lineage B.1), the Delta variant and the Omicron variant as the coating antigens, the binding capabilities between the RBDs and the antibodies in COVID-19 convalescent sera and vaccine sera after two doses of the inactivated vaccine produced by Sinopharm WIBP are compared with each other. The results showed that the Omicron variant may evade antibodies induced by the ancestral strain and by the inactivated vaccine, with significant reduction in the binding capability of its RBD much greater than that of the Delta variant. Full article

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15 pages, 1710 KiB

Open AccessArticle

Comparison of SARS-CoV-2 Evolution in Paediatric Primary Airway Epithelial Cell Cultures Compared with Vero-Derived Cell Lines

by Connor G. G. Bamford, Lindsay Broadbent, Elihu Aranday-Cortes, Mary McCabe, James McKenna, David G. Courtney, Olivier Touzelet, Ahlam Ali, Grace Roberts, Guillermo Lopez Campos, David Simpson, Conall McCaughey, Derek Fairley, Ken Mills, Ultan F. Power and on behalf of the Breathing Together Investigators

Viruses 2022, 14(2), 325; https://doi.org/10.3390/v14020325 - 5 Feb 2022

Cited by 4 | Viewed by 4563

Abstract

SARS-CoV-2 can efficiently infect both children and adults, albeit with morbidity and mortality positively associated with increasing host age and presence of co-morbidities. SARS-CoV-2 continues to adapt to the human population, resulting in several variants of concern (VOC) with novel properties, such as [...] Read more.

SARS-CoV-2 can efficiently infect both children and adults, albeit with morbidity and mortality positively associated with increasing host age and presence of co-morbidities. SARS-CoV-2 continues to adapt to the human population, resulting in several variants of concern (VOC) with novel properties, such as Alpha and Delta. However, factors driving SARS-CoV-2 fitness and evolution in paediatric cohorts remain poorly explored. Here, we provide evidence that both viral and host factors co-operate to shape SARS-CoV-2 genotypic and phenotypic change in primary airway cell cultures derived from children. Through viral whole-genome sequencing, we explored changes in genetic diversity over time of two pre-VOC clinical isolates of SARS-CoV-2 during passage in paediatric well-differentiated primary nasal epithelial cell (WD-PNEC) cultures and in parallel, in unmodified Vero-derived cell lines. We identified a consistent, rich genetic diversity arising in vitro, variants of which could rapidly rise to near fixation within two passages. Within isolates, SARS-CoV-2 evolution was dependent on host cells, with paediatric WD-PNECs showing a reduced diversity compared to Vero (E6) cells. However, mutations were not shared between strains. Furthermore, comparison of both Vero-grown isolates on WD-PNECs disclosed marked growth attenuation mapping to the loss of the polybasic cleavage site (PBCS) in Spike, while the strain with mutations in Nsp12 (T293I), Spike (P812R) and a truncation of Orf7a remained viable in WD-PNECs. Altogether, our work demonstrates that pre-VOC SARS-CoV-2 efficiently infects paediatric respiratory epithelial cells, and its evolution is restrained compared to Vero (E6) cells, similar to the case of adult cells. We highlight the significant genetic plasticity of SARS-CoV-2 while uncovering an influential role for collaboration between viral and host cell factors in shaping viral evolution and ultimately fitness in human respiratory epithelium. Full article

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8 pages, 503 KiB

Open AccessBrief Report

Spike Gene Evolution and Immune Escape Mutations in Patients with Mild or Moderate Forms of COVID-19 and Treated with Monoclonal Antibodies Therapies

by Aude Jary, Stéphane Marot, Antoine Faycal, Sacha Leon, Sophie Sayon, Karen Zafilaza, Emna Ghidaoui, Stéphanie Nguyen Quoc, Safaa Nemlaghi, Sylvain Choquet, Martin Dres, Valérie Pourcher, Vincent Calvez, Helga Junot, Anne-Geneviève Marcelin and Cathia Soulié

Viruses 2022, 14(2), 226; https://doi.org/10.3390/v14020226 - 24 Jan 2022

Cited by 20 | Viewed by 3312

Abstract

We explored the molecular evolution of the spike gene after the administration of anti-spike monoclonal antibodies in patients with mild or moderate forms of COVID-19. Four out of the 13 patients acquired a mutation during follow-up; two mutations (G1204E and E406G) appeared as [...] Read more.

We explored the molecular evolution of the spike gene after the administration of anti-spike monoclonal antibodies in patients with mild or moderate forms of COVID-19. Four out of the 13 patients acquired a mutation during follow-up; two mutations (G1204E and E406G) appeared as a mixture without clinical impact, while the Q493R mutation emerged in two patients (one receiving bamlanivimab and one receiving bamlanivimab/etesevimab) with fatal outcomes. Careful virological monitoring of patients treated with mAbs should be performed, especially in immunosuppressed patients. Full article

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17 pages, 5320 KiB

Open AccessArticle

Distinguishing Incubation and Acute Disease Stages of Mild-to-Moderate COVID-19

by Michael Müller, Johann Volzke, Behnam Subin, Christian Johann Schmidt, Hilte Geerdes-Fenge, Emil Christian Reisinger and Brigitte Müller-Hilke

Viruses 2022, 14(2), 203; https://doi.org/10.3390/v14020203 - 20 Jan 2022

Cited by 2 | Viewed by 4737

Abstract

While numerous studies have already compared the immune responses against SARS-CoV-2 in severely and mild-to-moderately ill COVID-19 patients, longitudinal trajectories are still scarce. We therefore set out to analyze serial blood samples from mild-to-moderately ill patients in order to define the immune landscapes [...] Read more.

While numerous studies have already compared the immune responses against SARS-CoV-2 in severely and mild-to-moderately ill COVID-19 patients, longitudinal trajectories are still scarce. We therefore set out to analyze serial blood samples from mild-to-moderately ill patients in order to define the immune landscapes for differently progressed disease stages. Twenty-two COVID-19 patients were subjected to consecutive venipuncture within seven days after diagnosis or admittance to hospital. Flow cytometry was performed to analyze peripheral blood immune cell compositions and their activation as were plasma levels of cytokines and SARS-CoV-2 specific immunoglobulins. Healthy donors served as controls. Integrating the kinetics of plasmablasts and SARS-CoV-2 specific antibodies allowed for the definition of three disease stages of early COVID-19. The incubation phase was characterized by a sharp increase in pro-inflammatory monocytes and terminally differentiated cytotoxic T cells. The latter correlated significantly with elevated concentrations of IP-10. Early acute infection featured a peak in PD-1⁺ cytotoxic T cells, plasmablasts and increasing titers of virus specific antibodies. During late acute infection, immature neutrophils were enriched, whereas all other parameters returned to baseline. Our findings will help to define landmarks that are indispensable for the refinement of new anti-viral and anti-inflammatory therapeutics, and may also inform clinicians to optimize treatment and prevent fatal outcomes. Full article

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12 pages, 768 KiB

Open AccessArticle

Using an Administrative and Clinical Database to Determine the Early Spread of COVID-19 at the US Department of Veterans Affairs during the Beginning of the 2019–2020 Flu Season: A Retrospective Longitudinal Study

by Lilia R. Lukowsky, Claudia Der-Martirosian, William Neil Steers, Kiran S. Kamble and Aram Dobalian

Viruses 2022, 14(2), 200; https://doi.org/10.3390/v14020200 - 20 Jan 2022

Cited by 2 | Viewed by 2914

Abstract

Background. Previous studies examining the early spread of COVID-19 have used influenza-like illnesses (ILIs) to determine the early spread of COVID-19. We used COVID-19 case definition to identify COVID-like symptoms (CLS) independently of other influenza-like illnesses (ILIs). Methods. Using data from Emergency Department [...] Read more.

Background. Previous studies examining the early spread of COVID-19 have used influenza-like illnesses (ILIs) to determine the early spread of COVID-19. We used COVID-19 case definition to identify COVID-like symptoms (CLS) independently of other influenza-like illnesses (ILIs). Methods. Using data from Emergency Department (ED) visits at VA Medical Centers in CA, TX, and FL, we compared weekly rates of CLS, ILIs, and non-influenza ILIs encounters during five consecutive flu seasons (2015–2020) and estimated the risk of developing each illness during the first 23 weeks of the 2019–2020 season compared to previous seasons. Results. Patients with CLS were significantly more likely to visit the ED during the first 23 weeks of the 2019–2020 compared to prior seasons, while ED visits for influenza and non-influenza ILIs did not differ substantially. Adjusted CLS risk was significantly lower for all seasons relative to the 2019–2020 season: RR15–16 = 0.72, 0.75, 0.72; RR16–17 = 0.81, 0.77, 0.79; RR17–18 = 0.80, 0.89, 0.83; RR18–19 = 0.82, 0.96, 0.81, in CA, TX, and FL, respectively. Conclusions. The observed increase in ED visits for CLS indicates the likely spread of COVID-19 in the US earlier than previously reported. VA data could potentially help identify emerging infectious diseases and supplement existing syndromic surveillance systems. Full article

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14 pages, 558 KiB

Open AccessArticle

Assessment of Inter-Laboratory Differences in SARS-CoV-2 Consensus Genome Assemblies between Public Health Laboratories in Australia

by Charles S. P. Foster, Sacha Stelzer-Braid, Ira W. Deveson, Rowena A. Bull, Malinna Yeang, Jane-Phan Au, Mariana Ruiz Silva, Sebastiaan J. van Hal, Rebecca J. Rockett, Vitali Sintchenko, Ki Wook Kim and William D. Rawlinson

Viruses 2022, 14(2), 185; https://doi.org/10.3390/v14020185 - 19 Jan 2022

Cited by 5 | Viewed by 2680

Abstract

Whole-genome sequencing of viral isolates is critical for informing transmission patterns and for the ongoing evolution of pathogens, especially during a pandemic. However, when genomes have low variability in the early stages of a pandemic, the impact of technical and/or sequencing errors increases. [...] Read more.

Whole-genome sequencing of viral isolates is critical for informing transmission patterns and for the ongoing evolution of pathogens, especially during a pandemic. However, when genomes have low variability in the early stages of a pandemic, the impact of technical and/or sequencing errors increases. We quantitatively assessed inter-laboratory differences in consensus genome assemblies of 72 matched SARS-CoV-2-positive specimens sequenced at different laboratories in Sydney, Australia. Raw sequence data were assembled using two different bioinformatics pipelines in parallel, and resulting consensus genomes were compared to detect laboratory-specific differences. Matched genome sequences were predominantly concordant, with a median pairwise identity of 99.997%. Identified differences were predominantly driven by ambiguous site content. Ignoring these produced differences in only 2.3% (5/216) of pairwise comparisons, each differing by a single nucleotide. Matched samples were assigned the same Pango lineage in 98.2% (212/216) of pairwise comparisons, and were mostly assigned to the same phylogenetic clade. However, epidemiological inference based only on single nucleotide variant distances may lead to significant differences in the number of defined clusters if variant allele frequency thresholds for consensus genome generation differ between laboratories. These results underscore the need for a unified, best-practices approach to bioinformatics between laboratories working on a common outbreak problem. Full article

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13 pages, 1759 KiB

Open AccessArticle

The Petasites hybridus CO₂ Extract (Ze 339) Blocks SARS-CoV-2 Replication In Vitro

by Lorena Urda, Matthias Heinrich Kreuter, Jürgen Drewe, Georg Boonen, Veronika Butterweck and Thomas Klimkait

Viruses 2022, 14(1), 106; https://doi.org/10.3390/v14010106 - 7 Jan 2022

Cited by 6 | Viewed by 3377

Abstract

The coronavirus disease 2019 (COVID-19), caused by a novel coronavirus (SARS-CoV-2), has spread worldwide, affecting over 250 million people and resulting in over five million deaths. Antivirals that are effective are still limited. The antiviral activities of the Petasites hybdridus CO₂ extract [...] Read more.

The coronavirus disease 2019 (COVID-19), caused by a novel coronavirus (SARS-CoV-2), has spread worldwide, affecting over 250 million people and resulting in over five million deaths. Antivirals that are effective are still limited. The antiviral activities of the Petasites hybdridus CO₂ extract Ze 339 were previously reported. Thus, to assess the anti-SARS-CoV-2 activity of Ze 339 as well as isopetasin and neopetasin as major active compounds, a CPE and plaque reduction assay in Vero E6 cells was used for viral output. Antiviral effects were tested using the original virus (Wuhan) and the Delta variant of SARS-CoV-2. The antiviral drug remdesivir was used as control. Pre-treatment with Ze 339 in SARS-CoV-2-infected Vero E6 cells with either virus variant significantly inhibited virus replication with IC₅₀ values of 0.10 and 0.40 μg/mL, respectively. The IC₅₀ values obtained for isopetasin ranged between 0.37 and 0.88 μM for both virus variants, and that of remdesivir ranged between 1.53 and 2.37 μM. In conclusion, Ze 339 as well as the petasins potently inhibited SARS-CoV-2 replication in vitro of the Wuhan and Delta variants. Since time is of essence in finding effective treatments, clinical studies will have to demonstrate if Ze339 can become a therapeutic option to treat SARS-CoV-2 infections. Full article

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6 pages, 682 KiB

Open AccessCommunication

SARS-CoV-2 T Cell Responses Elicited by COVID-19 Vaccines or Infection Are Expected to Remain Robust against Omicron

by Syed Faraz Ahmed, Ahmed Abdul Quadeer and Matthew R. McKay

Viruses 2022, 14(1), 79; https://doi.org/10.3390/v14010079 - 2 Jan 2022

Cited by 60 | Viewed by 24242

Abstract

Omicron, the most recent SARS-CoV-2 variant of concern (VOC), harbours multiple mutations in the spike protein that were not observed in previous VOCs. Initial studies suggest Omicron to substantially reduce the neutralizing capability of antibodies induced from vaccines and previous infection. However, its [...] Read more.

