Study of HIV type 1 gag/env variability in The Gambia, using a multiplex DNA polymerase chain reaction

A multiplex DNA PCR assay was developed for the simultaneous first-round am plification of HIV-1 gag and env fragments for the heteroduplex mobility as say (HMA). This assay was compared with the conventional amplification assa y, using DNA extracted from PBMC samples from 30 HIV-1-seropositive individ uals from The Gambia, who were enrolled between 1992 and 1997. From 27 of 3 0 (90%) samples both gag and env HMA fragments were amplified simultaneousl y. In one sample only the gag HMA fragment could be amplified by multiplex DNA PCR, and in two samples amplification was negative for both gag and env HMA in multiplex as well as the mono-DNA PCR. Of the 28 Gambian isolates s ubtyped by gag/env HMA or by sequencing and phylogenetic analysis, the majo rity (19 of 28; 68%) were intersubtype recombinant. Fifteen of 28 (53%) sam ples were circulating recombinant form (CRF) CRF02.AG variants. Two isolate s clustering with the previously documented Gambian isolate GM4 (previously described as an env GC recombinant) are classified as gag A/env J recombin ants.