Distinct rates and patterns of spread of the major HIV-1 subtypes in Central and East Africa

Author summary Since it emerged in human populations in the Democratic Republic of Congo (DRC) around 1920, HIV diversified in several virus lineages that spread across sub-Saharan Africa and beyond. While some lineages are rare and remain geographically confined to certain regions, e.g. subtypes H and J, others expanded rapidly across sub-Saharan Africa, e.g. subtype C. Here we conducted a spatial genetic analysis of the three main HIV-1 virus lineages, subtypes, A1, C and D, that co-circulate across 20 locations in central and East Africa, to investigate their spatial and temporal origins and their mode of spread across comparable geographic areas. We find that subtype C, currently the dominant lineage in sub-Saharan Africa, emerged in the southern DRC mining region, and spread 3-fold faster than other co-circulating lineages. Our study uncovers distinct patterns of spread of the main HIV-1 subtypes in a region that covers nearly half of all infected individuals in sub-Saharan Africa. Since the ignition of the HIV-1 group M pandemic in the beginning of the 20th century, group M lineages have spread heterogeneously throughout the world. Subtype C spread rapidly through sub-Saharan Africa and is currently the dominant HIV lineage worldwide. Yet the epidemiological and evolutionary circumstances that contributed to its epidemiological expansion remain poorly understood. Here, we analyse 346 novel pol sequences from the DRC to compare the evolutionary dynamics of the main HIV-1 lineages, subtypes A1, C and D. Our results place the origins of subtype C in the 1950s in Mbuji-Mayi, the mining city of southern DRC, while subtypes A1 and D emerged in the capital city of Kinshasa, and subtypes H and J in the less accessible port city of Matadi. Following a 15-year period of local transmission in southern DRC, we find that subtype C spread at least three-fold faster than other subtypes circulating in Central and East Africa. In conclusion, our results shed light on the origins of HIV-1 main lineages and suggest that socio-historical rather than evolutionary factors may have determined the epidemiological fate of subtype C in sub-Saharan Africa.