Virology Resistance

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Virology - Resistance

• Anna Maria Geretti
• Royal Free Hospital, London

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Treatment failure and resistance

• Low drug exposure
• Adherence
• PK
• Drug activation
• Drug penetration

Poor drug potency

• Host-related factors
• Viral load
• Immunity
• Genetics

Infection with resistant virus
Drug pressure
Persistent virus replication
Selection, emergence and evolution of drug
resistance
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Attachment Fusion
Release of RNA
Assembly
Reverse transcription Integration
Transcription
Maturation and budding
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• Mechanisms of genetic evolution
• Rapid evolution through point mutations
• RT error rate 1 per genome round
• Replication rate 109-1010 virus particles daily
• All possible mutations generated daily
• Genetic evolution through recombination
• Recombination rate 7-30 per genome round

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Emergence and evolution of resistance
selection
Emergence
Evolution towards high resistance and high fitness
Single mutant Double mutant
Triple mutant

• Increasing resistance and cross-resistance
• Accumulation of mutations on the same viral
  genome
• Compensatory changes that restore fitness

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Key principles of resistance

• Drug-resistant mutants are selected (not
  created) by drug pressure if virological
  suppression is incomplete
• Ongoing virus replication under drug pressure
  leads to the evolution of resistance and
  cross-resistance
• Resistant mutants often display reduced fitness
  but compensatory changes emerge over time that
  partially restore virus fitness
• If therapy is discontinued resistant mutants
  disappear from the dominant quasispecies,
  persisting as minority species and archived
  resistance in latently infected cells

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Clinical implications

• Continuing a failing treatment can be deleterious
  
• Use only for patients lacking effective treatment
  options
• Judicious selection of drugs
• Maintain for the shortest period possible pending
  the availability of new treatment options

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Viral load reduction during 3TC monotherapy
(NUCA3001)
0.5
0.0
-0.5
Mean change in HIV-1 RNA (log copies/ml)
-1.0
Emergence of M184V
-1.5
-2.0
0
4
8
12
16
20
24
28
32
36
40
44
48
52
Week
Eron J, N Eng J Med 1995
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3TC monotherapy vs treatment interruption (TI)
in patients with resistance
CD4
0

• Open-label study
• Patients on 3TC-based therapy with VLgt1000, CD4
  gt500
• M184V
• Randomized to 3TC or TI

50
100
Mean change in CD4 cells/mm3
150
200
250
pns
300
0
4
8
12
16
20
24
48
Weeks
2.00
Viral load
1.75
1.50
1.25
Mean change in HIV RNA log10 c/mL
1.00
0.75
0.50
p0.0015
0.25
0
0
4
8
12
16
20
24
36
48
Weeks
Castagna A, AIDS 2006
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Definitions

• Changes in the viral genetic sequence (mutations)
  that confer drug resistance - genotypic
  resistance
• Commonly reduce drug susceptibility compared with
  the susceptibility of wild-type viruses -
  phenotypic resistance
• Mediated by
• Changes in the molecular target of
  therapy(detected in routine tests)
• Changes in other viral proteins that indirectly
  interfere with drug activity (not routinely
  tested for)

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Mechanisms of NRTI resistance Primer unblocking

• Hydrolytic removal of the chain-terminating NRTI
  enables DNA synthesis to resume
• The hydrolytic removal requires a pyrophosphate
  donor, which in most cells is ATP (b)

Gotte, J Virol 2000
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Cut-offs for interpreting resistance
Lower cut-off Level of resistance beyond
which response begins to fall off
Upper cut-off Level of resistance beyond which
clinical response is lost
Zone of intermediate response
Response
Resistance
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Detection of resistant mutants
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20-30
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Clinical implications

• In treated persons, resistance test results
  obtained after therapy is discontinued are not
  reliable
• Resistance is long-lasting, even if undetectable
• Resistance results must be interpreted in the
  context of the patients treatment history

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Transmitted drug resistance (TDR) Stable after
transmission Gradual reversion over time, often
incomplete Persistence as low frequency
species Persistence in latently infected cells
Reversion rate Rapid K70R, M184V,
T215YIntermediate D67N, Y181C, T215S,
K219NSlow M41L, T69DN, G190S, L210W, T215LCE,
K219Q in RT and I84V, L90M in PR
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European surveys of resistance in newly
diagnosed patients
1Booth C, JAC 2007 2Wensing A, 3Vercauteren,
and 4Paraskevis, EHDRW 2006 5Oette, JAIDS 2006
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recent infection PBMC analysis
Geretti AM, Curr Opin Infect Dis 2007
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Diagnostic yield of allele-specific PCR vs
standard genotyping in drug-naïve patients

