Human Immunodeficiency Virus 1, Antiretroviral Drug Resistance Testing - HIV Drug Resistance

Dx
Monitor
Background
Lab Tests

Diagnosis

Indications for Testing

HIV patients prior to initial therapy
Patients on highly active antiretroviral therapy (HAART) experiencing treatment failure
Patients showing viral load rebound

Laboratory Testing

Baseline genotypic testing in patients from countries with evidence of HIV drug resistance may help determine etiology of treatment failure
- Test only if patient is highly adherent to antiretroviral therapy
- Most useful in initial evaluation or after failure of first- and second-line regimens
Phenotypic evaluation in combination with genotyping – most useful in patients with complex history of treatment failure
Specific drug resistance testing
- Integrase inhibitor resistance
- Trofile co-receptor tropism assay
  - Guides the use of maraviroc therapy in adult patients infected with CCR5-tropic HIV-1 virus strain resistant to multiple antiretroviral agents and who have evidence of viral replication and multidrug failure
- Abacavir genotyping
- For more information, refer to ViroSeq HIV-1 Antiretroviral Drug Resistance Report
- HIV retroviral drugs (see table below)

HIV Retroviral Drugs
Generic Name	Trade Name	Code
Nucleoside Reverse Transcriptase Inhibitors
Zidovudine Didanosine Lamivudine Stavudine Abacavir Tenofovir Emtricitabine	Retrovir^® Videx^® Epivir^® Zerit^® Ziagen^® Viread^® Emtriva^®	AZT, ZDV DDI 3TC D4T ABC TDF FTC
Protease Inhibitors
Saquinavir Ritonavir Indinavir Nelfinavir Lopinavir/Ritonavir Amprenavir Fosamprenavir Atazanavir Tipranavir Darunavir	Fortovase^® Norvir^® Crixivan^® Viracept^® Kaletra^® Agenerase^® Lexiva^® Reyataz^® Aptivus^® Prezista^®	SQV RTV IDV NFV LPV APV FOS ATV TPV DRV
Non-Nucleoside Reverse Transcriptase Inhibitor
Nevirapine Delavirdine Etravirine Efavirenz	Viramune^® Rescriptor^® Intelence^™ Sustiva^®	NVP DLV TMC125 EFV
Integrase Inhibitors
Raltegravir	Isentress^™	MK-0518
Receptor Inhibitors - CCR5
Maraviroc	Selzentry^®

Monitoring

HIV-1 RNA testing, quantitative – successful therapy results in suppression to <50 copies/mL (PCR) or <75 copies/mL (branded DNA) by 24 weeks
- Recommended by the International AIDS Society USA panel
- RNA measures 2-8 weeks after initiation of testing
- Every 4-8 weeks until suppressed
- Every 3-4 months the first year

Clinical Background

Drug-resistance testing is considered an important part of managing HIV-infected adults and is a widespread practice in the developed world.

Epidemiology

Prevalence – resistance to HIV therapy develops in 78% of patients worldwide
- In U.S., resistance rate is ~15% for any HIV drug (CDC 2003-2006)

Genetics

Histocompatibility – HLA-B*5701 genotype associated with abacavir sensitivity
- Autosomal dominant inheritance
- Most common in Indian and Thai individuals; less common in Caucasians; rare in East Asians

Pathophysiology

Reasons for failure include the following
- Lack of access to care
- Patient noncompliance
- Drug pharmacology issues – absorption, elimination, interactions
- Development of antiretroviral resistance
Highest resistance – nucleoside reverse transcriptase inhibitors
Role of resistance testing in primary infection
- Identify mutations present
- Identify etiology of treatment failures
Role of resistance testing in established infections that are currently treated
- Failure of current therapy – decreasing CD4 count, increasing viral load
- Patient noncompliance with highly active antiretroviral therapy (HAART) regimen
- Increased risk of resistance to newly resumed therapy
Patients at high risk of abacavir hypersensitivity reaction can be identified pre-therapeutically through laboratory detection of HLA-B*5701

Indications for Laboratory Testing

Tests generally appear in the order most useful for common clinical situations
Click on number for test-specific information in the ARUP Laboratory Test Directory

