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Viral Gastroenteritis 2022
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Viral Gastroenteritis 2022

A special issue of Viruses (ISSN 1999-4915). This special issue belongs to the section "Human Virology and Viral Diseases".

Deadline for manuscript submissions: closed (28 February 2023) | Viewed by 30353

Special Issue Editors

Dr. Adriana Luchs

E-Mail Website
Guest Editor
Virology Center, Enteric Disease Laboratory, Adolfo Lutz Institute, São Paulo 01246-902, SP, Brazil
Interests: molecular epidemiology of enteric viruses; viral interspecies transmission; public Health; viral genetic diversity; viral evolution
Dr. Jesús Rodríguez-Díaz

E-Mail Website
Guest Editor
Department of Microbiology, School of Medicine, University of Valencia, 46010 Valencia, Spain
Interests: molecular epidemiology of rotavirus and norovirus; virus–host interactions; microbiota
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Viral gastroenteritis is an intestinal infection that includes signs and symptoms such as watery diarrhea, stomach cramps, nausea/vomiting, and sometimes fever, affecting humans and many animal species. Several viruses, including rotavirus, norovirus, adenovirus, and astroviruses, account for most cases of acute viral gastroenteritis. They have a significant impact on global public health and are responsible for major economic losses in livestock and poultry. Viruses involved in gastroenteritis can be transmitted by the fecal–oral route directly or by indirect contact via contaminated fluids, including surface water, food, and carriers such as fomites. Recently, there has been a growing number of reports describing the interspecies transmission of enteric viruses from animals to humans, among animals or even from humans to animals. Therefore, viral gastroenteritis is a fertile and challenging field within the overarching domain of One Health surveillance.

This Special Issue on Viral Gastroenteritis invites the submission of manuscripts on epidemiology, diagnosis, host–virus interaction, surveillance, molecular epidemiology, pathogenesis, immunology, treatment and prevention, extra-intestinal dissemination, foodborne illness emergence and evolution, virus discovery, interspecies transmission, potential animal reservoirs, and any other aspects of viral gastroenteritis research. Under the One Health paradigm, collaboration between human health, animal health, environmental health and food safety fields is also particularly encouraged.

We look forward to receiving your submissions for this Special Issue.

Dr. Adriana Luchs
Dr. Jesús Rodríguez-Díaz
Guest Editors

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All submissions that pass pre-check are peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Viruses is an international peer-reviewed open access monthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 2600 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

  • viral gastroenteritis
  • host–virus interaction
  • molecular epidemiology
  • viral evolution
  • viral diversity
  • surveillance
  • vaccines

Published Papers (15 papers)

