Viruses

11 pages, 968 KiB

Open AccessArticle

Immunogenicity of Oral Rabies Vaccine Strain SPBN GASGAS in Local Dogs in Bali, Indonesia

by Irene Linda Megawati Saputra, Suwarno Suwarno, Wahid Fakhri Husein, Pebi Purwo Suseno, I Made Angga Prayoga, Ad Vos, I Made Arthawan, Luuk Schoonman, John Weaver and Nuryani Zainuddin

Viruses 2023, 15(6), 1405; https://doi.org/10.3390/v15061405 - 20 Jun 2023

Cited by 4 | Viewed by 2313

Abstract

Dog-mediated rabies is endemic in much of Indonesia, including Bali. Most dogs in Bali are free-roaming and often inaccessible for parenteral vaccination without special effort. Oral rabies vaccination (ORV) is considered a promising alternative to increase vaccination coverage in these dogs. This study [...] Read more.

Dog-mediated rabies is endemic in much of Indonesia, including Bali. Most dogs in Bali are free-roaming and often inaccessible for parenteral vaccination without special effort. Oral rabies vaccination (ORV) is considered a promising alternative to increase vaccination coverage in these dogs. This study assessed immunogenicity in local dogs in Bali after oral administration of the highly attenuated third-generation rabies virus vaccine strain SPBN GASGAS. Dogs received the oral rabies vaccine either directly or by being offered an egg-flavored bait that contained a vaccine-loaded sachet. The humoral immune response was then compared with two further groups of dogs: a group that received a parenteral inactivated rabies vaccine and an unvaccinated control group. The animals were bled prior to vaccination and between 27 and 32 days after vaccination. The blood samples were tested for the presence of virus-binding antibodies using ELISA. The seroconversion rate in the three groups of vaccinated dogs did not differ significantly: bait: 88.9%; direct-oral: 94.1%; parenteral: 90.9%; control: 0%. There was no significant quantitative difference in the level of antibodies between orally and parenterally vaccinated dogs. This study confirms that SPBN GASGAS is capable of inducing an adequate immune response comparable to a parenteral vaccine under field conditions in Indonesia. Full article

(This article belongs to the Section Viral Immunology, Vaccines, and Antivirals)

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11 pages, 280 KiB

Open AccessArticle

Influence of SARS-CoV-2 Status and Aging on the Nasal and Fecal Immunological Profiles of Elderly Individuals Living in Nursing Homes

by Claudio Alba, Marta Mozota, Rebeca Arroyo, Natalia Gómez-Torres, Irma Castro and Juan Miguel Rodríguez

Viruses 2023, 15(6), 1404; https://doi.org/10.3390/v15061404 - 20 Jun 2023

Viewed by 1531

Abstract

In the frame of SARS-CoV-2 infection, studies regarding cytokine profiling of mucosal-related samples are scarce despite being the primary infection sites. The objective of this study was to compare the nasal and fecal inflammatory profiles of elderly individuals living in a nursing home [...] Read more.

In the frame of SARS-CoV-2 infection, studies regarding cytokine profiling of mucosal-related samples are scarce despite being the primary infection sites. The objective of this study was to compare the nasal and fecal inflammatory profiles of elderly individuals living in a nursing home highly affected by COVID-19 (ELD1) with those of elderly individuals living in a nursing home with no cases of SARS-CoV-2 infection (ELD2) and, also, with those of healthy SARS-CoV-2-negative younger adults (YHA). BAFF/TNFSF13B, IL6, IL10 and TNF-α (immunological hallmarks of SARS-CoV-2 infection) were the only immune factors whose concentrations were different in the three groups. Their highest concentrations were achieved in the ELD1 group. Nasal and fecal concentrations of a wide number of pro-inflammatory cytokines were similar in the ELD1 and ELD2 groups but higher than those found in the YHA samples. These results reinforce the hypothesis that immunosenescence and inflammaging rendered the elderly as a highly vulnerable population to a neo-infection, such as COVID-19, which was evidenced during the first pandemic waves. Full article

(This article belongs to the Special Issue COVID-19 Diagnostics in Clinical Applications and Pandemic Controls 2023)

12 pages, 3761 KiB

Open AccessCommunication

Genetic Characterization and Pathogenesis of H5N1 High Pathogenicity Avian Influenza Virus Isolated in South Korea during 2021–2022

by Ra Mi Cha, Yu-Na Lee, Min-Ji Park, Yoon-Gi Baek, Jae-In Shin, Chang Hwa Jung, Mingeun Sagong, Gyeong-Beom Heo, Yong-Myung Kang, Kwang-Nyeong Lee, Youn-Jeong Lee and Eun-Kyoung Lee

Viruses 2023, 15(6), 1403; https://doi.org/10.3390/v15061403 - 20 Jun 2023

Cited by 5 | Viewed by 2636

Abstract

High pathogenicity avian influenza (HPAI) viruses of clade 2.3.4.4 H5Nx have been circulating in poultry and wild birds worldwide since 2014. In South Korea, after the first clade 2.3.4.4b H5N1 HPAI viruses were isolated from wild birds in October 2021, additional HPAIV outbreaks [...] Read more.

High pathogenicity avian influenza (HPAI) viruses of clade 2.3.4.4 H5Nx have been circulating in poultry and wild birds worldwide since 2014. In South Korea, after the first clade 2.3.4.4b H5N1 HPAI viruses were isolated from wild birds in October 2021, additional HPAIV outbreaks occurred in poultry farms until April 2022. In this study, we genetically characterized clade 2.3.4.4b H5N1 HPAIV isolates in 2021–2022 and examined the pathogenicity and transmissibility of A/mandarin duck/Korea/WA585/2021 (H5N1) (WA585/21) in chickens and ducks. Clade 2.3.4.4b H5N1 HPAI viruses caused 47 outbreaks in poultry farms and were also detected in multiple wild birds. Phylogenetic analysis of HA and NA genes indicated that Korean H5N1 HPAI isolates were closely related to Eurasian viruses isolated in 2021–2022. Four distinct genotypes of H5N1 HPAI viruses were identified in poultry, and the majority were also found in wild birds. WA585/21 inoculated chickens showed virulent pathogenicity with high mortality and transmission. Meanwhile, ducks infected with the virus showed no mortality but exhibited high rates of transmission and longer viral shedding than chickens, suggesting that they may play an important role as silent carriers. In conclusion, consideration of both genetic and pathogenic traits of H5N1 HPAI viruses is required for effective viral control. Full article

(This article belongs to the Special Issue Advances in Animal Influenza Virus Research)

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14 pages, 6190 KiB

Open AccessArticle

The Roles of the 5′ and 3′ Untranslated Regions in Human Astrovirus Replication

by Nicole Wildi and Torsten Seuberlich

Viruses 2023, 15(6), 1402; https://doi.org/10.3390/v15061402 - 20 Jun 2023

Cited by 2 | Viewed by 1684

Abstract

Astroviruses are small nonenveloped single-stranded RNA viruses with a positive sense genome. They are known to cause gastrointestinal disease in a broad spectrum of species. Although astroviruses are distributed worldwide, a gap in knowledge of their biology and disease pathogenesis persists. Many positive-sense [...] Read more.

Astroviruses are small nonenveloped single-stranded RNA viruses with a positive sense genome. They are known to cause gastrointestinal disease in a broad spectrum of species. Although astroviruses are distributed worldwide, a gap in knowledge of their biology and disease pathogenesis persists. Many positive-sense single-stranded RNA viruses show conserved and functionally important structures in their 5′ and 3′ untranslated regions (UTRs). However, not much is known about the role of the 5′ and 3′ UTRs in the viral replication of HAstV-1. We analyzed the UTRs of HAstV-1 for secondary RNA structures and mutated them, resulting in partial or total UTR deletion. We used a reverse genetic system to study the production of infectious viral particles and to quantify protein expression in the 5′ and 3′ UTR mutants, and we established an HAstV-1 replicon system containing two reporter cassettes in open reading frames 1a and 2, respectively. Our data show that 3′ UTR deletions almost completely abolished viral protein expression and that 5′ UTR deletions led to a reduction in infectious virus particles in infection experiments. This indicates that the presence of the UTRs is essential for the life cycle of HAstV-1 and opens avenues for further research. Full article

(This article belongs to the Section General Virology)

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13 pages, 3462 KiB

Open AccessEditor’s ChoiceArticle

Proteomics Identified UDP-Glycosyltransferase Family Members as Pro-Viral Factors for Turnip Mosaic Virus Infection in Nicotiana benthamiana

by Kaida Ding, Zhaoxing Jia, Penghuan Rui, Xinxin Fang, Hongying Zheng, Jianping Chen, Fei Yan and Guanwei Wu

Viruses 2023, 15(6), 1401; https://doi.org/10.3390/v15061401 - 20 Jun 2023

Cited by 3 | Viewed by 2177

Abstract

Viruses encounter numerous host factors that facilitate or suppress viral infection. Although some host factors manipulated by viruses were uncovered, we have limited knowledge of the pathways hijacked to promote viral replication and activate host defense responses. Turnip mosaic virus (TuMV) is one [...] Read more.

