Quarterly Report for Quarter Ending March 31, 2026 (Form 10-Q)

Management's Discussion and Analysis of Financial Condition and Results of Operations.

You should read the following discussion and analysis of our financial condition and results of operations together with our unaudited condensed consolidated financial statements and related notes included elsewhere in this Quarterly Report on Form 10-Q, as well as our audited consolidated financial statements and related notes as disclosed in our Annual Report on Form 10-K for the year ended December 31, 2025, filed with the Securities and Exchange Commission ("SEC") on March 5, 2026. This discussion contains forward-looking statements based upon current plans, expectations and beliefs involving risks and uncertainties. Our actual results may differ materially from those anticipated in these forward-looking statements as a result of various factors, including those set forth in Part II, Item 1A, "Risk Factors" and other factors set forth in other parts of this Quarterly Report on Form 10-Q.

Overview

We are a late-stage clinical biopharmaceutical company leveraging our deep understanding of antiviral drug development, medicinal chemistry, biochemistry and virology to discover, develop and commercialize novel, orally administered antivirals to treat serious viral diseases. Our current product candidate pipeline includes the regimen of bemnifosbuvir and ruzasvir which we believe has the potential to improve the current standard of care ("SOC") for the treatment of patients with hepatitis C virus ("HCV") infection and AT-587 which we believe has the potential to be the first direct-acting antiviral ("DAA") for the treatment of patients, particularly immunocompromised patients, with chronic hepatitis E virus ("HEV") infection.

HCV - Our Goal and our Program

The objective of our HCV development program is to improve upon the current SOC by offering bemnifosbuvir and ruzasvir as a differentiated pan-genotypic protease inhibitor-free, short-duration regimen for patients infected with HCV, if successfully developed and approved. We believe that a novel treatment regimen that can be easily prescribed will benefit today's HCV population, which is predominately young (20-49 years old) and non-cirrhotic, and it would be a significant improvement to the current SOC.

Presently, there are no short-course (i.e., eight week) nucleotide inhibitor-based, pan-genotypic HCV treatment regimens. Clinical and nonclinical results from studies conducted to date, including a global Phase 2 clinical trial which enrolled 275 HCV infected patients, have shown that the regimen of bemnifosbuvir and ruzasvir has high potency and has been well tolerated. These studies have also shown that the regimen has a low risk for drug-drug interactions with many commonly prescribed medications including proton pump inhibitors and offers the convenience of being able to be taken with or without food. This is a profile that we believe will offer a significant improvement to the current SOC, if approved.

The global HCV Phase 3 program we are conducting consists of two randomized, open label studies: C-BEYOND which has clinical trial sites in the United States ("US") and Canada, and C-FORWARD which has clinical trial sites in countries outside of North America. In these Phase 3 trials we are comparing our regimen of bemnifosbuvir and ruzasvir to an active comparator, the regimen of sofosbuvir and velpatasvir, in patients with chronic HCV infection. We are conducting the Phase 3 program in geographically diverse regions in order to enroll patients with a broad array of HCV genotypes.

C-BEYOND is fully enrolled with over 880 patients, and we expect to report topline results mid-2026. We anticipate completing enrollment of an additional 880 patients in C-FORWARD in mid-2026 and reporting topline C-FORWARD results at year-end 2026. Pending successful results from these Phase 3 clinical trials, we are targeting submission to the US Food and Drug Administration ("FDA") of a New Drug Application ("NDA") for marketing approval in March 2027.

We are executing a focused chemistry, manufacturing and controls ("CMC") strategy to provide fixed dose combination ("FDC") tablets for the completion of the Phase 3 program, to fulfill NDA requirements and to prepare us for potential launch with sufficient commercial supply for projected initial sales if the regimen of bemnifosbuvir and ruzasvir is approved for marketing.

Given the large number of patients currently infected with HCV, which is reported by the US Center for Disease Control and Prevention to be as many as four million persons in the US, and the incidence of newly reported chronic infections continuing to outpace rates of treatment, we expect that a substantial global market will exist for the foreseeable future. In 2025, global net sales of branded HCV therapeutics known in the US as Epclusa® (including the authorized generic copy of Epclusa) and Mavyret® exceeded $2.5 billion with the US accounting for approximately 50% of these sales.

