Issues to Consider in HIV Resistance Testing

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Issues to Consider in HIV Resistance Testing

• Jason Tokumoto, MD
• National HIV/AIDS Clinicians Consultation Center

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Issues in resistance testing

• How beneficial is resistance testing?
• What resistance test to use?
• Resistance testing in the multi-drug resistant
  patient.
• When to switch vs How to switch
• Genotype/phenotype discordance.
• Phenotypic hypersusceptibility.
• Replication capacity.

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Current guidelines for resistance testing

• DHHS
  IAS-USA
• Acute infection Yes Yes
• Chronic infection Consider Yes
• (lt 2 years)
• Treatment failure Yes Yes

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Benefit

• How beneficial is resistance testing(genotype,
  phenotype, virtual phenotype)?

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Clinical trials of resistance testing

• Genotype vs no testing Viradapt, ARGENTA, GART,
  Havana.
• Phenotype vs no testing VIRA3001, CCTG 575.
• Genotype vs phenotype vs no testing CERT,
  NARVAL.
• Genotype phenotype vs genotype ERA.
• Virtual phenotype vs measured phenotype
  GenPheRex, Realvirfen.

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Benefit

• Virologic benefit derived from the use of
  genotypic resistance tests relatively small.
• At 6 months, genotypic testing increased
  proportion of patients who achieved undetectable
  viral load by 11 compared with no resistance
  test. Mean viral load reduction was 0.25 log 10.
• No clear evidence of benefit associated with
  phenotype vs no test.
• Pandou E T. Limited benefit of antiretroviral
  resistance testing in treatment-experienced
  patients a meta-analysis. AIDS 2004

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Benefit

• Some of the phenotype studies used fold change
  cut-offs that have been replaced by more accurate
  cut-offs(clinical cut-offs).
• Some patients had very advanced disease with few
  antiretroviral options and achieving undetectable
  viral load was unlikely no matter what method was
  used to select subsequent regimens.
• In patients failing initial or early regimens,
  clinicians might have found it straightfoward to
  select a new regimen without the use of
  resistance testing making it harder to detect a
  difference between arms.
• Many of these studies were short term and thus
  long-term benefits of resistance testing not
  known.

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Benefit

• TORO 1 and 2 studies which assessed efficacy of
  T-20 showed that resistance testing was
  beneficial.
• These studies demonstrated that the number of
  drugs in the optimized background regimen to
  which the virus was sensitive as determined by
  genotype or phenotype was highly predictive of
  response to therapy.

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Benefit

• Resistance test results can help to avoid using
  drugs that may be of no benefit and thereby avoid
  unnecessary toxicity.

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Benefit

• Conclusion There is short term virological
  benefit from resistance test vs no test long
  term benefits(clinical benefits) unclear.

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Which resistance test to order?

• Advantages/disadvantages.
• But which resistance test should one use?

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Which test?

• Based on available clinical data, cannot be
  easily answered.

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Which test?

• Many experts feel that genotype is adequate in
  initial or early failure.
• Assessment of NNRTI resistance can readily be
  assessed by genotype.
• Many experts prefer phenotype(plus genotype) in
  multi-drug resistant patients.

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Issues in genotype interpretation in the
multi-drug resistant patient

• In highly experienced patients, the multitude of
  accumulated mutations may be complex.
• Mutations may interact with each other making
  interpretation difficult.
• Archived mutations.

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Issues in phenotype interpretation in the
multidrug resistant patient

• Phenotype
• Cut-off fold change above which a virus is not
  susceptible to an antiretroviral agent.
• Technical cut-off based on a single reference
  virus.
• Biological cut-off based on clinical samples
  from treatment-naïve patients.
• Clinical cut-off based on virological response
  to antiretroviral drugs in clinical trials.

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Resistance testing in the multi-drug resistant
patient

• Help identify agents that are likely to retain
  the most activity(even if that activity is only
  partial compared with activity against the
  wild-type). In this setting, a phenotype may be
  more useful.
• Help to assess whether a new agent can be used
  with adequate support from the background regimen
  or whether its use should be deferred until it
  can be combined with other new agents. In other
  words, resistance testing in this setting might
  be used to determine WHEN TO SWITCH rather than
  HOW TO SWITCH.

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When to switch?

• DHHS Guidelines(2004) There is no consensus on
  the optimal time to change therapy for
  virological failure. The most aggressive approach
  would be to change for any repeated, detectable
  viremia
• But,
• a decision to change regimens might reduce
  future treatment options for that patient. This
  consideration can influence the clinician to be
  more conservative when deciding to change
  therapy.