Omicron, the most recent SARS-CoV-2 variant of concern (VOC), harbours multiple mutations in the spike protein that were not observed in previous VOCs. Initial studies suggest Omicron to substantially reduce the neutralizing capability of antibodies induced from vaccines and previous infection. However, its effect on T cell responses remains to be determined. Here, we assess the effect of Omicron mutations on known T cell epitopes and report data suggesting T cell responses to remain broadly robust against this new variant. Full article

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11 pages, 259 KiB

Open AccessArticle

The Prevalence of Acute Respiratory Distress Syndrome (ARDS) and Outcomes in Hospitalized Patients with COVID-19—A Study Based on Data from the Polish National Hospital Register

by Mariusz Gujski, Mateusz Jankowski, Daniel Rabczenko, Paweł Goryński and Grzegorz Juszczyk

Viruses 2022, 14(1), 76; https://doi.org/10.3390/v14010076 - 1 Jan 2022

Cited by 17 | Viewed by 3517

Abstract

Acute respiratory distress syndrome (ARDS) is a serious complication of COVID-19. This study aimed to evaluate the prevalence of ARDS among patients hospitalized with COVID-19 in Poland as well as to characterize clinical outcomes in patients hospitalized with COVID-19-associated ARDS. This is a [...] Read more.

Acute respiratory distress syndrome (ARDS) is a serious complication of COVID-19. This study aimed to evaluate the prevalence of ARDS among patients hospitalized with COVID-19 in Poland as well as to characterize clinical outcomes in patients hospitalized with COVID-19-associated ARDS. This is a retrospective, secondary analysis of epidemiological data from 116,539 discharge reports on patients hospitalized with COVID-19 in Poland between March and December 2020. The overall prevalence of ARDS was 3.6%, respectively 2.9% among females, and 4.4% among males (p < 0.001). Of the 4237 patients hospitalized with COVID-19-associated ARDS, 3764 deaths were reported (88.8%). Participants aged 60 years and over had more than three times higher odds of COVID-19-associated ARDS. Men had higher odds of COVID-19-associated ARDS than women (OR = 1.55; 95% CI: 1.45–1.65; p < 0.001). Patients with COVID-19 and diabetes had higher odds of COVID-19-associated ARDS (OR = 1.16; 95% CI: 1.03–1.30; p = 0.01). Among patients with COVID-19-associated ARDS, older age, male sex (OR = 1.27; 95% CI: 1.03–1.56; p = 0.02), and presence of cardiovascular diseases (OR = 1.26; 95% CI: 1.00–1.59; p = 0.048) were significantly associated with the risk of in-hospital death. Among patients hospitalized with COVID-19 in Poland, the prevalence of ARDS was relatively low, but the in-hospital mortality rate in patients with COVID-19-associated ARDS was higher compared to other EU countries. Full article

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18 pages, 2017 KiB

Open AccessArticle

Symptom-Based Predictive Model of COVID-19 Disease in Children

by Jesús M. Antoñanzas, Aida Perramon, Cayetana López, Mireia Boneta, Cristina Aguilera, Ramon Capdevila, Anna Gatell, Pepe Serrano, Miriam Poblet, Dolors Canadell, Mònica Vilà, Georgina Catasús, Cinta Valldepérez, Martí Català, Pere Soler-Palacín, Clara Prats, Antoni Soriano-Arandes and the COPEDI-CAT Research Group

Viruses 2022, 14(1), 63; https://doi.org/10.3390/v14010063 - 30 Dec 2021

Cited by 8 | Viewed by 4028

Abstract

Background: Testing for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection is neither always accessible nor easy to perform in children. We aimed to propose a machine learning model to assess the need for a SARS-CoV-2 test in children (<16 years old), depending [...] Read more.

Background: Testing for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection is neither always accessible nor easy to perform in children. We aimed to propose a machine learning model to assess the need for a SARS-CoV-2 test in children (<16 years old), depending on their clinical symptoms. Methods: Epidemiological and clinical data were obtained from the REDCap^® registry. Overall, 4434 SARS-CoV-2 tests were performed in symptomatic children between 1 November 2020 and 31 March 2021, 784 were positive (17.68%). We pre-processed the data to be suitable for a machine learning (ML) algorithm, balancing the positive-negative rate and preparing subsets of data by age. We trained several models and chose those with the best performance for each subset. Results: The use of ML demonstrated an AUROC of 0.65 to predict a COVID-19 diagnosis in children. The absence of high-grade fever was the major predictor of COVID-19 in younger children, whereas loss of taste or smell was the most determinant symptom in older children. Conclusions: Although the accuracy of the models was lower than expected, they can be used to provide a diagnosis when epidemiological data on the risk of exposure to COVID-19 is unknown. Full article

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15 pages, 5780 KiB

Open AccessArticle

COVID-19: Multiorgan Dissemination of SARS-CoV-2 Is Driven by Pulmonary Factors

by Akmaljon Odilov, Alexey Volkov, Adhamjon Abdullaev, Tatiana Gasanova, Tatiana Lipina and Igor Babichenko

Viruses 2022, 14(1), 39; https://doi.org/10.3390/v14010039 - 26 Dec 2021

Cited by 10 | Viewed by 4383

Abstract

Multi-organ failure is one of the common causes of fatal outcome in COVID-19 patients. However, the pathogenetic association of the SARS-CoV-2 viral load (VL) level with fatal dysfunctions of the lungs, liver, kidneys, heart, spleen and brain, as well as with the risk [...] Read more.

Multi-organ failure is one of the common causes of fatal outcome in COVID-19 patients. However, the pathogenetic association of the SARS-CoV-2 viral load (VL) level with fatal dysfunctions of the lungs, liver, kidneys, heart, spleen and brain, as well as with the risk of death in COVID-19 patients remains poorly understood. SARS-CoV-2 VL in the lungs, heart, liver, kidneys, brain, spleen and lymph nodes have been measured by RT qPCR using the following formula: N^SARS-CoV−2/N^{ABL1 ×} 100. Dissemination of SARS-CoV-2 in 30.5% of cases was mono-organ, and in 63.9% of cases, it was multi-organ. The average SARS-CoV-2 VL in the exudative phase of diffuse alveolar damage (DAD) was 60 times higher than in the proliferative phase. The SARS-CoV-2 VL in the lungs ranged from 0 to 250,281 copies. The “pulmonary factors” of SARS-CoV-2 multi-organ dissemination are the high level of SARS-CoV-2 VL (≥4909) and the exudative phase of DAD. The frequency of SARS-CoV-2 dissemination to lymph nodes was 86.9%, heart–56.5%, spleen–52.2%, liver–47.8%, kidney–26%, and brain–13%. We found no link between the SARS-CoV-2 VL level in the liver, kidneys, and heart and the serum level of CPK, LDH, ALP, ALT, AST and Cr of COVID-19 patients. Isolated detection of SARS-CoV-2 RNA in the myocardium of COVID-19 patients who died from heart failure is possible. The pathogenesis of COVID-19-associated multi-organ failure requires further research in a larger cohort of patients. Full article

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14 pages, 2648 KiB

Open AccessArticle

Activity of Galidesivir in a Hamster Model of SARS-CoV-2

by Ray Taylor, Richard Bowen, James F. Demarest, Michael DeSpirito, Airn Hartwig, Helle Bielefeldt-Ohmann, Dennis M. Walling, Amanda Mathis and Yarlagadda S. Babu

Viruses 2022, 14(1), 8; https://doi.org/10.3390/v14010008 - 21 Dec 2021

Cited by 13 | Viewed by 37527

Abstract

Coronavirus disease 2019 (COVID-19) has claimed the lives of millions of people worldwide since it first emerged. The impact of the COVID-19 pandemic on public health and the global economy has highlighted the medical need for the development of broadly acting interventions against [...] Read more.

Coronavirus disease 2019 (COVID-19) has claimed the lives of millions of people worldwide since it first emerged. The impact of the COVID-19 pandemic on public health and the global economy has highlighted the medical need for the development of broadly acting interventions against emerging viral threats. Galidesivir is a broad-spectrum antiviral compound with demonstrated in vitro and in vivo efficacy against several RNA viruses of public health concern, including those causing yellow fever, Ebola, Marburg, and Rift Valley fever. In vitro studies have shown that the antiviral activity of galidesivir also extends to coronaviruses. Herein, we describe the efficacy of galidesivir in the Syrian golden hamster model of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection. Treatment with galidesivir reduced lung pathology in infected animals compared with untreated controls when treatment was initiated 24 h prior to infection. These results add to the evidence of the applicability of galidesivir as a potential medical intervention for a range of acute viral illnesses, including coronaviruses. Full article

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6 pages, 757 KiB

Open AccessCommunication

A Novel High-Throughput Nanopore-Sequencing-Based Strategy for Rapid and Automated S-Protein Typing of SARS-CoV-2 Variants

by Gabriel E. Wagner, Massimo G. Totaro, André Volland, Michaela Lipp, Sabine Saiger, Sabine Lichtenegger, Patrick Forstner, Dorothee von Laer, Gustav Oberdorfer and Ivo Steinmetz

Viruses 2021, 13(12), 2548; https://doi.org/10.3390/v13122548 - 19 Dec 2021

Cited by 6 | Viewed by 3211

Abstract

Rapid molecular surveillance of SARS-CoV-2 S-protein variants leading to immune escape and/or increased infectivity is of utmost importance. Among global bottlenecks for variant monitoring in diagnostic settings are sequencing and bioinformatics capacities. In this study, we aimed to establish a rapid and user-friendly [...] Read more.

Rapid molecular surveillance of SARS-CoV-2 S-protein variants leading to immune escape and/or increased infectivity is of utmost importance. Among global bottlenecks for variant monitoring in diagnostic settings are sequencing and bioinformatics capacities. In this study, we aimed to establish a rapid and user-friendly protocol for high-throughput S-gene sequencing and subsequent automated identification of variants. We designed two new primer pairs to amplify only the immunodominant part of the S-gene for nanopore sequencing. Furthermore, we developed an automated “S-Protein-Typer” tool that analyzes and reports S-protein mutations on the amino acid level including a variant of concern indicator. Validation of our primer panel using SARS-CoV-2-positive respiratory specimens covering a broad C_t range showed successful amplification for 29/30 samples. Restriction to the region of interest freed sequencing capacity by a factor of 12–13, compared with whole-genome sequencing. Using either the MinION or Flongle flow cell, our sequencing strategy reduced the time required to identify SARS-CoV-2 variants accordingly. The S-Protein-Typer tool identified all mutations correctly when challenged with our sequenced samples and 50 deposited sequences covering all VOCs (December 2021). Our proposed S-protein variant screening offers a simple, more rapid, and low-cost entry into NGS-based SARS-CoV-2 analysis, compared with current whole-genome approaches. Full article

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11 pages, 1526 KiB

Open AccessArticle

Antibody-Dependent Enhancement of SARS-CoV-2 Infection of Human Immune Cells: In Vitro Assessment Provides Insight in COVID-19 Pathogenesis

by Xu-Rui Shen, Qian Li, Hui-Ling Li, Xi Wang, Qi Wang, Xiao-Shuang Zheng, Rong Geng, Yu-Lan Zhang, Bei Li, Ren-Di Jiang, Mei-Qin Liu, Yan Zhu, Wei Zhang, Xing-Lou Yang, Ke Peng and Peng Zhou

Viruses 2021, 13(12), 2483; https://doi.org/10.3390/v13122483 - 11 Dec 2021

Cited by 11 | Viewed by 6457

Abstract

Patients with COVID-19 generally raise antibodies against SARS-CoV-2 following infection, and the antibody level is positively correlated to the severity of disease. Whether the viral antibodies exacerbate COVID-19 through antibody-dependent enhancement (ADE) is still not fully understood. Here, we conducted in vitro assessment [...] Read more.

