Bayesian phylogeographic analyses clarify the origin of the HIV-1 subtype A variant circulating in former Soviet Union's countries
Bayesian phylogeographic analyses clarify the origin of the HIV-1 subtype A variant circulating in former Soviet Union's countries
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DOI：
10.1016/j.meegid.2015.05.003
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发表时间：
2015-07-01
影响因子：
3.2
通讯作者：
Thomson, Michael M.
中科院分区：
文献类型：
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作者：
Diez-Fuertes, Francisco;Cabello, Marina;Thomson, Michael M.
在前苏联(FSU)国家HIV-1流行中占主导地位的HIV-1 A亚型变异株代表了HIV-1大流行的主要分支之一。据报道，这种变种于1994年底开始在乌克兰敖德萨市的注射吸毒者中传播。关于A(FSU)变异的祖先起源提出了两个相互竞争的假说，将其定位在刚果民主共和国(DRC)或几内亚共和国(RG)。支持这些假说的研究使用了系统发育分析来鉴定在FSU国家以外收集的与A(FSU)有祖先关系的HIV-1序列。这里采用了一种不同的方法，基于贝叶斯系统发育推断和基于合并的群体遗传学，来阐明这种HIV-1变异株的祖先，并提高我们对其在FSU国家传播的了解。使用HIV-1基因组的env(C2-V3-C3)和p24(Gag)片段进行分析。推测的HIV-1A(FSU)变异株的迁移只显示了一条显著支持的从非洲到东欧的迁移途径，支持其起源于刚果民主共和国的假设，并估计了祖传病毒在1970年左右从非洲迁移的上限。对RG原产地的支持微不足道。这些结果支持了敖德萨作为甲型流感(FSU)疫情中心的主要作用，测定了A(FSU)变异体的tMRCA大约在1984年，也就是在注射吸毒者中爆炸性扩张的10年前。据估计，造成IDU暴发的A(FSU)亚群的起源地也位于敖德萨，估计tMRCA大约在1993年。贝叶斯系统地理分析还推断了从敖德萨到乌克兰、俄罗斯、哈萨克斯坦、乌兹别克斯坦和白俄罗斯其他城市的统计支持的移民路线。这些结果为HIV-1A(FSU)变异株的起源和传播提供了新的线索。(C)2015年爱思唯尔西区。版权所有。
The HIV-1 subtype A variant dominating the HIV-1 epidemics in former Soviet Union (FSU) countries (A(FSU)) represents one of the major clades of the HIV-1 pandemic. This variant was reported to have begun spreading among injecting drug users (IDUs) in the Ukrainian city of Odessa in late 1994. Two competing hypotheses have been proposed on the ancestral origin of the A(FSU) variant, locating it either in the Democratic Republic of Congo (DRC) or in the Republic of Guinea (RG). The studies supporting these hypotheses employed phylogenetic analyses to identify HIV-1 sequences collected outside FSU countries ancestrally related to A(FSU). A different approach, based on Bayesian phylogenetic inference and coalescent-based population genetics, has been employed here to elucidate the ancestry of this HIV-1 variant and to improve our knowledge on its spread in FSU countries. The analyses were carried out using env (C2-V3-C3) and p24(gag) fragments of the HIV-1 genome. The inferred migration for the HIV-1 A(FSU) variant revealed only one significantly supported migration pathway from Africa to Eastern Europe, supporting the hypothesis of its origin in the DRC and estimating the upper limit of the migration of the ancestral virus from Africa around 1970. The support for an origin in the RG was negligible. The results supported the main role of Odessa as the epicenter of the A(FSU) epidemic, dating the tMRCA of the A(FSU) variant around 1984, ten years before its explosive expansion among IDUs. The estimated origin of the A(FSU) subcluster responsible for the IDU outbreak was also located in Odessa, with the estimated tMRCA around 1993. Statistically supported migration routes from Odessa to other cities of Ukraine, Russia, Kazakhstan, Uzbekistan and Belarus were also inferred by the Bayesian phylogeographic analysis. These results shed new light on the origin and spread of the HIV-1 A(FSU) variant. (C) 2015 Elsevier WV. All rights reserved.