Gastroenteritis Viruses 2021

A special issue of Viruses (ISSN 1999-4915). This special issue belongs to the section "Animal Viruses".

Deadline for manuscript submissions: closed (15 January 2022) | Viewed by 28915

Special Issue Editor

Departament Genètica, Microbiologia i Estadística, Secció Microbiologia, Virologia i Biotecnologia, Facultat Biologia, Universitat de Barcelona, Avda Diagonal 643, 08028 Barcelona, Spain
Interests: norovirus; astrovirus; hepatitis A and E viruses; environmental and food virology; epidemiology; virus-host interactions
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Special Issue Information

Dear Colleagues,

Viral gastroenteritis has an immense impact on global public health, with rotaviruses, noroviruses, astroviruses, sapoviruses, enteroviruses and coronaviruses amongst the etiological agents. Tremendous advances in the last several decades, such as for instance the implementation of rotavirus vaccine, have contributed to undoubted improvements in the control of these pathogens, but new emerging viruses, including SARS-CoV-2, have been related to gastrointestinal symptoms in a large proportion of patients, posing new challenges to the field.  

In this Special Issue, we will cover the following topics of interest for the understanding of the interplay between gastroenteritis disease and viral infections: burden assessment and epidemiology, diagnostics, basic molecular and cell virology, pathogenesis, host response and host factors affecting infection outcome, extra-intestinal dissemination, control and prevention measures, emergence and evolution, the role of animal reservoirs, and the use of metagenomics for novel gastroenteritis virus discoveries. 

Dr. Susana Guix
Guest Editor

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Keywords

  • epidemiology
  • diagnostic
  • basic Virology
  • virus-Host interactions
  • microbiome
  • extraintestinal dissemination
  • vaccines
  • control and prevention
  • emergence and evolution
  • animal reservoirs and zoonosis
  • viral discovery

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Published Papers (10 papers)

