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

Abstract

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.

Genomic Analyses of Human Sapoviruses Detected over a 40-Year Period Reveal Disparate Patterns of Evolution among Genotypes and Genome Regions

“…Based on the genetic differences of the VP1-encoding sequences, human sapoviruses are phylogenetically clustered into four genogroups (GI, GII, GIV and GV), with each genogroup further clustered into multiple genotypes [1,4]. Discrepancies in the phylogenetic clustering can occur when using different genomic regions, particularly those encoding the RdRp and VP1, and this has led to the identification of intra-and inter-genogroup recombinant strains [1,[5][6][7][8][9][10][11][12][13].…”

“…Indeed, recombination has been shown to be an important mechanism of diversification for norovirus and other caliciviruses [1,14,15]. Some of the recombination events reported for sapoviruses did not clearly describe both parental strains [5][6][7]10,13], thus the "recombination signal" might be confounded by the possibility of different evolutionary diversification patterns among sapovirus genomic regions [16].…”

An outbreak of gastroenteritis associated with a novel GII.8 sapovirus variant-transmitted by vomit in Shenzhen, China, 2019

“…Based on complete capsid gene (VP1) sequences, SaVs are classified into at least 15 genogroups (GI − GXV), four of which (GI, GII, GIV and GV) are known to infect humans. The human SaVs in genogroups GI, GII, GIV and GV are currently subdivided into 7 GI (GI.1-GI.7), 8 GII (GII.1-GII.8) and one GII.NA, 1 GIV (GIV.1) and 2 GV (GV.1 and GV.2) genotypes [11], and one additional genotype of GII.NA that has been reported recently [12].…”

An Outbreak of Gastroenteritis Associated with a Novel GII.8 Sapovirus Variant-Transmitted by Vomit in Shenzhen, China, 2019

“…Based on complete capsid gene (VP1) sequences, sapoviruses are classi ed into at least 15 genogroups (GI−GXV), four of which (GI, GII, GIV and GV) are known to infect humans. The human sapoviruses in genogroups GI, GII, GIV and GV are currently subdivided into 7 GI (GI.1-GI.7), 8 GII (GII.1-GII.8) and one GII.NA, 1 GIV (GIV.1) and 2 GV (GV.1 and GV.2) genotypes [11] , and one additional genotype of GII.NA that has been reported recently [12] .…”