1 HIV Drug Resistance Training Module 1: Introduction to HIV Drug Resistance

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HIV Drug Resistance Training

Module 1:

Introduction to HIV Drug Resistance

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Topics

Impact of HIV Drug Resistance Factors that Influence Development of Drug

Resistance How to Minimize Drug Resistance How to Respond to Detection of Drug

Resistance Drug Resistance Assays

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Objectives

Understand importance of measuring drug resistance for large-scale treatment programs.

Identify factors that influence drug resistance.

Understand the methods available for the measuring HIV drug resistance.

Identify strategies for minimizing development of drug resistance.

Identify strategies for responding to detection of moderate to high levels of drug resistant HIV.

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impact of drug resistance

Why is it important to measure drug resistance?How does it impact the success of large-scale treatment programs?

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What is Antiviral Drug Resistance?

Drugs no longer block virus replication Cause:

– Mutations in the viral genome One or more:

– Specific for an antiviral drug OR – Affecting related drugs (cross-resistance)

How much resistance? Which drugs?– Depends on type and number of mutations

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Total: 33 million (30 – 36 million)

Western & Central Europe

730 000730 000[580 000 – 1.0 million][580 000 – 1.0 million]

Middle East & North Africa

380 000380 000[280 000 – 510 000][280 000 – 510 000]Sub-Saharan Africa

22.0 million22.0 million[20.5 – 23.6 million][20.5 – 23.6 million]

Eastern Europe & Central Asia

1.5 million 1.5 million [1.1 – 1.9 million][1.1 – 1.9 million]

South & South-East Asia

4.2 million4.2 million[3.5 – 5.3 million][3.5 – 5.3 million]Oceania

74 00074 000[66 000 – 93 000][66 000 – 93 000]

North America1.2 million

[760 000 – 2.0 million]

Latin America1.7 million1.7 million

[1.5 – 2.1 million][1.5 – 2.1 million]

East Asia740 000740 000

[480 000 – 1.1 million][480 000 – 1.1 million]Caribbean230 000

[210 000 – 270 000]

Adults and Children Estimated to be Living with HIV, 2007

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Towards Universal Access – Scaling up priority HIV/AIDS interventions in the health sector. WHO/UNAIDS/UNICEF, June 2008

Number of People Receiving ARV Therapy In Low- and Middle-income Countries 2002-

2007

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Median Price (USD) of First-line ARV Regimens in Low-income Countries, 2004-

2007

51% 12% 14% 9%

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Median Price (USD) of second-line ARV regimens in Low-income Countries, 2004-

2007

AZT/3TC/EFV AZT/3TC/NVP d4T/3TC/EFV

d4T/3TC/NVP

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HIV Drug Resistance is Inevitable

HIV DR is an inevitable consequence of ART, influenced by:– Ability of regimens to suppress replication

completely– Adherence and tolerability of regimens – "Genetic barrier" to resistance– Relative fitness of resistant variant(s)– Pharmacokinetics (IQ)– Availability/continuity of drug supply– Removal of barriers to access to care

Therefore, efforts to minimize HIVDR should be focused on these factors

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HIV DR Testing in Resource Rich Settings

Prevalence of HIVDR at baseline

Utility of resistance testing before

initiating therapy

Individualization of 1st line regimen

Resistance developing on therapy

Resistance testing before switching

therapy (SOC)

Individualization of 2nd line and subsequent

regimens

24+ drugs from 6 classes

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HIV DR Testing in Resource Limited Settings


Utility of resistance testing before

initiating therapy

Individualization of 1st line regimen


Resistance testing before switching

therapy (SOC)

Individualization of 2nd line and subsequent

regimens

24+ drugs from 6 classes

~6 drugs from 3 classes


Prevalence and patterns of resistance

in population

Determination of standard 2nd line

regimens


Will standard 1st line regimens be effective?