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15 pages, 1132 KiB  
Article
Genomic Analysis of Rwandan G9P[8] Rotavirus Strains Pre- and Post-RotaTeq® Vaccine Reveals Significant Distinct Sub-Clustering in a Post-Vaccination Cohort
by Robyn-Lee Potgieter, Peter N. Mwangi, Milton T. Mogotsi, Jeannine Uwimana, Leon Mutesa, Narcisse Muganga, Didier Murenzi, Lisine Tusiyenge, Mapaseka L. Seheri, A. Duncan Steele, Jason M. Mwenda and Martin M. Nyaga
Viruses 2023, 15(12), 2321; https://doi.org/10.3390/v15122321 - 25 Nov 2023
Viewed by 973
Abstract
Although the introduction of rotavirus vaccines has substantially contributed to the reduction in rotavirus morbidity and mortality, concerns persist about the re-emergence of variant strains that might alter vaccine effectiveness in the long term. The G9 strains re-emerged in Africa during the mid-1990s [...] Read more.
Although the introduction of rotavirus vaccines has substantially contributed to the reduction in rotavirus morbidity and mortality, concerns persist about the re-emergence of variant strains that might alter vaccine effectiveness in the long term. The G9 strains re-emerged in Africa during the mid-1990s and have more recently become predominant in some countries, such as Ghana and Zambia. In Rwanda, during the 2011 to 2015 routine surveillance period, G9P[8] persisted during both the pre- and post-vaccine periods. The pre-vaccination cohort was based on the surveillance period of 2011 to 2012, and the post-vaccination cohort was based on the period of 2013 to 2015, excluding 2014. The RotaTeq® vaccine that was first introduced in Rwanda in 2012 is genotypically heterologous to Viral Protein 7 (VP7) G9. This study elucidated the whole genome of Rwandan G9P[8] rotavirus strains pre- and post-RotaTeq® vaccine introduction. Fecal samples from Rwandan children under the age of five years (pre-vaccine n = 23; post-vaccine n = 7), conventionally genotyped and identified as G9P[8], were included. Whole-genome sequencing was then performed using the Illumina® MiSeq platform. Phylogenetic analysis and pair-wise sequence analysis were performed using MEGA6 software. Distinct clustering of three post-vaccination study strains was observed in all 11 gene segments, compared to the other Rwandan G9P[8] study strains. Specific amino acid differences were identified across the gene segments of these three 2015 post-vaccine strains. Important amino acid differences were identified at position N242S in the VP7 genome segment of the three post-vaccine G9 strains compared to the other G9 strains. This substitution occurs at a neutralization epitope site and may slightly affect protein interaction at that position. These findings indicate that the Rwandan G9P[8] strains revealed a distinct sub-clustering pattern among post-vaccination study strains circulating in Rwanda, with changes at neutralization epitopes, which may play a role in neutralization escape from vaccine candidates. This emphasizes the need for continuous whole-genome surveillance to better understand the evolution and epidemiology of the G9P[8] strains post-vaccination. Full article
(This article belongs to the Special Issue Viral Gastroenteritis 2022)
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10 pages, 981 KiB  
Article
Epidemiologic and Clinical Characteristics of Human Bocavirus Infection in Children with or without Acute Gastroenteritis in Acre, Northern Brazil
by Fábyla D’ Tácia Brito Trindade, Endrya Socorro Foro Ramos, Patrícia Santos Lobo, Jedson Ferreira Cardoso, Edvaldo Tavares Penha Júnior, Delana Andreza Melo Bezerra, Mayara Annanda Oliveira Neves, Jorge Alberto Azevedo Andrade, Monica Cristina Moraes Silva, Joana D’Arc Pereira Mascarenhas, Sylvia Fátima Santos Guerra and Luana Silva Soares
Viruses 2023, 15(4), 1024; https://doi.org/10.3390/v15041024 - 21 Apr 2023
Cited by 1 | Viewed by 1578
Abstract
Human bocavirus (HBoV) is an emerging virus detected around the world that may be associated with cases of acute gastroenteritis (AGE). However, its contribution to AGE has not been elucidated. This study aimed to describe the frequency, clinical features, and HBoV species circulation [...] Read more.
Human bocavirus (HBoV) is an emerging virus detected around the world that may be associated with cases of acute gastroenteritis (AGE). However, its contribution to AGE has not been elucidated. This study aimed to describe the frequency, clinical features, and HBoV species circulation in children up to 5 years with or without AGE symptoms in Acre, Northern Brazil. A total of 480 stool samples were collected between January and December 2012. Fecal samples were used for extraction, nested PCR amplification, and sequencing for genotyping. Statistical analysis was applied to verify the association between epidemiological and clinical characteristics. Overall, HBoV-positivity was 10% (48/480), with HBoV-positive rates of 8.4% (19/226) and 11.4% (29/254) recorded in diarrheic and non-diarrheic children, respectively. The most affected children were in the age group ranging between 7 and 24 months (50%). HBoV infection was more frequent in children who live in urban areas (85.4%), use water from public networks (56.2%), and live with adequate sewage facilities (50%). Co-detection with other enteric viruses was 16.7% (8/48) and the most prevalent coinfection was RVA+ HBoV (50%, 4/8). HBoV-1 was the most frequent species detected in diarrheic and non-diarrheic children, responsible for 43.8% (21/48) of cases, followed by HBoV-3 (29.2%, 14/48) and HBoV-2 (25%, 12/48). In this study, HBoV infection was not always associated with AGE, as most HBoV cases belonged to the non-diarrheal group. Future studies are warranted in order to determine the role of HBoV in causing acute diarrhea disease. Full article
