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Viruses Jan 2021Inflammatory bowel diseases (IBD), including ulcerative colitis (UC) and Crohn's disease (CD), is a multifactorial disease in which dietary, genetic, immunological, and... (Review)
Review
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 and 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.
Topics: Animals; Autophagy; Biomarkers; Blood Group Antigens; Disease Management; Disease Susceptibility; Enterovirus; Enterovirus Infections; Gastrointestinal Microbiome; Host-Pathogen Interactions; Humans; Inflammatory Bowel Diseases; Microbial Interactions; Signal Transduction; Virome
PubMed: 33451106
DOI: 10.3390/v13010104 -
PloS One 2021Diarrhoea remains a major cause of childhood morbidity and mortality worldwide. This study aimed to monitor the aetiology of acute diarrhoea in children in Shanghai....
Diarrhoea remains a major cause of childhood morbidity and mortality worldwide. This study aimed to monitor the aetiology of acute diarrhoea in children in Shanghai. Paediatric outpatients with acute diarrhoea were enrolled in the study from Jan 2015 to Dec 2018. Faecal samples were collected for testing. Enteric bacteria were identified and typed by culture and serotyping, respectively. Enteric viruses were identified by real-time PCR. Enteric pathogens were identified in 1572 (58.4%) of the 2692 enrolled children with acute diarrhoea. Viruses were detected more frequently than bacteria (41.3% versus 25.0%). Nontyphoidal Salmonella spp. (NTS) was the most common (10.3%) bacteria isolated, followed by enteropathogenic Escherichia coli (EPEC) (6.5%), enteroaggregative Escherichia coli (EAEC) (6.2%), Campylobacter spp. (3.6%), enterotoxigenic Escherichia coli (ETEC) (1.1%), Shigella spp. (0.2%), and enterohemorrhagic Escherichia coli (EHEC) (0.1%). Rotavirus was the most common (16.0%) virus detected, followed by norovirus (15.5%), adenovirus (7.2%), sapovirus (3.0%) and astrovirus (2.7%). Rotavirus, norovirus and NTS were the major pathogens responsible for diarrhoea in Shanghainese children. Improving uptake of the rotavirus vaccine and strengthening foodborne-pathogen prevention will aid in reducing the burden of diarrhoeal disease in children in Shanghai.
Topics: Campylobacter; Child; Child, Preschool; China; Diarrhea; Enterotoxigenic Escherichia coli; Female; Humans; Infant; Infant, Newborn; Male; Norovirus; Rotavirus; Salmonella
PubMed: 33831124
DOI: 10.1371/journal.pone.0249888 -
Frontiers in Immunology 2019Noroviruses and Sapoviruses, classified in the family, are small positive-stranded RNA viruses, considered nowadays the leading cause of acute gastroenteritis globally... (Review)
Review
Noroviruses and Sapoviruses, classified in the family, are small positive-stranded RNA viruses, considered nowadays the leading cause of acute gastroenteritis globally in both children and adults. Although most noroviruses have been associated with gastrointestinal disease in humans, almost 50 years after its discovery, there is still a lack of comprehensive evidence regarding its biology and pathogenesis mainly because they can be neither conveniently grown in cultured cells nor propagated in animal models. However, other members of this family such as Feline calicivirus (FCV), Murine norovirus (MNV), Rabbit hemorrhagic disease virus (RHDV), and Porcine sapovirus (PS), from which there are accessible propagation systems, have been useful to study the calicivirus replication strategies. Using cell cultures and animal models, many of the functions of the viral proteins in the viral replication cycles have been well-characterized. Moreover, evidence of the role of viral proteins from different members of the family in the establishment of infection has been generated and the mechanism of their immunopathogenesis begins to be understood. In this review, we discuss different aspects of how caliciviruses are implicated in membrane rearrangements, apoptosis, and evasion of the immune responses, highlighting some of the pathogenic mechanisms triggered by different members of the family.
Topics: Adaptive Immunity; Animals; Antimicrobial Cationic Peptides; Apoptosis; Caliciviridae; Caliciviridae Infections; Cell Membrane; Cytopathogenic Effect, Viral; Disease Susceptibility; Gene Expression Regulation, Viral; Genome, Viral; Host-Pathogen Interactions; Humans; Immune Evasion; Immunity; Immunity, Innate; Immunomodulation; Microbial Interactions; Microbiota; Virus Replication
PubMed: 31632406
DOI: 10.3389/fimmu.2019.02334 -
Current Opinion in Infectious Diseases Oct 2020Sapovirus, a genus in the Caliciviridae family alongside norovirus, is increasingly recognized as an important cause of childhood diarrhea. Some challenges exist in our... (Review)
Review
PURPOSE OF REVIEW
Sapovirus, a genus in the Caliciviridae family alongside norovirus, is increasingly recognized as an important cause of childhood diarrhea. Some challenges exist in our ability to better understand sapovirus infections, including the inability to grow sapovirus in cell culture, which has hindered diagnosis and studies of immunity. Another challenge is that individuals with sapovirus infection are commonly coinfected with other enteric pathogens, complicating our ability to attribute the diarrhea episode to a single pathogen.
