Genetic characterization of human immunodeficiency virus type 1 in South Africa.

Abstract

A study was conducted to investigate the genetic diversity of HIV-1 in South Africa. Blood was collected from 172 HIV-1 seropositive individuals, representing different risk groups,and subtyped by heteroduplex mobility assay (HMA) using an -700-bp env region. HIV-1 subtype C predominated and was present in 97% of heterosexually infected individuals. Ninety three percent of individuals infected homosexually and 89% of recipients of contaminated blood products were infected with subtype B viruses. Four env subtype A viruses were also identified.In order to screen for recombinant viruses, 117 of these samples were also subtyped using a gag HMA based on an -540-bp gag region. There was concordance in 113 samples with both gag and env HMA identifying the same subtype. Four recombinant viruses were found which were mosaics between subtype C and regions belonging to either subtypes A or B. Thus, the prevalence of recombinant viruses in this study is relatively low (3%).

A second study examined the phylogenetic relationships between 44 HIV-1 isolates from 43 infected subjects employed by three adjacent South African gold mines. The patients were migrant workers originating from the rural areas of South Africa and neighbouring countries of Lesotho, Botswana, Swaziland and Mozambique. HIV-1 was subtyped by env HMA and sequence analysis was used to determine phylogenetic relationships between isolates. All isolates were identified as env subtype C. These isolates did not show a distinct phylogenetic relatedness based on the geographic origins of the migrant workers or show cki ,-c homology to other subtype C sequences from southern Africa or India. The heterogeneity among these samples suggests multiple introductions of HIV-1 subtype C into this population. However, five clusters of closely related sequences were identified, mainly involving miners of disparate geographic origins,suggesting possible epidemiological linkage in these few cases.

In summary, subtype C is the predominant HIV-1 subtype in Gauteng associated with heterosexual transmission. Globally, subtype C has become the most prevalent subtype and it is likely that future vaccine strategies will be directed towards this subtype. Continual genetic characterization of HIV in South Africa is important to monitor the ongoing evolution of this subtype and to document the emergence of new subtypes and inter-subtype recombinants.