A gag gene heteroduplex mobility assay for subtyping HIV-1

A heteroduplex mobility assay (HMA) using 753 and 446 base pair (bp) amplic ons of the p17/p24 region of the gag gene of HIV-1 has been developed and v alidated with reference clones and clinical samples representative of subty pes A, B, C, D, E, G, and H. There was complete concordance between the gag HMA assigned subtype and the subtype known from gag or env sequence data o r env HMA. The heteroduplexes from both amplicons can be clearly resolved o n either MetaPhor XR agarose or MDE polyacrylamide gels. The MetaPhor XR ge l system was the more convenient and is the preferred choice for routine HM A subtyping. This gag HMA provides a rapid, simple and inexpensive method f or subtyping HIV-1 based on a genomic region other than the commonly used e nv gene target. The incorporation of gag HMA into subtype determination alg orithms should allow the detection of gag/env recombinant strains of HIV-1. (C) 2000 Elsevier Science B.V. All rights reserved.