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AIDS Res Hum Retroviruses. 2008 Jul;24(7):1009-12. doi: 10.1089/aid.2008.0028.

Phylogenetic diversity and low level antiretroviral resistance mutations in HIV type 1 treatment-naive patients from Cape Town, South Africa.

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Division of Medical Virology, National Health Laboratory Service (NHLS) and University of Stellenbosch, Tygerberg 7505, Cape Town, South Africa.


We analyzed the HIV-1 pol gene from patients in Cape Town to determine the genetic diversity of HIV-1 in the region and to assess the baseline HIV-1 resistance level of treatment-naive patients. Plasma was collected prior to the national antiretroviral therapy (ART) program. RNA was extracted, followed by RT-PCR and automated DNA sequencing of the viral protease (PR) and reverse transcriptase (RT) coding region. Genotyping was done through phylogenetic analysis. The sequences were inspected for resistance-associated mutations against PR and RT inhibitors. A total of 140 pol sequences were analyzed, of which 133 (95%) belong to HIV-1 subtype C, five (3.6%) were subtype B, and one each was subtype G and CRF02_AG. Five sequences (3.6%) had resistance-associated mutations. These include three (2.1%) NNRTI mutations. With the progression of the national ART program, it is important to monitor the resistance profile of naive and treatment-experienced patients.

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