Viruses encounter numerous host factors that facilitate or suppress viral infection. Although some host factors manipulated by viruses were uncovered, we have limited knowledge of the pathways hijacked to promote viral replication and activate host defense responses. Turnip mosaic virus (TuMV) is one of the most prevalent viral pathogens in many regions of the world. Here, we employed an isobaric tag for relative and absolute quantitation (iTRAQ)-based proteomics approach to characterize cellular protein changes in the early stages of infection of Nicotiana benthamiana by wild type and replication-defective TuMV. A total of 225 differentially accumulated proteins (DAPs) were identified (182 increased and 43 decreased). Bioinformatics analysis showed that a few biological pathways were associated with TuMV infection. Four upregulated DAPs belonging to uridine diphosphate-glycosyltransferase (UGT) family members were validated by their mRNA expression profiles and their effects on TuMV infection. NbUGT91C1 or NbUGT74F1 knockdown impaired TuMV replication and increased reactive oxygen species production, whereas overexpression of either promoted TuMV replication. Overall, this comparative proteomics analysis delineates the cellular protein changes during early TuMV infection and provides new insights into the role of UGTs in the context of plant viral infection. Full article

(This article belongs to the Section Viruses of Plants, Fungi and Protozoa)

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10 pages, 808 KiB

Open AccessArticle

Validity of Rapid Antibody Testing for COVID-19 Vaccine in Homeless People

by Se-Min Hwang, Yun Jung, Jiyeon Seo, Yoomi Jung, Shinae Park and Haesook Seo

Viruses 2023, 15(6), 1400; https://doi.org/10.3390/v15061400 - 20 Jun 2023

Viewed by 1400

Abstract

(1) Background: There is a paucity of data regarding the validity of rapid antibody testing for SARS-CoV-2 vaccine response in homeless people worldwide. The objective of this study was to evaluate a rapid SARS-CoV-2 IgM/IgG antibody detection kit as a qualitative screen for [...] Read more.

(1) Background: There is a paucity of data regarding the validity of rapid antibody testing for SARS-CoV-2 vaccine response in homeless people worldwide. The objective of this study was to evaluate a rapid SARS-CoV-2 IgM/IgG antibody detection kit as a qualitative screen for vaccination in homeless people. (2) Methods: This study included 430 homeless people and 120 facility workers who had received one of BNT162b2, mRNA-1273, AZD1222/ChAdOx1, or JNJ-78436735/AD26.COV2.5 vaccines. They were tested for IgM/IgG antibodies to the SARS-CoV-2 spike protein with the STANDARD™ Q COVID-19 IgM/IgG Plus Test (QNCOV-02C). ELISA/competitive inhibition ELISA (CI-ELISA) was subsequently run to assess the validity of the serological antibody test. (3) Results: The sensitivity of homeless people was 43.5%. The status of homelessness was related to a lower agreement between serological antibody testing and CI-ELISA (adjusted OR (aOR), 0.35; 95% CI, 0.18–0.70). However, the Heterologous boost vaccine presented higher agreement between serological antibody testing and CI-ELISA (adjusted OR (aOR), 6.50; 95% CI, 3.19–13.27). (4) Conclusions: This study found weak agreement between the rapid IgG results and confirmatory CI-ELISA testing in homeless people. However, it can be used as a screening test for the acceptance of homeless people with heterologous boost vaccination in facilities. Full article

(This article belongs to the Section Viral Immunology, Vaccines, and Antivirals)

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17 pages, 647 KiB

Open AccessArticle

Unbiased Virus Detection in a Danish Zoo Using a Portable Metagenomic Sequencing System

by Anna S. Fomsgaard, Stamatios A. Tahas, Katja Spiess, Charlotta Polacek, Jannik Fonager and Graham J. Belsham

Viruses 2023, 15(6), 1399; https://doi.org/10.3390/v15061399 - 20 Jun 2023

Cited by 1 | Viewed by 2769

Abstract

Metagenomic next-generation sequencing (mNGS) is receiving increased attention for the detection of new viruses and infections occurring at the human–animal interface. The ability to actively transport and relocate this technology enables in situ virus identification, which could reduce response time and enhance disease [...] Read more.

Metagenomic next-generation sequencing (mNGS) is receiving increased attention for the detection of new viruses and infections occurring at the human–animal interface. The ability to actively transport and relocate this technology enables in situ virus identification, which could reduce response time and enhance disease management. In a previous study, we developed a straightforward mNGS procedure that greatly enhances the detection of RNA and DNA viruses in human clinical samples. In this study, we improved the mNGS protocol with transportable battery-driven equipment for the portable, non-targeted detection of RNA and DNA viruses in animals from a large zoological facility, to simulate a field setting for point-of-incidence virus detection. From the resulting metagenomic data, we detected 13 vertebrate viruses from four major virus groups: (+)ssRNA, (+)ssRNA-RT, dsDNA and (+)ssDNA, including avian leukosis virus in domestic chickens (Gallus gallus), enzootic nasal tumour virus in goats (Capra hircus) and several small, circular, Rep-encoding, ssDNA (CRESS DNA) viruses in several mammal species. More significantly, we demonstrate that the mNGS method is able to detect potentially lethal animal viruses, such as elephant endotheliotropic herpesvirus in Asian elephants (Elephas maximus) and the newly described human-associated gemykibivirus 2, a human-to-animal cross-species virus, in a Linnaeus two-toed sloth (Choloepus didactylus) and its enclosure, for the first time. Full article

(This article belongs to the Special Issue Applications of Next-Generation Sequencing in Virus Discovery 2.0)

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14 pages, 6617 KiB

Open AccessArticle

Structural Basis for the Enhanced Infectivity and Immune Evasion of Omicron Subvariants

by Yaning Li, Yaping Shen, Yuanyuan Zhang and Renhong Yan

Viruses 2023, 15(6), 1398; https://doi.org/10.3390/v15061398 - 20 Jun 2023

Cited by 2 | Viewed by 1949

Abstract

The Omicron variants of SARS-CoV-2 have emerged as the dominant strains worldwide, causing the COVID-19 pandemic. Each Omicron subvariant contains at least 30 mutations on the spike protein (S protein) compared to the original wild-type (WT) strain. Here we report the cryo-EM structures [...] Read more.

The Omicron variants of SARS-CoV-2 have emerged as the dominant strains worldwide, causing the COVID-19 pandemic. Each Omicron subvariant contains at least 30 mutations on the spike protein (S protein) compared to the original wild-type (WT) strain. Here we report the cryo-EM structures of the trimeric S proteins from the BA.1, BA.2, BA.3, and BA.4/BA.5 subvariants, with BA.4 and BA.5 sharing the same S protein mutations, each in complex with the surface receptor ACE2. All three receptor-binding domains of the S protein from BA.2 and BA.4/BA.5 are “up”, while the BA.1 S protein has two “up” and one “down”. The BA.3 S protein displays increased heterogeneity, with the majority in the all “up” RBD state. The different conformations preferences of the S protein are consistent with their varied transmissibility. By analyzing the position of the glycan modification on Asn343, which is located at the S309 epitopes, we have uncovered the underlying immune evasion mechanism of the Omicron subvariants. Our findings provide a molecular basis of high infectivity and immune evasion of Omicron subvariants, thereby offering insights into potential therapeutic interventions against SARS-CoV-2 variants. Full article

(This article belongs to the Special Issue The Secret Life of ACE2 as a Receptor for the Coronaviruses)

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18 pages, 2518 KiB

Open AccessArticle

Diversity of Human Enterovirus Co-Circulations in Five Kindergartens in Bangkok between July 2019 and January 2020

by Pichamon Sittikul, Elizabeth M. Batty, Prasert Yodsawat, Jiratchaya Nuanpirom, Nathamon Kosoltanapiwat, Unitsa Sangket, Supawat Chatchen, Nicholas P. J. Day and Janjira Thaipadungpanit

Viruses 2023, 15(6), 1397; https://doi.org/10.3390/v15061397 - 20 Jun 2023

Cited by 5 | Viewed by 2173

Abstract

Human enterovirus causes various clinical manifestations in the form of rashes, febrile illness, flu-like illness, uveitis, hand–foot–mouth disease (HFMD), herpangina, meningitis, and encephalitis. Enterovirus A71 and coxsackievirus are significant causes of epidemic HFMD worldwide, especially in children aged from birth to five years [...] Read more.

