Near full-length sequence analysis of HIV type 1 BF recombinants from Italy

Abstract

Recombination between HIV-1 subtypes B and F has generated several circulating and unique recombinant forms, particularly in Latin American areas. In Italy, subtype B is highly prevalent while subtype F is the most common pure non-B subtype. To investigate the recombination pattern in Italian BF recombinant viruses, we characterized full-length sequences derived from 15 adult patients, mostly Italian and infected by the heterosexual route. One of the BF mosaics was a CRF29, three sequences clustered with low bootstrap values with CRF39, CRF40, and CRF42. With the exception of the CRF29-like sequence, the other recombination patterns were unique, but two possible clusters were identified. Analysis of the gp120 V3 domain suggested a possible link with subtype F from Eastern Europe rather than from Latin America, favoring the hypothesis of local recombination between clade B and F viruses over that of import of BF recombinants from Latin America. HIV-1 subtypes B and F appear prone to generation of unique recombinants in Italy, warranting epidemiological surveillance and investigation of a possible clinical significance.

FIG. 1.

Neighbor-joining tree of near full-length BF recombinant sequences generated with the GTR + I + G maximum likelihood model. Black circles indicate BF recombinants sequenced in this study. Bootstrap values based on 100 replicates are shown at key nodes.

FIG. 2.

Schematic representation of near-full length genomes of 15 BF recombinant viruses from Italy. Subtype B and F1 regions are shown in dark and light gray, respectively. Genomic regions that were not sequenced are shown in white. Recombination breakpoint positions are referred to the HXB2 nucleotide coordinates. Pictures were generated using the “Recombinant drawing tool” available at the Los Alamos HIV Sequence database website.