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

Nuno R. Faria, Nicole Vidal, José Lourenco, Jayna Raghwani, Kim C.E. Sigaloff, Andy J. Tatem, David A.M. Van De Vijver, Andrea Clemencia Pineda-Peña, Rebecca Rose, Carole L. Wallis, Steve Ahuka-Mundeke, Jean Jacques Muyembe-Tamfum, Jérémie Muwonga, Marc A. Suchard, Tobias F.Rinke De Wit, Raph L. Hamers, Nicaise Ndembi, Guy Baele, Martine Peeters, Oliver G. PybusPhilippe Lemey, Simon Dellicour

Research output: Contribution to journalArticlepeer-review

32 Scopus citations


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.

Original languageEnglish (US)
Article numbere1007976
JournalPLoS Pathogens
Issue number12
StatePublished - 2019

All Science Journal Classification (ASJC) codes

  • Parasitology
  • Microbiology
  • Immunology
  • Molecular Biology
  • Genetics
  • Virology


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