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UNITED STATES

SECURITIES AND EXCHANGE COMMISSION

WASHINGTON, DC 20549

FORM 10-Q

(Mark One)


☒	QUARTERLY REPORT PURSUANT TO SECTION 13 OR 15(d) OF THE SECURITIES EXCHANGE ACT OF 1934

For the quarterly period ended June 30, 2025


☐	TRANSITION REPORT PURSUANT TO SECTION 13 OR 15(d) OF THE SECURITIES EXCHANGE ACT OF 1934

For the transition period from _______________ to _______________

Commission File Number: 001-39661

Atea Pharmaceuticals, Inc.

(Exact Name of Registrant as Specified in its Charter)


Delaware	46-0574869
(State or other jurisdiction of incorporation or organization)	(I.R.S. Employer Identification No.)
225 Franklin Street, Suite 2100 Boston, MA	02110
(Address of principal executive offices)	(Zip Code)

(857) 284-8891

(Registrant’s telephone number, including area code)

(Former name, former address and former fiscal year, if changed since last report)

Securities registered pursuant to Section 12(b) of the Act:

     Title of each class

     Trading
Symbol(s)

     Name of each exchange on which registered

     Common Stock, $0.001 par value per share

     AVIR

     The Nasdaq Global Select Market

Indicate by check mark whether the registrant (1) has filed all reports required to be filed by Section 13 or 15(d) of the Securities Exchange Act of 1934 during the preceding 12 months (or for such shorter period that the registrant was required to file such reports), and (2) has been subject to such filing requirements for the past 90 days. Yes ☒ No ☐

Indicate by check mark whether the registrant has submitted electronically every Interactive Data File required to be submitted pursuant to Rule 405 of Regulation S-T (§232.405 of this chapter) during the preceding 12 months (or for such shorter period that the registrant was required to submit such files). Yes ☒ No ☐

Indicate by check mark whether the registrant is a large accelerated filer, an accelerated filer, a non-accelerated filer, a smaller reporting company, or an emerging growth company. See the definitions of “large accelerated filer,” “accelerated filer,” “smaller reporting company,” and “emerging growth company” in Rule 12b-2 of the Exchange Act.

If an emerging growth company, indicate by check mark if the registrant has elected not to use the extended transition period for complying with any new or revised financial accounting standards provided pursuant to Section 13(a) of the Exchange Act. ☐

Indicate by check mark whether the registrant is a shell company (as defined in Rule 12b-2 of the Exchange Act). Yes ☐ No ☒

As of August 4, 2025, the registrant had 79,357,553 shares of common stock, $0.001 par value per share, outstanding.

SPECIAL NOTE REGARDING FORWARD-LOOKING STATEMENTS

This Quarterly Report on Form 10-Q contains forward-looking statements. We make such forward-looking statements pursuant to the safe harbor provisions of the Private Securities Litigation Reform Act of 1995 and other federal securities laws. 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 development timelines and results and other future conditions. The words “aim,” “anticipate,” “believe,” “contemplate,” “continue,” “could,” “estimate,” “expect,” “goal,” “intend,” “may,” "objective," "on track," “plan,” “possible,” “potential,” “predict,” “project,” “seek,” “should,” “target,” “will,” “would” or the negative of these terms or other similar expressions are intended to identify forward-looking statements, although not all forward-looking statements contain these identifying words.

These forward-looking statements include, among other things, statements about:

•

our expectations relating to clinical trials for our hepatitis C virus (“HCV”) product candidate and other potential product candidates, including projected costs, study designs and the timing for initiation, recruitment, completion, and reporting interim, top-line and final data;

•

the potential therapeutic benefit of our HCV product candidate and market opportunities therefor;

•

the safety profile and related adverse events of our HCV product candidate;

•

our plans to research, develop and commercialize our current and future product candidates;

•

the potential benefits of any future collaboration we may enter into;

•

the timing of and our ability to apply for, and if successful, obtain and maintain regulatory approvals for our product candidates;

•

the rate and degree of market acceptance and clinical utility of any products for which we may receive marketing approval;

•

our manufacturing and commercialization capabilities and strategy;

•

our estimates regarding future revenue, expenses and results of operations;

•

the progress of, timing of and amount of expenses associated with our research, development and commercialization activities;

•

our future financial position, capital requirements, cash runway, needs for additional financing and the availability of such financing;

•

our business strategy;

•

developments relating to our industry and our competitors, including competing HCV treatments;

•

our expectations regarding federal, state and foreign laws and regulations;

•

our share repurchase program; and

•

our ability to attract, motivate, and retain key personnel.

These forward-looking statements are based on management’s current expectations, estimates, forecasts and projections about our business and the industry in which we operate. 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 future results, performance or achievements expressed or implied by the forward-looking statements. Factors that may cause actual results to differ materially from current expectations include the initiation, execution and completion of clinical trials, uncertainties surrounding the timing of availability of data from our clinical trials, ongoing discussions with and actions by regulatory authorities, our development activities and those other factors we discuss in Part II, Item 1A. “Risk Factors” in this Quarterly Report on Form 10-Q. You should read these risk factors and the other cautionary statements made in this report as being applicable to all related forward-looking statements wherever they appear in this report. The risk factors are not exhaustive and other sections of this report may include additional factors which could adversely impact our business and financial performance.

Drug development and commercialization involve a high degree of risk, and only a small number of research and development programs result in commercialization of a product. Preliminary and interim results from any trial and results in early-stage clinical trials may not be indicative of full results or results from later stage or larger scale clinical trials and do not ensure regulatory approval. Moreover, we operate in a very competitive and rapidly changing environment. New risk factors emerge from time to time, and it is not possible for our management to predict all risk factors nor can we assess the impact of all factors on our business or the extent to which any factor, or combination of factors, may cause actual results to differ materially from those contained in, or implied by, any forward-looking statements.

Given these uncertainties, you should not rely on these forward-looking statements as predictions of future events. Except as required by law, we assume no obligation to update or revise these forward-looking statements for any reason, even if new information becomes available in the future.

As used in this Quarterly Report on Form 10-Q, unless otherwise specified or the context otherwise requires, the terms “we,” “our,” “us,” and the “Company” refer to Atea Pharmaceuticals, Inc. and its subsidiary. All brand names or trademarks appearing in this Quarterly Report on Form 10-Q are the property of their respective owners.

SUMMARY RISK FACTORS

Our business is subject to numerous risks and uncertainties, including those described in Part II, Item 1A. “Risk Factors” in this Quarterly Report on Form 10-Q. The principal risks and uncertainties affecting our business include the following:

•

We have a limited operating history and no history of successfully developing or commercializing any approved antiviral products, which may make it difficult to evaluate the success of our business to date and to assess the prospects for our future viability.

•

We have incurred significant operating expenses since inception. We expect our expenditures will increase for the foreseeable future. We have no products that have generated any commercial revenue and we may not again achieve or maintain profitability.

•

We may require substantial additional financing, which may not be available on acceptable terms, or at all. A failure to obtain this necessary capital when needed could force us to delay, limit, reduce or terminate our product development or commercialization efforts.

•

We may engage in strategic collaborations or other transactions that could disrupt our business, cause dilution to our stockholders, reduce our financial resources, and subject us to other risks.

•

Our ability to use our net operating loss carryforwards and other tax attributes to offset taxable income may be subject to certain limitations.

