title: HIV-1 subtypes and recombinants in Northern Tanzania: distribution of viral quasispecies.
abstract: This study analyzed the distribution and prevalence of HIV-1 subtypes, multiplicity of HIV-1 infection, and frequency of inter-subtype recombination among HIV-1-infected female bar and hotel workers in Moshi, Kilimanjaro Region, Tanzania, from 2004 to 2007. The HIV-1 viral sequences spanning the V1-C5 region of HIV-1 env gp120 were analyzed from 50 subjects by single genome amplification and sequencing (SGA/S) technique. A total of 1740 sequences were amplified and sequenced from the HIV-1 proviral DNA template. The median env sequences analyzed per subject per two time points was 38 (IQR 28-50) over one year of HIV infection. In a subset of 14 subjects, a total of 239 sequences were obtained from HIV-1 RNA template at the baseline visit. The most prevalent HIV-1 subtypes were A1 (56%) and C (30%), while HIV-1 subtype D and inter-subtype recombinant viruses were found in 6% and 8% of subjects respectively. Transmission of multiple HIV-1 variants was evident in 27% of the subjects infected with pure HIV-1 subtypes A1, C, or D. The HIV-1 inter-subtype recombinants were found in 8% including HIV-1 C/A, D/A, and complex mosaic recombinants. Multiple viral variants were found in two subjects infected with inter-subtype recombinants. One subject harbored quasispecies of both pure HIV-1 A1 and C/A recombinant. The other subject was infected with two complex mosaic inter-subtype recombinant variants belonging to subtype D. HIV-1 multiple infections and ongoing recombination contribute significantly to the genetic diversity of circulating HIV-1 in Tanzania and have important implications for vaccine design and the development of therapeutic strategies.
authors.affiliation: Kilimanjaro Christian Medical Centre and College, Tumaini University, Moshi, Tanzania.
authors.forename: Ireen E
authors.initials: IE
authors.lastname: Kiwelu
authors.forename: Vladimir
authors.initials: V
authors.lastname: Novitsky
authors.forename: Lauren
authors.initials: L
authors.lastname: Margolin
authors.forename: Jeannie
authors.initials: J
authors.lastname: Baca
authors.forename: Rachel
authors.initials: R
authors.lastname: Manongi
authors.forename: Noel
authors.initials: N
authors.lastname: Sam
authors.forename: John
authors.initials: J
authors.lastname: Shao
authors.forename: Mary F
authors.initials: MF
authors.lastname: McLane
authors.forename: Saidi H
authors.initials: SH
authors.lastname: Kapiga
authors.forename: M
authors.initials: M
authors.lastname: Essex
mesh_terms: D000293:Adolescent; D000328:Adult; D004279:DNA, Viral / Q000145:classification / Q000235:genetics; D005260:Female; D015694:Gene Products, rev / Q000235:genetics; D015658:HIV Infections / Q000235:genetics / Q000821:virology; D006679:HIV Seropositivity / Q000235:genetics; D015497:HIV-1 / Q000145:classification / Q000235:genetics / Q000472:pathogenicity; D006801:Humans; D008875:Middle Aged; D010802:Phylogeny; D011995:Recombination, Genetic; D017422:Sequence Analysis, DNA; D060386:Sex Workers; D013636:Tanzania
chemical_list: D004279:DNA, Viral; D015694:Gene Products, rev