title: Identification of Ugandan HIV type 1 variants with unique patterns of recombination in pol involving subtypes A and D.
abstract: Most HIV-1 infections in Uganda are caused by subtypes A and D. The prevalence of recombination and the sites of specific breakpoints between these subtypes have not been reported. HIV-1 pol sequences encoding protease (amino acids 1-99) and reverse transcriptase (amino acids 1-324) from 102 pregnant Ugandan women were analyzed by the Recombinant Identification Program, SimPlot, and examination of phylogenetically informative sites to identify sites of recombination between sequence segments belonging to different subtypes. Thirteen percent (13 of 102) of the pol sequences contained strong evidence of recombination between subtypes A and D. At least nine different patterns of recombination were observed. Five women infected with a recombinant virus transmitted the recombinant virus perinatally. In this population-based study, intersubtype recombinants were common. The large number of different types of pol recombinants identified suggests that recombination occurs readily in the pol region. Perinatal transmission of the recombinant viruses demonstrates their evolutionary stability.
authors.affiliation: Department of Pathology, Johns Hopkins Medical Institutions, Ross Building 646, 720 Rutland Avenue, Baltimore, MD 21205, USA. seshlem@jhmi.edu
authors.forename: Susan H
authors.initials: SH
authors.lastname: Eshleman
authors.forename: Matthew J
authors.initials: MJ
authors.lastname: Gonzales
authors.forename: Graziella
authors.initials: G
authors.lastname: Becker-Pergola
authors.forename: Shawn C
authors.initials: SC
authors.lastname: Cunningham
authors.forename: Laura A
authors.initials: LA
authors.lastname: Guay
authors.forename: J Brooks
authors.initials: JB
authors.lastname: Jackson
authors.forename: Robert W
authors.initials: RW
authors.lastname: Shafer
mesh_terms: D030561:Databases, Nucleic Acid; D005260:Female; D015751:Genes, pol; D014644:Genetic Variation; D015658:HIV Infections / Q000821:virology; D016333:HIV Protease / Q000235:genetics; D054303:HIV Reverse Transcriptase / Q000235:genetics; D015497:HIV-1 / Q000145:classification / Q000235:genetics*; D006801:Humans; D008969:Molecular Sequence Data; D011247:Pregnancy; D011995:Recombination, Genetic; D014454:Uganda
chemical_list: D054303:HIV Reverse Transcriptase; D016333:HIV Protease