Human enterovirus causes various clinical manifestations in the form of rashes, febrile illness, flu-like illness, uveitis, hand–foot–mouth disease (HFMD), herpangina, meningitis, and encephalitis. Enterovirus A71 and coxsackievirus are significant causes of epidemic HFMD worldwide, especially in children aged from birth to five years old. The enterovirus genotype variants causing HFMD epidemics have been reported increasingly worldwide in the last decade. We aim to use simple and robust molecular tools to investigate human enteroviruses circulating among kindergarten students at genotype and subgenotype levels. With the partial 5′-UTR sequencing analysis as a low-resolution preliminary grouping tool, ten enterovirus A71 (EV-A71) and coxsackievirus clusters were identified among 18 symptomatic cases and 14 asymptomatic cases in five kindergartens in Bangkok, Thailand, between July 2019 and January 2020. Two occurrences of a single clone causing an infection cluster were identified (EV-A71 C1-like subgenotype and coxsackievirus A6). Random amplification-based sequencing using MinION (Oxford Nanopore Technology) helped identify viral transmission between two closely related clones. Diverse genotypes co-circulating among children in kindergartens are reservoirs for new genotype variants emerging, which might be more virulent or better at immune escape. Surveillance of highly contagious enterovirus in communities is essential for disease notifications and controls. Full article

(This article belongs to the Special Issue Enteroviruses 2023)

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14 pages, 3497 KiB

Open AccessArticle

Virome Profiling, New Virus Identification and the Prevalence and Distribution of Viruses Infecting Chieh-Qua (Benincasa hispida Cogn. var. chieh-qua How) in China

by Haiyan Che, Yuxin Ma, Yating Lin, Tuizi Feng, Daquan Luo and Haibo Long

Viruses 2023, 15(6), 1396; https://doi.org/10.3390/v15061396 - 19 Jun 2023

Cited by 2 | Viewed by 1912

Abstract

The cucurbit vegetable chieh-qua (Benincasa hispida var. chieh-qua How) is an important crop in South China and southeast Asian countries. Viral diseases cause substantial loss of chieh-qua yield. To identify the viruses that affect chieh-qua in China, ribosomal RNA-depleted total RNA sequencing [...] Read more.

The cucurbit vegetable chieh-qua (Benincasa hispida var. chieh-qua How) is an important crop in South China and southeast Asian countries. Viral diseases cause substantial loss of chieh-qua yield. To identify the viruses that affect chieh-qua in China, ribosomal RNA-depleted total RNA sequencing was performed using chieh-qua leaf samples with typical viral symptoms. The virome of chieh-qua comprises four known viruses (melon yellow spot virus (MYSV), cucurbit chlorotic yellows virus (CCYV), papaya ringspot virus (PRSV) and watermelon silver mottle virus (WSMoV) and two novel viruses: cucurbit chlorotic virus (CuCV) in the genus Crinivirus and chieh-qua endornavirus (CqEV) in the genus Alphaendornavirus. The complete genomes of the two novel viruses in chieh-qua and three other isolates of CuCV in pumpkin, watermelon and cucumber were determined and the recombination signals of pumpkin and watermelon isolates of CuCV were detected. A reverse transcriptase PCR indicated that the dominant viruses of chieh-qua in Hainan are MYSV (66.67%) and CCYV (55.56%), followed by CuCV (27.41%), WSMoV (7.41%), cucumber mosaic virus (8.15%), zucchini yellow mosaic virus (6.67%), PRSV (6.67%) and CqEV (35.56%). Our findings support diagnostic and prevalence studies of viruses infecting chieh-qua in China, enabling sustainable control strategies for cucurbit viruses worldwide. Full article

(This article belongs to the Special Issue Next-Generation Sequencing in Plant Virology 2.0)

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14 pages, 1589 KiB

Open AccessArticle

Hantavirus in Panama: Twenty Years of Epidemiological Surveillance Experience

by Blas Armién, Carlos Muñoz, Hector Cedeño, Jacqueline R. Salazar, Tybbyssay P. Salinas, Publio González, José Trujillo, Deyanira Sánchez, Jamileth Mariñas, Ayvar Hernández, Harmodio Cruz, Leisy Yovany Villarreal, Elba Grimaldo, Samuel González, Heydy Nuñez, Susana Hesse, Fernando Rivera, George Edwards, Ricardo Chong, Ovidio Mendoza, Martín Meza, Milagro Herrera, Rudick Kant, Raul Esquivel, Dora Estripeaut, Demetrio Serracín, Bernardino Denis, Esthefani Robles, Yaxelis Mendoza, Gloria Gonzalez, Felicia Tulloch, Juan Miguel Pascale, Jonathan L. Dunnum, Joseph A. Cook, Anibal G. Armién, Fernando Gracia, Gladys Alicia Guerrero and Itza de Mosca Show full author list Hide full author list

Viruses 2023, 15(6), 1395; https://doi.org/10.3390/v15061395 - 19 Jun 2023

Cited by 7 | Viewed by 2738

Abstract

Twenty years have passed since the emergence of hantavirus zoonosis in Panama at the beginning of this millennium. We provide an overview of epidemiological surveillance of hantavirus disease (hantavirus pulmonary syndrome and hantavirus fever) during the period 1999–2019 by including all reported and [...] Read more.

Twenty years have passed since the emergence of hantavirus zoonosis in Panama at the beginning of this millennium. We provide an overview of epidemiological surveillance of hantavirus disease (hantavirus pulmonary syndrome and hantavirus fever) during the period 1999–2019 by including all reported and confirmed cases according to the case definition established by the health authority. Our findings reveal that hantavirus disease is a low-frequency disease, affecting primarily young people, with a relatively low case-fatality rate compared to other hantaviruses in the Americas (e.g., ANDV and SNV). It presents an annual variation with peaks every 4–5 years and an interannual variation influenced by agricultural activities. Hantavirus disease is endemic in about 27% of Panama, which corresponds to agroecological conditions that favor the population dynamics of the rodent host, Oligoryzomys costaricensis and the virus (Choclo orthohantavirus) responsible for hantavirus disease. However, this does not rule out the existence of other endemic areas to be characterized. Undoubtedly, decentralization of the laboratory test and dissemination of evidence-based surveillance guidelines and regulations have standardized and improved diagnosis, notification at the level of the primary care system, and management in intensive care units nationwide. Full article

(This article belongs to the Special Issue Hantavirus Ecology, Epidemiology, and Disease, in Memory of Dr. Ho Wang Lee)

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17 pages, 5083 KiB

Open AccessArticle

Investigation of the Molecular Epidemiology and Evolution of Circulating Severe Acute Respiratory Syndrome Coronavirus 2 in Thailand from 2020 to 2022 via Next-Generation Sequencing

by Jiratchaya Puenpa, Vorthon Sawaswong, Pattaraporn Nimsamer, Sunchai Payungporn, Patthaya Rattanakomol, Nutsada Saengdao, Jira Chansaenroj, Ritthideach Yorsaeng, Kamol Suwannakarn and Yong Poovorawan

Viruses 2023, 15(6), 1394; https://doi.org/10.3390/v15061394 - 19 Jun 2023

Cited by 4 | Viewed by 1832

Abstract

Coronavirus disease 2019 (COVID-19) is an infectious condition caused by the severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2), which surfaced in Thailand in early 2020. The current study investigated the SARS-CoV-2 lineages circulating in Thailand and their evolutionary history. Complete genome sequencing of 210 [...] Read more.