HEV - Our Goal and Our Program

We are developing AT-587 for the treatment of chronic HEV infection in immunocompromised patients. In this high-risk patient population, infection with HEV can rapidly progress to cirrhosis and other serious complications.

There are no DAAs currently available for the treatment of HEV. The most frequent interventions include reduction of immunosuppressive agents which, in solid organ transplant recipients, increases risk of transplant rejection, or off-label treatment with ribavirin which is indicated for treatment of other viruses but hindered by serious adverse events and limited HEV efficacy. The severity of disease in high-risk patients combined with the lack of approved HEV therapies is a substantial unmet medical need which we believe can be addressed if AT-587 is successfully developed.

AT-587 has demonstrated potent nanomolar antiviral activity against HEV in vitro. In single-dose in vivo nonclinical pharmacokinetic studies, high plasma concentrations of the surrogate to the active intracellular triphosphate metabolite were observed in all animal species tested. Results from in vitro toxicology, pharmacology and drug metabolism and pharmacokinetic studies indicate the potential for a favorable clinical profile for AT-587. Currently, we anticipate initiating clinical development of AT-587 with a first-in-human Phase 1 study in mid-2026.

Developing a treatment for HEV, particularly a product candidate derived from our proprietary platform, is a potentially important and advantageous strategic expansion of our antiviral pipeline. If both product candidates are successfully developed and approved, we will have a hepatology portfolio that we anticipate will improve upon the current SOC for HCV and introduce the first DAA for HEV.

Discovery efforts for other RNA virus infections

We have an extensive library of compounds that have been designed and generated by our medicinal chemists. Currently, we are evaluating select compounds derived from this library in in vitro and in vivo studies to assess the antiviral activity and other properties of such compounds against other RNA viral infections.

In all our discovery and preclinical efforts, we assess where there is a compelling market opportunity and then we aim to identify and advance only those candidates that we believe may have first- or best-in-class profiles with the potential to either become the SOC, or disrupt the existing SOC, and in each case, dramatically improve patient outcomes.

Financial Resources

We believe we are well capitalized to advance our current programs. We had $256.0 million in cash, cash equivalents and marketable securities at March 31, 2026.

We do not have any products approved for sale and have not generated any product revenue since inception. We do not anticipate generating any revenue from product sales for the foreseeable future. Our ability to generate product revenue will depend on the successful development, regulatory approval and eventual commercialization of one or more of our product candidates. Until such time as we can generate significant revenue from product sales, if ever, we expect to finance our operations through private or public equity or debt financings, collaborative or other arrangements with third parties, or through other sources of financing. Our failure to meet the primary efficacy endpoint of our COVID-19 SUNRISE-3 Phase 3 clinical trial may make such financing more difficult. Adequate funding may not be available to us on acceptable terms, or at all. If we fail to raise capital or enter into such agreements as and when needed, we may have to significantly delay, scale back or discontinue the development and commercialization of our product candidates.

We remain focused on identifying initiatives, investments and opportunities to maximize stockholder value.

In an effort to enhance efficiency in the management of infrastructure expenses, in the first quarter of 2025, we reduced our workforce by approximately 25%. This workforce reduction is expected to result in aggregate cost savings of approximately $15.0 million through 2027.

Additionally, in April 2025, our Board authorized a program to repurchase shares of our common stock ("Common Stock"). Under this authorization, we returned capital to our stockholders while maintaining the capacity to complete the Phase 3 clinical development of the regimen of bemnifosbuvir and ruzasvir and execute on our other strategic business plans. Under the share repurchase program, which was fully completed in 2025, we expended $25.5 million (including transaction costs and excise taxes) in connection with the repurchase of 7,673,792 shares of our Common Stock.

Expecting that the results of our HCV Phase 3 clinical development program, if successful, will drive stockholder value and catalyze business development discussions, in November 2025, we concluded the formal engagement to explore strategic partnerships which we previously entered into with Evercore LLC, a global independent investment bank. Currently, we expect to report topline results from our Phase 3 C-Beyond trial in mid-2026 and topline results from our Phase 3 C-Forward trial at year-end 2026. We remain open to consideration of strategic transactions and all other opportunities to drive stockholder value.

