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21 pages, 1842 KiB

Open AccessArticle

Virus Etiology, Diversity and Clinical Characteristics in South African Children Hospitalised with Gastroenteritis

by Esmari Rossouw, Marieke Brauer, Pieter Meyer, Nicolette M. du Plessis, Theunis Avenant and Janet Mans

Viruses 2021, 13(2), 215; https://doi.org/10.3390/v13020215 - 30 Jan 2021

Cited by 29 | Viewed by 5224

Abstract

Background: Viral gastroenteritis remains a major cause of hospitalisation in young children. This study aimed to determine the distribution and diversity of enteric viruses in children ≤5 years, hospitalised with gastroenteritis at Kalafong Provincial Tertiary Hospital, Pretoria, South Africa, between July 2016 and [...] Read more.

Background: Viral gastroenteritis remains a major cause of hospitalisation in young children. This study aimed to determine the distribution and diversity of enteric viruses in children ≤5 years, hospitalised with gastroenteritis at Kalafong Provincial Tertiary Hospital, Pretoria, South Africa, between July 2016 and December 2017. Methods: Stool specimens (n = 205) were screened for norovirus GI and GII, rotavirus, sapovirus, astrovirus and adenovirus by multiplex RT-PCR. HIV exposure and FUT2 secretor status were evaluated. Secretor status was determined by FUT2 genotyping. Results: At least one gastroenteritis virus was detected in 47% (96/205) of children. Rotavirus predominated (46/205), followed by norovirus (32/205), adenovirus (15/205), sapovirus (9/205) and astrovirus (3/205). Norovirus genotypes GI.3, GII.2, GII.3, GII.4, GII.7, GII.12, GII.21, and rotavirus strains G1P[8], G2P[4], G2P[6], G3P[4], G3P[8], G8P[4], G8P[6], G9P[6], G9P[8] and sapovirus genotypes GI.1, GI.2, GII.1, GII.4, GII.8 were detected; norovirus GII.4[P31] and rotavirus G3P[4] predominated. Asymptomatic norovirus infection (GI.3, GI.7, GII.4, GII.6, GII.13) was detected in 22% of 46 six-week follow up stools. HIV exposure (30%) was not associated with more frequent or severe viral gastroenteritis hospitalisations compared to unexposed children. Rotavirus preferentially infected secretor children (p = 0.143) and norovirus infected 78% secretors and 22% non-secretors. Conclusion: Rotavirus was still the leading cause of gastroenteritis hospitalisations, but norovirus caused more severe symptoms. Full article

(This article belongs to the Special Issue Gastroenteritis Viruses)

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12 pages, 3802 KiB

Open AccessArticle

Protein Disulfide Isomerase A4 Is Involved in Genome Uncoating during Human Astrovirus Cell Entry

by Nayeli Aguilar-Hernández, Lena Meyer, Susana López, Rebecca M. DuBois and Carlos F. Arias

Viruses 2021, 13(1), 53; https://doi.org/10.3390/v13010053 - 31 Dec 2020

Cited by 18 | Viewed by 3469

Abstract

Although human astroviruses (HAstVs) are important agents of gastroenteritis in young children, the studies aimed at characterizing their biology have been limited, in particular regarding their cell entry process. It has been shown that HAstV serotype 8 enters human cells by a classical [...] Read more.

Although human astroviruses (HAstVs) are important agents of gastroenteritis in young children, the studies aimed at characterizing their biology have been limited, in particular regarding their cell entry process. It has been shown that HAstV serotype 8 enters human cells by a classical clathrin-mediated endocytosis pathway; however, the cell receptor or other cell entry factors that may be relevant for an efficient viral infection are unknown. In this work we used a far-Western blotting approach to identify cellular proteins that interact with the recombinant capsid spike proteins of HAstV serotypes 1, 2, and 8, synthesized in Escherichia coli. We identified the 72 kDa protein disulfide isomerase A4 (PDIA4) as a binding partner for HAstV-1 and -8 spikes, but not for the HAstV-2 spike. In agreement with this observation, the PDI inhibitor 16F16 strongly blocked infection by HAstV serotypes 1 and 8, but not serotype 2. RNA interference of PDIA4 expression selectively blocked HAstV-8 infectivity. We also showed that the PDI activity does not affect virus binding or internalization but is required for uncoating of the viral genome. Full article

