Prevalence and clinical impact of minority resistant variants in patients failing an integrase inhibitor-based regimen by ultra-deep sequencing

T. Nguyen, DB Fofana, MP Lê, C. Charpentier, G. Peytavin, M. Wirden, S. Lambert-Niclot, N. Désiré, M. Grude, L. Morand-Joubert, P. Flandre, C. Katlama, D. Descamps, V. Calvez, E. Todesco, and AG Marcelin. Journal of Antimicrobial Chemotherapy, 2018; 73:2485-2492, doi:10.1093/jac/dky198 Advance Access publication 4 June 2018.  This email address is being protected from spambots. You need JavaScript enabled to view it.

Citation: "... Baseline samples of patients with virological failure (VF) (n=34) and of those with virological success (VS) (n=31) under INSTI treatment were sequenced by UDS. Data were analysed using the SmartGene platform, and resistance was interpreted according to the ANRS algorithm version 27 ... analyses were performed using a fully automated analysis pipeline commercially available via SmartGene (; SmartGene, Zug, Switzerland). Briefly, paired-end reads are merged and quality-filtered to remove noise. Alignment is performed using a target-specific profile and a consensus is produced based on a user-selected ambiguity threshold. Mutations are called by frame-aware alignment with reference sequence HXB2 ..."