1
Rationale and Uses For a Public HIV Drug
Resistance Database
Bob Shafer, MD
Professor of Medicine and by Courtesy Pathology
(Infectious Diseases)
2
Outline
• HIV drug therapy essentials
• HIVDB
• Examples of public health applications
• Surveillance of transmitted drug resistance
• Genetic mechanisms of acquired drug resistance
HIV-1 Genome
HIV Replication and Targets of Therapy
5
Antiretroviral Inhibitors (ARVs)
ddI
ddC
AZT
1990
Nucleoside
RT Inhibitor
3TC
d4T
NVP
IDV
RTV
SQV
EFV
DLV
APV
NFV
ABC
1995
LPV
TDF
2000
Protease
Inhibitor
Nonnucleoside
RT inhibitor
T20
MVC
ATV
FTC TPV DRV RAL ETR
2005
Fusion
Inhibitor
Integrase
Inhibitor
CCR5
Inhibitor
6
HIV Genetic Variation
• Generation of variation
• High mutation rate
• Recombination
• Proviral DNA “archive”
• Selective evolutionary pressures
• Immunological
• Antiretroviral drugs (ARVs)
Tebit DM, Arts EJ. Tracking a century of global expansion and evolution of HIV. Lancet Infect Dis 2011
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HIV-1 RT: Active Site, Template, Primer, and dNTP
Active site
Incoming nucleotide
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NNRTI Resistance Mutations
Active site
Etravirine
NNRTI resistance mutations
HIV-1 Protease Drug Resistance Mutations
Lopinavir
Major resistance mutations
Active site & substrate cleft
Minor resistance mutations
Models Relating HIV Drug Resistance to Treatment
Response
12
10 Million Patients on Antiretroviral Therapy
2013 Global AIDS Response Progress Reporting (WHO/UNICEF/UNAIDS)
13
Outline
• HIV drug therapy essentials
• HIVDB
• Examples of public health applications
• Surveillance for transmitted drug resistance
• Genetic mechanisms of acquired drug resistance
14
Database Rationale
• Drug resistance knowledge important for

Interpreting genotypic resistance tests

Designing surveillance studies and public health decisions

Assisting drug development.
15
How we know what we know about HIV
drug resistance mutations
• Genotype-treatment correlations – 1998
• Genotype-phenotype correlations – 2002
• Genotype-outcome correlations – 2005
16
Database Rationale
• Large amounts of drug resistance data are important for
generating drug-resistance knowledge.
• Uniform representation of 3 main data correlations
facilitates meta-analyses.
Genotype-Rx
Genotype-Phenotype
Genotype-Outcome
Clinical management
Epidemiologic studies
Drug development
http://hivdb.stanford.edu
Genotypic HIV Resistance Testing
CCTCAGATCACTCTTTGGCAACGACCCATAGTCACAATAAAGATAGCGGGACAACTAAAGGAAGCTCTATTAGATACAGGAGCAGATGATACA
GTATTAGAAGAAATGAATTTGCCAGGAAAATGGAAACCAAAAATAATAGTGGGAATTGGAGGGTTTACCAAAGTAAGACAGTATGATCATGTAC
AAATAGAAATCTGTGGACATAAAGTTATAGGTGCAGTATTAATAGGACCTACACCTGCCAATATAATTGGAAGAAATCTGTTGACTCAGCTTGGC
TGTACTTTAAATTTT
PQITLWQRPIVTIKIAGQLKEALLDTGADDTVLEEMNLPGKWKPKIIVGIGGFTKVRQYDHVQIEICGHKVIGAVLIGPTPANIIGR
NLLTQLGCTLNF
Differences from Consensus B:
L10I, G17R, K20I, E35D, N37S, M46I, I62V, L63P, A71I, G73S, I84V, L90M, I93L
HIV-1 Genotypic Resistance Testing: Online Interpretation
Meaningful Results
(1) Quality control
(2) Sequence Interpretation
(3) Literature references
(4) Clinical education / advice
Shafer RW et al. HIV-1 RT and Protease Search Engine for Queries. Nat Med 2000
HIVdb: Genotypic Resistance Interpretation
http://hivdb.stanford.edu
HIVdb: Genotypic Resistance Interpretation
HIVdb: Genotypic Resistance Interpretation
HIVdb: Genotypic Resistance Interpretation
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Surveillance for Transmitted Drug
Resistance
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Outline
• HIV drug therapy essentials
• HIVDB
• Examples of public health applications
• Surveillance for transmitted drug resistance
• Genetic mechanisms of acquired drug resistance
26
Rationale for Surveillance for Drug Resistance
in ARV-Naive Populations
• Assess extent of transmitted drug resistance (TDR).
