Comparative performance evaluation of the HIV-1 LiPA protease and reverse transcriptase resistance assay on clinical isolates

Tsongalis, Gregory J.; Gleeson, Timothy; Rodina, M A; Anamani, Denise E.; Ross, Jacqueline; Joanisse, I.; Tanimoto, Lorine; Ziermann, Rainer

doi:10.1016/j.jcv.2005.01.011

Cited by 9 publications

(4 citation statements)

References 11 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Several assays have been developed with improved sensitivity for resistant mutants (4,10,(13)(14)(15)(16)(17)20); however, their relative performances have not been assessed. In the current study, a panel of wild-type-mutant HIV-1 mixtures was created to evaluate the performance of these assays.…”

mentioning

confidence: 99%

“…Thirteen laboratories were selected with the goal of maximizing the number of technologies evaluated. The technologies included pyrosequencing of PCR products (15), real-time allele-specific RT-PCR (ASPCR) (10,13,17), oligonucleotide ligation-based assays (OLA) (4), a Ty1/HIV-1 RT hybrid system (TyHRT) (14), single-genome sequencing (SGS) (16), and a line probe assay (LiPA) (VERSANT HIV-RT Resistance Assay; Bayer, Berkley, CA) (20). Standard genotyping methods using FDAcleared kits were included (HIV-1 TRUGENE [Bayer, Tarrytown, NY] and ViroSeq v2.0 [Celera Diagnostics, Alameda, CA]).…”

mentioning

confidence: 99%

See 1 more Smart Citation

Blinded, Multicenter Comparison of Methods To Detect a Drug-Resistant Mutant of Human Immunodeficiency Virus Type 1 at Low Frequency

et al. 2006

View full text Add to dashboard Cite

We determined the abilities of 10 technologies to detect and quantify a common drug-resistant mutant of human immunodeficiency virus type 1 (lysine to asparagine at codon 103 of the reverse transcriptase) using a blinded test panel containing mutant-wild-type mixtures ranging from 0.01% to 100% mutant. Two technologies, allele-specific reverse transcriptase PCR and a Ty1HRT yeast system, could quantify the mutant down to 0.1 to 0.4%. These technologies should help define the impact of low-frequency drug-resistant mutants on response to antiretroviral therapy.

show abstract

mentioning

confidence: 99%

mentioning

confidence: 99%

Blinded, Multicenter Comparison of Methods To Detect a Drug-Resistant Mutant of Human Immunodeficiency Virus Type 1 at Low Frequency

et al. 2006

View full text Add to dashboard Cite

show abstract

“…Heteroduplex tracking assays and restriction fragment length polymorphism analysis are less costly and relative simple methods for SNP detection, but they are also less sensitive than desirable (they detect 5 to 10% of the SNPs present in an HIV-1 population). Finally, the INNOLiPA HIV-1 RT and PRO assays (Innogenetic, Ghent, Belgium) are oligonucleotide-based hybridization assays that can discriminate between wild-type and mutant sequences and that have the ability to detect low-frequency polymorphisms (21,48). All of these approaches, however, have limited functionality in probing for drug resistance mutations in diverse HIV-1 genomes.…”

mentioning

confidence: 99%

Sensitive Oligonucleotide Ligation Assay for Low-Level Detection of Nevirapine Resistance Mutations in Human Immunodeficiency Virus Type 1 Quasispecies

