Table_1_Genomic and evolutionary characteristics of G9P[8], the dominant group a rotavirus in China (2016–2018).DOCX

G9P[8] became the predominant rotavirus A (RVA) genotype in China in 2012. To evaluate its genetic composition at the whole-genome level, 115 G9P[8] RVA strains isolated from children under 5 years old were sequenced and characterized. All 13 strains in 2016 and 2017 and an additional 54 strains in 2018 were genotyped as G9-P[8]-I1-R1-C1-M1-A1-N1-T1-E1-H1. The other 48 strains in 2018 were all genotyped as G9-P[8]-I1-R1-C1-M1-A1-N1-T1-E2-H1, with the NSP4 gene characterized as a DS-1-like genotype. The time of the most recent common ancestor (tMRCA) and evolution rates of the VP7, VP4, and NSP4 (E1 and E2) genes of these strains were estimated by Bayesian evolutionary dynamics analysis. We estimated the evolution rates (nt substitutions per site per year) as 1.38 × 10–3 [the 95% highest posterior density (HPD) was 1.09–1.72 × 10–3] for VP7, 0.87 × 10–3 (95% HPD: 0.75–1.00 × 10–3) for VP4, 0.56 × 10–3 (95% HPD: 0.41–0.73 × 10–3) for NSP4-E1, and 1.35 × 10–3 (95% HPD: 0.92–1.86 × 10–3) for NSP4-E2. The tMRCA was estimated to be 1935.4 (95% HPD: 1892.4–1961.3) for VP7, 1894.3 (95% HPD: 1850.5–1937.8) for VP4, 1929.4 (95% HPD: 1892.4–1961.3) for NSP4-E1, and 1969.2 (95% HPD: 1942.2–1985.3) for NSP4-E2. The baseline genetic information in this study is expected to improve our understanding of the genomic and evolutionary characteristics of the rotavirus genome. Furthermore, it will provide a basis for the development of next-generation rotavirus vaccines for humans.

G9P[8]于2012年成为中国流行的主要轮状病毒A型（RVA）基因型。为评估其全基因组水平的遗传组成，对115株来自5岁以下儿童的G9P[8] RVA进行了测序和鉴定。2016年和2017年的13个菌株以及2018年的额外54个菌株被鉴定为G9-P[8]-I1-R1-C1-M1-A1-N1-T1-E1-H1基因型。2018年的其余48个菌株均被鉴定为G9-P[8]-I1-R1-C1-M1-A1-N1-T1-E2-H1基因型，其中NSP4基因被鉴定为DS-1型基因型。通过贝叶斯进化动力学分析，估计了这些菌株VP7、VP4和NSP4（E1和E2）基因的最近期共同祖先时间（tMRCA）和进化速率。我们估计的进化速率（每位点每年核苷酸替换数）为VP7为1.38 × 10–3[95%最高后验密度（HPD）为1.09–1.72 × 10–3]，VP4为0.87 × 10–3（95% HPD：0.75–1.00 × 10–3），NSP4-E1为0.56 × 10–3（95% HPD：0.41–0.73 × 10–3），NSP4-E2为1.35 × 10–3（95% HPD：0.92–1.86 × 10–3）。tMRCA估计为VP7为1935.4（95% HPD：1892.4–1961.3），VP4为1894.3（95% HPD：1850.5–1937.8），NSP4-E1为1929.4（95% HPD：1892.4–1961.3），NSP4-E2为1969.2（95% HPD：1942.2–1985.3）。本研究中的基线遗传信息有望提升我们对轮状病毒基因组及其进化特性的理解。此外，它将为开发针对人类的下一代轮状病毒疫苗提供基础。