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J Antimicrob Chemother. 2018 Nov 1;73(11):3122-3128. doi: 10.1093/jac/dky315.

Ultra-deep sequencing improves the detection of drug resistance in cellular DNA from HIV-infected patients on ART with suppressed viraemia.

Author information

1
Laboratoire de Virologie, Hôpital Henri Mondor, APHP, Créteil, France.
2
Université Paris Est Créteil, UPEC, U955 Inserm, Créteil, France.
3
Laboratoire de Virologie, Hôpital Saint-Louis, APHP, Paris, France.
4
Université Paris Diderot, Inserm U941, Paris, France.
5
INSERM SC 10, Villejuif, France.
6
Maladies infectieuses, Hôpital Saint-Louis, APHP, Paris, France.

Abstract

Background:

Standard genotypic tests performed on HIV DNA from patients on suppressive ART, with previous resistance-associated mutations (RAMs) detected in their plasma, underestimate resistance. We thus compared ultra-deep sequencing (UDS) with bulk sequencing of DNA to detect RAMs previously identified in plasma.

Methods:

We sequenced the DNA of 169 highly treatment experienced patients with suppressed viraemia (ANRS 138-EASIER trial). Protease (PR) and reverse transcriptase (RT) genes from HIV DNA were sequenced by bulk sequencing and UDS, comparing 1% and 20% as thresholds of detection for UDS.

Results:

Patients were highly treatment experienced (13.6 years). UDS of DNA was successful for the RT and PR genes in 133 (79%) and 137 (81%) patients, respectively. The detection of RAMs was similar by bulk sequencing and UDS with a 20% cut-off. However, the detection of RAMs by UDS with a 1% cut-off was significantly higher than that of bulk sequencing for RT codons D67N (65.4% versus 52.3%), M184V (66.2% versus 52.3%), L210W (48.9% versus 36.4%) and T215Y (57.9% versus 42.1%) and PR codons M46I (46% versus 26%), I54L (12.4% versus 3.9%), V82A (44.5% versus 29.9%) and L90M (57.7% versus 42.5%).

Conclusions:

Genotypic resistance testing of cellular HIV DNA of well-controlled patients should use UDS technology with a sensitivity threshold of 1% to improve the detection of the resistant reservoir.

PMID:
30137335
DOI:
10.1093/jac/dky315

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