(This article belongs to the Special Issue Viral Gastroenteritis 2022)
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23 pages, 7013 KiB  
Article
Characterization of Human Norovirus Nonstructural Protein NS1.2 Involved in the Induction of the Filamentous Endoplasmic Reticulum, Enlarged Lipid Droplets, LC3 Recruitment, and Interaction with NTPase and NS4
by Chien-Hui Hung, Ju-Bei Yen, Pey-Jium Chang, Lee-Wen Chen, Tsung-Yu Huang, Wan-Ju Tsai and Yu-Chin Tsai
Viruses 2023, 15(3), 812; https://doi.org/10.3390/v15030812 - 22 Mar 2023
Viewed by 1909
Abstract
Human noroviruses (HuNVs) are the leading cause of gastroenteritis worldwide. NS1.2 is critical for HuNV pathogenesis, but the function is still unclear. The GII NS1.2 of HuNVs, unlike GI NS1.2, was localized to the endoplasmic reticulum (ER) and lipid droplets (LDs) and is [...] Read more.
Human noroviruses (HuNVs) are the leading cause of gastroenteritis worldwide. NS1.2 is critical for HuNV pathogenesis, but the function is still unclear. The GII NS1.2 of HuNVs, unlike GI NS1.2, was localized to the endoplasmic reticulum (ER) and lipid droplets (LDs) and is accompanied by a distorted-filamentous ER morphology and aggregated-enlarged LDs. LC3 was recruited to the NS1.2-localized membrane through an autophagy-independent pathway. NS1.2, expressed from a cDNA clone of GII.4 norovirus, formed complexes with NTPase and NS4, which exhibited aggregated vesicle-like structures that were also colocalized with LC3 and LDs. NS1.2 is structurally divided into three domains from the N terminus: an inherently disordered region (IDR), a region that contains a putative hydrolase with the H-box/NC catalytic center (H-box/NC), and a C-terminal 251–330 a.a. region containing membrane-targeting domain. All three functional domains of NS1.2 were required for the induction of the filamentous ER. The IDR was essential for LC3 recruitment by NS1.2. Both the H-Box/NC and membrane-targeting domains are required for the induction of aggregated-enlarged LDs, NS1.2 self-assembly, and interaction with NTPase. The membrane-targeting domain was sufficient to interact with NS4. The study characterized the NS1.2 domain required for membrane targeting and protein–protein interactions, which are crucial for forming a viral replication complex. Full article
(This article belongs to the Special Issue Viral Gastroenteritis 2022)
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14 pages, 1655 KiB  
Article
Co-Surveillance of Rotaviruses in Humans and Domestic Animals in Central Uganda Reveals Circulation of Wide Genotype Diversity in the Animals
by Josephine Bwogi, Charles Karamagi, Denis Karuhize Byarugaba, Phionah Tushabe, Sarah Kiguli, Prossy Namuwulya, Samuel S. Malamba, Khuzwayo C. Jere, Ulrich Desselberger and Miren Iturriza-Gomara
Viruses 2023, 15(3), 738; https://doi.org/10.3390/v15030738 - 13 Mar 2023
Cited by 2 | Viewed by 1728
Abstract
Rotavirus genotypes are species specific. However, interspecies transmission is reported to result in the emergence of new genotypes. A cross-sectional study of 242 households with 281 cattle, 418 goats, 438 pigs, and 258 humans in Uganda was undertaken between 2013 and 2014. The [...] Read more.
Rotavirus genotypes are species specific. However, interspecies transmission is reported to result in the emergence of new genotypes. A cross-sectional study of 242 households with 281 cattle, 418 goats, 438 pigs, and 258 humans in Uganda was undertaken between 2013 and 2014. The study aimed to determine the prevalence and genotypes of rotaviruses across co-habiting host species, as well as potential cross-species transmission. Rotavirus infection in humans and animals was determined using NSP3 targeted RT-PCR and ProSpecT Rotavirus ELISA tests, respectively. Genotyping of rotavirus-positive samples was by G- and P-genotype specific primers in nested RT-PCR assays while genotyping of VP4 and VP7 proteins for the non-typeable human positive sample was done by Sanger sequencing. Mixed effect logistic regression was used to determine the factors associated with rotavirus infection in animals. The prevalence of rotavirus was 4.1% (95% CI: 3.0–5.5%) among the domestic animals and 0.8% (95% CI: 0.4–1.5%) in humans. The genotypes in human samples were G9P[8] and P[4]. In animals, six G-genotypes, G3(2.5%), G8(10%), G9(10%), G11(26.8%), G10(35%), and G12(42.5%), and nine P-genotypes, P[1](2.4%), P[4](4.9%), P[5](7.3%), P[6](14.6%), P[7](7.3%), P[8](9.8%), P[9](9.8%), P[10](12.2%), and P[11](17.1%), were identified. Animals aged 2 to 18 months were less likely to have rotavirus infection in comparison with animals below 2 months of age. No inter-host species transmission was identified. Full article
(This article belongs to the Special Issue Viral Gastroenteritis 2022)
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34 pages, 4219 KiB  
Article
Genomic Constellation of Human Rotavirus G8 Strains in Brazil over a 13-Year Period: Detection of the Novel Bovine-like G8P[8] Strains with the DS-1-like Backbone
by Roberta Salzone Medeiros, Yasmin França, Ellen Viana, Lais Sampaio de Azevedo, Raquel Guiducci, Daniel Ferreira de Lima Neto, Antonio Charlys da Costa and Adriana Luchs
Viruses 2023, 15(3), 664; https://doi.org/10.3390/v15030664 - 01 Mar 2023
Cited by 4 | Viewed by 1722
Abstract
Rotavirus (RVA) G8 is frequently detected in animals, but only occasionally in humans. G8 strains, however, are frequently documented in nations in Africa. Recently, an increase in G8 detection was observed outside Africa. The aims of the study were to monitor G8 infections [...] Read more.
