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Background:  Understanding the sequence diversity of protease and reverse transcriptase (RT) in all HIV-1 subtypes is crucial to rational design and assessment of drug therapy in developing countries.

Methods:  This study examined the protease and RT sequence in 34 therapy-naïve individuals participating in the HIVNET 028 study in Malawi, Zambia, Zimbabwe, and South Africa. The pol sequence was determined from frozen plasma samples using the ViroSeq Genotyping System (Applied Biosystems, Foster City, CA) and DNA sequencing on a 377. Analysis of the sequences was done using Sequencher and ClustalX for alignment, the National Institutes of Health’s Genotyping Tool, and Stanford University’s Sequence Analysis Program Web sites for classification, and the Los Alamos National Laboratory Antiviral Drug Resistance Analysis tool and Stanford University Web sites for base frequency analysis.

Results:  Sequencing was successful on 34 of 40 samples on which sequencing was attempted. All of the samples were HIV-1 subtype C.  No polymorphisms that would be called major resistance mutations in HIV-1 subtype B were observed in either the protease or RT regions. Polymorphisms potentially relevant to resistance are compared in the table below with frequencies of HIV-1 subtype B in the Stanford database.