Determination of standard 1st line

regimen

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Need for Population-based Therapies

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Need to Maintain Effectiveness

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Drug Resistance and HIV

HIV… evolves rapidly within human body has a high replication rate has a high mutation rate

Resistant strains can emerge within days if

drug pressure is not sufficient to suppress replication.

Resistant strains persist indefinitely and can re-emerge if same drugs are stopped and restarted (even if they are not detected by standard resistance assays).

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Review

Why is it important to measure drug resistance?

How does it impact the success of large-scale treatment programs?

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factors that influence development of drug resistanceWhat regimens influence drug resistance?What patient factors influence drug resistance?What public health approaches influence drug resistance?

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In Which Conditions is DR More Likely?

Treatment with <3 drugs Inappropriate selection of drugs Adding one drug to a failing regimen Interruption of treatment (even for a few

days) Prolonging a failing regimen

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In Which Conditions is DR Less Likely?Medication Factors

All patients treated with 3 or more drugs Use of appropriate drug regimens Can reliably suppress HIV replication to

levels of <50 copies/ml Use of fixed-dose combinations to support

adherence

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In Which Conditions is DR Less Likely?Systems Factors

Limited number of regimens Trained personnel, low turnover Supervision and monitoring Adequate lab services Drug supply and delivery systems

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In Which Conditions is DR Less Likely?Patient Factors

Adherence to treatment regimen Avoiding interruption of treatment, even if

only a few days Regular follow-up (going to clinic) Staying on uninterrupted first-line ART as

long as possible

CONTINUITY!

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Programmatic Factors Affecting Patient Compliance

Cost of treatment to patient Distance patient must travel to get

treatment Supply interruptions Availability of second-line regimens for

patients whose first-line regimens fail Timing of use of second-line regimens

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Discussion

What regimens influence drug resistance? What patient factors influence drug

resistance? What public health approaches influence

drug resistance?

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Reflection

What regimens do we use in our country? What systematic and programmatic

challenges do we face?

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how to minimize drug resistanceWhat can countries do to minimize or suppress drug resistance?

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Elements of a National HIVDR Prevention and Assessment Strategy

A. Development of a national HIVDR Working Group, five year plan and budget

B. Regular assessment of HIVDR early warning indicators (EWI) from all ART sites (or representative sites)

C. Surveys to monitor HIVDR and associated factors in sentinel ART sites

D. HIVDR transmission threshold surveys in geographic areas where ART has been widespread for > 3 years

E. HIVDR database developmentF. Designation of an in-country or regional WHO-accredited

HIVDR genotyping laboratoryG. HIVDR minimization activities review and supportH. Preparation of annual HIVDR report and

recommendations; use of data for ART and planning

Bennett, Bertagnolio, Sutherland and Gilks, Antiviral Therapy 13 Suppl 2:1–13, 2008

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Database, analysis

Transmission of DR HIV to uninfected individuals

Threshold Surveys(Surveillance)

Genotyping Laboratory

DR HIV prevalence < or ≥ 5%, 15%

To which drugs?

*Surveys to monitor HIV DR prevention and associated factors in sentinel ARV treatment sites

Emergence of HIVDR in treated

patients

Sentinel ART Site Monitoring Surveys*

Genotyping, VL Laboratory

HIVDR Prevention at 12 months; prevalence and

patterns of DR; associated factors

ART site factors associated with minimizing

HIVDR

Early Warning Indicators

Areas to directly target for improvement

PUBLIC HEALTH ACTION

Non-Laboratory Data collection

Relationship of Different Assessment Factors

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General WHO Strategies (1 of 2)

Strengthen existing programmes that minimize HIVDR

Form national HIV drug resistance working group

Monitor Early Warning Indicators Survey to monitor HIVDR prevention and

associated factors in sentinel ART sites Watch for transmitted HIVDR in recently

infected individuals

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General Strategies (2 of 2)

Designate one or more genotyping labs for HIVDR surveillance and monitoring

Maintain a national database to hold the HIV sequences collected through surveillance, monitoring, and research projects