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Research

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10 pages, 2563 KiB  
Article
Enteric Viruses Nucleic Acids Distribution along the Digestive Tract of Rhesus Macaques with Idiopathic Chronic Diarrhea
by Eric Delwart, David Merriam, Amir Ardeshir, Eda Altan, Yanpeng Li, Xutao Deng and Dennis J. Hartigan-O’Connor
Viruses 2022, 14(3), 638; https://0-doi-org.brum.beds.ac.uk/10.3390/v14030638 - 19 Mar 2022
Viewed by 1750
Abstract
Idiopathic chronic diarrhea (ICD) is a little understood common clinical problem in captive rhesus macaques claiming 33% of medical culls unrelated to research. The eukaryotic virome in digestive tract tissues collected at necropsy from nine animals with ICD was characterized using viral metagenomics. [...] Read more.
Idiopathic chronic diarrhea (ICD) is a little understood common clinical problem in captive rhesus macaques claiming 33% of medical culls unrelated to research. The eukaryotic virome in digestive tract tissues collected at necropsy from nine animals with ICD was characterized using viral metagenomics. We compared the distribution of viral reads in tissues and mucosal scrapings from the stomach, duodenum, jejunum, ileum, and the proximal, transverse, and distal colons. In situ hybridization (ISH) using viral probes were performed on fixed tissues. Deep sequencing revealed multiple viruses in the Parvoviridae and Picornaviridae family. Tissues and mucosal scraping from the same locations showed closely related viral reads contents while different gut tissues from the same animal varied widely. ISH showed punctuated staining for both RNA and DNA viruses in the distal colon. Parvovirus staining was also detected in the stomach/duodenum/jejunum in distinct oval-shaped structures. The location of enteric viral nucleic acid differed widely between different viral families and along the length of the digestive tract. Full article
(This article belongs to the Special Issue Gastroenteritis Viruses 2021)
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12 pages, 2201 KiB  
Article
Novel Cyclovirus Species in Dogs with Hemorrhagic Gastroenteritis
by Kerry Gainor, Yashpal S. Malik and Souvik Ghosh
Viruses 2021, 13(11), 2155; https://0-doi-org.brum.beds.ac.uk/10.3390/v13112155 - 26 Oct 2021
Cited by 3 | Viewed by 2335
Abstract
Nested PCRs with circovirus/cyclovirus pan-rep (replicase gene) primers detected eukaryotic circular Rep-encoding single-stranded DNA (CRESS DNA) viruses in three (samples CN9E, CN16E and CN34) of 18 canine parvovirus-2-positive fecal samples from household dogs with hemorrhagic gastroenteritis on the Caribbean island of Nevis. [...] Read more.
Nested PCRs with circovirus/cyclovirus pan-rep (replicase gene) primers detected eukaryotic circular Rep-encoding single-stranded DNA (CRESS DNA) viruses in three (samples CN9E, CN16E and CN34) of 18 canine parvovirus-2-positive fecal samples from household dogs with hemorrhagic gastroenteritis on the Caribbean island of Nevis. The complete genomes of CRESS DNA virus CN9E, CN16E and CN34 were determined by inverse nested PCRs. Based on (i) genome organization, (ii) location of the putative origin of replication, (iii) pairwise genome-wide sequence identities, (iv) the presence of conserved motifs in the putative replication-associated protein (Rep) and the arginine-rich region in the amino terminus of the putative capsid protein (Cp) and (v) a phylogenetic analysis, CN9E, CN16E and CN34 were classified as cycloviruses. Canine-associated cycloviruses CN16E and CN34 were closely related to each other and shared low genome-wide nucleotide (59.642–59.704%), deduced Rep (35.018–35.379%) and Cp (26.601%) amino acid sequence identities with CN9E. All the three canine-associated cycloviruses shared < 80% genome-wide pairwise nucleotide sequence identities with cycloviruses from other animals/environmental samples, constituting two novel species (CN9E and CN16E/34) within the genus Cyclovirus. Considering the feeding habits of dogs, we could not determine whether the cycloviruses were of dietary origin or infected the host. Interestingly, the CN9E putative Rep-encoding open reading frame was found to use the invertebrate mitochondrial genetic code with an alternative initiation codon (ATA) for translation, corroborating the hypothesis that cycloviruses are actually arthropod-infecting viruses. To our knowledge, this is the first report on the detection and complete genome analysis of cycloviruses from domestic dogs. Full article
(This article belongs to the Special Issue Gastroenteritis Viruses 2021)
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15 pages, 5460 KiB  
Article
Norovirus Epidemiology and Genetic Diversity in Leipzig, Germany during 2013–2017
by Nora Ennuschat, Sabine Härtel, Corinna Pietsch and Uwe G. Liebert
