To the Editor: Although international efforts to systematically collect, characterize, and classify HIV isolates from around the world have increased considerably, data on HIV-1 genetic variations in Puerto Rico are limited. This island (population 3.7 million) has one of the highest AIDS incidence rates in the United States (53.3 cases per 100,000) (1). To evaluate the potential for a multiple subtype distribution pattern in Puerto Rico, we analyzed genetic variations between HIV-1 strains isolated from peripheral blood mononuclear cells of 63 asymptomatic HIV-infected female commercial sex workers from 12 communities. These participants were part of 290 female commercial sex workers followed in a larger cross-sectional study of risk behavior (2).

HIV-1 subtypes F (n = 4) and B (n = 44) strains were identified in persons infected with a single viral subtype with a molecular screening assay based on restriction fragment length polymorphism (RFLP) analysis and with DNA sequencing of the viral protease gene-prot (3). The remaining 15 specimens were classified by RFLP as potential dual infections. Further cloning and sequencing of prot from three of these specimens confirmed one dual infection involving subtypes F and B viruses and identified two infections caused by genetically distinct quasispecies of subtype B variants.

In further detailed pairwise analysis of HIV-1 prot genes, a small nucleotide divergence of 0.3% (0.0 to 1.1) within subtype F contrasted with a typical value of 6.3% (5.1 to 7.8) for the intrasubtype distance within subtype B prot sequences (4). The 99% similarity between prot subtype F Puerto Rican sequences suggested an epidemiologic link or a recent introduction of subtype F in Puerto Rico. Comparative sequence analysis of the C2-V3 env is useful in establishing the time that elapsed from infection on the basis of an annual nucleotide divergence of 0.5% to 1% in this region (5). Such analysis has been used to study the epidemiologic link between cases (4,6). Thus, we compared env sequences from two of five persons infected with prot subtype F strains. This analysis provided several observations. Env nucleotide divergence of 13.2% did not support a direct epidemiologic link between these strains. Furthermore, the relatively high intrasubtype diversity between env sequences suggested that evolution from a common progenitor would have taken a minimum of approximately 13 years. Phylogenetic analysis classified these two env sequences as subtype B, indicating that at least some of Puerto Rican prot subtype F viruses represent HIV-1 mosaics involving closely related prot F and significantly divergent env B sequences. Overall, discrepancy in both subtype assignment and nucleotide diversities within prot and env regions may indicate that distinct F/B mosaics circulating in Puerto Rico were likely the result of recombination between highly homogeneous subtype F of relatively recent arrival and divergent resident subtype B viruses.

HIV-1 infections with subtype F strains including B/F mosaics have been reported in Brazil (3,7). To evaluate a potential HIV-1 linkage between Brazil and Puerto Rico, a comparative phylogenetic analysis was done on subtype F viral prot sequences from these countries. This analysis documented that HIV-1 subtype F strains in Puerto Rico are distinct from both Brazilian and Romanian viruses. Furthermore, our results show that genetic analysis of prot allows tracking of subtype F viruses of different origin. Recently, by this approach, HIV-1 prot subtype F of Puerto Rican origin and F prot/B env mosaic were identified in HIV-1-infected persons in New York city (8). Observation of HIV-1 subtype F strains in Puerto Rico together with the recent report describing the first cases of such infections in New York indicates the potential for further emergence of subtype F on the North American continent. The presence of a complex distribution pattern of subtype F infections in Puerto Rico has serious implications for the evaluation and development of HIV diagnostics and vaccines.

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