•

Our business is highly dependent on the success of our product candidate, the regimen of bemnifosbuvir and ruzasvir for the treatment of HCV infection. If we fail to successfully develop this product candidate or we are unable to obtain regulatory approval or successfully commercialize this or any other product candidates, or are significantly delayed in doing so, our business will be harmed.

•

The regulatory approval processes of the U.S. Food and Drug Administration (“FDA”) and comparable foreign regulatory authorities are lengthy, expensive, time-consuming and inherently unpredictable.

•

Clinical development, including enrollment of patients in clinical trials, is an expensive, lengthy and uncertain process. We may encounter substantial delays and costs in our clinical trials, or may not be able to conduct or complete our clinical trials on the timelines we expect, if at all.

•

We intend to develop certain of our product candidates in combination with other product candidates that we discover or acquire, which exposes us to additional risks.

•

Our product candidates may be associated with serious adverse events, undesirable side effects or have other properties that could halt their clinical development, prevent their regulatory approval, limit their commercial potential or result in significant negative consequences.

•

We currently conduct and may in the future conduct clinical trials of our product candidates in sites outside the United States (“US”). The FDA may not accept data from trials conducted in foreign locations.

•

Interim, topline and preliminary data from our clinical trials that we announce or publish from time to time may change as more data become available and are subject to audit and verification procedures that could result in material changes in the final data.

•

We may not be successful in our efforts to identify and successfully develop additional product candidates.

•

Risks related to healthcare laws and other legal compliance matters may materially and adversely affect our business and financial results.

•

Risks related to commercialization may materially and adversely affect our business and financial results.

•

Risks related to manufacturing and our dependence on third parties may materially and adversely affect our business and financial results.

•

Risks related to intellectual property may materially and adversely affect our business and financial results.

•

We are highly dependent on our management, directors and other key personnel.

iii

•

Our future success depends on our ability to retain officers, directors and key employee and to attract, retain and motivate qualified personnel.

•

Our business and operations may suffer in the event of system failures, security breaches, deficiencies or intrusions which could materially affect our results.

•

We or the third parties whom we depend upon may be adversely affected by natural disasters or other unforeseen events resulting in business interruptions and our business continuity and disaster recovery plans may not adequately protect us from such business interruptions.

•

Increased scrutiny of, and evolving expectations for, environmental, social, and governance initiatives could increase our costs, harm our reputation, or otherwise adversely impact our business and financial results.

•

Litigation against us could be costly and time-consuming to defend and could result in additional liabilities.

•

Unstable market and economic conditions may have serious adverse consequences on our business, financial condition and stock price.

•

Risks related to our common stock may materially and adversely affect our stock price.

•

If we fail to maintain effective internal control over financial reporting and effective disclosure controls and procedures, we may not be able to accurately report our financial results in a timely manner or prevent fraud, which may adversely affect investor confidence in our company.

Table of Contents


		Page
SPECIAL NOTE REGARDING FORWARD-LOOKING STATEMENTS		i
SUMMARY RISK FACTORS		iii

PART I.	FINANCIAL INFORMATION	1
Item 1.	Financial Statements (Unaudited)	1
	Condensed Consolidated Balance Sheets	1
	Condensed Consolidated Statements of Operations and Comprehensive Loss	2
	Condensed Consolidated Statements of Stockholders’ Equity	3
	Condensed Consolidated Statements of Cash Flows	4
	Notes to Condensed Consolidated Financial Statements	5
Item 2.	Management’s Discussion and Analysis of Financial Condition and Results of Operations	15
Item 3.	Quantitative and Qualitative Disclosures About Market Risk	26
Item 4.	Controls and Procedures	26

PART II.	OTHER INFORMATION	27
Item 1.	Legal Proceedings	27
Item 1A.	Risk Factors	27
Item 2.	Unregistered Sales of Equity Securities and Use of Proceeds	85
Item 5.	Other Information	86
Item 6.	Exhibits	87
SIGNATURES		88

PART I—FINANCIAL INFORMATION

Item 1. Financial Statements.

Atea Pharmaceuticals, Inc.

Condensed Consolidated Balance Sheets

(in thousands, except share and per share amounts)

(Unaudited)


	June 30, 2025			December 31, 2024
Assets
Current assets
Cash and cash equivalents	$	87,721		$	64,696
Marketable securities		291,992			390,025
Prepaid expenses and other current assets		5,891			7,634
Total current assets		385,604			462,355
Property and equipment, net		665			873
Other assets		4,394			197
Operating lease right-of-use assets, net		942			1,243
Total assets	$	391,605		$	464,668
Liabilities and Stockholders’ Equity
Current liabilities
Accounts payable	$	8,844		$	4,458
Accrued expenses and other current liabilities		10,454			13,345
Current portion of operating lease liabilities		821			800
Total current liabilities		20,119			18,603
Operating lease liabilities		425			842
Income taxes payable		6,645			6,356
Total liabilities		27,189			25,801
Commitments and contingencies (see Note 11)
Stockholders’ equity:
Preferred stock, $0.001 par value per share; 10,000,000 shares authorized; no shares issued and outstanding		—			—
Common stock, $0.001 par value; 300,000,000 shares authorized; 81,137,478 and 84,463,059 shares issued and outstanding as of June 30, 2025 and December 31, 2024, respectively		81			84
Additional paid-in capital		799,951			802,770
Accumulated other comprehensive gain		37			233
Accumulated deficit		(435,653	)		(364,220	)
Total stockholders’ equity		364,416			438,867
Total liabilities and stockholders’ equity	$	391,605		$	464,668

The accompanying notes are an integral part of these unaudited condensed consolidated financial statements.

Atea Pharmaceuticals, Inc.

Condensed Consolidated Statements of Operations and Comprehensive Loss

(in thousands, except share and per share amounts)

(Unaudited)


	Three Months Ended June 30,						Six Months Ended June 30,
	2025			2024			2025			2024
Operating expenses
Research and development	$	32,275		$	34,696		$	61,859		$	92,271
General and administrative		9,070			12,220			18,527			24,451
Total operating expenses		41,345			46,916			80,386			116,722
Loss from operations		(41,345	)		(46,916	)		(80,386	)		(116,722	)
Interest income and other, net		4,391			6,637			9,363			13,505
Loss before income taxes		(36,954	)		(40,279	)		(71,023	)		(103,217	)
Income tax expense		(207	)		(243	)		(410	)		(474	)
Net loss	$	(37,161	)	$	(40,522	)	$	(71,433	)	$	(103,691	)
Other comprehensive loss
Unrealized loss on available-for-sale investments		(81	)		(99	)		(196	)		(487	)
Comprehensive loss	$	(37,242	)	$	(40,621	)	$	(71,629	)	$	(104,178	)
Net loss per share — basic and diluted	$	(0.44	)	$	(0.48	)	$	(0.85	)	$	(1.23	)
Weighted-average number of common shares — basic and diluted		83,747,335			84,253,700			84,449,318			84,069,646

The accompanying notes are an integral part of these unaudited condensed consolidated financial statements.

Atea Pharmaceuticals, Inc.