Viruses 2021, 13(10), 1961; https://0-doi-org.brum.beds.ac.uk/10.3390/v13101961 - 29 Sep 2021
Cited by 7 | Viewed by 1837
Abstract
Globally and in all age groups, noroviruses are a main cause of gastroenteritis. To assess their local epidemiology and genetic diversity, stool samples of 7509 inpatients with gastrointestinal complaints from all age groups were analyzed. After detection of norovirus genogroup I and II [...] Read more.
Globally and in all age groups, noroviruses are a main cause of gastroenteritis. To assess their local epidemiology and genetic diversity, stool samples of 7509 inpatients with gastrointestinal complaints from all age groups were analyzed. After detection of norovirus genogroup I and II RNA by real-time RT-PCR, viral capsids were genotyped by partial nucleic acid sequencing. In the case of GII.2 strains, polymerase genotypes were also assessed. Between October 2013 and September 2017, presence of norovirus RNA was shown in 611 samples (8.1%), of which 610 (99.8%) were typed successfully. Norovirus positivity rate was higher in patients aged below five years (14.8%) than in older patients (5.7%). Among the 611 norovirus positive samples, GII.4 (56.6%) strains prevailed, followed by GII.6 (11.3%), GII.3 (11.0%) and GII.2 (9.5%). The most common genogroup I (GGI) genotype was GI.3 (3.6%). In addition, rare genotypes such as GII.13, GII.14 and GII.26 were detected. Interestingly, GII.3 infections were most common in children under the age of five years. Assessment of polymerase genotypes in GII.2 viruses showed a shift from P2 to P16, with higher diversity in P2 sequences. The varying distribution of norovirus genotypes depending on season, age and setting of infection highlights the importance of frequent genotyping as a basis for vaccine development and needful adjustments. Full article
(This article belongs to the Special Issue Gastroenteritis Viruses 2021)
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19 pages, 1358 KiB  
Article
Whole Genome Analysis of Human Rotaviruses Reveals Single Gene Reassortant Rotavirus Strains in Zambia
by Wairimu M. Maringa, Julia Simwaka, Peter N. Mwangi, Evans M. Mpabalwani, Jason M. Mwenda, M. Jeffrey Mphahlele, Mapaseka L. Seheri and Martin M. Nyaga
Viruses 2021, 13(9), 1872; https://0-doi-org.brum.beds.ac.uk/10.3390/v13091872 - 18 Sep 2021
Cited by 11 | Viewed by 2538
Abstract
Rotarix® vaccine was implemented nationwide in Zambia in 2013. In this study, four unusual strains collected in the post-vaccine period were subjected to whole genome sequencing and analysis. The four strains possessed atypical genotype constellations, with at least one reassortant genome segment [...] Read more.
Rotarix® vaccine was implemented nationwide in Zambia in 2013. In this study, four unusual strains collected in the post-vaccine period were subjected to whole genome sequencing and analysis. The four strains possessed atypical genotype constellations, with at least one reassortant genome segment within the constellation. One of the strains (UFS-NGS-MRC-DPRU4749) was genetically and phylogenetically distinct in the VP4 and VP1 gene segments. Pairwise analyses demonstrated several amino acid disparities in the VP4 antigenic sites of this strain compared to that of Rotarix®. Although the impact of these amino acid disparities remains to be determined, this study adds to our understanding of the whole genomes of reassortant strains circulating in Zambia following Rotarix® vaccine introduction. Full article
(This article belongs to the Special Issue Gastroenteritis Viruses 2021)
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9 pages, 424 KiB  
Article
Human Astrovirus Outbreak in a Daycare Center and Propagation among Household Contacts
by Ignacio Parrón, Elsa Plasencia, Thais Cornejo-Sánchez, Mireia Jané, Cristina Pérez, Conchita Izquierdo, Susana Guix, Àngela Domínguez and on behalf of the Working Group for the Study of Acute Gastroenteritis Outbreaks in Catalonia
Viruses 2021, 13(6), 1100; https://0-doi-org.brum.beds.ac.uk/10.3390/v13061100 - 09 Jun 2021
Cited by 3 | Viewed by 2093
Abstract
We investigated an outbreak of acute gastroenteritis due to human astrovirus in a daycare center, describing the transmission mechanism, the most affected age groups, conditioning factors and the extent of the outbreak among household contacts of the daycare center attenders. Data were collected [...] Read more.