RECENT FINDINGS
Development of molecular methods for sapovirus detection has increased our ability to measure disease prevalence. The prevalence of sapovirus varies between 1 and 17% of diarrhea episodes worldwide, with the highest burden in young children and older adults. Further, epidemiological studies have used novel approaches to account for the presence of coinfections with other enteric pathogens; one multisite cohort study of children under two years of age found that sapovirus had the second-highest attributable incidence among all diarrheal pathogens studied.
SUMMARY
Especially in settings where rotavirus vaccines have been introduced, efforts to reduce the overall burden of childhood diarrhea should focus on the reduction of sapovirus transmission and disease burden.
Topics: Adolescent; Adult; Aged; Aged, 80 and over; Caliciviridae Infections; Child; Child, Preschool; Cohort Studies; Coinfection; Diarrhea; Feces; Gastroenteritis; Genetic Variation; Genotype; Humans; Incidence; Infant; Infant, Newborn; Middle Aged; Risk Factors; Rotavirus Vaccines; Sapovirus; Young Adult
PubMed: 32796163
DOI: 10.1097/QCO.0000000000000671 -
Viruses Apr 2020In this review, we describe the distribution and genetic diversity of sapoviruses detected among humans, animals and the environment in African countries. Databases were... (Review)
Review
In this review, we describe the distribution and genetic diversity of sapoviruses detected among humans, animals and the environment in African countries. Databases were searched for studies conducted in African countries and published between Jan 2005 and Mar 2019. Only studies where RT- PCR was used for initial detection were included in the systematic review. We identified 27 studies from 14 African countries with 18 focused on human sapoviruses, two on animal sapoviruses and seven on sapoviruses observed in the environment. Samples. The overall estimated pooled prevalence of human sapovirus infections among symptomatic and asymptomatic individuals was similar at 5.0% (95% Confidence Interval (CI): 3.0-7.0) and 2.0% (95% CI: 1.0-3.0), respectively. In environmental samples sapovirus detection rates ranged from 0% to 90% while in animal studies it was 1.7% to 34.8%. Multiple causes of gastroenteritis, sensitivity of detection method used, diversity of sapovirus strains and rotavirus vaccine coverage rate are some of the factors that could have contributed to the wide range of sapovirus detection rates that were reported. The studies reported human genogroups GI, GII, and GIV, with genogroup GI being the most prevalent. Some potential novel strains were detected from animal samples. Most studies genotyped a small portion of either the capsid and/or polymerase region. However, this is a limitation as it does not allow for detection of recombinants that occur frequently in sapoviruses. More studies with harmonized genotyping protocols that cover longer ranges of the sapovirus genome are needed to provide more information on the genomic characterization of sapoviruses circulating in African countries. Further investigations on animal to human transmission for sapoviruses are needed as inter-species transmissions have been documented for other viruses.
Topics: Africa; Animals; Caliciviridae Infections; Gastroenteritis; Genetic Variation; Genotype; Humans; Phylogeny; Sapovirus
PubMed: 32349380
DOI: 10.3390/v12050490 -
Foods (Basel, Switzerland) Oct 2020In recent years, several foodborne viruses' outbreaks have been recorded worldwide. Μost of the foodborne viruses have a low infection dose, are stable and can persist... (Review)
Review
In recent years, several foodborne viruses' outbreaks have been recorded worldwide. Μost of the foodborne viruses have a low infection dose, are stable and can persist and survive in foods for a long time without loss of infectivity. The most important foodborne viruses are: human norovirus (HuNoV), human rotavirus (HRV), hepatitis A virus (HAV), hepatitis E virus (HEV), human astrovirus (HAstV), Aichi virus (AiV), sapovirus (SaV), human adenovirus (HAdV) and enterovirus (EV). In recent years, innovative non-thermal food-processing technologies including high-pressure processing (HPP), cold plasma (CP), ultraviolet light (UV), irradiation and pulsed electric field (PEF) for improving the quality and safety of foods, including foods of animal origin, have been under research. This review presents the recent data on foodborne viruses and reviews the innovative non-thermal technologies for the control of the foodborne viruses in foods.