Merck License Agreement

In December 2021, we entered into a license agreement ("Merck License Agreement") with MSD International GmbH, an affiliate of Merck & Co., Inc. ("Merck") for the development, manufacture and commercialization of ruzasvir. Ruzasvir is the investigational NS5A inhibitor we are developing in combination with bemnifosbuvir for the treatment of HCV.

Pursuant to the terms of the Merck License Agreement, we obtained from Merck an exclusive (subject to certain reserved rights to conduct internal research), sublicensable, and worldwide license under certain Merck patents and know-how to research, develop, manufacture, have manufactured, use, import, export, sell, offer for sale, and otherwise commercialize ruzasvir or products containing ruzasvir (each a "Product") for all therapeutic or prophylactic uses in humans.

In addition to a non-refundable upfront payment that we made in February 2022, we agreed to pay Merck milestone payments upon our achievement of certain development, regulatory and sales-based milestones. Additionally, we will pay Merck tiered royalties based on annual net sales of Products ranging from high single digits to mid-teens percentages. Our royalty payment obligations will continue until the later of (i) the expiration of the last to expire valid claim of a licensed Merck patent claiming such Product and (ii) a period of years after the first commercial sale of such Product in such country. We may terminate the Merck License Agreement for convenience upon prior written notice. The first milestone in the amount of $5.0 million became due and payable in April 2025 when we enrolled our first patient in C-BEYOND, the Phase 3 clinical trial that we are currently conducting in the US and Canada evaluating the regimen of bemnifosbuvir and ruzasvir for the treatment of HCV. The Company recognized this milestone payment as research and development expense in the three months ended June 30, 2025. The next potential milestone, in the amount of $10.0 million, is payable upon acceptance by the FDA of a new drug application covering a product candidate including ruzasvir. If we successfully complete the ongoing HCV Phase 3 clinical trials evaluating the regimen of bemnifosbuvir and ruzasvir and are able to complete and submit the NDA to the FDA on our current projected timeline, we anticipate that this next potential milestone may become due and payable during the three months ended June 30, 2027.

Financial Operations Overview

As of March 31, 2026, we had cash and investments of $256.0 million. Net cash used in operating activities was $46.4 million for the three months ended March 31, 2026.

Based on our current plans, we anticipate our existing financial resources will allow us to advance our current and planned clinical programs to and through key inflection points, prepare and submit an application for marketing approval of the regimen of bemnifosbuvir and ruzasvir, engage in pre-launch activities including the manufacture of the regimen of bemnifosbuvir and ruzasvir in commercial quantities sufficient to meet our initial sales projections and advance to late-stage clinical development of AT-587 for the treatment of HEV.

We expect that our net cash used in operating activities will remain significant as we complete the clinical development of the regimen of bemnifosbuvir and ruzasvir for the treatment of HCV, seek regulatory approval, manufacture such product at commercial scale and prepare for and, if approved, pursue commercialization activities; advance AT-587, our HEV product candidate through preclinical and clinical development; acquire, discover, validate and develop additional product candidates; obtain, maintain, protect and enforce our intellectual property portfolio; and, if necessary, hire additional personnel. In addition, we may incur additional costs as we continue to operate as a public company. We believe that our available cash, cash equivalents and marketable securities will be sufficient to fund our planned operations through 2027. We have based this estimate on assumptions that may prove to be wrong and we could exhaust our available capital resources sooner than we expect.

We do not have any products approved for sale and have not generated any product revenue since inception. We do not anticipate generating any revenue from product sales for the foreseeable future. Our ability to generate product revenue will depend on the successful development, regulatory approval and eventual commercialization of one or more of our product candidates. Until such time as we can generate significant revenue from product

sales, if ever, we expect to finance our operations through private or public equity or debt financings, collaborative or other arrangements with third parties, or through other sources of financing. Adequate funding may not be available to us on acceptable terms, or at all. If we fail to raise capital or enter into such agreements as and when needed, we may have to significantly delay, scale back or discontinue the development and commercialization of our product candidates.

We plan to continue to use third-party service providers, including clinical research organizations ("CROs") to carry out our preclinical and clinical development, and contract manufacturing organizations ("CMOs") to manufacture and supply the materials used during the development of our product candidates. Additionally, we expect to rely on CMOs for the manufacture of commercial supply of any product candidate we may successfully develop.

