High HIV Type 1 Subtype Diversity and Few Drug Resistance Mutations among Seropositive People Detected during the 2005 Second Generation HIV Surveillance in Madagascar

Subtype determination and detection of drug resistant-associated mutations (DRM) were performed on 31 HIV-1 Western blot-positive sera during the 2005 second-generation HIV surveillance in Madagascar. Amplification and sequencing of at least one of the partial reverse transcriptase, protease, and partial envelope genes were successful for all strains. All three gene sequences were obtained for 28 strains. A high degree of subtype or circulating recombinant forms (CRF) was observed for these 28 strains: A-A1 (eight cases), CRF02_–AG (six cases), B (five cases), C (three cases), CRF06_–cpx (three cases), CRF10_CD, BC_–CRF, and unique RF (one case each). According to the ANRS September 2005 DRM list and algorithm, no DRM was detected in the reverse transcriptase and only one strain bore three major DRM in the protease M46I, I84V, and L90M leading to resistance to indinavir, saquinavir, nelfinavir, atazanavir/ritonavir, and possibly lopinavir.