Chikungunya virus (CHIKV), an alphavirus of the Togaviridae family, is among the most medically significant mosquito-borne viruses, capable of causing major epidemics of febrile disease and severe, chronic arthritis. Identifying viral mutations is crucial for understanding virus evolution and evaluating those genetic determinants that directly impact pathogenesis and transmissibility. The present study was undertaken to expand on past CHIKV evolutionary studies through robust genome-scale phylogenetic analysis to better understand CHIKV genetic diversity and evolutionary dynamics since its reintroduction into India in 2005. We sequenced the complete genomes of fifty clinical isolates collected between 2010 and 2016 from two geographic locations, Delhi and Mumbai. We then analysed them along with 753 genomes available on the Virus Pathogen Database and Analysis Resource sampled over fifteen years (2005–20) from a range of locations across the globe and identified novel genetic variants present in samples from this study. Our analyses show evidence of frequent reintroduction of the virus into India and that the most recent CHIKV outbreak shares a common ancestor as recently as 2006.

中文翻译：

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自 2005 年重新出现以来印度基孔肯雅病毒的分子进化

基孔肯雅病毒 (CHIKV) 是披膜病毒科的甲病毒，是医学上最重要的蚊媒病毒之一，能够引起发热性疾病和严重慢性关节炎的主要流行病。识别病毒突变对于了解病毒进化和评估直接影响发病机制和传播性的遗传决定因素至关重要。本研究旨在通过稳健的基因组规模系统发育分析扩展过去的 CHIKV 进化研究，以更好地了解自 2005 年重新引入印度以来的 CHIKV 遗传多样性和进化动态。我们对 2010 年至 2016 年间收集的 50 个临床分离株的完整基因组进行了测序来自德里和孟买两个地理位置。然后，我们分析了它们以及病毒病原体数据库和分析资源中可用的 753 个基因组，这些基因组在十五年（2005-20 年）期间从全球多个地点采样，并确定了本研究样本中存在的新遗传变异。我们的分析表明，有证据表明该病毒频繁地重新引入印度，并且最近一次 CHIKV 爆发与 2006 年有共同的祖先。