(This article belongs to the Special Issue Gastroenteritis Viruses)

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19 pages, 1040 KiB

Open AccessArticle

Unveiling Viruses Associated with Gastroenteritis Using a Metagenomics Approach

by Xavier Fernandez-Cassi, Sandra Martínez-Puchol, Marcelle Silva-Sales, Thais Cornejo, Rosa Bartolome, Silvia Bofill-Mas and Rosina Girones

Viruses 2020, 12(12), 1432; https://doi.org/10.3390/v12121432 - 13 Dec 2020

Cited by 14 | Viewed by 3736

Abstract

Acute infectious gastroenteritis is an important illness worldwide, especially on children, with viruses accounting for approximately 70% of the acute cases. A high number of these cases have an unknown etiological agent and the rise of next generation sequencing technologies has opened new [...] Read more.

Acute infectious gastroenteritis is an important illness worldwide, especially on children, with viruses accounting for approximately 70% of the acute cases. A high number of these cases have an unknown etiological agent and the rise of next generation sequencing technologies has opened new opportunities for viral pathogen detection and discovery. Viral metagenomics in routine clinical settings has the potential to identify unexpected or novel variants of viral pathogens that cause gastroenteritis. In this study, 124 samples from acute gastroenteritis patients from 2012–2014 previously tested negative for common gastroenteritis pathogens were pooled by age and analyzed by next generation sequencing (NGS) to elucidate unidentified viral infections. The most abundant sequences detected potentially associated to acute gastroenteritis were from Astroviridae and Caliciviridae families, with the detection of norovirus GIV and sapoviruses. Lower number of contigs associated to rotaviruses were detected. As expected, other viruses that may be associated to gastroenteritis but also produce persistent infections in the gut were identified including several Picornaviridae members (EV, parechoviruses, cardioviruses) and adenoviruses. According to the sequencing data, astroviruses, sapoviruses and NoV GIV should be added to the list of viral pathogens screened in routine clinical analysis. Full article

(This article belongs to the Special Issue Gastroenteritis Viruses)

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11 pages, 956 KiB

Open AccessArticle

Involvement of Workers in Closed and Semiclosed Institutions in Outbreaks of Acute Gastroenteritis Due to Norovirus

by Ignacio Parrón, Irene Barrabeig, Miquel Alseda, Thais Cornejo-Sánchez, Susana Guix, Mireia Jané, Conchita Izquierdo, Cristina Rius, Àngela Domínguez and the Working Group for the Study of Acute Gastroenteritis Outbreaks in Catalonia

Viruses 2020, 12(12), 1392; https://doi.org/10.3390/v12121392 - 4 Dec 2020

Cited by 4 | Viewed by 1844

Abstract

Norovirus outbreaks frequently occur in closed or semiclosed institutions. Recent studies in Catalonia and various countries indicate that, during outbreaks in these institutions, norovirus is detected in between 23% and 60% of workers, and the prevalence of infection in asymptomatic workers involved in [...] Read more.

Norovirus outbreaks frequently occur in closed or semiclosed institutions. Recent studies in Catalonia and various countries indicate that, during outbreaks in these institutions, norovirus is detected in between 23% and 60% of workers, and the prevalence of infection in asymptomatic workers involved in outbreaks ranges from 17% to 40%. In this work, we carried out a prospective study to investigate the involvement of workers in closed and semiclosed institutions during outbreaks. The attack rates (ARs) and the rate ratios (RRs) were calculated according to the type of transmission and occupational category. The RRs and 95% confidence intervals (CIs) between workers and users were calculated. The mean cycle of quantification (Cq) values were compared according to the genogroup and the presence of symptoms. ARs were higher in person-to-person transmission than in common vehicle outbreaks, and 38.8% of workers were symptomatic. The RR between workers and users was 0.46 (95% CI 0.41–0.52). The ARs in workers were high, particularly in workers with closer contact with users. The mean Cq was lower in patients than in asymptomatic infected persons, although the difference was only significant for genogroup I (GI). The frequency of asymptomatic infected persons suggests that personal hygiene measures should be followed by all workers in the centers affected. Full article

