Frances Gotch, Pontiano Kaleebu, Alleluiah Rutemberwa, Jill Gilmour, Jimmy Whitworth and David Yirrell.

We are investigating the prevalence of inter-genic and intra-genic inter-subtype recombination events in HIV.1 in Ugandan populations of patients. We are evaluating the implications such data may have in our analyses of cross-clade cytotoxic T lymphocyte (CTL) activity in the same group of patients. We have shown that the majority of HIV.1 infected patients show cross-reactivity in their CTL responses as assessed using chromium release assays, and using ELISPOT assays employing both specific peptides and recombinant vaccinia viruses. All patients have been designated as being infected with a specific clade of HIV.1 based on envelope heteroduplex mobility analyses. We are however aware that in areas such as Uganda where HIV prevalence is high and where different subtypes of HIV.1 co-circulate, inter-subtype recombination is likely to take place. Such recombination events may have implications for our evaluation of the putative efficacy of cell mediated immune responses. We have examined sequence from the V3/V4 region of envelope and from a 700bpfragment of the gag gene encompassing the majority of p17 and p24 in 87 patients from two cohorts of HIV infected persons in Uganda. Our data shows 29.8% of viruses to be env/gag (inter-genic) recombinants, and 9.2% to be gag/gag (intra-genic) recombinants - the majority with breakpoints close to the p17/p24 junction. Our data is in concordance with previously published data from Rwanda. We have identified 15 different subtype assortments. The implications of the data will be discussed.