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1 JP Morgan Healthcare Conference January 15, 2026
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2 DISCLAIMERS Forward-Looking Statements This presentation contains “forward-looking statements” within the meaning of the Private Securities Litigation Reform Act of 1995. Forward-looking statements are neither historical facts nor assurances of fu ture performance. Instead, they are b ased on our current beliefs, expectations and assumptions regarding the future of our business, future plans and strategies, our clinical results and other future cond itions including without limitation the future of the HCV and HEV landscape and related commercial market opportunities. All statements other than statements of historical facts contained in this presentation are forward-looking statements, including statements by Atea Pharmaceuticals, Inc. (the “Company”) regarding future results of operations and financial position, includ ing our anticipated cash runway; business strategy; current and prospective product candidates; anticipated milestone events; potential benefits of our product candidates and market opportunity; clinical trials, including, without limitation, anticipated initiation, enrollment, regulatory submission and data readout timelines; preclinical activities; product approvals; manufacturing availability; degree of market acceptance of any products that may be approved; estimated total addressable market; research and development costs; prospective collaborations and strategic partnerships; and prospects and opportunities for investors. In some cases, you can identify forward-looking statements by terms such as “may,” “will,” “should,” “expects,” “plans,” “anticipates,” “could ,” “intends,” “targets,” “projects,” “contemplates,” “believes,” “estimates,” “predicts,” “potential” or “continue” or the negative of these terms or other similar expressions. The information in this p resentation, including without limitation the forward-looking statements contained herein, represent our views as of the d ate of this presentation. These statements are neither promises nor guarantees, but involve known and unknown risks, uncertainties and other important factors that may cause our actu al results, performance or achievements to be materially different from any anticipated results, performance or achievements expressed or implied b y the forward-looking statements. Risks and uncertainties that may cause actual results to differ materially include uncertainties inherent in the drug discovery and development process and the regulatory submission or approval process, unexpected or unfavorable safety or efficacy data or results observed during clinical trials or in data readouts; delays in or disruptions to clinical trials or our business; our reliance on third parties over which we may not always have full control, our ability to manu facture sufficient commercial product, competition from app roved treatments for HCV, and other important risks and uncertainties that are described in our Annual Report on Form 10-K filed for the year ended December 31, 2024 and ou r most recent quarterly report on Form 10-Q filed with the Securities and Exchange Commission (“SEC”) and our other filings with the SEC. New risk factors and uncertainties may emerge from time to time, and it is not possible to predict all risk factors and u ncertainties. Accordingly, you are cautioned not to place undue reliance on these forward-looking statements. Except as required by applicable law, we do not plan to publicly upd ate or revise any forward-looking statements contained herein, whether as a result of any new information, future events, changed circumstances or otherwise. No representations or warranties (expressed or implied) are made about the accuracy of any such forward-looking statements. Industry Information Market data and industry information u sed throughout this presentation are based on management’s knowledge of the industry and the good faith estimates of management. We also relied, to the extent available, upon management’s review of independent industry surveys and publications and other publicly available information prepared by a number of third-party sources. All of the market data and industry information used in this presentation involves a number of assumptions and limitations, and you are cautioned not to give undue weight to such estimates. Although we believe that these sou rces are reliable, we cannot guarantee the accuracy or completeness of this information, and we have not indep endently verified this information. While we believe the estimated market position, market op portu nity and market size information included in this presentation are generally reliab le, such information, which is d erived in p art from management’s estimates and beliefs, is inherently uncertain and imprecise. No representations or warranties are made by the Company or any of its affiliates as to the accuracy of any such statements or p rojections. Projections, assumptions and estimates of our future p erformance and the future performance of the industry in which we operate are necessarily subject to a high degree of uncertainty and risk due to a variety of factors, including those described above. These and other factors could cause results to differ materially from those expressed in our estimates and beliefs and in the estimates prepared by independent parties.