Produce an annual report summarizing results from all the above

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Strengthen Existing Programmes That Minimize HIVDR

Support for adherence and follow-up Removal of barriers to ART access Drug supply continuity at the individual,

ART site, and national levels

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Form National HIV Drug Resistance Working Group

Develop HIVDR prevention, surveillance and monitoring plan

Make evidence-based recommendations for HIVDR prevention

Includes epidemiologists, clinicians, researchers, and laboratorians

Collect indicators and implement surveys Develop evaluation strategies

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Monitor Early Warning Indicators

Routine collection of medical and pharmacy records

Monitor for factors associated with HIVDR prevention or emergence– Extent to which prescribing practices meet

national and international guidelines– % of patients still on first-line; % lost to follow-up– % patients with timely medication pick up and

clinical follow-up– Drug supply continuity at site– Adherence and viral load, if feasible

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HIVDR Early Warning Indicators (EWI)

Prescribing

practices

Proportion lost to follow-up during

the first 12 months of ART

Patient retention on first-line ART

On-time ARV drug pick up

ART appointment-keeping

Drug supply

continuity

Site-level ART Program

Function

Viral load suppressio

n @12 months

Pill count/ adherence

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HIVDR EWI Site-Based Report Example

Site

Months with no

ARV drug stockoutsTarget: 12

% appropriate Initial ART regimen

prescriptionsTarget: 100%

% starting first line ART lost to follow up at 12

monthsTarget: < 20%

% on ART keeping all clinical

appointments on time

Target: > 80%

% on ART picking up all ART drugs on

time Target: ≥ 90%

1 12 94/94 (100%) 4/96 (4%) 182/209 (87%) 184/192 (96%)

2 10 81/81 (100%) 9/74 (12%) 342/402 (85%) 176/220 (80%)

3 9 31/40 (78%) 12/37 (32%) 122/244 (50%) 144/206 (70%)

4 12 104/104 (100%) 10/99 (10%) 891/993 (90%) 483/508 (95%)

5 12 112/112(100%) 13/105 (12%) 262/305 (85%) 184/202 (91%)

6 11 98/101 (97%) 2/90 (2%) 416/442 (95%) 254/359 (71%)

7 12 98/98 (100%) 9/88 (10%) 602/683 (88%) 369/402 (95%)

8 12 203/203 (100%) 43 /195 (22%) 292/356 (82%) 254/284 (86%)

9 12 304/305 (99.7%) 117/260 (45%) 753/1506 (50%) 829/1202 (69%)

10...

12 94/94 (100%) 12/90 (13%) 271/305 (89%) 269/290 (93%)

152 12 33/33(100%) 4/31 (13%) 147/180 (82%) 143/159 (90%)

153 10 26/34 (76%) 7/35 (20%) 148/224 (66%) 129/182 (71%)

154 12 73/73(100%) 9/69 (16%) 178/203 (87% ) 146/154 (95%)

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For More Information

See Bennett, Bertagnolio, Sutherland and Gilks (2008). The World Health Organization’s global strategy for prevention and assessment of HIV drug resistance. Antiviral Therapy 13 Suppl 2:1-13.

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Implementation of the WHO HIVDR Strategy – June 2009

Implementation of at least 1 component of the HIVDR strategy in 41 countries

HIVDR transmission surveys completed in 11 countries

EWI piloted in 23 countries HIVDR training workshops:

– Africa (3), Asia, Caribbean 22 accredited HIVDR Genotyping labs HIVDR laboratory training package Annual external Quality Assurance (supported

by NIH, through the VQA)

Countries implementing or planning a national HIVDR strategy

Countries with a national HIVDR working group implementing > 1 assessment element as of 2/2009

Countries setting up a working group and planning to implement > 1 assessment element in 2009

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Other

Designate one or more genotyping labs for HIVDR surveillance and monitoring– The WHO offers accreditation, support, and

training through the WHO Global HIVDR laboratory network

Maintain a national database to hold the HIV sequences collected through surveillance, monitoring, and research projects

Produce an annual report summarizing results from all the above

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Discussion

What can countries do to minimize drug resistance?

