scholarly journals Wide Diversity of Recombinant Noroviruses Circulating in Spain, 2016 to 2020

2021 ◽  
Author(s):  
Noemi Navarro-Lleó ◽  
Cristina Santiso-Bellón ◽  
Susana Vila-Vicent ◽  
Noelia Carmona-Vicente ◽  
Roberto Gozalbo-Rovira ◽  
...  
Keyword(s):  
Enteric Virus ◽  
Viral Gastroenteritis ◽  
Junction Region ◽  
Predominant Genotype ◽  
Recombinant Strains ◽  
High Prevalence ◽  
Positive Rate ◽  
Sporadic Cases ◽  
Stool Samples

Noroviruses are the leading cause of sporadic cases and outbreaks of viral gastroenteritis. For more than 20 years most norovirus infections have been caused by the pandemic genotype GII.4, yet recent studies have reported the emergence of recombinant strains in many countries. In the present study, 4,950 stool samples collected between January 2016 and April 2020 in Valencia (Spain) from patients with acute gastroenteritis were analyzed to investigate the etiological agent. Norovirus was the most frequently detected enteric virus with a positive rate of 9.5% (471/4,950). Among 224 norovirus strains characterized, 175 belonged to genogroup GII and 49 to genogroup GI. Using dual genotyping based on sequencing the ORF1/ORF2 junction region we detected 25 different capsid-polymerase type associations. The most common GII capsid genotype was GII.4 Sydney 2012, followed by GII.2, GII.3, GII.6 and GII.17. A high prevalence of recombinant strains (90.4%) was observed among GII infections between 2018 and 2020. GII.4 Sydney[P16] was the predominant genotype from 2019 to 2020. In addition, GII.P16 polymerase was found harboring within six different capsid genes. A new subcluster of GII.4 Sydney associated with the P31 polymerase was identified by phylogenetic analysis. GI.4 and GI.3 were the predominant genotypes in genogroup GI, in which recombinant strains were also found, such as GI.3[P10], GI.3[P13] and GI.5[P4]. Interestingly, the GI.3[P10] strain could represent a new capsid genotype. This study shows the extensive diversity of recombinant noroviruses circulating in Spain and highlights the role of recombination events in the spread of noroviruses.

scholarly journals Enteric Viruses and Inflammatory Bowel Disease

Viruses ◽  
2021 ◽  
Vol 13 (1) ◽  
pp. 104
Author(s):  
Georges Tarris ◽  
Alexis de Rougemont ◽  
Maëva Charkaoui ◽  
Christophe Michiels ◽  
Laurent Martin ◽  
...  
Keyword(s):  
Association Studies ◽  
Enteric Viruses ◽  
Enteric Virus ◽  
Viral Gastroenteritis ◽  
Blood Group Antigens ◽  
Genome Wide Association Studies ◽  
Virus Infections ◽  
T Helper ◽  
Inflammatory Bowel

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.

scholarly journals Fecal Components Modulate Human Astrovirus Infectivity in Cells and Reconstituted Intestinal Tissues

mSphere ◽  
2019 ◽  
Vol 4 (6) ◽  
Author(s):  
Francisco J. Pérez-Rodriguez ◽  
Gael Vieille ◽  
Lara Turin ◽  
Soner Yildiz ◽  
Caroline Tapparel ◽  
...  
Keyword(s):  
Real Life ◽  
Enteric Viruses ◽  
Enteric Virus ◽  
Viral Gastroenteritis ◽  
Dependent Manner ◽  
Viral Genotype ◽  
Interindividual Differences ◽  
Human Astroviruses ◽  
Human Astrovirus