PubMed: 33113926
DOI: 10.3390/foods9111520 -
Microbiology Spectrum Aug 2023Norovirus is the primary cause of viral gastroenteritis (GE). To investigate norovirus epidemiology, there is a need for whole-genome sequencing and reference sets...
Norovirus is the primary cause of viral gastroenteritis (GE). To investigate norovirus epidemiology, there is a need for whole-genome sequencing and reference sets consisting of complete genomes. To investigate the potential of shotgun metagenomic sequencing on the Illumina platform for whole-genome sequencing, 71 reverse transcriptase quantitative PCR (RT-qPCR) norovirus positive-feces (threshold cycle [], <30) samples from norovirus surveillance within The Netherlands were subjected to metagenomic sequencing. Data were analyzed through an in-house next-generation sequencing (NGS) analysis workflow. Additionally, we assessed the potential of metagenomic sequencing for the surveillance of off-target viruses that are of importance for public health, e.g., sapovirus, rotavirus A, enterovirus, parechovirus, aichivirus, adenovirus, and bocaparvovirus. A total of 60 complete and 10 partial norovirus genomes were generated, representing 7 genogroup I capsid genotypes and 12 genogroup II capsid genotypes. In addition to the norovirus genomes, the metagenomic approach yielded partial or complete genomes of other viruses for 39% of samples from children and 6.7% of samples from adults, including adenovirus 41 ( = 1); aichivirus 1 ( = 1); coxsackievirus A2 ( = 2), A4 ( = 2), A5 ( = 1), and A16 ( = 1); bocaparvovirus 1 ( = 1) and 3 ( = 1); human parechovirus 1 ( = 2) and 3 ( = 1); Rotavirus A ( = 1); and a sapovirus GI.7 ( = 1). The sapovirus GI.7 was initially not detected through RT-qPCR and warranted an update of the primer and probe set. Metagenomic sequencing on the Illumina platform robustly determines complete norovirus genomes and may be used to broaden gastroenteritis surveillance by capturing off-target enteric viruses. Viral gastroenteritis results in significant morbidity and mortality in vulnerable individuals and is primarily caused by norovirus. To investigate norovirus epidemiology, there is a need for whole-genome sequencing and reference sets consisting of full genomes. Using surveillance samples sent to the Dutch National Institute for Public Health and the Environment (RIVM), we compared metagenomics against conventional techniques, such as RT-qPCR and Sanger-sequencing, with norovirus as the target pathogen. We determined that metagenomics is a robust method to generate complete norovirus genomes, in parallel to many off-target pathogenic enteric virus genomes, thereby broadening our surveillance efforts. Moreover, we detected a sapovirus that was not detected by our validated gastroenteritis RT-qPCR panel, which exemplifies the strength of metagenomics. Our study shows that metagenomics can be used for public health gastroenteritis surveillance, the generation of reference-sets for molecular epidemiology, and how it compares to current surveillance strategies.
Topics: Child; Adult; Humans; Infant; Public Health; Metagenomics; RNA, Viral; Gastroenteritis; Rotavirus; Viruses; Enteritis; Enterovirus Infections; Adenoviridae Infections; Norovirus; Adenoviridae; Adenovirus Infections, Human; Sapovirus; Enterovirus; Feces
PubMed: 37432120
DOI: 10.1128/spectrum.05022-22 -
PloS One 2022Norovirus and sapovirus are important causes of childhood acute gastroenteritis (AGE). Breastfeeding prevents AGE generally; however, it is unknown if breastfeeding...
BACKGROUND
Norovirus and sapovirus are important causes of childhood acute gastroenteritis (AGE). Breastfeeding prevents AGE generally; however, it is unknown if breastfeeding prevents AGE caused specifically by norovirus and sapovirus.
METHODS
We investigated the association between breastfeeding and norovirus or sapovirus AGE episodes in a birth cohort. Weekly data on breastfeeding and AGE episodes were captured during the first year of life. Stools were collected from children with AGE and tested by RT-qPCR for norovirus and sapovirus. Time-dependent Cox models estimated associations between weekly breastfeeding and time to first norovirus or sapovirus AGE.
FINDINGS
From June 2017 to July 2018, 444 newborns were enrolled in the study. In the first year of life, 69 and 34 children experienced a norovirus and a sapovirus episode, respectively. Exclusive breastfeeding lasted a median of 2 weeks, and any breastfeeding lasted a median of 43 weeks. Breastfeeding in the last week did not prevent norovirus (HR: 1.09, 95% CI: 0.62, 1.92) or sapovirus (HR: 1.00, 95% CI: 0.82, 1.21) AGE in a given week, adjusting for household sanitation, consumption of high-risk foods, and mother's and child's histo-blood group phenotypes. Maternal secretor-positive phenotype was protective against norovirus AGE, whereas child's secretor-positive phenotype was a risk factor for norovirus AGE.
