Genotyping and Drug Resistance in Clinical Practice

1
Genotyping and Drug Resistance in Clinical
Practice

• Donna E. Sweet, MDProfessor of MedicineThe
  University of Kansas School of Medicine -
  Wichita

2
Mutations Occur Spontaneously in the HIV Genome

• HIV makes copies of itself very rapidly 1-10
  billion new virus particles/day
• During its replication, HIV is prone to make
  errors when copying itself
• This results in mutations or errors in the
  genetic material of the virus which make the
  structure of the offspring virus slightly
  different to that of the parent virus
• Some of these mutations will result in an
  increased ability of the virus to grow in the
  presence of antiretroviral drugs

Marshall J Glesby MD PhD Associate Professor of
Medicine and Public Health Weill Medical College
of Cornell University March 2006
3
Drug Levels and Resistance ?1
Increased risk of side effects
Drug concentration
MEC (Minimum Effective Concentratin)
Increased risk of resistance
0
dose
dose
dose
dose
Marshall J Glesby MD PhD Associate Professor of
Medicine and Public Health Weill Medical College
of Cornell University March 2006
4
Drug Levels and Resistance ?2
Increased risk of side effects
Drug concentration
MEC (Minimum Effective Concentratin)
Increased risk of resistance
0
missed dose
late dose
dose
dose
dose
Marshall J Glesby MD PhD Associate Professor of
Medicine and Public Health Weill Medical College
of Cornell University March 2006
5
CDC Surveillance of Resistance Mutations In
Naive Patients
7.8
8

• 633 newly diagnosed patients genotyped at 89
  sites in 6 states in 2003-2004
• 14.5 prevalence of resistance mutations
• NRTI, 7.8
• NNRTI, 3.0
• PI, 0.7
• Multiclass, 0.7

6
Prevalence ()
4
2
0
NRTI
NNRTI
PI
Multi
Bennett D et al. 12th CROI 2005 abstract 674
6
Guidelines Treatment-Naive Patients
7
Prevalence of Resistance in Acute/Recent HIV
Infection
STARHS Serologic Testing Algorithm for Recent
HIV Seroconversions surveillance data
1. Resistance Workshop 2003. Abstract 117. 2.
Ibid, Abstract 119. 3. Ibid, Abstract 120. 4.
CROI. 2004. Abstract 682. 5. Resistance Workshop
2003. Abstract 121. 6. Ibid, Abstract 122. 7.
Ibid, Abstract 123. 8. Ibid, Abstract 124. 9.
Ibid, Abstract 130. 10. CROI. 2004. Abstract 680.
8
Recommendations for Resistance Tests
Clinical Setting

• Virologic failure
• Suboptimal virologic suppression
• Acute HIV infection

Recommended

• Chronic HIV infection prior to starting ART

Consider

• gt4 weeks after ART drugs are stopped
• Viral load levels lt1000 cpm

Not generally recommended
DHHS Guidelines, 4/7/05
9
Testing for Drug Resistance

• Adjunct to guide antiretroviral therapy
• Combine with obtaining a drug history and
  maximizing drug adherence
• Research supports use in certain settings
• Genotyping vs. phenotyping
• Limitations of resistance testing and specific
  indications

10
The Use of Drug Resistance Testing
11
The Use of Drug Resistance Testing
12
Testing for Drug Resistance

• Recommended in case of virologic failure, to
  determine role of resistance and maximize the
  number of active drugs in a new regimen
• Combine with obtaining a drug history and
  maximizing drug adherence
• Research supports use in certain settings
• Perform while patient is taking ART (or within 4
  weeks of regimen discontinuation)

13
Genotyping

• Detects drug resistance mutations in specific
  genes, e.g., reverse transcriptase and protease
• Sequencing or probing
• Results within 1-2 weeks
• Interpretation of mutations and cross-resistance
  is complex
• Consultation with specialists is recommended

14
Phenotyping

• Measures the ability of viruses to grow in
  various concentrations of antiretroviral drugs
• Results within 2-3 weeks
• More expensive than genotyping
• The ratio of the IC50s of the test and reference
  viruses is reported as the fold increase in IC50,
  or fold resistance
• Interpretation may be complex
• Consultation with specialists is recommended

