Simplified strategy for detection of recombinant human immunodeficiency virus type 1 group M isolates by gag/env heteroduplex mobility assay

We developed a heteroduplex mobility assay in the gag gene (gag HMA) for th e identification of group M subtypes A to H. The assay covers the region co ding for amino acid 132 of p24 to amino acid 20 of p7 (according to human i mmunodeficiency virus type 1 [HIV-1] ELI, 460 bp). The gag HMA was compared with sequencing and phylogenetic analysis of an evaluation panel of 79 HIV -1 group M isolates isolated from infected individuals from different geogr aphic regions. Application of gag HMA in combination with env HMA on 252 HI V-1-positive plasma samples from Benin, Cameroon, Kenya, and Zambia reveale d a high prevalence of a variety of intersubtype recombinants in Yaounde, C ameroon (53.8%); Kisumu, Kenya (26.8%); and Cotonou, Benin (41%); no recomb inants were identified among the samples from Ndola, Zambia. The AG(IbNG) c irculating recombinant form, as determined by gag HMA, was found to be the most common intersubtype recombinant in Yaounde (39.4%) and Cotonou (38.5%) . Using a one-tube reverse transcriptase PCR protocol, this gag HMA in comb ination with env HMA is a useful tool for rapidly monitoring the prevalence of the various genetic subtypes as well as of recombinants of HIV-1. Moreo ver, this technology can easily be applied in laboratories in developing co untries.