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Reflection

What are our highest-priority “next steps” for minimizing drug resistance?

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how to respond to detection of drug resistanceWhat can be done if widespread drug resistance is found?

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Response to Detection of Transmitted Drug Resistance

If the prevalence of transmitted resistance to important drugs or drug classes is 5-15% or > 15%, surveys should be repeated in the original areas annually and extended to additional areas

Consider changing standard 1st line regimen

Monitor Early Warning Indicators for clues about what can be improved at a programmatic level

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Response to Results from Monitoring Surveys

If the patterns of resistance indicate reduced susceptibility to 2nd line drugs, surveys should be repeated in the original areas annually and extended to additional areas.

Consider changing standard 2nd line regimen.

Monitor Early Warning Indicators for clues about what can be improved at a programmatic level.

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hiv drug resistance assays

What are the different types of resistance assays?What are the advantages and limitations of these assays?What results can we expect from these tests?What if the results from one type of test are inconsistent with results from another?

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Clinical Use of Resistance Data

Resistance tests are most accurate in assessing resistance to current regimen

Absence of resistance to previously used drug does not rule out reservoirs of resistant virus that might emerge after re-initiation of that drug

If resistance to given drug has ever been detected, that drug should probably not be used again, even if current test results suggest viral susceptibility

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Conditions for Drug Resistance Testing:Individual Patient Management

When to use:– When there are treatment options– To indicate drug exposure– While patient is on therapy or before starting for

the 1st time What to consider:

– Treatment history, other reasons for therapy failure

– Lab-to-lab variability of results and interpretations– Requires expert advice for optimal use– Only test single agents, not combinations

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Conditions for Drug Resistance Testing: Public Health Applications

When to use:– When making decisions for national treatment

guidelines• 1st line regimens (based on results of surveillance

for transmitted drug resistant HIV)• 2nd line regimens (based on patterns of resistance

in treated patients)– To monitor program effectiveness minimizing

HIVDR What to consider:

– Early Warning Indicators, programme and site factors

– Treatment history, other reasons for therapy failure

– Lab-to-lab variability of results and interpretations

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Limitations of Resistance Testing:

Only possible in case of a detectable viral load

Lack of consistent quality control (see ENVA)

Current assays do not pick up “minority species;” information is given on predominant strain

Assays have mostly been studied in “late” failures; what is their value in early failures?

Susceptibility is not equal to activity (clinical efficacy)

Clinical validation: more data necessary

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Reflection

What benefits do I hope to see through DR testing in our country?

What are my concerns right now about this type of testing?

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Types of Resistance Assays

Genotypic Testing: Prediction of phenotype based on sequence

Phenotypic Testing: Measure of susceptibility to specific drugs– Recombinant Assays: RT/PCR portion of patient

virus and transfer into a vector• Several different versions commercialized,

automated and regulated– PBMC Assay: Culture virus from patient

• Largely replaced by recombinant assays due to difficulties in reproducibility and throughput

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Genotype Assays: Generic Procedure

Patient virus

PR-RT DNA

RT-PCR

Protein Sequence

Sequencing

Resistance Mutations

Selection

Prediction of Drug

Susceptibility

Interpretation

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Sources and Types of Genotype Assays

Reference Labs (North America and Europe)– Send blood sample in, receive results on report

• LabCorp, Quest, AML, Specialty, Mayo, etc.• Monogram Biosciences, Virco

Commercial kits– Can be performed on site (in laboratory)

• TruGene (Siemens)• ViroSeq (Abbott/Celera)

In-house assays– "home brew" assay performed at one site

(clinical, hospital or research laboratory)– Must be validated and approved if used for

patient management

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Data Analysis (TruGene)

