Increasing prevalence of non-clade BHIV-1 strains in heterosexual men and women, as monitored by analysis of reverse transcriptase and protease sequences

Objective: We evaluated the prevalence of HIV-1 non-clade B over time in a formerly clade B-restricted area. Protease and reverse transcriptase region s of the pot gene were used for phylogenetic and recombination analysis and for clade assignment to HIV-1 A-D, F-H, J, and K strains of the M group. Methods: The pot gene of 349 HIV-1 patients belonging to the Italian Cohort Naive for Antiretrovirals (ICONA) were genotypically analyzed to study the prevalence of antiretroviral-associated resistance mutations. All HIV-1 po t sequences and 32 HIV reference strains were analyzed, including the refer ence strains for the major HIV-1 subtypes. The non-clade B sequences accord ing to the HIV-1 Subtyping Tool program were further studied by a bootscan analysis (SimPlot) to investigate the likelihood of recombination between s ubtypes. Results: Phylogenetic analysis detected 19 of 349 (5.4%) non-clade B subtyp es. The proportions of patients carrying non-clade B virus before and after 1997 were 1.9% and 8.4%, respectively (p = .008). Among whites, heterosexu al infection and female gender were significantly associated with the prese nce of non-clade B subtypes (p = .001 and .005, respectively). Non-clade B HIV-1 was harbored by 14.5% of the heterosexuals who were found to be HIV-1 positive after 1997, 60% of whom were women. Bootscan analysis identified four strains as F, two as A, one as C, one as G, and 11 (57.9 %) as non-cla de B recombinant subtypes. Conclusion: Detection of HIV-1 subtypes and intersubtype recombinants in a previously clade B-homogeneous area indicates that the HIV-1 epidemic is ev olving in Italy and that heterosexuals and women are at increased risk of i nfection with non-clade B HIV-1 subtypes. Sequences inferred from the pot g ene yield to establish the subtype of circulating HIV-1 strains. As a conse quence, genotyping of pot gene for testing resistance to antiretrovirals wa rrants concomitant surveillance of non-clade B subtypes.