Molecular characterization of human astrovirus genotypes and recombinant strains circulating in pediatric patients with acute gastroenteritis

Abstract

Human astrovirus (HAstV) is the common cause of acute gastroenteritis in children. The investigation of molecular epidemiology of HAstV is essential for monitoring the emergence and/or re-emergence of new HAstV genotypes, as well as understanding the evolution of HAstV circulating in children suffering from acute gastroenteritis. The present study aimed to investigate the prevalence and distribution of HAstV strains circulating in children hospitalized with acute gastroenteritis in Chiang Mai, Thailand during 2019 to 2020 and the emergence of HAstV recombinant strains in pediatric patients hospitalized with acute gastroenteritis in Chiang Mai, Thailand, spanning of 2011 to 2020. A total of 623 fecal specimens collected from children with acute gastroenteritis were screened for HAstV by RT-PCR that targeted the partial RdRp in ORF 1b and strains were characterized by sequencing and phylogenetic analysis. Of 623 fecal samples, 11 (1.8%) were positive for HAstV. Of these, both classic and novel HAstV genotypes, including classic HAstV1-HAstV5 and novel HAstV-MLB1, were detected. The classic HAstV1 was detected as the most common genotype at a prevalence of 0.64% (4 of 623), followed by classic HAstV4 and novel HAstV-MLB1 each of 0.32% (2 of 623), and classic HAstV2, HAstV3, and HAstV5 each of 0.16% (1 of 623). For the HAstV recombinant strains detection, a total of 92 archival HAstV strains collected from pediatric patients with acute gastroenteritis during the period of 2011 to 2020 were further

characterized to identify the recombinant strains. The ORF1b (RdRp) and ORF2 (capsid) junction region of each strain was amplified and sequenced. The obtained sequences were analysed in comparison with the reference sequences retrieved from GenBank database. Their genotypes were assigned using MEGA X software based on the partial ORF1b and ORF2 regions, and the recombination breakpoints of recombinant strains were determined by SimPlot and RDP4 analyses. Five inter-genotype recombinant strains with three recombination patterns of ORF1b/ORF2 of classic HAstV, HAstV8/HAstV1, HAstV8/HAstV3, and HAstV3/HAstV2, were detected. The recombination breakpoints were located at 3'-end region of ORF1b close to the ORF1b/ORF2 junction. In conclusion, the data in this study revealed a relatively high divergence of HAstV genotypes circulating in pediatric patients admitted to the hospitals with acute gastroenteritis in Chiang Mai, Thailand during 2019 to 2020. The classic HAstV1 was the predominant genotype. In addition, several novel inter-genotype recombinant strains of classic HAstV genotypes were detected in pediatric patients with acute gastroenteritis in Chiang Mai, Thailand, during the period of ten years from 2011 to 2020.