ABSTRACT Human astroviruses (HAstV) are among the most common causative agents of viral gastroenteritis, especially in children, and extraintestinal manifestations have also been described. These viruses are transmitted by the fecal-oral route, implying that stool composition and the gut microbiota may impact their ability to remain infectious. For some enteric viruses, individual bacterial envelope components and other polysaccharide-containing molecules, which are abundant in stools, have been shown to enhance capsid stability. However, the role of the complex stool environment and, most importantly, the role of interindividual differences have been poorly studied. We used HAstV as a model to investigate how the stool environment in itself, its interindividual variability, and some specific stool components could affect HAstV stability and infectivity. Using two different HAstV genotypes, we found that stools as a whole modulate astrovirus infectivity not only in an individual-dependent manner but also in a manner that depends on the viral genotype. A virus-protective effect was observed after incubation with various Gram-positive and Gram-negative bacteria as well as with bacterial components, such as lipopolysaccharide and peptidoglycan. These results were further confirmed in human intestinal tissues, a more physiologically relevant system. Astrovirus infectivity was also preserved by mucin, a major component of intestinal mucus. We further confirmed that these components stabilize the viral capsid. These results show that although HAstV benefits from the stabilizing effect of fecal components, the complexity and variability of the stool composition and the multiple potential interactions may explain the interindividual differences in viral transmission observed in real life. IMPORTANCE To ensure transmission, enteric viruses must maintain their infectivity during the various environmental challenges that they face in transit within and between hosts. Increased knowledge of the factors affecting enteric virus survival may help to control their transmission. This study reveals that specific fecal bacterial components preserve classic human astrovirus infectivity by stabilizing viral particles. However, the outcomes of stool-virus interactions are very variable, ranging from protection to a reduction of viral infectivity, depending on the viral genotype and the individual from whom the stool has been collected. We show that the transmissibility of enteric viruses is dependent on the intestinal contents of the infected individual and highlight the complex multiple interactions that could explain the stochastic nature of enteric virus transmission in humans.

scholarly journals Norovirus Infections and Disease in Lower‐Middleand Low‐Income Countries, 1997–2018

Viruses ◽  
2019 ◽  
Vol 11 (4) ◽  
pp. 341 ◽  
Author(s):  
Mans
Keyword(s):  
Low Income ◽  
Low Income Countries ◽  
Viral Gastroenteritis ◽  
Healthy Controls ◽  
Limited Data ◽  
Middle Income ◽  
Predominant Genotype ◽  
Middle Income Countries ◽  
High Prevalence ◽  
Polymerase Chain

Noroviruses are a major cause of viral gastroenteritis. The burden of the norovirus in lowresourcesettings is not well‐established due to limited data. This study reviews the norovirusprevalence, epidemiology, and genotype diversity in lower‐middle‐income countries (LMIC) andin low‐income countries (LIC). PubMed was searched up to 14 January 2019 for norovirus studiesfrom all LIC and LMIC (World Bank Classification). Studies that tested gastroenteritis cases and/orasymptomatic controls for norovirus by reverse transcription‐polymerase chain reaction (RT‐PCR)were included. Sixty‐four studies, the majority on children <5 years of age, were identified, and 14%(95% confidence interval; CI 14–15, 5158/36,288) of the gastroenteritis patients and 8% (95% CI 7–9,423/5310) of healthy controls tested positive for norovirus. In LMIC, norovirus was detected in 15%(95% CI 15–16) of cases and 8% (95% CI 8–10) of healthy controls. In LIC, 11% (95% CI 10–12) ofsymptomatic cases and 9% (95% CI 8–10) of asymptomatic controls were norovirus positive.Norovirus genogroup II predominated overall. GII.4 was the predominant genotype in all settings,followed by GII.3 and GII.6. The most prevalent GI strain was GI.3. Norovirus causes a significantamount of gastroenteritis in low‐resource countries, albeit with high levels of asymptomaticinfection in LIC and a high prevalence of coinfections

First detection of human astrovirus in gastroenteritis outbreak in Hungary

2011 ◽  
Vol 152 (2) ◽  
pp. 45-50 ◽  
Author(s):  
Péter Pankovics ◽  
Ákos Boros ◽  
Melinda Rovács ◽  
Erika Nagy ◽  
Erika Krisztián ◽  
...  
Keyword(s):  
Nucleotide Sequence ◽  
Care Center ◽  
Epidemiological Data ◽  
Oral Route ◽  
Viral Gastroenteritis ◽  
Gastroenteritis Outbreak ◽  
Etiological Role ◽  
Human Astroviruses ◽  
Stool Samples