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3 Focused Antiviral Pipeline with De-risked Phase 3 Program Program Therapeutic/ Indication Preclinical Phase 1 Phase 2 Phase 3 Milestone Flaviviridae Hepatitis C Virus (HCV) Fixed Dose Combination: Bemnifosbuvir (BEM) Nucleotide Ruzasvir (RZR) NS5A Inhibitor Ph 3 C-BEYOND trial (US / Canada) enrollment completed (n=> 880); results expected mid-2026 Ph 3 C-FORWARD trial (outside North America) full patient enrollment (n=880) expected mid-2026; results expected year-end 2026 Hepeviridae Hepatitis E Virus (HEV) Nucleotide Prodrug AT-587 Phase 1 initiation targeted mid-2026 Cash and investments: $301.8 million at 12/31/25 Cash runway anticipated through 2027 New Program
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4 US New Chronic HCV Infections Continue to Increase Despite Availability of Curative Direct-Acting Antivirals Removal of HCV prescribing barriers by payors
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5 BEM/RZR Potential Best-in-Class Regimen for Treatment of HCV Profile
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6 • HCV product candidate is regimen of BEM, the most potent nucleotide inhibitor, and RZR, a highly potent NS5A inhibitor* • Demonstrated: Efficacy and tolerability Low risk of drug-drug interactions, including proton pump inhibitors Convenient dosing with short 8-week treatment duration** and no food effect • Phase 2 results (n=275) -- BEM and RZR combination regimen achieved primary endpoints of sustained virologic response and safety • 98% sustained virologic response at 12 weeks post-treatment (SVR12) • No drug-related serious adverse events • Chronic HCV , patients stratified by cirrhosis and genotype, HIV-co- infected allowed • Global Clinical Phase 3 program: First head-to-head against sofosbuvir (SOF) /velpatasvir (VEL)† 2 trials with ~1,760 total patients; up to 240 sites globally Phase 3 BEM / RZR vs. Active Comparator Robust Phase 2 Results Achieved Primary Endpoints Potential Best -In-Class Treatment for HCV BEM/RZR: Potential Best-in-Class Treatment for HCV *BEM in vitro studies; RZR preclinical and clinical studies ** in non-cirrhotic patients; †brand name product marketed as Epclusa® First Head-to-Head Phase 3 Program in HCV
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7 BEM/RZR KOL Feedback Test-and-Treat & Market Research BEM/RZR Market Research
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8 KOLS: BEM/RZR Profile Well Suited for Rapid Test-and-Treat Care While you're waiting, they're spreading HCV. You want to to poke a patient's finger, get a result and give the course of medication… If you have short duration, less pill burden, no food effect, minimal DDIs, you're perfectly aligned with a test-and-treat model. Anthony Martinez, MD, University of Buffalo, Erie County Medical Center …Shorter is better. It's just a simple fact. If we're able to enlarge number of healthcare providers that treat HCV, the multiplier effect on getting treatment across the US is exponential… A regimen is needed that is uncomplicated and easy to use and providers aren't afraid of or worried about. Eric Lawitz, MD, Texas Liver Institute, UT Health San Antonio …People say 8 versus 12 weeks, maybe not that big a deal, but actually, the focus on a shorter duration is very, very important. What we found is that if we can get them on to their first dose of medication, our success rate of getting people to complete treatment is incredibly high... Jordan Feld, MD, MPH, University of Toronto, Toronto General Hospital, Canada Delay in treatment increases the risk of transmission. You now have to treat a lot more individuals than you would have if you treated someone earlier in their infection . Nancy Reau, MD, Rush University Medical Center, Chicago
