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5 pages, 209 KiB

Open AccessEditorial

Special Issue “Emerging Viruses 2021: Surveillance, Prevention, Evolution and Control”

by Fabrício Souza Campos, Maité Freitas Silva Vaslin and Luciana Barros de Arruda

Viruses 2022, 14(4), 815; https://doi.org/10.3390/v14040815 - 15 Apr 2022

Viewed by 1728

Abstract

Virus replication frequently results in the accumulation, re-assortment and re-combination of mutations, which contributes to their rapid adaptation to environmental changes and often advances the emergence of new virus variants or species [...] Full article

(This article belongs to the Special Issue Emerging Viruses 2021: Surveillance, Prevention, Evolution and Control)

4 pages, 651 KiB

Open AccessEditorial

Epidemic Spread of SARS-CoV-2 Lineage B.1.1.7 in Brazil

by Filipe R. R. Moreira, Diego M. Bonfim, Danielle A. G. Zauli, Joice P. Silva, Aline B. Lima, Frederico S. V. Malta, Alessandro C. S. Ferreira, Victor C. Pardini, Wagner C. S. Magalhães, Daniel C. Queiroz, Rafael M. Souza, Victor E. V. Geddes, Walyson C. Costa, Rennan G. Moreira, Nuno R. Faria, Carolina M. Voloch, Renan P. Souza and Renato S. Aguiar

Viruses 2021, 13(6), 984; https://doi.org/10.3390/v13060984 - 26 May 2021

Cited by 13 | Viewed by 4307

Abstract

The emergence of diverse lineages harboring mutations with functional significance and potentially enhanced transmissibility imposes an increased difficulty on the containment of the SARS-CoV-2 pandemic [...] Full article

(This article belongs to the Special Issue Emerging Viruses 2021: Surveillance, Prevention, Evolution and Control)

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Research

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18 pages, 4088 KiB

Open AccessArticle

Complete Genome Characterization of Reticuloendotheliosis Virus Detected in Chickens with Multiple Viral Coinfections

by Ruy D. Chacón, Benjy Sedano-Herrera, Elizabeth Regina Alfaro-Espinoza, Wilma Ursula Quispe, Arturo Liñan-Torres, David De la Torre, Anderson de Oliveira, Claudete S. Astolfi-Ferreira and Antonio J. Piantino Ferreira

Viruses 2022, 14(4), 798; https://doi.org/10.3390/v14040798 - 13 Apr 2022

Cited by 9 | Viewed by 3323

Abstract

Reticuloendotheliosis virus (REV) is a retroviral pathogen capable of infecting several avian hosts and is associated with immunosuppression, anemia, proventriculitis, neoplasia, and runting–stunting syndrome. Its genome contains the three major genes, gag, pol, and env, and two flanking long terminal [...] Read more.

Reticuloendotheliosis virus (REV) is a retroviral pathogen capable of infecting several avian hosts and is associated with immunosuppression, anemia, proventriculitis, neoplasia, and runting–stunting syndrome. Its genome contains the three major genes, gag, pol, and env, and two flanking long terminal repeat (LTR) regions. Complete genome sequences of REV are limited in terms of geographical origin. The aim of this study was to characterize the complete genome of REV detected in Brazilian chickens with multiple viral coinfections and analyze the polymorphisms in the deduced amino acids sequences corresponding to its encoded proteins. We tested the presence and completeness of REV as well as other viral pathogens in samples from Brazilian poultry farms by qPCR. The complete genomes of two REV strains were sequenced by overlapping fragments through the dideoxy method. Phylogenetic analysis, pairwise identity matrix, polymorphism identification and protein modeling were performed along the entire genome. We detected REV in 65% (26/40) of the tested samples. Concomitant viral infections were detected in 82.5% (33/40) of the samples and in 90% (9/10) of the farms. Multiple infections included up to seven viruses. Phylogenetic analysis classified both Brazilian strains into REV subtype 3, and the pairwise comparison indicated that strains from the USA and fowlpox virus (FWPV)-related strains were the most identical. The subdomain p18 in gag, the reverse transcriptase/ribonuclease H in pol, and the surface (SU) in the env protein were the most polymorphic in genomic comparisons. The relevant motifs for each protein were highly conserved, with fewer polymorphisms in the fusion peptide, immunosuppression domain, and disulfide bonds on the surface (SU) and transmembrane (TM) of env. This is the first study to include complete genomes of REV in Brazil and South America detected in farms with multiple viral coinfections. Our findings suggest an involvement of REV as an immunosuppressor and active agent in the emergence and progression of multiple infectious diseases. We also found a possible etiological relationship between Brazilian strains and the USA and FWPV recombinant strains. This information highlights the need for epidemiological vigilance regarding REV in association with another pathogens. Full article

(This article belongs to the Special Issue Emerging Viruses 2021: Surveillance, Prevention, Evolution and Control)

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23 pages, 5182 KiB

Open AccessArticle

Outbreaks of Avipoxvirus Clade E in Vaccinated Broiler Breeders with Exacerbated Beak Injuries and Sex Differences in Severity

by Ruy D. Chacón, Claudete S. Astolfi-Ferreira, Patrícia C. Pereira, Mario S. Assayag, Jr., Antony B. Campos-Salazar, David De la Torre, Lilian R. M. de Sá, Sonia R. Yokomizo de Almeida, Rose Elí Grassi Rici and Antonio J. Piantino Ferreira

Viruses 2022, 14(4), 773; https://doi.org/10.3390/v14040773 - 8 Apr 2022

Cited by 6 | Viewed by 3465

Abstract

Avipoxvirus affects chickens and wild birds, and it is characterized by lesions on the nonfeathered parts of the body (the cutaneous form), or necrotic lesions in the upper respiratory tract (the diphtheritic form). In poultry farming, avian pox is usually controlled by live [...] Read more.

