Molecular epidemiology of HIV in two highly endemic areas of northeastern South Africa

Abstract

There is paucity of data on the genetic landscape of HIV-1 viruses circulating in the Limpopo Province of northeastern South Africa. Here, we examine the genetic diversity of viruses from Bela-Bela and Musina, two towns with high HIV prevalence. Between June 2007 and March 2008, blood samples were collected from antiretroviral-drug-naïve individuals. Viruses were analyzed for genetic subtypes and drug resistance mutations. All of the viruses in these samples were shown by phylogenetic analysis based on gag p17, gag p24, reverse transcriptase, protease and envelope C2-C3 gene regions to belong to HIV-1 subtype C. Two of 44 reverse transcriptase sequences (4.5%) contained N rather than the consensus K at position 103. The K103N mutation is normally associated with resistance to NNRTIs. No major mutations were observed in the protease gene. However, several polymorphisms and amino acid changes normally considered to be minor drug resistance mutations were observed in the protease sequences. These results suggest that HIV-1 subtype C remains the predominant variant responsible for the epidemic in northeastern South Africa and that the prevalence of drug-resistant viruses among the naïve population is low.

Fig. 1. Phylogenetic relationships of gag p24 nucleotide sequences from northeastern South Africa

Sequences were aligned with reference HIV-1 subtype A-K sequences, and a phylogenetic tree was constructed by the neighbor-joining method implemented in ClustalX. Test sequences (in boldface) cluster and intermingle with subtype C reference sequences. Bootstraps values above 70% of 1000 replicates are indicated

Fig. 2. Phylogenetic relationship of partial reverse transcriptase nucleotide sequences from northeastern South Africa

The sequences cluster and intermingle with subtype C reference sequences, indicating that they are HIV-1 subtype C. The tree was constructed by the neighbor-joining method as implemented in the ClustalX2 program. The validity of the branching orders was estimated with 1000 replicates. Bootstrap values above 70% of 1000 replicates are indicated

Fig. 3. Phylogenetic analysis of the env C2-C3 nucleotide sequences from northeastern South Africa

Test sequences (in boldface) cluster and intermingle with HIV-1 subtype C reference sequences with a bootstrap value of 91% of 1000 replicates

Fig. 4. Predicted V-3 loop amino acid sequences and biotypes of HIV from northeastern South Africa

The multiple aligned sequences were compared to the consensus of the test sequences with those of the global subtype C consensus sequence and the South African vaccine strain AY043173_ZA. Underlined are the glycosylation sites and the GPGQ motif. Four viruses are X4 viruses, as predicted by webPSSM. The consensus of the test sequences showed close amino acid similarity to the global subtype C consensus sequence and the South African vaccine strain, except at position 32 for the consensus sequence and 25 and 29 for AY043173_ZA