Skip to main page content
U.S. flag

An official website of the United States government

Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation
Comparative Study
. 2001 Feb;39(2):454-9.
doi: 10.1128/JCM.39.2.454-459.2001.

Comparison of DNA sequencing and a line probe assay for detection of human immunodeficiency virus type 1 drug resistance mutations in patients failing highly active antiretroviral therapy

Affiliations
Comparative Study

Comparison of DNA sequencing and a line probe assay for detection of human immunodeficiency virus type 1 drug resistance mutations in patients failing highly active antiretroviral therapy

J Servais et al. J Clin Microbiol. 2001 Feb.

Abstract

The resistance of human immunodeficiency virus type 1 (HIV-1) to drugs is a major cause of antiretroviral treatment failure. We have compared direct sequencing to a line probe assay (LiPA) for the detection of drug resistance-related mutations in 197 clinical samples, and we have investigated the sequential appearance of mutations under drug pressure. For 26 patients with virological failure despite the use of two nucleoside analogues and one protease inhibitor (indinavir [n = 6], ritonavir [n = 10], and saquinavir [n = 10]), genotypic resistance assays were carried out retrospectively every 3 months for up to 2 years by using direct sequencing (TruGene; Visible Genetics) and a LiPA for detection of mutations in the reverse transcriptase (INNO-LiPA HIV-1 RT; Innogenetics) and the protease (INNO-LiPA HIV Protease, prototype version; Innogenetics) genes. Comparison of the results from both assays found rare major discrepancies (<1% of codons analyzed). INNO-LiPA detected more wild-type-mutant mixtures than sequencing but suffered from a high rate of codon hybridization failures for the reverse transcriptase. LiPA detected earlier and more frequently than sequencing the transient mixed virus population that contained I84V, which appears before V82A in the protease sequence. Mutations M461, G48V, and L90M were often transient and drug pressure related. In conclusion, direct sequencing and LiPAs give concordant results for most clinical isolates. LiPAs are more sensitive for the detection of mixed virus populations. Mutation I84V appears in minor populations in the early steps of the pathways of resistance to indinavir and ritonavir. The fact that some mutations can be found only transiently and in minor virus populations highlights the importance of a low detection limit for resistance assays.

PubMed Disclaimer

Figures

FIG. 1
FIG. 1
(a) LiPA results for key positions in the PRO and RT genes. Results for wild-type (white bars), mixed wild-type and mutant (gray bars), and mutant (black bars) populations, viruses with other rare amino acid substitutions (PRO, V82F/T/I; RT, T215F) (gray bars with white dots [in PRO codon 82]), and viruses with negative results (bars with white and black lines) are shown. (b) Sequencing results for key positions in the PRO and RT genes. Results for wild-type (white bars), mixed mutant and wild-type (gray bars), and mutant (black bars) populations, viruses with other rare amino acid substitutions (PRO, M46L, I54T, V82F, and I84M, RT, T69N, codon 69 serine-serine insertion, and M184I) (gray bars with white dots [in PRO, codons 46, 54, 82, and 84; in RT, codons 69, 74, and 184]), and viruses with negative results (bars with white and black lines) are shown. (c) Comparison (percent concordance) of genotyping results obtained by LiPA and DNA sequencing. Concordance is shown as white bars, minor discrepancies are shown as gray bars, major discrepancies are shown as black bars, and unexpected amino acid substitutions are shown as gray bars with white dots (in PRO, codons 46, 54, and 84; in RT, codons 69, 74, and 184 [for RT L74I/F and M184I; for PRO, M46L, I54T, and I84M]).

Similar articles

Cited by

References

    1. Collier A, Coombs R W, Schoenfeld D A, Bassett R L, Timpone J, Baruch A, Jones M, Facey K, Whitacre C, McAuliffe V J, Friedman H M, Merigan T C, Reichman R C, Hooper C, Corey L. Treatment of human immunodeficiency virus infection with saquinavir, zidovudine, and zalcitabine. N Engl J Med. 1996;334:1011–1017. - PubMed
    1. Condra J H, Holder D J, Schleif W A, Blahy O M, Danovich R M, Gabryelski L J, Graham D J, Laird D, Quintero J C, Rhodes A, Robbins H L, Roth E, Shivaprakash M, Yang T, Chodakewitz J A, Deutsch P J, Leavitt R Y, Massari F E, Mellors J W, Squires K E, Steigbigel R T, Teppler H, Emini E A. Genetic correlates of in vivo viral resistance to indinavir, a human immunodeficiency virus type 1 inhibitor. J Virol. 1996;70:8270–8276. - PMC - PubMed
    1. Condra J H, Schleif W A, Blahy O M, Gabryelski L J, Graham D J, Quintero J C, Rhodes A, Robbins H L, Roth E, Shivaprakash M, Titus D, Yang T, Teppler H, Squires K E, Deutsch P J, Emini E A. In vivo emergence of HIV-1 variants resistant to multiple protease inhibitors. Nature. 1995;374:569–571. - PubMed
    1. Descamps D, Calvez V, Collin G, Cécille A, Apetrei C, Damond F, Katlama C, Matheron S, Huraux J M, Brun-Vézinet F. Line probe assay for detection of human immunodeficiency virus type 1 mutations conferring resistance to nucleoside inhibitors of reverse transcriptase: comparison with sequence analysis. J Clin Microbiol. 1998;36:2143–2145. - PMC - PubMed
    1. Devereux H L, Youle M, Johnson M A, Loveday C. Rapid decline in detectability of HIV-1 drug resistance mutations after stopping therapy. AIDS. 1999;13:123–127. - PubMed

Publication types

MeSH terms