Avipoxvirus affects chickens and wild birds, and it is characterized by lesions on the nonfeathered parts of the body (the cutaneous form), or necrotic lesions in the upper respiratory tract (the diphtheritic form). In poultry farming, avian pox is usually controlled by live attenuated vaccines. However, there have been many reports of outbreaks, even in flocks of vaccinated birds. In the present study, different outbreaks of the emerging clade E avipoxvirus were detected in commercial breeder flocks of chickens vaccinated against fowlpox virus in Southeast Brazil. Clinical manifestations of these outbreaks included a marked prevalence of moderate to severe progressive lesions in the beaks of affected birds, especially in roosters with increased mortality (up to 8.48%). Also, a reduced hatchability (up to 20.77% fewer hatching eggs) was observed in these flocks. Analysis of clinical samples through light and transmission electron microscopy revealed the presence of Bollinger bodies and poxvirus particles in epithelial cells and affecting chondrocytes. PCR, sequencing, and phylogenetic analysis of major core protein (P4b) and DNA polymerase (pol) genes identified this virus as clade E avipoxvirus. We also developed qPCR assays for open reading frames (ORFs) 49, 114, and 159 to detect and quantify this emergent virus. These results show the arrival and initial spread of this pathogen in the poultry industry, which was associated with harmful outbreaks and exacerbated clinical manifestations in vaccinated commercial breeder flocks. This study also highlights the relevance of permanent vigilance and the need to improve sanitary and vaccination programs. Full article

(This article belongs to the Special Issue Emerging Viruses 2021: Surveillance, Prevention, Evolution and Control)

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9 pages, 857 KiB

Open AccessCommunication

Nucleocapsid (N) Gene Mutations of SARS-CoV-2 Can Affect Real-Time RT-PCR Diagnostic and Impact False-Negative Results

by Jéssika Cristina Chagas Lesbon, Mirele Daiana Poleti, Elisângela Chicaroni de Mattos Oliveira, José Salvatore Leister Patané, Luan Gaspar Clemente, Vincent Louis Viala, Gabriela Ribeiro, Marta Giovanetti, Luiz Carlos Junior de Alcantara, Olivia Teixeira, Maria Cristina Nonato, Loyze Paola Oliveira de Lima, Antonio Jorge Martins, Claudia Renata dos Santos Barros, Elaine Cristina Marqueze, Jardelina de Souza Todão Bernardino, Debora Botequio Moretti, Ricardo Augusto Brassaloti, Raquel de Lello Rocha Campos Cassano, Pilar Drummond Sampaio Correa Mariani, Svetoslav Nanev Slavov, Rafael Bezerra dos Santos, Evandra Strazza Rodrigues, Elaine Vieira Santos, Josiane Serrano Borges, Debora Glenda Lima de La Roque, Joao Paulo Kitajima, Bibiana Santos, Patricia Akemi Assato, Felipe Allan da Silva da Costa, Cecilia Artico Banho, Livia Sacchetto, Marilia Mazzi Moraes, Melissa Palmieri, Fabiana Erica Vilanova da Silva, Rejane Maria Tommasini Grotto, Jayme A. Souza-Neto, Mauricio Lacerda Nogueira, Luiz Lehman Coutinho, Rodrigo Tocantins Calado, Raul Machado Neto, Dimas Tadeu Covas, Simone Kashima, Maria Carolina Elias, Sandra Coccuzzo Sampaio and Heidge Fukumasu Show full author list Hide full author list

Viruses 2021, 13(12), 2474; https://doi.org/10.3390/v13122474 - 10 Dec 2021

Cited by 30 | Viewed by 5576 | Correction

Abstract

The current COVID-19 pandemic demands massive testing by Real-time RT-PCR (Reverse Transcription Polymerase Chain Reaction), which is considered the gold standard diagnostic test for the detection of the SARS-CoV-2 virus. However, the virus continues to evolve with mutations that lead to phenotypic alterations [...] Read more.

The current COVID-19 pandemic demands massive testing by Real-time RT-PCR (Reverse Transcription Polymerase Chain Reaction), which is considered the gold standard diagnostic test for the detection of the SARS-CoV-2 virus. However, the virus continues to evolve with mutations that lead to phenotypic alterations as higher transmissibility, pathogenicity or vaccine evasion. Another big issue are mutations in the annealing sites of primers and probes of RT-PCR diagnostic kits leading to false-negative results. Therefore, here we identify mutations in the N (Nucleocapsid) gene that affects the use of the GeneFinder COVID-19 Plus RealAmp Kit. We sequenced SARS-CoV-2 genomes from 17 positive samples with no N gene detection but with RDRP (RNA-dependent RNA polymerase) and E (Envelope) genes detection, and observed a set of three different mutations affecting the N detection: a deletion of 18 nucleotides (Del28877-28894), a substitution of GGG to AAC (28881-28883) and a frameshift mutation caused by deletion (Del28877-28878). The last one cause a deletion of six AAs (amino acids) located in the central intrinsic disorder region at protein level. We also found this mutation in 99 of the 14,346 sequenced samples by the Sao Paulo state Network for Pandemic Alert of Emerging SARS-CoV-2 variants, demonstrating the circulation of the mutation in Sao Paulo, Brazil. Continuous monitoring and characterization of mutations affecting the annealing sites of primers and probes by genomic surveillance programs are necessary to maintain the effectiveness of the diagnosis of COVID-19. Full article

(This article belongs to the Special Issue Emerging Viruses 2021: Surveillance, Prevention, Evolution and Control)

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20 pages, 991 KiB

Open AccessArticle

Semi-Supervised Pipeline for Autonomous Annotation of SARS-CoV-2 Genomes

by Kristen L. Beck, Edward Seabolt, Akshay Agarwal, Gowri Nayar, Simone Bianco, Harsha Krishnareddy, Timothy A. Ngo, Mark Kunitomi, Vandana Mukherjee and James H. Kaufman

Viruses 2021, 13(12), 2426; https://doi.org/10.3390/v13122426 - 3 Dec 2021

Cited by 5 | Viewed by 3001

Abstract

SARS-CoV-2 genomic sequencing efforts have scaled dramatically to address the current global pandemic and aid public health. However, autonomous genome annotation of SARS-CoV-2 genes, proteins, and domains is not readily accomplished by existing methods and results in missing or incorrect sequences. To overcome [...] Read more.