Human astroviruses are one of the known pathogens of gastroenteritis in infants, children and rarely in elderly. It causes 4.2-7.3% of the sporadic gastroenteritis cases with diarrhea and vomiting in children. The etiological role of astrovirus has not been confirmed yet in outbreaks of gastroenteritis in Hungary. Aims: The first description of the detection and molecular epidemiology of astrovirus in outbreaks of gastroenteritis in Hungary. Materials and methods: Stool samples originated from Komárom-Esztergom County, from a day-care center (nursery) where a gastroenteritis outbreak occurred in June, 2010. Astrovirus was detected by RT-PCR methods. The nucleotide sequence of the nearly complete genome was sequenced. Clinical and epidemiological data were collected by epidemiological investigation. Results: Out of the 29 exposed persons (24 children and 5 adults) 7 (24.1%) children had gastroenteritis with diarrhea, and vomiting in one case, in the period of June 4-15, 2010. Bacterial pathogens, rotavirus, adenovirus and norovirus were not detected, but genotype 1 astrovirus could be identified in 3 (42.8%) stool samples (HQ398856). The nucleotide sequence of the astrovirus ORF1a/ORF1b/ORF2/3’UTR regions was determined. The source of the outbreak was presumably the firstly recognized ill child and the virus was spread by fecal-oral route with direct contact in the children community. Conclusions: Epidemiologic and clinical characteristics of the astrovirus outbreak in the nursery are described in details to prove that the possible etiological role of astroviruses in viral gastroenteritis which should not forget in order after rotaviruses, caliciviruses (norovirus and sapovirus) and enteric adenoviruses. Orv. Hetil., 2011, 152, 45–50.

scholarly journals Epidemiological and Genetic Characterization of Sapovirus in Patients with Acute Gastroenteritis in Valencia (Spain)

Viruses ◽  
2021 ◽  
Vol 13 (2) ◽  
pp. 184
Author(s):  
Sibele de Oliveira-Tozetto ◽  
Cristina Santiso-Bellón ◽  
Josep M. Ferrer-Chirivella ◽  
Noemi Navarro-Lleó ◽  
Susana Vila-Vicent ◽  
...  
Keyword(s):  
Acute Gastroenteritis ◽  
Age Groups ◽  
Enteric Virus ◽  
Diagnostic Procedures ◽  
University Hospital ◽  
Molecular Diagnostic ◽  
Positive Rate ◽  
Enteric Infections ◽  
Stool Samples

Sapovirus is a common cause of acute gastroenteritis in all age groups. Sapovirus infections are seldom investigated in Spain, and its epidemiology in the country is not well known. The use of molecular diagnostic procedures has allowed a more frequent detection of sapoviruses in patients with diarrhea. A total of 2545 stool samples from patients with acute gastroenteritis attended from June 2018 to February 2020 at the Clinic University Hospital in Valencia, Spain, were analyzed by reverse transcription (RT) and real-time multiplex PCR (RT-PCR) to investigate the etiology of enteric infections. Sapovirus was the second enteric virus detected with a positive rate of 8%, behind norovirus (12.2%) and ahead of rotavirus (7.1%), astrovirus (4.9%) and enteric adenoviruses (2.9%). Most sapovirus infections occurred in infants and young children under 3 years of age (74%) with the highest prevalence in autumn and early winter. Coinfections were found in 25% of the patients with sapovirus diarrhea, mainly with other enteric viruses. Genotyping demonstrated the circulation of seven different genotypes during the study period, with a predominance of genotypes GI.1, GI.2, and GII.1. Phylogenetic analysis showed that genogroup GII strains form a cluster separated from genogroup GI and GV, being genotype GV.1 strains related to genotype GI.1 and GI.2 strains.

scholarly journals Genetic recombination and diversity of sapovirus in pediatric patients with acute gastroenteritis in Thailand, 2010–2018

