Objectives: To determine HIV-1 env and gag subtypes in male homosexual and heterosexual populations in Cape Town, South Africa.
Design: DNA was isolated from blood originating from 61 patients attending local clinics. Samples were divided according to presumed mode of transmission: male homosexual (n = 26), heterosexual/vertical (n = 32), blood transfusion (n = 1) and unknown (n = 2).
Methods: Proviral HIV-1 DNA was subtyped by heteroduplex mobility assay (HMA) based on the 799 base-pair V3-V5 region of the env gene (n = 47) or by sequence analysis of the p17 region of the gag gene (n = 33), or both. For HMA, reference plasmids were constructed containing the V1-V5 env region sequences (1.2-kb) representative of local subtypes. Subtype designation of reference subtypes was confirmed by sequence analysis of the V3-loop region.
Results: Analysis of the partial gag sequences and HMA of the V3-V5 env region identified three subtypes: B, C and D. A fourth env subtype, subtype E, was also identified by HMA. Subtypes were found to segregate according to mode of transmission, with subtype B viruses found in 96% (25 out of 26) of the male homosexual group and subtype C viruses found in 81% (26 out of 32) of the heterosexual/vertical transmission group. Subtype B viruses were also found in four heterosexual patients, one patient infected by blood transfusion and in two patients with unknown mode of transmission. Subtype D viruses were found in one male homosexual patient and one heterosexual patient. A subtype E virus was identified in a heterosexual patient. No discrepancy was found in subtype designation in samples analysed in both between the gag and env regions (n = 19).
Conclusions: Subtype B viruses were associated with male homosexual transmission and subtype C viruses with heterosexual transmission, suggesting two independent epidemics. This data may have implications in the selection of appropriate vaccines for different risk groups in the country.
PIP: Investigations of the genetic heterogeneity of human immunodeficiency virus (HIV) -1 are important both to monitor the spread of the virus to new population groups and to the development of vaccines the efficacy of which could be influenced by virus variations. This study analyzed serum samples from 61 HIV-1 infected individuals recruited from clinics in Cape Town, South Africa. The mode of transmission was male homosexual in 26 cases, heterosexual/vertical in 32 cases, blood transfusion in 1 case, and unknown in 2 cases. Proviral HIV-1 DNA was subtyped by heteroduplex mobility assay (HMA) based on the 700 base-pair V3-V5 region of the env gene or by sequence analysis of the p17 region of the gag gene. This process identified 3 subtypes: B, C, and D. A fourth env subtype (E) was also identified by HMA. Subtypes were significantly (p 0.001) associated with the mode of HIV transmission. Subtype B viruses were found in 96% of male homosexual sera and subtype C viruses were identified in 81% of the heterosexual/vertical transmission group. Subtype B viruses were also identified in 4 heterosexuals, 1 person infected through blood transfusion, and the 2 cases where the mode of transmission was unknown. Subtype D viruses were found in 1 male homosexual and 1 heterosexual, while a subtype E virus was identified in a heterosexual patient. These findings imply that heterosexual and homosexual HIV-1 epidemics in South Africa were independent. Both epidemiological and molecular data suggest that the initial epidemic in South Africa was, in part, a result of the introduction of HIV-1 by homosexuals who had sexual contacts with men in the US or Europe. The second, heterosexual epidemic was most likely a result of regional spread.