Fujii Yoshiki, Doan Yen Hai, Suzuki Yoshiyuki, Nakagomi Toyoko, Nakagomi Osamu, Katayama Kazuhiko
Department of Virology II, National Institute of Infectious Diseases, Tokyo, Japan.
Graduate School of Natural Sciences, Nagoya City University, Nagoya, Japan.
Front Microbiol. 2019 Jan 31;10:38. doi: 10.3389/fmicb.2019.00038. eCollection 2019.
A comprehensive molecular epidemiological study using next-generation sequencing technology was conducted on 333 rotavirus A (RVA)-positive specimens collected from six sentinel hospitals across Japan over three consecutive seasons (2012-2014). The majority of the RVA isolates were grouped into five genotype constellations: Wa-like G1P[8], DS-1-like G1P[8], G2P[4], G3P[8] and G9P[8]. Phylogenetic analysis showed that the distribution of strains varied by geographical locations and epidemic seasons. The VP7 genes of different G types were estimated to evolve at 7.26 × 10-1.04 × 10 nucleotide substitutions per site per year. The Bayesian time-scaled tree of VP7 showed that the time to the most recent common ancestor of epidemic strains within a region was 1-3 years, whereas that of the epidemic strains across the country was 2-6 years. This study provided, for the first time, the timeframe during which an epidemic strain spread locally and within the country and baseline information needed to predict how rapidly RVAs spread.
我们使用下一代测序技术，对在连续三个季节（2012 - 2014年）从日本六家哨点医院收集的333份轮状病毒A（RVA）阳性标本进行了全面的分子流行病学研究。大多数RVA分离株被分为五个基因型组合：Wa样G1P[8]、DS - 1样G1P[8]、G2P[4]、G3P[8]和G9P[8]。系统发育分析表明，毒株的分布因地理位置和流行季节而异。不同G型的VP7基因估计每年每个位点的核苷酸替换率为7.26×10 - 1.04×10。VP7的贝叶斯时间尺度树显示，一个地区内流行毒株最近共同祖先的时间为1 - 3年，而全国流行毒株的时间为2 - 6年。本研究首次提供了流行毒株在当地和国内传播的时间框架，以及预测RVA传播速度所需的基线信息。
