title: Phylogenetics of HIV-1 subtype G env: Greater complexity and older origins than previously reported.
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.
authors.affiliation: International Centre for Genetic Engineering and Biotechnology (ICGEB), Cape Town, South Africa; Division of Immunology, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa; Division of Medical Virology, Faculty of Health Sciences, and Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa; Institute of Medical Research and Study of Medicinal plants (IMPM), Yaoundé, Cameroon.
authors.forename: Marcel
authors.initials: M
authors.lastname: Tongo
authors.affiliation: International Centre for Genetic Engineering and Biotechnology (ICGEB), Cape Town, South Africa; Division of Immunology, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa.
authors.forename: René G
authors.initials: RG
authors.lastname: Essomba
authors.affiliation: Computational Biology Group, Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa.
authors.forename: Frederick
authors.initials: F
authors.lastname: Nindo
authors.affiliation: International Centre for Genetic Engineering and Biotechnology (ICGEB), Cape Town, South Africa.
authors.forename: Fatima
authors.initials: F
authors.lastname: Abrahams
authors.affiliation: Centre International de Référence «Chantal Biya» pour la recherche sur la prévention et la prise en charge du VIH/SIDA (CIRCB), Yaoundé, Cameroon.
authors.forename: Aubin Joseph
authors.initials: AJ
authors.lastname: Nanfack
authors.affiliation: Centre International de Référence «Chantal Biya» pour la recherche sur la prévention et la prise en charge du VIH/SIDA (CIRCB), Yaoundé, Cameroon; Faculty of Medicine and Surgery, University of Rome Tor Vergata, Rome, Italy.
authors.forename: Joseph
authors.initials: J
authors.lastname: Fokam
authors.affiliation: Centre International de Référence «Chantal Biya» pour la recherche sur la prévention et la prise en charge du VIH/SIDA (CIRCB), Yaoundé, Cameroon.
authors.forename: Desire
authors.initials: D
authors.lastname: Takou
authors.affiliation: Centre International de Référence «Chantal Biya» pour la recherche sur la prévention et la prise en charge du VIH/SIDA (CIRCB), Yaoundé, Cameroon; Faculty of Medicine and Biomedical Sciences, University of Yaounde I, Yaounde, Cameroon.
authors.forename: Judith N
authors.initials: JN
authors.lastname: Torimiro
authors.affiliation: Institute of Medical Research and Study of Medicinal plants (IMPM), Yaoundé, Cameroon.
authors.forename: Eitel
authors.initials: E
authors.lastname: Mpoudi-Ngole
authors.affiliation: Division of Medical Virology, Faculty of Health Sciences, and Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa.
authors.forename: Wendy A
authors.initials: WA
authors.lastname: Burgers
authors.affiliation: Computational Biology Group, Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa.
authors.forename: Darren P
authors.initials: DP
authors.lastname: Martin
authors.affiliation: International Centre for Genetic Engineering and Biotechnology (ICGEB), Cape Town, South Africa; Division of Immunology, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa. Electronic address: jeffrey.dorfman@icgeb.org.
authors.forename: Jeffrey R
authors.initials: JR
authors.lastname: Dorfman
mesh_terms: D000350:Africa, Central; D000810:Angola; D015658:HIV Infections / Q000821:virology*; D015497:HIV-1 / Q000145:classification* / Q000235:genetics / Q000302:isolation & purification* / Q000378:metabolism; D006801:Humans; D008969:Molecular Sequence Data; D010802:Phylogeny; D058974:Phylogeography; D011995:Recombination, Genetic; D054299:env Gene Products, Human Immunodeficiency Virus / Q000235:genetics*
chemical_list: D054299:env Gene Products, Human Immunodeficiency Virus
keywords: CRF; HIV-1; Phylogenetic analysis; Subtype G