HIV-1 Quantification with Reflex to Genotypic Drug Resistance Analysis and Phenotypic Resistance Prediction, Plasma
Method Description Describes how the test is performed and provides a method-specific reference
Detection and Quantification
COBAS AmpliPrep/COBAS TaqMan HIV-1 Test, version 2.0, is an in vitro nucleic acid amplification test for the quantification of HIV-1 RNA in human plasma, using the COBAS AmpliPrep instrument for automated viral nucleic acid extraction (generic silica-based capture technique) and the COBAS TaqMan analyzer for automated amplification and detection of the viral nucleic acid target. To accommodate the polymorphism within the HIV-1 genomic target sequence, this assay employs multiple PCR primers for 2 target sequences (HIV-1 gag and LTR regions). The HIV-1 Quantitation Standards is used to detect and compensate for possible PCR inhibition and as a control for target amplification and detection processes. Dual-labeled fluorescent oligonucleotide probes are utilized to detect amplified material. Quantification of target sequences is monitored using the emission intensity of fluorescent reporter dyes released during the amplification process.(Package insert: COBAS AmpliPrep/COBAS TaqMan HIV-1 Test, version 2.0, Roche Molecular Systems Inc., Branchburg, NJ, 6/2010)
Genotypic Resistance Analysis (GHIVR/88782 HIV-1 Genotypic Drug Resistance Mutation Analysis, with Reflex to Phenotypic Drug Resistance Prediction, Plasma)
HIV-1 genotyping is performed using the TruGene HIV-1 assay, which determines the nucleotide bases by simultaneous bidirectional sequencing (1.9 kb total) of the viral reverse transcriptase (1,600 nucleotide) and protease (300 nucleotide) genes of HIV-1 in a blood specimen and identifies any mutations. An automated DNA sequencing system (OpenGene computer software) compares the specimen genotype to the known resistance mutations and generates a list of the mutations present and the antiviral drugs to which the mutations confer resistance.(Package insert: TruGene HIV-1 Genotyping Assay, Siemens Healthcare Diagnostics, Tarrytown, NY)
Phenotype Analysis (VPHIV/88781 HIV-1 Phenotypic Drug Resistance Prediction [Add-On])
HIV-1 target genomic sequence obtained from the genotyping test is analyzed by a proprietary software application with a large correlative database of approximately 30,000 matching clinical HIV-1 genotypes and phenotypes at Virco Lab Inc. USA (Bridgewater, NJ). The analysis identifies all the mutations that can affect resistance to each drug and then interrogates the database for phenotypic drug resistance patterns from previous clinical samples that match these patterns of genotypic mutations.
When all matches have been identified, the software further analyzes the data for all the matches using the Virtual Phenotype-LM linear regression modeling application, which takes into account the weighted contribution of individual mutations and mutation pairs to make fold change (FC) predictions for each drug. This predicted FC in IC50 for each drug is typically based on data from thousands of real phenotypes with the same patterns of genotypic mutations. Clinically relevant interpretation of predicted FC is based on comparison between the FC in IC50 and the clinical cutoff (CCO) values for the given drug. The CCO values are derived from a clinical outcomes database containing clinical data from more than 17,000 patients, including treatment history, current treatment, and changes in viral load and CD4 count after modifying treatment based on drug resistance testing results. When CCO values for a given drug are not available from the database, biological cutoff value derived from in vitro susceptibility testing is used for comparison.(www.vircolab.com)
Day(s) and Time(s) Test Performed Outlines the days and times the test is performed. This field reflects the day and time the sample must be in the testing laboratory to begin the testing process and includes any specimen preparation and processing time required before the test is performed. Some tests are listed as continuously performed, which means assays are performed several times during the day.
HIV-1 quantification: Monday through Saturday; 7 a.m.-4 p.m.
HIV-1 genotyping: varies; test will be performed in batches of 4.
Analytic Time Defines the amount of time it takes the laboratory to setup and perform the test. This is defined in number of days. The shortest interval of time expressed is "same day/1 day," which means the results may be available the same day that the sample is received in the testing laboratory. One day means results are available 1 day after the sample is received in the laboratory.
Maximum Laboratory Time Defines the maximum time from specimen receipt at Mayo Medical Laboratories until the release of the test result
Specimen Retention Time Outlines the length of time after testing that a specimen is kept in the laboratory before it is discarded
Performing Laboratory Location The location of the laboratory that performs the test