利用早期样本重建布基纳法索和西非的HIV-1 CRF02_AG和CRF06_cpx流行情况。
Reconstructing the HIV-1 CRF02_AG and CRF06_cpx epidemics in Burkina Faso and West Africa using early samples.
作者信息
Yebra Gonzalo, Kalish Marcia L, Leigh Brown Andrew J
机构信息
Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK.
Institute for Global Health, Vanderbilt University, Nashville, TN, USA.
出版信息
Infect Genet Evol. 2016 Dec;46:209-218. doi: 10.1016/j.meegid.2016.03.038. Epub 2016 Apr 6.
BACKGROUND
HIV-1 circulating recombinant forms (CRFs) represent viral recombinant lineages that play a significant role in the global epidemic. Two of them dominate the epidemic in Burkina Faso: CRF06_cpx (first described in this country) and CRF02_AG. We reconstructed the phylodynamics of both recombinant viruses in Burkina Faso and throughout West Africa.
METHODS
We analysed CRF06_cpx and CRF02_AG sequences (protease/gp41) from early samples collected in Burkina Faso in 1986 together with other GenBank sequences (1984-2013) in 4 datasets: African CRF06_cpx (210/60); down-sampled CRF06_cpx (146/45); Burkina Faso CRF02_AG (130/39) and West/Central African CRF02_AG (691/298). For each dataset, we analysed both protease and gp41 jointly using the BEAST multilocus analysis and conducted phylogeographic analysis to reconstruct the early migration routes between countries.
RESULTS
The time to the most recent common ancestor (tMRCA) of CRF06_cpx was 1979 (1973-1983) for protease and 1981 (1978-1983) for gp41. The gp41 analysis inferred the origin of CRF06_cpx (or at least its parental subtype G lineage) in the Democratic Republic of Congo but migrated to Burkina Faso soon after (1982). Both genes showed that CRF06_cpx radiated to the rest of West Africa predominantly after around 1990. These results were robust to the oversampling of Burkina Faso sequences as they were confirmed in the down-sampled dataset. The tMRCA of the Burkina Faso CRF02_AG lineage was 1979 (1977-1983) for protease and 1980 (1978-1981) for gp41. However, we reconstructed its presence in West Africa much earlier (mid-1960s), with an initial origin in Cameroon and/or Nigeria, and its phylogeographic analysis revealed much interconnection within the region with a lack of country-specific phylogenetic patterns, which prevents tracking its exact migration routes.
CONCLUSIONS
Burkina Faso presents a relatively young HIV epidemic, with the diversification of the current in-country CRF02_AG and CRF06_cpx lineages taking place around 1980. This country represents the main source of CRF06_cpx in West Africa. The CRF02_AG epidemic started at least a decade earlier and showed much interchange between West African countries (especially involving coastal countries) suggesting great population mobility and an extensive viral spread in the region.
背景
HIV-1循环重组型（CRF）代表了在全球流行中起重要作用的病毒重组谱系。其中两种在布基纳法索的疫情中占主导地位：CRF06_cpx（最早在该国被描述）和CRF02_AG。我们重建了布基纳法索以及整个西非这两种重组病毒的系统发育动力学。
方法
我们分析了1986年在布基纳法索采集的早期样本中的CRF06_cpx和CRF02_AG序列（蛋白酶/gp41），以及4个数据集中的其他GenBank序列（1984 - 2013年）：非洲CRF06_cpx（210/60）；下采样的CRF06_cpx（146/45）；布基纳法索CRF02_AG（130/39）和西非/中非CRF02_AG（691/298）。对于每个数据集，我们使用BEAST多位点分析联合分析蛋白酶和gp41，并进行系统发育地理分析以重建各国之间的早期迁移路线。
结果
CRF06_cpx的最近共同祖先时间（tMRCA），蛋白酶为1979年（1973 - 1983年），gp41为1981年（1978 - 1983年）。gp41分析推断CRF06_cpx（或至少其亲本亚型G谱系）起源于刚果民主共和国，但随后不久（1982年）迁移到了布基纳法索。两个基因均显示CRF06_cpx主要在1990年左右辐射到西非其他地区。这些结果对于布基纳法索序列的过采样具有稳健性，因为它们在下采样数据集中得到了证实。布基纳法索CRF02_AG谱系的tMRCA，蛋白酶为1979年（1977 - 1983年），gp41为1980年（1978 - 1981年）。然而，我们重建其在西非的存在要早得多（20世纪60年代中期），最初起源于喀麦隆和/或尼日利亚，其系统发育地理分析显示该区域内存在大量相互联系，缺乏特定国家的系统发育模式，这使得追踪其确切迁移路线变得困难。
结论
布基纳法索呈现出相对年轻的HIV疫情，当前国内CRF02_AG和CRF06_cpx谱系的多样化大约发生在1980年左右。该国是西非CRF06_cpx的主要来源。CRF02_AG疫情至少在十年前就已开始，并且显示出西非国家之间（特别是沿海国家）有大量的交流，这表明该地区人口流动性大且病毒传播广泛。
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