Viral metagenomics reveals sapoviruses of different genogroups in stool samples from children with acute gastroenteritis in Jiangsu, China

Abstract

Sapoviruses (SAVs), including several genogroups (GI to GV), are one of the causes of acute gastroenteritis (AGE). In this study, viral metagenomics revealed the presence of sapoviruses of different genogroups in stool from children with AGE. Eight different complete SAV genomes were determined, of which five belonged to GI and the other three belonged to GII, GIV and GV, respectively. Although they were highly similar to published sequences, the GIV and GV were the first complete genome sequences of these SAVs found in China. In a prevalence investigation, 19% of subjects with AGE were positive for SAVs, while none of the control group was positive.Publisher's Note Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.

Molecular Epidemiology of Sapovirus in Children Living in the Northwest Amazon Region

“…Sapoviruses are now recognized as an important cause of AGE in children [ 3 , 29 , 30 , 31 , 32 ]. In this study, we investigated the genetic variability of sapoviruses in children in the Amazon region.…”

“…Genetic characterization of sapoviruses using molecular methods can be difficult due to the genetic variability of the region encoding the major structural VP1 protein, requiring the design of new primers. The application of primer-independent metagenomic sequencing approaches for identification of human sapovirus has also been reported recently and is able to characterize the presence of sapoviruses of different genogroups in feces from children with AGE [ 31 ]. We observed a heterogeneity and spread of sapovirus genotypes throughout the Amazon region where the children live.…”

Metagenomic Detection and Genetic Characterization of Human Sapoviruses among Children with Acute Flaccid Paralysis in Nigeria

“…Viral metagenomics has proven to be an effective technique for discovering new viruses and expanding our understanding of the diversity of viruses found in clinical samples, including the identification of new SaV strains [ 29 , 31 ]. Metagenomic analyses using whole genome sequencing are becoming more common in clinical settings, and they have been used for the in-depth genomic analysis of SaVs in four different countries in the Americas [ 32 ] and China [ 33 , 34 ]. The use of whole genome rather than short genome sequences has improved the in-depth analysis of viral genomes, including members in the Caliciviridae family that have the capability to rapidly evolve, recombine, and acquire mutations [ 32 , 35 ].…”

Polymerase chain reaction primer sets for the detection of genetically diverse human sapoviruses

“…Human sapoviruses are currently assigned to one of four genogroups (GI, GII, GIV, and GV) and are further classified into at least 18 genotypes (GI.1-7, GII.1-8, GIV.1, and GV.1-2) based on their VP1 sequences [ 7 ]. Nucleic acid detection methods, especially reverse transcription (RT)- polymerase chain reaction (PCR) and real-time RT-PCR assays, are widely used for the screening of human sapoviruses [ 1 ]; however, the application of primer-independent metagenomic sequencing approaches for identification of human sapoviruses has also been reported recently [ 8 – 10 ]. Multiple primer sets for RT-PCR have been designed to detect human sapoviruses [ 1 ], but their reactivity with different human sapovirus genotypes has not been experimentally demonstrated except in our recent real-time RT-PCR study [ 11 ].…”