Patients with COVID-19 generally raise antibodies against SARS-CoV-2 following infection, and the antibody level is positively correlated to the severity of disease. Whether the viral antibodies exacerbate COVID-19 through antibody-dependent enhancement (ADE) is still not fully understood. Here, we conducted in vitro assessment of whether convalescent serum enhanced SARS-CoV-2 infection or induced excessive immune responses in immune cells. Our data revealed that SARS-CoV-2 infection of primary B cells, macrophages and monocytes, which express variable levels of FcγR, could be enhanced by convalescent serum from COVID-19 patients. We also determined the factors associated with ADE, and found which showed a time-dependent but not viral-dose dependent manner. Furthermore, the ADE effect is not associated with the neutralizing titer or RBD antibody level when testing serum samples collected from different patients. However, it is higher in a medium level than low or high dilutions in a given sample that showed ADE effect, which is similar to dengue. Finally, we demonstrated more viral genes or dysregulated host immune gene expression under ADE conditions compared to the no-serum infection group. Collectively, our study provides insight into the understanding of an association of high viral antibody titer and severe lung pathology in severe patients with COVID-19. Full article

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13 pages, 1578 KiB

Open AccessArticle

by Ana C. Moreira, Maria Jose Teles, Tânia Silva, Clara M. Bento, Inês Simões Alves, Luisa Pereira, João Tiago Guimarães, Graça Porto, Pedro Oliveira and Maria Salomé Gomes

Viruses 2021, 13(12), 2482; https://doi.org/10.3390/v13122482 - 10 Dec 2021

Cited by 15 | Viewed by 3268

Abstract

Large variability in COVID-19 clinical progression urges the need to find the most relevant biomarkers to predict patients’ outcomes. We evaluated iron metabolism and immune response in 303 patients admitted to the main hospital of the northern region of Portugal with variable clinical [...] Read more.

Large variability in COVID-19 clinical progression urges the need to find the most relevant biomarkers to predict patients’ outcomes. We evaluated iron metabolism and immune response in 303 patients admitted to the main hospital of the northern region of Portugal with variable clinical pictures, from September to November 2020. One hundred and twenty-seven tested positive for SARS-CoV-2 and 176 tested negative. Iron-related laboratory parameters and cytokines were determined in blood samples collected soon after admission. Demographic data, comorbidities and clinical outcomes were recorded. Patients were assigned into five groups according to severity. Serum iron and transferrin levels at admission were lower in COVID-19-positive than in COVID-19-negative patients. The levels of interleukin (IL)-6 and monocyte chemoattractant protein 1 (MCP-1) were increased in COVID-19-positive patients. The lowest serum iron and transferrin levels at diagnosis were associated with the worst outcomes. Iron levels negatively correlated with IL-6 and higher levels of this cytokine were associated with a worse prognosis. Serum ferritin levels at diagnosis were higher in COVID-19-positive than in COVID-19-negative patients. Serum iron is the simplest laboratory test to be implemented as a predictor of disease progression in COVID-19-positive patients. Full article

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12 pages, 1636 KiB

Open AccessArticle

COVID-19 Modulates Inflammatory and Renal Markers That May Predict Hospital Outcomes among African American Males

by Wendy Fonseca, Nobuhiro Asai, Kazuma Yagi, Carrie-Anne Malinczak, Gina Savickas, Christine C. Johnson, Shannon Murray, Edward M. Zoratti, Nicholas W. Lukacs, Jia Li and Charles F. Schuler IV

Viruses 2021, 13(12), 2415; https://doi.org/10.3390/v13122415 - 2 Dec 2021

Cited by 5 | Viewed by 2404

Abstract

Background and Objectives: African Americans and males have elevated risks of infection, hospitalization, and death from SARS-CoV-2 in comparison with other populations. We report immune responses and renal injury markers in African American male patients hospitalized for COVID-19. Methods: This was a single-center, [...] Read more.

Background and Objectives: African Americans and males have elevated risks of infection, hospitalization, and death from SARS-CoV-2 in comparison with other populations. We report immune responses and renal injury markers in African American male patients hospitalized for COVID-19. Methods: This was a single-center, retrospective study of 56 COVID-19 infected hospitalized African American males 50+ years of age selected from among non-intensive care unit (ICU) and ICU status patients. Demographics, hospitalization-related variables, and medical history were collected from electronic medical records. Plasma samples collected close to admission (≤2 days) were evaluated for cytokines and renal markers; results were compared to a control group (n = 31) and related to COVID-19 in-hospital mortality. Results: Among COVID-19 patients, eight (14.2%) suffered in-hospital mortality; seven (23.3%) in the ICU and one (3.8%) among non-ICU patients. Interleukin (IL)-18 and IL-33 were elevated at admission in COVID-19 patients in comparison with controls. IL-6, IL-18, MCP-1/CCL2, MIP-1α/CCL3, IL-33, GST, and osteopontin were upregulated at admission in ICU patients in comparison with controls. In addition to clinical factors, MCP-1 and GST may provide incremental value for risk prediction of COVID-19 in-hospital mortality. Conclusions: Qualitatively similar inflammatory responses were observed in comparison to other populations reported in the literature, suggesting non-immunologic factors may account for outcome differences. Further, we provide initial evidence for cytokine and renal toxicity markers as prognostic factors for COVID-19 in-hospital mortality among African American males. Full article

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15 pages, 1593 KiB

Open AccessArticle

Potential of an Eco-Sustainable Probiotic-Cleaning Formulation in Reducing Infectivity of Enveloped Viruses

by Maria D’Accolti, Irene Soffritti, Francesco Bonfante, Walter Ricciardi, Sante Mazzacane and Elisabetta Caselli

Viruses 2021, 13(11), 2227; https://doi.org/10.3390/v13112227 - 4 Nov 2021

Cited by 16 | Viewed by 6641

Abstract

The COVID-19 pandemic has deeply influenced sanitization procedures, and high-level disinfection has been massively used to prevent SARS-CoV-2 spread, with potential negative impact on the environment and on the threat of antimicrobial resistance (AMR). Aiming to overcome these concerns, yet preserving the effectiveness [...] Read more.

The COVID-19 pandemic has deeply influenced sanitization procedures, and high-level disinfection has been massively used to prevent SARS-CoV-2 spread, with potential negative impact on the environment and on the threat of antimicrobial resistance (AMR). Aiming to overcome these concerns, yet preserving the effectiveness of sanitization against enveloped viruses, we assessed the antiviral properties of the Probiotic Cleaning Hygiene System (PCHS), an eco-sustainable probiotic-based detergent previously proven to stably abate pathogen contamination and AMR. PCHS (diluted 1:10, 1:50 and 1:100) was tested in comparison to common disinfectants (70% ethanol and 0.5% sodium hypochlorite), in suspension and carrier tests, according with the European UNI EN 14476:2019 and UNI EN 16777:2019 standards. Human alpha- and beta-coronaviruses hCoV-229E and SARS-CoV-2, human herpesvirus type 1, human and animal influenza viruses, and vaccinia virus were included in the study. The results showed that PCHS was able to inactivate 99.99% of all tested viruses within 1–2 h of contact, both in suspension and on surface. Notably, while control disinfectants became inactive within 2 h after application, the PCHS antiviral action persisted up to 24 h post-application, suggesting that its use may effectively allow a continuous prevention of virus spread via contaminated environment, without worsening environmental pollution and AMR concern. Full article

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11 pages, 1257 KiB

Open AccessArticle

Dynamics of Viral Shedding and Symptoms in Patients with Asymptomatic or Mild COVID-19

by Seongman Bae, Ji Yeun Kim, So Yun Lim, Heedo Park, Hye Hee Cha, Ji-Soo Kwon, Mi Hyun Suh, Hyun Jung Lee, Joon Seo Lim, Jiwon Jung, Min Jae Kim, Yong Pil Chong, Sang-Oh Lee, Sang-Ho Choi, Yang Soo Kim, Ho Young Lee, Sohyun Lee, Man-Seong Park and Sung-Han Kim

Viruses 2021, 13(11), 2133; https://doi.org/10.3390/v13112133 - 22 Oct 2021

Cited by 17 | Viewed by 3920

Abstract

We conducted a prospective cohort study at a community facility designated for the isolation of individuals with asymptomatic or mild COVID-19 between 10 January and 22 February 2021 to investigate the relationship of viral shedding with symptom changes of COVID-19. In total, 89 [...] Read more.

We conducted a prospective cohort study at a community facility designated for the isolation of individuals with asymptomatic or mild COVID-19 between 10 January and 22 February 2021 to investigate the relationship of viral shedding with symptom changes of COVID-19. In total, 89 COVID-19 adult patients (12 asymptomatic, 16 presymptomatic, 61 symptomatic) were enrolled. Symptom scores, the genomic RNA and subgenomic RNA of SARS-CoV-2 from saliva samples with a cell culture were measured. Asymptomatic COVID-19 patients had a similar viral load to symptomatic patients during the early course of the disease, but exhibited a rapid decrease in viral load with the loss of infectivity. Subgenomic RNA and viable virus by cell culture in asymptomatic patients were detected only until 3 days after diagnosis, and the positivity of the subgenomic RNA and cell culture in symptomatic patients gradually decreased in both from 40% in the early disease course to 13% at 10 days and 4% at 8 days after the symptom onset, respectively. In conclusion, symptomatic patients have a high infectivity with high symptom scores during the early disease course and gradually lose infectivity depending on the symptom. Conversely, asymptomatic patients exhibit a rapid decrease in viral load with the loss of infectivity, despite a similar viral load during the early disease course. Full article

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13 pages, 2077 KiB

Open AccessArticle

Clusters of SARS-CoV-2 Lineage B.1.1.7 Infection after Vaccination with Adenovirus-Vectored and Inactivated Vaccines

by William M. de Souza, Stéfanie P. Muraro, Gabriela F. Souza, Mariene R. Amorim, Renata Sesti-Costa, Luciana S. Mofatto, Julia Forato, Priscilla P. Barbosa, Daniel A. Toledo-Teixeira, Karina Bispo-dos-Santos, Pierina L. Parise, Natalia S. Brunetti, Joselia C. O. Moreira, Vitor A. Costa, Daniela M. Cardozo, Maria L. Moretti, Silvia Barros-Mazon, Gabriela F. Marchesi, Christiane Ambrosio, Fernando R. Spilki, Valeria C. Almeida, Andre S. Vieira, Lair Zambon, Alessandro S. Farias, Marcelo Addas-Carvalho, Bruno D. Benites, Rafael E. Marques, Ester C. Sabino, Andrea B. Von Zuben, Scott C. Weaver, Nuno R. Faria, Fabiana Granja, Rodrigo N. Angerami and José Luiz Proença-Módena Show full author list Hide full author list

Viruses 2021, 13(11), 2127; https://doi.org/10.3390/v13112127 - 22 Oct 2021

Cited by 6 | Viewed by 4019

Abstract

A SARS-CoV-2 B.1.1.7 variant of concern (VOC) has been associated with increased transmissibility, hospitalization, and mortality. This study aimed to explore the factors associated with B.1.1.7 VOC infection in the context of vaccination. On March 2021, we detected SARS-CoV-2 RNA in nasopharyngeal samples [...] Read more.

A SARS-CoV-2 B.1.1.7 variant of concern (VOC) has been associated with increased transmissibility, hospitalization, and mortality. This study aimed to explore the factors associated with B.1.1.7 VOC infection in the context of vaccination. On March 2021, we detected SARS-CoV-2 RNA in nasopharyngeal samples from 14 of 22 individuals vaccinated with a single-dose of ChAdOx1 (outbreak A, n = 26), and 22 of 42 of individuals with two doses of the CoronaVac vaccine (outbreak B, n = 52) for breakthrough infection rates for ChAdOx1 of 63.6% and 52.4% for CoronaVac. The outbreaks were caused by two independent clusters of the B.1.1.7 VOC. The serum of PCR-positive symptomatic SARS-CoV-2-infected individuals had ~1.8–3.4-fold more neutralizing capacity against B.1.1.7 compared to the serum of asymptomatic individuals. These data based on exploratory analysis suggest that the B.1.1.7 variant can infect individuals partially immunized with a single dose of an adenovirus-vectored vaccine or fully immunized with two doses of an inactivated vaccine, although the vaccines were able to reduce the risk of severe disease and death caused by this VOC, even in the elderly. Full article

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7 pages, 506 KiB

Open AccessCommunication

Viral Shedding among Re-Positive Severe Acute Respiratory Syndrome Coronavirus-2 Positive Individuals in Republic of Korea

by Jeong-Min Kim, Boyeong Ryu, Young June Choe, Hye-Jun Jo, Hyeokjin Lee, Heui Man Kim, Nam-Joo Lee, Jee Eun Rhee, Yoon-Seok Chung, Myung-Guk Han, Eun-Jin Kim, Youngjoon Park, Jin Gwack, Yeowon Jin, Jeongsuk Song, Seunghee Seo, Byoungchul Gill, Hyunyeong Kim, Yeeun Park, Cheon Kwon Yoo and Eun Kyeong Jeong Show full author list Hide full author list

Viruses 2021, 13(10), 2089; https://doi.org/10.3390/v13102089 - 17 Oct 2021

Cited by 4 | Viewed by 4934

Abstract

This study investigated the infectivity of severe acute respiratory syndrome (SARS-CoV-2) in individuals who re-tested positive for SARS-CoV-2 RNA after recovering from their primary illness. We investigated 295 individuals with re-positive SARS-CoV-2 polymerase chain reaction (PCR) test results and 836 of their close [...] Read more.