We investigated an outbreak of acute gastroenteritis due to human astrovirus in a daycare center, describing the transmission mechanism, the most affected age groups, conditioning factors and the extent of the outbreak among household contacts of the daycare center attenders. Data were collected from persons exposed at the daycare center and their home contacts. Fecal samples from affected and non-affected daycare center attenders were analyzed for viruses causing acute gastroenteritis by RT-PCR. The percentage of households affected and the attack rates (AR) were calculated. The attack rates were compared using the rate ratio (RR) with 95% confidence intervals. Information was obtained from 245 people (76 attenders and 169 contacts) of whom 49 were clinical cases. Five HAstV-4, two HAstV-8 and three non-typable HAstV cases were identified (six from clinical cases and four from asymptomatic infected people). The global AR was 20% (41.2% in children aged < 2 years). Data were obtained from 67 households: 20 households of affected attenders and 47 of non-affected attendees. Household contacts of affected attenders had a higher AR (74.3%) than that of non-affected attendees (2.4%). We found asymptomatic infections amongst daycare attendees. The transmission of HAstV during the outbreak was not limited to the daycare center but extended to household contacts of both affected and non-affected attenders. Full article
(This article belongs to the Special Issue Gastroenteritis Viruses 2021)
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14 pages, 2254 KiB  
Article
Evidence of Circulation of Several HAV Genetic Variants and Emergence of Potential Antigenic Variants in an Endemo-Epidemic Country before Vaccine Introduction
by Kaouther Ayouni, Anissa Chouikha, Oussema Khamessi, Henda Touzi, Walid Hammemi and Henda Triki
Viruses 2021, 13(6), 1056; https://0-doi-org.brum.beds.ac.uk/10.3390/v13061056 - 03 Jun 2021
Cited by 1 | Viewed by 2366
Abstract
Similar to several other countries in the world, the epidemiology of hepatitis A virus changed from high to intermediate endemicity level in Tunisia, which led to the occurrence of outbreaks. This study aimed to determine the genetic and antigenic variability of HAV strains [...] Read more.
Similar to several other countries in the world, the epidemiology of hepatitis A virus changed from high to intermediate endemicity level in Tunisia, which led to the occurrence of outbreaks. This study aimed to determine the genetic and antigenic variability of HAV strains circulating in Tunisia during the last few years. Genotyping using complete VP1 gene and VP1-2A junction confirmed the predominance of genotype IA, with co-circulation of several genetic and antigenic variants. Phylogenetic analysis including Tunisian and strains from other regions of the world showed the presence of at least two IA-variants within IA subgenotype. Amino-acid analysis showed several mutations in or close to epitope regions in the VP1-region. This study provides a baseline on the genetic and antigenic variability of HAV circulating strains before the introduction of vaccination into the national immunization schedule. Full article
(This article belongs to the Special Issue Gastroenteritis Viruses 2021)
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13 pages, 3960 KiB  
Article
Human Astroviruses: A Tale of Two Strains
by Virginia Hargest, Amy E. Davis, Shaoyuan Tan, Valerie Cortez and Stacey Schultz-Cherry
Viruses 2021, 13(3), 376; https://0-doi-org.brum.beds.ac.uk/10.3390/v13030376 - 27 Feb 2021
Cited by 9 | Viewed by 2819
Abstract
Since the 1970s, eight closely related serotypes of classical human astroviruses (HAstV) have been associated with gastrointestinal illness worldwide. In the late 2000s, three genetically unique human astrovirus clades, VA1-VA3, VA2-VA4, and MLB, were described. While the exact disease associated with these clades [...] Read more.
Since the 1970s, eight closely related serotypes of classical human astroviruses (HAstV) have been associated with gastrointestinal illness worldwide. In the late 2000s, three genetically unique human astrovirus clades, VA1-VA3, VA2-VA4, and MLB, were described. While the exact disease associated with these clades remains to be defined, VA1 has been associated with central nervous system infections. The discovery that VA1 could be grown in cell culture, supports exciting new studies aimed at understanding viral pathogenesis. Given the association of VA1 with often lethal CNS infections, we tested its susceptibility to the antimicrobial drug, nitazoxanide (NTZ), which we showed could inhibit classical HAstV infections. Our studies demonstrate that NTZ inhibited VA1 replication in Caco2 cells even when added at 12 h post-infection, which is later than in HAstV-1 infection. These data led us to further probe VA1 replication kinetics and cellular responses to infection in Caco-2 cells in comparison to the well-studied HAstV-1 strain. Overall, our studies highlight that VA1 replicates more slowly than HAstV-1 and elicits significantly different cellular responses, including the inability to disrupt cellular junctions and barrier permeability. Full article
(This article belongs to the Special Issue Gastroenteritis Viruses 2021)
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Review

