Antiretroviral Drug Resistance

Anna Maria GerettiUCL Medical School &

Royal Free Hampstead Medical School, London

Drug-related factors•Potency•PK properties•Genetic barrier

Host-related factors•Adherence•Tolerability•Immunity•Genetics

Drug pressure

Emergence and evolution

of drug resistance

Virus-related factors•Viral load•Drug susceptibility•Fitness

Persistent virus replication during HAART

Attachment Fusion Release of RNA

Reverse transcription Integration Transcription

Maturation and budding

Assembly

Characteristics of HIV-1 infection

1. High virus replication rate (109-1010 virus particles / day)

2. Rapid virus clearance (T½ cells producing virus: <1 day; T½ free virus in plasma: a few hrs)

3. Virus latency (1:106 resting CD4 T cells)

4. Chronic immune activation and inflammation

5. CD4 T-cell depletion (108-109 cells lost daily)

6. Progressive immune deficient state

7. Continuous virus genetic evolution

Wong 1997; Chun 1997; Siliciano 2003; Strain 2003; Han 2007

Mechanisms of HIV genetic evolution1. RT-driven mutagenesis

– Rate: ~1 wrong incorporation per genome round– All possible point mutations generated daily

2. APOBEC-driven mutagenesis– Deamination of cytosine residues in nascent DNA– GA hypermutation

3. Recombination– Rate: 7-30 per genome round– Hybrid virus progeny produced from different strains

Dominant quasispecies

Escape from pressure

Preserved fitness

rapid turnover rapid adaptation

Consequences of HIV genetic variability

At the population level

Continuous emergence of new variants

At the patient level

Escape from immune pressure

Escape from drug pressure

Increased fitness and pathogenicity

Challenge for diagnostic and monitoring assays

Emergence and evolution of resistance

Increasing number of mutations Accumulation of mutations on the same viral genome Initially reduced viral fitness Compensatory changes restore fitness

Evolution Emergence

Single mutant Double mutant Triple mutant

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

Plasma HIV RNAViral gene (e.g., RT)

PCR

Sequencing Mutations

RT M184V

Methionine Valine

@ codon 184 of RT

ATG / AUG GTG / GUG

Detection of resistant mutants

0.001

0.01

0.1

1

10

100

Detected by ultrasensitive methods

Mu

tatio

n F

requ

enc

yDetected by routine methods

Natural background

Low-frequency resistance in the FIRST study

Mutations Resistance test P

Standard

UDS

NNRTI 7% 15% <0.001

NRTI 6% 14% <0.001

PI 2% 5% 0.03

Any 14% 28% <0.001

N=258

Risk of failure of first-line NNRTI-based ART in patients with NNRTI resistance

Bulk resistance: HR 12.4 [3.4-45.1]

UDS resistance: HR 2.5 [1.2-5.4]

Siemen, JID 2009USD = Ultra deep sequencing

Drug pressureResistant

Wild-type

20-3

0%

Limit of detection

Key principles of resistance

Once drug pressure is removed, resistant mutants are outgrown by fitter wild-type virus and become undetectable by routine tests

Resistance test results obtained after therapy is discontinued are not reliable

Resistant mutants persist at low frequency in plasma and are “archived” in latently infected cells

Resistance is long-lasting

Resistance test results must be interpreted in the context of the patient’s treatment history

Wild-type Resistant

Ms S., 35 yr Δ HIV+ Dec 1997

10

1000

100000

Dec-97 Jun-98 Dec-98 Jun-99 Dec-99 Jun-00 Dec-00 Jun-01 Dec-01 Jun-02 Dec-02

d4T 3TC NVP

d4T 3TC NVP

VL

<50

M184V

Y181C

M184V

Y181C

M184V = 3TC, FTC

Y181C = NNRTIs

Drug pressure

Transmission

Transmitted drug resistance

Stable after transmissionGradual reversion over time, sometimes incompletePersistence at low frequency in plasmaPersistence in latently infected cells

Genetic barrier

Key concepts

Genetic barrier to resistance

Defined by:

Number of mutations required to compromise activity

Impact of each mutation on drug susceptibility

Interactions between mutations

Fitness cost of resistance

Drug concentration

Resistant

Wild-type

Genetic barrier – A simplified overview

Class ARVs Genetic barrier

NRTIs

ZDV/3TC, d4T/3TC ++

ABC/3TC, TDF/3TC +

TDF/FTC ++

NNRTIsEFV, NVP, ETV, RPV +

ETV, RPV +/++

PIs Boosted +++/++++

Fusion inhibitors T20 +

CCR5 antagonists MVC ++ (for R5 virus)