This study investigated the infectivity of severe acute respiratory syndrome (SARS-CoV-2) in individuals who re-tested positive for SARS-CoV-2 RNA after recovering from their primary illness. We investigated 295 individuals with re-positive SARS-CoV-2 polymerase chain reaction (PCR) test results and 836 of their close contacts. We attempted virus isolation in individuals with re-positive SARS-CoV-2 PCR test results using cell culture and confirmed the presence of neutralizing antibodies using serological tests. Viral culture was negative in all 108 individuals with re-positive SARS-CoV-2 PCR test results in whom viral culture was performed. Three new cases of SARS-CoV-2 infection were identified among household contacts using PCR. Two of the three new cases had had contact with the index patient during their primary illness, and all three had antibody evidence of past infection. Thus, there was no laboratory evidence of viral shedding and no epidemiological evidence of transmission among individuals with re-positive SARS-CoV-2 PCR test results. Full article

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20 pages, 3078 KiB

Open AccessArticle

Imbalanced Immune Response of T-Cell and B-Cell Subsets in Patients with Moderate and Severe COVID-19

by Alexey Golovkin, Olga Kalinina, Vadim Bezrukikh, Arthur Aquino, Ekaterina Zaikova, Tatyana Karonova, Olesya Melnik, Elena Vasilieva and Igor Kudryavtsev

Viruses 2021, 13(10), 1966; https://doi.org/10.3390/v13101966 - 30 Sep 2021

Cited by 43 | Viewed by 4338

Abstract

Background: The immunological changes associated with COVID-19 are largely unknown. Methods: Patients with COVID-19 showing moderate (n = 18; SpO2 > 93%, respiratory rate > 22 per minute, CRP > 10 mg/L) and severe (n = 23; SpO₂ < 93%, [...] Read more.

Background: The immunological changes associated with COVID-19 are largely unknown. Methods: Patients with COVID-19 showing moderate (n = 18; SpO2 > 93%, respiratory rate > 22 per minute, CRP > 10 mg/L) and severe (n = 23; SpO₂ < 93%, respiratory rate >30 per minute, PaO₂/FiO₂ ≤ 300 mmHg, permanent oxygen therapy, qSOFA > 2) infection, and 37 healthy donors (HD) were enrolled. Circulating T- and B-cell subsets were analyzed by flow cytometry. Results: CD4+Th cells were skewed toward Th2-like phenotypes within CD45RA+CD62L− (CM) and CD45RA–CD62L− (EM) cells in patients with severe COVID-19, while CM CCR6+ Th17-like cells were decreased if compared with HD. Within CM Th17-like cells “classical” Th17-like cells were increased and Th17.1-like cells were decreased in severe COVID-19 cases. Circulating CM follicular Th-like (Tfh) cells were decreased in all COVID-19 patients, and Tfh17-like cells represented the most predominant subset in severe COVID-19 cases. Both groups of patients showed increased levels of IgD-CD38++ B cells, while the levels of IgD+CD38− and IgD–CD38− were decreased. The frequency of IgD+CD27+ and IgD–CD27+ B cells was significantly reduced in severe COVID-19 cases. Conclusions: We showed an imbalance within almost all circulating memory Th subsets during acute COVID-19 and showed that altered Tfh polarization led to a dysregulated humoral immune response. Full article

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9 pages, 1112 KiB

Open AccessCommunication

Lack of Evidence of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) Spillover in Free-Living Neotropical Non-Human Primates, Brazil

by Lívia Sacchetto, Bárbara Aparecida Chaves, Edson Rodrigues Costa, Aline Souza de Menezes Medeiros, Marcelo Gordo, Danielle Bastos Araújo, Danielle Bruna Leal Oliveira, Ana Paula Betaressi da Silva, Andréia Francesli Negri, Edison Luiz Durigon, Kathryn A. Hanley, Nikos Vasilakis, Marcus Vinícius Guimarães de Lacerda and Maurício Lacerda Nogueira

Viruses 2021, 13(10), 1933; https://doi.org/10.3390/v13101933 - 25 Sep 2021

Cited by 8 | Viewed by 4728

Abstract

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the agent of coronavirus disease 2019 (COVID-19), is responsible for the worst pandemic of the 21st century. Like all human coronaviruses, SARS-CoV-2 originated in a wildlife reservoir, most likely from bats. As SARS-CoV-2 has spread [...] Read more.

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the agent of coronavirus disease 2019 (COVID-19), is responsible for the worst pandemic of the 21st century. Like all human coronaviruses, SARS-CoV-2 originated in a wildlife reservoir, most likely from bats. As SARS-CoV-2 has spread across the globe in humans, it has spilled over to infect a variety of non-human animal species in domestic, farm, and zoo settings. Additionally, a broad range of species, including one neotropical monkey, have proven to be susceptible to experimental infection with SARS-CoV-2. Together, these findings raise the specter of establishment of novel enzootic cycles of SARS-CoV-2. To assess the potential exposure of free-living non-human primates to SARS-CoV-2, we sampled 60 neotropical monkeys living in proximity to Manaus and São José do Rio Preto, two hotspots for COVID-19 in Brazil. Our molecular and serological tests detected no evidence of SAR-CoV-2 infection among these populations. While this result is reassuring, sustained surveillance efforts of wildlife living in close association with human populations is warranted, given the stochastic nature of spillover events and the enormous implications of SARS-CoV-2 spillover for human health. Full article

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16 pages, 29732 KiB

Open AccessArticle

COVID-19 Infection in Pregnancy: PCR Cycle Thresholds, Placental Pathology, and Perinatal Outcomes

by Estibalitz Laresgoiti-Servitje, Jorge Arturo Cardona-Pérez, Rosa Gabriela Hernández-Cruz, Addy Cecilia Helguera-Repetto, María Yolotzin Valdespino-Vázquez, Elsa Romelia Moreno-Verduzco, Isabel Villegas-Mota, Sandra Acevedo-Gallegos, Mario Rodríguez-Bosch, Moisés León-Juárez, Mónica Aguinaga-Ríos, Irma Coronado-Zarco, Alejandro Ortiz-Calvillo, María Antonieta Rivera-Rueda, Carolina Valencia-Contreras, María de Lourdes Gómez-Sousa, Mario Solis-Paredes, Juan Carlos Rodriguez-Aldama, Rafael Galván-Contreras, Ricardo Figueroa-Damián, Manuel Cortés-Bonilla, Guadalupe Estrada-Gutierrez, Salvador Espino-y-Sosa and Claudine Irles Show full author list Hide full author list

Viruses 2021, 13(9), 1884; https://doi.org/10.3390/v13091884 - 21 Sep 2021

Cited by 16 | Viewed by 4991

Abstract

(1) This study aimed to evaluate characteristics, perinatal outcomes, and placental pathology of pregnant women with or without SARS-CoV-2 infection in the context of maternal PCR cycle threshold (C_T) values. (2) This was a retrospective case-control study in a third-level health [...] Read more.

(1) This study aimed to evaluate characteristics, perinatal outcomes, and placental pathology of pregnant women with or without SARS-CoV-2 infection in the context of maternal PCR cycle threshold (C_T) values. (2) This was a retrospective case-control study in a third-level health center in Mexico City with universal screening by RT-qPCR. The association of COVID-19 manifestations, preeclampsia, and preterm birth with maternal variables and C_T values were assessed by logistic regression models and decision trees. (3) Accordingly, 828 and 298 women had a negative and positive test, respectively. Of those positive, only 2.6% of them presented mild to moderate symptoms. Clinical characteristics between both groups of women were similar. No associations between C_T values were found for maternal features, such as pre-gestational BMI, age, and symptomatology. A significantly higher percentage of placental fibrinoid was seen with women with low C_Ts (<25; p < 0.01). Regarding perinatal outcomes, preeclampsia was found to be significantly associated with symptomatology but not with risk factors or C_T values (p < 0.01, aOR = 14.72). Moreover, 88.9% of women diagnosed with COVID-19 at <35 gestational weeks and symptomatic developed preeclampsia. (4) The data support strong guidance for pregnancies with SARS-CoV-2 infection, in particular preeclampsia and placental pathology, which need further investigation. Full article

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11 pages, 3806 KiB

Open AccessArticle

Kinetics of Nucleocapsid, Spike and Neutralizing Antibodies, and Viral Load in Patients with Severe COVID-19 Treated with Convalescent Plasma

by Thomas P. Thomopoulos, Margherita Rosati, Evangelos Terpos, Dimitris Stellas, Xintao Hu, Sevasti Karaliota, Anthi Bouchla, Ioannis Katagas, Anastasia Antoniadou, Andreas Mentis, Sotirios G. Papageorgiou, Marianna Politou, Jenifer Bear, Duncan Donohue, Anastasia Kotanidou, Ioannis Kalomenidis, Eleni Korompoki, Robert Burns, Maria Pagoni, Elisavet Grouzi, Stavroula Labropoulou, Kostantinos Stamoulis, Aristotelis Bamias, Sotirios Tsiodras, Meletios-Athanasios Dimopoulos, George N. Pavlakis, Vasiliki Pappa and Barbara K. Felber Show full author list Hide full author list

Viruses 2021, 13(9), 1844; https://doi.org/10.3390/v13091844 - 15 Sep 2021

Cited by 4 | Viewed by 3460

Abstract

COVID-19 is an ongoing pandemic with high morbidity and mortality. Despite meticulous research, only dexamethasone has shown consistent mortality reduction. Convalescent plasma (CP) infusion might also develop into a safe and effective treatment modality on the basis of recent studies and meta-analyses; however, [...] Read more.

COVID-19 is an ongoing pandemic with high morbidity and mortality. Despite meticulous research, only dexamethasone has shown consistent mortality reduction. Convalescent plasma (CP) infusion might also develop into a safe and effective treatment modality on the basis of recent studies and meta-analyses; however, little is known regarding the kinetics of antibodies in CP recipients. To evaluate the kinetics, we followed 31 CP recipients longitudinally enrolled at a median of 3 days post symptom onset for changes in binding and neutralizing antibody titers and viral loads. Antibodies against the complete trimeric Spike protein and the receptor-binding domain (Spike-RBD), as well as against the complete Nucleocapsid protein and the RNA binding domain (N-RBD) were determined at baseline and weekly following CP infusion. Neutralizing antibody (pseudotype NAb) titers were determined at the same time points. Viral loads were determined semi-quantitatively by SARS-CoV-2 PCR. Patients with low humoral responses at entry showed a robust increase of antibodies to all SARS-CoV-2 proteins and Nab, reaching peak levels within 2 weeks. The rapid increase in binding and neutralizing antibodies was paralleled by a concomitant clearance of the virus within the same timeframe. Patients with high humoral responses at entry demonstrated low or no further increases; however, virus clearance followed the same trajectory as in patients with low antibody response at baseline. Together, the sequential immunological and virological analysis of this well-defined cohort of patients early in infection shows the presence of high levels of binding and neutralizing antibodies and potent clearance of the virus. Full article

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10 pages, 8759 KiB

Open AccessArticle

Just Seeing Is Not Enough for Believing: Immunolabelling as Indisputable Proof of SARS-CoV-2 Virions in Infected Tissue

by Andreja Erman, Karmen Wechtersbach, Daniel Velkavrh, Jerica Pleško, Maja Frelih and Nika Kojc

Viruses 2021, 13(9), 1816; https://doi.org/10.3390/v13091816 - 13 Sep 2021

Cited by 2 | Viewed by 3069

Abstract

Background: There is increasing evidence that identification of SARS-CoV-2 virions by transmission electron microscopy could be misleading due to the similar morphology of virions and ubiquitous cell structures. This study thus aimed to establish methods for indisputable proof of the presence of SARS-CoV-2 [...] Read more.

