title: Estimating the rate of intersubtype recombination in early HIV-1 group M strains.
abstract: West Central Africa has been implicated as the epicenter of the HIV-1 epidemic, and almost all group M subtypes can be found there. Previous analysis of early HIV-1 group M sequences from Kinshasa in the Democratic Republic of Congo, formerly Zaire, revealed that isolates from a number of individuals fall in different positions in phylogenetic trees constructed from sequences from opposite ends of the genome as a result of recombination between viruses of different subtypes. Here, we use discrete ancestral trait mapping to develop a procedure for quantifying HIV-1 group M intersubtype recombination across phylogenies, using individuals' gag (p17) and env (gp41) subtypes. The method was applied to previously described HIV-1 group M sequences from samples obtained in Kinshasa early in the global radiation of HIV. Nine different p17 and gp41 intersubtype recombinant combinations were present in the data set. The mean number of excess ancestral subtype transitions (NEST) required to map individuals' p17 subtypes onto the gp14 phylogeny samples, compared to the number required to map them onto the p17 phylogenies, and vice versa, indicated that excess subtype transitions occurred at a rate of approximately 7 × 10(-3) to 8 × 10(-3) per lineage per year as a result of intersubtype recombination. Our results imply that intersubtype recombination may have occurred in approximately 20% of lineages evolving over a period of 30 years and confirm intersubtype recombination as a substantial force in generating HIV-1 group M diversity.
authors.affiliation: University of Edinburgh, Institute of Evolutionary Biology, Ashworth Laboratories, Edinburgh, United Kingdom.
authors.forename: Melissa J
authors.initials: MJ
authors.lastname: Ward
authors.forename: Samantha J
authors.initials: SJ
authors.lastname: Lycett
authors.forename: Marcia L
authors.initials: ML
authors.lastname: Kalish
authors.forename: Andrew
authors.initials: A
authors.lastname: Rambaut
authors.forename: Andrew J
authors.initials: AJ
authors.lastname: Leigh Brown
mesh_terms: D016000:Cluster Analysis; D015023:Democratic Republic of the Congo / Q000453:epidemiology; D005838:Genotype; D015488:HIV Antigens / Q000235:genetics; D015700:HIV Envelope Protein gp41 / Q000235:genetics; D015658:HIV Infections / Q000453:epidemiology* / Q000821:virology*; D015497:HIV-1 / Q000145:classification* / Q000235:genetics* / Q000302:isolation & purification; D006801:Humans; D017720:Molecular Epidemiology; D010802:Phylogeny; D011995:Recombination, Genetic; D017422:Sequence Analysis, DNA; D054301:gag Gene Products, Human Immunodeficiency Virus / Q000235:genetics
chemical_list: D015488:HIV Antigens; D015700:HIV Envelope Protein gp41; D054301:gag Gene Products, Human Immunodeficiency Virus; C514787:gp41 protein, Human immunodeficiency virus 1; C054858:p17 protein, Human Immunodeficiency Virus Type 1