SARS-CoV-2 genomic sequencing efforts have scaled dramatically to address the current global pandemic and aid public health. However, autonomous genome annotation of SARS-CoV-2 genes, proteins, and domains is not readily accomplished by existing methods and results in missing or incorrect sequences. To overcome this limitation, we developed a novel semi-supervised pipeline for automated gene, protein, and functional domain annotation of SARS-CoV-2 genomes that differentiates itself by not relying on the use of a single reference genome and by overcoming atypical genomic traits that challenge traditional bioinformatic methods. We analyzed an initial corpus of 66,000 SARS-CoV-2 genome sequences collected from labs across the world using our method and identified the comprehensive set of known proteins with 98.5% set membership accuracy and 99.1% accuracy in length prediction, compared to proteome references, including Replicase polyprotein 1ab (with its transcriptional slippage site). Compared to other published tools, such as Prokka (base) and VAPiD, we yielded a 6.4- and 1.8-fold increase in protein annotations. Our method generated 13,000,000 gene, protein, and domain sequences—some conserved across time and geography and others representing emerging variants. We observed 3362 non-redundant sequences per protein on average within this corpus and described key D614G and N501Y variants spatiotemporally in the initial genome corpus. For spike glycoprotein domains, we achieved greater than 97.9% sequence identity to references and characterized receptor binding domain variants. We further demonstrated the robustness and extensibility of our method on an additional 4000 variant diverse genomes containing all named variants of concern and interest as of August 2021. In this cohort, we successfully identified all keystone spike glycoprotein mutations in our predicted protein sequences with greater than 99% accuracy as well as demonstrating high accuracy of the protein and domain annotations. This work comprehensively presents the molecular targets to refine biomedical interventions for SARS-CoV-2 with a scalable, high-accuracy method to analyze newly sequenced infections as they arise. Full article

(This article belongs to the Special Issue Emerging Viruses 2021: Surveillance, Prevention, Evolution and Control)

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22 pages, 6762 KiB

Open AccessArticle

Changes of Host Immunity Mediated by IFN-γ⁺ CD8⁺ T Cells in Children with Adenovirus Pneumonia in Different Severity of Illness

by Ruilin Zheng, Yinghua Li, Danyang Chen, Jingyao Su, Ning Han, Haitian Chen, Zhihui Ning, Misi Xiao, Mingqi Zhao and Bing Zhu

Viruses 2021, 13(12), 2384; https://doi.org/10.3390/v13122384 - 28 Nov 2021

Cited by 17 | Viewed by 2350

Abstract

The host immunity of patients with adenovirus pneumonia in different severity of illness is unclear. This study compared the routine laboratory tests and the host immunity of human adenovirus (HAdV) patients with different severity of illness. A co-cultured cell model in vitro was [...] Read more.

The host immunity of patients with adenovirus pneumonia in different severity of illness is unclear. This study compared the routine laboratory tests and the host immunity of human adenovirus (HAdV) patients with different severity of illness. A co-cultured cell model in vitro was established to verify the T cell response in vitro. Among 140 patients with confirmed HAdV of varying severity, the number of lymphocytes in the severe patients was significantly reduced to 1.91 × 10⁹/L compared with the healthy control (3.92 × 10⁹/L) and the mild patients (4.27 × 10⁹/L). The levels of IL-6, IL-10, and IFN-γ in patients with adenovirus pneumonia were significantly elevated with the severity of the disease. Compared with the healthy control (20.82%) and the stable patients (33.96%), the percentage of CD8⁺ T cells that produced IFN-γ increased to 56.27% in the progressing patients. Adenovirus infection increased the percentage of CD8⁺ T and CD4⁺ T cells that produce IFN-γ in the co-culture system. The hyperfunction of IFN-γ⁺ CD8⁺ T cells might be related to the severity of adenovirus infection. The in vitro co-culture cell model could also provide a usable cellular model for subsequent experiments. Full article

(This article belongs to the Special Issue Emerging Viruses 2021: Surveillance, Prevention, Evolution and Control)

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26 pages, 10872 KiB

Open AccessArticle

Kite-Shaped Molecules Block SARS-CoV-2 Cell Entry at a Post-Attachment Step

by Shiu-Wan Chan, Talha Shafi and Robert C. Ford

Viruses 2021, 13(11), 2306; https://doi.org/10.3390/v13112306 - 19 Nov 2021

Cited by 7 | Viewed by 2697

Abstract

Anti-viral small molecules are currently lacking for treating coronavirus infection. The long development timescales for such drugs are a major problem, but could be shortened by repurposing existing drugs. We therefore screened a small library of FDA-approved compounds for potential severe acute respiratory [...] Read more.