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9 Annual New HCV Infections in US Exceed Annual Treatments Test-and-Treat Can Expand Diagnosis and Treatment of HCV Infections 1. CDC; 2. The CDA Foundation, Lafayette, CO 2025. Hepatitis C – United States. Available from https://cdafound.org/Polaris/database-query/ (Accessed 1/8/2026); 3. IQVIA 2024; 4. U.S. Net Sales of Mavyret, Epclusa (and its authorized copy) from AbbVie and Gilead 2024 Annual Reports EXPANSION OF TEST-AND-TREAT MODEL OF CARE CRITICAL TO ACCELERATE HCV ELIMINATION IN US Potential US government initiatives to eradicate HCV US HCV INFECTIONS GROWING FASTER THAN TREATED PATIENTS TEST TREAT AND • Rapid diagnosis and treatment at the same time • Reduces barriers to treatment prescribing / initiation • Short treatment duration with low-risk of drug-drug interactions optimal for physicians and patients • Bipartisan legislative efforts underway with goal to eliminate HCV in US with test-and-treat model ~4 Million Infected Individuals1 >160 Thousand New Chronic Annual Infections2 ~90 Thousand Treated Annually with Epclusa or Mavyret3 ~$1.5B US net sales in 20244
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10 Highly Attractive BEM/RZR Commercial Profile 1. Predicted share of patients between BEM/RZR, Epclusa, and Mavyret. Atea Custom Market Research, IQVIA, June 2025; 2. Atea Custom Market Research, Formulary Insights, June 2024; 3. IQVIA 2022 % of patients likely to be prescribed BEM/RZR1 High willingness to add BEM/RZR regimen onto formulary2 • Distribution of HCV prescribers by IQVIA3 • Specialty Care Sales Force Required ~6,000 Prescribers write ~80% Direct Acting Antiviral Prescriptions • Limited competition with no competitors in clinical development Concentrated Prescriber Base Research of Payors Covering >130M Lives Quantitative Market Research of High DAA Prescribers Non-Cirrhotic Patients Compensated Cirrhotic Patients 48% 49% PRESCRIBERS PAYORS MARKET BEM/RZR Has Potential to Become Most Prescribed Treatment in HCV Market
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11 BEM/RZR Potential Best-in-Class Regimen for Treatment of HCV Global Phase 3 Program Update
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12 C-BEYOND • ~120 sites in US and Canada • Enrollment completed • Cirrhotic population target achieved • Results expected mid-2026 • ~120 sites in 17 countries outside of North America • Enrollment completion expected mid-2026 • Results expected year-end 2026 C-FORWARD On Track: Global HCV Phase 3 Program
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13 Global HCV Phase 3 Program: C-BEYOND (US/Canada) and C-FORWARD (Outside North America) Open-label: BEM/RZR Regimen vs Active Comparator in Chronic HCV Patients Randomized (1:1) Primary Endpoint - Encompasses SVR12 in All Arms* • No Cirrhosis: 8 weeks of BEM/RZR vs 12 weeks of active comparator • Compensated Cirrhosis: 12 weeks of BEM/RZR vs active comparator Primary Endpoint 1:1 SVR = Sustained Virologic Response FDC = Fixed Dose Combination (Dose 2 tb QD BEM/RZR) SOF/VEL = sofosbuvir/velpatasvir *HCV RNA < lower limit of quantification 24 weeks from start of treatment Non-Cirrhotic US / Canada Trial Enrollment Completed Outside North America Trial N= ~704 Cirrhotic US / Canada Trial Enrollment Completed Outside North America Trial N= ~176 8 weeks BEM/RZR FDC 12 weeks SOF/VEL FDC 12 weeks BEM/RZR FDC 12 weeks SOF/VEL FDC Treatment Duration (Weeks) 1:1 Chronic HCV, patients stratified by cirrhosis and genotype, HIV co- infected allowed, prior DAA excluded Two Phase 3 Trials: 1) N= >880 trial US / Canada (C-BEYOND) 2) N= ~880 trial Outside North America (C-FORWARD) N= ~1,760 total patients 1280 Post-Treatment (Weeks)
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14 Predicted Median Time to Viral Clearance by Fibrosis Stage Based on Ph 2 Results Zitzmann C et al. Presented at The Liver Meeting® 2025, American Association for the Study of Liver Diseases (AASLD), November 7–11, 2025, Washington, D.C., USA MEDIAN TIME TO LLOQ BASED ON MODEL PREDICTION: • F0–F3: 12 days [CI 95:2—27] • F4: 16 days [CI 95:4—41] MEDIAN TIME TO CURE BASED ON MODEL PREDICTION: • F0–F3: 7.3 weeks [CI 95:5—14] • F4: 8.2 weeks [CI 95:5—16] VIROLOGIC RESPONSE (VR) BASED ON MODEL PREDICTION: RAPID VR: 95.4% OVERALL • 97.8% in F0 –F3 [CI95:94.5—99.1] • 82.4% in F4 [CI 95:66.5—91.7] (BEM/RZR) (BEM/RZR) Time to Cure Estimates Support 8-Week Treatment for Non-cirrhotic and 12-Week Treatment for Compensated Cirrhosis