Background: There is increasing evidence that identification of SARS-CoV-2 virions by transmission electron microscopy could be misleading due to the similar morphology of virions and ubiquitous cell structures. This study thus aimed to establish methods for indisputable proof of the presence of SARS-CoV-2 virions in the observed tissue. Methods: We developed a variant of the correlative microscopy approach for SARS-CoV-2 protein identification using immunohistochemical labelling of SARS-CoV-2 proteins on light and electron microscopy levels. We also performed immunogold labelling of SARS-CoV-2 virions. Results: Immunohistochemistry (IHC) of SARS-CoV-2 nucleocapsid proteins and subsequent correlative microscopy undoubtedly proved the presence of SARS-CoV-2 virions in the analysed human nasopharyngeal tissue. The presence of SARS-CoV-2 virions was also confirmed by immunogold labelling for the first time. Conclusions: Immunoelectron microscopy is the most reliable method for distinguishing intracellular viral particles from normal cell structures of similar morphology and size as virions. Furthermore, we developed a variant of correlative microscopy that allows pathologists to check the results of IHC performed first on routinely used paraffin-embedded samples, followed by semithin, and finally by ultrathin sections. Both methodological approaches indisputably proved the presence of SARS-CoV-2 virions in cells. Full article

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16 pages, 1142 KiB

Open AccessArticle

One Health Investigation of SARS-CoV-2 Infection and Seropositivity among Pets in Households with Confirmed Human COVID-19 Cases—Utah and Wisconsin, 2020

by Grace W. Goryoka, Caitlin M. Cossaboom, Radhika Gharpure, Patrick Dawson, Cassandra Tansey, John Rossow, Victoria Mrotz, Jane Rooney, Mia Torchetti, Christina M. Loiacono, Mary L. Killian, Melinda Jenkins-Moore, Ailam Lim, Keith Poulsen, Dan Christensen, Emma Sweet, Dallin Peterson, Anna L. Sangster, Erin L. Young, Kelly F. Oakeson, Dean Taylor, Amanda Price, Tair Kiphibane, Rachel Klos, Darlene Konkle, Sanjib Bhattacharyya, Trivikram Dasu, Victoria T. Chu, Nathaniel M. Lewis, Krista Queen, Jing Zhang, Anna Uehara, Elizabeth A. Dietrich, Suxiang Tong, Hannah L. Kirking, Jeffrey B. Doty, Laura S. Murrell, Jessica R. Spengler, Anne Straily, Ryan Wallace and Casey Barton Behravesh Show full author list Hide full author list

Viruses 2021, 13(9), 1813; https://doi.org/10.3390/v13091813 - 12 Sep 2021

Cited by 39 | Viewed by 4987

Abstract

Approximately 67% of U.S. households have pets. Limited data are available on SARS-CoV-2 in pets. We assessed SARS-CoV-2 infection in pets during a COVID-19 household transmission investigation. Pets from households with ≥1 person with laboratory-confirmed COVID-19 were eligible for inclusion from April–May 2020. [...] Read more.

Approximately 67% of U.S. households have pets. Limited data are available on SARS-CoV-2 in pets. We assessed SARS-CoV-2 infection in pets during a COVID-19 household transmission investigation. Pets from households with ≥1 person with laboratory-confirmed COVID-19 were eligible for inclusion from April–May 2020. We enrolled 37 dogs and 19 cats from 34 households. All oropharyngeal, nasal, and rectal swabs tested negative by rRT-PCR; one dog’s fur swabs (2%) tested positive by rRT-PCR at the first sampling. Among 47 pets with serological results, eight (17%) pets (four dogs, four cats) from 6/30 (20%) households had detectable SARS-CoV-2 neutralizing antibodies. In households with a seropositive pet, the proportion of people with laboratory-confirmed COVID-19 was greater (median 79%; range: 40–100%) compared to households with no seropositive pet (median 37%; range: 13–100%) (p = 0.01). Thirty-three pets with serologic results had frequent daily contact (≥1 h) with the index patient before the person’s COVID-19 diagnosis. Of these 33 pets, 14 (42%) had decreased contact with the index patient after diagnosis and none were seropositive; of the 19 (58%) pets with continued contact, four (21%) were seropositive. Seropositive pets likely acquired infection after contact with people with COVID-19. People with COVID-19 should restrict contact with pets and other animals. Full article

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16 pages, 2955 KiB

Open AccessArticle

Dating the Common Ancestor from an NCBI Tree of 83688 High-Quality and Full-Length SARS-CoV-2 Genomes

by Xuhua Xia

Viruses 2021, 13(9), 1790; https://doi.org/10.3390/v13091790 - 8 Sep 2021

Cited by 11 | Viewed by 4760

Abstract

All dating studies involving SARS-CoV-2 are problematic. Previous studies have dated the most recent common ancestor (MRCA) between SARS-CoV-2 and its close relatives from bats and pangolins. However, the evolutionary rate thus derived is expected to differ from the rate estimated from sequence [...] Read more.

All dating studies involving SARS-CoV-2 are problematic. Previous studies have dated the most recent common ancestor (MRCA) between SARS-CoV-2 and its close relatives from bats and pangolins. However, the evolutionary rate thus derived is expected to differ from the rate estimated from sequence divergence of SARS-CoV-2 lineages. Here, I present dating results for the first time from a large phylogenetic tree with 86,582 high-quality full-length SARS-CoV-2 genomes. The tree contains 83,688 genomes with full specification of collection time. Such a large tree spanning a period of about 1.5 years offers an excellent opportunity for dating the MRCA of the sampled SARS-CoV-2 genomes. The MRCA is dated 16 August 2019, with the evolutionary rate estimated to be 0.05526 mutations/genome/day. The Pearson correlation coefficient (r) between the root-to-tip distance (D) and the collection time (T) is 0.86295. The NCBI tree also includes 10 SARS-CoV-2 genomes isolated from cats, collected over roughly the same time span as human COVID-19 infection. The MRCA from these cat-derived SARS-CoV-2 is dated 30 July 2019, with r = 0.98464. While the dating method is well known, I have included detailed illustrations so that anyone can repeat the analysis and obtain the same dating results. With 16 August 2019 as the date of the MRCA of sampled SARS-CoV-2 genomes, archived samples from respiratory or digestive tracts collected around or before 16 August 2019, or those that are not descendants of the existing SARS-CoV-2 lineages, should be particularly valuable for tracing the origin of SARS-CoV-2. Full article

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12 pages, 1408 KiB

Open AccessArticle

Doxycycline Inhibition of a Pseudotyped Virus Transduction Does Not Translate to Inhibition of SARS-CoV-2 Infectivity

by Luisa Diomede, Sara Baroni, Ada De Luigi, Arianna Piotti, Jacopo Lucchetti, Claudia Fracasso, Luca Russo, Valerio Bonaldo, Nicolò Panini, Federica Filippini, Fabio Fiordaliso, Alessandro Corbelli, Marten Beeg, Massimo Pizzato, Francesca Caccuri, Marco Gobbi, Emiliano Biasini, Arnaldo Caruso and Mario Salmona

Viruses 2021, 13(9), 1745; https://doi.org/10.3390/v13091745 - 1 Sep 2021

Cited by 5 | Viewed by 3623

Abstract

The rapid spread of the pandemic caused by the SARS-CoV-2 virus has created an unusual situation, with rapid searches for compounds to interfere with the biological processes exploited by the virus. Doxycycline, with its pleiotropic effects, including anti-viral activity, has been proposed as [...] Read more.

The rapid spread of the pandemic caused by the SARS-CoV-2 virus has created an unusual situation, with rapid searches for compounds to interfere with the biological processes exploited by the virus. Doxycycline, with its pleiotropic effects, including anti-viral activity, has been proposed as a therapeutic candidate for COVID-19 and about twenty clinical trials have started since the beginning of the pandemic. To gain information on the activity of doxycycline against SARS-CoV-2 infection and clarify some of the conflicting clinical data published, we designed in vitro binding tests and infection studies with a pseudotyped virus expressing the spike protein, as well as a clinically isolated SARS-CoV-2 strain. Doxycycline inhibited the transduction of the pseudotyped virus in Vero E6 and HEK-293 T cells stably expressing human receptor angiotensin-converting enzyme 2 but did not affect the entry and replication of SARS-CoV-2. Although this conclusion is apparently disappointing, it is paradigmatic of an experimental approach aimed at developing an integrated multidisciplinary platform which can shed light on the mechanisms of action of potential anti-COVID-19 compounds. To avoid wasting precious time and resources, we believe very stringent experimental criteria are needed in the preclinical phase, including infectivity studies with clinically isolated SARS-CoV-2, before moving on to (futile) clinical trials. Full article

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16 pages, 2521 KiB

Open AccessArticle

Processing Hundreds of SARS-CoV-2 Samples with an In-House PCR-Based Method without Robotics

by Theresa Mair, Maja Ivankovic, Christian Paar, Helmut J. F. Salzer, Angelika Heissl, Bernd Lamprecht, Elisabeth Schreier-Lechner and Irene Tiemann-Boege

Viruses 2021, 13(9), 1712; https://doi.org/10.3390/v13091712 - 28 Aug 2021

Cited by 1 | Viewed by 2843

Abstract

The SARS-CoV-2 pandemic has required the development of multiple testing systems to monitor and control the viral infection. Here, we developed a PCR test to screen COVID-19 infections that can process up to ~180 samples per day without the requirement of robotics. For [...] Read more.

The SARS-CoV-2 pandemic has required the development of multiple testing systems to monitor and control the viral infection. Here, we developed a PCR test to screen COVID-19 infections that can process up to ~180 samples per day without the requirement of robotics. For this purpose, we implemented the use of multichannel pipettes and plate magnetics for the RNA extraction step and combined the reverse transcription with the qPCR within one step. We tested the performance of two RT-qPCR kits as well as different sampling buffers and showed that samples taken in NaCl or PBS are stable and compatible with different COVID-19 testing systems. Finally, we designed a new internal control based on the human RNase P gene that does not require a DNA digestion step. Our protocol is easy to handle and reaches the sensitivity and accuracy of the standardized diagnostic protocols used in the clinic to detect COVID-19 infections. Full article

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13 pages, 936 KiB

Open AccessArticle

The Emergence of SARS-CoV-2 within the Dog Population in Croatia: Host Factors and Clinical Outcome

by Vladimir Stevanovic, Irena Tabain, Tatjana Vilibic-Cavlek, Maja Mauric Maljkovic, Iva Benvin, Zeljka Hruskar, Snjezana Kovac, Iva Smit, Gorana Miletic, Suzana Hadina, Vilim Staresina, Lada Radin, Valentina Plichta, Branimir Skrlin, Zoran Vrbanac, Mirna Brkljacic, Marija Cvetnic, Josipa Habus, Kresimir Martinkovic, Iva Zecevic, Gabrijela Jurkic, Ivana Ferencak, Zinka Stritof, Matko Perharic, Lovro Bucic and Ljubo Barbic Show full author list Hide full author list

Viruses 2021, 13(8), 1430; https://doi.org/10.3390/v13081430 - 22 Jul 2021

Cited by 18 | Viewed by 4775

Abstract

Over a year into the COVID-19 pandemic, there is growing evidence that SARS-CoV-2 infections among dogs are more common than previously thought. In this study, the prevalence of SARS-CoV-2 antibodies was investigated in two dog populations. The first group was comprised of 1069 [...] Read more.

Over a year into the COVID-19 pandemic, there is growing evidence that SARS-CoV-2 infections among dogs are more common than previously thought. In this study, the prevalence of SARS-CoV-2 antibodies was investigated in two dog populations. The first group was comprised of 1069 dogs admitted to the Veterinary Teaching Hospital for any given reason. The second group included dogs that shared households with confirmed COVID-19 cases in humans. This study group numbered 78 dogs. In COVID-19 infected households, 43.9% tested ELISA positive, and neutralising antibodies were detected in 25.64% of dogs. Those data are comparable with the secondary attack rate in the human population. With 14.69% of dogs in the general population testing ELISA positive, there was a surge of SARS-CoV-2 infections within the dog population amid the second wave of the pandemic. Noticeably seroprevalence of SARS-CoV-2 in the dog and the human population did not differ at the end of the study period. Male sex, breed and age were identified as significant risk factors. This study gives strong evidence that while acute dog infections are mostly asymptomatic, they can pose a significant risk to dog health. Due to the retrospective nature of this study, samples for viral isolation and PCR were unavailable. Still, seropositive dogs had a 1.97 times greater risk for developing central nervous symptoms. Full article

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14 pages, 47663 KiB

Open AccessArticle

Viral Load and Patterns of SARS-CoV-2 Dissemination to the Lungs, Mediastinal Lymph Nodes, and Spleen of Patients with COVID-19 Associated Lymphopenia

by Adhamjon Abdullaev, Akmaljon Odilov, Maxim Ershler, Alexey Volkov, Tatiana Lipina, Tatiana Gasanova, Yuri Lebedin, Igor Babichenko and Andrey Sudarikov

Viruses 2021, 13(7), 1410; https://doi.org/10.3390/v13071410 - 20 Jul 2021

Cited by 11 | Viewed by 5210

Abstract

Lymphopenia is a frequent hematological manifestation, associated with a severe course of COVID-19, with an insufficiently understood pathogenesis. We present molecular genetic immunohistochemical, and electron microscopic data on SARS-CoV-2 dissemination and viral load (VL) in lungs, mediastinum lymph nodes, and the spleen of [...] Read more.