(This article belongs to the Special Issue Gastroenteritis Viruses)

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14 pages, 1031 KiB

Open AccessArticle

Detection of Norovirus in Saliva Samples from Acute Gastroenteritis Cases and Asymptomatic Subjects: Association with Age and Higher Shedding in Stool

by Eduard Anfruns-Estrada, Aurora Sabrià, Cristina Fuentes, Sara Sabaté, Efrén Razquin, Thais Cornejo, Rosa Bartolomé, Nuria Torner, Conchita Izquierdo, Nuria Soldevila, Lorena Coronas, Angela Dominguez, Rosa M. Pintó, Albert Bosch, Susana Guix and on behalf of the Working Group for the Study of Outbreaks of Acute Gastroenteritis in Catalonia (PI16/02005)

Viruses 2020, 12(12), 1369; https://doi.org/10.3390/v12121369 - 30 Nov 2020

Cited by 15 | Viewed by 3252

Abstract

Norovirus infections are a leading cause of acute gastroenteritis outbreaks worldwide and across all age groups, with two main genogroups (GI and GII) infecting humans. The aim of our study was to investigate the occurrence of norovirus in saliva samples from individuals involved [...] Read more.

Norovirus infections are a leading cause of acute gastroenteritis outbreaks worldwide and across all age groups, with two main genogroups (GI and GII) infecting humans. The aim of our study was to investigate the occurrence of norovirus in saliva samples from individuals involved in outbreaks of acute gastroenteritis in closed and semiclosed institutions, and its relationship with the virus strain, virus shedding in stool, the occurrence of symptoms, age, and the secretor status of the individual. Epidemiological and clinical information was gathered from norovirus outbreaks occurring in Catalonia, Spain during 2017–2018, and stool and saliva samples were collected from affected and exposed resident individuals and workers. A total of 347 saliva specimens from 25 outbreaks were analyzed. Further, 84% of individuals also provided a paired stool sample. For GII infections, norovirus was detected in 17.9% of saliva samples from symptomatic cases and 5.2% of asymptomatic individuals. Positivity in saliva occurred in both secretors and nonsecretors. None of the individuals infected by norovirus GI was positive for the virus in saliva. Saliva positivity did not correlate with any of the studied symptoms but did correlate with age ≥ 65 years old. Individuals who were positive in saliva showed higher levels of virus shedding in stool. Mean viral load in positive saliva was 3.16 ± 1.08 log₁₀ genome copies/mL, and the predominance of encapsidated genomes was confirmed by propidium monoazide (PMA)xx-viability RTqPCR assay. The detection of norovirus in saliva raises the possibility of oral-to-oral norovirus transmission during the symptomatic phase and, although to a lesser extent, even in cases of asymptomatic infections. Full article

(This article belongs to the Special Issue Gastroenteritis Viruses)

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13 pages, 4899 KiB

Open AccessArticle

Phylogenetic Investigation of Norovirus Transmission between Humans and Animals

by Nele Villabruna, Ray W. Izquierdo Lara, Judit Szarvas, Marion P. G. Koopmans and Miranda de Graaf

Viruses 2020, 12(11), 1287; https://doi.org/10.3390/v12111287 - 10 Nov 2020

Cited by 9 | Viewed by 2706

Abstract

Norovirus infections are a leading cause of acute gastroenteritis worldwide, affecting people of all ages. There are 10 norovirus genogroups (GI-GX) that infect humans and animals in a host-specific manner. New variants and genotypes frequently emerge, and their origin is not well understood. [...] Read more.

Norovirus infections are a leading cause of acute gastroenteritis worldwide, affecting people of all ages. There are 10 norovirus genogroups (GI-GX) that infect humans and animals in a host-specific manner. New variants and genotypes frequently emerge, and their origin is not well understood. One hypothesis is that new human infections may be seeded from an animal reservoir, as human noroviruses have occasionally been detected in animal species. The majority of these sequences were identified as older GII.4 variants, but a variety of other GIIs and GIs have been detected as well. While these sequences share at least 94% nt similarity with human strains, most of them are >98% identical to human strains. The fact that these strains were detected in animals after they had been detected through human surveillance to be already circulating in humans suggests human-to-animal transmission. Full article

(This article belongs to the Special Issue Gastroenteritis Viruses)