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15 Phase 3 Endpoints, Patient Populations and Analyses *post-hoc analyses Modified Intent-To-Treat (mITT) Per-Protocol (PP) Population: All randomized and dosed All randomized, study drug compliant (≥80% pill count) and SVR assessment at Week 24 (or with SVR12) Considerations: Overall SVR rate will reflect non-drug related discontinuations (as rate does not consider compliance or lost to follow-up) Overall SVR rate will better reflect true efficacy (as rate does consider compliance and lost to follow-up) Ph 2 SVR12 rates w/ above handling* 95% 98% • Modified intent-to-treat is FDA preferred and per -protocol is EMA preferred • The same methods for assessing non -inferiority will be conducted in both Phase 3 studies and in both populations • The reported overall SVR (primary analysis) for each study will differ because of the population used • Phase 3 studies powered 90% with 5% non -inferiority for expected rate approximating 95% in mITT population C-BEYOND (US/CANADA) C-FORWARD (Outside North America) Primary Efficacy Endpoint SVR at Week 24 mITT population SVR at Week 24 PP population Major Secondary Efficacy Endpoint SVR at Week 24 PP population SVR at Week 24 mITT population
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16 Commercial Supply Available for Launch at NDA Approval BEM/RZR Commercial Readiness Expected Short Time to Profitability Post Launch All components and processes for large scale manufacturing are in place Manufacture of commercial launch supply underway Blister card for convenience and patient adherence Simple weekly dosing package 4 weekly blister cards packaged into a carton for 1-month supply Low cost of goods relative to net price (low single digit percent)
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17 Product Candidate AT-587 New Program Hepatitis E Virus
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18 1. WHO most recent estimate. http://www.who.int/mediacentre/factsheets/fs280/en/ Accessed 1/8/2026. 2. Adapted from Khuroo MS, Khuroo MS, Khuroo NS. Hepatitis E: Discovery, global impact, control and cure. World J Gastroenterol 2016; 22(31): 7030-7045 WHO estimates up to 20 million global HEV infections annually1 Hepatitis E Virus (HEV) Overview Waterborne transmission causes acute epidemics in developing countries Foodborne transmission causes chronic infection in the immunocompromised in developed countries HEV2 GT 1,2 HEV-1 HEV-2 HEV-3 HEV-4 HEV2 GT 3,4
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19 1. Alexandrova R, et al. HV Infection Among Immunocompromised Individuals: A Brief Narrative Review. Infection and Drug Resistance. 2014;17 2. Kamar N et al. Factors Associated with Chronic Hepatitis in HEV with SOT. Gastroenter. 2011(140). 3. Dalton H et al. EASL Clinical Practice Guidelines on hepatitis E virus infection. J Hepatology. 2018;16. 1256-1271 Chronic HEV Infection Among Immunocompromised Individuals with GT-3 and GT-4 Can Lead to Rapid Progression to Cirrhosis At-Risk Populations1 • Solid organ transplant recipients • Hematopoietic stem cell transplant (HSCT) recipients • Patients with hematologic malignancies • Patients with pre-existing liver disease Step Current Interventions3 Rationale Risks First Line Reduce Immunosuppression Restore Host Immunity Organ Rejection / Reinfection Second Line Ribavirin (3 months) Direct Antiviral Effect Not Approved / Side Effects / Intolerance Guideline Differences • WHO: Focus on Epidemic HEV (GT1, GT2) • EASL: Focus on Chronic HEV (GT3) Reflects Distinct Local Epidemiology of infected SOT recipients with chronic HEV rapidly develop cirrhosis in 3-5 years2 15% No approved HEV treatments
