Evolutionary analysis of the Chikungunya virus epidemic in Mexico reveals intra-host mutational hotspots in the E1 protein

The epidemic potential of Chikungunya virus (CHIKV) was recently made evident by its introduction and rapid expansion in the Caribbean and the Americas. We sought to gain a detailed understanding of the dynamics of the epidemic in Mexico, the country with the highest number of confirmed CHIKV cases in the Americas, and to characterise viral evolution at the population and intra-host level. Analysis of the spatiotemporal distribution of 2,739 diagnosed cases in Mexico from December 2014 to December 2015 showed a rapid nationwide expansion of the epidemic with focalisation in the South West of the country. We sequenced the envelope glycoprotein 1 gene (E1) from 25 patients using the Illumina MiSeq platform and report synonymous and non-synonymous consensus mutations. Bayesian phylogenetic analysis using 249 Asian lineage E1 sequences gave updated estimates of nucleotide substitution rates for E1 and time to most recent common ancestor of major lineages. The analysis indicates phylogenetically-related emergent Latin American clusters in South Western Mexico, Nicaragua and Honduras and transmission of American strains in the Pacific islands. Detailed analysis showed that intra-host changes in E1 mainly occurred in two variable regions (E1:189–220 and E1:349–358) in domains II and III, respectively, in residues involved in inter and intra-envelope spike interactions. At the population level, this study sheds light on the introduction and evolutionary dynamics of CHIKV in the Americas. At the intra-host level, this study identifies mutational hotspots of the E1 protein with implications for understanding the relationship between the CHIKV quasispecies, viral fitness and pathogenesis.

基孔肯雅病毒（Chikungunya virus, CHIKV）的流行潜力近期已通过其传入加勒比地区及美洲并快速扩散得到充分证实。本研究旨在深入解析美洲地区确诊基孔肯雅病毒病例数最多的墨西哥的疫情动态，并从群体及宿主内层面刻画病毒的进化特征。本研究对2014年12月至2015年12月间墨西哥境内2739例确诊病例的时空分布开展分析，结果显示疫情在全国范围内快速扩散，并在该国西南部呈现局灶性聚集特征。本研究利用Illumina MiSeq测序平台，对25名患者的包膜糖蛋白1（envelope glycoprotein 1 gene, E1）基因进行测序，报告了其同义与非同义共识突变情况。基于249条亚洲谱系E1序列开展的贝叶斯系统发育分析，更新了E1基因的核苷酸替换速率及各主要谱系最近共同祖先时间的估算结果。分析结果显示，墨西哥西南部、尼加拉瓜及洪都拉斯存在系统发育相关的新兴拉丁美洲进化聚类群，且美洲毒株在太平洋岛屿存在传播事件。详细分析表明，E1基因的宿主内变异主要集中在两个可变区域（分别对应E1蛋白189–220位与349–358位氨基酸），即结构域II与结构域III中参与包膜刺突蛋白间及内部相互作用的氨基酸残基区域。在群体层面，本研究阐明了基孔肯雅病毒传入美洲后的引入过程与进化动态；在宿主内层面，本研究鉴定出E1蛋白的突变热点，为理解基孔肯雅病毒准种、病毒适合度与致病机制之间的关联提供了重要启示。