INTERPRETATION
Exclusive breastfeeding in this population was short-lived, and no conclusions could be drawn about its potential to prevent norovirus or sapovirus AGE. Non-exclusive breastfeeding did not prevent norovirus or sapovirus AGE in the first year of life. However, maternal secretor-positive phenotype was associated with a reduced hazard of norovirus AGE.
Topics: Birth Cohort; Blood Group Antigens; Caliciviridae Infections; Enteritis; Enterovirus Infections; Feces; Gastroenteritis; Humans; Norovirus; Sapovirus
PubMed: 36240197
DOI: 10.1371/journal.pone.0267689 -
Pediatrics Jan 2022To inform next steps in pediatric diarrhea burden reduction by understanding the shifting enteropathogen landscape after rotavirus vaccine implementation.
OBJECTIVES
To inform next steps in pediatric diarrhea burden reduction by understanding the shifting enteropathogen landscape after rotavirus vaccine implementation.
METHODS
We conducted a case-control study of 1788 medically attended children younger than 5 years, with and without gastroenteritis, after universal rotavirus vaccine implementation in Peru. We tested case and control stools for 5 viruses, 19 bacteria, and parasites; calculated coinfection-adjusted attributable fractions (AFs) to determine pathogen-specific burdens; and evaluated pathogen-specific gastroenteritis severity using Clark and Vesikari scales.
RESULTS
Six pathogens were independently positively associated with gastroenteritis: norovirus genogroup II (GII) (AF 29.1, 95% confidence interval [CI]: 28.0-32.3), rotavirus (AF 8.9, 95% CI: 6.8-9.7), sapovirus (AF 6.3, 95% CI: 4.3-7.4), astrovirus (AF 2.8, 95% CI: 0.0-4.0); enterotoxigenic Escherichia coli heat stable and/or heat labile and heat stable (AF 2.4, 95% CI: 0.6-3.1), and Shigella spp. (AF 2.0, 95% CI: 0.4-2.2). Among typeable rotavirus cases, we most frequently identified partially heterotypic strain G12P[8] (54 of 81, 67%). Mean severity was significantly higher for norovirus GII-positive cases relative to norovirus GII-negative cases (Vesikari [12.7 vs 11.8; P < .001] and Clark [11.7 vs 11.4; P = .016]), and cases in the 6- to 12-month age range relative to cases in other age groups (Vesikari [12.7 vs 12.0; P = .0002] and Clark [12.0 vs 11.4; P = .0016]).
CONCLUSIONS
Norovirus is well recognized as the leading cause of pediatric gastroenteritis in settings with universal rotavirus vaccination. However, sapovirus is often overlooked. Both norovirus and sapovirus contribute significantly to the severe pediatric disease burden in this setting. Decision-makers should consider multivalent vaccine acquisition strategies to target multiple caliciviruses in similar countries after successful rotavirus vaccine implementation.
Topics: Case-Control Studies; Child, Preschool; Diarrhea; Feces; Gastroenteritis; Genotype; Humans; Norovirus; Peru; Prospective Studies; Rotavirus; Rotavirus Infections; Rotavirus Vaccines; Sapovirus; Severity of Illness Index
PubMed: 34918158
DOI: 10.1542/peds.2020-049884 -
Animal Diseases 2021Bile acids (BAs) are evolutionally conserved molecules synthesized in the liver from cholesterol to facilitating the absorption of fat-soluble nutrients. In the... (Review)
Review
Bile acids (BAs) are evolutionally conserved molecules synthesized in the liver from cholesterol to facilitating the absorption of fat-soluble nutrients. In the intestines, where enteric viruses replicate, BAs also act as signaling molecules that modulate various biological functions activation of specific receptors and cell signaling pathways. To date, BAs present either pro-viral or anti-viral effects for the replication of enteric viruses and . In this review, we summarized current information on biosynthesis, transportation and metabolism of BAs and the role of BAs in replication of enteric caliciviruses, rotaviruses, and coronaviruses. We also discussed the application of BAs for cell culture adaptation of fastidious enteric caliciviruses and control of virus infection, which may provide novel insights into the development of antivirals and/or disinfectants for enteric viruses.
PubMed: 34778876
DOI: 10.1186/s44149-021-00003-x