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17 pages, 19819 KiB

Open AccessArticle

Whole Genome Sequence Analysis of Porcine Astroviruses Reveals Novel Genetically Diverse Strains Circulating in East African Smallholder Pig Farms

by Joshua O. Amimo, Eunice M. Machuka, Edward O. Abworo, Anastasia N. Vlasova and Roger Pelle

Viruses 2020, 12(11), 1262; https://doi.org/10.3390/v12111262 - 5 Nov 2020

Cited by 8 | Viewed by 2718

Abstract

Astroviruses (AstVs) are widely distributed and are associated with gastroenteritis in human and animals. The knowledge of the genetic diversity and epidemiology of AstVs in Africa is limited. This study aimed to characterize astroviruses in asymptomatic smallholder piglets in Kenya and Uganda. Twenty-four [...] Read more.

Astroviruses (AstVs) are widely distributed and are associated with gastroenteritis in human and animals. The knowledge of the genetic diversity and epidemiology of AstVs in Africa is limited. This study aimed to characterize astroviruses in asymptomatic smallholder piglets in Kenya and Uganda. Twenty-four samples were randomly selected from a total of 446 piglets aged below 6 months that were initially collected for rotavirus study and sequenced for whole genome analysis. Thirteen (13/24) samples had contigs with high identity to genus Mamastrovirus. Analysis of seven strains with complete (or near complete) AstV genome revealed variable nucleotide and amino acid sequence identities with known porcine astrovirus (PoAstV) strains. The U083 and K321 strains had nucleotide sequence identities ranging from 66.4 to 75.4% with the known PoAstV2 strains; U460 strain had nucleotide sequence identities of 57.0 to 65.1% regarding the known PoAstV3; and K062, K366, K451, and K456 strains had nucleotide sequence identities of 63.5 to 80% with the known PoAstV4 strains. The low sequence identities (<90%) indicate that novel genotypes of PoAstVs are circulating in the study area. Recombination analysis using whole genomes revealed evidence of multiple recombination events in PoAstV4, suggesting that recombination might have contributed to the observed genetic diversity. Linear antigen epitope prediction and a comparative analysis of capsid protein of our field strains identified potential candidate epitopes that could help in the design of immuno-diagnostic tools and a subunit vaccine. These findings provide new insights into the molecular epidemiology of porcine astroviruses in East Africa. Full article

(This article belongs to the Special Issue Gastroenteritis Viruses)

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13 pages, 715 KiB

Open AccessArticle

Diversity of Noroviruses throughout Outbreaks in Germany 2018

by Sandra Niendorf, Mirko Faber, Andrea Tröger, Julian Hackler and Sonja Jacobsen

Viruses 2020, 12(10), 1157; https://doi.org/10.3390/v12101157 - 13 Oct 2020

Cited by 10 | Viewed by 2488

Abstract

Human norovirus accounts for the majority of viral gastroenteritis cases worldwide. It is a fast evolving virus generating diversity via mutation and recombination. Therefore, new variants and new recombinant strains emerge in the norovirus population. We characterized norovirus positive stool samples from one [...] Read more.

Human norovirus accounts for the majority of viral gastroenteritis cases worldwide. It is a fast evolving virus generating diversity via mutation and recombination. Therefore, new variants and new recombinant strains emerge in the norovirus population. We characterized norovirus positive stool samples from one intensively studied district Märkisch-Oderland state Brandenburg with the samples from other states of Germany in order to understand the molecular epidemiological dynamics of norovirus outbreaks in Germany 2018. PCR systems, Sanger sequencing, and phylogenetic analyses were used for genotyping. Noroviruses of 250 outbreaks in Germany were genotyped, including 39 outbreaks for the district Märkisch-Oderland. Viral diversity in Märkisch-Oderland as compared to Germany was similar, but not identical. The predominant genogroup in Germany was GII with predominate genotype GII.P16-GII.4 Sydney, whereas GII.P31-GII.4 Sydney was the most frequent in Märkisch-Oderland. Genogroup I viruses were less frequently detected, regional and national. Within the sequences of GII.4 recombinants, two distinct clusters were identified with outbreaks from Märkisch-Oderland. Further analysis of sequence data and detailed epidemiological data are needed in order to understand the link between outbreaks in such clusters. Molecular surveillance should be based on samples collected nationally in order to trace comprehensive virus distribution and recombination events in virus population. Full article