Anti-viral small molecules are currently lacking for treating coronavirus infection. The long development timescales for such drugs are a major problem, but could be shortened by repurposing existing drugs. We therefore screened a small library of FDA-approved compounds for potential severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) antivirals using a pseudovirus system that allows a sensitive read-out of infectivity. A group of structurally-related compounds, showing moderate inhibitory activity with IC₅₀ values in the 2–5 μM range, were identified. Further studies demonstrated that these “kite-shaped” molecules were surprisingly specific for SARS-CoV-1 and SARS-CoV-2 and that they acted early in the entry steps of the viral infectious cycle, but did not affect virus attachment to the cells. Moreover, the compounds were able to prevent infection in both kidney- and lung-derived human cell lines. The structural homology of the hits allowed the production of a well-defined pharmacophore that was found to be highly accurate in predicting the anti-viral activity of the compounds in the screen. We discuss the prospects of repurposing these existing drugs for treating current and future coronavirus outbreaks. Full article

(This article belongs to the Special Issue Emerging Viruses 2021: Surveillance, Prevention, Evolution and Control)

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10 pages, 984 KiB

Open AccessArticle

Hypovitaminosis D Is Associated with Higher Levels of Inflammatory Cytokines and with HAM/TSP in HTLV-Infected Patients

by Elaine Coutinho Netto, Alfredo Carlos Silva, Célia Pedroso and Carlos Brites

Viruses 2021, 13(11), 2223; https://doi.org/10.3390/v13112223 - 4 Nov 2021

Cited by 6 | Viewed by 1873 | Correction

Abstract

Recent studies have shown the effects of vitamin D on host response to infectious diseases. Some studies detected a high prevalence of hypovitaminosis D in HIV-infected patients, but scarce information exists for HTLV-1 infection. We conducted a cross-sectional study to evaluate the frequency [...] Read more.

Recent studies have shown the effects of vitamin D on host response to infectious diseases. Some studies detected a high prevalence of hypovitaminosis D in HIV-infected patients, but scarce information exists for HTLV-1 infection. We conducted a cross-sectional study to evaluate the frequency of hypovitaminosis D in HTLV-1 patients and its relationship with their immune response in HTLV-infected patients and in age- and gender-matched controls at a Brazilian rehabilitation hospital. We compared vitamin D, interleukin-6 (IL-6), tumoral necrosis factor-alpha (TNF-α) and interferon-gamma (IFN-γ) levels across groups. Logistic regression was utilized to assess the association between hypovitaminosis D and cytokine levels. We enrolled 161 HTLV-infected subjects (129 HTLV-associated myelopathy/tropical spastic paraparesis (HAM/TSP) patients, 32 asymptomatic HTLV carriers) and equal number of HTLV-negative controls. We observed a significantly higher prevalence of hypovitaminosis D in patients with HAM/TSP than in HTLV asymptomatic carriers (p < 0.001), or controls (p < 0.001). HAM/TSP patients also had higher levels of IL-6 and IFN-γ than asymptomatic carriers. Patients with HAM/TSP and hypovitaminosis D had higher levels of TNF-α than asymptomatic HTLV carriers. These findings suggest hypovitaminosis D plays a role in HAM/TSP pathogenesis, and it needs to be evaluated in further studies. Full article

(This article belongs to the Special Issue Emerging Viruses 2021: Surveillance, Prevention, Evolution and Control)

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12 pages, 32758 KiB

Open AccessArticle

Mutational Hotspot in the SARS-CoV-2 Spike Protein N-Terminal Domain Conferring Immune Escape Potential

by Slawomir Kubik, Nils Arrigo, Jaume Bonet and Zhenyu Xu

Viruses 2021, 13(11), 2114; https://doi.org/10.3390/v13112114 - 20 Oct 2021

Cited by 11 | Viewed by 3171

Abstract

Global efforts are being made to monitor the evolution of SARS-CoV-2, aiming for early identification of genotypes providing increased infectivity or virulence. However, viral lineage-focused tracking might fail in early detection of advantageous mutations emerging independently across phylogenies. Here, the emergence patterns of [...] Read more.

Global efforts are being made to monitor the evolution of SARS-CoV-2, aiming for early identification of genotypes providing increased infectivity or virulence. However, viral lineage-focused tracking might fail in early detection of advantageous mutations emerging independently across phylogenies. Here, the emergence patterns of Spike mutations were investigated in sequences deposited in local and global databases to identify mutational hotspots across phylogenies and we evaluated their impact on SARS-CoV-2 evolution. We found a striking increase in the frequency of recruitment of diverse substitutions at a critical residue (W152), positioned in the N-terminal domain (NTD) of the Spike protein, observed repeatedly across independent phylogenetic and geographical contexts. These mutations might have an impact on the evasion of neutralizing antibodies. Finally, we found that NTD is a region exhibiting particularly high frequency of mutation recruitments, suggesting an evolutionary path in which the virus maintains optimal efficiency of ACE2 binding combined with the flexibility facilitating the immune escape. We conclude that adaptive mutations, frequently present outside of the receptor-binding domain, can emerge in virtually any SARS-CoV-2 lineage and at any geographical location. Therefore, surveillance should not be restricted to monitoring defined lineages alone. Full article

(This article belongs to the Special Issue Emerging Viruses 2021: Surveillance, Prevention, Evolution and Control)