As we continue to advance our programs, we expect to incur significant expenses over the next several years, as we:

Components of Results of Operations

Revenue

We do not have any products approved for sale and we have not generated any revenue in the periods presented.

If our product candidate development efforts are successful and result in commercialization, we may generate revenue in the future from product sales. Additionally, we may generate revenue from collaboration or license agreements that we may enter into with third parties.

Operating Expenses

Research and Development Expenses

Substantially all of our research and development expenses consist of expenses incurred in connection with the discovery and development of our product candidates. These expenses include external costs consisting of fees paid to third parties, including CROs and CMOs, to conduct certain research and development activities on our behalf and consulting costs, as well as internal costs consisting of payroll and personnel-related expenses, including salaries and bonuses, employee benefit costs and stock-based compensation expenses for our research and development employees and allocated overhead, including rent, equipment, depreciation, information technology costs and utilities attributable to our research and development personnel. We expense both internal and external research and development expenses as they are incurred. In circumstances where amounts have been paid in advance or in excess of costs incurred, we record a prepaid expense, which is expensed as services are performed or goods are delivered.

A significant portion of our research and development costs have been external costs, which we track by therapeutic area. We have not historically tracked our internal research and development expenses by therapeutic area as they are deployed across multiple programs.

The following table summarizes our external research and development expenses by indication and internal research and development expenses:

Substantially all of our resources are focused on the development of our product candidates. We expect our research and development expenses to vary quarter over quarter particularly as we complete our Phase 3 HCV clinical program, manufacture commercial launch supply for the possible commercialization of the regimen of bemnifosbuvir and ruzasvir and advance AT-587 for the treatment of HEV. Predicting the timing or cost to complete our clinical programs, validate our commercial manufacturing and supply processes and manufacture of product at commercial scale is difficult and delays may occur because of many factors, including factors outside of our control. For example, if the FDA or other regulatory authorities were to require us to conduct clinical trials beyond those that we currently anticipate or the time to complete planned clinical trials is extended due to delays in enrollment or otherwise, we could be required to expend significant additional financial resources and time on the completion of clinical development. Furthermore, we are unable to predict with any certainty when our HCV and HEV product candidates or any other product candidate we may develop will, if ever, receive regulatory approval.

Early stage discovery activities include assessing the antiviral activity, pharmacokinetics, toxicity and other properties of select compounds derived from our nucleos(t)ide library in an effort to identify promising potential product candidates for the treatment of RNA viral infections for which there is no currently approved DAA or for which we believe the current SOC can be improved to address unmet medical needs.

General and Administrative Expenses

General and administrative expenses consist principally of payroll and personnel expenses, including salaries and bonuses, benefits and stock-based compensation expenses, professional fees for legal, consulting, accounting and tax services, business insurance, allocated overhead, including rent, equipment, depreciation, information technology costs and utilities, and other general operating expenses not otherwise classified as research and development expenses.

We anticipate that our general and administrative expenses may increase, including in connection with any future expansion of our organization for potential commercialization of our product candidates, as a result of increased personnel costs, expanded infrastructure, increased consulting, legal and accounting services, costs associated with complying with Nasdaq and SEC requirements and increased investor relations costs.

Interest Income and Other, Net

Interest income and other, net, consists primarily of interest income earned on our cash and investments.

Income Taxes

Income taxes consists primarily of federal and state current income taxes.

Results of Operations

Comparison of the Three Months Ended March 31, 2026 and 2025

The following table summarizes our results of operations for the periods indicated:

Research and Development Expenses

Research and development expenses increased by $11.6 million from $29.6 million for the three months ended March 31, 2025 to $41.1 million for the three months ended March 31, 2026. The net increase was primarily driven by an increase in external spend for our HCV Phase 3 clinical development and HEV preclinical development activities. The increase was partially offset by lower internal research and development expenses primarily related to lower salaries and wages and lower stock-based compensation expense in the three months ended March 31, 2026.

General and Administrative Expenses

General and administrative expenses decreased by $2.6 million from $9.5 million for the three months ended March 31, 2025 to $6.9 million for the three months ended March 31, 2026. The net decrease was primarily related to lower salaries and wages, lower stock-based compensation expense and lower professional fees.

Interest Income and Other, Net

Interest income and other, net, decreased by $2.4 million for the three months ended March 31, 2026 compared to the three months ended March 31, 2025, primarily due to lower investment balances.