(This article belongs to the Special Issue Gastroenteritis Viruses)

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12 pages, 1011 KiB

Open AccessArticle

Ecology of Porcine Astrovirus Type 3 in a Herd with Associated Neurologic Disease

by Gaurav Rawal, Franco Matias Ferreyra, Nubia R. Macedo, Laura K. Bradner, Karen M. Harmon, Grant Allison, Daniel C. L. Linhares and Bailey L. Arruda

Viruses 2020, 12(9), 992; https://doi.org/10.3390/v12090992 - 7 Sep 2020

Cited by 16 | Viewed by 3448

Abstract

Astroviruses (AstVs) cause disease in a wide variety of species. Porcine AstVs are highly genetically diverse and conventionally assigned to five genetic lineages (PoAstV1-5). Due to the increasing evidence that porcine astrovirus type 3 (PoAstV3) is a cause of encephalomyelitis in swine and [...] Read more.

Astroviruses (AstVs) cause disease in a wide variety of species. Porcine AstVs are highly genetically diverse and conventionally assigned to five genetic lineages (PoAstV1-5). Due to the increasing evidence that porcine astrovirus type 3 (PoAstV3) is a cause of encephalomyelitis in swine and to elucidate important ecologic characteristics, the infection dynamics and environmental distribution of PoAstV3 were investigated in a herd with PoAstV3-associated neurologic disease. Over a 22 week period, the frequency of PoAstV3 fecal shedding varied by pig and age. The peak detection by RT-qPCR of PoAstV3 on fecal swabs (95%; 61 of 64) occurred at 3 weeks of age. The lowest frequency of detection was at 21 weeks of age (4%; 2 of 47); however, the frequency increased to 41% (19 of 46) at the final sampling time point (25 weeks of age). Viremia was rare (0.9%: 4 of 433). Detection in oral fluid was consistent with 75% to 100% of samples positive at each time point. Pens and feeders also had a high rate of detection with a majority of samples positive at a majority of sampling time points. Based on the data presented, PoAstV3 can be consistently detected in the environment with a majority of pigs being infected and a subset intermittently shedding the virus in feces out to 25 weeks of age. These findings suggest the importance of as-yet unidentified risk factors associated with the development of PoAstV3-associated polioencephalomyelitis. Full article

(This article belongs to the Special Issue Gastroenteritis Viruses)

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17 pages, 1915 KiB

Open AccessArticle

A Targeted Metagenomics Approach to Study the Diversity of Norovirus GII in Shellfish Implicated in Outbreaks

by Marion Desdouits, Candice Wacrenier, Joanna Ollivier, Julien Schaeffer and Françoise S. Le Guyader

Viruses 2020, 12(9), 978; https://doi.org/10.3390/v12090978 - 3 Sep 2020

Cited by 15 | Viewed by 2865

Abstract

Human noroviruses (NoV) cause epidemics of acute gastroenteritis (AGE) worldwide and can be transmitted through consumption of contaminated foods. Fresh products such as shellfish can be contaminated by human sewage during production, which results in the presence of multiple virus strains, at very [...] Read more.

Human noroviruses (NoV) cause epidemics of acute gastroenteritis (AGE) worldwide and can be transmitted through consumption of contaminated foods. Fresh products such as shellfish can be contaminated by human sewage during production, which results in the presence of multiple virus strains, at very low concentrations. Here, we tested a targeted metagenomics approach by deep-sequencing PCR amplicons of the capsid (VP1) and polymerase (RdRp) viral genes, on a set of artificial samples and on shellfish samples associated to AGE outbreaks, to evaluate its advantages and limitations in the identification of strains from the NoV genogroup (G) II. Using artificial samples, the method allowed the sequencing of most strains, but not all, and displayed variability between replicates especially with lower viral concentrations. Using shellfish samples, targeted metagenomics was compared to Sanger-sequencing of cloned amplicons and was able to identify a higher diversity of NoV GII and GIV strains. It allowed phylogenetic analyses of VP1 sequences and the identification, in most samples, of GII.17[P17] strains, also identified in related clinical samples. Despite several limitations, combining RdRp- and VP1-targeted metagenomics is a sensitive approach allowing the study NoV diversity in low-contaminated foods and the identification of NoV strains implicated in outbreaks. Full article