PeerJ ◽  
2020 ◽  
Vol 8 ◽  
pp. e8520 ◽  
Author(s):  
Kattareeya Kumthip ◽  
Pattara Khamrin ◽  
Hiroshi Ushijima ◽  
Limin Chen ◽  
Shilin Li ◽  
...  
Keyword(s):  
Acute Gastroenteritis ◽  
Genetic Recombination ◽  
Age Groups ◽  
Etiologic Agent ◽  
Rt Pcr ◽  
Chiang Mai ◽  
Predominant Genotype ◽  
Recombinant Strains ◽  
Stool Samples ◽  
First Time

Background Human sapovirus (SaV) is an etiologic agent of acute gastroenteritis (AGE) in all age groups worldwide. Genetic recombination of SaV has been reported from many countries. So far, none of SaV recombinant strain has been reported from Thailand. This study examined the genetic recombination and genotype diversity of SaV in children hospitalized with AGE in Chiang Mai, Thailand. Methods Stool samples were collected from children suffering from diarrhea who admitted to the hospitals in Chiang Mai, Thailand between 2010 and 2018. SaV was detected by RT-PCR and the polymerase and capsid gene sequences were analysed. Results From a total of 3,057 samples tested, 50 (1.6%) were positive for SaV. Among positive samples, SaV genotype GI.1 was the most predominant genotype (40%; 20/50), followed by GII.1 and GII.5 (each of 16%; 8/50), GI.2 (14%; 7/50), GIV.1 (4%; 2/50), and GI.5 (2%; 1/50). In addition, 4 SaV recombinant strains of GII.1/GII.4 were identified in this study (8%; 4/50). Conclusions The data revealed the genetic diversity of SaV circulating in children with AGE in Chiang Mai, Thailand during 2010 to 2018 and the intragenogroup SaV recombinant strains were reported for the first time in Thailand.

scholarly journals Parasitic Infections among Children of Squatter Community in Dharan Municipality, Sunsari, Nepal

2016 ◽  
Vol 4 (2) ◽  
pp. 203-206 ◽  
Author(s):  
R. Chongbang ◽  
P. Dongol ◽  
A. Chakrawarti ◽  
H. Khanal
Keyword(s):  
Technical College ◽  
Intestinal Parasites ◽  
Parasitic Infection ◽  
Epidemiological Studies ◽  
Parasitic Infections ◽  
Management Actions ◽  
High Prevalence ◽  
Positive Rate ◽  
Awareness Programs ◽  
Stool Samples

Background and Objective: Children of squatter community are more prone to many infections and epidemiological studies provide to develop suitable preventive plans. Thus, the main objective of the present study was to determine the prevalence of parasitic infections among children of Squatter Community of Dharan Municipality.Methodology: Altogether 184 stool samples were collected from June 2014 to January 2015. The samples were examined using direct microscopy by saline wet mount technique in the microbiology laboratory of Sunsari Technical College, Dharan.Results: The overall prevalence of intestinal parasites was found to be 41.4% with male children more infected (45.8%) than female children (37.5%). Children between 4-8 years of age were most infected (48.1%). Among 4 species of parasites detected Ascaris lumbricoides (18.1%) was the commonest helminths and Giardia lamblia (74.02%) was the commonest protozoa. Positive rate was higher in Dalits (59.7%, 43/72) and the least in Tibeto-Burman (27.1%, 22/81) (p<0.05) ethnic groups.52.5% of children not using water and 33.6% of children using bucket water at toilet after defecation were infected. Children using soap for hand washing after defecation were less infected (32.02%) than other children (55.1%). Children taking the anti-parasitic drug in last six months had significantly low positive rate (9.3%) than others (51.7%) (p<0.05).Conclusion: High prevalence of parasitic infection was observed among children in Squatter community of Dharan Municipality. Thus, health education along with infection management actions and the awareness programs for sanitation improvements are required to reduce the parasitosis.Int J Appl Sci Biotechnol, Vol 4(2): 203-206

scholarly journals Evaluation of the BioFire Gastrointestinal Panel to Detect Diarrheal Pathogens in Pediatric Patients