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13 pages, 1592 KiB

Open AccessArticle

Turnover of SARS-CoV-2 Lineages Shaped the Pandemic and Enabled the Emergence of New Variants in the State of Rio de Janeiro, Brazil

by Ronaldo da Silva Francisco Junior, Alessandra P Lamarca, Luiz G P de Almeida, Liliane Cavalcante, Douglas Terra Machado, Yasmmin Martins, Otávio Brustolini, Alexandra L Gerber, Ana Paula de C Guimarães, Reinaldo Bellini Gonçalves, Cassia Alves, Diana Mariani, Thais Felix Cruz, Isabelle Vasconcellos de Souza, Erika Martins de Carvalho, Mario Sergio Ribeiro, Silvia Carvalho, Flávio Dias da Silva, Márcio Henrique de Oliveira Garcia, Leandro Magalhães de Souza, Cristiane Gomes da Silva, Caio Luiz Pereira Ribeiro, Andréa Cony Cavalcanti, Claudia Maria Braga de Mello, Cláudio J. Struchiner, Amilcar Tanuri and Ana Tereza R de Vasconcelos Show full author list Hide full author list

Viruses 2021, 13(10), 2013; https://doi.org/10.3390/v13102013 - 7 Oct 2021

Cited by 13 | Viewed by 3416

Abstract

In the present study, we provide a retrospective genomic epidemiology analysis of the SARS-CoV-2 pandemic in the state of Rio de Janeiro, Brazil. We gathered publicly available data from GISAID and sequenced 1927 new genomes sampled periodically from March 2021 to June 2021 [...] Read more.

In the present study, we provide a retrospective genomic epidemiology analysis of the SARS-CoV-2 pandemic in the state of Rio de Janeiro, Brazil. We gathered publicly available data from GISAID and sequenced 1927 new genomes sampled periodically from March 2021 to June 2021 from 91 out of the 92 cities of the state. Our results showed that the pandemic was characterized by three different phases driven by a successive replacement of lineages. Interestingly, we noticed that viral supercarriers accounted for the overwhelming majority of the circulating virus (>90%) among symptomatic individuals in the state. Moreover, SARS-CoV-2 genomic surveillance also revealed the emergence and spread of two new variants (P.5 and P.1.2), firstly reported in this study. Our findings provided important lessons learned from the different epidemiological aspects of the SARS-CoV-2 dynamic in Rio de Janeiro. Altogether, this might have a strong potential to shape future decisions aiming to improve public health management and understanding mechanisms underlying virus dispersion. Full article

(This article belongs to the Special Issue Emerging Viruses 2021: Surveillance, Prevention, Evolution and Control)

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16 pages, 3747 KiB

Open AccessArticle

An Antigenic Space Framework for Understanding Antibody Escape of SARS-CoV-2 Variants

by Nathaniel L. Miller, Thomas Clark, Rahul Raman and Ram Sasisekharan

Viruses 2021, 13(10), 2009; https://doi.org/10.3390/v13102009 - 6 Oct 2021

Cited by 7 | Viewed by 3473

Abstract

The evolution of mutations in SARS-CoV-2 at antigenic sites that impact neutralizing antibody responses in humans poses a risk to immunity developed through vaccination and natural infection. The highly successful RNA-based vaccines have enabled rapid vaccine updates that incorporate mutations from current variants [...] Read more.

The evolution of mutations in SARS-CoV-2 at antigenic sites that impact neutralizing antibody responses in humans poses a risk to immunity developed through vaccination and natural infection. The highly successful RNA-based vaccines have enabled rapid vaccine updates that incorporate mutations from current variants of concern (VOCs). It is therefore important to anticipate future antigenic mutations as the virus navigates the heterogeneous global landscape of host immunity. Toward this goal, we survey epitope-paratope interfaces of anti-SARS-CoV-2 antibodies to map an antigenic space that captures the role of each spike protein residue within the polyclonal antibody response directed against the ACE2-receptor binding domain (RBD) or the N-terminal domain (NTD). In particular, the antigenic space map builds on recently published epitope definitions by annotating epitope overlap and orthogonality at the residue level. We employ the antigenic space map as a framework to understand how mutations on nine major variants contribute to each variant’s evasion of neutralizing antibodies. Further, we identify constellations of mutations that span the orthogonal epitope regions of the RBD and NTD on the variants with the greatest antibody escape. Finally, we apply the antigenic space map to predict which regions of antigenic space—should they mutate—may be most likely to complementarily augment antibody evasion for the most evasive and transmissible VOCs. Full article

(This article belongs to the Special Issue Emerging Viruses 2021: Surveillance, Prevention, Evolution and Control)

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11 pages, 3940 KiB

Open AccessArticle

Outbreak of a Systemic Form of Camelpox in a Dromedary Herd (Camelus dromedarius) in the United Arab Emirates

by Sunitha Joseph, Joerg Kinne, Péter Nagy, Jutka Juhász, Rajib Barua, Nissy Annie Georgy Patteril, Donata Hoffmann, Florian Pfaff, Bernd Hoffmann and Ulrich Wernery

Viruses 2021, 13(10), 1940; https://doi.org/10.3390/v13101940 - 28 Sep 2021

Cited by 11 | Viewed by 2298

Abstract

Camelpox virus (CMLV) is the causative agent of camelpox, which frequently occurs in the Old World camelids-rearing countries except for Australia. It has also been described in experimentally inoculated New World camelids. Camelpox outbreaks are often experienced shortly after the rainy season, which [...] Read more.

