HIV type 1 diversity and the reliability of the heteroduplex mobility assay

Abstract

We investigated HIV-1 diversity by means of heteroduplex mobility assay (HMA) genotyping. We studied 199 samples from patients originating from 26 countries and living in France. The HMA successfully genotyped 182 (91 %) of these samples, as follows : 77 (42 %) subtype A, 57 (31 %) subtype B, 5 (3 %) subtype C, 5 (3 %) subtype D, 8 (4 %) subtype E, 22 (12 %) subtype F, 5 (3 %) subtype G, and 3 (2 %) subtype H. We were not able to genotype 12 samples by means of the HMA. These latter strains were sequenced, and phylogenetic analyses revealed that they were highly divergent subtype A-, D-, or G-related strains. Eight (of 12) subtype D strains were indeterminate by HMA, owing to the broad intrasubtype diversity, suggesting that new reference subtype D plasmids are required, as previously proposed. Thirty-seven strains belonging to the different subtypes were sequenced, and the results showed perfect concordance with the HMA results. Interlaboratory quality controls confirmed the reliability of the HMA for HIV-1 subtyping, despite the extensive viral variability. However, plasmid selection must be continuously revised to cover viral diversification. (Résumé d'auteur