Income Taxes

Income tax expense was $0.1 and $0.2 million for the three months ended March 31, 2026 and 2025, respectively.

Liquidity and Capital Resources

Sources of Liquidity

As of March 31, 2026, we had cash, cash equivalents and marketable securities of $256.0 million. We believe that our available cash and investments will be sufficient to fund our planned operations through 2027 including the completion of the Phase 3 program evaluating the regimen of bemnifosbuvir and ruzasvir for the treatment of HCV. We have based this estimate on assumptions that may prove to be wrong and we could exhaust our available capital resources sooner than we expect.

We are party to an amended and restated open market sales agreement ("Sales Agreement") with Jefferies LLC ("Jefferies"), pursuant to which we may from time to time offer and sell shares of our Common Stock for an aggregate offering price of up to $200.0 million, through or to Jefferies, acting as sales agent or principal. We have agreed to pay Jefferies a commission of up to 3.0% of the aggregate gross proceeds from each sale of shares, reimburse legal fees and disbursements and provide Jefferies with customary indemnification and contribution rights. As of March 31, 2026, no shares have been issued under the Sales Agreement. The shares

will be offered and sold under the Company's shelf registration statement on Form S-3 declared effective by the SEC on November 19, 2024.

Future Funding Requirements

To date, we have not generated any product revenue. We do not expect to generate any product revenue unless and until we obtain regulatory approval of and commercialize any of our product candidates and we do not know when, or if, this will occur. We expect to continue to incur significant expenditures for the foreseeable future as we continue the development of, and seek regulatory approvals for, our product candidates, and prepare for and begin to commercialize any approved products. We are subject to all of the risks typically related to the development of new product candidates, and we may encounter unforeseen expenses, difficulties, complications, delays and other unknown factors that may adversely affect our business. Moreover, we expect to incur additional general and administrative costs, including selling costs, as we continue to operate as a public company and potentially expand our organization to support and otherwise initiate additional activities in preparation for potential commercialization of the regimen of bemnifosbuvir and ruzasvir.

We will continue to invest significant capital to develop our product candidates and fund operations for the foreseeable future. To fund such investment, we may seek to raise capital through public or private equity or debt financings, collaborative arrangements with third parties, or through other sources of financing. We anticipate that we may need to raise substantial additional capital, the requirements for which will depend on many factors, including:

A change in the outcome of any of these or other variables with respect to any of our product candidates could significantly change the costs and timing associated with the development or potential commercialization of one or more of our product candidates. Furthermore, our operating plans may change in the future, and we will continue to require additional capital to meet operational needs and capital requirements associated with such operating plans. If we raise additional funds by issuing equity securities, our stockholders may experience dilution. Any future debt financing that we enter into may impose upon us additional covenants that restrict our operations, including limitations on our ability to incur liens or additional debt, pay dividends, repurchase our Common Stock, make certain investments or engage in certain merger, consolidation or asset sale transactions. Any debt financing or additional equity that we raise may contain terms that are not favorable to us or our stockholders.

Adequate funding may not be available to us on acceptable terms or at all. Our failure to raise capital as and when needed could have a negative impact on our financial condition and our ability to pursue our business strategies. If we are unable to raise additional funds when needed, we may be required to delay, reduce, or terminate some or all of our development programs, clinical trials and commercialization activities or we may also be required to sell or license to others rights to our product candidates in certain territories or indications that we would prefer to develop and commercialize ourselves. If we are required to enter into collaborations and other arrangements to supplement our funds, we may have to give up certain rights that limit our ability to develop and commercialize our product candidates or may have other terms that are not favorable to us or our stockholders, which could materially affect our business and financial condition.

Market volatility, inflation, interest rate fluctuations and other macroeconomic trends and geopolitical events, including civil or political unrest and terrorism, may have a significant impact on the availability of funding sources and the terms on which any funding may be available.

See Part II, Item 1A,"Risk Factors" for additional risks associated with our substantial capital requirements.

Summary Statements of Cash Flows

The following table sets forth the primary sources and uses of cash and cash equivalents for each of the periods presented below:

Cash Flows from Operating Activities

Net cash used in operating activities for the three months ended March 31, 2026 was $46.4 million. Cash used in operating activities was primarily due to a net loss of $45.4 million, accretion of premium and discounts on marketable securities of $0.6 million, a decrease in accounts payable and accrued expenses and other liabilities of $6.2 million, partially offset by stock-based compensation expense of $3.7 million and a decrease in prepaid expenses and other assets of $2.0 million.

