A comparison of HIV‐1 drug susceptibility as provided by conventional phenotyping and by a phenotype prediction tool based on viral genotype

Abstract

Concordance between the conventional HIV-1 phenotypic drug resistance assay, PhenoSense (PS), and vircoTYPE HIV-1 (vT), a drug resistance assay based on prediction of the phenotype, was investigated in a data set from the Stanford HIV Resistance database (hivdb). Depending on the drug, between 287 and 902 genotype-phenotype data pairs were available for comparisons. Test results (fold-change values) in the two assays were highly correlated, with an overall mean correlation coefficient of 0.90 using single PS measurements. This coefficient rose to 0.94 when the vT results were compared to the mean of repeat PS measurements. These results are comparable with the corresponding correlation coefficients of 0.87 and 0.95, calculated using single measurements, and the mean of repeat measurements, respectively, as obtained in the Antivirogram assay, the conventional HIV-1 phenotypic drug resistance test on which vT is based. The proportion of resistance calls resulting in a "major" discordance (fully susceptible or maximal response by one assay but fully resistant or minimal response by the other) ranged from 0% to 8.1% for drugs for which two clinical test cut-offs were available in both assays (didanosine, abacavir, tenofovir, saquinavir/r, fosamprenavir/r, and lopinavir/r), from 2.4% to 8.1% for the drugs for which two clinical test cut-offs were available in the vT assay and one clinical test cut-off in the PS assay (lamivudine, stavudine, indinavir/r, and atazanavir/r) and from 3.1% to 10.3% for drugs for which biological test cut-offs were used (zidovudine, nevirapine, delavirdine, efavirenz, indinavir, ritonavir, nelfinavir, saquinavir, and fosamprenavir). Our analyses suggest that these assays provide comparable resistance information, which will be of value to physicians who may be presented with either or both types of test report in their practice.

Novel Method for Simultaneous Quantification of Phenotypic Resistance to Maturation, Protease, Reverse Transcriptase, and Integrase HIV Inhibitors Based on 3′Gag(p2/p7/p1/p6)/PR/RT/INT-Recombinant Viruses: a Useful Tool in the Multitarget Era of Antiretroviral Therapy

“…Multiple studies have compared different genotypic assays (8,20,25,64,85), genotype versus phenotype (8,16,49,72), and different phenotypic (52,64,76,86) drug resistance assays. In the case of phenotypic assays, agreement among the tests varies with drug classes, usually showing better a correlation for PIs and lower correlation for NRTIs (64,86).…”

Characterization of the E138K Resistance Mutation in HIV-1 Reverse Transcriptase Conferring Susceptibility to Etravirine in B and Non-B HIV-1 Subtypes

“…The data were analyzed by using Prism software (version 5.0; GraphPad, Inc.) to determine the EC 50 for each drug tested. Resistance to a given drug was determined based on the published lower clinical cutoff (CCO), which determines the cutoff fold change value for the sensitivity of NNRTIs (46,48). These values are 3.0 for ETR, 3.4 for EFV, and 5.5 for NVP (46,48).…”

Development and Performance of Conventional HIV-1 Phenotyping (Antivirogram®) and Genotype-Based Calculated Phenotyping Assay (virco®TYPE HIV-1) on Protease and Reverse Transcriptase Genes to Evaluate Drug Resistance

“…Therefore, an internal phenotyping (inclusive genotyping) proficiency testing is executed with a well-characterized panel of five recombinant virus stocks, which demonstrates resistance for drugs or drug classes and is tested on a quarterly basis. Biological test cutoffs, separating HIV-1 strains with a normal range of susceptibility from viral strains with reduced susceptibility, were determined for the Antivirogram assay (Version 2.5.01) by defining the 97.5th percentile of the fold-change values determined in vitro on genetically wild-type viruses [1]. …”

“…The Gag (p7/p1-p1/p6)-PR-RT coding sequence, containing the downstream part of Gag and about two thirds of the adjacent 5′-end of the polymerase gene (POL) region, was reverse transcribed and amplified in a one-step RT-PCR (35 µl final volume, Superscript III HF, Invitrogen) using PRTO5 [1] and OUT3 [1], followed by a nested PCR (Expand High Fidelity Polymerase, Roche), using 3′-In, 5′-CATCTACATAGAAAGTTTCTGCTCC-3′ and 5′-In, 5′-CTAGGAAAAAGGGCTGTTGGAAATG-3′. Negative and positive controls were included in each run.…”

“…A third method is a hybrid approach or system which uses genotypic data to predict phenotypic susceptibility. This method requires a large database of paired geno- and phenotypes but predicts phenotypic susceptibility as rapidly as genotypic testing and with comparable accuracy [1] and specificity compared to the actual laboratory-performed phenotype.…”