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Genotype Report (TruGene)

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Genotype Report (ViroSeq)

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Genotyping: Pros and Cons

Advantages

Can be performed rapidly (days)

Relatively inexpensive ($100 - $400)

Available in many labs

Disadvantages

Does not directly measure susceptibility

Sometimes difficult to interpret results

Not all patterns of resistance mutations are known (esp. for new drugs and combinations)

Generally qualitative Subjectivity in mixture

detection

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Phenotype Assays: Generic Procedure

Patient virus

PR-RT DNA

RT-PCR

(Resistance Test Vector)

(Vector Assembly)

Recombinant Virus

Transfection

Measure of Drug

Susceptibility

Infection

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Commercially Available Phenotypic Assays

All are recombinant virus phenotypic assays

Antivirogram (Virco)– Homologous recombination used to generate

vector– Replication occurs over multiple cycles

PhenoSense (Monogram)– Vector generated directly by digestion and

ligation– Replication limited to single cycle– High precision and reproducibility

Phenoscript (VIRalliance)– Homologous recombination used to generate

vector– Uses VSV-G protein for virus entry– Replication limited to single cycle

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Phenotype Report (Monogram)

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Phenotype Report (Virco)

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Phenotyping: Pros and Cons

Advantages

Direct measure of drug susceptibility

Quantitative Can immediately test

new RT and PR inhibitors

Disadvantages

Longer time to obtain results (weeks)

Relatively complex technology

More expensive than genotypic assays

Available in fewer labs

Clinical cutoff values for drug resistance not clearly defined for all drugs

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GENO vs PHENO?

A gross oversimplification:– Utility of genotypic testing greatest earlier in

treatment continuum– Utility of phenotypic testing increases with

subsequent treatment rounds

Genotypic testing Genotypic testing

Phenotypic testing

Treatment rounds

Utility

Increasing Genetic Complexity

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Phenotype/Genotype Discordance

GenotypePatient virus

PR-RT DNA

RT-PCR

Protein Sequence

Sequencing

Resistance Mutations

Selection

Prediction of Drug

Susceptibility

Interpretation

PhenotypePatient virus

PR-RT DNA

RT-PCR

(Resistance Test Vector)

(Vector Assembly)

Recombinant Virus

Transfection

Measure of Drug

Susceptibility

Infection

?

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PhenoSense GT Report Form (Monogram)

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3 Types of Phenotype-Genotype Discordance

Genotype predicts resistance, not reflected in phenotype ("PT-S, GT-R"); mixtures of resistant and sensitive viruses are present in the specimen

Genotype predicts resistance, not reflected in phenotype ("PT-S, GT-R"); not explained by mixtures

Genotype predicts susceptibility, but phenotype detects reduced susceptibility or resistance ("PT-R, GT-S")

Parkin et al. JAIDS 2002

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Genotype/Phenotype “Discordance”

Previously unrecognized cross-resistance (or lack of expected cross-resistance).

Previously unrecognized resistance-associated mutations (“RAMs”).

New amino acids at known positions.– e.g. N88S, I84A, K103S, I47A, K101P, V106M…

Effect of recognized RAMs tempered by other mutations.– e.g. L90M, V82A, K103N, suppression of ZDV by

184, etc. Particular combinations of polymorphisms

or “secondary” mutations– e.g. K103R/V179D

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Discussion

What are the different types of resistance assays?

What are the advantages and limitations of these assays?

What results can we expect from these tests?

What if the results from one type of test are inconsistent with results from another?

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Reflection

What type of DR assay is most appropriate for our situation?

What results can we expect? What factors should we keep in mind about

this type of assay?

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Summary

Impact of HIV Drug Resistance Factors that Influence Development of Drug

Resistance How to Minimize Drug Resistance How to Respond to Detection of Drug

Resistance Drug Resistance Assays

Documents

1 HIV Drug Resistance Training Module 1: Introduction to HIV Drug Resistance