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23 pages, 855 KiB  
Review
Serological Humoral Immunity Following Natural Infection of Children with High Burden Gastrointestinal Viruses
by Mark R. Zweigart, Sylvia Becker-Dreps, Filemón Bucardo, Fredman González, Ralph S. Baric and Lisa C. Lindesmith
Viruses 2021, 13(10), 2033; https://0-doi-org.brum.beds.ac.uk/10.3390/v13102033 - 09 Oct 2021
Cited by 11 | Viewed by 3270
Abstract
Acute gastroenteritis (AGE) is a major cause of morbidity and mortality worldwide, resulting in an estimated 440,571 deaths of children under age 5 annually. Rotavirus, norovirus, and sapovirus are leading causes of childhood AGE. A successful rotavirus vaccine has reduced rotavirus hospitalizations by [...] Read more.
Acute gastroenteritis (AGE) is a major cause of morbidity and mortality worldwide, resulting in an estimated 440,571 deaths of children under age 5 annually. Rotavirus, norovirus, and sapovirus are leading causes of childhood AGE. A successful rotavirus vaccine has reduced rotavirus hospitalizations by more than 50%. Using rotavirus as a guide, elucidating the determinants, breath, and duration of serological antibody immunity to AGE viruses, as well as host genetic factors that define susceptibility is essential for informing development of future vaccines and improving current vaccine candidates. Here, we summarize the current knowledge of disease burden and serological antibody immunity following natural infection to inform further vaccine development for these three high-burden viruses. Full article
(This article belongs to the Special Issue Gastroenteritis Viruses 2021)
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19 pages, 1161 KiB  
Review
Organoids to Dissect Gastrointestinal Virus–Host Interactions: What Have We Learned?
by Sue E. Crawford, Sasirekha Ramani, Sarah E. Blutt and Mary K. Estes
Viruses 2021, 13(6), 999; https://0-doi-org.brum.beds.ac.uk/10.3390/v13060999 - 27 May 2021
Cited by 10 | Viewed by 4229
Abstract
Historically, knowledge of human host–enteric pathogen interactions has been elucidated from studies using cancer cells, animal models, clinical data, and occasionally, controlled human infection models. Although much has been learned from these studies, an understanding of the complex interactions between human viruses and [...] Read more.
Historically, knowledge of human host–enteric pathogen interactions has been elucidated from studies using cancer cells, animal models, clinical data, and occasionally, controlled human infection models. Although much has been learned from these studies, an understanding of the complex interactions between human viruses and the human intestinal epithelium was initially limited by the lack of nontransformed culture systems, which recapitulate the relevant heterogenous cell types that comprise the intestinal villus epithelium. New investigations using multicellular, physiologically active, organotypic cultures produced from intestinal stem cells isolated from biopsies or surgical specimens provide an exciting new avenue for understanding human specific pathogens and revealing previously unknown host–microbe interactions that affect replication and outcomes of human infections. Here, we summarize recent biologic discoveries using human intestinal organoids and human enteric viral pathogens. Full article
(This article belongs to the Special Issue Gastroenteritis Viruses 2021)
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21 pages, 3485 KiB  
Review
Bile Goes Viral
by Victoria R. Tenge, Kosuke Murakami, Wilhelm Salmen, Shih-Ching Lin, Sue E. Crawford, Frederick H. Neill, B. V. Venkataram Prasad, Robert L. Atmar and Mary K. Estes
Viruses 2021, 13(6), 998; https://0-doi-org.brum.beds.ac.uk/10.3390/v13060998 - 27 May 2021
Cited by 6 | Viewed by 3689
Abstract
Laboratory cultivation of viruses is critical for determining requirements for viral replication, developing detection methods, identifying drug targets, and developing antivirals. Several viruses have a history of recalcitrance towards robust replication in laboratory cell lines, including human noroviruses and hepatitis B and C [...] Read more.
Laboratory cultivation of viruses is critical for determining requirements for viral replication, developing detection methods, identifying drug targets, and developing antivirals. Several viruses have a history of recalcitrance towards robust replication in laboratory cell lines, including human noroviruses and hepatitis B and C viruses. These viruses have tropism for tissue components of the enterohepatic circulation system: the intestine and liver, respectively. The purpose of this review is to discuss how key enterohepatic signaling molecules, bile acids (BAs), and BA receptors are involved in the replication of these viruses and how manipulation of these factors was useful in the development and/or optimization of culture systems for these viruses. BAs have replication-promoting activities through several key mechanisms: (1) affecting cellular uptake, membrane lipid composition, and endocytic acidification; (2) directly interacting with viral capsids to influence binding to cells; and (3) modulating the innate immune response. Additionally, expression of the Na+-taurocholate cotransporting polypeptide BA receptor in continuous liver cell lines is critical for hepatitis B virus entry and robust replication in laboratory culture. Viruses are capable of hijacking normal cellular functions, and understanding the role of BAs and BA receptors, components of the enterohepatic system, is valuable for expanding our knowledge on the mechanisms of norovirus and hepatitis B and C virus replication. Full article
(This article belongs to the Special Issue Gastroenteritis Viruses 2021)
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