Rotavirus (RVA) G8 is frequently detected in animals, but only occasionally in humans. G8 strains, however, are frequently documented in nations in Africa. Recently, an increase in G8 detection was observed outside Africa. The aims of the study were to monitor G8 infections in the Brazilian human population between 2007 and 2020, undertake the full-genotype characterization of the four G8P[4], six G8P[6] and two G8P[8] RVA strains and conduct phylogenetic analysis in order to understand their genetic diversity and evolution. A total of 12,978 specimens were screened for RVA using ELISA, PAGE, RT-PCR and Sanger sequencing. G8 genotype represented 0.6% (15/2434) of the entirely RVA-positive samples. G8P[4] comprised 33.3% (5/15), G8P[6] 46.7% (7/15) and G8P[8] 20% (3/15). All G8 strains showed a short RNA pattern. All twelve selected G8 strains displayed a DS-1-like genetic backbone. The whole-genotype analysis on a DS-1-like backbone identified four different genotype-linage constellations. According to VP7 analysis, the Brazilian G8P[8] strains with the DS-1-like backbone strains were derived from cattle and clustered with newly DS-1-like G1/G3/G9/G8P[8] strains and G2P[4] strains. Brazilian IAL-R193/2017/G8P[8] belonged to a VP1/R2.XI lineage and were grouped with bovine-like G8P[8] strains with the DS-1-like backbone strains detected in Asia. Otherwise, the Brazilian IAL-R558/2017/G8P[8] possess a “Distinct” VP1/R2 lineage never previously described and grouped apart from any of the DS-1-like reference strains. Collectively, our findings suggest that the Brazilian bovine-like G8P[8] strains with the DS-1-like backbone strains are continuously evolving and likely reassorting with local RVA strains rather than directly relating to imports from Asia. The Brazilian G8P[6]-DS-1-like strains have been reassorted with nearby co-circulating American strains of the same DS-1 genotype constellation. However, phylogenetic analyses revealed that these strains have some genetic origin from Africa. Finally, rather than being African-born, Brazilian G8P[4]-DS-1-like strains were likely imported from Europe. None of the Brazilian G8 strains examined here exhibited signs of recent zoonotic reassortment. G8 strains continued to be found in Brazil according to their intermittent and localized pattern, thus, does not suggest that a potential emergence is taking place in the country. Our research demonstrates the diversity of G8 RVA strains in Brazil and adds to the understanding of G8P[4]/P[6]/P[8] RVA genetic diversity and evolution on a global scale. Full article
(This article belongs to the Special Issue Viral Gastroenteritis 2022)
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10 pages, 1395 KiB  
Article
Genetic Diversity of Norovirus in Children with Acute Gastroenteritis in Southwest Nigeria, 2015–2017
by Kafayat O. Arowolo, Christianah I. Ayolabi, Isaac A. Adeleye, Bruna A. Lapinski, Jucelia S. Santos and Sonia M. Raboni
Viruses 2023, 15(3), 644; https://doi.org/10.3390/v15030644 - 28 Feb 2023
Cited by 2 | Viewed by 1778
Abstract
Norovirus (NoV) is a leading cause of viral gastroenteritis globally, especially in children below five years. Epidemiological studies on the diversity of NoV in middle- and low-income countries, including Nigeria, are limited. This study aimed to determine the genetic diversity of NoV in [...] Read more.
Norovirus (NoV) is a leading cause of viral gastroenteritis globally, especially in children below five years. Epidemiological studies on the diversity of NoV in middle- and low-income countries, including Nigeria, are limited. This study aimed to determine the genetic diversity of NoV in children below five years with acute gastroenteritis at three hospitals in Ogun State, Nigeria. A total of 331 fecal samples were collected from February 2015 to April 2017, while 175 were randomly selected and analyzed using RT-PCR, partial sequencing and phylogenetic analyses of both the polymerase (RdRp) and capsid (VP1) genes. NoV was detected in 5.1% (9/175; RdRp) and 2.3% (4/175; VP1) of samples, with 55.6% (5/9) co-infection with other enteric viruses. A diverse genotype distribution was identified, and GII.P4 was the dominant RdRp genotype detected (66.7%), with two genetic clusters, followed by GII.P31 (22.2%). The rare GII.P30 genotype (11.1%) was detected at a low rate for the first time in Nigeria. Based on the VP1 gene, GII.4 was the dominant genotype (75%), with two variants, Sydney 2012 and possibly New Orleans 2009, co-circulating during the study. Interestingly, both intergenotypic, GII.12(P4) and GII.4 New Orleans(P31), and intra-genotypic, GII.4 Sydney(P4) and GII.4 New Orleans(P4), putative recombinant strains were observed. This finding suggests the first likely report of GII.4 New Orleans(P31) in Nigeria. In addition, GII.12(P4) was first described in Africa and globally in this study, to the best of our knowledge. This study provided insights into the genetic diversity of NoV circulating in Nigeria, which would be useful for ongoing and future vaccine design and monitoring of emerging genotypes and recombinant strains. Full article
(This article belongs to the Special Issue Viral Gastroenteritis 2022)
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18 pages, 2297 KiB  
Article
Genomic Analysis of G2P[4] Group A Rotaviruses in Zambia Reveals Positive Selection in Amino Acid Site 7 of Viral Protein 3
by Peter N. Mwangi, Robyn-Lee Potgieter, Julia Simwaka, Evans M. Mpabalwani, Jason M. Mwenda, Milton T. Mogotsi, Nonkululeko Magagula, Mathew D. Esona, A. Duncan Steele, Mapaseka L. Seheri and Martin M. Nyaga
Viruses 2023, 15(2), 501; https://doi.org/10.3390/v15020501 - 11 Feb 2023
Cited by 1 | Viewed by 1723
Abstract
The G2P[4] genotype is among the rotavirus strains that circulate commonly in humans. Several countries have reported its immediate upsurge after the introduction of rotavirus vaccination, raising concern about sub-optimal vaccine effectiveness against this genotype in the long term. This study aimed to [...] Read more.
