The recombinant and parental sequences of each pair of isolates tested were aligned using CLUSTAL X [43] . The breakpoint location of each recombinant was determined as being the central position of the interval bounded by the two closest nucleotide sites that were characteristic of each of the parental sequences). Recombination rates were calculated as follows. We define each recombination window studied with each pair of parental sequences as RwXY a-b , for a recombination window involving isolates X and Y, spanning position a to position b of env (reference sequence HXB2); a 50 nucleotides window was then considered (XY a-b Sw i , for a sliding window starting at position i of env), beginning from the 59 border of the sequence studied and the number of breakpoints (indicated as XY a-b n i ) falling within the window was counted. The resulting recombination rate per nucleotide in the sliding window XY a-b Sw i is