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

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
    • Drug hypersensitivity screening
      • Abacavir genotyping (HLA-B*5701)
    • 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 Follow Up
Human Immunodeficiency Virus 1, Genotype by Sequencing 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 Type 1 (HIV-1) Drug Resistance (GenoSURE PRIme) 2008438
Method: Polymerase Chain Reaction/Sequencing 

Detect resistance in HIV-1 to antiretroviral drugs

Requires specimens with HIV-1 RNA plasma levels of >500 copies/mL

Provides susceptibility information for NRTIs, NNRTIs, PIs, and INIs

If there is insufficient virus to produce results, viral load is confirmed by HIV-1 RNA quantitation

   
HIV1 Genotype and Integrase Inhibitor Resistance by Sequencing 2009256
Method: Polymerase Chain Reaction/Sequencing

Detect changes in viral genome associated with drug resistance

Predict HIV-1 drug resistance to integrase inhibitors

Requires specimens with HIV-1 RNA plasma levels of >1,000 copies/mL

   
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 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

Identify individuals at risk for abacavir sulfate hypersensitivity reaction (ABC HSR) prior to therapeutic treatment

Screening prior to reinitiation of treatment in individuals who have previously tolerated abacavir but whose HLA-B*5701 status is unknown

Clinical sensitivity/specificity – for immunologically confirmed ABC HSR, 98% and 99%, respectively

Analytical sensitivity/specificity – 99% for prediction of HLA-B*5701 carrier status by SNP rs2395029 genotyping

Diagnostic errors can occur due to rare sequence variations

Rare recombination events between HCP5 SNP rs2395029 and HLA-B*5701 may occur

Nongenetic factors that may affect drug sensitivity are not identified

Testing for a genetic variant associated with ABC HSR does not replace the need for therapeutic drug or other clinical monitoring