Condensed Consolidated Statements of Stockholders’ Equity

(in thousands, except share amounts)

(Unaudited)


	Common Stock						Additional			Accumulated Other			Accumulated			Total
	Shares			Amount			Paid-in Capital			Comprehensive Gain (Loss)			Deficit			Stockholders' Equity
Balance—January 1, 2025		84,463,059		$	84		$	802,770		$	233		$	(364,220	)	$	438,867
Issuance of common stock upon vesting of restricted stock units, net of employee tax obligations		1,062,120			1			(486	)		—			—			(485	)
Issuance of common stock under employee stock purchase plan		54,296			—			138			—			—			138
Stock-based compensation expense		—			—			6,951			—			—			6,951
Other comprehensive income (loss)		—			—			—			(115	)		—			(115	)
Net loss		—			—			—			—			(34,272	)		(34,272	)
Balance—March 31, 2025		85,579,475			85			809,373			118			(398,492	)		411,084
Issuance of common stock upon vesting of restricted stock units		177,600			1			(1	)		—			—			—
Repurchase of common stock		(4,619,597	)		(5	)		(14,088	)		—			—			(14,093	)
Stock-based compensation expense		—			—			4,667			—			—			4,667
Other comprehensive income (loss)		—			—			—			(81	)		—			(81	)
Net loss		—			—			—			—			(37,161	)		(37,161	)
Balance—June 30, 2025		81,137,478		$	81		$	799,951		$	37		$	(435,653	)	$	364,416


	Common Stock				Additional			Accumulated Other			Accumulated			Total
	Shares		Amount		Paid-in Capital			Comprehensive Gain (Loss)			Deficit			Stockholders' Equity
Balance—January 1, 2024		83,435,513	$	83	$	750,737		$	207		$	(195,835	)	$	555,192
Issuance of common stock upon vesting of restricted stock units		729,032		1		(1	)		—			—			—
Issuance of common stock under employee stock purchase plan		58,555		—		150			—			—			150
Stock-based compensation expense		—		—		12,586			—			—			12,586
Other comprehensive income (loss)		—		—		—			(388	)		—			(388	)
Net loss		—		—		—			—			(63,169	)		(63,169	)
Balance—March 31, 2024		84,223,100		84		763,472			(181	)		(259,004	)		504,371
Issuance of common stock upon vesting of restricted stock units		198,900		—		—			—			—			—
Stock-based compensation expense		—		—		12,720			—			—			12,720
Other comprehensive income (loss)		—		—		—			(99	)		—			(99	)
Net loss		—		—		—			—			(40,522	)		(40,522	)
Balance—June 30, 2024		84,422,000	$	84	$	776,192		$	(280	)	$	(299,526	)	$	476,470

The accompanying notes are an integral part of these unaudited condensed consolidated financial statements.

Atea Pharmaceuticals, Inc.

Condensed Consolidated Statements of Cash Flows

(in thousands)

(Unaudited)


	Six Months Ended June 30,
	2025			2024
Cash flows from operating activities
Net loss	$	(71,433	)	$	(103,691	)
Adjustments to reconcile net loss to net cash used in operating activities:
Stock-based compensation expense		11,618			25,306
Depreciation and amortization expense		208			208
Accretion of premium and discounts on marketable securities		(3,061	)		(6,512	)
Changes in operating assets and liabilities:
Prepaid expenses and other current assets		1,743			8,194
Other assets		(4,197	)		—
Accounts payable		4,386			1,218
Accrued expenses and other liabilities		(2,602	)		(6,703	)
Operating lease liabilities		(95	)		(87	)
Net cash used in operating activities		(63,433	)		(82,067	)
Cash flows from investing activities
Purchases of marketable securities		(223,368	)		(174,460	)
Sales and maturities of marketable securities		324,266			355,948
Net cash provided by investing activities		100,898			181,488
Cash flows from financing activities
Proceeds from issuance of common stock under ESPP		138			150
Repurchase of common stock		(14,093	)		—
Issuance of restricted stock units		(485	)		—
Net cash (used in) provided by financing activities		(14,440	)		150
Net increase in cash and cash equivalents		23,025			99,571
Cash and cash equivalents at the beginning of period		64,696			143,823
Cash and cash equivalents at the end of period	$	87,721		$	243,394

The accompanying notes are an integral part of these unaudited condensed consolidated financial statements.

Atea Pharmaceuticals, Inc.

Notes to Condensed Consolidated Financial Statements

(in thousands, except share and per share amounts)

(Unaudited)

1. Nature of Business

Business Overview

Atea Pharmaceuticals, Inc., together with its wholly owned subsidiary, Atea Pharmaceuticals Securities Corporation, is referred to herein on a consolidated basis as “Atea” or the “Company”.

The Company is a clinical-stage biopharmaceutical company focused on discovering, developing and commercializing oral antiviral therapeutics to improve the lives of patients suffering from serious viral infections. The Company’s lead product candidate, the regimen of bemnifosbuvir, a nucleotide NS5B inhibitor, and ruzasvir, an NS5A inhibitor is being developed for the treatment of hepatitis C virus (“HCV”). In April 2025, the Company commenced enrollment of patients in the HCV Phase 3 program evaluating the regimen.

Liquidity and Capital Resources

As of June 30, 2025, the Company had $379.7 million in cash, cash equivalents and marketable securities, which the Company believes will be sufficient to fund the share repurchase program discussed in Note 6 and its operations for a period through at least twelve months from the issuance date of these consolidated financial statements.

The Company is a party to an amended and restated open market sales agreement (“Sales Agreement”) with Jefferies LLC (“Jefferies”), under which the Company may from time to time offer and sell shares of its common stock (“Common Stock”) for an aggregate offering price of up to $200.0 million, through or to Jefferies, acting as sales agent or principal. The shares will be offered and sold under the Company’s shelf registration statement on Form S-3 and a related prospectus declared effective by the Securities and Exchange Commission (the “SEC”) on November 19, 2024. The Company has agreed to pay Jefferies a commission of 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 June 30, 2025, no shares have been issued under the Sales Agreement.

Risks and Uncertainties

The Company is subject to risks and uncertainties common to clinical-stage biopharmaceutical companies. These risks include, but are not limited to, potential failure of preclinical and clinical studies, uncertainties associated with research and development activities generally, competition from technical innovations of others, dependence upon key personnel, compliance with governmental regulations, the need to obtain marketing approval for any product candidate that the Company may develop, the need to gain broad acceptance among patients, payers and health care providers to successfully commercialize any product for which marketing approval is obtained and the need to secure and maintain adequate intellectual property protection for the Company’s proprietary technology and products. Further, the Company is currently dependent on third-party service providers for much of its preclinical research, clinical development and manufacturing activities. Product candidates currently under development, including most notably the regimen of bemnifosbuvir and ruzasvir for the treatment of HCV, will require significant amounts of additional capital and additional research and development efforts, and all will require regulatory approval, prior to commercialization. Even if the Company is able to generate revenues from the sale of its product candidates, if any are approved and commercialized, it may not become profitable. If the Company fails to become profitable or is unable to sustain profitability on a continuing basis, then it may be unable to continue its operations at planned levels and be forced to reduce its operations.

The Company may seek additional capital through one or more of a combination of financing through the sale of additional equity securities, debt financing, or funding in connection with any new collaborative relationships it may enter into or other arrangements. There can be no assurance that the Company will be able to obtain such additional funding, on terms acceptable to the Company, on a timely basis or at all. The terms of any financing may adversely affect the holdings or the rights of the Company’s existing stockholders. The Company’s cost of financing and its access to potential sources of future liquidity may be adversely impacted by a number of factors,

including, without limitation, then current geopolitical events and the conditions in the financial markets including market volatility and rates of interest and inflation.