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20 1. 2023 SOT patients transplanted in US, EU & UK. Newsletter Transplant: International Figures on Donation and Transplantation 2023. EDQM Vol 29 2024. 2. 2022 HSCT patients transplanted in EU & UK. Passweg, J.R., et al.Utilization of hematopoietic cell transplantation and cellular therapy technology in Europe and associated Countries.Bone Marrow Transplant 60, 227–236 (2025) and 2023 HSCT patients transplanted in US. Health Resources and Service Administration. 3. 2022 Leukemia and non-Hodgkins Lymphoma patients in US, EU & UK. WHO International Agency for Research on Cancer. https://gco.iarc.who.int/today/en Accessed 10/20/25. 4. Hansrivijit P. Et al. HEV in SOT Recipients. World J Gastroenterol. 2021(27). 12. 5. Kamar N et al. Factors Associated with Chronic Hepatitis in HEV with SOT. Gastroenter. 2011(140) A growing number of patients in high -risk populations in US & EU with no approved treatment Estimated HEV Infection Among High-Risk Populations in US & EU Leads to Commercial Opportunity of $750M-$1B* ~3%** of at-risk patients develop chronic HEV4,5 Solid Organ Transplant (SOT)1 Recipients ~80K HSCT Recipients 2 ~37K Hematologic Malignancies3 ~334K Incidence among at-risk populations Potential Treatment Population of ~13.5K Patients Annually Incidence rate of chronic HEV *Assumes pricing estimates of $200K per course of therapy based on similar HDV pricing *Assumes ~30% treated **Assumes similar incidence rates of chronic HEV in HSCT and Hematologic Malignancies as with SOT Commercial Opportunity $750M-$1B*
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21 • AT-587 is potent against various HEV GT-3 strains and remains active against clinical ribavirin RAS • Antiviral activity of AT-587 confirmed in primary human hepatocytes infected with HEV • An animal model confirmed in vivo potency of BEM at 250 mg/kg/day (unpublished data) Compound HEV-3 p6 WT HEV-3 p6 G1634R (RBV RAS)* HEV-3 83.2.27 Bemnifosbuvir 477 ± 121 (n=4) --- --- AT-587 86.1 ± 20.1 (n=5) 83.9 ± 1.6 142.2 ± 1.6 Ribavirin > 10,000 (n=5) 12,793 ± 945 19,111 ± 335 Fitness (%) 100.0 144.2* 115.0 EC50 VALUES (NM) AGAINST HEV STRAINS IN HUH7 CELLS n = minimum of 2 except where indicated * The G1634R mutation confers an advantage for viral replication in vitro, which contributes to treatment failure, yet does not appear to alter its sensitivity to ribavirin AT-587: Potent Antiviral Activity Against Multiple HEV-3 Strains and Ribavirin Resistant Virus in Replicons
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22 Comparable Exposure of Active Triphosphate Metabolite Surrogate Achieved with AT-587 and Bemnifosbuvir Following a Single Oral Dose to Rats and Monkeys Bemnifosbuvir AT-587 Species PK Parameter Parent Drug Surrogate Metabolite Species PK Parameter Parent Drug Surrogate Metabolite Monkey¹ Dose (mg/kg) 100 Monkey Dose (mg/kg) 100 AUClast (ng·h/mL) 1,100 3,032 AUClast (ng·h/mL) 3,321 3,723 Cmax (ng/mL) 783 131 Cmax (ng/mL) 1,819 331 Tmax (h) 1-2 4 Tmax (h) 1 4 Rat² Dose (mg/kg) 500; adjusted to 100 Rat Dose (mg/kg) 100 AUClast (ng·h/mL) 16 1,928 AUClast (ng·h/mL) ND 1,913 Cmax (ng/mL) 12 108 Cmax (ng/mL) < 1.0 176 Tmax (h) 0.25 6-8 Tmax (h) ND 4 ¹ Doses administered as powder in capsules ² Doses administered in suspension in aqueous 0.5% CMC/0.5% Tween 80 Doses administered as homogeneous suspension (0.5% CMC + 1% Tween 80)
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23 AT-587 Forms High Levels of Active Triphosphate Metabolite (AT-9068) in Human Hepatocytes (Site of Viral Replication) Triphosphate AUC0-24h (h*pmol /106 cells) • No inhibition of α, β, γ human DNA polymerases by active triphosphate (AT -9068) • Negative in screening in vitro genetox assays (2-strain AMES, chromosomal aberration) • Clean in screening hERG assay • No toxicity to human iPS cardiomyocytes • Minor effect on bone marrow CD34 + cells, with mean IC 50 > 30 uM • IND/CTA enabling studies ongoing with GLP toxicology studies Human hepatocytes 1,360 3,920 CELLS AT-9068 (AT-587) AT-9010 (BEM)
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24 Upcoming Key Milestones Across Antiviral Pipeline enabling studies 20272026 BEM/RZR REGIMEN - PHASE 3 PROGRAM FOR HCV AT-587- PROGRAM FOR HEV Mid-2026 • Completion of C- FORWARD patient enrollment • Topline Phase 3 results for C-BEYOND Year-end 2026 • Topline Phase 3 results for C-FORWARD 2027 • Anticipated Q1 NDA submission Ongoing • IND/CTA enabling studies 2H 2026 • Initiation POC clinical study 2H 2027 • Initiation Phase 2/3 trial Mid-2026 • Phase 1 clinical study Cash and investments: $301.8 million at 12/31/25 Cash runway anticipated through 2027 Ongoing • Two Phase 3 Trials
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