(This article belongs to the Special Issue Gastroenteritis Viruses)

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13 pages, 2271 KiB

Open AccessArticle

Attach Me If You Can: Murine Norovirus Binds to Commensal Bacteria and Fungi

by Jasmine L. Madrigal, Sutonuka Bhar, Samantha Hackett, Haley Engelken, Ross Joseph, Nemat O. Keyhani and Melissa K. Jones

Viruses 2020, 12(7), 759; https://doi.org/10.3390/v12070759 - 14 Jul 2020

Cited by 18 | Viewed by 5167

Abstract

The presence of commensal bacteria enhances both acute and persistent infection of murine noroviruses. For several enteric viral pathogens, mechanisms by which these bacteria enhance infection involve direct interactions between the virus and bacteria. While it has been demonstrated that human noroviruses bind [...] Read more.

The presence of commensal bacteria enhances both acute and persistent infection of murine noroviruses. For several enteric viral pathogens, mechanisms by which these bacteria enhance infection involve direct interactions between the virus and bacteria. While it has been demonstrated that human noroviruses bind to a variety of commensal bacteria, it is not known if this is also true for murine noroviruses. The goal of this study was to characterize interactions between murine noroviruses and commensal bacteria and determine the impact of bacterial growth conditions, incubation temperature and time, on murine norovirus attachment to microbes that comprise the mammalian microbiome. We show that murine noroviruses bind directly to commensal bacteria and show similar patterns of attachment as human norovirus VLPs examined under the same conditions. Furthermore, while binding levels are not impacted by the growth phase of the bacteria, they do change with time and incubation temperature. We also found that murine norovirus can bind to a commensal fungal species, Candida albicans. Full article

(This article belongs to the Special Issue Gastroenteritis Viruses)

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16 pages, 1595 KiB

Open AccessArticle

Beclin1 Binds to Enterovirus 71 3D Protein to Promote the Virus Replication

by Qi Xiang, Pin Wan, Ge Yang, Siyu Huang, Mengying Qin, Hua Yang, Zhen Luo, Kailang Wu and Jianguo Wu

Viruses 2020, 12(7), 756; https://doi.org/10.3390/v12070756 - 14 Jul 2020

Cited by 11 | Viewed by 4038

Abstract

Enterovirus 71 (EV71) is the main pathogen causing hand-foot-mouth disease (HFMD) in infants and children, which can also lead to severe neurological diseases and even death. Therefore, understanding the replication mechanism of EV71 is of great significance for the prevention and control of [...] Read more.

Enterovirus 71 (EV71) is the main pathogen causing hand-foot-mouth disease (HFMD) in infants and children, which can also lead to severe neurological diseases and even death. Therefore, understanding the replication mechanism of EV71 is of great significance for the prevention and control of EV71-induced diseases. Beclin1 (BECN1, a mammalian homologue of ATG6 in yeast) is an important core protein for the initiation and the normal process of autophagy in cells. In addition to its involvement in autophagy, Beclin1 has also been reported to play an important role in cancer and innate immune signaling pathways. However, the role of Beclin1 in EV71 replication remains elusive. Here, we primarily found that Beclin1 facilitates EV71 replication in human rhabdomyosarcoma (RD) cells and the autophagy was actually induced, but Beclin1 was not significantly affected at either mRNA level or protein level during early EV71 infection. Further studies discovered that Beclin1 could interacts with EV71 non-structural protein 3D mainly through its evolutionary conserved domain (ECD) and coiled-coiled domain (CCD), thus promoting the replication of EV71 in human rhabdomyosarcoma (RD) cells and human astroglioma (U251) cells. Collectively, we reveal a novel regulatory mechanism associated with Beclin1 to promote EV71 replication, thus providing a potential therapeutic target for the prevention and control of EV71-associated diseases. Full article

(This article belongs to the Special Issue Gastroenteritis Viruses)

