Kobayashi Miho, Yoshizumi Shima, Kogawa Sayaka, Takahashi Tomoko, Ueki Yo, Shinohara Michiyo, Mizukoshi Fuminori, Tsukagoshi Hiroyuki, Sasaki Yoshiko, Suzuki Rieko, Shimizu Hideaki, Iwakiri Akira, Okabe Nobuhiko, Shirabe Komei, Shinomiya Hiroto, Kozawa Kunihisa, Kusunoki Hideki, Ryo Akihide, Kuroda Makoto, Katayama Kazuhiko, Kimura Hirokazu
Gunma Prefectural Institute of Public Health and Environmental Science, Maebashi-shi, Gunma 371-0052, Japan.
Hokkaido Institute of Public Health, Sapporo-shi, Hokkaido 060-0819, Japan.
Sci Rep. 2015 Sep 4;5:13806. doi: 10.1038/srep13806.
We studied the molecular evolution of the capsid gene in all genotypes (genotypes 1-9) of human norovirus (NoV) genogroup I. The evolutionary time scale and rate were estimated by the Bayesian Markov chain Monte Carlo (MCMC) method. We also performed selective pressure analysis and B-cell linear epitope prediction in the deduced NoV GI capsid protein. Furthermore, we analysed the effective population size of the virus using Bayesian skyline plot (BSP) analysis. A phylogenetic tree by MCMC showed that NoV GI diverged from the common ancestor of NoV GII, GIII, and GIV approximately 2,800 years ago with rapid evolution (about 10(-3) substitutions/site/year). Some positive selection sites and over 400 negative selection sites were estimated in the deduced capsid protein. Many epitopes were estimated in the deduced virus capsid proteins. An epitope of GI.1 may be associated with histo-blood group antigen binding sites (Ser377, Pro378, and Ser380). Moreover, BSP suggested that the adaptation of NoV GI strains to humans was affected by natural selection. The results suggested that NoV GI strains evolved rapidly and date back to many years ago. Additionally, the virus may have undergone locally affected natural selection in the host resulting in its adaptation to humans.
我们研究了人诺如病毒（NoV）基因组I所有基因型（基因型1 - 9）的衣壳基因的分子进化。通过贝叶斯马尔可夫链蒙特卡罗（MCMC）方法估计进化时间尺度和速率。我们还对推导的NoV GI衣壳蛋白进行了选择压力分析和B细胞线性表位预测。此外，我们使用贝叶斯天际线图（BSP）分析了病毒的有效种群大小。由MCMC构建的系统发育树表明，NoV GI大约在2800年前从NoV GII、GIII和GIV的共同祖先分化出来，进化迅速（约10⁻³ 替换/位点/年）。在推导的衣壳蛋白中估计出一些正选择位点和400多个负选择位点。在推导的病毒衣壳蛋白中估计出许多表位。GI.1的一个表位可能与组织血型抗原结合位点（Ser377、Pro378和Ser380）有关。此外，BSP表明NoV GI毒株对人类的适应性受到自然选择的影响。结果表明，NoV GI毒株进化迅速，可追溯到多年前。此外，该病毒可能在宿主中经历了局部影响的自然选择，从而导致其对人类的适应性。