• Increased diagnostic yield by 5 (K103N) to
  344 (T215F)

Johnson J, CROI 2007
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Time to failure of NNRTI-based HAART with and
without baseline NNRTI resistance
Estimated with failure at 12 months 72.7 with
NNRTI resistance vs 28.0 without RT mutations
(p0.006)
Siemen, IHDRW 2007
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Prevalence of resistance among treated patients
undergoing testing in the UK
Prevalence () of resistance
Geretti AM, IHDRW 2008
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Predictors of detectable resistance -
multivariate analysis
No significant effect of gender, age or risk group
Geretti AM, IHDRW 2008
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HAART regimens have a different genetic barrier
to the emergence of resistance
2NRTI PI/r
3TC ZDV NNRTI 3TC ABC NNRTI 3TC ABC ZDV 3TC TDF
EFV FTC TDF EFV
2NRTI PI
TDF 3TC ABC TDF 3TC ddI ABC ddI d4T TDF ddI EFV
Genetic barrier defined by Speed of emergence
of detectable resistance No. of mutations
required to compromise drug activity
Kempf D, JID 2004 Phillips A, AIDS 2005
Gulick, ICDTHI 2004 Cahn P, IAS 2001 Feinberg
J, IAC 2002 Molina JM, IAC 2004 MacManus S,
AIDS 2004 Ananworanich J, IAS 2005 Malan R,
CROI 2006 Miller MD, CDTHI 2002 Arribas JR,
CDTHI 2004 Molina JM, IAC 2004
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Relative genetic barrier of PI/s

• NFV
• SQV, IDV
• ATV
• LPV, FPV
• TPV, DRV

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Resistance in clinical trials of first-line HAART
wk 48
Gallant JE, IAC 2006 Gazzard B, ICAAC Miller M,
ICDTHI 2002 De Jesus E, ICAAC 2003 Molina JM,
IAS 2005 MacManus S, AIDS 2004
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NRTI resistance in patients receiving ZDV/3TC/TDF
in Uganda and Zimbabwe (DART)

• Resistance test results available in subset of
  patients with viral load gt1000 c/ml at wk 24
  (n26/43) and wk 48 (n35/64)

Pillay D, CROI 2007
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Cross-resistance potential

• NRTIs significant to complete
• NNRTIs complete for NVP and EFV
• PIs grows with increasing mutations
• Entry Inhibitors complete for MRC and VRC
• Integrase Inhibitors complete for RAL and ELV

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Can we predict emerging resistance during failure
of first-line NNRTI-based therapy?

• Regimen Detection Drugs affected
• ZDV 3TC NNRTI Early 3TC, NVP, EFV
• ZDV 3TC NNRTI Late ZDV, d4T, ABC gt ddI,
  TDF
• d4T 3TC NNRTI Early 3TC, NVP, EFV
• d4T 3TC NNRTI Late ZDV, d4T, ABC
  gt ddI, TDF
• ABC 3TC NNRTI Early 3TC, NVP, EFV
• ABC 3TC NNRTI Intermediate ABC, ddI
• ABC 3TC NNRTI Late TDF, d4T
• TDF FTC NNRTI Early 3TC, NVP, EFV
• TDF FTC NNRTI Intermediate TDF, ABC,
  ddI, d4T

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DUET studies Virological response according to
baseline ETV RAMs

• ETV RAMs
• V90I A98G
• L100I K101E/P
• V106I V179D/F
• Y181C/I/V G190A/S

Vingerhoets, IHDRW 2007
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PI cross-resistance
Parkin N, CROI 2007
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Clinical implications

• Resistance to NRTIs, 2nd generation NNRTIs and
  PI/r is a continuum
• Intermediate levels of drug activity can play an
  important part in a successful drug regimen
• Support from other active drugs essential to
  ensure responses are maintained

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POWER Virological response by baseline number of
DRV/r mutations
All DRV/r 600/100 mg bd
Adapted from Cohen C, IDSA 2006
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Thank you

• Comprehensive long-term management of HIV
  infected patients must strive to minimise drug
  resistance as a key goal

a.geretti_at_medsch.ucl.ac.uk