Genetic diversity and drug resistance mutations in HIV type 1 from untreated patients in Bamako, Mali.

OBJECTIVE To determine the genetic diversity of HIV-1 reverse transcriptase (RT) and protease sequences and the presence of mutations linked to antiretroviral (ARV) resistance in treatment-naive, HIV-1-infected individuals living in Mali. METHODS Ninety-eight samples from ARV drug-naive, HIV-1-infected patients were collected in one clinical centre in Bamako, Mali in 2005. RT and protease genes were sequenced in order to perform phylogenetic and resistance analyses. RESULTS The most prevalent subtype was CRF02-AG (75% of cases), followed by the CRF06-cpx subtype (20%). Intersubtype recombinants between CRF02-AG, CRF01-AE and CRF06-cpx were also described in 5% of cases. After 4 years of ARV use in Mali, two previously untreated individuals (2%; 95% CI: 0.00-4.77%) were found to have resistant viruses, one with a single nucleoside mutation and one with K103N non-nucleoside reverse transcriptase inhibitor resistance mutation. No evidence of transmitted protease inhibitor resistance mutations was found. CONCLUSION These data provide direct evidence for the circulation of HIV-1 isolates containing resistance mutations in treatment-naive patients in Mali. Since ARV use in Mali began, more than 5000 patients have started treatment, mostly with Triomune (stavudine/lamivudine/nevirapine). The resistance-associated mutations detected in the present study are consistent with this treatment regimen. Continued surveillance will be required to monitor the emergence of ARV resistance in this country.