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

Abstract

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.

HIV-1 Transmission Patterns Within and Between Risk Groups in Coastal Kenya

“…This indicates that the elapsed time A Bayesian Skygrid plot showing population dynamics of the HIV-1 sub-subtype A1 injecting drug users' sub-epidemic in coastal Kenya. Since the IDU pol sequence alignment did not contain temporal information (all sequences were sampled in 2010), the node height for this cluster was calibrated using information from the tMRCA posterior distribution obtained from dating the origin of subtype A1 Kenyan clusters 64 . Median estimates of the number of injecting drug users contributing to new infections are shown as a continuous black line.…”

Current and historic HIV-1 molecular epidemiology in paediatric and adult population from Kinshasa in the Democratic Republic of Congo

“…The DRC is known as the origin of HIV-1 pandemic and the epicenter for the selection and spreading of many HIV-1 variants to neighboring countries 28 . As a consequence of high HIV-1 genetic heterogenicity (probably the highest diversity rate in the world), the accurate phylogenetic reconstructions have not been easy to interpret 29 .…”

Accommodating individual travel history, global mobility, and unsampled diversity in phylogeography: a SARS-CoV-2 case study

“…We summarize posterior tree distributions https://github.com/beast-dev/beast-mcmc ) and associated R package constructs these estimates. We also visualize posterior expected Markov jumps estimates between all locations using circular migration flow plots, which have been successfully used to visualize migration data 39 , including phylogeographic estimates 40 . When summarizing these jumps from analyses that include unsampled diversity, we ignore branches that only have unsampled taxa as descendants.…”