title: Genetic diversity and high proportion of intersubtype recombinants among HIV type 1-infected pregnant women in Kisumu, western Kenya.
abstract: The high genetic diversity of HIV-1 continues to complicate effective vaccine development. To better understand the extent of genetic diversity, intersubtype recombinants and their relative contribution to the HIV epidemic in Kenya, we undertook a detailed molecular epidemiological investigation on HIV-1-infected women attending an antenatal clinic in Kisumu, Kenya. Analysis of gag-p24 region from 460 specimens indicated that 310 (67.4%) were A, 94 (20.4%) were D, 28 (6.1%) were C, 9 (2.0%) were A2, 8 (1.7%) were G, and 11 (2.4%) were unclassifiable. Analysis of the env -gp41 region revealed that 326 (70.9%) were A, 85 (18.5%) D, 26 (5.7%) C, 9 (2.0%) each of A2 and G, 4(0.9%) unclassifiable, and 1 (0.2%) CRF02_AG. Parallel analyses of the gag-p24 and env-gp41 regions indicated that 344 (74.8%) were concordant subtypes, while the remaining 116 (25.2%) were discordant subtypes. The most common discordant subtypes were D/A (40, 8.7%), A/D (27, 5.9%), C/A (11, 2.4%), and A/C (8, 1.7%). Further analysis of a 2.1-kb fragment spanning the gag-pol region from 38 selected specimens revealed that 19 were intersubtype recombinants and majority of them were unique recombinant forms. Distribution of concordant and discordant subtypes remained fairly stable over the 4-year period (1996-2000) studied. Comparison of amino acid sequences of gag-p24 and env-gp41 regions with the subtype A consensus sequence or Kenyan candidate vaccine antigen (HIVA) revealed minor variations in the immunodominant epitopes. These data provide further evidence of high genetic diversity, with subtype A as the predominant subtype and a high proportion of intersubtype recombinants in Kenya.
authors.affiliation: Division of AIDS, STD, and TB Laboratory Research, National Center for HIV, STD and TB prevention, Centers for Disease Control and Prevention, Atlanta, Georgia 30333, USA.
authors.forename: Chunfu
authors.initials: C
authors.lastname: Yang
authors.forename: Ming
authors.initials: M
authors.lastname: Li
authors.forename: Ya-Ping
authors.initials: YP
authors.lastname: Shi
authors.forename: Jorn
authors.initials: J
authors.lastname: Winter
authors.forename: Anna M
authors.initials: AM
authors.lastname: van Eijk
authors.forename: John
authors.initials: J
authors.lastname: Ayisi
authors.forename: Dale J
authors.initials: DJ
authors.lastname: Hu
authors.forename: Richard
authors.initials: R
authors.lastname: Steketee
authors.forename: Bernard L
authors.initials: BL
authors.lastname: Nahlen
authors.forename: Renu B
authors.initials: RB
authors.lastname: Lal
mesh_terms: D015492:AIDS Serodiagnosis; D001483:Base Sequence; D017931:DNA Primers; D005260:Female; D015752:Genes, env; D015750:Genes, gag; D014644:Genetic Variation; D015658:HIV Infections / Q000150:complications / Q000175:diagnosis / Q000821:virology*; D015497:HIV-1 / Q000145:classification / Q000235:genetics*; D006801:Humans; D007630:Kenya; D008969:Molecular Sequence Data; D010802:Phylogeny; D011247:Pregnancy; D011251:Pregnancy Complications, Infectious / Q000175:diagnosis / Q000821:virology*; D011995:Recombination, Genetic; D020133:Reverse Transcriptase Polymerase Chain Reaction; D013045:Species Specificity
chemical_list: D017931:DNA Primers