Abstract
Background: Rotavirus (RV) A is one of the major reasons which causes acute dehydration and diarrhea. It is also one of the highest morbid diseases in children. There are only a few reports about the changes in prevalence and VP4/VP7 genotype of RVs in southwest China. Here is the report about the prevalence of RVs from 2015 to 2020 in Yunnan, southwest China. Methods: The virus genes were extracted from RV positive samples, then VP4/VP7 genes were amplified, followed by sequencing and gene typing, phylogenetic analysis, antigenic epitope variation analysis, and selective pressure analysis were also performed. Results: A total of 135 VP4 gene sequences and 143 VP7 gene sequences were obtained from stool samples during 2015-2020. Of them, P[8] genotype accounted for 97.0% of the total, while the P[4] genotype accounted for 3.0%. As for the VP7 genotype, G9 genotype accounted for 86.0% of the total, the G3 genotype accounted for 9.1%, and the G2 genotype accounted for 4.9%. G9P[8] was identified as the predominant RV strain during the epidemic season in Yunnan during 2015-2020. Phylogenetic analysis showed that G9 genotype sequences were primarily similar to African strains (KJ753473, KY661937), while P[8] genotype sequences were close to Southeast Asian strains (JQ837878, KX362594). In antigenic epitope variation analysis, among 37 epitopes of P[8] genotype, the RotaTeq™ vaccine strain covers 31 amino acid positions, Rotarix™ covers 28 amino acid positions, while LLR covers only 9. In the representative sequence of the G9 genotype, RotaTeq™ vaccine strains cover 27 out of 29 amino acid positions, Rotarix™ covers 16 positions, and LLR covers 16 positions. The results of the selective pressure analysis indicated potential positive sites for the G9P[8] genotype located at vp7-44, vp7-100, vp7-221, vp7-278, vp4-3, and vp4-4. Conclusions: Our study shows that G9P[8] is the most dominant RV genotype in Yunnan, China. Consistent with the recent epidemic trend of RV strains in China, this study could provide new perspectives on vaccine research.