• Monitor the expected efficacy of first-line therapies.
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Challenges to ARV-Resistance Surveillance
• There is no perfect definition of genotypic resistance.
•
There are many different drug-resistance mutations (DRMs).
•
Drug resistance mutations occasionally occur in the absence
of selective drug pressure. Therefore, not all drug-resistance
mutations are evidence for transmitted drug resistance
(TDR).
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Challenges to ARV-Resistance Surveillance
• More than 300 studies of genotypic resistance in ARVnaïve patients have been published.
• Findings differ by region, time, study population, and
potentially study methods.
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Surveillance Drug Resistance Mutations (SDRMs)
• Drug-resistance mutations with a high sensitivity and specificity
for detecting selective ARV pressure.
• Nonpolymorphic.
•
Applicable to all HIV-1 subtypes.
Shafer RW, et al. HIV drug resistance mutations for
drug resistance surveillance. AIDS 2007
30
HIV-1 Resistance in ARV-Naïve Populations:
Analysis of Published RT and PR Sequences
• Well-characterized representative population of ARVnaïve persons.
• Country and year of virus isolation known.
• HIV-1 RT ± PR sequence is publicly available.
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Calibrated Population Resistance Analysis Tool
• Applies SDRM list to a
set of sequences
•
•
Standardized approach
to handling missing data
and poor sequence
quality.
Backward-compatibility
Gifford, RJ et al. The calibrated population resistance tool: standardized
genotypic estimation of transmitted HIV-1 drug resistance. AIDS 2008
HIV-1 Resistance in ARV-Naïve Populations:
Prevalence by Region
Region
No.
Studies
No.
Persons
% Resistance
Median
% Resistance
IQR
North America
24
11,038
11.4
8.8 – 14.0
Europe
44
11,419
9.3
6.0 – 15.1
Latin America
39
5,802
7.6
4.0 – 10.1
High-income Asia
11
3,190
5.5
3.5 – 9.0
Former Soviet Union
11
1,124
3.4
0.0 – 6.4
South/Southeast Asia
49
4,181
3.3
2.0 – 5.3
Sub-Saharan Africa
86
9,904
2.8
1.1 – 5.7
264
46,660
HIV-1 Resistance in ARV-Naïve Populations:
Sub-Saharan Africa
Sub-Saharan Africa
Overall
8
4
0
887
1529
<=1
1538
<=3
1343
4
1803
<=6
1200
7
1449
<=14
%Resistance
Years Since AR
NRTI
8
4
0
NNRTI
8
4
0
PI
8
4
0
http://hivdb.stanford.edu/surveillance/map/
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HIV-1 Resistance in ARV-Naïve Populations:
South / Southeast Asia
South/Southeast Asia
Overall
8
4
0
495
512
858
556
877
811
<=2
3
4
<=6
<=9
%Resistance
Years Since AR
NRTI
8
4
0
NNRTI
8
4
0
PI
8
4
0
http://hivdb.stanford.edu/surveillance/map/
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HIV-1 Resistance in ARV-Naïve Populations:
Most Common SDRMs by Region and ARV Class
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HIV-1 Resistance in ARV-Naïve Populations:
Conclusions
• Significant differences in prevalence of resistance in ARVnaïve patients by region and year.
• Transmitted NNRTI resistance is increasing in SubSaharan Africa and South/Southeast Asia.
• Analysis of data from many studies is required to obtain
meaningful estimates of transmitted drug resistance.
36
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Outline
• HIV drug therapy essentials
• HIVDB
• Examples of public health applications
• Surveillance for transmitted drug resistance
• Genetic mechanisms of acquired drug resistance
38
Rationale
• In resource-limited regions, ~25% of patients receiving
first-line ART develop virological failure within 1 year.