Coronavirus disease 2019 (COVID-19) is an infectious condition caused by the severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2), which surfaced in Thailand in early 2020. The current study investigated the SARS-CoV-2 lineages circulating in Thailand and their evolutionary history. Complete genome sequencing of 210 SARS-CoV-2 samples collected from collaborating hospitals and the Institute of Urban Disease Control and Prevention over two years, from December 2020 to July 2022, was performed using next-generation sequencing technology. Multiple lineage introductions were observed before the emergence of the B.1.1.529 omicron variant, including B.1.36.16, B.1.351, B.1.1, B.1.1.7, B.1.524, AY.30, and B.1.617.2. The B.1.1.529 omicron variant was subsequently detected between January 2022 and June 2022. The evolutionary rate for the spike gene of SARS-CoV-2 was estimated to be between 0.87 and 1.71 × 10⁻³ substitutions per site per year. There was a substantial prevalence of the predominant mutations C25672T (L94F), C25961T (T190I), and G26167T (V259L) in the ORF3a gene during the Thailand outbreaks. Complete genome sequencing can enhance the prediction of future variant changes in viral genomes, which is crucial to ensuring that vaccine strains are protective against worldwide outbreaks. Full article

(This article belongs to the Special Issue Applications of Next-Generation Sequencing in Virus Discovery 2.0)

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9 pages, 1726 KiB

Open AccessBrief Report

Genetic Variability in the E6/E7 Region of Human Papillomavirus 16 in Women from Ecuador

by Alicia Zhingre, César Bedoya-Pilozo, Diana Gutiérrez-Pallo, Inés Badano, Andrés Herrera-Yela, Zoila Salazar, Damaris Alarcón, Natali Argüello-Bravo, Maylen Espinoza, Patricio Ponce, Yudira Soto and Andrés Carrazco-Montalvo

Viruses 2023, 15(6), 1393; https://doi.org/10.3390/v15061393 - 19 Jun 2023

Viewed by 2342

Abstract

Human Papillomavirus (HPV) infection is associated with intraepithelial neoplasia and cervical cancer (CC). Ecuador has a high prevalence of cervical cancer, with more than 1600 new cases diagnosed annually. This study aimed to analyze oncogenes E6 and E7 of HPV16 in samples collected [...] Read more.

Human Papillomavirus (HPV) infection is associated with intraepithelial neoplasia and cervical cancer (CC). Ecuador has a high prevalence of cervical cancer, with more than 1600 new cases diagnosed annually. This study aimed to analyze oncogenes E6 and E7 of HPV16 in samples collected from women with cancerous and precancerous cervical lesions from the Ecuadorian coast. Twenty-nine women, including six with ASCUS, three with LSIL, thirteen with HSIL, and seven with Cacu, were analyzed. The most common SNPs were E6 350G or L83V (82.6%) and E6 145T/286A/289G/335T/350G or Q14H/F78Y/L83V (17.4%). Both variants are reported to be associated with an increased risk of cervical cancer in worldwide studies. In contrast, all E7 genes have conserved amino-acid positions. Phylogenetic trees showed the circulation of the D (26.1%) and A (73.9) lineages. The frequency of D was higher than that reported in other comparable studies in Ecuador and Latin America, and may be related to the ethnic composition of the studied populations. This study contributes to the characterization of the potential risk factors for cervical carcinogenesis associated with Ecuadorian women infected with HPV16. Full article

(This article belongs to the Section Human Virology and Viral Diseases)

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14 pages, 3603 KiB

Open AccessArticle

Genomic Characterization of a Halovirus Representing a Novel Siphoviral Cluster

by Kaixin Diao, Guohui Li, Xueqin Sun, Hao Yi, Shiying Zhang and Wei Xiao

Viruses 2023, 15(6), 1392; https://doi.org/10.3390/v15061392 - 19 Jun 2023

Cited by 1 | Viewed by 2057

Abstract

Salt mines are a special type of hypersaline environment. Current research mainly focuses on prokaryotes, and the understanding of viruses in salt mines remains limited. Understanding viruses in hypersaline environments is of great significance for revealing the formation and maintenance of microbial communities, [...] Read more.

Salt mines are a special type of hypersaline environment. Current research mainly focuses on prokaryotes, and the understanding of viruses in salt mines remains limited. Understanding viruses in hypersaline environments is of great significance for revealing the formation and maintenance of microbial communities, energy flow and element cycling, and host ecological functions. A phage infecting Halomonas titanicae was isolated from Yipinglang Salt Mine in China, designated Halomonas titanicae phage vB_HtiS_YPHTV-1 (YPHTV-1). Transmission electron microscopy revealed that YPHTV-1 had an icosahedral head with a diameter of 49.12 ± 0.15 nm (n = 5) and a long noncontractile tail with a length of 141.7 ± 0.58 nm (n = 5), indicating that it was a siphovirus. The one-step growth curve showed that the burst size of YPHTV-1 was 69 plaque forming units (PFUs) cell⁻¹. The genome of YPHTV-1 was 37,980 bp with a GC content of 36.2%. The phylogenetic analysis of the six conserved proteins indicated that YPHTV-1 formed a cluster with Bacillus phages and was separated from phages infecting Halomonas. The average nucleotide identity (ANI), phylogenetic, and network analyses indicated that the phage YPHTV-1 represented a new genus under Caudoviricetes. In total, 57 open reading frames (ORFs) were predicted in the YPHTV-1 genome, 30 of which could be annotated in the database. Notably, several auxiliary metabolic genes were encoded by YPHTV-1, such as ImmA/IrrE family metalloendopeptidase, mannose-binding lectin (MBL) folding metallohydrolase, M15 family of metal peptidases, MazG-like family protein, O antigen ligase, and acyltransferase. These genes potentially enabled the host bacterium to resist ionizing radiation, ultraviolet light (UV), mitomycin C, β-lactam antibiotic, high osmotic pressure, and nutritional deficiencies. These findings highlight the role of haloviruses in the life cycle of halobacteria. Full article

(This article belongs to the Special Issue Virus Bioinformatics 2023)

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15 pages, 4780 KiB

Open AccessArticle

CoVigator—A Knowledge Base for Navigating SARS-CoV-2 Genomic Variants

by Thomas Bukur, Pablo Riesgo-Ferreiro, Patrick Sorn, Ranganath Gudimella, Johannes Hausmann, Thomas Rösler, Martin Löwer, Barbara Schrörs and Ugur Sahin

Viruses 2023, 15(6), 1391; https://doi.org/10.3390/v15061391 - 17 Jun 2023

Cited by 3 | Viewed by 2126

Abstract

Background: The outbreak of the severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) resulted in the global COVID-19 pandemic. The urgency for an effective SARS-CoV-2 vaccine has led to the development of the first series of vaccines at unprecedented speed. The discovery of SARS-CoV-2 spike-glycoprotein [...] Read more.