Diagnostics ◽  
2021 ◽  
Vol 12 (1) ◽  
pp. 34
Author(s):  
Sung Jin Jo ◽  
Hyun Mi Kang ◽  
Jung Ok Kim ◽  
Hanwool Cho ◽  
Woong Heo ◽  
...  
Keyword(s):  
Pediatric Patients ◽  
Enteric Virus ◽  
Rapid Identification ◽  
Health Concern ◽  
True Positive ◽  
Comparator Method ◽  
Molecular Tests ◽  
Discrepancy Analysis ◽  
Positive Rate ◽  
Stool Samples

Infectious diarrhea is a global pediatric health concern; therefore, rapid and accurate detection of enteropathogens is vital. We evaluated the BioFire® FilmArray® Gastrointestinal (GI) Panel with that of comparator laboratory tests. Stool samples of pediatric patients with diarrhea were prospectively collected and tested. As a comparator method for bacteria, culture, conventional PCR for diarrheagenic E. coli, and Allplex GI-Bacteria(I) Assay were tested. For discrepancy analysis, BD MAX Enteric Bacterial Panel was used. As a comparator method for virus, BD MAX Enteric Virus Panel and immunochromatography was used and Allplex GI-Virus Assay was used for discrepancy analysis. The “true positive” was defined as culture-positive and/or positive results from more than two molecular tests. Of the 184 stool samples tested, 93 (50.5%) were true positive for 128 pathogens, and 31 (16.9%) were positive for multiple pathogens. The BioFire GI Panel detected 123 pathogens in 90 of samples. The BioFire GI Panel demonstrated a sensitivity of 100% for 12 targets and a specificity of >95% for 16 targets. The overall positive rate and multiple pathogen rate among patients in the group without underlying diseases were significantly higher than those in the group with hematologic disease (57.0% vs. 28.6% (p = 0.001) and 20.4% vs. 4.8% (p = 0.02), respectively). The BioFire GI Panel provides comprehensive results within 2 h and may be useful for the rapid identification of enteropathogens.

Molecular Detection of Group A Rotavirus in under Five Years Old Children with Acute Diarrhoea Admitted to Yangon Children’s Hospital

2019 ◽  
Vol 31 (1) ◽  
pp. 87-92
Keyword(s):  
Acute Diarrhoea ◽  
Enzyme Linked Immunosorbent Assay ◽  
Viral Gastroenteritis ◽  
Cross Sectional ◽  
Under Five ◽  
Group A Rotavirus ◽  
Rotavirus Vaccination ◽  
Group A ◽  
Stool Samples ◽  
Considerable Morbidity

Rotaviruses are regarded as the most common cause of viral gastroenteritis and are responsible for considerable morbidity and mortality among children especially under five years of age worldwide. In developing countries like Myanmar, where diarrhoea is in the priority childhood disease, rotavirus surveillance and detection of rotavirus genotypes are utmost important. A hospital-based, cross-sectional descriptive study was conducted at Yangon Children‟s Hospital among under five children admitted for acute diarrhoea from January to October 2016. This study includes detection of Group A rotavirus antigen by commercial enzyme-linked immunosorbent assay (ELISA) and genotyping by multiplex RT-PCR. From a total of 488 collected samples, rotavirus antigen was detected in 219 samples (45%). Rotavirus diarrhoea was most common among the age of 6-11 months (38.8%) followed by 12-23 months (37.9%). The results showed that boys were more commonly affected than girls. Detection of rotavirus positivity was peak in February (57.6 %). Out of 219 stool samples with positive ELISA result, 40 stool samples with high optical density value were proceeded for further determination of G and P genotypes. Regarding distribution of G genotypes, the most common G genotype was G9 which comprised 45%, and that of P genotype was P[8] which comprised 92.5%. Regarding combination of G and P genotypes, the most frequent combination is G9P[8], and it constituted 42.5%. Untypable genotypes were seen in 30% of G and 2.5% of P typing. As rotavirus infection can be prevented by vaccine, WHO recommended that rotavirus vaccination should be included in national immunization program especially in countries where prevalence of rotavirus is high. The distribution of G and P genotypes is important in consideration of appropriate vaccine in pre-vaccination and evaluation of effectiveness of vaccine in post-vaccination period. Therefore, the information on currently circulating genotypes of rotavirus in this study will serve as valuable data for vaccination programme.

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