TY - JOUR
T1 - Distinct rates and patterns of spread of the major HIV-1 subtypes in Central and East Africa
AU - Faria, Nuno R.
AU - Vidal, Nicole
AU - Lourenco, José
AU - Raghwani, Jayna
AU - Sigaloff, Kim C.E.
AU - Tatem, Andy J.
AU - Van De Vijver, David A.M.
AU - Pineda-Peña, Andrea Clemencia
AU - Rose, Rebecca
AU - Wallis, Carole L.
AU - Ahuka-Mundeke, Steve
AU - Muyembe-Tamfum, Jean Jacques
AU - Muwonga, Jérémie
AU - Suchard, Marc A.
AU - De Wit, Tobias F.Rinke
AU - Hamers, Raph L.
AU - Ndembi, Nicaise
AU - Baele, Guy
AU - Peeters, Martine
AU - Pybus, Oliver G.
AU - Lemey, Philippe
AU - Dellicour, Simon
N1 - Publisher Copyright:
© 2019 Faria et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
PY - 2019
Y1 - 2019
N2 - 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.
AB - 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.
UR - http://www.scopus.com/inward/record.url?scp=85076317941&partnerID=8YFLogxK
UR - http://www.scopus.com/inward/citedby.url?scp=85076317941&partnerID=8YFLogxK
U2 - 10.1371/journal.ppat.1007976
DO - 10.1371/journal.ppat.1007976
M3 - Article
C2 - 31809523
AN - SCOPUS:85076317941
SN - 1553-7366
VL - 15
JO - PLoS Pathogens
JF - PLoS Pathogens
IS - 12
M1 - e1007976
ER -
