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


CONCLUSIONS
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.
Yirrell
David L
DL
Centre for HIV Research, ICAPB, University of Edinburgh, Edinburgh, UK.
Kaleebu
Pontiano
P
Morgan
Dilys
D
Watera
Christine
C
Magambo
Brian
B
Lyagoba
Frederick
F
Whitworth
James
J
D000328:Adult; D001483:Base Sequence; D015331:Cohort Studies; D004279:DNA, Viral; D015683:Gene Products, gag / Q000235:genetics; D015488:HIV Antigens / Q000235:genetics; D016655:HIV Core Protein p24 / Q000235:genetics; D015699:HIV Envelope Protein gp120 / Q000235:genetics; D015658:HIV Infections / Q000097:blood / Q000821:virology*; D015497:HIV-1 / Q000145:classification / Q000235:genetics*; D006801:Humans; D008969:Molecular Sequence Data; D010446:Peptide Fragments / Q000235:genetics; D010802:Phylogeny; D011995:Recombination, Genetic; D012424:Rural Population; D014454:Uganda; D014505:Urban Population; D014764:Viral Proteins; D054301:gag Gene Products, Human Immunodeficiency Virus
D004279:DNA, Viral; D015683:Gene Products, gag; D015488:HIV Antigens; D016655:HIV Core Protein p24; D015699:HIV Envelope Protein gp120; C059762:HIV envelope protein gp120 (305-321); D010446:Peptide Fragments; D014764:Viral Proteins; D054301:gag Gene Products, Human Immunodeficiency Virus; C054858:p17 protein, Human Immunodeficiency Virus Type 1