Camelpox virus (CMLV) is the causative agent of camelpox, which frequently occurs in the Old World camelids-rearing countries except for Australia. It has also been described in experimentally inoculated New World camelids. Camelpox outbreaks are often experienced shortly after the rainy season, which occurs twice a year on the Arabian Peninsula because of the increased density of the insect population, particularly mosquitos. A systemic form of camelpox outbreak in seven dromedary camels was diagnosed by histology, virus isolation, and PCR. A phylogenetic analysis using full length CMLV genomes of the isolated CMLV strains showed a single phylogenetic unit without any distinctive differences between them. The United Arab Emirates (UAE) isolate sequences showed phylogenetical relatedness with CMLV isolates from Israel with only minor sequence differences. Although the sequences of viruses from both countries were closely related, the disease manifestation was vastly different. Our study shows that the virulence is not only determined by genetic features of CMLV alone but may also depend on other factors such as unknown aspects of the host (e.g., age, overall fitness), management, and the environment. Full article

(This article belongs to the Special Issue Emerging Viruses 2021: Surveillance, Prevention, Evolution and Control)

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22 pages, 6737 KiB

Open AccessArticle

Genetic Characterization and Pathogenesis of Avian Influenza Virus H7N3 Isolated from Spot-Billed Ducks in South Korea, Early 2019

by Thuy-Tien Thi Trinh, Indira Tiwari, Kaliannan Durairaj, Bao Tuan Duong, Anh Thi Viet Nguyen, Hien Thi Tuong, Vui Thi Hoang, Duong Duc Than, SunJeong Nam, Seon-Ju Yeo and Hyun Park

Viruses 2021, 13(5), 856; https://doi.org/10.3390/v13050856 - 7 May 2021

Cited by 7 | Viewed by 3734

Abstract

Low-pathogenicity avian influenza viruses (LPAIV) introduced by migratory birds circulate in wild birds and can be transmitted to poultry. These viruses can mutate to become highly pathogenic avian influenza viruses causing severe disease and death in poultry. In March 2019, an H7N3 avian [...] Read more.

Low-pathogenicity avian influenza viruses (LPAIV) introduced by migratory birds circulate in wild birds and can be transmitted to poultry. These viruses can mutate to become highly pathogenic avian influenza viruses causing severe disease and death in poultry. In March 2019, an H7N3 avian influenza virus—A/Spot-billed duck/South Korea/WKU2019-1/2019 (H7N3)—was isolated from spot-billed ducks in South Korea. This study aimed to evaluate the phylogenetic and mutational analysis of this isolate. Molecular analysis revealed that the genes for HA (hemagglutinin) and NA (neuraminidase) of this strain belonged to the Central Asian lineage, whereas genes for other internal proteins such as polymerase basic protein 1 (PB1), PB2, nucleoprotein, polymerase acidic protein, matrix protein, and non-structural protein belonged to that of the Korean lineage. In addition, a monobasic amino acid (PQIEPR/GLF) at the HA cleavage site, and the non-deletion of the stalk region in the NA gene indicated that this isolate was a typical LPAIV. Nucleotide sequence similarity analysis of HA revealed that the highest homology (99.51%) of this isolate is to that of A/common teal/Shanghai/CM1216/2017 (H7N7), and amino acid sequence of NA (99.48%) was closely related to that of A/teal/Egypt/MB-D-487OP/2016 (H7N3). An in vitro propagation of the A/Spot-billed duck/South Korea/WKU2019-1/2019 (H7N3) virus showed highest (7.38 Log₁₀ TCID₅₀/mL) virus titer at 60 h post-infection, and in experimental mouse lungs, the virus was detected at six days’ post-infection. Our study characterizes genetic mutations, as well as pathogenesis in both in vitro and in vivo model of a new Korea H7N3 viruses in 2019, carrying multiple potential mutations to become highly pathogenic and develop an ability to infect humans; thus, emphasizing the need for routine surveillance of avian influenza viruses in wild birds. Full article

(This article belongs to the Special Issue Emerging Viruses 2021: Surveillance, Prevention, Evolution and Control)

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2 pages, 210 KiB

Open AccessCorrection

Correction: Lesbon et al. Nucleocapsid (N) Gene Mutations of SARS-CoV-2 Can Affect Real-Time RT-PCR Diagnostic and Impact False-Negative Results. Viruses 2021, 13, 2474

by Jéssika Cristina Chagas Lesbon, Mirele Daiana Poleti, Elisângela Chicaroni de Mattos Oliveira, José Salvatore Leister Patané, Luan Gaspar Clemente, Vincent Louis Viala, Gabriela Ribeiro, Marta Giovanetti, Luiz Carlos Junior de Alcantara, Olivia Teixeira, Maria Cristina Nonato, Loyze Paola Oliveira de Lima, Antonio Jorge Martins, Claudia Renata dos Santos Barros, Elaine Cristina Marqueze, Jardelina de Souza Todão Bernardino, Debora Botequio Moretti, Ricardo Augusto Brassaloti, Raquel de Lello Rocha Campos Cassano, Pilar Drummond Sampaio Correa Mariani, Svetoslav Nanev Slavov, Rafael Bezerra dos Santos, Evandra Strazza Rodrigues, Elaine Vieira Santos, Josiane Serrano Borges, Debora Glenda Lima de La Roque, Joao Paulo Kitajima, Bibiana Santos, Patricia Akemi Assato, Felipe Allan da Silva da Costa, Cecilia Artico Banho, Livia Sacchetto, Marilia Mazzi Moraes, Melissa Palmieri, Fabiana Erica Vilanova da Silva, Rejane Maria Tommasini Grotto, Jayme A. Souza-Neto, Mauricio Lacerda Nogueira, Luiz Lehman Coutinho, Rodrigo Tocantins Calado, Raul Machado Neto, Dimas Tadeu Covas, Simone Kashima, Maria Carolina Elias, Sandra Coccuzzo Sampaio and Heidge Fukumasu Show full author list Hide full author list

Viruses 2022, 14(9), 1967; https://doi.org/10.3390/v14091967 - 5 Sep 2022

Viewed by 1492

Abstract

The authors hereby request the inclusion of two authors (Olivia Teixeira and Maria Cristina Nonato) in the recently published article in Viruses entitled “Nucleocapsid (N) gene mutations of SARS-CoV-2 can affect real-time RT-PCR diagnostic and impact false-negative results” [...] Full article