Lymphopenia is a frequent hematological manifestation, associated with a severe course of COVID-19, with an insufficiently understood pathogenesis. We present molecular genetic immunohistochemical, and electron microscopic data on SARS-CoV-2 dissemination and viral load (VL) in lungs, mediastinum lymph nodes, and the spleen of 36 patients who died from COVID-19. Lymphopenia <1 × 10⁹/L was observed in 23 of 36 (63.8%) patients. In 12 of 36 cases (33%) SARS-CoV-2 was found in lung tissues only with a median VL of 239 copies (range 18–1952) SARS-CoV-2 cDNA per 100 copies of ABL1. Histomorphological changes corresponding to bronchopneumonia and the proliferative phase of DAD were observed in these cases. SARS-CoV-2 dissemination into the lungs, lymph nodes, and spleen was detected in 23 of 36 patients (58.4%) and was associated with the exudative phase of DAD in most of these cases. The median VL in the lungs was 12,116 copies (range 810–250281), lymph nodes—832 copies (range 96–11586), and spleen—71.5 copies (range 0–2899). SARS-CoV-2 in all cases belonged to the 19A strain. A immunohistochemical study revealed SARS-CoV-2 proteins in pneumocytes, alveolar macrophages, and bronchiolar epithelial cells in lung tissue, sinus histiocytes of lymph nodes, as well as cells of the Billroth pulp cords and spleen capsule. SARS-CoV-2 particles were detected by transmission electron microscopy in the cytoplasm of the endothelial cell, macrophages, and lymphocytes. The infection of lymphocytes with SARS-CoV-2 that we discovered for the first time may indicate a possible link between lymphopenia and SARS-CoV-2-mediated cytotoxic effect. Full article

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6 pages, 244 KiB

Open AccessCase Report

First Detection of SARS-CoV-2 B.1.1.7 Variant of Concern in an Asymptomatic Dog in Spain

by Sandra Barroso-Arévalo, Belén Rivera, Lucas Domínguez and José M. Sánchez-Vizcaíno

Viruses 2021, 13(7), 1379; https://doi.org/10.3390/v13071379 - 15 Jul 2021

Cited by 33 | Viewed by 4592

Abstract

Natural SARS-CoV-2 infection in pets has been widely documented during the last year. Although the majority of reports suggested that dogs’ susceptibility to the infection is low, little is known about viral pathogenicity and transmissibility in the case of variants of concern, such [...] Read more.

Natural SARS-CoV-2 infection in pets has been widely documented during the last year. Although the majority of reports suggested that dogs’ susceptibility to the infection is low, little is known about viral pathogenicity and transmissibility in the case of variants of concern, such as B.1.1.7 in this species. Here, as part of a large-scale study on SARS-CoV-2 prevalence in pets in Spain, we have detected the B.1.1.7 variant of concern (VOC) in a dog whose owners were infected with SARS-CoV-2. The animal did not present any symptoms, but viral loads were high in the nasal and rectal swabs. In addition, viral isolation was possible from both swabs, demonstrating that the dog was shedding infectious virus. Seroconversion occurred 23 days after the first sampling. This study documents the first detection of B.1.1.7 VOC in a dog in Spain and emphasizes the importance of performing active surveillance and genomic investigation on infected animals. Full article

9 pages, 709 KiB

Open AccessCommunication

Serum Neutralizing Activity against B.1.1.7, B.1.351, and P.1 SARS-CoV-2 Variants of Concern in Hospitalized COVID-19 Patients

by Claudia Maria Trombetta, Serena Marchi, Simonetta Viviani, Alessandro Manenti, Linda Benincasa, Antonella Ruello, Emilio Bombardieri, Ilaria Vicenti, Maurizio Zazzi and Emanuele Montomoli

Viruses 2021, 13(7), 1347; https://doi.org/10.3390/v13071347 - 12 Jul 2021

Cited by 11 | Viewed by 2701

Abstract

The recent spreading of new SARS-CoV-2 variants, carrying several mutations in the spike protein, could impact immune protection elicited by natural infection or conferred by vaccination. In this study, we evaluated the neutralizing activity against the viral variants that emerged in the United [...] Read more.

The recent spreading of new SARS-CoV-2 variants, carrying several mutations in the spike protein, could impact immune protection elicited by natural infection or conferred by vaccination. In this study, we evaluated the neutralizing activity against the viral variants that emerged in the United Kingdom (B.1.1.7), Brazil (P.1), and South Africa (B.1.351) in human serum samples from hospitalized patients infected by SARS-CoV-2 during the first pandemic wave in Italy in 2020. Of the patients studied, 59.5% showed a decrease (≥2 fold) in neutralizing antibody titer against B.1.1.7, 83.3% against P.1, and 90.5% against B.1.351 with respect to the original strain. The reduction in antibody titers against all analyzed variants, and in particular P.1 and B.1.351, suggests that previous symptomatic infection might be not fully protective against exposure to SARS-CoV-2 variants carrying a set of relevant spike mutations. Full article

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12 pages, 1994 KiB

Open AccessArticle

Previous SARS-CoV-2 Infection Increases B.1.1.7 Cross-Neutralization by Vaccinated Individuals

by Benjamin Trinité, Edwards Pradenas, Silvia Marfil, Carla Rovirosa, Víctor Urrea, Ferran Tarrés-Freixas, Raquel Ortiz, Jordi Rodon, Júlia Vergara-Alert, Joaquim Segalés, Victor Guallar, Rosalba Lepore, Nuria Izquierdo-Useros, Glòria Trujillo, Jaume Trapé, Carolina González-Fernández, Antonia Flor, Rafel Pérez-Vidal, Ruth Toledo, Anna Chamorro, Roger Paredes, Ignacio Blanco, Eulàlia Grau, Marta Massanella, Jorge Carrillo, Bonaventura Clotet and Julià Blanco Show full author list Hide full author list

Viruses 2021, 13(6), 1135; https://doi.org/10.3390/v13061135 - 12 Jun 2021

Cited by 14 | Viewed by 4484

Abstract

With the spread of new variants of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), there is a need to assess the protection conferred by both previous infections and current vaccination. Here we tested the neutralizing activity of infected and/or vaccinated individuals against pseudoviruses [...] Read more.

With the spread of new variants of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), there is a need to assess the protection conferred by both previous infections and current vaccination. Here we tested the neutralizing activity of infected and/or vaccinated individuals against pseudoviruses expressing the spike of the original SARS-CoV-2 isolate Wuhan-Hu-1 (WH1), the D614G mutant and the B.1.1.7 variant. Our data show that parameters of natural infection (time from infection and nature of the infecting variant) determined cross-neutralization. Uninfected vaccinees showed a small reduction in neutralization against the B.1.1.7 variant compared to both the WH1 strain and the D614G mutant. Interestingly, upon vaccination, previously infected individuals developed more robust neutralizing responses against B.1.1.7, suggesting that vaccines can boost the neutralization breadth conferred by natural infection. Full article

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19 pages, 5043 KiB

Open AccessArticle

Full-Length Computational Model of the SARS-CoV-2 Spike Protein and Its Implications for a Viral Membrane Fusion Mechanism

by Wataru Nishima and Marta Kulik

Viruses 2021, 13(6), 1126; https://doi.org/10.3390/v13061126 - 11 Jun 2021

Cited by 7 | Viewed by 5821

Abstract

The SARS-CoV-2 virus has now become one of the greatest causes of infectious death and morbidity since the 1918 flu pandemic. Substantial and unprecedented progress has been made in the elucidation of the viral infection process in a short time; however, our understanding [...] Read more.

The SARS-CoV-2 virus has now become one of the greatest causes of infectious death and morbidity since the 1918 flu pandemic. Substantial and unprecedented progress has been made in the elucidation of the viral infection process in a short time; however, our understanding of the structure–function dynamics of the spike protein during the membrane fusion process and viral uptake remains incomplete. Employing computational approaches, we use full-length structural models of the SARS-CoV-2 spike protein integrating Cryo-EM images and biophysical properties, which fill the gaps in our understanding. We propose a membrane fusion model incorporating structural transitions associated with the proteolytic processing of the spike protein, which initiates and regulates a series of events to facilitate membrane fusion and viral genome uptake. The membrane fusion mechanism highlights the notable role of the S1 subunit and eventual mature spike protein uptake through the host membrane. Our comprehensive view accounts for distinct neutralizing antibody binding effects targeting the spike protein and the enhanced infectivity of the SARS-CoV-2 variant. Full article

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23 pages, 1998 KiB

Open AccessArticle

Estimates and Determinants of SARS-Cov-2 Seroprevalence and Infection Fatality Ratio Using Latent Class Analysis: The Population-Based Tirschenreuth Study in the Hardest-Hit German County in Spring 2020

by Ralf Wagner, David Peterhoff, Stephanie Beileke, Felix Günther, Melanie Berr, Sebastian Einhauser, Anja Schütz, Hans Helmut Niller, Philipp Steininger, Antje Knöll, Matthias Tenbusch, Clara Maier, Klaus Korn, Klaus J. Stark, André Gessner, Ralph Burkhardt, Michael Kabesch, Holger Schedl, Helmut Küchenhoff, Annette B. Pfahlberg, Iris M. Heid, Olaf Gefeller and Klaus Überla Show full author list Hide full author list

Viruses 2021, 13(6), 1118; https://doi.org/10.3390/v13061118 - 10 Jun 2021

Cited by 21 | Viewed by 5018

Abstract

SARS-CoV-2 infection fatality ratios (IFR) remain controversially discussed with implications for political measures. The German county of Tirschenreuth suffered a severe SARS-CoV-2 outbreak in spring 2020, with particularly high case fatality ratio (CFR). To estimate seroprevalence, underreported infections, and IFR for the Tirschenreuth [...] Read more.

SARS-CoV-2 infection fatality ratios (IFR) remain controversially discussed with implications for political measures. The German county of Tirschenreuth suffered a severe SARS-CoV-2 outbreak in spring 2020, with particularly high case fatality ratio (CFR). To estimate seroprevalence, underreported infections, and IFR for the Tirschenreuth population aged ≥14 years in June/July 2020, we conducted a population-based study including home visits for the elderly, and analyzed 4203 participants for SARS-CoV-2 antibodies via three antibody tests. Latent class analysis yielded 8.6% standardized county-wide seroprevalence, a factor of underreported infections of 5.0, and 2.5% overall IFR. Seroprevalence was two-fold higher among medical workers and one third among current smokers with similar proportions of registered infections. While seroprevalence did not show an age-trend, the factor of underreported infections was 12.2 in the young versus 1.7 for ≥85-year-old. Age-specific IFRs were <0.5% below 60 years of age, 1.0% for age 60–69, and 13.2% for age 70+. Senior care homes accounted for 45% of COVID-19-related deaths, reflected by an IFR of 7.5% among individuals aged 70+ and an overall IFR of 1.4% when excluding senior care home residents from our computation. Our data underscore senior care home infections as key determinant of IFR additionally to age, insufficient targeted testing in the young, and the need for further investigations on behavioral or molecular causes of the fewer infections among current smokers. Full article

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14 pages, 670 KiB

Open AccessArticle

Prevalence, Persistence, and Factors Associated with SARS-CoV-2 IgG Seropositivity in a Large Cohort of Healthcare Workers in a Tertiary Care University Hospital in Northern Italy

by Gitana Scozzari, Cristina Costa, Enrica Migliore, Maurizio Coggiola, Giovannino Ciccone, Luigi Savio, Antonio Scarmozzino, Enrico Pira, Paola Cassoni, Claudia Galassi, Rossana Cavallo and The Collaborative Group

Viruses 2021, 13(6), 1064; https://doi.org/10.3390/v13061064 - 3 Jun 2021

Cited by 19 | Viewed by 3672

Abstract

This observational study evaluated SARS-CoV-2 IgG seroprevalence and related clinical, demographic, and occupational factors among workers at the largest tertiary care University-Hospital of Northwestern Italy and the University of Turin after the first pandemic wave of March–April 2020. Overall, about 10,000 individuals were [...] Read more.

This observational study evaluated SARS-CoV-2 IgG seroprevalence and related clinical, demographic, and occupational factors among workers at the largest tertiary care University-Hospital of Northwestern Italy and the University of Turin after the first pandemic wave of March–April 2020. Overall, about 10,000 individuals were tested; seropositive subjects were retested after 5 months to evaluate antibodies waning. Among 8769 hospital workers, seroprevalence was 7.6%, without significant differences related to job profile; among 1185 University workers, 3.3%. Self-reporting of COVID-19 suspected symptoms was significantly associated with positivity (Odds Ratio (OR) 2.07, 95%CI: 1.76–2.44), although 27% of seropositive subjects reported no previous symptom. At multivariable analysis, contacts at work resulted in an increased risk of 69%, or 24% for working in a COVID ward; contacts in the household evidenced the highest risk, up to more than five-fold (OR 5.31, 95%CI: 4.12–6.85). Compared to never smokers, being active smokers was inversely associated with seroprevalence (OR 0.60, 95%CI: 0.48–0.76). After 5 months, 85% of previously positive subjects still tested positive. The frequency of SARS-COV-2 infection among Health Care Workers was comparable with that observed in surveys performed in Northern Italy and Europe after the first pandemic wave. This study confirms that infection frequently occurred as asymptomatic and underlines the importance of household exposure, seroprevalence (OR 0.60, 95%CI: 0.48–0.76). Full article

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12 pages, 2104 KiB

Open AccessArticle

Correlating qRT-PCR, dPCR and Viral Titration for the Identification and Quantification of SARS-CoV-2: A New Approach for Infection Management

by Martina Brandolini, Francesca Taddei, Maria Michela Marino, Laura Grumiro, Agata Scalcione, Maria Elena Turba, Fabio Gentilini, Michela Fantini, Silvia Zannoli, Giorgio Dirani and Vittorio Sambri

Viruses 2021, 13(6), 1022; https://doi.org/10.3390/v13061022 - 28 May 2021

Cited by 29 | Viewed by 6083

Abstract

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) was first identified in Wuhan, China, in late 2019 and is the causative agent of the coronavirus disease 2019 (COVID-19) pandemic. Quantitative reverse-transcription polymerase chain reaction (qRT-PCR) represents the gold standard for diagnostic assays even if [...] Read more.

