Performance comparison of deep sequencing platforms for detecting HIV-1 variants in the pol gene

Journal of Medical Virology
Florence NicotJacques Izopet

Abstract

The present study compares the performances of an in-house sequencing protocol developed on MiSeq, the Sanger method, and the 454 GS-FLX for detecting and quantifying drug-resistant mutations (DRMs) in the human immunodeficiency virus polymerase gene (reverse transcriptase [RT] and protease [PR]). MiSeq sequencing identified all the resistance mutations detected by bulk sequencing (n = 84). Both the MiSeq and 454 GS-FLX platforms identified 67 DRMs in the RT and PR regions, but a further 25 DRMs were identified by only one or other of them. Pearson's analysis showed good concordance between the percentage of drug-resistant variants determined by MiSeq and 454 GS-FLX sequencing (ρ = .77, P < .0001). The MiSeq platform is as accurate as the 454 GS-FLX Roche system for determining RT and PR DRMs and could be used for monitoring human immunodeficiency virus type 1 drug resistance.

References

Aug 2, 2005·Nature·Marcel MarguliesJonathan M Rothberg
Nov 9, 2010·Journal of Clinical Virology : the Official Publication of the Pan American Society for Clinical Virology·Karin J MetznerHauke Walter
Apr 7, 2011·JAMA : the Journal of the American Medical Association·Jonathan Z LiDaniel R Kuritzkes
Sep 6, 2011·Clinical Infectious Diseases : an Official Publication of the Infectious Diseases Society of America·Luke C SwensonP Richard Harrigan
Dec 3, 2011·Proceedings of the National Academy of Sciences of the United States of America·Cassandra B JabaraRonald Swanstrom
Apr 24, 2012·Nature Biotechnology·Nicholas J LomanMark J Pallen
Jul 24, 2012·Journal of Clinical Virology : the Official Publication of the Pan American Society for Clinical Virology·F NicotJ Izopet
Nov 21, 2012·PloS One·John ArcherMiguel E Quiñones-Mateu
Feb 7, 2013·Journal of Virological Methods·Max W ChangBruce E Torbett
Oct 23, 2014·The Journal of Antimicrobial Chemotherapy·Alessandro Cozzi-LepriUNKNOWN CHAIN Minority HIV-1 Variants Working Group
Aug 19, 2015·Antimicrobial Agents and Chemotherapy·H R LapointeC J Brumme
Nov 21, 2015·Journal of Clinical Virology : the Official Publication of the Pan American Society for Clinical Virology·Jannik FonagerThea Kølsen Fischer
Oct 31, 2016·Genomics, Proteomics & Bioinformatics·Hengyun LuZemin Ning
Feb 12, 2017·Scientific Reports·Stéphanie RaymondJacques Izopet

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