Background: The outbreak of the severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) resulted in the global COVID-19 pandemic. The urgency for an effective SARS-CoV-2 vaccine has led to the development of the first series of vaccines at unprecedented speed. The discovery of SARS-CoV-2 spike-glycoprotein mutants, however, and consequentially the potential to escape vaccine-induced protection and increased infectivity, demonstrates the persisting importance of monitoring SARS-CoV-2 mutations to enable early detection and tracking of genomic variants of concern. Results: We developed the CoVigator tool with three components: (1) a knowledge base that collects new SARS-CoV-2 genomic data, processes it and stores its results; (2) a comprehensive variant calling pipeline; (3) an interactive dashboard highlighting the most relevant findings. The knowledge base routinely downloads and processes virus genome assemblies or raw sequencing data from the COVID-19 Data Portal (C19DP) and the European Nucleotide Archive (ENA), respectively. The results of variant calling are visualized through the dashboard in the form of tables and customizable graphs, making it a versatile tool for tracking SARS-CoV-2 variants. We put a special emphasis on the identification of intrahost mutations and make available to the community what is, to the best of our knowledge, the largest dataset on SARS-CoV-2 intrahost mutations. In the spirit of open data, all CoVigator results are available for download. The CoVigator dashboard is accessible via covigator.tron-mainz.de. Conclusions: With increasing demand worldwide in genome surveillance for tracking the spread of SARS-CoV-2, CoVigator will be a valuable resource of an up-to-date list of mutations, which can be incorporated into global efforts. Full article

(This article belongs to the Special Issue Virus Bioinformatics 2023)

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15 pages, 2530 KiB

Open AccessArticle

Two Decades of Wildlife Pathogen Surveillance: Case Study of Choclo orthohantavirus and Its Wild Reservoir Oligoryzomys costaricensis

by Publio Gonzalez, Jacqueline R. Salazar, Tybbysay P. Salinas, Mario Avila, Jocelyn P. Colella, Jonathan L. Dunnum, Gregory E. Glass, Gloria Gonzalez, Enos Juarez, Kimberly Lindblade, Edwin Pile, Yaxelis Mendoza, Juan Miguel Pascale, Anibal G. Armien, Joseph A. Cook and Blas Armien

Viruses 2023, 15(6), 1390; https://doi.org/10.3390/v15061390 - 17 Jun 2023

Cited by 4 | Viewed by 2248

Abstract

The Costa Rican pygmy rice rat (Oligoryzomys costaricensis) is the primary reservoir of Choclo orthohantavirus (CHOV), the causal agent of hantavirus disease, pulmonary syndrome, and fever in humans in Panama. Since the emergence of CHOV in early 2000, we have systematically [...] Read more.

The Costa Rican pygmy rice rat (Oligoryzomys costaricensis) is the primary reservoir of Choclo orthohantavirus (CHOV), the causal agent of hantavirus disease, pulmonary syndrome, and fever in humans in Panama. Since the emergence of CHOV in early 2000, we have systematically sampled and archived rodents from >150 sites across Panama to establish a baseline understanding of the host and virus, producing a permanent archive of holistic specimens that we are now probing in greater detail. We summarize these collections and explore preliminary habitat/virus associations to guide future wildlife surveillance and public health efforts related to CHOV and other zoonotic pathogens. Host sequences of the mitochondrial cytochrome b gene form a single monophyletic clade in Panama, despite wide distribution across Panama. Seropositive samples were concentrated in the central region of western Panama, consistent with the ecology of this agricultural commensal and the higher incidence of CHOV in humans in that region. Hantavirus seroprevalence in the pygmy rice rat was >15% overall, with the highest prevalence in agricultural areas (21%) and the lowest prevalence in shrublands (11%). Host–pathogen distribution, transmission dynamics, genomic evolution, and habitat affinities can be derived from the preserved samples, which include frozen tissues, and now provide a foundation for expanded investigations of orthohantaviruses in Panama. Full article

(This article belongs to the Special Issue Hantavirus Ecology, Epidemiology, and Disease, in Memory of Dr. Ho Wang Lee)

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22 pages, 2328 KiB

Open AccessReview

Hepatitis E Virus Infections: Epidemiology, Genetic Diversity, and Clinical Considerations

by Busara Songtanin, Adebayo J. Molehin, Kevin Brittan, Wuttiporn Manatsathit and Kenneth Nugent

Viruses 2023, 15(6), 1389; https://doi.org/10.3390/v15061389 - 17 Jun 2023

Cited by 15 | Viewed by 4458

Abstract

According to the World Health Organization, approximately 20 million people worldwide are infected annually with the hepatitis E virus (HEV). There are four main genotypes of HEV. Genotype 1 and genotype 2 are common in developing countries and are transmitted by contaminated water [...] Read more.

According to the World Health Organization, approximately 20 million people worldwide are infected annually with the hepatitis E virus (HEV). There are four main genotypes of HEV. Genotype 1 and genotype 2 are common in developing countries and are transmitted by contaminated water from a fecal–oral route. Genotype 3 and genotype 4 are common in developed countries and can lead to occasional transmission to humans via undercooked meat. Hepatitis E virus 1 and HEV3 can lead to fulminant hepatitis, and HEV3 can lead to chronic hepatitis and cirrhosis in immunocompromised patients. The majority of patients with HEV infection are asymptomatic and usually have spontaneous viral clearance without treatment. However, infection in immunocompromised individuals can lead to chronic HEV infection. Both acute and chronic HEV infections can have extrahepatic manifestations. No specific treatment is required for acute HEV infection, no treatment has been approved in chronic infection, and no HEV vaccine has been approved by the (United States) Food and Drug Administration. This review focuses on the molecular virology (HEV life cycle, genotypes, model systems, zoonosis), pathogenesis, clinical manifestation, and treatment of chronic HEV infection, especially in immunocompromised patients, to provide clinicians a better understanding of the global distribution of these infections and the significant effect they can have on immunocompromised patients. Full article

(This article belongs to the Special Issue Hepatitis E: Molecular Virology, Pathogenesis, and Treatment)

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15 pages, 1060 KiB

Open AccessReview

Conditional Cell Reprogramming and Air–Liquid Interface Modeling Life Cycle of Oncogenic Viruses (HPV and EBV) in Epithelial Cells and Virus-Associated Human Carcinomas

by Abdul Qawee Rani, Dilber Nurmemet, Joseph Liffick, Anam Khan, Darrion Mitchell, Jenny Li, Bo Zhao and Xuefeng Liu

Viruses 2023, 15(6), 1388; https://doi.org/10.3390/v15061388 - 17 Jun 2023

Cited by 4 | Viewed by 2636

Abstract

Several oncogenic viruses are associated with approximately 20% of human cancers. Experimental models are crucial for studying the pathogenicity and biological aspects of oncogenic viruses and their potential mechanisms in tumorigenesis. Current cell models have considerable limitations such as: their low yield, genetic [...] Read more.

Several oncogenic viruses are associated with approximately 20% of human cancers. Experimental models are crucial for studying the pathogenicity and biological aspects of oncogenic viruses and their potential mechanisms in tumorigenesis. Current cell models have considerable limitations such as: their low yield, genetic and epigenetic modification, and reduction in tumor heterogeneity during long propagation. Cancer cell lines are limited and not appropriate for studying the viral life cycle, for example, natural viral life cycles of HPV and EBV, and their persistence and latency in epithelial cells are poorly understood, since these processes are highly related to epithelial differentiation. Therefore, there is an urgent need of reliable human physiological cell models to study viral life cycle and cancer initiation. Conditional cell reprogramming (CCR) is a rapid and robust cell culture system, where the cells can be established from minimally invasive or noninvasive specimens and their lineage functions preserved during the long-term culture. These CR cells retain their ability to differentiate at air–liquid interface (ALI). Here, we recapitulated the applications of CR and ALI approaches in modeling host–virus interactions and viral-mediated tumorigenesis. Full article

(This article belongs to the Special Issue Conditional Cell Reprogramming: Applications in Virology)

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13 pages, 2719 KiB

Open AccessArticle

The Evolution of Highly Pathogenic Avian Influenza A (H5) in Poultry in Nigeria, 2021–2022

by Clement Meseko, Adelaide Milani, Bitrus Inuwa, Chinonyerem Chinyere, Ismaila Shittu, James Ahmed, Edoardo Giussani, Elisa Palumbo, Bianca Zecchin, Francesco Bonfante, Silvia Maniero, Angélique Angot, Mamadou Niang, Alice Fusaro, Federica Gobbo, Calogero Terregino, Taiwo Olasoju, Isabella Monne and Maryam Muhammad

Viruses 2023, 15(6), 1387; https://doi.org/10.3390/v15061387 - 17 Jun 2023

Cited by 7 | Viewed by 3409

Abstract

In 2021, amidst the COVID-19 pandemic and global food insecurity, the Nigerian poultry sector was exposed to the highly pathogenic avian influenza (HPAI) virus and its economic challenges. Between 2021 and 2022, HPAI caused 467 outbreaks reported in 31 of the 37 administrative [...] Read more.

