The investigator proposes to employ polymerase chain reaction (PCR), DNA cloning and sequencing techniques to attempt to determine diversity in the HIV genome encoding the V3 loop in about 300 representative isolates from endemic localities in Uganda. Lysates of infected mononuclear cells obtained from AIDS patients in geographically distinct regions will be used as the source of viral isolates. The HIV genome segment comprising nucleotide residues 6597-6955 which encode the entire V3 loop will be amplified by PCR using primer #1 (5'-CGCTGCAGAAGAAGAGGTAGTAATTAGAT) and primer #2 (5'-CCCTGCAGTAGAAAAATTCCCCTCTACAA). The amplified DNA will be electroeluted from 5%-10% polyacrylamide gradient gels and then subcloned into the pst I site in pGEM-blue plasmids. The inserts will be expanded in Escherichia coli and then sequenced by means of dideoxynucleotide chain termination. The sequence data obtained from the Ugandan isolates will be compared with each other and with those of standard American strains currently in use for vaccine design and development.
