Field evaluation of the gag-based heteroduplex mobility assay for genetic subtyping of circulating recombinant forms of human immunodeficiency virus type 1 in Abidjan, Côte d'Ivoire

Abstract

The gag-based heteroduplex mobility assay (gag-HMA) was evaluated for its ease and reliability in subtyping circulating recombinant forms (CRFs) of human immunodeficiency virus type 1 (HIV-1) in Côte d'Ivoire. One hundred thirty-two plasma samples were analyzed blindly for HIV-1 subtypes by sequencing the pol gene and by gag-HMA. DNA sequencing was used as the "gold standard." Of the 132 samples sequenced, 108 (82%) were CRF02_AG, 14 (11%) were pure subtype A, 5 (4%) were subtype G, 3 (2%) were subtype D, 1 was CRF01_AE, and 1 was subtype H. The gag-HMA correctly classified 126 (95.5%) of the samples. Of the 108 samples that were classified as CRF02_AG by DNA sequencing, 107 (99%) were correctly identified by gag-HMA, resulting in a positive predictive value of 96.4%. The gag-HMA seems to be a valuable tool for understanding the molecular epidemiology of HIV-1 CRF02_AG in Côte d'Ivoire and West Africa, which could be important for developing and evaluating AIDS vaccines, although DNA sequencing remains necessary for accurate molecular epidemiology.

FIG. 1.

Typical profile of a CRF02_AG (IBNG-like) sample, CI00297, with undifferentiated and differentiated heteroduplexes. Letters above the gel indicate reference plasmids used in determining subtypes in the HMA. Subtype assignment was based on heteroduplex migration pattern. CRF01_AE, CRF02_AG, and “pure” A were differentiated by altering the gel condition by increasing the urea concentration to 30% and extending the electrophoresis time for up to 3 h. The heteroduplexes formed by the sample and the references that migrate faster (close to the homoduplexes at the bottom of the gel) are most closely related to the specific reference plasmid. On a 20% urea gel, not all the recombinants (CRF_02 and CRF_01) could be differentiated from pure subtype A because they are closer. However, at 30% urea, by increasing the denaturing condition of the gel, the recombinants could be distinguished from the pure subtype A.