Integrase inhibitors RAL, ELV +

Common NRTI resistance patterns

NRTIs Mutations ZDV d4T ABC ddI TDF 3TC FTC

ZDV 3TC

d4T 3TC

M184V

TAMs

+ TAMs

d4T 3TCTDF 3TCTDF FTC

M184V

K65R

ABC 3TC

M184V

L74V

K65R Y115F

TAMs = thymidine analogue mutations: M41L, D67N, K70R, L210W, T215Y/F, L219Q/E

Resistance with first-line HAART

Study ART wk Tests

K65R L74V M184V TAMs 3rd drug

GS903 n=299 TDF 3TC EFV 48 29 24% 0 41% 0 EFVR 55%

GS934 n=244 TDF FTC EFV 96 14 0 0 14% 0 EFVR 71%

GS934 n=243 ZDV 3TC EFV 96 29 0 0 31% 3% EFVR 62%

CNA30021 n=770 ABC 3TC EFV 48 38 3% 21% 47% 0 EFVR 58%

ABT418 n=190 TDF FTC LPV/r 96 23 0 0 17% 0 PIR 0

SOLO n=190 ABC 3TC FPV/r 48 32 0 0 12% 0 PIR 0

ARTEMIS n=343 TDF FTC DRV/r 96 31 0 0 6% 0 PIR 0

STARTMRK n=281 TDF FTC RAL 96 13 0 0 38% 0 RALR 33%

Margot, HIV Med 2006; Margot, JAIDS 2009; Moyle, JAIDS 2005; Molina, IAC 2004; Gathe, AIDS 2004; Mills, AIDS 2009; Lennox, Lamcet 2009.

1st and 2nd generation NNRTIs

Nevirapine Efavirenz Etravirine

Major resistance mutationsL100I, K101E/PK103N/SV106A/ME138K, V179FY181C/I/V, Y188L/H/C, G190A/S/EF227C, M230L, K238T

Rilpivirine

Activity of ETV with a strong backboneDUET studies: OBR (with DRV/r) + ETV or Placebo

0 2 4 8 12 16 20 24 32 40 48

40%

p<0.0001*Res

pond

ers

(%)

± 95

% C

I

100

90

80

70

60

50

40

30

20

10

0

Time (weeks)

Patients with VL <50 copies/ml at wk 48 (ITT-TLOVR)

ETV + OBR (n=599)

Placebo + OBR (n=604)

61%

Katlama, AIDS 2009

ART-experienced patients with documented NNRTI and PI resistance

Activity of ETV with a weak backboneStudy TMC125-C227: 2 NRTIs + ETV or PI

Ruxrungtham, HIV Med 2008

ART-experienced, PI-naive patients with documented NNRTI resistance

The genetic barrier of PIs in vitro

De Meyer, Antimicrob Agents Chemother 2005;De Meyer, IHDRW 2006

Time (days)

Incr

ease

i n P

I se l

e cti

on

c o

nce

nt r

a tio

n

0

50

100

150

200

250

300

350

400

450

0 100 300 500 700 900 1100

DRV (R41T, K70E)

RTV (G16E, M46I, V82F, I84V)

SQV (G48V, A71V, G73S, I84V, L90M)

NFV (L10F, D30N, R41K, K45I, M46I, V77I, I84V, N88D)

APV (L10F, V32I, L33F, M46I, I47V, I50V)LPV (L10F, L23I, M46I, I50V, I54V, L63P, V82A)

TPV (L33V, M46L, V82T)ATV (L10F, V32I, M46I, I62V, A71V, I84V, N88S)

Hypersusceptibility

Key concepts

Mechanisms of NRTI resistance: Primer unblocking

T215Y-mediated resistance

Hydrolytic removal of the chain-terminating NRTI enables DNA synthesis to resume

The pyrophosphate donor in most cells is ATP

M184V antagonizes the process

3TC partially restores susceptibility to ZDV,d4T and TDF in the presence of TAMs

3TC antagonizes the emergence of TAMs P P P

P

PP

P

P

PP

P

PP

P

P

P

Gotte, J Virol 2000

Residual activity

Key concepts

Res

po

nse

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

Resistance as a continuum

Partial treatment interruption in patients with resistance reveals residual activity

NRTI PI NNRTI T20–0.5

0.0

0.5

1.0

Discontinued treatment class

Change in plasma

viral load

Week 2 change in VL

Deeks, CROI 2005

Key principles of resistance

Resistance moves along a continuum and increasing numbers of mutations lead to progressive loss of responses

Residual activity is possible despite the presence of extensive resistance (best evidence for the NRTIs)

Resistance carries a fitness cost that reduces viral replication

Antagonistic effects between mutations can have beneficial effects

Clinical implications for patients with treatment failure

The likelihood of drug-resistance depends upon the drug, the regimen and the level of adherence

When selecting a new regimen, aim for at least 2 fully active drugs

Avoid functional monotherapy with drugs that have a low genetic barrier

If options are limited, exploit residual activity and hypersusceptibility effects – continue the NRTIs rather than stopping therapy

Thank you