Diversity of the human immunodeficiency virus type 1 envelope glycoprotein in San Francisco Men's Health Study participants.
Multiple genetic subtypes of HIV-1, differing by up to 30% of nucleotides in their envelope coding sequences, have been identified in the global epidemic. In the United States, where HIV-1 infection with subtype B predominates, the interisolate diversity in envelope is 15% or more. It is recognized that geographic, temporal, and demographic variables can affect the genetic diversity of HIV-1 strains, but there have been few opportunities to evaluate these factors by population-based sampling. We have evaluated HIV-1 envelope diversity among participants in the San Francisco Men's Health Study (SFMHS), which represents a geographically, temporally, and demographically defined subset of HIV-1 infections in the United States. DNA was extracted from primary PBMCs obtained within 6 months of seroconversion and from individuals whose HIV-1 infection occurred between 1985 and 1989. The full-length envelope gene was PCR amplified, cloned, and sequenced from 17 different individuals. The sequences were compared within the cohort and with reference sequences from the United States and overseas, and their relationship to vaccine prototype strains LAI, MN, and SF2 was evaluated. SFMHS participants harbored HIV-1 subtype B infections with limited interpatient variation and a higher proportion of atypical V3 loop crown sequences than reference sequences of this subtype. Throughout gp160, the MN strain was less representative than LAI or SF2 among the patients examined. The geographic component of variation was apparently more substantial than the temporal, emphasizing the need for widely distributed geographic sampling in estimations of HIV diversity.
McCutchan
F E
FE
Henry M. Jackson Foundation for the Advancement of Military Medicine, Rockville, Maryland 20850, USA.
Sanders-Buell
E
E
Salminen
M O
MO
Carr
J K
JK
Sheppard
W H
WH
D016915:AIDS Vaccines / Q000235:genetics; D000595:Amino Acid Sequence; D001483:Base Sequence; D017931:DNA Primers / Q000235:genetics; D004279:DNA, Viral / Q000235:genetics; D015752:Genes, env; D014644:Genetic Variation; D015699:HIV Envelope Protein gp120 / Q000235:genetics; D015658:HIV Infections / Q000453:epidemiology* / Q000821:virology*; D006679:HIV Seropositivity / Q000821:virology; D015497:HIV-1 / Q000145:classification* / Q000235:genetics* / Q000302:isolation & purification; D006801:Humans; D008297:Male; D017720:Molecular Epidemiology; D008969:Molecular Sequence Data; D010446:Peptide Fragments / Q000235:genetics; D016133:Polymerase Chain Reaction; D012495:San Francisco / Q000453:epidemiology; D017386:Sequence Homology, Amino Acid
D016915:AIDS Vaccines; D017931:DNA Primers; D004279:DNA, Viral; D015699:HIV Envelope Protein gp120; C059762:HIV envelope protein gp120 (305-321); D010446:Peptide Fragments