Net cash used in operating activities for the three months ended March 31, 2025 was $30.6 million. Cash used in operating activities was primarily due to a net loss of $34.3 million, accretion of premium and discounts on marketable securities of $1.7 million, and an increase in other assets of $4.2 million, partially offset by stock-based compensation expense of $7.0 million and an increase in accounts payable and accrued expenses of $3.3 million.

Cash Flows from Investing Activities

Net cash provided by investing activities for the three months ended March 31, 2026 was $29.7 million and consisted of sales and maturities of marketable securities of $104.3 million partially offset by purchases of marketable securities of $74.5 million.

Net cash provided by investing activities for the three months ended March 31, 2025 was $85.6 million and consisted of sales and maturities of marketable securities of $208.2 million partially offset by purchases of marketable securities of $122.6 million.

Cash Flows from Financing Activities

Net cash provided by financing activities for the three months ended March 31, 2026 was $0.3 million and consisted of $0.9 million in proceeds from the exercise of stock options and $0.1 million in proceeds from the issuance of our Common Stock under our employee stock purchase plan offset by $0.7 million used in connection with the net settlement of vested restricted stock units.

Net cash used in financing activities for the three months ended March 31, 2025 was $0.3 million and consisted of $0.4 million related to the net settlement of vested restricted stock units partially offset by proceeds of $0.1 million from the sale of our Common Stock under our employee stock purchase plan.

Contractual Obligations and Commitments

There have been no material changes to our contractual obligations during the three months ended March 31, 2026 from those previously disclosed in our Annual Report on Form 10-K for the year ended December 31, 2025.

We enter into contracts in the normal course of business with CROs for preclinical and clinical studies and testing, CMOs for manufacture and supply of our clinical trial materials and other third parties for other services and products used for operating purposes. These contracts do not contain any minimum purchase commitments and generally provide for termination following a certain period after notice, and therefore we believe that our non-cancelable obligations under these agreements are not material. Payments due upon cancelation principally consist only of payments for services provided and expenses incurred up to the date of cancelation.

Critical Accounting Policies and Estimates

Our financial statements have been prepared in accordance with US generally accepted accounting principles ("GAAP"). The preparation of these financial statements requires us to make estimates and assumptions that affect the reported amounts of assets and liabilities, the disclosure of contingent assets and liabilities at the date of the financial statements and the reported expenses incurred during the reporting periods. Our estimates are based on our historical experience and on various other factors that we believe are reasonable under the circumstances, the results of which form the basis for making judgments about the carrying value of assets and liabilities that are not readily apparent from other sources. Actual results may differ from these estimates. The effects of material revisions in estimates, if any, will be reflected in the consolidated financial statements prospectively from the date of change in estimates.

Our critical accounting policies are those policies that require the most significant judgments and estimates in the preparation of the financial statements. Management has determined that our most critical accounting policies are those relating to revenue recognition, accrued research and development expenses and stock-based compensation.

Indemnification Agreements

We enter into standard indemnification arrangements in the ordinary course of business. Pursuant to these arrangements, we indemnify, hold harmless and agree to reimburse the indemnified parties for losses suffered or incurred by the indemnified party, including in connection with any trade secret, copyright, patent or other intellectual property infringement claim by any third party with respect to its technology. The term of these indemnification agreements is generally perpetual any time after the execution of the agreement. The maximum potential amount of future payments we could be required to make under these arrangements is not determinable. We have never incurred costs to defend lawsuits or settle claims related to these indemnification agreements. As a result, we believe the fair value of these agreements is minimal.

We have also agreed to indemnify our directors and officers for certain events or occurrences while the director or officer is, or was serving, at our request in such capacity. The indemnification period covers all pertinent events and occurrences during the director's or officer's service. The maximum potential amount of future payments we could be required to make under these indemnification agreements is not specified in the agreements; however, we have director and officer insurance coverage that is intended to reduce our exposure and enable us to recover a portion of any future amounts paid. We believe the estimated fair value of these indemnification agreements in excess of applicable insurance coverage is minimal.