Kuroda Makoto, Niwa Shoichi, Sekizuka Tsuyoshi, Tsukagoshi Hiroyuki, Yokoyama Masaru, Ryo Akihide, Sato Hironori, Kiyota Naoko, Noda Masahiro, Kozawa Kunihisa, Shirabe Komei, Kusaka Takashi, Shimojo Naoki, Hasegawa Shunji, Sugai Kazuko, Obuchi Masatsugu, Tashiro Masato, Oishi Kazunori, Ishii Haruyuki, Kimura Hirokazu
Pathogen Genomics Center, National Institute of Infectious Diseases, 1-23-1 Toyama, Shinjuku-ku, Tokyo 162-8640, Japan.
Gunma Prefectural Institute of Public Health and Environmental Sciences, 378 Kamioki-machi, Maebashi-shi, Gunma 371-0052, Japan.
Sci Rep. 2015 Feb 2;5:8185. doi: 10.1038/srep08185.
Human rhinovirus species C (HRV-C) was recently discovered, and this virus has been associated with various acute respiratory illnesses (ARI). However, the molecular evolution of the major antigens of this virus, including VP1, VP2, and VP3, is unknown. Thus, we performed complete VP1, VP2, and VP3 gene analyses of 139 clinical HRV-C strains using RT-PCR with newly designed primer sets and next-generation sequencing. We assessed the time-scale evolution and evolutionary rate of these genes using the Bayesian Markov chain Monte Carlo method. In addition, we calculated the pairwise distance and confirmed the positive/negative selection sites in these genes. The phylogenetic trees showed that the HRV-C strains analyzed using these genes could be dated back approximately 400 to 900 years, and these strains exhibited high evolutionary rates (1.35 to 3.74 × 10(-3) substitutions/site/year). Many genotypes (>40) were confirmed in the phylogenetic trees. Furthermore, no positively selected site was found in the VP1, VP2, and VP3 protein. Molecular modeling analysis combined with variation analysis suggested that the exterior surfaces of the VP1, VP2 and VP3 proteins are rich in loops and are highly variable. These results suggested that HRV-C may have an old history and unique antigenicity as an agent of various ARI.
人鼻病毒C种（HRV-C）最近被发现，并且这种病毒已与各种急性呼吸道疾病（ARI）相关联。然而，该病毒主要抗原（包括VP1、VP2和VP3）的分子进化情况尚不清楚。因此，我们使用新设计的引物对通过逆转录聚合酶链反应（RT-PCR）和下一代测序对139株临床HRV-C毒株进行了完整的VP1、VP2和VP3基因分析。我们使用贝叶斯马尔可夫链蒙特卡罗方法评估了这些基因的时间尺度进化和进化速率。此外，我们计算了成对距离并确定了这些基因中的正/负选择位点。系统发育树表明，使用这些基因分析的HRV-C毒株可以追溯到大约400至900年前，并且这些毒株表现出较高的进化速率（1.35至3.74×10⁻³替换/位点/年）。在系统发育树中确认了许多基因型（>40种）。此外，在VP1、VP2和VP3蛋白中未发现正选择位点。结合变异分析的分子建模分析表明，VP1、VP2和VP3蛋白的外表面富含环结构且高度可变。这些结果表明，HRV-C作为各种ARI的病原体可能具有悠久的历史和独特的抗原性。