• Drug-resistance mutations are detected in 50% to 90%
of patients with virological failure.
• Regimens used in resource-limited countries differ from
those used in well-resourced countries.
• Patients in resource-limited countries are monitored
infrequently and second-line therapy is chosen without
genotypic resistance testing.
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Genetic Mechanisms of Resistance in Patients
with Virological Failure
• Choosing second-line therapy.
• Developing point-of-care (POC) diagnostic tests.
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WHO-Recommended First-Line ARV Regimens
WHO-Recommended Regimens, 2016 to 2013
NRTI
NRTI
NNRTI / PI
d4T (being phased out)
3TC (or FTC)
EFV
AZT
NVP
TDF
LPV (PI, 2nd line)
ABC (children)
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Number of Patients by Regimen and Subtype
Data summary from mid 2012
A
B
C
AE
AG
D
G
Misc
Total
d4T/3TC/NVP
50
55
121
430
123
27
122
40
1121
AZT/3TC/NVP
45
99
394
45
50
42
46
21
469
d4T/3TC/EFV
13
92
188
16
9
2
3
11
540
AZT/3TC/EFV
25
244
274
45
20
17
26
11
576
133
490
977
536
202
88
197
83
2706
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Sources of Patient Data and Sequences
Data summary from mid 2012
Number Studies
Number Patients
%
10 largest
1,409
51%
20 largest
1,981
72%
50 largest
2,640
98%
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Question From WHO: Which NRTI should be
substituted in patients stopping d4T?
• Patients with virological failure on d4T can develop resistance by
two mutually exclusive mutational pathways:
•
Thymidine analog mutations: cross-resistance to AZT
•
Non-thymidine analog mutations particularly K65R: cross-resistance to
TDF and increased susceptibility to AZT
• In vitro studies have shown that viruses belonging to subtype C
are at increased risk for developing K65R.
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Impact of NNRTI, Subtype, and Years on NRTIResistance Mutations in 1,840 Patients Receiving d4T
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Impact of Subtype on AZT and TDF Cross-Resistance in
1,840 Patients Receiving d4T
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Rationale for Point-Of-Care (POC) Resistance Testing
in Low/Middle-Income Countries?
• POC test for detecting virological failure have been
developed.
• A POC resistance test for a limited number of the most
important mutations could be used:
•
To confirm virological failure
•
To suggest among second-line therapy options
•
Be used prior to therapy in regions with elevated TDR or in
patients with uncertain treatment history.
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Sensitivity for Detecting Resistance after 1st-Line
Failure: 4 NNRTI and 6 NRTI-Resistance Mutations
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Sensitivity for Detecting Resistance in Untreated
Patients: 4 NNRTI and 6 NRTI-Resistance Mutations
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Conclusions
• Drug resistance knowledge is important for interpreting genotypic
resistance tests, designing surveillance studies, and drug
development.
• Large amounts of drug resistance data are important for
generating drug-resistance knowledge.
• Drug-resistance data consists mostly of correlations between
genotype-treatment, genotype-phenotype, and genotypevirological outcome.
50
Acknowledgements
Database / Data analysis
Soo-Yon Rhee, M.S.
Tommy Liu, B.S.
Michele Tang, M.D.
Vici Varghese, Ph.D.
Funding
NIAID – Division of AIDS
Bill and Melinda Gates Foundation
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HIV-1 Evolution and Drug Resistance:
An Example
A
B
HIV-1 levels prior to TMB-202
HIV-1 levels during and following TMB-202
June
2009
2009
April 2010
Plasma HIV-1 RNA log copies / ml
1997
6.0
5.0
ENF
4.0
DRV + RAL
3.0
EFV
2.0
Below the level of quantification
Below the level of quantification
1.0
97
98
99
00
01
02
03
04
05
06
07
08
09
-4
0
4
8
12
16
20
24 28
32
36
40
44
Ibalizumab Infusions
Accompanying antiretrovirals: etravirine + enfuvirtide
Fessel WJ, et al. The efficacy of an anti-CD4 monoclonal
antibody for HIV-1 treatment. Antivir Res 2011