In 2021, amidst the COVID-19 pandemic and global food insecurity, the Nigerian poultry sector was exposed to the highly pathogenic avian influenza (HPAI) virus and its economic challenges. Between 2021 and 2022, HPAI caused 467 outbreaks reported in 31 of the 37 administrative regions in Nigeria. In this study, we characterized the genomes of 97 influenza A viruses of the subtypes H5N1, H5N2, and H5N8, which were identified in different agro-ecological zones and farms during the 2021–2022 epidemic. The phylogenetic analysis of the HA genes showed a widespread distribution of the H5Nx clade 2.3.4.4b and similarity with the HPAI H5Nx viruses that have been detected in Europe since late 2020. The topology of the phylogenetic trees indicated the occurrence of several independent introductions of the virus into the country, followed by a regional evolution of the virus that was most probably linked to its persistent circulation in West African territories. Additional evidence of the evolutionary potential of the HPAI viruses circulating in this region is the identification in this study of a putative H5N1/H9N2 reassortant virus in a mixed-species commercial poultry farm. Our data confirm Nigeria as a crucial hotspot for HPAI virus introduction from the Eurasian territories and reveal a dynamic pattern of avian influenza virus evolution within the Nigerian poultry population. Full article

(This article belongs to the Special Issue Drivers of Evolution of Animal RNA Viruses, Volume II)

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15 pages, 2712 KiB

Open AccessSystematic Review

Viral Loads in Skin Samples of Patients with Monkeypox Virus Infection: A Systematic Review and Meta-Analysis

by Isha Rani, Prakasini Satapathy, Anmol Goyal, Muhammad Aaqib Shamim, Amit Pal, Rosanna Squitti, Kalyan Goswami, Keerti Bhusan Pradhan, Sarvesh Rustagi, Alaa Hamza Hermis, Joshuan J. Barboza, Alfonso J. Rodriguez-Morales, Ranjit Sah and Bijaya K. Padhi

Viruses 2023, 15(6), 1386; https://doi.org/10.3390/v15061386 - 17 Jun 2023

Cited by 6 | Viewed by 3259

Abstract

Despite monkeypox (mpox) being a public health emergency, there is limited knowledge about the risk of infectivity from skin viral loads during mpox infection. Thus, the aim of this study was to estimate cutaneous viral loads among mpox patients globally. Several databases, including [...] Read more.

Despite monkeypox (mpox) being a public health emergency, there is limited knowledge about the risk of infectivity from skin viral loads during mpox infection. Thus, the aim of this study was to estimate cutaneous viral loads among mpox patients globally. Several databases, including Cochrane, EBSCOHost, EMBASE, ProQuest, PubMed, Scopus, and Web of Science, and preprint servers were searched concerning skin mpox viral loads in confirmed mpox subjects. In this systematic review and meta-analysis, a total of 331 articles were initially screened after the removal of duplicate entries. A total of nine articles were included in the systematic review and meta-analysis for the overall estimation of viral loads (Ct) using a random-effect model. The pooled cutaneous mpox viral load (lower Ct) was 21.71 (95% CI: 20.68–22.75) with a majority of positivity rates being 100%, highlighting a higher infectivity risk from skin lesions. The current results strongly support that skin mpox viral loads may be a dominant source of rapid transmission during current multi-national outbreaks. This important finding can help in constructing useful measures in relevant health policy. Full article

(This article belongs to the Topic Discovery and Development of Monkeypox Disease Treatments)

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30 pages, 1375 KiB

Open AccessReview

The Pathogenesis of Cytomegalovirus and Other Viruses Associated with Hearing Loss: Recent Updates

by Xinyu Shi, Xiaozhou Liu and Yu Sun

Viruses 2023, 15(6), 1385; https://doi.org/10.3390/v15061385 - 16 Jun 2023

Cited by 6 | Viewed by 5062

Abstract

Virus infection is one of the most common etiologies of hearing loss. Hearing loss associated with viral infection can be unilateral or bilateral, mild or severe, sudden or progressive, and permanent or recoverable. Many viruses cause hearing loss in adults and children; however, [...] Read more.

Virus infection is one of the most common etiologies of hearing loss. Hearing loss associated with viral infection can be unilateral or bilateral, mild or severe, sudden or progressive, and permanent or recoverable. Many viruses cause hearing loss in adults and children; however, the pathogenesis of hearing loss caused by viral infection is not fully understood. This review describes cytomegalovirus, the most common virus causing hearing loss, and other reported hearing loss-related viruses. We hope to provide a detailed description of pathogenic characteristics and research progress on pathology, hearing phenotypes, possible associated mechanisms, treatment, and prevention measures. This review aims to provide diagnostic and treatment assistance to clinical workers. Full article

(This article belongs to the Section Human Virology and Viral Diseases)

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11 pages, 1325 KiB

Open AccessArticle

Overview of Mpox Outbreak in Greece in 2022–2023: Is It Over?

by Kassiani Mellou, Kyriaki Tryfinopoulou, Styliani Pappa, Kassiani Gkolfinopoulou, Sofia Papanikou, Georgia Papadopoulou, Evangelia Vassou, Evangelia-Georgia Kostaki, Kalliopi Papadima, Elissavet Mouratidou, Maria Tsintziloni, Nikolaos Siafakas, Zoi Florou, Antigoni Katsoulidou, Spyros Sapounas, George Sourvinos, Spyridon Pournaras, Efthymia Petinaki, Maria Goula, Vassilios Paparizos, Anna Papa, Theoklis Zaoutis and Dimitrios Paraskevis Show full author list Hide full author list

Viruses 2023, 15(6), 1384; https://doi.org/10.3390/v15061384 - 16 Jun 2023

Cited by 3 | Viewed by 3691

Abstract

In May 2022, for the first time, multiple cases of mpox were reported in several non-endemic countries. The first ever case of the disease in Greece was confirmed on 8 June 2022, and a total of 88 cases were reported in the country [...] Read more.

In May 2022, for the first time, multiple cases of mpox were reported in several non-endemic countries. The first ever case of the disease in Greece was confirmed on 8 June 2022, and a total of 88 cases were reported in the country until the end of April 2023. A multidisciplinary response team was established by the Greek National Public Health Organization (EODY) to monitor and manage the situation. EODY’s emergency response focused on enhanced surveillance, laboratory testing, contact tracing, medical countermeasures, and the education of health care providers and the public. Even though management of cases was considered successful and the risk from the disease was downgraded, sporadic cases continue to occur. Here, we provide epidemiological and laboratory features of the reported cases to depict the course of the disease notification rate. Our results suggest that measures for raising awareness as well as vaccination of high-risk groups of the population should be continued. Full article

(This article belongs to the Special Issue Zoonotic Viral Diseases)

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21 pages, 9729 KiB

Open AccessArticle

The Molecular Epidemiology of Clade 2.3.4.4B H5N1 High Pathogenicity Avian Influenza in Southern Africa, 2021–2022

by Celia Abolnik, Thandeka Phiri, Belinda Peyrot, Renee de Beer, Albert Snyman, David Roberts, Katrin Ludynia, Frances Jordaan, Michele Maartens, Zehaad Ismail, Christine Strydom, Gerbrand van der Zel, Jade Anthony, Nadine Daniell, Liesl De Boni, John Grewar, Adriaan Olivier and Laura Roberts

Viruses 2023, 15(6), 1383; https://doi.org/10.3390/v15061383 - 16 Jun 2023

Cited by 18 | Viewed by 3633

Abstract

In southern Africa, clade 2.3.4.4B H5N1 high pathogenicity avian influenza (HPAI) was first detected in South African (SA) poultry in April 2021, followed by outbreaks in poultry or wild birds in Lesotho and Botswana. In this study, the complete or partial genomes of [...] Read more.

