Spatiotemporal Dynamics of the HIV-1 Subtype G Epidemic in West and Central Africa

The human immunodeficiency virus type 1 (HIV-1) subtype G is the second most prevalent HIV-1 clade in West Africa, accounting for nearly 30% of infections in the region. There is no information about the spatiotemporal dynamics of dissemination of this HIV-1 clade in Africa. To this end, we analyzed a total of 305 HIV-1 subtype G pol sequences isolated from 11 different countries from West and Central Africa over a period of 20 years (1992 to 2011). Evolutionary, phylogeographic and demographic parameters were jointly estimated from sequence data using a Bayesian coalescent-based method. Our analyses indicate that subtype G most probably emerged in Central Africa in 1968 (1956–1976). From Central Africa, the virus was disseminated to West and West Central Africa at multiple times from the middle 1970s onwards. Two subtype G strains probably introduced into Nigeria and Togo between the middle and the late 1970s were disseminated locally and to neighboring countries, leading to the origin of two major western African clades (GWA-I and GWA-II). Subtype G clades circulating in western and central African regions displayed an initial phase of exponential growth followed by a decline in growth rate since the early/middle 1990s; but the mean epidemic growth rate of GWA-I (0.75 year−1) and GWA-II (0.95 year−1) clades was about two times higher than that estimated for central African lineages (0.47 year−1). Notably, the overall evolutionary and demographic history of GWA-I and GWA-II clades was very similar to that estimated for the CRF06_cpx clade circulating in the same region. These results support the notion that the spatiotemporal dissemination dynamics of major HIV-1 clades circulating in western Africa have probably been shaped by the same ecological factors.人类免疫缺陷病毒1型（human immunodeficiency virus type 1, HIV-1）G亚型是西非地区流行率第二高的HIV-1进化支（clade），约占该地区近30%的感染病例。目前尚无针对该HIV-1进化支在非洲的传播时空动态的研究报道。为此，我们对1992年至2011年这20年间，从西非与中非11个国家分离得到的共计305条HIV-1 G亚型pol基因序列（pol gene）进行了分析。我们采用基于贝叶斯溯祖的分析方法（Bayesian coalescent-based method），从序列数据中联合估算了进化、系统发育地理学（phylogeographic）以及群体动力学参数（demographic parameters）。分析结果表明，G亚型最有可能于1968年（1956–1976年）在中非地区起源。自20世纪70年代中期起，该病毒多次从中非传播至西非及中西非地区。两株分别于20世纪70年代中后期传入尼日利亚与多哥的G亚型毒株，在当地及周边国家扩散传播，由此演化出西非两大主要进化支（GWA-I与GWA-II）。西非与中非地区流行的G亚型进化支均呈现出初始指数增长阶段，自20世纪90年代早中期起增长速率逐步下降；但GWA-I（0.75 年⁻¹）与GWA-II（0.95 年⁻¹）进化支的平均疫情增长速率约为中非进化支（0.47 年⁻¹）的两倍。值得注意的是，GWA-I与GWA-II进化支的整体进化与群体动力学历史，与同期在该地区流行的CRF06_cpx进化支的估算结果高度相似。上述结果支持这一假说：西非地区流行的主要HIV-1进化支的时空传播动态，可能由相同的生态因素所塑造。