After the 2005-2009 chikungunya epidemic, intermittent outbreaks were reported in many parts of India. The outbreaks were caused by either locally circulating strains or imported viruses. Virus transmission routes can be traced by complete genome sequencing studies. We investigated two outbreaks in 2014 and 2019 in Kerala, India. Chikungunya virus (CHIKV) was isolated from the samples, and whole genomes were sequenced for a 2014 isolate and a 2019 isolate. Phylogenetic analysis revealed that the isolates formed a separate group with a 2019 isolate from Pune, Maharashtra, and belonged to the East/Central/South African (ECSA) genotype, Indian subcontinent sublineage of the Indian Ocean Lineage (IOL). A novel mutation at amino acid position 76 of the E2 gene was observed in the group. The phylogenetic results suggest that the outbreaks might have been caused by a virus that had been circulating in India since 2014. A detailed study is needed to investigate the evolution of CHIKV in India.

中文翻译：

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2014-2019 年印度喀拉拉邦两次局部暴发的基孔肯雅病毒分离株的分子特征。

在 2005-2009 年基孔肯雅热流行之后，印度许多地区报告了间歇性爆发。爆发是由本地传播的毒株或输入的病毒引起的。病毒传播途径可以通过完整的基因组测序研究来追踪。我们调查了 2014 年和 2019 年在印度喀拉拉邦发生的两次疫情。从样本中分离出基孔肯雅病毒 (CHIKV)，并对 2014 年分离株和 2019 年分离株的全基因组进行测序。系统发育分析显示，这些分离株与来自马哈拉施特拉邦浦那的 2019 年分离株形成了一个单独的组，属于东/中/南非 (ECSA) 基因型，印度洋谱系 (IOL) 的印度次大陆亚谱系。在该组中观察到 E2 基因第 76 位氨基酸的新突变。