Analysis of full-length human immunodeficiency virus type 1 genome reveals a variable spectrum of subtypes B and F recombinants in Sao Paulo, Brazil

Recombination is one of the major mechanisms contributing to human immunodeficiency virus type I (HIV-1) variability. Analysis of pol gene sequences of 215 HIV-1 samples from Sao Paulo, Brazil classified 189 sequences as subtype B (87.9%), 8 sequences as subtype F (3.7%), and 18 sequences (8.4%) as B/F recombinants. After the analysis of the pol gene, a subset of six recombinant samples composed of sequences with a related recombinant pol structure was selected for full-length genome analysis to identify a possible circulating recombinant form. According to full-length genome analysis, recombination was higher in gag, protease, reverse transcriptase, integrase, and vif. Identification of many distinct recombinant forms and the absence of an identifiable HIV-1 circulating recombinant form suggest that a high frequency of dual infections between HIV-1 subtypes B and F is occurring in Sao Paulo, Brazil.