The molecular detection and genetic characterization of human norovirus and sapovirus in pediatric patients with acute diarrhea in Chiang Mai, Thailand

Abstract

Human enteric pathogens in the family Caliciviridae including norovirus (NoV) and sapovirus (SaV) are associated with acute diarrheal disease globally and are considered as one of the viruses with high genetic diversity. In order to investigate the epidemiology of NoV and SaV in pediatric patients with acute diarrhea in Chiang Mai, Thailand from January 2019 to December 2020, a total of 675 stool specimens were collected and tested for the presence of NoV and SaV by RT-multiplex PCR. The results showed that 126 (18.7%) and 6 (0.9%) stool samples were positive for NoV and SaV, respectively. Mixed infection of NoV and SaV was detected in one patient (0.2%). Among 10 different NoV strains detected in this study, NoV genogroup II genotype 4 (GII.4) was the most predominant genotype followed by GII.3, GII.2, GII.6, GII.12, GII.7, GII.17, GI.4, GII.14, and GI.3. For GII.4 variants, Sydney 2012 was the most predominant variant. Interestingly, monthly distribution of NoV genotypes revealed that NoV GII.3 increased dramatically in August 2019, suggesting an outbreak of NoV GII.3 in the community. In addition, 3 genotypes of SaV were detected in this study. Of these, SaV GI.1 was the most predominant genotype followed by GI.2 and GII.5. For the dual-typing of NoV GII, 64 out of 124 NoV strains detected in this study were successfully amplified for the partial RdRp/VP1 region by semi-nested PCR. Of these, NoV GII.4 Sydney 2012[P16] was the most prevalent type, followed by GII.3[P12], GII.4 Sydney 2012[P31], GII.2[P16], GII.12[P16], GII.6[P7], GII.17[P17], and GII.7[P7]. In conclusion, this study demonstrates the prevalence and genetic diversity of NoV and SaV circulating in pediatric patients with acute gastroenteritis in Chiang Mai, Thailand during 2019 to 2020 and an emergence of NoV GII.3 infection in 2019.