Slides
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1 Third Quarter Financial and Business Update November 12, 2025
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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 future performance. Instead, they are based on our current beliefs, expectations and assumptions regarding the future of our business, future plans and strategies, our clinical results and other future conditions including without limitation the future of the HCV 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, including 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 presentation, including without limitation the forward-looking statements contained herein, represent our views as of the date 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 actual results, performance or achievements to be materially different from any anticipated results, performance or achievements expressed or implied by 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 manufacture sufficient commercial pr oduct, competition from approved 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 our 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 uncertainties. 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 update 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 used 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 estimat es. Although we believe that these sources are reliable, we cannot guarantee the accuracy or completeness of this information, and we have not independently verified this information. While we believe the estimated mar ket position, market opportunity and market size information included in this presentation are generally reliable, such information, which is derived in part 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 projections. Projections, assumptions and estimates of our future performance an d 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 ca use 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) full patient enrollment (n=880) expected YE 2025; results anticipated mid-2026 Ph 3 C-FORWARD trial (outside North America) full patient enrollment (n=880) expected mid-2026; results anticipated year-end 2026 Hepeviridae Hepatitis E Virus (HEV) Nucleotide Prodrug AT-587, AT-2490 Phase 1 initiation targeted mid-2026 Cash, cash equivalents & marketable securities: $329.3M at 9/30/25 Cash runway anticipated through 2027 New Program
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4 BEM/RZR Recent Program Highlights New Data Presented at The Liver Meeting 2025
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5 New Data Presented at The Liver Meeting ® November 7-11, 2025 Posters are available on Atea’s website https://ir.ateapharma.com/news -and-events/publications Three Presentations at the American Association for the Study of Liver Diseases (AASLD) The Liver Meeting 2025 0089 Oral Presentation Multiscale Modeling of Results from a Phase 2 Study of an 8-week Combination Regimen of Bemnifosbuvir and Ruzasvir in Patients with Chronic Hepatitis C Virus Infection Presenting Author: Carolin Zitzmann Poster Number: 1381, Identified as a Poster of Distinction Title: No Impact of RASs on the High Efficacy of Bemnifosbuvir and Ruzasvir in Combination: Resistance Analysis from a Ph 2 Study in HCV-Infected Patients Presenting Author: Qi Huang Poster Number: 1398 Title: Bemnifosbuvir and Ruzasvir Provided as a Fixed-dose Combination Demonstrates High Relative Bioavailability to Their Individual Formulations and Can Be Dosed with No Regard to Food Presenting Author: Xiao-Jian Zhou AASLD Logo
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6 HCV KOL Panel Event to be Held on November 13, 2025 Our panel features leaders in hepatology, gastroenterology, infectious diseases and HCV research, including: Jordan Feld, MD, MPH – University of Toronto, Toronto General Hospital, Canada Eric Lawitz, MD – Texas Liver Institute, University of Texas Health San Antonio, US Anthony Martinez, MD – University of Buffalo, Erie County Medical Center, US Nancy Reau, MD – Rush University Medical Center, Chicago, US
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7 BEM/RZR Potential Best-in-Class Regimen Global Phase 3 Program Update
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8 • HCV program is a 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 (new data) 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 safety and sustained virologic response • 98% sustained virologic response at 12 weeks post-treatment (SVR12) • No drug-related serious adverse events or treatment discontinuations • 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 First Head-to-Head Phase 3 Program in HCV SOF/VEL = sofosbuvir/velpatasvir – brand name product marketed as Epclusa®; *BEM in vitro studies; RZR preclinical and clinical studies Positive results of robust Phase 2 studies of antiviral therapies for HCV have historically led to a high probability of success in Phase 3 trials
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9 Global HCV Phase 3 Program C-BEYOND in US / Canada & 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 < LLOQ 24 weeks from start of treatment Non-Cirrhotic US / Canada Trial ~N=~748 Outside North America Trial N= ~704 Cirrhotic US / Canada ~N=132 Outside North America 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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10 C-BEYOND • ~120 sites in US and Canada • Enrollment completion expected year end 2025 • Data expected mid-2026 • ~120 sites in 16 countries outside of North America • Enrollment completion expected mid-2026 • Data expected year-end 2026 C-FORWARD On Track: Global HCV Phase 3 Program
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11 BEM New Mechanism of Action (MoA) Against HCV Dual Mechanism of Action
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12 BEM’s Unique Dual Mechanism of Action (MoA) Against HCV • BEM’s established MoA is an inhibition of HCV RNA production / replication via chain termination like all nucleotide analogs such as sofosbuvir (SOF) • Modeling of HCV viral kinetics data from Phase I BEM monotherapy trial suggests BEM has an additional MoA* – inhibiting HCV viral assembly/secretion – a mechanism previously only associated with NS5a inhibitors such as velpatasvir (VEL) and ruzasvir (RZR) * Los Alamos National Labs (Alan Perelson) replication / production assembly/ secretion Viral Kinetics
