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

Abstract

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.

Phylogenetics of HIV-1 subtype G env: Greater complexity and older origins than previously reported

“…Our analysis does not therefore support the hypothesis that HIV-1 subtype G travelled directly from Angola to either Cuba (Bártolo et al, 2009;Delatorre and Bello, 2013a) or the Iberian peninsula (Bártolo et al, 2009). It also does not support the conclusion that the MRCA of subtype G existed in Angola, the DRC or the Republic of Congo, as has been previously suggested with an analysis of partial pol gene sequences (Delatorre et al, 2014). Our analysis instead suggests two other possibilities: (1) that subtype G originated in Cameroon and moved directly to the Iberian peninsula, or (2) that it originated in Cameroon and moved to Cuba, Spain and Portugal, perhaps via Angola.…”

“…Our estimated timing of the subtype G env MRCA is about 15 years earlier than that previously reported for publically available subtype G gag, env (Abecasis et al, 2009) or pol (Delatorre et al, 2014) sequences. We also trace the origins of subtype G env sequences sampled in Cuba and Europe and conclude that subtype G env sequences appear to have moved to Europe directly from Africa.…”

“…The time of the most recent common ancestor (tMRCA) for subtype G env sequences was estimated to be 1953 (95%HPD 1929(95%HPD -1964: about 15 years earlier than prior estimates for subtype G based upon partial gag, env and pol sequences (1968)(1969) (Abecasis et al, 2009;Delatorre et al, 2014). As noted above, the Bayesian MCC tree supported the existence of the same seven major lineages (G1-G7) that were found in the ML tree ( Fig.…”

“…It has been previously inferred based on pol sequence analyses that subtype G originated in or near Angola (Delatorre et al, 2014) and that subtype G migrated from Angola to the Iberian peninsula and Cuba (Bártolo et al, 2009;Delatorre et al, 2014); however, with the exception of one sequence from Gabon, there were no available full-length env sequences from this region in the LANL database. We therefore searched Genbank for any partial env sequences from Cameroon, Nigeria, the DRC, the Republic of Congo, Gabon and Angola that could be subtype G sequences by the multi-step process described in Section 2.…”

Viral Genetic Diversity and Polymorphisms in a Cohort of HIV-1-Infected Patients Eligible for Initiation of Antiretroviral Therapy in Abuja, Nigeria

“…The three major subtype G clusters were reported previously as G WA-I , G WA-II , and G CA 6,22,63 However, within a G cluster, different strains may be present. For example, in the G3 cluster, there are possibly four different strains, denoted as G3A–D (Fig.…”