Distinct Rates and Patterns of Spread of the Major HIV-1 Subtypes in Central and East Africa

Overview

Journal PLoS Pathog

Specialty Microbiology

Date 2019 Dec 7

PMID 31809523

Citations 23

Authors

Nuno R Faria

Nicole Vidal

Jose Lourenco

Jayna Raghwani

Kim C E Sigaloff

Andy J Tatem

David A M van de Vijver

Andrea-Clemencia Pineda-Pena

Rebecca Rose

Carole L Wallis

Steve Ahuka-Mundeke

Jean-Jacques Muyembe-Tamfum

Jeremie Muwonga

Marc A Suchard

Tobias F Rinke de Wit

Raph L Hamers

Nicaise Ndembi

Guy Baele

Martine Peeters

Oliver G Pybus

Philippe Lemey

Simon Dellicour

Affiliations

Soon will be listed here.

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.

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References

Worobey M, Gemmel M, Teuwen D, Haselkorn T, Kunstman K, Bunce M . Direct evidence of extensive diversity of HIV-1 in Kinshasa by 1960. Nature. 2008; 455(7213):661-4. PMC: 3682493. DOI: 10.1038/nature07390. View

Bartolo I, Calado R, Borrego P, Leitner T, Taveira N . Rare HIV-1 Subtype J Genomes and a New H/U/CRF02_AG Recombinant Genome Suggests an Ancient Origin of HIV-1 in Angola. AIDS Res Hum Retroviruses. 2016; 32(8):822-8. PMC: 5335814. DOI: 10.1089/AID.2016.0084. View

Abecasis A, Vandamme A, Lemey P . Quantifying differences in the tempo of human immunodeficiency virus type 1 subtype evolution. J Virol. 2009; 83(24):12917-24. PMC: 2786833. DOI: 10.1128/JVI.01022-09. View

Li G, Piampongsant S, Faria N, Voet A, Pineda-Pena A, Khouri R . An integrated map of HIV genome-wide variation from a population perspective. Retrovirology. 2015; 12:18. PMC: 4358901. DOI: 10.1186/s12977-015-0148-6. View

Bartolo I, Rocha C, Bartolomeu J, Gama A, Marcelino R, Fonseca M . Highly divergent subtypes and new recombinant forms prevail in the HIV/AIDS epidemic in Angola: new insights into the origins of the AIDS pandemic. Infect Genet Evol. 2008; 9(4):672-82. DOI: 10.1016/j.meegid.2008.05.003. View

Lihana R, Ssemwanga D, Abimiku A, Ndembi N . Update on HIV-1 diversity in Africa: a decade in review. AIDS Rev. 2012; 14(2):83-100. View

Minin V, Suchard M . Counting labeled transitions in continuous-time Markov models of evolution. J Math Biol. 2007; 56(3):391-412. DOI: 10.1007/s00285-007-0120-8. View

Ssemwanga D, Ndembi N, Lyagoba F, Magambo B, Kapaata A, Bukenya J . Transmitted antiretroviral drug resistance among drug-naive female sex workers with recent infection in Kampala, Uganda. Clin Infect Dis. 2012; 54 Suppl 4:S339-42. DOI: 10.1093/cid/cir937. View

Hemelaar J, Elangovan R, Yun J, Dickson-Tetteh L, Fleminger I, Kirtley S . Global and regional molecular epidemiology of HIV-1, 1990-2015: a systematic review, global survey, and trend analysis. Lancet Infect Dis. 2018; 19(2):143-155. DOI: 10.1016/S1473-3099(18)30647-9. View

10.

Muwonga J, Edidi S, Butel C, Vidal N, Monleau M, Okenge A . Resistance to antiretroviral drugs in treated and drug-naive patients in the Democratic Republic of Congo. J Acquir Immune Defic Syndr. 2011; 57 Suppl 1:S27-33. DOI: 10.1097/QAI.0b013e31821f596c. View

11.

OBrien J, Minin V, Suchard M . Learning to count: robust estimates for labeled distances between molecular sequences. Mol Biol Evol. 2009; 26(4):801-14. PMC: 2734148. DOI: 10.1093/molbev/msp003. View

12.

Talbi C, Lemey P, Suchard M, Abdelatif E, Elharrak M, Nourlil J . Phylodynamics and human-mediated dispersal of a zoonotic virus. PLoS Pathog. 2010; 6(10):e1001166. PMC: 2965766. DOI: 10.1371/journal.ppat.1001166. View

13.

Hamers R, Wallis C, Kityo C, Siwale M, Mandaliya K, Conradie F . HIV-1 drug resistance in antiretroviral-naive individuals in sub-Saharan Africa after rollout of antiretroviral therapy: a multicentre observational study. Lancet Infect Dis. 2011; 11(10):750-9. DOI: 10.1016/S1473-3099(11)70149-9. View

14.

Parker J, Rambaut A, Pybus O . Correlating viral phenotypes with phylogeny: accounting for phylogenetic uncertainty. Infect Genet Evol. 2007; 8(3):239-46. DOI: 10.1016/j.meegid.2007.08.001. View

15.

Tee K, Pybus O, Parker J, Ng K, Kamarulzaman A, Takebe Y . Estimating the date of origin of an HIV-1 circulating recombinant form. Virology. 2009; 387(1):229-34. DOI: 10.1016/j.virol.2009.02.020. View

16.

Chitnis A, Rawls D, Moore J . Origin of HIV type 1 in colonial French Equatorial Africa?. AIDS Res Hum Retroviruses. 2000; 16(1):5-8. DOI: 10.1089/088922200309548. View

17.

Sigaloff K, Mandaliya K, Hamers R, Otieno F, Jao I, Lyagoba F . Short communication: High prevalence of transmitted antiretroviral drug resistance among newly HIV type 1 diagnosed adults in Mombasa, Kenya. AIDS Res Hum Retroviruses. 2011; 28(9):1033-7. DOI: 10.1089/AID.2011.0348. View

18.

Arien K, Abraha A, Quinones-Mateu M, Kestens L, Vanham G, Arts E . The replicative fitness of primary human immunodeficiency virus type 1 (HIV-1) group M, HIV-1 group O, and HIV-2 isolates. J Virol. 2005; 79(14):8979-90. PMC: 1168791. DOI: 10.1128/JVI.79.14.8979-8990.2005. View

19.

Villabona Arenas C, Vidal N, Ahuka Mundeke S, Muwonga J, Serrano L, Muyembe J . Divergent HIV-1 strains (CRF92_C2U and CRF93_cpx) co-circulating in the Democratic Republic of the Congo: Phylogenetic insights on the early evolutionary history of subtype C. Virus Evol. 2017; 3(2):vex032. PMC: 5724398. DOI: 10.1093/ve/vex032. View

20.

Arien K, Vanham G, Arts E . Is HIV-1 evolving to a less virulent form in humans?. Nat Rev Microbiol. 2007; 5(2):141-51. PMC: 7097722. DOI: 10.1038/nrmicro1594. View