The G2P[4] genotype is among the rotavirus strains that circulate commonly in humans. Several countries have reported its immediate upsurge after the introduction of rotavirus vaccination, raising concern about sub-optimal vaccine effectiveness against this genotype in the long term. This study aimed to gain insight into the evolution of post-vaccine Zambian G2P[4] group A rotavirus (RVA) strains and their overall genetic make-up by analysis of sequence alignments at the amino acid (AA) level. Twenty-nine Zambian G2P[4] rotavirus strains were subjected to whole-genome sequencing using the Illumina MiSeq® platform. All the strains exhibited the typical DS-1-like genotype constellation, and the nucleotide sequences of the 11 genome segments showed high nucleotide similarities (>97%). Phylogenetic analyses together with representative global G2P[4] RVA showed that Zambian strains clustered into human lineages IV (for VP2, VP4, VP7, NSP1, and NSP5), V (for VP1, VP3, VP6, NSP2, and NSP3), and XXIII (for NSP4). The AA differences between the lineages where the study strains clustered and lineages of global reference strains were identified and analyzed. Selection pressure analysis revealed that AA site seven in the Viral Protein 3 (VP3) genome segment was under positive selection. This site occurs in the region of intrinsic disorder in the VP3 protein, and Zambian G2P[4] strains could potentially be utilizing this intrinsically disordered region to survive immune pressure. The Zambian G2P[4] strains from 2012 to 2016 comprised the G2P[4] strains that have been circulating globally since the early 2000s, highlighting the epidemiological fitness of these contemporary G2P[4] strains. Continuous whole-genome surveillance of G2P[4] strains remains imperative to understand their evolution during the post-vaccination period. Full article
(This article belongs to the Special Issue Viral Gastroenteritis 2022)
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14 pages, 563 KiB  
Article
The Association between Symptomatic Rotavirus Infection and Histo-Blood Group Antigens in Young Children with Diarrhea in Pretoria, South Africa
by Kebareng Rakau, Maemu Gededzha, Ina Peenze, Pengwei Huang, Ming Tan, Andrew Duncan Steele and Luyanda Mapaseka Seheri
Viruses 2022, 14(12), 2735; https://doi.org/10.3390/v14122735 - 08 Dec 2022
Cited by 2 | Viewed by 1614
Abstract
Objectives: Recently, histo-blood group antigens (HBGAs) have been identified as receptors or attachment factors of several viral pathogens. Among rotaviruses, HBGAs interact with the outer viral protein, VP4, which has been identified as a potential susceptibility factor, although the findings are inconsistent throughout [...] Read more.
Objectives: Recently, histo-blood group antigens (HBGAs) have been identified as receptors or attachment factors of several viral pathogens. Among rotaviruses, HBGAs interact with the outer viral protein, VP4, which has been identified as a potential susceptibility factor, although the findings are inconsistent throughout populations due to HBGA polymorphisms. We investigated the association between HBGA phenotypes and rotavirus infection in children with acute gastroenteritis in northern Pretoria, South Africa. Methods: Paired diarrheal stool and saliva samples were collected from children aged ≤ 59 months (n = 342) with acute moderate to severe diarrhea, attending two health care facilities. Rotaviruses in the stool samples were detected by commercial EIA and the rotavirus strains were characterized by RT-PCR targeting the outer capsid VP7 (G-type) and VP4 (P-type) antigens for genotyping. Saliva-based ELISAs were performed to determine A, B, H, and Lewis antigens for blood group typing. Results: Blood type O was the most common blood group (62.5%) in this population, followed by groups A (26.0%), B (9.3%), and AB (2.2%). The H1-based secretors were common (82.7%) compared to the non-secretors (17.3%), and the Lewis antigen positive phenotypes (Le(a+b+)) were predominant (54.5%). Blood type A children were more likely to be infected by rotavirus (38.8%) than any other blood types. P[4] rotaviruses (21/49; 42.9%) infected only secretor individuals, whereas P[6] rotaviruses (3/49; 6.1%) only infected Le(a−b−), although the numbers were very low. On the contrary, P[8] rotaviruses infected children with a wide range of blood group phenotypes, including Le(a−b−) and non-secretors. Conclusions: Our findings demonstrated that Lewis antigens, or the lack thereof, may serve as susceptibility factors to rotaviral infection by specific VP4 genotypes as observed elsewhere. Potentially, the P[8] strains remain the predominant human VP4 genotype due to their ability to bind to a variety of HBGA phenotypes. Full article
(This article belongs to the Special Issue Viral Gastroenteritis 2022)
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17 pages, 3008 KiB  
Article
Detection and Molecular Characterization of Enteric Viruses in Bivalve Mollusks Collected in Arraial do Cabo, Rio de Janeiro, Brazil
by Lilian Gonçalves do Nascimento, Sylvia Kahwage Sarmento, Raphael Leonardo, Meylin Bautista Gutierrez, Fábio Correia Malta, Jaqueline Mendes de Oliveira, Caroline Rezende Guerra, Ricardo Coutinho, Marize Pereira Miagostovich and Tulio Machado Fumian
Viruses 2022, 14(11), 2359; https://doi.org/10.3390/v14112359 - 26 Oct 2022
Cited by 5 | Viewed by 2331
Abstract
Viral bivalve contamination is a recognized food safety hazard. Therefore, this study investigated the detection rates, seasonality, quantification, and genetic diversity of enteric viruses in bivalve samples (mussels and oysters). We collected 97 shellfish samples between March 2018 and February 2020. The screening [...] Read more.
