Rega Institute, Katholieke Universiteit Leuven, Leuven, Belgium.
Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK.
J Gen Virol. 2012 Apr;93(Pt 4):889-899. doi: 10.1099/vir.0.038638-0. Epub 2011 Dec 21.
Human immunodeficiency virus type 2 (HIV-2) emerged in West Africa and has spread further to countries that share socio-historical ties with this region. However, viral origins and dispersal patterns at a global scale remain poorly understood. Here, we adopt a Bayesian phylogeographic approach to investigate the spatial dynamics of HIV-2 group A (HIV-2A) using a collection of 320 partial pol and 248 partial env sequences sampled throughout 19 countries worldwide. We extend phylogenetic diffusion models that simultaneously draw information from multiple loci to estimate location states throughout distinct phylogenies and explicitly attempt to incorporate human migratory fluxes. Our study highlights that Guinea-Bissau, together with Côte d'Ivoire and Senegal, have acted as the main viral sources in the early stages of the epidemic. We show that convenience sampling can obfuscate the estimation of the spatial root of HIV-2A. We explicitly attempt to circumvent this by incorporating rate priors that reflect the ratio of human flow from and to West Africa. We recover four main routes of HIV-2A dispersal that are laid out along colonial ties: Guinea-Bissau and Cape Verde to Portugal, Côte d'Ivoire and Senegal to France. Within Europe, we find strong support for epidemiological linkage from Portugal to Luxembourg and to the UK. We demonstrate that probabilistic models can uncover global patterns of HIV-2A dispersal providing sampling bias is taken into account and we provide a scenario for the international spread of this virus.
人类免疫缺陷病毒 2 型（HIV-2）在西非出现，并进一步传播到与该地区有社会历史联系的国家。然而，病毒的起源和在全球范围内的扩散模式仍知之甚少。在这里，我们采用贝叶斯系统地理学方法，利用在全球 19 个国家采集的 320 个部分 pol 和 248 个部分 env 序列，对 HIV-2 组 A（HIV-2A）的空间动态进行了研究。我们扩展了同时从多个基因座提取信息的系统发育扩散模型，以估计整个不同系统发育树中的位置状态，并明确尝试纳入人类迁徙通量。我们的研究表明，几内亚比绍与科特迪瓦和塞内加尔一起，在该疾病的早期阶段充当了主要的病毒来源。我们表明，方便抽样可能会混淆对 HIV-2A 空间根源的估计。我们明确地试图通过纳入反映从和到西非的人类流动比率的速率先验来避免这一点。我们恢复了 HIV-2A 传播的四条主要途径，这些途径是沿着殖民关系铺设的：几内亚比绍和佛得角到葡萄牙，科特迪瓦和塞内加尔到法国。在欧洲内部，我们发现从葡萄牙到卢森堡和英国的流行病学联系有很强的支持。我们证明，概率模型可以揭示 HIV-2A 传播的全球模式，前提是考虑到抽样偏差，并且我们为该病毒的国际传播提供了一个情景。
