Background:  Surveillance for transmitted HIV-1 drug resistance was conducted among drug-naïve, recently infected subjects in South Africa, where single-dose nevirapine (NVP) has been in use since 2002 and a treatment program started in 2004.

Methods:  All subjects were from the Gauteng Province and were part of the 2002 and 2004 annual ante-natal HIV seroprevalence survey conducted by the South African National Department of Health. All subjects met the inclusion criteria as set out by the WHO guidelines for HIV-1 transmitted drug resistance surveillance (women <21 years of age and in first pregnancy). Genotyping was performed on plasma viral RNA by sequencing the protease and reverse transcriptase genes. Samples were also tested for the K103N mutation using a highly sensitive allele-specific real time polymerase chain reaction (PCR) assay (ASC-PCR).

Results:  Of 151 eligible participants from 2002, 66 (44%) were successfully amplified. None of the samples from 2002 had evidence of resistance mutations on genotyping or by ASC-PCR. Of 163 eligible participants from 2004, 60 (37%) samples were successfully amplified. Of these, 4 (2.5%) had K103N by genotyping, 1 of which also contained the M184V mutation and a further 2 had the K70R or T69D resistance mutations. In total, 6 (3.7%) participants showed evidence of resistance mutations on genotyping. All samples clustered phylogenetically with HIV-1 subtype C, the predominant subtype circulating in South Africa. By ASC-PCR, 5 samples (3.1%) were positive for K103N including the 4 that were genotype positive.

Conclusions:  The K103N ASC-PCR may represent a suitable screening method for drug-resistance surveillance as this mutation is commonly selected by NVP and can persist for extended periods in untreated persons. These data suggest that resistant variants may be circulating at a low frequency in South Africa and that annual surveillance among untreated populations should be conducted to determine whether this increases with time.