In southern Africa, clade 2.3.4.4B H5N1 high pathogenicity avian influenza (HPAI) was first detected in South African (SA) poultry in April 2021, followed by outbreaks in poultry or wild birds in Lesotho and Botswana. In this study, the complete or partial genomes of 117 viruses from the SA outbreaks in 2021–2022 were analyzed to decipher the sub-regional spread of the disease. Our analysis showed that seven H5N1 sub-genotypes were associated with the initial outbreaks, but by late 2022 only two sub-genotypes still circulated. Furthermore, SA poultry was not the source of Lesotho’s outbreaks, and the latter was most likely an introduction from wild birds. Similarly, SA and Botswana’s outbreaks in 2021 were unrelated, but viruses of Botswana’s unique sub-genotype were introduced into SA later in 2022 causing an outbreak in ostriches. At least 83% of SA’s commercial poultry cases in 2021–2022 were point introductions from wild birds. Like H5N8 HPAI in 2017–2018, a coastal seabird-restricted sub-lineage of H5N1 viruses emerged in the Western Cape province in 2021 and spread to Namibia, causing mortalities in Cape Cormorants. In SA ~24,000 of this endangered species died, and the loss of >300 endangered African penguins further threatens biodiversity. Full article

(This article belongs to the Section Animal Viruses)

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18 pages, 2151 KiB

Open AccessArticle

The Lambda Variant in Argentina: Analyzing the Evolution and Spread of SARS-CoV-2 Lineage C.37

by Mercedes Soledad Nabaes Jodar, Carolina Torres, Laura Mojsiejczuk, Dolores Acuña, Laura Elena Valinotto, Stephanie Goya, Monica Natale, Silvina Lusso, Sofia Alexay, Ariel Amadio, Matias Irazoqui, Franco Fernandez, Maria Elina Acevedo, Cristina Alvarez Lopez, Andres Angelletti, Paula Aulicino, Elisa Bolatti, Bettina Brusés, Marco Cacciahue, Ana Cavatorta, Agustina Cerri, Andres Cordero, Humberto Debat, Maria Jose Dus Santos, Maria Florencia Eberhardt, Regina Ercole, Carlos Espul, Marisa Farber, Fabián Fay, Ailen Fernandez, Florencia Ferrini, Laura Formichelli, Santiago Ceballos, Fernando Gallego, Adriana Giri, Maria Gismondi, Raul Maximiliano Acevedo, Ivan Gramundi, María Eugenia Ibañez, Guido Konig, Viviana Leiva, Melina Lorenzini Campos, Horacio Lucero, Nathalie Marquez, Melina Mazzeo, Alicia Susana Mistchenko, Luciana Montoto, Marianne Muñoz, Victoria Nadalich, Cristina Nardi, Belén Ortiz, Luis Pianciola, Carolina Pintos, Andrea Puebla, Carolina Rastellini, Alejandro Ezequiel Rojas, Javier Sfalcin, Ariel Suarez, Clara Theaux, Guillermo Thomas, Estefania Tittarelli, Rosana Toro, Vanina Villanova, Gretel Wenk, Cecilia Ziehm, Maria Carla Zimmermann, Sebastian Zunino, Proyecto PAIS and Mariana Viegas Show full author list Hide full author list

Viruses 2023, 15(6), 1382; https://doi.org/10.3390/v15061382 - 16 Jun 2023

Cited by 2 | Viewed by 2242

Abstract

The second wave of COVID-19 occurred in South America in early 2021 and was mainly driven by Gamma and Lambda variants. In this study, we aimed to describe the emergence and local genomic diversity of the SARS-CoV-2 Lambda variant in Argentina, from its [...] Read more.

The second wave of COVID-19 occurred in South America in early 2021 and was mainly driven by Gamma and Lambda variants. In this study, we aimed to describe the emergence and local genomic diversity of the SARS-CoV-2 Lambda variant in Argentina, from its initial entry into the country until its detection ceased. Molecular surveillance was conducted on 9356 samples from Argentina between October 2020 and April 2022, and sequencing, phylogenetic, and phylogeographic analyses were performed. Our findings revealed that the Lambda variant was first detected in Argentina in January 2021 and steadily increased in frequency until it peaked in April 2021, with continued detection throughout the year. Phylodynamic analyses showed that at least 18 introductions of the Lambda variant into the country occurred, with nine of them having evidence of onward local transmission. The spatial–-temporal reconstruction showed that Argentine clades were associated with Lambda sequences from Latin America and suggested an initial diversification in the Metropolitan Area of Buenos Aires before spreading to other regions in Argentina. Genetic analyses of genome sequences allowed us to describe the mutational patterns of the Argentine Lambda sequences and detect the emergence of rare mutations in an immunocompromised patient. Our study highlights the importance of genomic surveillance in identifying the introduction and geographical distribution of the SARS-CoV-2 Lambda variant, as well as in monitoring the emergence of mutations that could be involved in the evolutionary leaps that characterize variants of concern. Full article

(This article belongs to the Special Issue Molecular Epidemiology of SARS-CoV-2)

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21 pages, 6011 KiB

Open AccessArticle

m⁶A Regulates the Stability of Cellular Transcripts Required for Efficient KSHV Lytic Replication

by Oliver Manners, Belinda Baquero-Perez, Timothy J. Mottram, Ivaylo D. Yonchev, Christopher J. Trevelyan, Katherine L. Harper, Sarah Menezes, Molly R. Patterson, Andrew Macdonald, Stuart A. Wilson, Julie L. Aspden and Adrian Whitehouse

Viruses 2023, 15(6), 1381; https://doi.org/10.3390/v15061381 - 16 Jun 2023

Cited by 2 | Viewed by 2040

Abstract

The epitranscriptomic modification N⁶-methyladenosine (m⁶A) is a ubiquitous feature of the mammalian transcriptome. It modulates mRNA fate and dynamics to exert regulatory control over numerous cellular processes and disease pathways, including viral infection. Kaposi’s sarcoma-associated herpesvirus (KSHV) reactivation from [...] Read more.

The epitranscriptomic modification N⁶-methyladenosine (m⁶A) is a ubiquitous feature of the mammalian transcriptome. It modulates mRNA fate and dynamics to exert regulatory control over numerous cellular processes and disease pathways, including viral infection. Kaposi’s sarcoma-associated herpesvirus (KSHV) reactivation from the latent phase leads to the redistribution of m⁶A topology upon both viral and cellular mRNAs within infected cells. Here we investigate the role of m⁶A in cellular transcripts upregulated during KSHV lytic replication. Our results show that m⁶A is crucial for the stability of the GPRC5A mRNA, whose expression is induced by the KSHV latent–lytic switch master regulator, the replication and transcription activator (RTA) protein. Moreover, we demonstrate that GPRC5A is essential for efficient KSHV lytic replication by directly regulating NFκB signalling. Overall, this work highlights the central importance of m⁶A in modulating cellular gene expression to influence viral infection. Full article

(This article belongs to the Special Issue Herpesvirus Manipulation of Cellular Processes 2.0)

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14 pages, 3916 KiB

Open AccessArticle

The Virome of Babaco (Vasconcellea × heilbornii) Expands to Include New Members of the Rhabdoviridae and Bromoviridae

by Edison G. Reyes-Proaño, Maria G. Cañada-Bautista, Juan F. Cornejo-Franco, Robert A. Alvarez-Quinto, Dimitre Mollov, Eduardo Sanchez-Timm and Diego F. Quito-Avila

Viruses 2023, 15(6), 1380; https://doi.org/10.3390/v15061380 - 16 Jun 2023

Cited by 2 | Viewed by 1938

Abstract

Babaco (Vasconcellea × heilbornii) is a subtropical species in the Caricaceae family. The plant is native to Ecuador and represents an important crop for hundreds of families. The objective of this study was to characterize, at the genomic level, two new [...] Read more.

Babaco (Vasconcellea × heilbornii) is a subtropical species in the Caricaceae family. The plant is native to Ecuador and represents an important crop for hundreds of families. The objective of this study was to characterize, at the genomic level, two new babaco viruses identified by high-throughput sequencing. The viruses, an ilarvirus and a nucleorhabdovirus, were found in a symptomatic babaco plant from a commercial nursery in the Azuay province of Ecuador. The tripartite genome of the new ilarvirus, provisionally named babaco ilarvirus 1 (BabIV-1), is related to subgroup 3 ilarviruses, including apple mosaic virus, apple necrotic mosaic virus, and prunus necrotic ringspot virus as the closest relatives. The genome of the nucleorhabdovirus, provisionally named babaco nucleorhabdovirus 1 (BabRV-1), showed the closest relation with joa yellow blotch-associated virus and potato yellow dwarf nucleorhabdovirus. Molecular-based detection methods found BabIV-1 and BabRV-1 in 21% and 36%, respectively, of plants surveyed in a commercial babaco nursery, highlighting the importance of enforcing virus testing and nursery certification programs for babaco. Full article

(This article belongs to the Special Issue Next-Generation Sequencing in Plant Virology 2.0)

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12 pages, 880 KiB

Open AccessArticle

Evidence of a Link between Hepatitis E Virus Exposure and Glomerulonephritis Development

by Mohamed A. El-Mokhtar, Ayat M. Kamel, Ehsan M. W. El-Sabaa, Sahar A. Mandour, Ahmed Shawkat Abdelmohsen, Abdelmajeed M. Moussa, Eman H. Salama, Sahar Aboulfotuh, Lobna Abdel-Wahid, Essam M. Abdel Aziz, Nashwa Mostafa A. Azoz, Ibrahim M. Sayed and Amal A. Elkhawaga

Viruses 2023, 15(6), 1379; https://doi.org/10.3390/v15061379 - 15 Jun 2023

Cited by 4 | Viewed by 1787

Abstract

Viruses can trigger glomerulonephritis (GN) development. Hepatitis viruses, especially Hepatitis C virus and Hepatitis B viruses, are examples of the viruses that trigger GN initiation or progression. However, the proof of a correlation between GN and Hepatitis E virus infection is not clear. [...] Read more.

