Phylogenetics of HIV-1 subtype G env: Greater complexity and older origins than previously reported |
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| Affiliation: | 1. Laboratoire de Biologie Moléculaire et Immunologie (BIOLIM/FSS/UL), Faculté des Sciences de la Santé, Université de Lomé, Togo;2. UMI 233, Institut de Recherche pour le Développement (IRD), INSERM U1175 and Université de Montpellier, Montpellier, France;3. Association Arc-en-Ciel, Lomé, Togo;4. Programme National de Lutte contre le Sida et les IST/Togo (PNLS/IST/Togo), Lomé, Togo;5. Université de Lomé, Département de Santé Publique, Lomé, Togo;6. Université de Bordeaux, ISPED, Centre INSERM U1219-Epidemiologie-Biostatistique, F-33000 Bordeaux, France;7. Conseil National de Lutte contre le SIDA (CNLS) et Faculté des Sciences de la Santé, Lomé, Togo;1. Centre for HIV & STIs, National Institute for Communicable Diseases, National Health Laboratory Service, Johannesburg, South Africa;2. Department of Medical Virology, Faculty of Health Sciences, University of Pretoria, Pretoria, South Africa;3. Paediatric HIV Diagnostics Syndicate, Wits Health Consortium, Johannesburg, South Africa;4. School of Public Health, Faculty of Health Sciences, University of the Witwatersrand, South Africa;5. PathCare Reference Laboratory and Stellenbosch University, Cape Town, South Africa;6. Department of Paediatrics & Child Health, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa |
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| Abstract: | ![]()
HIV-1 subtype G has played an early and central role in the emergent complexity of the HIV-1 group M (HIV-1M) epidemic in central/west Africa. Here, we analysed new subtype G env sequences sampled from 8 individuals in Yaoundé, Cameroon during 2007–2010, together with all publically available subtype G-attributed full-length env sequences with known sampling dates and locations. We inferred that the most recent common ancestor (MRCA) of the analysed subtype G env sequences most likely occurred in ∼1953 (95% Highest Posterior Density interval [HPD] 1939–1963): about 15 years earlier than previous estimates. We found that the subtype G env phylogeny has a complex structure including seven distinct lineages, each likely dating back to the late 1960s or early 1970s. Sequences from Angola, Gabon and the Democratic Republic of Congo failed to group consistently in these lineages, possibly because they are related to more ancient sequences that are poorly sampled. The circulating recombinant form (CRF), CRF06_cpx env sequences but not CRF25_cpx env sequences are phylogenetically nested within the subtype G clade. This confirms that the CRF06_cpx env plausibly was derived through recombination from a subtype G parent, and suggests that the CRF25_cpx env was likely derived from an HIV-1M lineage related to the MRCA of subtype G that has remained undiscovered and may be extinct. Overall, this fills important gaps in our knowledge of the early events in the spread of HIV-1M. |
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| Keywords: | HIV-1 Subtype G Phylogenetic analysis CRF |
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