Genetic diversity of sapovirus in non-hospitalized adults with sporadic cases of acute gastroenteritis in Shanghai, China

SUMMARYSapoviruses (SaVs) are responsible for sporadic cases and outbreaks of acute gastroenteritis. Despite this, few studies in India have focused on the epidemiological investigation of SaV in cases of acute gastroenteritis. The aim of this study was to understand the molecular epidemiology, genetic diversity and clinical impact of SaV in diarrhoeic children from Pune, Western India. Between 2007 and 2011, a total of 985 faecal samples from diarrhoeic cases and non-diarrhoeic controls were collected and examined for the presence of SaV by nested RT–PCR. SaV was detected in 2·7% (21/778) of the cases and 1·9% (4/207) of the controls. We observed that the majority of SaV mono-infections caused severe gastroenteritis (67%) with clinical manifestations of diarrhoea (100%), vomiting (73%) and dehydration (80%). All known human SaV genogroups were detected in the study. At least eight genotypes were identified from cases and controls. Genogroups GIV and GV, along with genotypes GI.5, GII.4 and GII.6, were discovered for the first time in India. Two GII.4 study strains were found to be 98·5–99% identical, having a novel intra-genogroup recombinant (GII.1/GII.4) recently reported from the Philippines, suggesting probable evidence of recombination. The circulation pattern of SaV genotypes varied during the study period, with GII.1 being predominant in 2007 and 2009, GIV.1 in 2008, and GV.1 in 2011.

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Molecular Epidemiology of Oyster-Related Human Noroviruses and Their Global Genetic Diversity and Temporal-Geographical Distribution from 1983 to 2014

Applied and Environmental Microbiology ◽

10.1128/aem.01729-15 ◽

2015 ◽

Vol 81 (21) ◽

pp. 7615-7624 ◽

Cited By ~ 32

Author(s):

Yongxin Yu ◽

Hui Cai ◽

Linghao Hu ◽

Rongwei Lei ◽

Yingjie Pan ◽

...

Keyword(s):

Genetic Diversity ◽

Quality Control ◽

Molecular Epidemiology ◽

Geographical Distribution ◽

Acute Gastroenteritis ◽

Phylogenetic Analyses ◽

Disease Outbreaks ◽

Temporal Distribution ◽

Global Scale ◽

Sporadic Cases

ABSTRACTNoroviruses (NoVs) are a leading cause of epidemic and sporadic cases of acute gastroenteritis worldwide. Oysters are well recognized as the main vectors of environmentally transmitted NoVs, and disease outbreaks linked to oyster consumption have been commonly observed. Here, to quantify the genetic diversity, temporal distribution, and circulation of oyster-related NoVs on a global scale, 1,077 oyster-related NoV sequences deposited from 1983 to 2014 were downloaded from both NCBI GenBank and the NoroNet outbreak database and were then screened for quality control. A total of 665 sequences with reliable information were obtained and were subsequently subjected to genotyping and phylogenetic analyses. The results indicated that the majority of oyster-related NoV sequences were obtained from coastal countries and regions and that the numbers of sequences in these regions were unevenly distributed. Moreover, >80% of human NoV genotypes were detected in oyster samples or oyster-related outbreaks. A higher proportion of genogroup I (GI) (34%) was observed for oyster-related sequences than for non-oyster-related outbreaks, where GII strains dominated with an overwhelming majority of >90%, indicating that the prevalences of GI and GII are different in humans and oysters. In addition, a related convergence of the circulation trend was found between oyster-related NoV sequences and human pandemic outbreaks. This suggests that oysters not only act as a vector of NoV through environmental transmission but also serve as an important reservoir of human NoVs. These results highlight the importance of oysters in the persistence and transmission of human NoVs in the environment and have important implications for the surveillance of human NoVs in oyster samples.

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Molecular epidemiology and genetic diversity of norovirus infection in children with acute gastroenteritis in Bangladesh, 2014‐2019

Journal of Medical Virology ◽

10.1002/jmv.26772 ◽

2021 ◽

Author(s):

Shuvra Kanti Dey ◽

Nadim Sharif ◽

Baki Billah ◽

Tanjir Tarek Ibn Siddique ◽

Tarequl Islam ◽

...

Keyword(s):

Genetic Diversity ◽

Molecular Epidemiology ◽

Acute Gastroenteritis

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Prevalence and Genetic Diversity of Group A Rotavirus Genotypes in Moscow (2019–2020)

Pathogens ◽

10.3390/pathogens10060674 ◽

2021 ◽

Vol 10 (6) ◽

pp. 674

Author(s):

Anton Yuzhakov ◽

Ksenia Yuzhakova ◽

Nadezhda Kulikova ◽

Lidia Kisteneva ◽

Stanislav Cherepushkin ◽

...