Viral bivalve contamination is a recognized food safety hazard. Therefore, this study investigated the detection rates, seasonality, quantification, and genetic diversity of enteric viruses in bivalve samples (mussels and oysters). We collected 97 shellfish samples between March 2018 and February 2020. The screening of samples by qPCR or RT-qPCR revealed the detection of norovirus (42.3%), rotavirus A (RVA; 16.5%), human adenovirus (HAdV; 24.7%), and human bocavirus (HBoV; 13.4%). There was no detection of hepatitis A virus. In total, 58.8% of shellfish samples tested positive for one or more viruses, with 42.1% of positive samples contaminated with two or more viruses. Norovirus showed the highest median viral load (3.3 × 106 GC/g), followed by HAdV (median of 3.5 × 104 GC/g), RVA (median of 1.5 × 103 GC/g), and HBoV (median of 1.3 × 103 GC/g). Phylogenetic analysis revealed that norovirus strains belonged to genotype GII.12[P16], RVA to genotype I2, HAdV to types -C2, -C5, and -F40, and HBoV to genotypes -1 and -2. Our results demonstrate the viral contamination of bivalves, emphasizing the need for virological monitoring programs to ensure the quality and safety of shellfish for human consumption and as a valuable surveillance tool to monitor emerging viruses and novel variants. Full article
(This article belongs to the Special Issue Viral Gastroenteritis 2022)
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6 pages, 926 KiB  
Article
Phylogeography of Rotavirus G8P[8] Detected in Argentina: Evidence of Transpacific Dissemination
by Juan Ignacio Degiuseppe, Carolina Torres, Viviana Andrea Mbayed and Juan Andrés Stupka
Viruses 2022, 14(10), 2223; https://doi.org/10.3390/v14102223 - 09 Oct 2022
Cited by 4 | Viewed by 1575
Abstract
Rotavirus is one of the leading causes of diarrhea in children. In 2018, G8P[8], an unusual association of genotypes, was detected with moderate frequency in symptomatic children in Argen-tina, unlike a previous sporadic identification in 2016. The aim of this study was to [...] Read more.
Rotavirus is one of the leading causes of diarrhea in children. In 2018, G8P[8], an unusual association of genotypes, was detected with moderate frequency in symptomatic children in Argen-tina, unlike a previous sporadic identification in 2016. The aim of this study was to analyze the dissemination pattern of the G8P[8]-lineage IV strains detected in Argentina. Nucleotide sequences of the VP7 gene of Argentine G8P[8] strains (2016, 2018 and 2019) were studied by discrete phylodynamic analyses, together with other worldwide relevant G8-lineage IV strains. Bayes Factor (BF) was used to assess the strength of the epidemiological association between countries. Phylodynamic analyses determined an evolutionary rate of 3.7 × 10−3 (HDP95%: 1.4 × 10−3–8.2 × 10−3) substitutions/site/year. Likewise, the most recent common ancestor was 32.2 years old, dating back to 1986 (HDP95% = 1984–1988). The spatiotemporal dynamics analysis revealed South Korea as being the country of origin of the Argentine strains (posterior probability of the ancestral state: 0.8471), which was also evidenced by a significant rate of diffusion from South Korea to Argentina (BF: 55.1). The detection of G8 in South America in 2016–2017 was not related to the cases detected in 2018–2019, revealing a new G8 introduction to the region and supporting a transpacific dissemination. Full article
(This article belongs to the Special Issue Viral Gastroenteritis 2022)
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12 pages, 1397 KiB  
Article
Isolation and Genotyping of Adenoviruses from Wastewater and Diarrheal Samples in Egypt from 2016 to 2020
by Abdou Kamal Allayeh, Sahar Abd Al-Daim, Nehal Ahmed, Mona El-Gayar and Ahmed Mostafa
Viruses 2022, 14(10), 2192; https://doi.org/10.3390/v14102192 - 04 Oct 2022
Cited by 7 | Viewed by 2244
Abstract
Human adenoviruses (HAdV) are a prevalent cause of diarrhea in children all over the world. Adenoviral infections are responsible for 2% to 10% of diarrheic cases. A long-term investigation was required to gain better knowledge about the incidence of HAdV in Egypt. Herein, [...] Read more.
Human adenoviruses (HAdV) are a prevalent cause of diarrhea in children all over the world. Adenoviral infections are responsible for 2% to 10% of diarrheic cases. A long-term investigation was required to gain better knowledge about the incidence of HAdV in Egypt. Herein, we conducted 5 years of detection, isolation, and genotyping of HAdV in fecal and sewage samples from 2016 to 2020, in Cairo, Egypt using molecular and cell culture assays. Human adenoviruses were identified in 35 of 447 fecal samples (7.8%), but only 53.3% (64/120) of the sewage samples. Children under the age of two had the highest positive rate for HAdV infection (77.1%). Species F of HAdV was the most common prevalent genotype in fecal and sewage samples, at 88.5% and 85.9%, respectively. The most prevalent genotypes detected in fecal samples were HAdV-41 (71.2%), HAdV-40 (17.2%), HAdV-6 (5.7%), and HAdV-1 (5.7%). In contrast, the most common genotypes in sewage samples were HAdV-41 (64%), HAdVs-40 (21.8%), HAdV-6 (7.8%), HAdV-1 (4.7%), and HAdV-2 (1.6%). HAdV was detected in all months of the year, with a peak period for clinical samples from December to February (p < 0.001), which matched Egypt’s rainy season, while the monthly distribution of HAdV in sewage samples remained consistent throughout the year, with no statistically significant peak period. Interestingly, the HAdV-type 41 genotype was the most common genotype during all of the years of this study. Throughout a 5-year period, our work revealed the infection rate, seasonal distribution, virus isolates, and genetic diversity of HAdV infections in environmental and clinical samples in Cairo, Egypt. Non-enteric adenovirus types (1, 2 and 6), as well as enteric adenovirus (41 and 40), may play a key role in gastroenteritis in Egypt. Full article