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) was first identified in Wuhan, China, in late 2019 and is the causative agent of the coronavirus disease 2019 (COVID-19) pandemic. Quantitative reverse-transcription polymerase chain reaction (qRT-PCR) represents the gold standard for diagnostic assays even if it cannot precisely quantify viral RNA copies. Thus, we decided to compare qRT-PCR with digital polymerase chain reaction (dPCR), which is able to give an accurate number of RNA copies that can be found in a specimen. However, the aforementioned methods are not capable to discriminate if the detected RNA is infectious or not. For this purpose, it is necessary to perform an endpoint titration on cell cultures, which is largely used in the research field and provides a tissue culture infecting dose per mL (TCID50/mL) value. Both research and diagnostics call for a model that allows the comparison between the results obtained employing different analytical methods. The aim of this study is to define a comparison among two qRT-PCR protocols (one with preliminary RNA extraction and purification and an extraction-free qRT-PCR), a dPCR and a titration on cell cultures. The resulting correlations yield a faithful estimation of the total number of RNA copies and of the infectious viral burden from a Ct value obtained with diagnostic routine tests. All these estimations take into consideration methodological errors linked to the qRT-PCR, dPCR and titration assays. Full article

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16 pages, 12500 KiB

Open AccessArticle

COVID-19 Severity Potentially Modulated by Cardiovascular-Disease-Associated Immune Dysregulation

by Abby C. Lee, Grant Castaneda, Wei Tse Li, Chengyu Chen, Neil Shende, Jaideep Chakladar, Pam R. Taub, Eric Y. Chang and Weg M. Ongkeko

Viruses 2021, 13(6), 1018; https://doi.org/10.3390/v13061018 - 28 May 2021

Cited by 9 | Viewed by 3759

Abstract

Patients with underlying cardiovascular conditions are particularly vulnerable to severe COVID-19. In this project, we aimed to characterize similarities in dysregulated immune pathways between COVID-19 patients and patients with cardiomyopathy, venous thromboembolism (VTE), or coronary artery disease (CAD). We hypothesized that these similarly [...] Read more.

Patients with underlying cardiovascular conditions are particularly vulnerable to severe COVID-19. In this project, we aimed to characterize similarities in dysregulated immune pathways between COVID-19 patients and patients with cardiomyopathy, venous thromboembolism (VTE), or coronary artery disease (CAD). We hypothesized that these similarly dysregulated pathways may be critical to how cardiovascular diseases (CVDs) exacerbate COVID-19. To evaluate immune dysregulation in different diseases, we used four separate datasets, including RNA-sequencing data from human left ventricular cardiac muscle samples of patients with dilated or ischemic cardiomyopathy and healthy controls; RNA-sequencing data of whole blood samples from patients with single or recurrent event VTE and healthy controls; RNA-sequencing data of human peripheral blood mononuclear cells (PBMCs) from patients with and without obstructive CAD; and RNA-sequencing data of platelets from COVID-19 subjects and healthy controls. We found similar immune dysregulation profiles between patients with CVDs and COVID-19 patients. Interestingly, cardiomyopathy patients display the most similar immune landscape to COVID-19 patients. Additionally, COVID-19 patients experience greater upregulation of cytokine- and inflammasome-related genes than patients with CVDs. In all, patients with CVDs have a significant overlap of cytokine- and inflammasome-related gene expression profiles with that of COVID-19 patients, possibly explaining their greater vulnerability to severe COVID-19. Full article

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15 pages, 4537 KiB

Open AccessReview

The Spike of Concern—The Novel Variants of SARS-CoV-2

by Anna Winger and Thomas Caspari

Viruses 2021, 13(6), 1002; https://doi.org/10.3390/v13061002 - 27 May 2021

Cited by 95 | Viewed by 15189

Abstract

The high sequence identity of the first SARS-CoV-2 samples collected in December 2019 at Wuhan did not foretell the emergence of novel variants in the United Kingdom, North and South America, India, or South Africa that drive the current waves of the pandemic. [...] Read more.

The high sequence identity of the first SARS-CoV-2 samples collected in December 2019 at Wuhan did not foretell the emergence of novel variants in the United Kingdom, North and South America, India, or South Africa that drive the current waves of the pandemic. The viral spike receptor possesses two surface areas of high mutagenic plasticity: the supersite in its N-terminal domain (NTD) that is recognised by all anti-NTD antibodies and its receptor binding domain (RBD) where 17 residues make contact with the human Ace2 protein (angiotensin I converting enzyme 2) and many neutralising antibodies bind. While NTD mutations appear at first glance very diverse, they converge on the structure of the supersite. The mutations within the RBD, on the other hand, hone in on only a small number of key sites (K417, L452, E484, N501) that are allosteric control points enabling spike to escape neutralising antibodies while maintaining or even gaining Ace2-binding activity. The D614G mutation is the hallmark of all variants, as it promotes viral spread by increasing the number of open spike protomers in the homo-trimeric receptor complex. This review discusses the recent spike mutations as well as their evolution. Full article

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12 pages, 1128 KiB

Open AccessOpinion

Repeated Exposure to Subinfectious Doses of SARS-CoV-2 May Promote T Cell Immunity and Protection against Severe COVID-19

by Maria Laura De Angelis, Federica Francescangeli, Rachele Rossi, Alessandro Giuliani, Ruggero De Maria and Ann Zeuner

Viruses 2021, 13(6), 961; https://doi.org/10.3390/v13060961 - 22 May 2021

Cited by 9 | Viewed by 20796

Abstract

Europe is experiencing a third wave of COVID-19 due to the spread of highly transmissible SARS-CoV-2 variants. A number of positive and negative factors constantly shape the rates of COVID-19 infections, hospitalization, and mortality. Among these factors, the rise in increasingly transmissible variants [...] Read more.

Europe is experiencing a third wave of COVID-19 due to the spread of highly transmissible SARS-CoV-2 variants. A number of positive and negative factors constantly shape the rates of COVID-19 infections, hospitalization, and mortality. Among these factors, the rise in increasingly transmissible variants on one side and the effect of vaccinations on the other side create a picture deeply different from that of the first pandemic wave. Starting from the observation that in several European countries the number of COVID-19 infections in the second and third pandemic wave increased without a proportional rise in disease severity and mortality, we hypothesize the existence of an additional factor influencing SARS-CoV-2 dynamics. This factor consists of an immune defence against severe COVID-19, provided by SARS-CoV-2-specific T cells progressively developing upon natural exposure to low virus doses present in populated environments. As suggested by recent studies, low-dose viral particles entering the respiratory and intestinal tracts may be able to induce T cell memory in the absence of inflammation, potentially resulting in different degrees of immunization. In this scenario, non-pharmaceutical interventions would play a double role, one in the short term by reducing the detrimental spreading of SARS-CoV-2 particles, and one in the long term by allowing the development of a widespread (although heterogeneous and uncontrollable) form of immune protection. Full article

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14 pages, 2103 KiB

Open AccessArticle

SARS-CoV-2 Disinfection of Air and Surface Contamination by TiO₂ Photocatalyst-Mediated Damage to Viral Morphology, RNA, and Protein

by Ryosuke Matsuura, Chieh-Wen Lo, Satoshi Wada, Junichi Somei, Heihachiro Ochiai, Takeharu Murakami, Norihito Saito, Takayo Ogawa, Atsushi Shinjo, Yoshimi Benno, Masaru Nakagawa, Masami Takei and Yoko Aida

Viruses 2021, 13(5), 942; https://doi.org/10.3390/v13050942 - 20 May 2021

Cited by 63 | Viewed by 12896

Abstract

SARS-CoV-2 is the causative agent of COVID-19, which is a global pandemic. SARS-CoV-2 is transmitted rapidly via contaminated surfaces and aerosols, emphasizing the importance of environmental disinfection to block the spread of virus. Ultraviolet C radiation and chemical compounds are effective for SARS-CoV-2 [...] Read more.

SARS-CoV-2 is the causative agent of COVID-19, which is a global pandemic. SARS-CoV-2 is transmitted rapidly via contaminated surfaces and aerosols, emphasizing the importance of environmental disinfection to block the spread of virus. Ultraviolet C radiation and chemical compounds are effective for SARS-CoV-2 disinfection, but can only be applied in the absence of humans due to their toxicities. Therefore, development of disinfectants that can be applied in working spaces without evacuating people is needed. Here we showed that TiO₂-mediated photocatalytic reaction inactivates SARS-CoV-2 in a time-dependent manner and decreases its infectivity by 99.9% after 20 min and 120 min of treatment in aerosol and liquid, respectively. The mechanistic effects of TiO₂ photocatalyst on SARS-CoV-2 virion included decreased total observed virion count, increased virion size, and reduced particle surface spike structure, as determined by transmission electron microscopy. Damage to viral proteins and genome was further confirmed by western blotting and RT-qPCR, respectively. The multi-antiviral effects of TiO₂-mediated photocatalytic reaction implies universal disinfection potential for different infectious agents. Notably, TiO₂ has no adverse effects on human health, and therefore, TiO₂-induced photocatalytic reaction is suitable for disinfection of SARS-CoV-2 and other emerging infectious disease-causing agents in human habitation. Full article

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17 pages, 34250 KiB

Open AccessArticle

Prediction and Evolution of the Molecular Fitness of SARS-CoV-2 Variants: Introducing SpikePro

by Fabrizio Pucci and Marianne Rooman

Viruses 2021, 13(5), 935; https://doi.org/10.3390/v13050935 - 18 May 2021

Cited by 22 | Viewed by 5434

Abstract

The understanding of the molecular mechanisms driving the fitness of the SARS-CoV-2 virus and its mutational evolution is still a critical issue. We built a simplified computational model, called SpikePro, to predict the SARS-CoV-2 fitness from the amino acid sequence and structure of [...] Read more.

The understanding of the molecular mechanisms driving the fitness of the SARS-CoV-2 virus and its mutational evolution is still a critical issue. We built a simplified computational model, called SpikePro, to predict the SARS-CoV-2 fitness from the amino acid sequence and structure of the spike protein. It contains three contributions: the inter-human transmissibility of the virus predicted from the stability of the spike protein, the infectivity computed in terms of the affinity of the spike protein for the ACE2 receptor, and the ability of the virus to escape from the human immune response based on the binding affinity of the spike protein for a set of neutralizing antibodies. Our model reproduces well the available experimental, epidemiological and clinical data on the impact of variants on the biophysical characteristics of the virus. For example, it is able to identify circulating viral strains that, by increasing their fitness, recently became dominant at the population level. SpikePro is a useful, freely available instrument which predicts rapidly and with good accuracy the dangerousness of new viral strains. It can be integrated and play a fundamental role in the genomic surveillance programs of the SARS-CoV-2 virus that, despite all the efforts, remain time-consuming and expensive. Full article

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13 pages, 2793 KiB

Open AccessArticle

Critical Aspects Concerning the Development of a Pooling Approach for SARS-CoV-2 Diagnosis Using Large-Scale PCR Testing

by Daniel Cruceriu, Oana Baldasici, Loredana Balacescu, Stefana Gligor-Popa, Mirela Flonta, Milena A. Man, Simona Visan, Catalin Vlad, Adrian P. Trifa, Ovidiu Balacescu and Patriciu Achimas-Cadariu

Viruses 2021, 13(5), 902; https://doi.org/10.3390/v13050902 - 13 May 2021

Cited by 2 | Viewed by 4078

Abstract

The primary approach to controlling the spread of the pandemic SARS-CoV-2 is to diagnose and isolate the infected people quickly. Our paper aimed to investigate the efficiency and the reliability of a hierarchical pooling approach for large-scale PCR testing for SARS-CoV-2 diagnosis. To [...] Read more.