2. Summary of Significant Accounting Policies

Basis of Presentation and Use of Estimates

The unaudited interim condensed consolidated financial statements of the Company included herein have been prepared in accordance with accounting principles generally accepted in the United States (“GAAP”) as found in the Accounting Standards Codification (“ASC”), Accounting Standards Update (“ASU”) of the Financial Accounting Standards Board (“FASB”) and the rules and regulations of the SEC. Certain information and footnote disclosures normally included in financial statements prepared in accordance with GAAP have been condensed or omitted from this report, as is permitted by such SEC rules and regulations. Accordingly, these unaudited condensed consolidated financial statements should be read in conjunction with the Company’s audited consolidated financial statements and the notes thereto for the year ended December 31, 2024 included in the Company’s Annual Report on Form 10-K filed with the SEC on March 6, 2025.

Unaudited Interim Financial Information

The accompanying condensed consolidated balance sheet as of June 30, 2025, the condensed consolidated statements of operations and comprehensive loss for the three and six months ended June 30, 2025 and 2024, the condensed consolidated statements of stockholders’ equity for the three and six months ended June 30, 2025 and 2024, and the condensed consolidated statements of cash flows for the six months ended June 30, 2025 and 2024 are unaudited. The unaudited interim financial statements have been prepared on the same basis as the audited annual financial statements and, in the opinion of management, reflect all adjustments, which include only normal recurring adjustments, necessary for the fair statement of the Company’s financial position as of June 30, 2025, the results of its operations for the three and six months ended June 30, 2025 and 2024 and its cash flows for the six months ended June 30, 2025 and 2024. The results for the three and six months ended June 30, 2025 are not necessarily indicative of results to be expected for the year ending December 31, 2025, or any other interim period.

Principles of Consolidation

The condensed consolidated financial statements include the accounts of Atea Pharmaceuticals, Inc. and its wholly-owned subsidiary, Atea Pharmaceuticals Securities Corporation. All intercompany amounts have been eliminated in consolidation.

Significant Accounting Policies

The significant accounting policies used in the preparation of these condensed consolidated financial statements are consistent with those as described in the Annual Report on Form 10-K for the year ended December 31, 2024 filed with the SEC on March 6, 2025.

Recently Issued Accounting Pronouncements

From time to time, new accounting pronouncements are issued by the FASB or other standard setting bodies that the Company adopts as of the specified effective date. The Company does not believe that the adoption of recently issued standards have or may have a material impact on its condensed consolidated financial statements and disclosures.

3. Marketable Securities


								As of June 30, 2025
	Amortized Cost		Unrealized Gains		Unrealized Losses			Fair Value
Marketable Securities
US Treasury obligations	$	88,518	$	16	$	(9	)	$	88,525
US Government agency securities		6,958		1		(3	)		6,956
Asset-backed securities		42,883		29		(4	)		42,908
Commercial paper		3,914		—		(2	)		3,912
Corporate bonds		149,682		34		(25	)		149,691
Total	$	291,955	$	80	$	(43	)	$	291,992


								As of December 31, 2024
	Amortized Cost		Unrealized Gains		Unrealized Losses			Fair Value
Marketable Securities
US Treasury obligations	$	108,967	$	69	$	—		$	109,036
US Government agency securities		25,083		19		(8	)		25,094
Asset-backed securities		60,002		77		(8	)		60,071
Commercial paper		21,850		7		—			21,857
Corporate bonds		173,890		125		(48	)		173,967
Total	$	389,792	$	297	$	(64	)	$	390,025

As of June 30, 2025 and December 31, 2024, the Company held 46 and 21 securities that were in an unrealized loss position of $43 and $64, respectively. The Company has the intent and ability to hold such securities until recovery. As a result, the Company did not record any charges for credit-related impairments for its marketable debt securities for the six months ended June 30, 2025.

As of June 30, 2025 and December 31, 2024, none of the securities had remaining maturities longer than one year.

The Company received proceeds of $324,266 and $355,948 from sales and maturities of marketable securities during the six months ended June 30, 2025 and 2024.

4. Fair Value Measurements

The following tables present information about the Company’s financial assets measured at fair value on a recurring basis and indicate the level of the fair value hierarchy utilized to determine such fair values:


	Fair Value Measurements as of June 30, 2025
	Level 1		Level 2		Level 3		Total
Cash equivalents
Money market funds	$	76,900	$	—	$	—	$	76,900
Marketable Securities
US Treasury obligations		—		88,525		—		88,525
US Government agency securities		—		6,956		—		6,956
Asset-backed securities		—		42,908		—		42,908
Commercial paper		—		3,912		—		3,912
Corporate bonds		—		149,691		—		149,691
Total	$	76,900	$	291,992	$	—	$	368,892


	Fair Value Measurements as of December 31, 2024
	Level 1		Level 2		Level 3		Total
Cash equivalents
Money market funds	$	60,984	$	—	$	—	$	60,984
Marketable Securities
US Treasury obligations		—		109,036		—		109,036
US Government agency securities		—		25,094		—		25,094
Asset-backed securities		—		60,071		—		60,071
Commercial paper		—		21,857		—		21,857
Corporate bonds		—		173,967		—		173,967
Total	$	60,984	$	390,025	$	—	$	451,009

The Company’s assets with fair value categorized as Level 1 within the fair value hierarchy include money market funds. Money market funds are publicly traded mutual funds and are presented as cash equivalents on the unaudited condensed consolidated balance sheets as of June 30, 2025 and December 31, 2024.

The Company’s assets with fair value categorized as Level 2 within the fair value hierarchy include treasury obligations, government agency securities, asset-backed securities, commercial paper and corporate bonds with fair values determined by utilizing information from third party pricing sources for identical or similar assets and liabilities in active market.

There were no transfers between Level 1, Level 2 or Level 3 categories during the six months ended June 30, 2025.

5. Accrued Expenses and Other Current Liabilities

Accrued expenses and other current liabilities consist of the following:


	June 30, 2025		December 31, 2024
Research and development, including manufacturing and clinical expenditures	$	6,076	$	6,940
Payroll and payroll related		3,721		5,904
Professional fees and other		657		501
Total accrued expenses and other current liabilities	$	10,454	$	13,345

6. Common Stock

As of June 30, 2025, the authorized capital of the Company included 300,000,000 shares of Common Stock, of which 81,137,478 shares of the Common Stock were issued and outstanding. On all matters to be voted upon by the holders of the Common Stock, holders of the Common Stock are entitled to one vote per share. The holders of the Common Stock have no preemptive, redemption or conversion rights.

In April 2025, the Company’s Board of Directors authorized the Company to repurchase an aggregate amount of $25,000 of Common Stock. During the three months ended June 30, 2025, the Company repurchased 4,619,597 shares of Common Stock for an aggregate price of $14,093 (including transaction costs). As of June 30, 2025 $11,091 remained authorized for future repurchases. The repurchased shares of Common Stock were retired immediately upon receipt and returned to authorized and unissued status. Repurchased Common Stock is reflected as a reduction of stockholders’ equity. Any excess of cost over par value is charged to additional paid-in capital.