Test Name and Number	Recommended Use	Limitations
Human Immunodeficiency Virus 1, Genotyping 0055670 Method: Reverse Transcription Polymerase Chain Reaction/Sequencing	Detect changes in viral genome associated with drug resistance Use in conjunction with CD4 measurement to monitor treatment efficacy Requires specimens with HIV-1 RNA plasma levels of >1,000 copies/mL	Treatment failure can be caused by factors other than drug resistance; interpretation of resistance genotyping results must be done in conjunction with other clinical and laboratory information Sequenced using the Viroseq™ HIV-1 Genotyping System; some insertions or deletions may be difficult to detect Absence of resistance mutations does not rule out presence of reservoirs of resistant viruses that cannot be detected Does not detect minor HIV-1 populations <20% of the total population
HIV PhenoSense GT® 0092399 Method: Phenotyping/Genotyping	Estimate the ability of patient’s cloned virus to replicate in cell culture in the presence of a drug Determine the drug dosage needed to inhibit viral replication in vitro and generally report the concentration of drug required to inhibit viral replication by 50%, or IC₅₀ Determine cause of treatment failure Clarify and confirm results from HIV genotyping tests Requires specimens with HIV-1 RNA plasma levels of >500 copies/mL	Treatment failure can be caused by factors other than drug resistance; interpretation of resistance genotyping results must be done in conjunction with other clinical and laboratory information Comparisons between assays performed in different laboratories are not recommended; no standardization exists among methods of HIV-1 drug resistance testing Absence of resistance mutations does not rule out the presence of reservoirs of resistant viruses that cannot be detected
Human Immunodeficiency Virus (HIV) Phenotype Comprehensive 0092050 Method: Drug Susceptibility using HIV Culture (Cell Culture)	Measure the ability of patient’s virus to replicate in cell culture in the presence of a drug Determine the drug dosage needed to inhibit viral replication in vitro and generally report the concentration of drug required to inhibit viral replication by 50%, or the IC₅₀ Determine the cause of treatment failure When used in conjunction with genotyping, can provide a complete picture of antiretroviral susceptibility to HIV Requires specimens with HIV-1 RNA plasma levels of >500 copies/mL	Treatment failure can be caused by factors other than drug resistance; interpretation of resistance genotyping results must be done in conjunction with other clinical and laboratory information Comparisons between assays performed in different laboratories are not recommended; no standardization exists among methods of HIV-1 drug resistance testing Absence of resistance mutations does not rule out the presence of reservoirs of resistant viruses that cannot be detected
Human Immunodeficiency Virus 1, vircoTYPE 0051186 Method: Reverse Transcription Polymerase Chain Reaction/Sequencing/Phenotype Interpretation	Predict HIV-1 drug resistance from the nucleic acid sequence of the human immunodeficiency virus Requires specimens with HIV-1 RNA plasma levels of >1,000 HIV-1 copies/mL	Treatment failure can be caused by factors other than drug resistance; interpretation of resistance genotyping results must be done in conjunction with other clinical and laboratory information Virus sequenced at ARUP Laboratories and then sent to Virco (vircolab.com) for analysis using the Virtual Phenotype Linear Modeling analysis Comparisons between assays performed in different laboratories are not recommended Absence of resistance mutations does not rule out the presence of reservoirs of resistant viruses that cannot be detected
HIV-1 Integrase Inhibitor Resistance by Sequencing 2004457 Method: Reverse Transcription Polymerase Chain Reaction/Sequencing	Predict HIV drug resistance to integrase inhibitors	Mutations in viral sub-populations <20% of total may not be detected
Trofile Co-Receptor Tropism Assay 0093370 Method: Recombinant virus, single replication	Identify R5 virus infection to guide use of maraviroc therapy Requires specimens with HIV-1 RNA plasma levels of >1,000 HIV-1 copies/mL Note – Maraviroc therapy has been approved by the FDA for combination antiretroviral treatment of adults infected with only CCR5-tropic HIV-1 who have evidence of viral replication and have HIV-1 strains resistant to multiple antiretroviral agents
Trofile™ DNA Co-Receptor Tropism Assay 2004747 Method: CD4 Cell Culture Assay for Phenotypic Recombinant-virus Co-receptor Tropism	Recommended for patients with undetectable viral loads; identify therapeutic risk
HLA-B*5701 Associated Variant Genotyping for Abacavir Sensitivity 2002429 Method: Polymerase Chain Reaction/Fluorescence Monitoring	Use to determine risk of abacavir hypersensitivity reaction	Rare diagnostic errors may occur due to primer site mutations Rare recombination events between HCP5 SNP rs2395029 and HLA-B5701 may occur Alleles other than HLA-B**5701 will not be detected Non-genetic factors that may affect drug sensitivity are not identified