15
Genopheno An Example
RT Q102K, D123E, I142V, C162S, V179I, T200A,
I202V, R211Q, R277K, T286P, E297A PR K14R, I15V,
M36A, R41K, K55R, I62V, I66L, G68E, H69Y, K70KIK,
I93L
16
Drug Resistance Testing Limitations

• Lack of uniform quality assurance
• Relatively high cost
• Insensitivity for minor viral species (lt10-20)

17
Drug Resistance Testing

• Resistance assays should be performed while the
  patient is taking antiretroviral regimen
• Data suggesting the absence of resistance should
  be interpreted carefully in relation to the prior
  treatment history

18
Drug Resistance Testing
19
Drug Resistance Testing
20
Drug Resistance Testing
21
When is Resistance Testing Recommended?
US Dept of Health Human Services (7/03)
International AIDS Society-USA (7/03)
Yes
Yes
When drugs stop working
Yes
Yes
When drugs dont work well enough
Same as for other patients
Yes
Pregnant women starting treatment
Recently infected
Yes
Yes
Consider
Yes (if within 2 years)
Chronic infection, treatment naive
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Can we afford this?

• Resistance testing after first virologic failure
  increases life expectancy by 3 months costing
  17,900 per QALY gained.
• Resistance testing before start of first HAART
  costs 22,300 per QALY gained at 20 prevalence
  of transmitted drug resistance (San Diego
  prevalence).
• At 4 prevalence 69,000 per QALY

Weinstein et al. Ann. Intern Med 2001
23
Perspective

• Sulfa prophylaxis for PCP 16,000/QALY
• Azithromycin prophy for MAC 35,000/QALY
• Fluconazole prophy for Crypto 100,000/QALY
• Gancyclovir prohpy for CMV 314,000/QALY
• Even at a prevalence of 4 resistance testing
  before start of HAART may be worth it.
• This does not even take into account the savings
  of wasting drugs in a regimen doomed to fail
  because there is underlying resistance to one
  drug in the regimen.

Saag. Ann. Intern Med 2001
24
Rationale for Early Detection

• Disease prognosis nadir CD4 cell count first 30
  days, symptom severity, setpoint VL
• Access to ARV therapy
• Risk-reduction counseling
• Partner notification and referral for testing
• Provide better estimates of HIV incidence rates
  (esp. with use of detuned EIA)
• Screening for transmitted drug resistance

25
Frequency and Treatment-Related Predictors of
Thymidine-Analogue Mutation Patterns in HIV-1
Isolates after Unsuccessful Antiretroviral
Therapy

• In 1465 genotypes from 684 patients in whom
  highly active antiretroviral therapy (HAART) was
  unsuccessful, predictors of this pattern were the
  number of previous HAART regimens undergone
• Use of stavudine/lamivudine
• Use of nevirapine
• Use of efavirenz
• Use of ritonavir

Frequency and Treatment-Related Predictors of
Thymidine-Analogue Mutation Patterns in HIV-1
Isolates after Unsuccessful Antiretroviral
Therapy The Journal of Infectious
Diseases 20061931219-1222
26
Frequency and Treatment-Related Predictors of
Thymidine-Analogue Mutation Patterns in HIV-1
Isolates after Unsuccessful Antiretroviral
Therapy
Frequency and Treatment-Related Predictors of
Thymidine-Analogue Mutation Patterns in HIV-1
Isolates after Unsuccessful Antiretroviral
Therapy The Journal of Infectious
Diseases 20061931219-1222
27
Version 1
Mutations Selected by nRTIs
28
Mutations Selected by nRTIs (cont)
Version 1
29
Mutations Selected by nRTIs
Version 2
30
Version 2
Mutations Selected by nRTIs (cont)
31
Mutations Selected by NNRTIs
32
Mutations Selected by PIs
82
FIRV
33
Mutations Selected by PIs (cont)
34
Mutations in the gp41 Envelope Gene Associated
With Resistance to Entry Inhibitors
Enfuvirtide
35
Darunivir Resistance (Tibotec 114)
Three mutations were associated with a decreased
virologic response to TMC-114, using a stepwise
regression model V32I, I47V, and I54M.
Source Brian A. Boyle, MD in Tribulations and
Trials in HIV Disease, Part 2. AIDS Reader.
2006 16291 294