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HelpTest Code LAB9253 HIV-1 Genotypic Drug Resistance to Reverse Transcriptase, Protease, and Integrase Inhibitors, Plasma
Additional Codes
HIVDR
Ordering Guidance
This test is intended for detection and identification of drug resistance-associated HIV-1 genotypic mutations in plasma specimens of individuals prior to or while receiving combination antiretroviral therapy.
Prior to requesting this test, patients must have a confirmed plasma HIV-1 RNA level (ie, viral load) of 1000 copies/mL or higher within the preceding 30 days. HIVQN / HIV-1 RNA Detection and Quantification, Plasma is available to provide this prerequisite test result. Alternately, if the patient's viral load is unknown, order HIQDR / HIV-1 RNA Quantification with Reflex to Genotypic Drug Resistance to Reverse Transcriptase, Protease, and Integrase Inhibitors, Plasma, which will perform viral load followed by genotype, if appropriate.
For initial diagnosis of HIV, order HIVDX / HIV-1 and HIV-2 Antigen and Antibody Diagnostic Evaluation, Plasma.
Additional Testing Requirements
Shipping Instructions
If shipment will be delayed for more than 24 hours, freeze plasma specimen at -70° C (up to 60 days) until shipment on dry ice.
Necessary Information
The following ask-at-order entry question must be answered at the time of test ordering (mark answer on the test request form if not ordering electronically):
HIV-1 RNA level copies/mL in last 30 days = (select answer option)
<1000
1000 to 1,000,000
1,000,001 to 10,000,000
>10,000,000
Note: Test requests for submitted specimens with less than 1000 copies/mL (not sufficient amount for testing), “No,†or no response entered will be canceled.
Specimen Required
Supplies: Sarstedt Aliquot Tube, 5 mL (T914)
Collection Container/Tube: Lavender top (EDTA)
Submission Container/Tube: Plastic vial
Specimen Volume: 2.2 mL
Collection Instructions:
1. Centrifuge blood collection tube and aliquot plasma into plastic vial per collection tube manufacturer's instructions (eg, centrifuge and aliquot within 2 hours of collection for BD Vacutainer tubes).
2. Freeze aliquoted plasma for shipment.
Additional Information: Specimens submitted for HIV-1 genotyping must contain 1000 copies/mL or more of HIV-1 RNA.
Secondary ID
616052Useful For
Identifying HIV-1 genotypic mutations associated with resistance to nucleotide and non-nucleoside reverse-transcriptase inhibitors, protease inhibitors, and integrase strain transfer inhibitors
Guiding initiation or change of combination antiretroviral therapy in individuals, including children, with HIV-1 infection
Method Name
Reverse Transcription Polymerase Chain Reaction (RT-PCR) followed by Targeted Next-Generation Sequencing (NGS)
Specimen Type
Plasma EDTASpecimen Minimum Volume
0.8 mL
Specimen Stability Information
| Specimen Type | Temperature | Time | Special Container |
|---|---|---|---|
| Plasma EDTA | Frozen (preferred) | 60 days | |
| Refrigerated | 7 days |
On-campus collections: Tube to 99 or deliver to University Extension Hospital Room EH318
Send plasma in plastic vial, Frozen. DO NOT SHARE!
Off-campus collections: Centrifuge and aliquot within 2 hours. Specimen to be stored/transported at Frozen temp. DO NOT SHARE!
Reject Due To
| Gross hemolysis | OK |
| Gross lipemia | OK |
| Gross icterus | OK |
Reference Values
An interpretive report will be provided.
Interpretation
Detectable HIV-1 genotypic mutations conferring resistance to an antiviral drug are reported as amino acid codon changes (eg, M184V) resulting from the nucleic acid base alterations, according to the interpretative algorithm of the Stanford HIV Database program. The codon mutations are categorized and interpreted in relation to previously published data of phenotypic antiviral susceptibility tests on virus that harbor such mutations. Each codon mutation is assigned a drug penalty score. The total score generated from all mutations relevant to the specific antiviral drug is used to estimate the level of resistance to that drug. These interpretive rules may be updated periodically by the Stanford HIV Database Team after reviewing newly published data on HIV-1 genotypic drug resistance-associated codon mutations.
Susceptible (SUSC) indicates that the codon mutations present in patient's HIV-1 strain have not been associated with resistance to the specific drug (Stanford HIVdb total score 0 to 9).
Potential Low-Level Resistance (PLR) indicates that codon mutations detected have been associated with possible reduction in susceptibility to the specific drug (Stanford HIVdb score 10 to 14).
Low-Level Resistance (LR) indicates that codon mutations detected have been associated with reduction in susceptibility to the specific drug (Stanford HIVdb score 15 to 29).
Intermediate Resistance (IR) indicates that codon mutations detected have been associated with reduction in susceptibility to the specific drug (Stanford HIVdb score 30 to 59).
High-level Resistant (HR) indicates that codon mutations detected have been associated with maximum reduction in susceptibility to the specific drug (Stanford HIVdb ≥ 60).