Keyword(s):

Infectious Disease ◽

Genetic Diversity ◽

Acute Gastroenteritis ◽

Rt Pcr ◽

Clinical Hospital ◽

Group A Rotavirus ◽

Group A ◽

First Time ◽

Common Combination ◽

Children Under 5

Group A rotavirus (RVA) infection is the leading cause of hospitalization of children under 5 years old, presenting with symptoms of acute gastroenteritis. The aim of our study was to explore the genetic diversity of RVA among patients admitted to Moscow Infectious Disease Clinical Hospital No. 1 with symptoms of acute gastroenteritis. A total of 653 samples were collected from May 2019 through March 2020. Out of them, 135 (20.67%) fecal samples were found to be positive for rotavirus antigen by ELISA. RT-PCR detected rotavirus RNA in 80 samples. Seven G-genotypes (G1, G2, G3, G4, G8, G9, and G12) and three P-genotypes (P[8], P[4], and P[6]) formed 9 different combinations. The most common combination was G9P[8]. However, for the first time in Moscow, the combination G3P[8] took second place. Moreover, all detected viruses of this combination belonged to Equine-like G3P[8] viruses that had never been detected in Russia before. The genotype G8P[8] and G9P[4] rotaviruses were also detected in Moscow for the first time. Among the studied rotaviruses, there were equal proportions of Wa and DS-1-like strains; previous studies showed that Wa-like strains accounted for the largest proportion of rotaviruses in Russia.

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Changing pattern of prevalence, genetic diversity, and mixed infections of viruses associated with acute gastroenteritis in pediatric patients in New Delhi, India

Journal of Medical Virology ◽

10.1002/jmv.24980 ◽

2017 ◽

Vol 90 (3) ◽

pp. 469-476 ◽

Cited By ~ 8

Author(s):

Shipra Gupta ◽

Anuja Krishnan ◽

Sumit Sharma ◽

Praveen Kumar ◽

Satinder Aneja ◽

...

Keyword(s):

Genetic Diversity ◽

Acute Gastroenteritis ◽

Pediatric Patients ◽

Mixed Infections ◽

New Delhi

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Clinico-epidemiology and genetic diversity of Salivirus in acute gastroenteritis cases from Pune, Western India: 2007–2011

Infection Genetics and Evolution ◽

10.1016/j.meegid.2016.07.047 ◽

2016 ◽

Vol 44 ◽

pp. 425-430 ◽

Cited By ~ 3

Author(s):

N. Lasure. ◽

V. Gopalkrishna.

Keyword(s):

Genetic Diversity ◽

Acute Gastroenteritis ◽

Western India

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Epidemiology and genetic diversity of human parechoviruses circulating among children hospitalised with acute gastroenteritis in Pune, Western India: a 5-years study

Epidemiology and Infection ◽

10.1017/s095026881700262x ◽

2017 ◽

Vol 146 (1) ◽

pp. 11-18 ◽

Cited By ~ 12

Author(s):

P. R. PATIL ◽

N. N. GANORKAR ◽

V. GOPALKRISHNA

Keyword(s):

Genetic Diversity ◽

Acute Gastroenteritis ◽

Clinical Manifestations ◽

Western India ◽

Vp1 Gene ◽

Rt Pcr ◽

Chain Reaction ◽

Predominant Genotype ◽

Stool Specimens ◽

Polymerase Chain

SUMMARYHuman parechoviruses (HPeVs) are known to cause various clinical manifestations including acute gastroenteritis. Although HPeV infections and their genotypes have been detected in human patients worldwide, no such reports are available from India to ascertain the association of HPeVs in acute gastroenteritis. The present study was conducted to determine the clinical features and genetic diversity of HPeVs detected in children hospitalised for acute gastroenteritis. Stool specimens (n= 979) collected from children aged ⩽5 years hospitalised for acute gastroenteritis in Pune, western India during January 2006–December 2010 were included. HPeV RNA was detected by reverse transcription-polymerase chain reaction (RT-PCR) (5′UTR) followed by genotyping using VP1 gene-based PCR and phylogenetic analysis. HPeV was detected in 13·9% (136/979) of the cases, co-infections with other enteric viruses were found in 43·4%. HPeV was more frequent in children ⩽1 year age with infections reported throughout the year. A total of 102/136 (75%) HPeV strains were genotyped, which comprised 13 different HPeV genotypes. Of these, HPeV1 was the most predominant genotype detected and phylogenetically clustered with the Harris strain which is rarely reported. The study documents circulation of heterogeneous HPeV genotypes. Two variant strains of HPeV4 and ‘RGD absent’ HPeV5 and 6 strains were also detected. This is the first report of HPeV with diversified genotypes identified in acute gastroenteritis patients from India.

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