In recent decades, chikungunya virus (CHIKV) has become geographically widespread. In 2004, the CHIKV East/Central/South African (ECSA) genotype moved from Africa to Indian ocean islands and India followed by a large epidemic in Southeast Asia. In 2013, the CHIKV Asian genotype drove an outbreak in the Americas. Since 2016, CHIKV has re-emerged in the Indian subcontinent and Southeast Asia. In the present study, CHIKVs were obtained from Bangladesh in 2017 and Thailand in 2019, and their nearly full genomes were sequenced. Phylogenetic analysis revealed that the recent CHIKVs were of Indian Ocean Lineage (IOL) of genotype ECSA, similar to the previous outbreak. However, these CHIKVs were all clustered into a new distinct sub-lineage apart from the past IOL CHIKVs, and they lacked an alanine-to-valine substitution at position 226 of the E1 envelope glycoprotein, which enhances CHIKV replication in Aedes albopictus. Instead, all the re-emerged CHIKVs possessed mutations of lysine-to-glutamic acid at position 211 of E1 and valine-to-alanine at position 264 of E2. Molecular clock analysis suggested that the new sub-lineage CHIKV was introduced to Bangladesh around late 2015 and Thailand in early 2017. These results suggest that re-emerged CHIKVs have acquired different adaptations than the previous CHIKVs.

中文翻译：

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基孔肯雅病毒东亚/中亚/南非基因型印​​度洋血统的新型亚系导致孟加拉国和泰国的顺序暴发

在最近几十年中，基孔肯雅病毒（CHIKV）在地理上已经广泛传播。2004年，CHIKV东/中/南非（ECSA）基因型从非洲转移到印度洋诸岛和印度，随后在东南亚流行。2013年，CHIKV亚洲人基因型在美洲爆发。自2016年以来，CHIKV已重新出现在印度次大陆和东南亚。在本研究中，CHIKVs分别于2017年和2019年从孟加拉国和泰国获得，并对其近乎完整的基因组进行了测序。系统发育分析表明，最近的CHIKVs是基因型ECSA的印度洋谱系（IOL），与之前的暴发相似。但是，除了过去的IOL CHIKV之外，这些CHIKV都聚集成了新的独特子系，白纹伊蚊。相反，所有重新出现的CHIKVs在E1的211位具有赖氨酸-谷氨酸突变，在E2的264位具有缬氨酸-谷氨酸突变。分子钟分析表明，新的子系CHIKV于2015年底前后引入了孟加拉国，并于2017年初引入了泰国。这些结果表明，与以前的CHIKV相比，重新出现的CHIKV获得了不同的适应性。