(This article belongs to the Special Issue Emerging Viruses 2021: Surveillance, Prevention, Evolution and Control)

1 pages, 439 KiB

Open AccessCorrection

Correction: Netto et al. Hypovitaminosis D Is Associated with Higher Levels of Inflammatory Cytokines and with HAM/TSP in HTLV-Infected Patients. Viruses 2021, 13, 2223

by Elaine Coutinho Netto, Alfredo Carlos Silva, Célia Pedroso and Carlos Brites

Viruses 2022, 14(8), 1633; https://doi.org/10.3390/v14081633 - 26 Jul 2022

Cited by 1 | Viewed by 874

Abstract

In the original publication [...] Full article

(This article belongs to the Special Issue Emerging Viruses 2021: Surveillance, Prevention, Evolution and Control)

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14 pages, 910 KiB

Open AccessConference Report

The 32nd Brazilian Society of Virology (SBV) 2021 Annual Meeting

by Maite Freitas Silva Vaslin, Alessandra Alevato Leal, Larissa Mayumi Bueno, Cíntia Bittar, Gabriela Fabiano de Souza, Karine Lourenço, Gustavo Peixoto Duarte da Silva, Maria Isabel Maldonado Coelho Guedes, José Luiz Proença-Módena, João Pessoa Araújo Junior, Helena Lage Ferreira and Flávio Guimarães da Fonseca

Viruses 2022, 14(3), 644; https://doi.org/10.3390/v14030644 - 20 Mar 2022

Cited by 1 | Viewed by 2276

Abstract

The Brazilian Society of Virology has been organizing annual meetings for 32 years now. The 32nd annual meeting, which occurred in 2021, was once again an online meeting in consequence of the issues imposed by COVID-19, even with the vaccination advances. As in [...] Read more.

The Brazilian Society of Virology has been organizing annual meetings for 32 years now. The 32nd annual meeting, which occurred in 2021, was once again an online meeting in consequence of the issues imposed by COVID-19, even with the vaccination advances. As in the 2020 meeting, the number of attendees was high, with considerable participation by undergraduate, graduate, and postdoc students. Distinguished scientists from different countries offered high-quality conferences, and oral presentation sessions were presented by young scientists showing their newest research results. For almost five hours a day during five days, attendees discussed high-quality science related to all areas of virology. Even with the difficulties imposed by another pandemic year, the 32nd SBV annual meeting achieved its most important goal—to inspire young scientists and discuss high-quality virology research. Full article

(This article belongs to the Special Issue Emerging Viruses 2021: Surveillance, Prevention, Evolution and Control)

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9 pages, 1589 KiB

Open AccessCase Report

An Outbreak in Pigeons Caused by the Subgenotype VI.2.1.2 of Newcastle Disease Virus in Brazil

by Luciano M. Thomazelli, Juliana A. Sinhorini, Danielle B. L. Oliveira, Terezinha Knöbl, Tatiana C. M. Bosqueiro, Elder Sano, Gladyston C. V. Costa, Cairo Monteiro, Erick G. Dorlass, Nathalia Utecht, Guilherme P. Scagion, Carla Meneguin, Laura M. N. Silva, Maria Vitória S. Moraes, Larissa M. Bueno, Dilmara Reischak, Adriano O. T. Carrasco, Clarice W. Arns, Helena L. Ferreira and Edison L. Durigon

Viruses 2021, 13(12), 2446; https://doi.org/10.3390/v13122446 - 6 Dec 2021

Cited by 9 | Viewed by 6747

Abstract

Newcastle disease virus (NDV) can infect over 250 bird species with variable pathogenicity; it can also infect humans in rare cases. The present study investigated an outbreak in feral pigeons in São Paulo city, Brazil, in 2019. Affected birds displayed neurological signs, and [...] Read more.

Newcastle disease virus (NDV) can infect over 250 bird species with variable pathogenicity; it can also infect humans in rare cases. The present study investigated an outbreak in feral pigeons in São Paulo city, Brazil, in 2019. Affected birds displayed neurological signs, and hemorrhages were observed in different tissues. Histopathology changes with infiltration of mononuclear inflammatory cells were also found in the brain, kidney, proventriculus, heart, and spleen. NDV staining was detected by immunohistochemistry. Twenty-seven out of thirty-four tested samples (swabs and tissues) were positive for Newcastle disease virus by RT-qPCR test, targeting the M gene. One isolate, obtained from a pool of positive swab samples, was characterized by the intracerebral pathogenicity index (ICPI) and the hemagglutination inhibition (HI) tests. This isolate had an ICPI of 0.99, confirming a virulent NDV strain. The monoclonal antibody 617/161, which recognizes a distinct epitope in pigeon NDV strains, inhibited the isolate with an HI titer of 512. A complete genome of NDV was obtained using next-generation sequencing. Phylogenetic analysis based on the complete CDS F gene grouped the detected isolate with other viruses from subgenotype VI.2.1.2, class II, including one previously reported in Southern Brazil in 2014. This study reports a comprehensive characterization of the subgenotype VI.2.1.2, which seems to have been circulating in Brazilian urban areas since 2014. Due to the zoonotic risk of NDV, virus surveillance in feral pigeons should also be systematically performed in urban areas. Full article

(This article belongs to the Special Issue Emerging Viruses 2021: Surveillance, Prevention, Evolution and Control)

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15 pages, 1391 KiB

Open AccessBrief Report

Global Discrepancies between Numbers of Available SARS-CoV-2 Genomes and Human Development Indexes at Country Scales

by Philippe Colson and Didier Raoult

Viruses 2021, 13(5), 775; https://doi.org/10.3390/v13050775 - 28 Apr 2021

Cited by 7 | Viewed by 2374

Abstract

It has now been over a year since SARS-CoV-2 first emerged in China, in December 2019, and it has spread rapidly around the world. Some variants are currently considered of great concern. We aimed to analyze the numbers of SARS-CoV-2 genome sequences obtained [...] Read more.