Viruses can trigger glomerulonephritis (GN) development. Hepatitis viruses, especially Hepatitis C virus and Hepatitis B viruses, are examples of the viruses that trigger GN initiation or progression. However, the proof of a correlation between GN and Hepatitis E virus infection is not clear. Some studies confirmed the development of GN during acute or chronic HEV infections, mainly caused by genotype 3. While others reported that there is no relation between HEV exposure and GN development. A recent study showed that a reduced glomerular filtration rate was developed in 16% of acute HEV genotype 1 (HEV-1) infections that returned to normal during recovery. HEV-1 is endemic in Egypt with a high seroprevalence among villagers and pregnant women. There is no available data about a link between HEV and GN in Egypt. Methods: GN patients (n = 43) and matched healthy subjects (n = 36) enrolled in Assiut University hospitals were included in this study. Blood samples were screened for hepatotropic pathogens. Tests for HEV markers such as HEV RNA and anti-HEV antibodies (IgM and IgG) were performed. Laboratory parameters were compared in HEV-seropositive and HEV-seronegative GN patients. Results: Anti-HEV IgG was detected in 26 (60.5%) out of 43 GN patients. HEV seroprevalence was significantly higher in GN than in healthy controls, suggesting that HEV exposure is a risk factor for GN development. None of the GN patients nor the healthy subjects were positive for anti-HEV IgM or HEV RNA. There was no significant difference between seropositive and seronegative GN patients in terms of age, gender, albumin, kidney function profiles, or liver transaminases. However, anti-HEV IgG positive GN patients had higher bilirubin levels than anti-HEV IgG negative GN patients. HEV-seropositive GN patients had a significantly elevated AST level compared to HEV-seropositive healthy subjects. Conclusion: exposure to HEV infection could be complicated by the development of GN. Full article

(This article belongs to the Special Issue Hepatitis E: Molecular Virology, Pathogenesis, and Treatment)

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12 pages, 1273 KiB

Open AccessReview

Application of Flow Cytometry in the Diagnosis of Bovine Epidemic Disease

by Zhilin Liu, Yuliang Zhang, Donghui Zhao, Yunjiao Chen, Qinglei Meng, Xin Zhang, Zelin Jia, Jiayu Cui and Xueli Wang

Viruses 2023, 15(6), 1378; https://doi.org/10.3390/v15061378 - 15 Jun 2023

Cited by 2 | Viewed by 2196

Abstract

As science and technology continue to advance, the use of flow cytometry is becoming more widespread. It can provide important information about cells in the body by detecting and analysing them, thereby providing a reliable basis for disease diagnosis. In the diagnosis of [...] Read more.

As science and technology continue to advance, the use of flow cytometry is becoming more widespread. It can provide important information about cells in the body by detecting and analysing them, thereby providing a reliable basis for disease diagnosis. In the diagnosis of bovine epidemic diseases, flow cytometry can be used to detect bovine viral diarrhoea, bovine leukaemia, bovine brucellosis, bovine tuberculosis, and other diseases. This paper describes the structure of a flow cytometer (liquid flow system, optical detection system, data storage and analysis system) and its working principles for rapid quantitative analysis and sorting of single cells or biological particles. Additionally, the research progress of flow cytometry in the diagnosis of bovine epidemic diseases was reviewed in order to provide a reference for future research and application of flow cytometry in the diagnosis of bovine epidemic diseases. Full article

(This article belongs to the Special Issue Veterinary Virology and Disease Control in China 2023)

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14 pages, 1482 KiB

Open AccessArticle

Antiviral Activity of Catechin against Dengue Virus Infection

by Bowen Yi, Benjamin Xuan Zheng Chew, Huixin Chen, Regina Ching Hua Lee, Yuhui Deborah Fong, Wei Xin Chin, Chee Keng Mok and Justin Jang Hann Chu

Viruses 2023, 15(6), 1377; https://doi.org/10.3390/v15061377 - 15 Jun 2023

Cited by 5 | Viewed by 3240

Abstract

Dengue virus (DENV) is the cause of dengue fever, infecting 390 million people worldwide per year. It is transmitted to humans through the bites of mosquitoes and could potentially develop severe symptoms. In spite of the rising social and economic impact inflicted by [...] Read more.

Dengue virus (DENV) is the cause of dengue fever, infecting 390 million people worldwide per year. It is transmitted to humans through the bites of mosquitoes and could potentially develop severe symptoms. In spite of the rising social and economic impact inflicted by the disease on the global population, a conspicuous lack of efficacious therapeutics against DENV still persists. In this study, catechin, a natural polyphenol compound, was evaluated as a DENV infection inhibitor in vitro. Through time-course studies, catechin was shown to inhibit a post-entry stage of the DENV replication cycle. Further investigation revealed its role in affecting viral protein translation. Catechin inhibited the replication of all four DENV serotypes and chikungunya virus (CHIKV). Together, these results demonstrate the ability of catechin to inhibit DENV replication, hinting at its potential to be used as a starting scaffold for further development of antivirals against DENV infection. Full article

(This article belongs to the Special Issue Novel Antiviral Targets against Emerging Viruses)

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16 pages, 340 KiB

Open AccessOpinion

Prevention of Congenital Cytomegalovirus Infection: Review and Case Series of Valaciclovir versus Hyperimmune Globulin Therapy

by Giovanni Nigro, Mario Muselli and on behalf of the Congenital Cytomegalic Disease Collaborating Group

Viruses 2023, 15(6), 1376; https://doi.org/10.3390/v15061376 - 15 Jun 2023

Cited by 10 | Viewed by 2392

Abstract

Cytomegalovirus (CMV) is the most common cause of congenital infections in developed countries because is capable of infecting the fetus after both primary and recurrent maternal infection, and because the virus may be spread for years through infected children. Moreover, CMV is the [...] Read more.

Cytomegalovirus (CMV) is the most common cause of congenital infections in developed countries because is capable of infecting the fetus after both primary and recurrent maternal infection, and because the virus may be spread for years through infected children. Moreover, CMV is the most serious congenital infection associated with severe neurological and sensorineural sequelae, which can occur at birth or develop later on. Hygienic measures can prevent CMV transmission, which mainly involve contact with children under 3 years of age and attending a nursery or daycare. In animal and human pregnancies, many observational and controlled studies have shown that CMV-specific hyperimmune globulin (HIG) is safe and can significantly decrease maternal–fetal transmission of CMV infection and, mostly, the occurrence of CMV disease. Recently, valaciclovir at the dosage of 8 g/day was also reported to be capable of decreasing the rates of congenital infection and disease. However, comparing the results of our two recent case series, the infants born to women treated with HIG showed significantly lower rates of CMV DNA positivity in urine (9.7% vs. 75.0%; p < 0.0001) and abnormalities after follow-up (0.0% vs. 41.7%; p < 0.0001). The implementation of CMV screening would enable primary prevention via hygiene counseling, improve the understanding and awareness of congenital CMV infection, and increase the knowledge of the potential efficacy of preventive or therapeutic HIG or antiviral administration. Full article

(This article belongs to the Special Issue Congenital Cytomegalovirus Infection)

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Viruses, Volume 15, Issue 6 (June 2023) – 188 articles

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