Supplementary Material for: Genetic and Antigenic Variability in VP4 and VP7 of Group A Human Rotavirus in Yunnan, China from 2015-2020.

Background: Rotavirus(RVs) A is one of major reasons which causes severe dehydration diarrhea. It is also one of the high morbidity disease 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 RV 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: 135 VP4 gene sequences and 143 VP7 gene sequences were obtained from stool samples during 2015 to 2020. Of them, P[8] genotype accounted for 97.0% of total, while the P[4] genotype accounted for 3.0%. As for the VP7 genotype, G9 genotype accounted for 86.0% of 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 to 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 epitope 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™ cover 16 positions, and LLR cover 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 rotavirus genotype in Yunnan China. Consistent with the recent epidemic trend of RV strains in China, this study could provide new perspectives on vaccine research.

背景：轮状病毒A组（Rotavirus A）是引发重症脱水性腹泻的主要病因之一，亦是儿童高发疾病之一。目前针对中国西南地区轮状病毒流行率及VP4/VP7基因型（VP4/VP7 genotype）变化的相关研究报道较少。本研究针对中国西南云南省2015至2020年的轮状病毒流行情况展开报告。
方法：研究人员从轮状病毒阳性样本中提取病毒基因，随后对VP4基因（VP4 gene）与VP7基因（VP7 gene）进行扩增，继而开展测序与基因分型、系统发育分析、抗原表位变异分析及选择压力分析。
结果：2015至2020年间，研究人员从粪便样本中获得135条VP4基因序列与143条VP7基因序列。其中P[8]基因型占总样本的97.0%，P[4]基因型占3.0%。VP7基因型方面，G9基因型占总样本的86.0%，G3基因型占9.1%，G2基因型占4.9%。G9P[8]被确定为2015至2020年云南地区流行季的优势轮状病毒毒株。系统发育分析显示，G9基因型序列与非洲毒株（KJ753473、KY661937）高度同源，而P[8]基因型序列与东南亚毒株（JQ837878、KX362594）亲缘关系较近。抗原表位变异分析结果表明，P[8]基因型的37个表位中，RotaTeq™疫苗株覆盖31个氨基酸位点，Rotarix™覆盖28个氨基酸位点，LLR仅覆盖9个。在G9基因型的代表性序列中，RotaTeq™疫苗株覆盖29个氨基酸位点中的27个，Rotarix™覆盖16个位点，LLR同样覆盖16个位点。选择压力分析结果显示，G9P[8]基因型存在潜在阳性选择位点：vp7-44、vp7-100、vp7-221、vp7-278、vp4-3及vp4-4。
结论：本研究表明，G9P[8]是中国云南地区最主要的轮状病毒基因型。本研究结果与中国近期轮状病毒毒株的流行趋势相符，可为疫苗研发提供新的研究视角。