It has now been over a year since SARS-CoV-2 first emerged in China, in December 2019, and it has spread rapidly around the world. Some variants are currently considered of great concern. We aimed to analyze the numbers of SARS-CoV-2 genome sequences obtained in different countries worldwide until January 2021. On 28 January 2021, we downloaded the deposited genome sequence origin from the GISAID database, and from the “Our world in data” website we downloaded numbers of SARS-CoV-2-diagnosed cases, numbers of SARS-CoV-2-associated deaths, population size, life expectancy, gross domestic product (GDP) per capita, and human development index per country. Files were merged and data were analyzed using Microsoft Excel software. A total of 450,968 SARS-CoV-2 genomes originating from 135 countries on the 5 continents were available. When considering the 19 countries for which the number of genomes per 100 deaths was >100, six were in Europe, while eight were in Asia, three were in Oceania and two were in Africa. Six (30%) of these countries are beyond rank 75, regarding the human development index and four (20%) are beyond rank 80 regarding GDP per capita. Moreover, the comparisons of the number of genomes sequenced per 100 deaths to the human development index by country show that some Western European countries have released similar or lower numbers of genomes than many African or Asian countries with a lower human development index. Previous data highlight great discrepancies between the numbers of available SARS-CoV-2 genomes per 100 cases and deaths and the ranking of countries regarding wealth and development. Full article

(This article belongs to the Special Issue Emerging Viruses 2021: Surveillance, Prevention, Evolution and Control)

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9 pages, 529 KiB

Open AccessOpinion

Within-Host and Between-Host Evolution in SARS-CoV-2—New Variant’s Source

by Karin Moelling

Viruses 2021, 13(5), 751; https://doi.org/10.3390/v13050751 - 25 Apr 2021

Cited by 28 | Viewed by 5525

Abstract

Some of the newly emerging corona viral variants show high numbers of mutations. This is unexpected for a virus with a low mutation rate due to an inherent proof-reading system. Could such a variant arise under very special conditions occurring in a host [...] Read more.

Some of the newly emerging corona viral variants show high numbers of mutations. This is unexpected for a virus with a low mutation rate due to an inherent proof-reading system. Could such a variant arise under very special conditions occurring in a host where the virus replicates and mutates in a rather unlimited fashion, such as in immune compromised patients? The virus was shown to replicate in an immunosuppressed cancer patient for more than 105 days and might be a source of new variants. These patients are asymptomatic and the virus may therefore escape detection and attention and be high-risk. Similarly, HIV-infected individuals may be immunocompromised and support coronavirus replication with increased mutation rates. The patients may promote “within-host evolution”. Some of the viruses present in such a highly mutagenic swarm or quasispecies within one patient may become founders and cause a pandemic by further “between-host evolution”. B.1.1.7 with 23 mutations may be such a case. Immunosuppressed patients can be identified and treated by the synthetic antibody cocktails as passive immunization and kept under control. Immunosuppressed patients can be easily identified and supervised by healthcare workers—once they become aware of the risk—to avoid new variants with pandemic potential. Full article

(This article belongs to the Special Issue Emerging Viruses 2021: Surveillance, Prevention, Evolution and Control)

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10 pages, 350 KiB

Open AccessConference Report

31st Brazilian Online Society for Virology (SBV) 2020 Annual Meeting

by Luciana Barros de Arruda, Fabrício Souza Campos, Jônatas Santos Abrahão, Flávio Guimarães da Fonseca, João Pessoa Araújo Junior and Fernando Rosado Spilki

Viruses 2021, 13(3), 414; https://doi.org/10.3390/v13030414 - 5 Mar 2021

Cited by 2 | Viewed by 2639

Abstract

The year 2020 was profoundly marked by the emergence and spread of SARS-CoV-2, causing COVID-19, which represents the greatest pandemic of the 21st century until now, and a major challenge for virologists in the scientific and medical communities. Increased numbers of SARS-CoV-2 infection [...] Read more.

The year 2020 was profoundly marked by the emergence and spread of SARS-CoV-2, causing COVID-19, which represents the greatest pandemic of the 21st century until now, and a major challenge for virologists in the scientific and medical communities. Increased numbers of SARS-CoV-2 infection all over the world imposed social and travel restrictions, including avoidance of face-to-face scientific meetings. Therefore, for the first time in history, the 2020 edition of the Brazilian Society of Virology (SBV) congress was totally online. Despite the challenge of the new format, the Brazilian society board and collaborators were successful in virtually congregating more than 921 attendees, which was the greatest SBV participant number ever reached. Seminal talks from prominent national and international researchers were presented every night, during a week, and included discussions about environmental, basic, animal, human, plant and invertebrate virology. A special roundtable debated exclusively new data and perspectives regarding COVID-19 by some of the greatest Brazilian virologists. Women scientists were very well represented in another special roundtable called “Young Women Inspiring Research”, which was one of the most viewed and commented section during the meeting, given the extraordinary quality of the presented work. Finally, SBV offered the Helio Gelli Pereira award for one graduate and one undergraduate student, which has also been a fruitful collaboration between the society and Viruses journal. The annual SBV meeting has, therefore, reached its goals to inspire young scientists, stimulate high-quality scientific discussion and to encourage global collaboration between virologists. Full article

(This article belongs to the Special Issue Emerging Viruses 2021: Surveillance, Prevention, Evolution and Control)

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