(This article belongs to the Special Issue Viral Gastroenteritis 2022)
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15 pages, 1777 KiB  
Article
Long Term Norovirus Infection in a Patient with Severe Common Variable Immunodeficiency
by Loa Ottosson, Marie Hagbom, Rikard Svernlöv, Sofia Nyström, Beatrice Carlsson, Mattias Öman, Magnus Ström, Lennart Svensson, Åsa Nilsdotter-Augustinsson and Johan Nordgren
Viruses 2022, 14(8), 1708; https://doi.org/10.3390/v14081708 - 02 Aug 2022
Cited by 3 | Viewed by 2615
Abstract
Norovirus is the most common cause of acute non-bacterial gastroenteritis. Immunocompromised patients can become chronically infected, with or without symptoms. In Europe, common variable immunodeficiency (CVID) is one of the most common inborn errors of immunity. A potentially severe complication is CVID-associated enteropathy, [...] Read more.
Norovirus is the most common cause of acute non-bacterial gastroenteritis. Immunocompromised patients can become chronically infected, with or without symptoms. In Europe, common variable immunodeficiency (CVID) is one of the most common inborn errors of immunity. A potentially severe complication is CVID-associated enteropathy, a disorder with similar histopathology to celiac disease. Studies suggest that chronic norovirus infection may be a contributor to CVID enteropathy, and that the antiviral drug ribavirin can be effective against norovirus. Here, a patient with CVID-like disease with combined B- and T-cell deficiency, had chronic norovirus infection and enteropathy. The patient was routinely administered subcutaneous and intravenous immunoglobulin replacement therapy (SCIg and IVIg). The patient was also administered ribavirin for ~7.5 months to clear the infection. Stool samples (collected 2013–2016) and archived paraffin embedded duodenal biopsies were screened for norovirus by qPCR, confirming a chronic infection. Norovirus genotyping was done in 25 stool samples. For evolutionary analysis, the capsid (VP1) and polymerase (RdRp) genes were sequenced in 10 and 12 stool samples, respectively, collected before, during, and after ribavirin treatment. Secretor phenotyping was done in saliva, and serum was analyzed for histo-blood group antigen (HBGA) blocking titers. The chronic norovirus strain formed a unique variant subcluster, with GII.4 Den Haag [P4] variant, circulating around 2009, as the most recent common ancestor. This corresponded to the documented debut of symptoms. The patient was a secretor and had HBGA blocking titers associated with protection in immunocompetent individuals. Several unique amino acid substitutions were detected in immunodominant epitopes of VP1. However, HBGA binding sites were conserved. Ribavirin failed in treating the infection and no clear association between ribavirin-levels and quantity of norovirus shedding was observed. In conclusion, long term infection with norovirus in a patient with severe CVID led to the evolution of a unique norovirus strain with amino acid substitutions in immunodominant epitopes, but conservation within HBGA binding pockets. Regularly administered SCIg, IVIg, and ~7.5-month ribavirin treatment failed to clear the infection. Full article
(This article belongs to the Special Issue Viral Gastroenteritis 2022)
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12 pages, 1615 KiB  
Article
A New Circular Single-Stranded DNA Virus Related with Howler Monkey Associated Porprismacovirus 1 Detected in Children with Acute Gastroenteritis
by Fabiola Villanova, Flávio Augusto de Padua Milagres, Rafael Brustulin, Emerson Luiz Lima Araújo, Ramendra Pati Pandey, V. Samuel Raj, Xutao Deng, Eric Delwart, Adriana Luchs, Antonio Charlys da Costa and Élcio Leal
Viruses 2022, 14(7), 1472; https://doi.org/10.3390/v14071472 - 04 Jul 2022
Cited by 2 | Viewed by 1771
Abstract
Putative replication-associated protein (REP) and capsid-like (CAP) proteins are encoded by circular single-stranded DNA viruses (CRESS DNA), which have been found in samples from most eukaryotic groups. However, the details of these viruses’ life cycles and their significance in diseases have yet to [...] Read more.
Putative replication-associated protein (REP) and capsid-like (CAP) proteins are encoded by circular single-stranded DNA viruses (CRESS DNA), which have been found in samples from most eukaryotic groups. However, the details of these viruses’ life cycles and their significance in diseases have yet to be established. We presented and analyzed two full-length CRESS DNA genomes acquired from two children diagnosed with acute gastroenteritis (GI) in the northeast state of Tocantins, Brazil, using next-generation sequencing and a virus-like filtration approach. Both sequences (named SmaCV3BR08 and SmaCV3BR291) are closely similar to a prior CRESS DNA sequence discovered in the feces of a new world monkey (Alouatta caraya) from the United States in 2009 and termed Howler monkey-associated porprismacovirus 1 (Genbank ID: NC 026317). According to our comparative study, these porprismacovirus genomes deviate by 10% at the nucleotide level. For comparative reasons, the divergence between our sequences (SmaCV3BR08 and SmaCV3BR291) and a porprismacovirus recently identified in a human fecal sample from Peru is 37%. These data suggest that there is a great diversity of porprismacoviruses in South America, perhaps more than two species. In addition, the finding of closely related sequences of porprismacoviruses in humans and native monkeys highlights the zoonotic potential of these viruses. Full article
(This article belongs to the Special Issue Viral Gastroenteritis 2022)
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Review

