Inter- and intra-genic intersubtype HIV-1 recombination in rural and semi-urban Uganda

Publication Date: 
Friday, January 25, 2002
Yirrell DL, Kaleebu P, Morgan D, Watera C, Magambo B, Lyagoba F and Whitworth J

OBJECTIVE:
To investigate the number and variety of viruses with discrepant subtypes between env and gag and within gag in two cohorts in Uganda.

METHODS:
Sequences were generated from PCR products amplified directly (without cloning) from patient blood and compared in the v3/v4 region of env and the p17 and p24 regions of gag to reference subtype strains by phylogenetic analysis. Gag sequences with a discrepant subtype between p17 and p24 were analysed further to indicate approximate sites of recombination.

RESULTS:
Envelope subtypes D and A were predominant, but subtypes B, C and G were also found. From analysis of three short regions of the HIV genome we found 15 different combinations of subtype assortment, including 11 different recombinant permutations. Approximately 30% of viruses (29/104) in this part of Uganda appear to be recombinants between the env and gag genes and 10% (11/104) are recombinant within the gag gene. There was no clear pattern of crossover points within the gag gene. There seems to be no evidence of new circulating recombinant forms.

CONCLUSION:
Both inter-genic and intra-genic inter-subtype recombination appear to be a relatively common occurrence in this geographical region where two subtypes of virus co-circulate. These results have implications for cross-clade vaccine design.

Publisher: 
AIDS
MRC/UVRI Authors: