Evaluation of the ABL NGS assay for HIV-1 drug resistance testing
Thomas Lhossein,
Karine Sylvain,
Véronique Descamps,
Virginie Morel,
Baptiste Demey,
Etienne Brochot
Affiliations
Thomas Lhossein
Department of Virology, Amiens University Medical Center, Amiens, France; Agents Infectieux Résistance et Chimiothérapie Research Unit, UR4294, Jules Verne University of Picardie, Amiens, France
Karine Sylvain
Department of Virology, Amiens University Medical Center, Amiens, France
Véronique Descamps
Department of Virology, Amiens University Medical Center, Amiens, France; Agents Infectieux Résistance et Chimiothérapie Research Unit, UR4294, Jules Verne University of Picardie, Amiens, France
Virginie Morel
Department of Virology, Amiens University Medical Center, Amiens, France; Agents Infectieux Résistance et Chimiothérapie Research Unit, UR4294, Jules Verne University of Picardie, Amiens, France
Baptiste Demey
Department of Virology, Amiens University Medical Center, Amiens, France; Agents Infectieux Résistance et Chimiothérapie Research Unit, UR4294, Jules Verne University of Picardie, Amiens, France
Etienne Brochot
Department of Virology, Amiens University Medical Center, Amiens, France; Agents Infectieux Résistance et Chimiothérapie Research Unit, UR4294, Jules Verne University of Picardie, Amiens, France; Corresponding author. Laboratoire de Virologie Centre de Biologie Humaine - CHU Amiens, F-80054, Amiens, cedex 1, France.
HIV evolution and variability around the world requires special monitoring of the viral strains in infected people. High-throughput HIV sequencing and drug resistance testing techniques have become routinely available over the last few years.We conducted a study to assess the new CE-marked ABL NGS HIV genotyping assay on an Illumina® platform, to compare the results (the detection of resistance associated mutations (RAMs) detected in the three main targets: reverse transcriptase, protease, and integrase) with those produced by three Sanger-based assays, and to compare the assays’ respective costs.For the 10 samples and a 20 % sensitivity threshold for the NGS technology, the percent agreement between the four assays ranged from 99.5 % to 100 %. We detected 4 more and 10 more RAMs of interest when we lowered the NGS assay's threshold to 10 % and 3 %, respectively. At a threshold of 3 %, the antiretroviral sensitivity interpretation algorithm (for protease inhibitors) was modified for only two patients. The NGS assay's unit cost fell rapidly as the number of samples per run increased.Compared with Sanger sequencing, the ABL NGS HIV genotyping assay is just as robust and somewhat more expensive but opens up interesting multiplexing perspectives for virology laboratories.