7. Stock-based Compensation

In October 2020, the Company’s shareholders approved the Company’s 2020 Incentive Award Plan (“2020 Plan”). The 2020 Plan initially provided for the issuance of up to 7,924,000 shares of Common Stock and for the grant of incentive stock options or other incentive awards to employees, officers, directors and consultants of the Company. The number of shares of Common Stock that may be issued under the 2020 Plan is also subject to

increase on the first day of each calendar year equal to the lesser of i) 5% of the aggregate number of shares of Common Stock outstanding on the final day of the immediately preceding calendar year or ii) such smaller number of shares as is determined by the board of directors. Through December 31, 2024, the shares available under the 2020 Plan were increased by 16,622,139 shares since the inception of the 2020 Plan. In January 2025, the shares of the Common Stock available under the 2020 Plan were increased by 4,223,152 shares. As of June 30, 2025, 5,056,452 shares of Common Stock were available for future issuance under the 2020 Plan.

The 2020 Plan replaced and is the successor of the Company’s 2013 Equity Incentive Plan, as amended (“2013 Plan”). In the event of any cancellation of an outstanding option award under the 2013 Plan, the shares underlying the cancelled option award will be made available for grant under the 2020 Plan.

Stock Options

The following table summarizes stock option activity:


	Number of Shares			Weighted Average Exercise Price Per Share		Weighted Average Remaining Contractual Term (years)		Aggregate Intrinsic Value ($000s)
Outstanding at January 1, 2025		20,166,069		$	13.51		6.6	$	6,095
Granted		3,345,228		$	3.09
Exercised		—		$	—
Cancelled		(621,500	)	$	7.50
Outstanding at June 30, 2025		22,889,797		$	12.15		6.4	$	8,659
Vested and expected to vest at June 30, 2025		22,889,797		$	12.15		6.4	$	8,659
Vested and exercisable at June 30, 2025		16,430,540		$	15.36		5.4	$	7,131

During the six months ended June 30, 2025, the Company granted 3,345,228 stock options with an aggregate grant date fair value of $7,339.

The aggregate intrinsic value of options granted is calculated as the difference between the exercise price of the options and the estimated fair value of the Common Stock for those options that had exercise prices lower than the fair value of the Common Stock.

Option grants generally vest over a service period of three or four years. All options have a contractual term of ten years. As of June 30, 2025, total unrecognized compensation expense related to stock option awards was $18,575, which is being recognized over a remaining weighted average period of 2.4 years.

Restricted Stock Units

During the six months ended June 30, 2025, the Company granted 1,091,064 restricted stock units to employees and directors under the 2020 Plan with an aggregate grant date fair market value of $3,372.

The restricted stock unit awards granted to employees vest in three annual installments. The restricted stock unit awards granted to directors vest in one annual installment. Below is the activity related to restricted stock units for the six months ended June 30, 2025.


	Number of Shares			Weighted Average Grant Date Fair Value
Outstanding at January 1, 2025		2,523,052		$	4.42
Granted		1,091,064		$	3.09
Released		(1,216,965	)	$	4.43
Cancelled		(150,087	)	$	4.03
Unvested at June 30, 2025		2,247,064		$	3.79

As of June 30, 2025, total unrecognized compensation expense related to restricted stock units was $6,441, which is being recognized over a remaining weighted average period of 1.65 years.

Performance-based Restricted Stock Units

During the six months ended June 30, 2022 the Company granted 724,970 performance-based restricted stock units (“2022 PSUs”) to employees with an aggregate grant fair value of $5,298. The performance period for the 2022 PSUs ran from February 1, 2022 through January 31, 2025 to achieve up to six defined performance metrics. The Company achieved two metrics which results in 50% of the grant date fair value being recognized as expense. Of the total 2022 PSUs granted, 25% vested on January 31, 2025, and 25% will vest on January 31, 2026 subject to continued employment. The Company recorded compensation expense of $81 and $0 for the three months ended June 30, 2025 and 2024, respectively. The Company recorded compensation expense of $197 and $0 for the six months ended June 30, 2025 and 2024, respectively. Expense is being recognized through January 31, 2026 for the 2022 PSUs that may vest on that date.

During the six months ended June 30, 2024, the Company granted 1,057,900 performance-based restricted stock units (“2024 PSUs”) to employees with an aggregate grant date fair value of $4,401. The 2024 PSUs provide for a performance period from February 1, 2024 through January 31, 2027 to achieve up to four defined performance metrics. The percentage of 2024 PSUs eligible to vest will be determined based on the number of metrics achieved during the performance period and may range from 0% to 200%. As of June 30, 2025, two of the 2024 PSU metrics were deemed probable of achievement resulting in expense recognition of 75% of the grant date value of the 2024 PSUs. Compensation expense is being recognized from the grant date through the final vest date of January 31, 2027. The Company recorded compensation expense of $274 and $183 for the three months ended June 30, 2025 and 2024, respectively. The Company recorded compensation expense of $545 and $303 for the six months ended June 30, 2025 and 2024, respectively.

During the six months ended June 30, 2025, the Company granted 1,045,600 performance-based restricted stock units (“2025 PSUs”) to employees with an aggregate grant date fair value of $3,200. The 2025 PSUs provide for a performance period from February 1, 2025 through January 31, 2028 to achieve up to four defined performance metrics. The percentage of 2025 PSUs eligible to vest will be determined based on the number of metrics achieved during the performance period and may range from 0% to 200%. As of June 30, 2025, none of the 2025 PSU metrics were deemed probable of achievement. The Company recorded no compensation expense for the three and six months ended June 30, 2025.

The following table summarizes the activity related to performance-based restricted stock units:


	Number of Shares			Weighted Average Grant Date Fair Value
Outstanding at January 1, 2025		1,782,870		$	5.37
Granted		1,045,600		$	3.06
Released		(181,242	)	$	7.14
Cancelled		(181,243	)	$	7.14
Unvested at June 30, 2025		2,465,985		$	4.13

As of June 30, 2025, total unrecognized compensation expense related to performance-based restricted stock units was $1,937, which is being recognized over weighted average period of 1.9 years.

Employee Stock Purchase Plan

In October 2020, the Company’s shareholders approved the employee stock purchase plan (“ESPP”). The Company initially reserved a total of 1,187,000 shares of its Common Stock for issuance under the ESPP. The ESPP provides that the number of shares reserved and available for issuance under the ESPP will be increased on January 1 of each calendar year by 1% of the number of shares of the Common Stock issued and outstanding on the final day of the immediately preceding calendar year or such lesser amount as specified by the board of directors. Through December 31, 2024, the number of shares of the Common Stock available for issuance under the ESPP was increased by 1,667,231. In January 2025 the number of shares of the Common Stock available for issuance under the ESPP was increased by 844,630.

The Company issued 54,296 and 58,555 shares for proceeds of $138 and $150 during the six months ended June 30, 2025 and 2024, respectively.

Stock-based Compensation Expense

Stock-based compensation expense by award type included within the unaudited condensed consolidated statements of operations and comprehensive loss was as follows:


	Three Months Ended June 30,				Six Months Ended June 30,
	2025		2024		2025		2024
Stock options	$	2,917	$	11,131	$	8,073	$	22,272
Restricted stock units		1,394		1,372		2,771		2,662
Performance-based restricted stock units		355		183		742		303
Employee stock purchase plan		1		34		32		69
Total stock-based compensation expense	$	4,667	$	12,720	$	11,618	$	25,306

Stock-based compensation expense is classified as follows:


	Three Months Ended June 30,				Six Months Ended June 30,
	2025		2024		2025		2024
Research and development expense	$	2,419	$	6,073	$	5,859	$	12,054
General and administrative expense		2,248		6,647		5,759		13,252
Total stock-based compensation expense	$	4,667	$	12,720	$	11,618	$	25,306

8. Net Loss Per Share

Basic and diluted earnings per share are calculated as follows:


	Three Months Ended June 30,						Six Months Ended June 30,
	2025			2024			2025			2024
Net loss	$	(37,161	)	$	(40,522	)	$	(71,433	)	$	(103,691	)
Weighted-average common shares outstanding — basic and diluted		83,747,335			84,253,700			84,449,318			84,069,646
Net loss per share — basic and diluted	$	(0.44	)	$	(0.48	)	$	(0.85	)	$	(1.23	)

The following shares were excluded from the computation of the net loss per share for the three and six months ended June 30, 2025 and 2024, respectively, due to the net loss during the periods as their effect is antidilutive.


