Genetic characterization of human immunodeficiency virus type 1 from Beira, Mozambique

In this report, we examined the genetic diversity of HIV-1 strains circulating in the city of Beira, the second largest metropolitan area in Mozambique. A total of 131 blood samples, collected between August and October 2003 from antiretroviral-naive individuals, were characterized with a combined approach consisting of heteroduplex mobility assay (HMA) subtyping for gag (n = 74) and/or env (n = 117) genes, and DNA sequence analysis of proviral env (C2V3C3, n = 52) LTR (n = 30) and/or pol (n = 43) genomic regions. Aside from the identification, by bootscanning analysis, of a viral strain with a C/A(1) mosaic C2V3C3 structure, classified as subtype A by env HMA, phylogenetic inference studies of the sequence data demonstrated the circulation of genetically diverse subtype C viruses, predominantly of the R5 type. Inspection of the LTR sequences revealed a pattern of structural and regulatory elements typical of subtype C, with 63.3% of the viruses showing three NF-kappa B binding sites. Analysis of the predicted protease sequences enabled us to detect a single primary mutation (184V, n = 1) associated with resistance to protease inhibitors (PI), while secondary mutations were highly prevalent, some of them in combinations which may confer PI resistance. Although an unexpectedly high rate (11.6%) of reverse transcriptase key mutations (V75A, K103N, Y181C, M184I, or P236L) was detected in the sequences analyzed, our data suggest the non-epidemic circulation of resistant viruses, and the absence of multi-class drug resistant viral strains.