The analysis of near full-length genome sequences of human immunodeficiency virus type 1 BF intersubtype recombinant viruses from Chile, Venezuela and Spain reveals their relationship to diverse lineages of recombinant viruses related to CRF12_BF.

Human immunodeficiency virus type 1 (HIV-1) BF intersubtype recombinant viruses are common in Argentina and Uruguay, where CRF12_BF and related recombinants are frequently found, and, in a lower proportion, in Brazil. Full-length genome sequences have been characterized in several of these recombinant viruses. Here, we analyze six newly derived near full-length genome sequences of BF recombinant viruses, three from Chile, one from Venezuela and two from Spain. Five of them had known epidemiological links to Argentina. Genomes were amplified by PCR from plasma RNA or from peripheral blood mononuclear cells' DNA. Mosaic structures and phylogenetic relationships were analyzed by bootscanning, neighbour-joining phylogenetic trees and by examination of subtype signature nucleotides. One virus from Spain had a mosaic structure fully coincident with CRF12_BF. The others had unique mosaic structures, except the viruses from two Chilean sisters infected vertically from the same mother, who showed identical recombination patterns. Each of the unique recombinants had one to six breakpoints coincident with CRF12_BF and three also had two or three breakpoints coincident with a previously characterized unique recombinant from Argentina (A025) related to CRF12_BF. A phylogenetic tree of concatenated subtype F segments supported the relationship of five recombinants with CRF12_BF. In trees of partial subtype F and B segments, four recombinants clustered with A025. The examination of CRF12_BF signature amino acids and nucleotides supported the common ancestry of all the analyzed viruses. Based on these results, a model of generation of HIV-1 BF recombinants of Argentinean ancestry by successive rounds of recombination along diverse lineages deriving from a common BF recombinant ancestor related to CRF12_BF is proposed.

High HIV-1 genetic diversity in Cuba.

BACKGROUND: HIV-1 subtype B is largely predominant in the Caribbean, although other subtypes have been recently identified in Cuba. OBJECTIVES: To examine HIV-1 genetic diversity in Cuba. METHODS: The study enrolled 105 HIV-1-infected individuals, 93 of whom had acquired the infection in Cuba. DNA from peripheral blood mononuclear cells was used for polymerase chain reaction amplification and sequencing of pol (protease-reverse transcriptase) and env (V3 region) segments. Phylogenetic trees were constructed using the neighbour-joining method. Intersubtype recombination was analysed by bootscanning. RESULTS: Of the samples, 50 (48%) were of subtype B and 55 (52%) of diverse non-B subtypes and recombinant forms. Among non-B viruses, 12 were non-recombinant, belonging to six subtypes (C, D, F1, G, H and J), the most frequent of which was subtype G (n = 5). The remaining 43 (78%) non-B viruses were recombinant, with 14 different forms, the two most common of which were Dpol/Aenv (n = 21) and U(unknown)pol/Henv (n = 7), which grouped in respective monophyletic clusters. Twelve recombinant viruses were mosaics of different genetic forms circulating in Cuba. Overall, 21 genetic forms were identified, with all known HIV-1 group M subtypes present in Cuba, either as non-recombinant viruses or as segments of recombinant forms. Non-B subtype viruses were predominant among heterosexuals (72%) and B subtype viruses among homo- or bisexuals (63%). CONCLUSION: An extraordinarily high diversity of HIV-1 genetic forms, unparalleled in the Americas and comparable to that found in Central Africa, is present in Cuba.