	Three Months Ended June 30,				Six Months Ended June 30,
	2025		2024		2025		2024
Stock options		22,889,797		20,158,002		22,889,797		20,158,002
Restricted stock units		2,247,064		2,523,052		2,247,064		2,523,052
Performance-based restricted stock units		2,465,985		1,782,870		2,465,985		1,782,870
Employee stock purchase plan		21,588		26,189		21,588		26,189

9. Leases

The Company has a non-cancelable operating lease agreement for its office space in Boston, Massachusetts at 225 Franklin Street ("225 Lease"). The 225 Lease commencement date was January 1, 2022 and the 225 Lease runs through December 31, 2026. The 225 Lease does not contain any options for renewal or extension.

The following assets and liabilities are recorded on the Company’s condensed consolidated balance sheet as of June 30, 2025.


	As of June 30,
	2025
Right-of-use asset	$	942
Current lease liability		821
Non-current lease liability		425

Future minimum payments under the 225 Lease, currently the Company’s only operating lease as of June 30, 2025 were as follows.


	As of June 30,
	2025
Remainder of 2025	$	419
2026		855
Total lease payments		1,274
Less amount representing implied interest		28
Total lease liability	$	1,246
Current portion of operating lease liabilities	$	821
Non-current portion of operating lease liabilities	$	425

For each of the three and six months ended June 30, 2025 and 2024, the Company recorded operating lease costs of $162 and $323, respectively, relating to its operating lease agreements.

10. Income Taxes

The Company recorded income tax expense of $207 and $243 for the three months ended June 30, 2025 and 2024, respectively. The Company recorded income tax expense of $410 and $474 for the six months ended June 30, 2025 and 2024, respectively.

The Company maintained a full valuation allowance through June 30, 2025 due to uncertainty regarding its ability to utilize deferred tax assets.

11. Commitments and Contingencies

License Agreement

In December 2021, the Company 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 NS5A inhibitor the Company is developing in combination with bemnifosbuvir for the treatment of HCV.

Pursuant to the terms of the Merck License Agreement, the Company obtained from Merck a worldwide exclusive (subject to certain reserved rights to conduct internal research) and sublicensable 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 the Company made in February 2022, the Company will be required to pay Merck milestone payments upon its achievement of certain development, regulatory and sales-based milestones. Additionally, the Company will pay Merck tiered royalties based on annual net sales of Products ranging from high single digits to mid-teens percentages. The Company’s 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. The Company may terminate the Merck License Agreement for convenience upon prior written notice. The first milestone in the amount of $5,000 became due and payable and the related expense was recognized in April 2025 upon the initiation of the HCV Phase 3 clinical trial referred to as C-Beyond. The next potential milestone under the Merck License Agreement, in the amount of $10,000, is payable upon the acceptance by the US Food

and Drug Administration of a new drug application covering a product candidate including ruzasvir which the Company expects will be the regimen of bemnifosbuvir and ruzasvir for the treatment of HCV.

Contingent Consulting Fee

The Company has an agreement with a consultant that requires payment of a success fee calculated as a percentage of certain product sales, subject to a cumulative maximum payout of $5,000. This success payment is contingent upon the occurrence of future events and the timing and likelihood of such payment is neither probable nor estimable.

Indemnification

The Company enters into certain types of contracts that contingently requires the Company to indemnify various parties against claims from third parties. These contracts primarily relate to (i) the Company’s bylaws, under which the Company must indemnify directors and executive officers, and may indemnify other officers and employees, for liabilities arising out of their relationship with the Company, (ii) contracts under which the Company must indemnify directors and certain officers and consultants for liabilities arising out of their relationship with the Company, and (iii) procurement, service or license agreements under which the Company may be required to indemnify vendors, service providers or licensees for certain claims, including claims that may be brought against them arising from the Company’s acts or omissions with respect to the Company’s products, technology, intellectual property or services.

From time to time, the Company may receive indemnification claims under these contracts in the normal course of business. In the event that one or more of these matters were to result in a claim against the Company, an adverse outcome, including a judgment or settlement, may cause a material adverse effect on the Company’s future business, operating results or financial condition. It is not possible to determine the maximum potential amount payable under these contracts since the Company has no history of prior indemnification claims and the unique facts and circumstances involved in each particular claim will be determinative.

12. Benefit Plan

The Company’s defined contribution plan under Section 401(k) of the Internal Revenue Code (“401(k) Plan”) covers substantially all employees who meet minimum age and service requirements. Under the terms of the 401(k) Plan, the Company records matching contributions up to 4% of the participant’s eligible compensation. During the three months ended June 30, 2025 and 2024, the Company recognized expense of $138 and $161, respectively, relating to matching contributions to the 401(k) Plan. During the six months ended June 30, 2025 and 2024, the Company recognized expense of $455 and $562, respectively, relating to matching contributions to the 401(k) Plan.

13. Related Party Transactions

During the year ended December 31, 2021, the Company entered into a consulting agreement with an entity controlled by one of its directors. The agreement provides for an annual retainer of $110. The Company recognized expense in the amount of $27 and $54 for each of the three and six months ended June 30, 2025 and 2024.

In May 2022, the Company entered into a consulting agreement with one of its directors. No expense related to this agreement was recognized during any of the three and six months ended June 30, 2025 and 2024.

14. Segment Information

The Company operates as one operating segment, focused on discovering, developing and commercializing antiviral therapeutics. The determination of a single business segment is consistent with the consolidated financial information regularly provided to the Company’s Chief Executive Officer (“CEO”) who is also the Chief Operating Decision Maker (“CODM”). As CODM, the CEO, uses consolidated, single-segment financial information for purposes of evaluating performance, making operating decisions, allocating resources, and planning and forecasting for future periods.

The CODM assesses performance and decides how to allocate resources based on consolidated net loss. This measure is used to monitor budget versus actual results to evaluate the performance of the segment.

The CODM reviews cash, cash equivalents and marketable securities as a measure of segment assets. As of June 30, 2025 and December 31, 2024, the Company’s cash, cash equivalents and marketable securities were $379,713 and $454,721, respectively.

