Stephanie Cox Gilead Sciences - PowerPoint Presentation

1. Stephanie CoxGilead SciencesFoster City, CAULTRASENSITIVE HIV-1 DRUG RESISTANCE ANALYSIS IN THE DISCOVER PREP TRIALFull-time employee and stockholder of Gilead.

2. Randomized1:1Double blinded,active controlledMSM or TGWaged ≥18 yWeek 048+14496100%participants50%participantsPrimary endpointF/TAF 200/25 mg qd n=2700F/TDF 200/300 mg qd n=2669F/TAFOL option144Study DesignAdherence and Resistance Analyses of HIV Infections*TFV-DP in DBS lowTFV-DP in DBS medium/highSuspected baseline infectionParticipants, n21811164111DISCOVER: a Randomized, Double Blind, Noninferiority TrialOngoing noninferiority study of F/TAF vs F/TDF for PrEP (NCT02842086)Eligibility criteria:High sexual risk of contracting HIV:≥2 episodes of condomless anal sex with ≥2 unique partners in 12 wk prior to enrollmentDiagnosis of rectal gonorrhea, chlamydia, or syphilis in 24 wk prior to enrollmentHIV and HBV negative, prior use of PrEP allowed*Updated with data cut through Week 118; adherence cutoffs, fmol/punches: emtricitabine/tenofovir alafenamide (F/TAF): low, <450; medium, ≥450–<900; high, ≥900; emtricitabine/tenofovir disoproxil fumarate (F/TDF): low, <350; medium ≥350–<700; high ≥700. DBS, dried blood spot; HBV, hepatitis B virus; MSM, men who have sex with men; OL, open label; PrEP, pre-exposure prophylaxis; TFV-DP, tenofovir-diphosphate; TGW, transgender women.Of the 5335 analysis-set participants, 27 (0.5%) acquired HIV-1 infection through Week 144 (open label Week 48) on study5 participants had suspected baseline infections and 20 had low levels of TFV-DP found by DBS analysis2

3. UMI-NGS: HIV Drug Resistance Assay**HIV gene-specific primers with unique molecular identifiers (UMIs) were used to synthesize complementary DNA (cDNA) from extracted HIV RNA from plasma samples; library preparation for next generation sequencing (NGS) included 2 rounds of polymerase chain reaction (PCR) amplification of the cDNA molecules with UMI and ligation of adaptor linkers; bioinformatics analysis was performed with an in-house pipeline that builds template consensus sequences of reads sharing identical UMI sequences at 80% majority base calling; UMI-based consensus building allows for correction of PCR/sequencing error and accurate assessment of sampling depth per sample. †For DISCOVER samples, UMI-NGS assay amplification regions were RT 63–131 and 152–211.MutantWild-typeAddition of UMI adaptor during cDNA synthesisUMIAmplification† and adaptor ligationBias and error correction through UMI consensus buildingMutant (75%)Wild-type (25%)AdaptorUMIsTrue variantPCR/sequencing error (false variant)True variant present in all fragments carrying same UMIFalse variant present in some fragments carrying same UMI3

4. FTC and TFV Resistance in the DISCOVER StudyIn the DISCOVER study, development of resistance was seen infrequently and most commonly with suspected baseline infections, as reported previously*Samples did not amplify for UMI-NGS testing; †Imputed, DBS not available at time of diagnosis; §No sample available for UMI-NGS or standard NGS testing.4Study Week at Time of InfectionM184V (2%)M184V (86%) M184I (6%)M184V (45%) M184I (41%)M184V (40%) M184I (60%)M184V (90%) M184I (10%)DBS TFV-DP lowDBS TFV-DP mediumDBS TFV-DP highF/TFV NRTI-R mutation††OL 24F/TAFF/TDF**§

5. Participants With Resistance: ART Regimens Initiated and OutcomesOut of 13 participants, 10 participants with follow up data were shown to be virologically suppressed; the other 3 participants were lost to follow up—, no resistance mutations; 3TC, lamivudine; ABC, abacavir; ART, antiretroviral therapy; B, bictegravir; C, cobicistat; DRV, darunavir; DTG, dolutegravir; E, elvitegravir; INSTI, integrase strand transfer inhibitor; ND, no data available; PI, protease inhibitor; RAL, raltegravir.5TxParticipantF/TFV-RTransmitted Drug Resistance Mutations (% Mutant)NRTI* (% Mutant)NNRTI* (% Mutant)INSTI* (% Mutant)ART RegimensSuppressedPINRTINNRTIINSTIF/TAF4M184V ————DRV/C/F/TAF + RALYes6————T66A (25)F/TAF + DTGND7———V106I (>99)N155H (5)F/TDF + DRV/coYes8——V118I (>99)——NDYesF/TDF12M184V/I————E/C/F/TAF + DRVYes13———V90I (>99)—NDYes17M184V/IM46I (4)—K103N (>99)—DTG + DRV/cYes18———K103N (>99)—E/C/F/TAF Yes19————Y143C (10), Q148R (4)DRV/C/F/TAFND20M184V/I———E92G (2)B/F/TAFYes22M184V/I—T69N (>99), K219E (>99)Y188L (>99)—ABC/DTG/3TCYes23———V90I (>99), K103N (>99)—ABC/DTG/3TCYes25———V106I (>99)—DRV/c + FTC + TAFND

6. ConclusionsResistance data were similar between standard and ultrasensitive sequencing evaluating mutations down to 1% of the viral population4 participants in the F/TDF arm had M184V/I: all 4 had suspected baseline infections1 participant in the F/TAF arm had M184V seen by UMI-NGS sequencing but not by standard sequencing methods including traditional NGSAll participants with viruses with resistance to study drugs were successfully treated with ARV regimensTransmitted drug resistance was seen in the PR, RT, and IN genes in 11 out of 25 participants evaluated by NGSConsistent with PrEP literature, HIV infections were uncommon in individuals who take PrEP as directed, and when they occurred, resistance was rareWe extend our thanks to the participants, their families, and all participating study investigators and staff. This study was funded by Gilead Sciences, Inc.6