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Background:  Baseline data on HIV genetic drug resistance mutations in South Africa is limited. Information in this regard may assist in deciding whether to perform resistance studies before the initiation of antiretroviral therapy. We have examined the protease region of 40 previously classified HIV-1 subtype C primary isolates obtained from drug-naive patients from Gauteng and Limpopo Provinces of South Africa for mutations that could signify resistance to protease inhibitors based on subtype-B data.

Methods:  Viral RNA was isolated from plasma using the Qiagen viral RNA kit. The protease gene coding for amino acids 1 to 99 was amplified by a nested reverse transcription PCR using consensus subtype-C primers. Nucleotide sequences edited were submitted to the Stanford sequence database (HIV-SEQ and beta test) for the detection of mutations associated with drug resistance.

Results:  No mutations characteristic of primary resistance to protease inhibitors were detected. However M36I and I93L, which are known secondary drug resistance mutations in subtype-B infections, each occurred in 36 (90%) of these subtype-C isolates. Additional amino acid substitutions associated with secondary drug resistance included K20R (18/40), L63P/T/V (21/40), and V77I (6/40). Ten isolates had a combination of K20R/M36I known to contribute to indinavir and ritonavir resistance. Also, a V82I substitution associated with low level resistance to nelfinavir was detected in 3 isolates. We are currently building these mutations into a subtype-C molecular clone to directly test resistance to protease inhibitors.

Conclusions:  Although this analysis revealed several potential secondary resistance mutations, it would still be expected that many or most of the sequenced viruses would be susceptible to currently available protease inhibitors. However, the effect of secondary resistance mutations and polymorphism on the propensity to develop resistance once drug pressure is applied is unknown. There is therefore need to evaluate apparent polymorphisms and continuous surveillance among patients failing antiretroviral therapies in South Africa to determine the resistance patterns among subtype-C viruses, the predominant variant responsible for the southern African epidemic.

Keywords: HIV-1 subtype C; Protease resistance mutations; South Africa