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% Cl: 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 5,000 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.