Unable to genotype indicates that the sequence data obtained are of poor quality to determine the presence or absence of resistance-associated codon mutations in the patient's HIV-1 strain. Probable causes of such poor sequence data include polymorphism in the region of the sequencing primers interfering with primer binding and subsequent sequencing reaction, or low viral load (ie, <1000 copies/mL).
Inconclusive indicates inability of the assay to reliably determine antiviral resistance because of the presence of polymerase chain reaction inhibitors or ambiguous or incomplete viral target sequences generated from the assay.
Method Description
This test utilizes the US Food and Drug Administration-approved, commercially available Sentosa SQ HIV-1 Genotyping Assay, which is a next-generation sequencing assay based on a "sequencing by synthesis" method. The assay is designed to generate 2 amplicons (approximately 1500 base pairs [bp] and approximately 1000 bp in length) spanning the PR / RT- and INT-coding regions, respectively, of the HIV-1 genome for sequencing. Codon positions 1 to 99, 1 to 387, and 1 to 288 in the PR-, RT-, and INT-coding regions, respectively, are subsequently analyzed by the assay software for clinically relevant codon substitutions.
Clinical plasma specimens are subjected to automated HIV-1 RNA extraction and purification, followed by reverse-transcription polymerase chain reaction of HIV-1 target sequences, with both a system control and a positive control included in each assay run for quality control purposes. Automated DNA library preparation is performed using the amplified products, including enzymatic shearing, adapter ligation, purification, and normalization, prior to DNA template preparation and sequencing. Sequencing reactions are conducted with the Sentosa SQ301 sequencer, and the assembled sequence data are analyzed using proprietary analysis and interpretive software applications. HIV-1 antiviral drug-resistance interpretations are based on algorithms implemented in the most current version of the Stanford University HIV Drug Resistance Database (HIVdb; Stanford University) using a 5% variant detection cutoff threshold set by the assay manufacturer.(Instruction manual: Sentosa SQ HIV-1 Genotyping Assay User Manual. Vela Diagnostics; Version 1.3, 05/2023)
Day(s) Performed
Monday through Friday
Report Available
3 to 10 daysSpecimen Retention Time
60 daysPerforming Laboratory
Mayo Clinic Laboratories in Rochester
CPT Code Information
0219U
LOINC Code Information
| Test ID | Test Order Name | Order LOINC Value |
|---|---|---|
| HIVDR | HIV-1 Genotypic Drug Resistance, P | 90901-0 |
| Result ID | Test Result Name | Result LOINC Value |
|---|---|---|
| 616052 | HIV-1 Genotypic Drug Resistance, P | 80689-3 |
| 616729 | HIV-1 group M subtype | 100984-4 |
| 616737 | Nucleos(t)ide RT mutations | 45175-7 |
| 616918 | Reverse Transcriptase failed codons | 100983-6 |
| 616738 | Abacavir | 30287-7 |
| 616739 | Didanosine | 30284-4 |
| 616740 | Emtricitabine | 41402-9 |
| 616741 | Lamivudine | 30283-6 |
| 616742 | Stavudine | 30286-9 |
| 616743 | Tenofovir | 41396-3 |
| 616744 | Zidovudine | 30282-8 |
| 616745 | Nonnucleoside RT mutations | 45176-5 |
| 616746 | Doravirine | 91897-9 |
| 616747 | Efavirenz | 30291-9 |
| 616748 | Etravirine | 52749-9 |
| 616749 | Nevirapine | 30289-3 |
| 616750 | Rilpivirine | 68463-9 |
| 616751 | Protease Mutations | 33630-5 |
| 616919 | Protease failed codons | 100985-1 |
| 616752 | Atazanavir + Ritonavir | 49618-2 |
| 616753 | Darunavir + Ritonavir | 49630-7 |
| 616754 | Fosamprenavir + Ritonavir | 51409-1 |
| 616755 | Indinavir + Ritonavir | 49619-0 |
| 616756 | Lopinavir + Ritonavir | 42000-0 |
| 616757 | Nelfinavir | 30294-3 |
| 616758 | Saquinavir + Ritonavir | 49621-6 |
| 616759 | Tipranavir + Ritonavir | 49622-4 |
| 616760 | Integrase mutations | 61199-6 |
| 616920 | Integrase failed codons | 100986-9 |
| 616761 | Bictegravir | 90080-3 |
| 616762 | Cabotegravir | 96566-5 |
| 616763 | Dolutegravir | 72857-6 |
| 616764 | Elvitegravir | 72526-7 |
| 616765 | Raltegravir | 72525-9 |
| HIRVL | HIV RNA level copies/mL <30 days = | 89543-3 |
| 618206 | HIVDR_PR-RT_SEQ: | No LOINC Needed |
| 618207 | HIVDR_INT_SEQ: | No LOINC Needed |
Forms
If not ordering electronically, complete, print, and send a Microbiology Test Request (T244) with the specimen.
Testing Algorithm
For information see HIV Treatment Monitoring Algorithm