title: A molecular epidemiologic survey of HIV in Uganda. HIV Variant Working Group.
abstract: OBJECTIVE
  Previous data, based on a small sampling of convenience, reported subtypes A, B, C, D, and G in Uganda, but neither the extent nor the proportion of these subtypes could be evaluated. To establish correctly the prevalence and distribution of HIV-1 subtypes, we analysed viral clades in 739 HIV-1-seropositive specimens from different areas of Uganda.
  
  
  METHODS
  Blood specimens from 1100 patients were collected in five districts of Uganda. Within this collection, 929 HIV-1-seroreactive samples underwent analysis of viral DNA, and 739 were selected for further subtyping in env or pol regions.
  
  
  RESULTS
  Using a combination of subtype A- and D-specific probes to C2-V3 region and DNA sequencing, HIV-1 env subtypes were determined in 594 specimens: 341 were of subtype A (57.4%), 250 of subtype D (42.1%), and three of subtype C (0.5%). Sixty-two samples showed reactivity with both probes, suggesting potential mixed infections, cross-reactivity to probes, or possibly other subtypes. Subsequent sequence analysis of 19 randomly selected specimens revealed subtypes A (n = 4), D (n = 12), and C (n = 3). Sequence analysis of the 27 samples chosen from the remaining 83 samples, which could be amplified only with viral gp41 or protease gene primers, classified them as subtypes A (n = 13) and D (n = 14). No significant clinical, demographic, or geographic differences were found between HIV-1 infections with viruses of subtypes A and D, despite considerable genetic diversity within these clades.
  
  
  CONCLUSIONS
  This is the first major population-based study of the prevalent HIV-1 strains in an African country selected for vaccine trials. The subtyping methods we describe should be of use to investigators seeking to conduct large-scale screening for HIV variants in other populations.
authors.affiliation: HIV/Retrovirus Diseases Branch, Division of AIDS, STD and TB Laboratory Research, National Center for Infectious Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia 30333, USA.
authors.forename: M A
authors.initials: MA
authors.lastname: Rayfield
authors.forename: R G
authors.initials: RG
authors.lastname: Downing
authors.forename: J
authors.initials: J
authors.lastname: Baggs
authors.forename: D J
authors.initials: DJ
authors.lastname: Hu
authors.forename: D
authors.initials: D
authors.lastname: Pieniazek
authors.forename: C C
authors.initials: CC
authors.lastname: Luo
authors.forename: B
authors.initials: B
authors.lastname: Biryahwaho
authors.forename: R A
authors.initials: RA
authors.lastname: Otten
authors.forename: S D
authors.initials: SD
authors.lastname: Sempala
authors.forename: T J
authors.initials: TJ
authors.lastname: Dondero
mesh_terms: D000328:Adult; D015342:DNA Probes; D004279:DNA, Viral; D005260:Female; D015752:Genes, env; D014644:Genetic Variation; D015658:HIV Infections / Q000453:epidemiology*; D015497:HIV-1 / Q000145:classification / Q000235:genetics*; D006801:Humans; D008297:Male; D017720:Molecular Epidemiology; D010802:Phylogeny; D016133:Polymerase Chain Reaction; D017422:Sequence Analysis, DNA; D014454:Uganda / Q000453:epidemiology
chemical_list: D015342:DNA Probes; D004279:DNA, Viral