Origin, evolution, and phylogeography of recent epidemic CHIKV strains
Origin, evolution, and phylogeography of recent epidemic CHIKV strains
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DOI：
10.1016/j.meegid.2011.12.015
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发表时间：
2012-03-01
影响因子：
3.2
通讯作者：
Rezza, Giovanni
中科院分区：
文献类型：
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作者：
Lo Presti, Alessandra;Ciccozzi, Massimo;Rezza, Giovanni
基孔肯雅病毒（CHIKV）是一种由节肢动物传播的阿尔法病毒属病毒，由伊蚊属传播给人类。本文对近年来CHIKV大流行的系统发育和地理分布进行了分析。我们估计了祖先病毒的起源时间，A226 V突变发生的时间和地点，以及病毒株从一个地区流向另一个地区。贝叶斯系统发育和地理分析是在整个数据集上进行的，该数据集由195个El（包膜1）CHIKV序列组成，并在一个子集（D2）上进行，该子集包括195个先前序列中的146个。使用放松的时钟模型，我们估计了CHIKV El平均进化速率，（在整个数据集中）1.4 x 10（-3）置换/研究中心/年（95%最高后验密度区间HPD 6.4 x 10（-4）-2.5 x 10（-3））和2.2 x 10（-3））（95%HPD 9.6 x 10（-4）-3.8 x 10（-3）），仅包括最近印度洋流行病涉及的菌株。地理分布分析表明CHIKV起源于非洲，tMRCA为146年，对应于1863年（95% HPD 1741-1941）。此外，D2亚群最可能起源于肯尼亚，tMRCA对应于2002年（2000-2004年95%的HPD），然后沿着两条不同的途径传播：一个在整个印度洋（留尼旺，科摩罗）和另一个从印度出发，然后分散在东南亚，到达意大利。总之，我们重建了上一次流行浪潮期间CHIKV的地理传播，其中显示了从非洲到印度洋岛屿再到印度，再从那里到其他东南亚国家的一条向东路径。A226 V变异体是否遵循相同的迁移路径仍然不确定，因为不能排除局部独立突变，随后由于更好地适应局部感染载体而赋予的选择性优势而固定。(C)2012 Elsevier BM. All rights reserved.
Chikungunya virus (CHIKV) is an arthropod-borne virus of the Alphavinis genus, which is transmitted to humans by Aedes spp. mosquitoes and was firstly identified in Tanzania in the mid 1950s.In this article, the findings of a phylogenetic and phylogeographic analysis of the recent CHIKV pandemic are reported. We estimated time of origin of the ancestral virus, time and place of occurrence of A226V mutation, and the flow of viral strains from an area to the other.The Bayesian phylogenetic and phylogeographic analysis was performed on the whole dataset, which consisted of 195 El (envelope 1) CHIKV sequences, and on a subset (D2), including 146 of the 195 previous sequences. Using the relaxed clock model, we estimated a CHIKV El mean evolutionary rate (in the whole dataset) of 1.4 x 10(-3) substitution/site/year (95% highest posterior density interval HPD 6.4 x 10(-4)-2.5 x 10(-3)), and of 2.2 x 10(-3) (95% HPD 9.6 x 10(-4)-3.8 x 10(-3)) in the D2 subset, including only the strains involved in the recent Indian Ocean epidemic. The phylogeographical analysis suggested an African origin of CHIKV with a tMRCA of 146 years corresponding to 1863 (95% HPD 1741-1941). Moreover D2 subset most probably originated in Kenya, with a tMRCA corresponding to the year 2002 (95% HPD 2000-2004), then spread following two distinct routes: one throughout the Indian Ocean (Reunion, Comoros) and the other moving from India then scattered in the South East Asia and reached Italy.In conclusion, we reconstructed the geographic spread of CHIKV during the last epidemic wave, which showed an eastward path from Africa to Indian Ocean island to India, and from there to other South East Asian countries. Whether A226V variants followed the same migration path remains undefined, since local independent mutations, followed by fixation due to selective advantage conferred by better adaptation to local vectors of infection, cannot be excluded. (C) 2012 Elsevier BM. All rights reserved.