The following table illustrates information about significant segment expenses and segment operating loss for the three and six months ended June 30, 2025 and 2024:


	Three Months Ended June 30,						Six Months Ended June 30,
	2025			2024			2025			2024
Research and development expense (1)
COVID-19 external costs (2)	$	(78	)	$	11,297		$	1,156		$	50,348
HCV external costs (2)		24,285			10,501			41,869			16,454
Early stage discovery external costs (2)		265			212			596			413
Compensation and related expenses		4,419			5,346			10,456			11,021
Consulting and professional fees		568			799			1,087			1,095
Other research and development expenses		397			468			836			886
Total research and development expense		29,856			28,623			56,000			80,217
General and administrative (3)
Compensation and related expenses		2,212			2,454			4,890			4,995
Consulting and professional fees		4,185			2,710			7,124			5,295
Other general and administrative		425			409			754			909
Total general and administrative		6,822			5,573			12,768			11,199
Stock based compensation		4,667			12,720			11,618			25,307
Other segment items (4)		(4,184	)		(6,394	)		(8,953	)		(13,032	)
Net loss	$	(37,161	)	$	(40,522	)	$	(71,433	)	$	(103,691	)

(1)Research and development expense for the three months ended June 30, 2025 and 2024 excludes stock based compensation of $2,419 and $6,073, respectively. Research and development expense for the six months ended June 30, 2025 and 2024 excludes stock based compensation of $5,859 and $12,054, respectively.

(2)External costs consist primarily of preclinical, clinical and manufacturing related activities.

(3)General and administrative expense for the three months ended June 30, 2025 and 2024 excludes stock based compensation of $2,248 and $6,647, respectively. General and administrative expense for the six months ended June 30, 2025 and 2024 excludes stock based compensation of $5,759 and $13,252, respectively.

(4)Other segment items include interest income and other, net and income tax expense.

15. Subsequent Event

On July 4, 2025, the U.S enacted the budget reconciliation bill H.R. 1 into law, which included significant changes to U.S. income tax laws. Corporate tax provisions in the law include the restoration of 100% bonus depreciation, immediate expensing for domestic research and experimental expenditures, changes to Section 163(j) interest limitations, modifications to the U.S.’s international tax framework, and expanded Section 162(m) aggregation requirements. The Company is in the process of evaluating the impact of these changes, and an estimate of the financial effect is not yet available.

Item 2. 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, 2024, filed with the Securities and Exchange Commission (“SEC”) on March 6, 2025. 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 clinical-stage biopharmaceutical company leveraging our deep understanding of antiviral drug development, medicinal chemistry, biology, biochemistry and virology to discover and develop novel orally administered product candidates to treat serious viral diseases. Our lead product candidate is the regimen consisting of bemnifosbuvir and ruzasvir, which we are developing for the treatment of hepatitis C virus (“HCV”) infection. Currently, we are evaluating the regimen in a Phase 3 clinical development program which includes two Phase 3 clinical trials namely “C-Beyond” which is the clinical trial we are conducting in the United States (“US”) and Canada and “C-Forward” which is the clinical trial we are conducting outside of North America. Patient enrollment in C-Beyond and C-Forward began in April and June 2025, respectively, and is currently ongoing.

HCV

HCV is a blood-borne, positive-sense, single-stranded ribonucleic acid ("RNA") virus that primarily infects liver cells. HCV is a leading cause of chronic liver disease, liver transplants and liver cancer in the US, Europe and Japan.

Despite the availability of direct-acting antiviral (“DAA”) oral combination treatment regimens and eradication efforts by the World Health Organization and others, HCV continues to be a serious viral disease. An estimated 50 million people globally live with chronic HCV infection, with approximately 1 million new infections occurring each year. It is estimated that HCV leads to 240,000 deaths per year. These deaths are primarily attributable to cirrhosis and hepatocellular cancer, each of which are serious long-term consequences resulting from prolonged exposure to HCV infection.

In the US, it is estimated that there are between 2.4 and 4.0 million persons infected with untreated HCV. Further it is reported that on an annual basis in the US, there are greater than 160,000 newly reported HCV infections. This incidence of newly reported infections outpaces substantially stagnant rates of treatment.

In the US and elsewhere, HCV is increasingly affecting younger people, with high case rates among those between 20 to 49 years of age. Since recently infected and younger patient populations are less likely to have developed cirrhosis given the relatively shorter cumulative exposure to the virus, there has been a trend in the US of decreasing incidence of cirrhosis among individuals with HCV infection. It is estimated that less than 10% of the HCV-infected population in the US has cirrhosis.

In 2024, global net sales of branded HCV therapeutics known in the US as Epclusa® and Mavyret® together with the authorized generic copies of Epclusa exceeded $2.9 billion with the US contributing approximately 50% of these sales. Given the large number of patients currently infected with HCV and high rates of annual incidence, it is expected that a substantial global market will exist for the foreseeable future.

Our Goal

The objective of our HCV development program, which is now enrolling patients in two Phase 3 clinical trials, is to improve upon the current standard of care ("SOC") by offering, the regimen of bemnifosbuvir and ruzasvir, if successfully developed and approved, as a differentiated pan-genotypic protease inhibitor-free therapeutic for HCV-infected patients, many of whom take medications for other conditions. We believe that a novel treatment, with a profile that can be easily prescribed for and administered to today’s population of HCV-infected patients (e.g. young, newly infected, non-cirrhotic) would be a significant improvement to the current SOC.

Presently, there are no short-course (i.e., eight week) nucleoside inhibitor-based, pan-genotypic HCV treatment regimens. Results from the clinical and nonclinical studies we have 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

offers high potency, a low risk for drug-drug interactions, good tolerability and convenience in that it can be taken with or without food which we believe would offer a significant improvement to the current SOC, if approved.

Phase 3 Clinical Development

The global HCV Phase 3 program we are currently conducting includes two randomized, open label Phase 3 trials comparing the regimen of bemnifosbuvir and ruzasvir to sofosbuvir and velpatasvir in patients with chronic HCV infection. The overall clinical trial design is identical for each trial. The Phase 3 trial being conducted in the US and Canada is referred to as C-Beyond and the Phase 3 clinical trial being conducted outside of North America is referred to as C-Forward.

Each of C-Beyond and C-Forward is expected to enroll approximately 880 treatment-naïve patients, both with and without compensated cirrhosis. Patients are being stratified by genotype and cirrhosis status, and patients with human immunodeficiency virus (“HIV”) co-infection may be enrolled. For non-cirrhotic patients, eight weeks of treatment with the regimen of bemnifosbuvir and ruzasvir will be compared to 12 weeks of sofosbuvir and velpatasvir. For cirrhotic patients, 12 weeks of bemnifosbuvir and ruzasvir will be compared to 12 weeks of sofosbuvir and velpatasvir. The global geographic footprint of the Phase 3 program is to assist us in enrolling patients with varied HCV genotypes.

Key Clinical Trial Results – Phase 2 and Phase 1

In December 2024, we announced that the global Phase 2 study evaluating the regimen of bemnifosbuvir and ruzasvir had met its primary endpoints of safety and sustained virologic response (“SVR”) at 12 weeks post treatment (“SVR12”). The regimen of bemnifosbuvir and ruzasvir was generally well-tolerated with no drug-related serious adverse events (“SAEs”) or treatment discontinuations.

Primary efficacy endpoint results showed a 98% (208/213) SVR12 rate in the per-protocol treatment adherent patient population after eight weeks of treatment with the regimen. The efficacy evaluable patient population, which included 17% treatment non-adherent patients, achieved a 95% (242/256) SVR12 rate. Additional results from the Phase 2 study showed in treatment adherent patients who were non-cirrhotic and infected with genotypes 1-4, an SVR12 rate of 99% (178/179) was achieved, demonstrating pan-genotypic potency. Treatment adherent patients with cirrhosis achieved an 88% (30/34) SVR12 rate. Although viral kinetics were slower in cirrhotic patients, all cirrhotic patients (100%; 34/34) achieved an end of treatment response at Week 8.

