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

Distinct rates and patterns of spread of the major HIV-1 subtypes in Central and East Africa
Distinct rates and patterns of spread of the major HIV-1 subtypes in Central and East 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.
1553-7366
1-23
Faria, Nuno R.
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Vidal, Nicole
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Raghwani, Jayna
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Sigaloff, Kim C. E.
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Tatem, Andy J.
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van de Vijver, David A. M.
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Pineda-Pena, Andrea-Clemencia
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Rose, Rebecca
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Wallis, Carole L.
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Ahuka-Mundeke, Steve
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Muyembe-Tamfum, Jean-Jacques
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Muwonga, Jeremie
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Suchard, Marc A.
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Rinke de Wit, T.F.
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Hamers, Raph L.
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Ndembi, Nicaise
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Baele, Guy
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Peeters, Martine
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Pybus, Oliver G.
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Lemey, Philippe
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Dellicour, Simon
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Faria, Nuno R.
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Vidal, Nicole
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Raghwani, Jayna
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Sigaloff, Kim C. E.
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Tatem, Andy J.
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van de Vijver, David A. M.
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Pineda-Pena, Andrea-Clemencia
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Rose, Rebecca
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Wallis, Carole L.
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Ahuka-Mundeke, Steve
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Muyembe-Tamfum, Jean-Jacques
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Muwonga, Jeremie
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Suchard, Marc A.
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Rinke de Wit, T.F.
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Hamers, Raph L.
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Ndembi, Nicaise
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Baele, Guy
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Peeters, Martine
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Pybus, Oliver G.
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Lemey, Philippe
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Dellicour, Simon
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Faria, Nuno R., Vidal, Nicole, Raghwani, Jayna, Sigaloff, Kim C. E., Tatem, Andy J., van de Vijver, David A. M., Pineda-Pena, Andrea-Clemencia, Rose, Rebecca, Wallis, Carole L., Ahuka-Mundeke, Steve, Muyembe-Tamfum, Jean-Jacques, Muwonga, Jeremie, Suchard, Marc A., Rinke de Wit, T.F., Hamers, Raph L., Ndembi, Nicaise, Baele, Guy, Peeters, Martine, Pybus, Oliver G., Lemey, Philippe and Dellicour, Simon (2019) Distinct rates and patterns of spread of the major HIV-1 subtypes in Central and East Africa. PLoS Pathogens, 15 (12), 1-23, [1007976]. (doi:10.1371/journal.ppat.1007976).

Record type: Article

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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Accepted/In Press date: 11 July 2019
e-pub ahead of print date: 6 December 2019
Published date: 6 December 2019

Identifiers

Local EPrints ID: 444255
URI: http://eprints.soton.ac.uk/id/eprint/444255
ISSN: 1553-7366
PURE UUID: bcbd3c52-8278-4db9-aa71-b567a932151b
ORCID for Andy J. Tatem: ORCID iD orcid.org/0000-0002-7270-941X

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Date deposited: 06 Oct 2020 20:13
Last modified: 07 Oct 2020 02:01

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Contributors

Author: Nuno R. Faria
Author: Nicole Vidal
Author: Jayna Raghwani
Author: Kim C. E. Sigaloff
Author: Andy J. Tatem ORCID iD
Author: David A. M. van de Vijver
Author: Andrea-Clemencia Pineda-Pena
Author: Rebecca Rose
Author: Carole L. Wallis
Author: Steve Ahuka-Mundeke
Author: Jean-Jacques Muyembe-Tamfum
Author: Jeremie Muwonga
Author: Marc A. Suchard
Author: T.F. Rinke de Wit
Author: Raph L. Hamers
Author: Nicaise Ndembi
Author: Guy Baele
Author: Martine Peeters
Author: Oliver G. Pybus
Author: Philippe Lemey
Author: Simon Dellicour

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