Improving PI drug resistance scores. Jens Verheyen, MD Institute of Virology University Duisburg-Essen

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1 Improving PI drug resistance scores Jens Verheyen, MD Institute of Virology University Duisburg-Essen

2 Overview Why can all PI drug resistance scores be improved? Do we still need to improve PI drug resistance scores, today? How to improve PI drug resistance scores?

3 Failure of antiretroviral therapy HIV-1 Viruslast

4 Genotypic HIV drug resistance test LPV/r ATV FPV NFV d4t ddc DLV NVP RAL EVG MV C T-20 TPV IDV ddi EFV DGV DRV SQV 3TC ETV RTV ABC RPV APV TDF AZT FTC

5 HIV-1 drug resistance - black and white - NRTI: 3TC / FTC M184V NNRTI: NVP K103N, Y181C EFV K103N, Y188L RPV E138K PI: NFV D30N, L90M SQV G48V, I84V, L90M INI: RAL Y143R, Q148HRK, N155H EVG S147G, Q148R, N155H

6 HIV-1 drug resistance - complex resistance profiles - PI: DRV 11I, 32I, 33F, 47V, 50V, 54LM; 74P, 76V, 84V, 89V 50L ATV I50L, I84V, N88S 76V, 50L LPV TPV V32I, M46I, I47A, I50V, I54VTALM, L76V, V82ATFS, I84V 47V/74P/82LT/83D; 58E/84V; 36I/43T/54AMV; 10I/33F/46L 50L 24I, 76V, 50LV, 54L

7 Maturation: complex interplay of enzyme and substrate maturation Virale protease Precursor proteins (Gag and Gag-Pol) XX X X X X Protease-inhibitor

8 PI drug resistance: PR and Gag mutations Gag mutations protease mutations compensatory mutations Do Gag mutations also directly confer PI drug resistance? resistance mutations compensatory mutations

9 PI failure without PR mutations M ARTEMIS HIV RNA >50 Kopien/ml (%) LPV/r (n=326) 33 % Percent failure n=108 GT: 51 PR: 0 RT: 19 PRmutations % Percent failure DRV/r (n=343) n=72 GT: 31 PR: 0 RT: 2 PRmutations 29 % Percent failure LPV/r (n=346) n=100 GT: 46 PR: 0 RT: 5 PRmutations RTmutations RTmutations RTmutations 1. Walmsley S, et al. NEJM 2002;346: ;

10 Failure of a double PI treatment regimen Patient: 56 years, HIV-1 positive (FD: 1997) Previously used PI: SQV, NFV, LPV, ATV/r, FPV/r Current ART: SQV, FPV/r HIV-1 genotype: PR: 46L HIV RNA remained detectable ( cop/ml) TDM: therapeutic drug levels for both drugs HIV-1 genotype: PR: 46L Gag: 431V, 436R Therapy switch: DRV/r, ETR, MVC, RAL (VL: <40 cop/ml) Verheyen et al., unpublished data

11 Gag CS mutations confer PI drug resistance IVS-1: IVS-32: IVS-34: K436E, I437T I437V I437T Nijhuis et al., PLoS medicine, 2007

12 Gag CS mutations confer PI drug resistance Nijhuis et al., JID, 2009

13 Can Gag mutations confer PI drug resistance? Yes!! Do Gag and PR mutations cooperate?

14 Prevalence of C-terminal Gag CS mutations in HIV-1 Percent of CS positive HIV Major- PR mutations: 24I, 32I, 46I/L, 50V/L, 54V/L/M/S/T/A, 82A/F/T/S, 84V, 90M Verheyen IHDRW 2006

15 200 Interplay of Gag and PR mutations Dam et al., PloS path, LPV (RF) PI resistant HIV Variants Chimeric HIV: Gag and PRRT Gag alons 0 Gag + PRRT Gag alone Gag + PRRT Gag alone Gag + PRRT Gag alone Gag + PRRT Gag alone Gag + PRRT Gag alone Gag + PRRT Gag alone : impaired replicationcapacity 300 Replication capacity Gag + PRRT Gag alone Gag + PRRT Gag alone Gag + PRRT Gag alone Gag + PRRT Gag alone Gag + PRRT Gag alone Gag + PRRT Gag alone

16 Interplay of Gag and PR mutations LPV (RF) Dam et al., PloS path, 2009 PI resistant HIV Variants Chimeric HIV: Gag and PRRT Gag alons 0 Gag PRRT Gag + alone alone PRRT Gag PRRT Gag + alone alone PRRT Gag PRRT Gag + alone alone PRRT Gag PRRT Gag + alone alone PRRT Gag PRRT Gag + alone alone PRRT Gag PRRT Gag + alone alone PRRT : impaired replicationcapacity HIV-Grade ANRS HIVdb Rega Highest drug resistance Gag and PRRT HIV variants HIV-Grade ANRS HIVdb Rega HIV-Grade ANRS HIVdb Rega Both PR and Gag mutations contribute to PI drug resistance but only PR mutations are scored by all interpretation tools

17 Can Gag mutations confer PI drug resistance? Yes!! Do Gag and PR mutations cooperate? Yes!! Can Gag mutations pave the way for PR mutations?