Jump to: Research, Other

26 pages, 488 KiB  
Review
Zoonotic RVA: State of the Art and Distribution in the Animal World
by Ricardo Gabriel Díaz Alarcón, Domingo Javier Liotta and Samuel Miño
Viruses 2022, 14(11), 2554; https://doi.org/10.3390/v14112554 - 18 Nov 2022
Cited by 13 | Viewed by 2334
Abstract
Rotavirus species A (RVA) is a pathogen mainly affecting children under five years old and young animals. The infection produces acute diarrhea in its hosts and, in intensively reared livestock animals, can cause severe economic losses. In this study, we analyzed all RVA [...] Read more.
Rotavirus species A (RVA) is a pathogen mainly affecting children under five years old and young animals. The infection produces acute diarrhea in its hosts and, in intensively reared livestock animals, can cause severe economic losses. In this study, we analyzed all RVA genomic constellations described in animal hosts. This review included animal RVA strains in humans. We compiled detection methods, hosts, genotypes and complete genomes. RVA was described in 86 animal species, with 52% (45/86) described by serology, microscopy or the hybridization method; however, strain sequences were not described. All of these reports were carried out between 1980 and 1990. In 48% (41/86) of them, 9251 strain sequences were reported, with 28% being porcine, 27% bovine, 12% equine and 33% from several other animal species. Genomic constellations were performed in 80% (32/40) of hosts. Typical constellation patterns were observed in groups such as birds, domestic animals and artiodactyls. The analysis of the constellations showed RVA’s capacity to infect a broad range of species, because there are RVA genotypes (even entire constellations) from animal species which were described in other studies. This suggests that this virus could generate highly virulent variants through gene reassortments and that these strains could be transmitted to humans as a zoonotic disease, making future surveillance necessary for the prevention of future outbreaks. Full article
(This article belongs to the Special Issue Viral Gastroenteritis 2022)

Other

Jump to: Research, Review

13 pages, 293 KiB  
Conference Report
The Challenges and Opportunities of Next-Generation Rotavirus Vaccines: Summary of an Expert Meeting with Vaccine Developers
by Jessie Chen, Stephanie Grow, Miren Iturriza-Gómara, William P. Hausdorff, Alan Fix and Carl D. Kirkwood
Viruses 2022, 14(11), 2565; https://doi.org/10.3390/v14112565 - 19 Nov 2022
Cited by 4 | Viewed by 1998
Abstract
The 2nd Next Generation Rotavirus Vaccine Developers Meeting, sponsored by PATH and the Bill and Melinda Gates Foundation, was held in London, UK (7–8 June 2022), and attended by vaccine developers and researchers to discuss advancements in the development of next-generation rotavirus vaccines [...] Read more.
The 2nd Next Generation Rotavirus Vaccine Developers Meeting, sponsored by PATH and the Bill and Melinda Gates Foundation, was held in London, UK (7–8 June 2022), and attended by vaccine developers and researchers to discuss advancements in the development of next-generation rotavirus vaccines and to consider issues surrounding vaccine acceptability, introduction, and uptake. Presentations included updates on rotavirus disease burden, the impact of currently licensed oral vaccines, various platforms and approaches for next generation rotavirus vaccines, strategies for combination pediatric vaccines, and the value proposition for novel parenteral rotavirus vaccines. This report summarizes the information shared at the convening and poses various topics worthy of further exploration. Full article
(This article belongs to the Special Issue Viral Gastroenteritis 2022)
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