et al. 2007

View full text Add to dashboard Cite

This study has adapted the oligonucleotide ligation assay (OLA) to probe for low-level nevirapine (NVP) resistance mutations K103N and Y181C in the human immunodeficiency virus type 1 (HIV-1) population of infected mother-infant pairs from Uganda. When NVP is used to prevent perinatal transmission, NVPresistant HIV-1 clones may be rapidly selected due to a low barrier for mutation and a relatively high level of fitness (compared to that of other drug-resistant HIV-1 clones). Monitoring for even a low frequency of NVP resistance mutations may help predict the success of subsequent treatment or warrant the use of another regimen to prevent transmission in a subsequent pregnancy. The standard OLA was optimized by using nonstandard bases in oligonucleotides to allow promiscuous base pairing and accommodate significant HIV-1 heterogeneity. Radiolabeled as opposed to fluorescently tagged oligonucleotides increased the sensitivity, whereas alteration of the template, oligonucleotides, salt, and thermostable DNA ligase concentrations increased the specificity for the detection of minority codons. This modified OLA is now capable of detecting mutants with the K103N or the Y181C mutation present in an HIV-1 population at a frequency of ϳ0.4% and is at least 10-to 30-fold more sensitive than the original protocol. A cohort of 19 Ugandan mothers who received NVP treatment perinatally were sampled 6 weeks postdelivery. Ten of 19 HIV-1 DNA samples extracted from peripheral blood mononuclear cells had a detectable K103N (0.5 to 44%) or Y181C (0.8 to 92.5%) mutation, but only one plasma HIV-1 RNA sample had a viral population with the Y181C mutation. These findings suggest that OLA is a robust, sensitive, and specific method for the detection of low-frequency drug resistance mutations in an intrapatient HIV-1 population.Three types of antiretroviral drugs (ARVs) are now used for the treatment of human immunodeficiency virus type 1 (HIV-1) infections, but only reverse transcriptase (RT) inhibitors are readily available to the vast majority of HIV-1-infected individuals in the developing world. The treatment regimen of choice is a combination of a nonnucleoside RT inhibitor (almost exclusively nevirapine [NVP]) and two nucleoside RT inhibitors, i.e., zidovudine (AZT) or stavudine plus lamivudine or didanosine.In addition to being the backbone of most treatment regimens, NVP is provided as a single dose to block the motherto-child transmission (MTCT) of HIV-1 in developing countries. In the absence of antiretroviral therapy, the frequency of MTCT is approximately 25 to 48% (2, 36, 38), whereas the administration of a short course of AZT therapy near the end of gestation (7,8,49) or the administration of a single dose of NVP at labor can reduce the rate of perinatal transmission to less than 20% (22,25,32,35,37). Although NVP remains very effective in the prevention of MTCT (22,32), the administration of even a single dose of NVP to

show abstract

“…Single-genome sequencing is an ultrasensitive method for identifying the presence of resistant subpopulations, but it is highly labor intensive (17). More recently, a series of less-demanding yet sensitive approaches have been reported, including a line-probe assay based on hybridization to probes, real-time PCR-based assays, and phenotypic detection utilizing a hybrid element of retrotransposon TY1 and HIV-1 reverse transcriptase (RT) (6,8,11,14,15,20,22). Although these assays demonstrated the ability to detect several drug resistance mutations, none were reported to detect the K65R mutation of HIV-1 RT from clinical patient specimens.…”

mentioning

confidence: 99%

MultiCode-RTx Real-Time PCR System for Detection of Subpopulations of K65R Human Immunodeficiency Virus Type 1 Reverse Transcriptase Mutant Viruses in Clinical Samples

Svarovskaia

Moser²,

Bae

et al. 2006

J Clin Microbiol

View full text Add to dashboard Cite

We report a real-time PCR assay capable of detecting drug-resistant human immunodeficiency virus type 1 reverse transcriptase K65R mutant virus at a level of 0.5% in polymorphic patient plasma specimens. Fiftythree treatment-naïve and 20 treatment-experienced specimens were successfully genotyped with the new method. Results were in agreement with population sequencing and the labor-intensive single-genome sequencing method.Human immunodeficiency virus type 1 (HIV-1) exhibits tremendous genetic variation, allowing virus to escape host immune response and develop drug resistance to antiretroviral therapeutics (1). To manage HIV-1 infection, genotypic and phenotypic methods are widely used to monitor drug-resistant viruses within infected individuals. Standard methods determine the majority genotype or phenotype present in the plasma virus population but have limited ability to detect minor subpopulations (Ͻ25%) of drugresistant virus (9,12,18). Minor subpopulations of resistant virus can arise during antiretroviral therapy, from transmission of drug-resistant virus, and from discontinuation of a drug treatment (2, 15, 16). The clinical relevance of minor resistant subpopulations on treatment outcome has not been well established due, in part, to a limited ability to detect and quantify such subpopulations. Single-genome sequencing is an ultrasensitive method for identifying the presence of resistant subpopulations, but it is highly labor intensive (17). More recently, a series of less-demanding yet sensitive approaches have been reported, including a line-probe assay based on hybridization to probes, real-time PCR-based assays, and phenotypic detection utilizing a hybrid element of

show abstract

Comparative performance evaluation of the HIV-1 LiPA protease and reverse transcriptase resistance assay on clinical isolates

Cited by 9 publications

References 11 publications

Blinded, Multicenter Comparison of Methods To Detect a Drug-Resistant Mutant of Human Immunodeficiency Virus Type 1 at Low Frequency

Blinded, Multicenter Comparison of Methods To Detect a Drug-Resistant Mutant of Human Immunodeficiency Virus Type 1 at Low Frequency

Sensitive Oligonucleotide Ligation Assay for Low-Level Detection of Nevirapine Resistance Mutations in Human Immunodeficiency Virus Type 1 Quasispecies

MultiCode-RTx Real-Time PCR System for Detection of Subpopulations of K65R Human Immunodeficiency Virus Type 1 Reverse Transcriptase Mutant Viruses in Clinical Samples

Contact Info

Product

Resources

About