Intersubtype recombinant HIV-1 Sequences.

Retroviruses are highly recombinogenic, but recombination can only occur between genomes packaged within the same virion. Until about 1994, it was generally thought that individuals do not become infected with multiple distinct HIV-1 strains, and so the possibility that recombination between divergent viruses could contribute to the evolution of HIV-1 was not widely considered. However, not long after the recognition that the considerable global diversity of the major (M) group of HIV-1 could be described in terms of discrete sequence subtypes, it was also realized that a significant fraction of HIV-1 strains are in fact intersubtype recombinants [1,2]. Analyses of viruses characterized over the last few years have confirmed that substantial numbers of HIV-1 isolates have mosaic genomes [3–16]. The finding of such hybrid viruses has a number of implications both for attempts at viral characterization (phylogenetic analyses, and tracking of the epidemic), and for concerns about the future genetic diversity of HIV-1 and its impact on vaccine development.