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J Med Virol. 2018 Sep;90(9):1486-1492. doi: 10.1002/jmv.25224. Epub 2018 May 25.

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

Author information

1
Laboratoire de Virologie, CHU de Toulouse, Hôpital Purpan, Toulouse, France.
2
INSERM, U1043, Toulouse, France.
3
Faculté de Médecine Toulouse-Purpan, Université Toulouse III Paul-Sabatier, Toulouse, France.
4
CHU de Toulouse, Hôpital Purpan, Service des Maladies Infectieuses et Tropicales, Toulouse, France.

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.

KEYWORDS:

MiSeq; deep sequencing; polymerase drug resistance

PMID:
29750364
DOI:
10.1002/jmv.25224
[Indexed for MEDLINE]

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