HIV-1 recombination between different subtypes has a major impact on the global epidemic. The generation of these intersubtype recombinants follows a defined set of events starting with dual infection of a host cell, heterodiploid virus production, strand transfers during reverse transcription, and then selection. In this study, recombination frequencies were measured in the C1-C4 regions of the envelope gene in the presence (using a multiple cycle infection system) and absence (in vitro reverse transcription and single cycle infection systems) of selection for replication-competent virus. Ugandan subtypes A and D HIV-1 env sequences (115-A, 120-A, 89-D, 122-D, 126-D) were employed in all three assay systems. These subtypes co-circulate in East Africa and frequently recombine in this human population.
Baird, H. A., Gao, Y., Galetto, R., Lalonde, M., Anthony, R. M., Giacomoni, V., … Arts, E. J. (2006). Influence of sequence identity and unique breakpoints on the frequency of intersubtype HIV-1 recombination. Retrovirology, 3. https://doi.org/10.1186/1742-4690-3-91