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The big question

• If the decision is made not to switch based on
  resistance test results(and of course
  CLINICALLY), WHAT TO DO IN THE MEANTIME?

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Genotype-phenotype discordance

• In the multi-drug resistant patient, you may have
  both genotype and phenotype results.
• In analyzing the data, you realize there is
  discordance between the genotype and phenotype.

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Phenotype/genotype discordance

• Not uncommon.
• In one study(ViroLogic), which included over
  30,000 matched genotypes and phenotypes
• 67 of viruses discordant for 1 or gt drugs
• 45 of viruses discordant for 2 or gt drugs
• 30 of viruses discordant for 3 or gt drugs

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Reasons for genotype-phenotype discordance

• Presence of mixtures.
• Incomplete genotype interpretation data(not
  accounting for novel or unknown mutations or
  unrecognized effects of mutations).
• Re-sensitization caused by a specific
  mutations.

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Case

• 44 year old male with AIDS with an initial CD4
  nadir of 50 and viral load of 100,000. Has been
  on multiple antiretroviral regimens in the past.
  The specific regimens are not known but he has
  been on AZT, 3TC, DDI, abacavir, sustiva. He may
  have been on crixivan, saquinavir, nelfinavir in
  the past. He is currently on tenofovir, ddi-ec,
  kaletra with an HIV viral load of 50,000. You
  obtain both a genotype and phenotype.

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Genotype/Phenotype discordance

• Nucleoside analogues
• Genotype K65K/R M184M/V
• Resistant to abacavir, ddi, 3tc, tenofovir.
• PhenoSense
• Sensitive to abacavir(1.18), ddi(1.29),
  3tc(2.98), d4t, azt, tenofovir(0.78)
• IS THE VIRUS RESISTANT or SENSITIVE to abacavir,
  ddi, 3tc, tenofovir?

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Genotype/phenotype discordance

• Mixtures
• Genotype will report as resistant.
• Phenotype may or may not call it resistant it
  depends on the proportion of the mixture.
• When there are mixtures ,the genotype is likely
  to be the more reliable.
• Therefore, virus probably resistant to abacavir,
  ddi, 3tc, tenofovir.

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Genotype/phenotype discordance

• Protease inhibitors
• Genotype L10F, K20I, L24I, M46I, L63P, V77V/I
• Resistant to atazanavir, crixivan
• Sensitive to amprenavir, lopinavir, nelfinavir,
  
• ritonavir, saquinavir
  
  
  
  
  
  
  
  
  
• Phenotype(fold change)
• Resistant to amprenavir(13), crixivan(22),
  lopinavir(22),nelfinavir(7.01), ritonavir(8.23)
• Sensitive to atazanavir(2.10), saquinavir(1.58)
• IS THE VIRUS SENSITIVE OR RESISTANT TO
  AMPRENAVIR, ATAZANAVIR, LOPINAVIR, NELFINAVIR,
  RITONAVIR?

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Genotype/Phenotype discordance

• Incomplete genotypic data
• Genotype not accounting for novel or unknown
  mutations or for unrecognized effects of
  mutations.
• In cases where the phenotype demonstrates
  resistance but the genotype indicates
  susceptibility, the phenotype is more likely to
  be the accurate of the two.
• Virus resistant to amprenavir,lopinavir,
  nelfinavir, ritonavir virus sensitive to
  atazanavir.

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Genotype-phenotype discordance

• Re-sensitization caused by a specific mutation.
• Genotype M184V, M41L, K70R, L210W
• Tenofovir-resistant
• Phenotype Sensitive to tenofovir

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Phenotypic hypersuceptibility

• Clinical significant hypersuceptibility
• M184V affecting azt, d4t, tenofovir
• K65R hypersensitizing azt
• TAMS causing hypersusceptibility to NNRTIs.

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Replication capacity(RC)

• Viral fitness ability of entire virus to
  replicate in a defined environment.
• Replication capacity an in-vitro measure of a
  single replication cycle of the plasma
  HIV-derived pol gene.

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Replication capacity

• May have prognostic value
• Overall better CD4 cell response when RC lt65.
• Among multidrug resistant patients whose HIV
  viral load not suppressed, gt65 RC correlated
  with worse virologic response at 3 months.
• (CROI 2005)
• However, the role of RC in the management of
  antiretroviral therapy remains to be defined.