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13 Loyola University In Vitro Data Confirm Additional MoA for BEM Comparison of BEM and SOF Inhibition Kinetics Intracellular HCV RNA Extracellular HCV RNA BEM exposure results in much lower extracellular HCV RNA levels as compared to SOF Concentrations of BEM and SOF selected to effect similar intracellular HCV RNA levels Untreated SOF (4 uM) BEM (250 nM) MoA Slide 1/2
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14 Concentrations of BEM and VEL selected to effect similar intracellular HCV RNA levels In Vitro Data Confirm Additional MoA for BEM Comparison of BEM and VEL Inhibition Kinetics Intracellular HCV RNA Extracellular HCV RNA Loyola University Untreated VEL (150 pM) BEM (250 nM) Extracellular HCV RNA levels were comparable with exposure of BEM or VEL, demonstrating that BEM also inhibits HCV secretion / assembly , in addition to viral replication MoA Slide 2/2
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15 15 HCV Lifecycle Bemnifosbuvir has been shown to inhibit viral replication inside the cell – reducing intracellular HCV RNA Bemnifosbuvir also inhibits the viral assembly and secretion of new HCV virions into the bloodstream, significantly reducing extracellular HCV RNA Bemnifosbuvir Bemnifosbuvir blocks the virus from making copies inside the cells Bemnifosbuvir blocks new HCV RNA from entering the bloodstream BEM’s Unique Dual MoA against HCV Intracellular HCV RNA Extracellular HCV RNA
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16 BEM: Potent Nucleotide with a Differentiated MoA for Treatment of HCV Next generation nucleotide with a dual mechanism of action against HCV Additional MoA may explain the higher potencyof BEM as compared to SOF Even in the presence of NS5A resistance, BEM would continue to block assembly / secretion due to its dual MoA These MoA data highlight the unique and differentiated profile of BEM / RZR regimen
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17 AT-587 and AT-2490 New Preclinical Program Hepatitis E Virus
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18 1. WHO most recent estimate. http://www.who.int/mediacentre/factsheets/fs280/en/ Accessed 10/23/25. 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 annually 1 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 Resis tance. 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 Interventions 3 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 a 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 Transplantatio n 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 t echnology 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 Accesse d 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 treatments Estimated HEV Infection Among High -Risk Populations in US & EU Leads to Market Opportunity of $500M -$750M ~3%* of at-risk patients develop chronic HEV 4,5 Solid Organ Transplant (SOT)1 Recipients ~80K HSCT Recipients 2 ~37K Hematologic Malignancies 3 ~334K Incidence among at-risk populations Potential Treatment Population of ~13.5K Patients Annually Incidence rate of chronic HEV Assumes pricing estimates of $150K per course of therapy based on similar HDV pricing *Assumes similar incidence rates of chronic HEV in HSCT and Hematologic Malignancies as with SOT Market Opportunity $500M-$750M
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21 Potent Inhibition of Hepatitis E Virus Replication Demonstrated by Atea Nucleotide Prodrugs Note: Antiviral activity of AT-2490 and AT-587 confirmed in primary human hepatocytes infected with HEV • Nanomolar potency of AT-587 and AT-2490 against HEV GT-1 and GT-3 confirmed at second laboratory (Virginia T ech) • Antiviral activity of BEM confirmed in HEV animal model at 250 mg/kg/day (unpublished data) and additional studies with AT-587 and AT-2490 HEV inhibitors are planned • Composition of matter patent issued in major territories; HEV use patent application pending Compound EC50 mean ± SD (nM; n=2) AT-587 66.9 ± 19.1 AT-2490 29.4 ± 8.3 BEM 530 (n=1) SOF 1,914 ± 309.7 Ribavirin ~10,000 Activity in Huh7 HEV -3 Kernow-C1 p6/Gluc replicon cells (Ruhr University)
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22 AT-587 and AT-2490 Form High Levels of Active Triphosphate Metabolite (AT-9068) in Human Hepatocytes AT-9068 Triphosphate AUC0-24h (h*pmol /106 cells) • AT-9068 does not inhibit α, β, γ DNA polymerases (IC50 > 100 uM) • Biochemical studies ongoing to evaluate HEV polymerase inhibition by AT-9068 and AT-9010 • Clean preclinical profile in several in vitro tests including Ames, hERG, chromosomal aberrations and human cardiomyocyte cytotoxicity assays Huh-7 4,050 3,583 5,965 Human hepatocytes 3,920 9,297 1,054; 1,673 CELL LINE AT-9068 (AT-587) AT-9010 (AT-511) AT-9068 (AT-2490) AT-9010
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23 Financial and Business Update 3rd Quarter 2025 Results
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24 Financial Update
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25 Financial Update
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26 Strong Execution Across a Growing Antiviral Pipeline On track with global Phase 3 program for the treatment of HCV; North America results expected mid-2026 and ex-North American results expected year-end 2026 Presented new data at The Liver Meeting 2025 supporting BEM/RZR as a potential best-in- class therapy with a differentiated profile for HCV; current global HCV annual net sales ~$3B New data demonstrate dual MoA of BEM, highlights its unique and differentiated profile, and explains the potency of BEM/RZR regimen for the treatment of HCV Antiviral pipeline expansion into HEV aims to address unmet clinical need with no approved therapies, presenting an estimated $500-750M market opportunity (US & EU)
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