18 Emergence of PR mutation 76V in HIV-1 failing PI therapies Emergence of PR mutation 76V: Comparison of genotypes before and after failure of ART n=2 431V 46I 76V n=3 46I 76V n=3 431V 76V 431V 46I 76V 46I 76V 431V 76V Verheyen et al. (2010) AIDS

19 Mtreemix-analysis of PI drug resistant HIV variants Evolutionary pathways were estimated from our crosssectional data using the mtreemix package. 57% of the observed mutational patterns could be explained by the assumption of an ordered accumulation along two pathways. Verheyen et al. (2006) AVT

20 Can Gag mutations confer PI drug resistance? Yes!! Do Gag and PR mutations cooperate? Yes!! Can Gag mutations pave the way for PR mutations? Yes!!

21 Gag mutations contribute to PI drug resistance: either alone or in combination with PR mutations either directly (resistance-conferring) or indirectly (compensatory) are integral part of evolutionary processes resulting in PI drug resistance Why not? Are PI drug resistance scores already perfect? geno2pheno

22 PI drug resistant HIV in Europe (n=29): Germany (Essen, Cologne, Erlangen), Belgium (Leuven) Italy (Rome), Spain (Barcelona) PI-R: n=29 NRTI-R: n=27 NNRTI-R: n=17 INI-R: n=6 X4: n=10 HIV-Grade ANRS HIVdb REGA

23 Carlo Perno, HIV in Europe 2020 what will it look like? - Cases of PI failure - Resistance will always be with us but we care Gag mutations contribute to PI drug resistance: Why not? either alone or in combination with PR mutations either directly (resistance-conferring) or indirectly (compensatory) are integral part of evolutionary processes resulting in PI drug resistance Are PI drug resistance scores already perfect? No!! Are PIs obsolete for ART 2016? PIs are still recommended 1 st line therapies. PIs are part of dual drug concepts. 22% PIs will remain essential for 2 nd /3 rd all around the world. line therapies We still detect PR mutations and even in TN-HIV (Hofstra O_05) and Harrigan et al. CROI2016

24 Gag mutations contribute to PI drug resistance: either alone or in combination with PR mutations either directly (resistance-conferring) or indirectly (compensatory) are integral part of evolutionary processes resulting in PI drug resistance Why not? Are PI drug resistance scores already perfect? No!! Are PIs obsolete for ART 2016? No!! Are there technical problems? C-terminal Gag seem to be more important than the N-terminal part. The new NGS technology facilitate Gag sequencing. Ehret et al, O_04: Relevance of minorities of 1% or 2% Li et al., Retrovirology 2015 How wide is wide enough? instead of How deep is deep enough?

25 Gag mutations contribute to PI drug resistance: either alone or in combination with PR mutations either directly (resistance-conferring) or indirectly (compensatory) are integral part of evolutionary processes resulting in PI drug resistance Why not? Are PI drug resistance scores already perfect? No!! Are PIs obsolete for ART 2016? No!! Are there technical problems? No!! With evidence that Gag mutations are important and in the absence of opposing factors we decided to include Gag mutations in the Rega drug resistance score

26 REGA 10.0 algorithm (PR and Gag mutations) Input: nucleic sequence (fasta-file) Output (rules based): Scoring of Gag and PR mutations Di Carlo et al., O_06 Correlation of failure only with combined resistance to TDF/FTC and RPV. Validation: data set

27 Thank you Institute of Virology, Section Virology-Venereology University Duisburg-Essen Marek Widera Barbara Bleekmann Miriam Dirks KU Leuven Rega Institute for Medical Research Annemie Vandamme Kristel Van Laethem Ricardo Camacho Department Biomedicine, University of Basel Thomas Klimkait HIV Unit and irsicaixa AIDS Research Institute Barcelona Roger Paredes University of Rome Tor Vergata, Department of Experimental Medicine and Surgery Institute of Virology, University of Cologne: Rolf Kaiser Elena Knops Department of Medical Microbiology, Virology, University Medical Center Utrecht Annemarie Wensing Monique Nijhuis Institute of Immunology and Genetics, Kaiserslautern Alexander Thielen Martin Däumer Francesca Ceccherini-Silberstein Valentina Svicher Matteo Surdo Romina Salpini