Molecular characterization of Rotaviruses detected in pediatric patients with Acute Gastroenteritis in Chiang Mai, Thailand

Abstract

Rotaviruses (RVs) are the major viruses that cause acute gastroenteritis in children younger than 5 years, especially in developing countries in Asia and Africa. The objectives of this study were to investigate the prevalence and genotype distribution of group A rotaviruses (RVAs) circulating in children with acute gastroenteritis in Chiang Mai, Thailand in 2018 and 2019 before the implementation of RVA vaccine in the childhood immunization programme in 2020. A total of 1,170 stool specimens were collected from children admitted to hospitals with acute gastroenteritis in Chiang Mai and screened for RVA by reverse transcription-polymerase chain reaction (RT-PCR). The RVA genotypes were determined by multiplex PCR with genotype specific primers or nucleotide sequencing. The nucleotide sequences were analyzed for their genetic relationship with other reference strains in GenBank database by phylogenetic analysis. Out of 1,170 stool specimens, 209 (17.9%) were positive for RVA. The identification of RV genotypes revealed wide variety of G and P genotype combinations. It was found that RVA genotype G9P[8] (24.4%) was detected as the most dominant genotype, followed by G3P[8] (22.9%), G8P[8] (22.0%), GIP[8] (16.7%), G2P[4] (6.7%), GIP[6] (2.3%), G1P[4] (1.0%), G3P[4] (1.0%),G9P[4] (1.0%), mixed infections of G1P[4]+G1P[8] (1.0%), and GXP[8] (0.5%). Moreover, this study was detected the uncommon RVA strain G3P[10] (0.5%) bearing bat-like RVA genome. In conclusion, this study demonstrates the prevalence and genetic diversity of RVA genotypes in children with acute gastroenteritis in Chiang Mai. The knowledge obtained from this study is useful for understanding the epidemiology of rotavirus before the introduction of RVA vaccine in Thailand. In addition, the emergence of uncommon G-P combination RVA strains provides an important evidence for interspecies transmission of human and animal rotaviruses.