The primary approach to controlling the spread of the pandemic SARS-CoV-2 is to diagnose and isolate the infected people quickly. Our paper aimed to investigate the efficiency and the reliability of a hierarchical pooling approach for large-scale PCR testing for SARS-CoV-2 diagnosis. To identify the best conditions for the pooling approach for SARS-CoV-2 diagnosis by RT-qPCR, we investigated four manual methods for both RNA extraction and PCR assessment targeting one or more of the RdRp, N, S, and ORF1a genes, by using two PCR devices and an automated flux for SARS-CoV-2 detection. We determined the most efficient and accurate diagnostic assay, taking into account multiple parameters. The optimal pool size calculation included the prevalence of SARS-CoV-2, the assay sensitivity of 95%, an assay specificity of 100%, and a range of pool sizes of 5 to 15 samples. Our investigation revealed that the most efficient and accurate procedure for detecting the SARS-CoV-2 has a detection limit of 2.5 copies/PCR reaction. This pooling approach proved to be efficient and accurate in detecting SARS-CoV-2 for all samples with individual quantification cycle (Cq) values lower than 35, accounting for more than 94% of all positive specimens. Our data could serve as a comprehensive practical guide for SARS-CoV-2 diagnostic centers planning to address such a pooling strategy. Full article

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9 pages, 1309 KiB

Open AccessBrief Report

Performance of Self-Collected Saliva Testing Compared with Nasopharyngeal Swab Testing for the Detection of SARS-CoV-2

by Florence Carrouel, Martine Valette, Hervé Perrier, Maude Bouscambert-Duchamp, Claude Dussart, Paul Tramini and Denis Bourgeois

Viruses 2021, 13(5), 895; https://doi.org/10.3390/v13050895 - 12 May 2021

Cited by 12 | Viewed by 3090

Abstract

The aim of this study was to determine whether self-collected pure saliva (SCPS) is comparable to nasopharyngeal (NP) swabs in the quantitative detection of SARS-CoV-2 by RT-PCR in asymptomatic, mild patients with confirmed COVID-19. Thirty-one patients aged from 18 to 85 years were [...] Read more.

The aim of this study was to determine whether self-collected pure saliva (SCPS) is comparable to nasopharyngeal (NP) swabs in the quantitative detection of SARS-CoV-2 by RT-PCR in asymptomatic, mild patients with confirmed COVID-19. Thirty-one patients aged from 18 to 85 years were included between 9 June and 11 December 2020. A SCPS sample and a NP sample were taken for each patient. Quantitative PCR was performed to detect SARS-CoV-2 viral load. Results of SCPS vs. NP samples testing were compared. Statistical analyses were performed. Viral load was significantly correlated (r = 0.72). The concordance probability was estimated at 73.3%. In symptomatic adults, SCPS performance was similar to that of NP swabs (Percent Agreement = 74.1%; p = 0.11). Thus, the salivary test based on pure oral saliva samples easily obtained by noninvasive techniques has a fair agreement with the nasopharyngeal one in asymptomatic, mild patients with a confirmed diagnosis of COVID-19. Full article

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15 pages, 5287 KiB

Open AccessArticle

Scalable, Micro-Neutralization Assay for Assessment of SARS-CoV-2 (COVID-19) Virus-Neutralizing Antibodies in Human Clinical Samples

by Richard S. Bennett, Elena N. Postnikova, Janie Liang, Robin Gross, Steven Mazur, Saurabh Dixit, Gregory Kocher, Shuiqing Yu, Shalamar Georgia-Clark, Dawn Gerhardt, Yingyun Cai, Lindsay Marron, Vladimir V. Lukin and Michael R. Holbrook

Viruses 2021, 13(5), 893; https://doi.org/10.3390/v13050893 - 12 May 2021

Cited by 24 | Viewed by 3832

Abstract

As the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic expanded, it was clear that effective testing for the presence of neutralizing antibodies in the blood of convalescent patients would be critical for development of plasma-based therapeutic approaches. To address the need for [...] Read more.

As the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic expanded, it was clear that effective testing for the presence of neutralizing antibodies in the blood of convalescent patients would be critical for development of plasma-based therapeutic approaches. To address the need for a high-quality neutralization assay against SARS-CoV-2, a previously established fluorescence reduction neutralization assay (FRNA) against Middle East respiratory syndrome coronavirus (MERS-CoV) was modified and optimized. The SARS-CoV-2 FRNA provides a quantitative assessment of a large number of infected cells through use of a high-content imaging system. Because of this approach, and the fact that it does not involve subjective interpretation, this assay is more efficient and more accurate than other neutralization assays. In addition, the ability to set robust acceptance criteria for individual plates and specific test wells provided further rigor to this assay. Such agile adaptability avails use with multiple virus variants. By February 2021, the SARS-CoV-2 FRNA had been used to screen over 5000 samples, including acute and convalescent plasma or serum samples and therapeutic antibody treatments, for SARS-CoV-2 neutralizing titers. Full article

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11 pages, 1633 KiB

Open AccessArticle

Genomic Surveillance of Circulating SARS-CoV-2 in South East Italy: A One-Year Retrospective Genetic Study

by Loredana Capozzi, Angelica Bianco, Laura Del Sambro, Domenico Simone, Antonio Lippolis, Maria Notarnicola, Graziano Pesole, Lorenzo Pace, Domenico Galante and Antonio Parisi

Viruses 2021, 13(5), 731; https://doi.org/10.3390/v13050731 - 22 Apr 2021

Cited by 8 | Viewed by 4318

Abstract

In order to provide insights into the evolutionary and epidemiological viral dynamics during the current COVID-19 pandemic in South Eastern Italy, a total of 298 genomes of SARS-CoV-2 strains collected in the Apulia and Basilicata regions, between March 2020 and January 2021, were [...] Read more.

In order to provide insights into the evolutionary and epidemiological viral dynamics during the current COVID-19 pandemic in South Eastern Italy, a total of 298 genomes of SARS-CoV-2 strains collected in the Apulia and Basilicata regions, between March 2020 and January 2021, were sequenced. The genomic analysis performed on the draft genomes allowed us to assign the genetic clades and lineages of belonging to each sample and provide an overview of the main circulating viral variants. Our data showed the spread in Apulia and Basilicata of SARS-CoV-2 variants which have emerged during the second wave of infections and are being currently monitored worldwide for their increased transmission rate and their possible impact on vaccines and therapies. These results emphasize the importance of genome sequencing for the epidemiological surveillance of the new SARS-CoV-2 variants’ spread. Full article

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17 pages, 3797 KiB

Open AccessArticle

Arthropod Ectoparasites Have Potential to Bind SARS-CoV-2 via ACE

by Su Datt Lam, Paul Ashford, Sandra Díaz-Sánchez, Margarita Villar, Christian Gortázar, José de la Fuente and Christine Orengo

Viruses 2021, 13(4), 708; https://doi.org/10.3390/v13040708 - 19 Apr 2021

Cited by 9 | Viewed by 5612

Abstract

Coronavirus-like organisms have been previously identified in Arthropod ectoparasites (such as ticks and unfed cat flea). Yet, the question regarding the possible role of these arthropods as SARS-CoV-2 passive/biological transmission vectors is still poorly explored. In this study, we performed in silico structural [...] Read more.

Coronavirus-like organisms have been previously identified in Arthropod ectoparasites (such as ticks and unfed cat flea). Yet, the question regarding the possible role of these arthropods as SARS-CoV-2 passive/biological transmission vectors is still poorly explored. In this study, we performed in silico structural and binding energy calculations to assess the risks associated with possible ectoparasite transmission. We found sufficient similarity between ectoparasite ACE and human ACE2 protein sequences to build good quality 3D-models of the SARS-CoV-2 Spike:ACE complex to assess the impacts of ectoparasite mutations on complex stability. For several species (e.g., water flea, deer tick, body louse), our analyses showed no significant destabilisation of the SARS-CoV-2 Spike:ACE complex, suggesting these species would bind the viral Spike protein. Our structural analyses also provide structural rationale for interactions between the viral Spike and the ectoparasite ACE proteins. Although we do not have experimental evidence of infection in these ectoparasites, the predicted stability of the complex suggests this is possible, raising concerns of a possible role in passive transmission of the virus to their human hosts. Full article

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8 pages, 1317 KiB

Open AccessCommunication

SARS-CoV-2 Reinfection in a Healthcare Worker Despite the Presence of Detectable Neutralizing Antibodies

by Thomas Theo Brehm, Susanne Pfefferle, Ronald von Possel, Robin Kobbe, Dominik Nörz, Stefan Schmiedel, Adam Grundhoff, Flaminia Olearo, Petra Emmerich, Alexis Robitaille, Thomas Günther, Platon Braun, Gabriele Andersen, Johannes K. Knobloch, Marylyn M. Addo, Ansgar W. Lohse, Martin Aepfelbacher, Nicole Fischer, Julian Schulze zur Wiesch and Marc Lütgehetmann

Viruses 2021, 13(4), 661; https://doi.org/10.3390/v13040661 - 12 Apr 2021

Cited by 21 | Viewed by 5303

Abstract

So far, only a few reports about reinfections with SARS-CoV-2 have been published, and they often lack detailed immunological and virological data. We report about a SARS-CoV-2 reinfection with a genetically distinct SARS-CoV-2 variant in an immunocompetent female healthcare worker that has led [...] Read more.

So far, only a few reports about reinfections with SARS-CoV-2 have been published, and they often lack detailed immunological and virological data. We report about a SARS-CoV-2 reinfection with a genetically distinct SARS-CoV-2 variant in an immunocompetent female healthcare worker that has led to a mild disease course. No obvious viral escape mutations were observed in the second virus variant. The infectious virus was shed from the patient during the second infection episode despite the presence of neutralizing antibodies in her blood. Our data indicate that a moderate immune response after the first infection, but not a viral escape, did allow for reinfection and live virus shedding. Full article

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9 pages, 246 KiB

Open AccessArticle

Comparison of Throat Washings, Nasopharyngeal Swabs and Oropharyngeal Swabs for Detection of SARS-CoV-2

by Florian Hitzenbichler, Stilla Bauernfeind, Bernd Salzberger, Barbara Schmidt and Jürgen J. Wenzel

Viruses 2021, 13(4), 653; https://doi.org/10.3390/v13040653 - 10 Apr 2021

Cited by 20 | Viewed by 3180

Abstract

Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) RNA is detected by reverse-transcription quantitative real-time PCR (RT-qPCR) from respiratory specimens. This study compares throat washings (TW), nasopharyngeal swabs (NS) and oropharyngeal swabs (OS). A total of 102 samples from 34 adult patients with confirmed [...] Read more.

Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) RNA is detected by reverse-transcription quantitative real-time PCR (RT-qPCR) from respiratory specimens. This study compares throat washings (TW), nasopharyngeal swabs (NS) and oropharyngeal swabs (OS). A total of 102 samples from 34 adult patients with confirmed SARS-CoV-2 infection were analysed by RT-qPCR with absolute quantification. The median concentrations and diagnostic sensitivities were

5.8 \times 10^{4}

copies/mL, 85% (NS),

1.4 \times 10^{4}

, 79% (OS) and

4.3 \times 10^{3}

, 85% (TW). Concentration differences were significant between NS and TW (P = 0.019). Saliva (SA) was available from 21 patients (median

3.4 \times 10^{3}

). OS and TW can be considered for SARS-CoV-2 diagnostics, although with slightly lower concentrations. Full article

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11 pages, 3530 KiB

Open AccessArticle

Nosocomial Outbreak of SARS-CoV-2 in a “Non-COVID-19” Hospital Ward: Virus Genome Sequencing as a Key Tool to Understand Cryptic Transmission

by Vítor Borges, Joana Isidro, Filipe Macedo, José Neves, Luís Silva, Mário Paiva, José Barata, Judite Catarino, Liliana Ciobanu, Sílvia Duarte, Luís Vieira, Raquel Guiomar and João Paulo Gomes

Viruses 2021, 13(4), 604; https://doi.org/10.3390/v13040604 - 1 Apr 2021

Cited by 43 | Viewed by 3901

Abstract

Dissemination of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in healthcare institutions affects both patients and health-care workers (HCW), as well as the institutional capacity to provide essential health services. Here, we investigated an outbreak of SARS-CoV-2 in a “non-COVID-19” hospital ward unveiled [...] Read more.

Dissemination of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in healthcare institutions affects both patients and health-care workers (HCW), as well as the institutional capacity to provide essential health services. Here, we investigated an outbreak of SARS-CoV-2 in a “non-COVID-19” hospital ward unveiled by massive testing, which challenged the reconstruction of transmission chains. The contacts network during the 15-day period before the screening was investigated, and positive SARS-CoV-2 RNA samples were subjected to virus genome sequencing. Of the 245 tested individuals, 48 (21 patients and 27 HCWs) tested positive for SARS-CoV-2. HCWs were mostly asymptomatic, but the mortality among patients reached 57.1% (12/21). Phylogenetic reconstruction revealed that all cases were part of the same transmission chain. By combining contact tracing and genomic data, including analysis of emerging minor variants, we unveiled a scenario of silent SARS-CoV-2 dissemination, mostly driven by the close contact within the HCWs group and between HCWs and patients. This investigation triggered enhanced prevention and control measures, leading to more timely detection and containment of novel outbreaks. This study shows the benefit of combining genomic and epidemiological data for disclosing complex nosocomial outbreaks, and provides valuable data to prevent transmission of COVID-19 in healthcare facilities. Full article

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