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14 pages, 4973 KiB

Open AccessArticle

Detection of Astrovirus in a Cow with Neurological Signs by Nanopore Technology, Italy

by Guendalina Zaccaria, Alessio Lorusso, Melanie M. Hierweger, Daniela Malatesta, Sabrina VP Defourny, Franco Ruggeri, Cesare Cammà, Pasquale Ricci, Marco Di Domenico, Antonio Rinaldi, Nicola Decaro, Nicola D’Alterio, Antonio Petrini, Torsten Seuberlich and Maurilia Marcacci

Viruses 2020, 12(5), 530; https://doi.org/10.3390/v12050530 - 11 May 2020

Cited by 7 | Viewed by 5493

Abstract

In this study, starting from nucleic acids purified from the brain tissue, Nanopore technology was used to identify the etiological agent of severe neurological signs observed in a cow which was immediately slaughtered. Histological examination revealed acute non-suppurative encephalomyelitis affecting the brainstem, cerebrum, [...] Read more.

In this study, starting from nucleic acids purified from the brain tissue, Nanopore technology was used to identify the etiological agent of severe neurological signs observed in a cow which was immediately slaughtered. Histological examination revealed acute non-suppurative encephalomyelitis affecting the brainstem, cerebrum, cerebellum, and medulla oblongata, while by using PCR-based assays, the nucleic acids of major agents for neurological signs were not detected. By using Nanopore technology, 151 sequence reads were assigned to Bovine Astrovirus (BoAstV). Real-time RT-PCR and in situ hybridization (ISH) confirmed the presence of viral RNA in the brain. Moreover, using the combination of fluorescent ISH and immunofluorescence (IF) techniques, it was possible to detect BoAstV RNA and antigens in the same cells, suggesting the active replication of the virus in infected neurons. The nearly whole genome of the occurring strain (BoAstV PE3373/2019/Italy), obtained by Illumina NextSeq 500, showed the highest nucleotide sequence identity (94.11%) with BoAstV CH13/NeuroS1 26,730 strain, an encephalitis-associated bovine astrovirus. Here, we provide further evidence of the role of AstV as a neurotropic agent. Considering that in a high proportion of non-suppurative encephalitis cases, which are mostly indicative of a viral infection, the etiologic agent remains unknown, our result underscores the value and versatility of Nanopore technology for a rapid diagnosis when the PCR-based algorithm gives negative results. Full article

(This article belongs to the Special Issue Gastroenteritis Viruses)

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13 pages, 1145 KiB

Open AccessReview

Enteric Viruses and Inflammatory Bowel Disease

by Georges Tarris, Alexis de Rougemont, Maëva Charkaoui, Christophe Michiels, Laurent Martin and Gaël Belliot

Viruses 2021, 13(1), 104; https://doi.org/10.3390/v13010104 - 13 Jan 2021

Cited by 39 | Viewed by 7581

Abstract

Inflammatory bowel diseases (IBD), including ulcerative colitis (UC) and Crohn’s disease (CD), is a multifactorial disease in which dietary, genetic, immunological, and microbial factors are at play. The role of enteric viruses in IBD remains only partially explored. To date, epidemiological studies have [...] Read more.

Inflammatory bowel diseases (IBD), including ulcerative colitis (UC) and Crohn’s disease (CD), is a multifactorial disease in which dietary, genetic, immunological, and microbial factors are at play. The role of enteric viruses in IBD remains only partially explored. To date, epidemiological studies have not fully described the role of enteric viruses in inflammatory flare-ups, especially that of human noroviruses and rotaviruses, which are the main causative agents of viral gastroenteritis. Genome-wide association studies have demonstrated the association between IBD, polymorphisms of the FUT2 and FUT3 genes (which drive the synthesis of histo-blood group antigens), and ligands for norovirus and rotavirus in the intestine. The role of autophagy in defensin-deficient Paneth cells and the perturbations of cytokine secretion in T-helper 1 and T-helper 17 inflammatory pathways following enteric virus infections have been demonstrated as well. Enteric virus interactions with commensal bacteria could play a significant role in the modulation of enteric virus infections in IBD. Based on the currently incomplete knowledge of the complex phenomena underlying IBD pathogenesis, future studies using multi-sampling and data integration combined with new techniques such as human intestinal enteroids could help to decipher the role of enteric viruses in IBD. Full article

(This article belongs to the Special Issue Gastroenteritis Viruses)

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