The global Phase 2 study enrolled 275 HCV treatment-naïve patients, both with and without compensated cirrhosis. The study was designed to evaluate the safety and efficacy of eight weeks of treatment with the regimen consisting of once-daily bemnifosbuvir 550 mg and ruzasvir 180 mg. The primary endpoints were safety and SVR12 in the per-protocol treatment adherent population. Secondary and other endpoints included SVR12 in the efficacy evaluable population (a broader analysis population which included treatment non-adherent patients), SVR at 24 weeks post treatment (“SVR24”), virologic failure and resistance.

The Phase 2 study results were presented in May 2025 at the European Association for the Study of Liver (“EASL”) Congress 2025. Additionally, at EASL in May 2025, we presented results from three Phase 1 studies. These studies included a pharmacokinetic study, a drug-drug interaction study and a renal impairment study.

The results from the Phase 1 pharmacokinetic study, which evaluated a single 550 mg dose of bemnifosbuvir in healthy participants with varying degrees of hepatic impairment, support the administration of bemnifosbuvir without dose adjustment in patients with hepatic impairment. The results from the Phase 1 drug-drug interaction study in healthy participants showed that co-administration of bemnifosbuvir and ruzasvir with the standard HIV regimen bictegravir/emtricitabine/tenofovir alafenamide (B/FTC/TAF) resulted in no clinically significant pharmacokinetic changes. The results from the Phase 1 renal impairment study in healthy participants showed that a single 550 mg dose of bemnifosbuvir was well-tolerated across participants with normal kidney function, moderate-to-severe renal impairment, and those with end-stage renal disease on hemodialysis. These data suggest bemnifosbuvir may be administered without dose adjustment in patients with renal dysfunction, including those undergoing dialysis.

COVID-19

In September 2024 we announced the outcome of the global Phase 3 SUNRISE-3 trial evaluating bemnifosbuvir versus placebo for the treatment of Coronavirus Disease 2019 ("COVID-19"). The trial did not meet the primary endpoint of a statistically significant reduction in all-cause hospitalization or death through Day 29 in the monotherapy cohort of 2,221 high-risk patients with mild to moderate COVID-19. We believe that the unfavorable results from this study were impacted by the constantly evolving variants of COVID-19 and rapidly changing

natural history of the disease, which during the study period trended toward a milder disease. This led us to discontinue efforts to develop bemnifosbuvir for the treatment of COVID-19. In SUNRISE-3, bemnifosbuvir was generally safe and well tolerated. In April 2025, we completed the close out of the study.

Respiratory and Other RNA Virus Infections

Separately, we are engaged in efforts to discover a product candidate for the treatment of respiratory diseases resulting from infection with single stranded RNA viruses. Additionally, we engaged in efforts to screen compounds which are a part of our compound library to assess antiviral activity against other RNA viral infections. Each of these efforts are at early stages and no clinical candidates have yet to be nominated.

Financial Resources

We believe we are well capitalized to advance our current programs. We had $379.7 million in cash, cash equivalents and marketable securities at June 30, 2025.

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.

In April 2025, our Board of Directors (the “Board”) authorized the repurchase of up to $25.0 million of our common stock (“Share Repurchase Program”). This authorization reflects our commitment to return 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 strategic business plans. Repurchases under the Share Repurchase Program may be made in the open market, in privately negotiated transactions or otherwise, with the amount and timing of repurchases to be determined at our discretion, or under a trading plan intended to satisfy the affirmative defense conditions of Rule 10b5-1(c)(1) under the Exchange Act.

During the three months ended June 30, 2025 we repurchased 4,619,597 shares of our common stock for an aggregate price of approximately $14.1 million (including transaction costs). As of June 30, 2025, approximately $11.1 million remained authorized for future repurchases. Repurchased shares of our common stock were retired immediately upon receipt and returned to authorized and unissued status.

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.

As previously announced, in December 2024, we engaged Evercore LLC, a global independent investment bank, to assist us in the identification of additional opportunities to enhance stockholder value. This process includes a review of a broad range of strategic alternatives, including strategic partnerships, acquisition, merger, or other business combination, sale of assets or other strategic transactions. As a part of this process, we continue to evaluate all options to maximize stockholder value. There is no assurance that the process will result in the completion of any specific transaction or outcome.

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 are required 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 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. 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 which we currently anticipate will be the regimen of bemnifosbuvir and ruzasvir for the treatment of HCV.

Financial Operations Overview

As of June 30, 2025, we had cash, cash equivalents and marketable securities of $379.7 million. Net cash used in operating activities was $63.4 million for the six months ended June 30, 2025. 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 million through 2027. As noted above, in April 2025, our Board authorized the Share Repurchase Program. This authorization reflects our commitment to return capital to our stockholders while maintaining the capacity to complete our Phase 3 clinical development of the regimen of bemnifosbuvir and ruzasvir and execute on our strategic business plans. 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 including the completion of clinical development of the regimen of bemnifosbuvir and ruzasvir for the treatment of HCV.

We expect that our net cash used in operating activities will remain significant as we advance our HCV product candidate through preclinical and clinical development, seek regulatory approval, and prepare for and, if approved, manufacture such product at commercial scale and otherwise pursue commercialization activities; 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. Our failure to meet the primary 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 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:

•

conduct Phase 3 clinical development of the regimen of bemnifosbuvir and ruzasvir for the treatment of HCV which includes the purchase of comparator drug;

•

continue discovery and IND-enabling activities to identify other potential product candidates for the treatment of diseases caused by single stranded RNA viruses;

•

initiate clinical development of product candidates for the treatment of respiratory and other diseases resulting from infection with single stranded RNA viruses;

•

manufacture the regimen of bemnifosbuvir and ruzasvir in fixed dose tablets for use in the Phase 3 clinical trials, regulatory approvals, and, if approved, for potential commercialization, for the treatment of HCV;

•

seek market approval and prepare for potential commercialization of any product candidates that we may successfully develop;

•

acquire or in-license clinical stage drug candidates, form strategic alliances or establish collaborations with third parties;

•

maintain, expand, protect and enforce our intellectual property portfolio;

•

hire additional personnel, if necessary, to support our activities; and

•

establish commercialization capabilities if we are successful in developing our product candidates.

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, consulting costs and in the case of our HCV Phase 3 program, costs to purchase comparator drug. Research and development expenses also include 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 or early stage discovery costs by therapeutic area as they are deployed across multiple programs. Early stage discovery activities consist of assessing the antiviral activity and other properties of select compounds derived from our compound library against respiratory and other RNA viral infections.

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


	Three Months Ended June 30,					Six Months Ended June 30,
	2025			2024		2025		2024
	(in thousands)					(in thousands)
COVID-19 external costs	$	(78	)	$	11,487	$	1,156	$	50,739
HCV external costs		24,285			10,501		41,869		16,454
Early stage discovery external costs		265			22		596		22
Internal research and development costs		7,803			12,686		18,238		25,056
Total research and development costs	$	32,275		$	34,696	$	61,859	$	92,271

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 advance our Phase 3 HCV clinical program and prepare for the possible commercialization of the regimen of bemnifosbuvir and ruzasvir if the Phase 3 clinical development is successful. 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 product candidate or any other product candidate we may develop will receive regulatory approval, if ever.

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 The Nasdaq Global Select Market and Securities and Exchange Commission 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, cash equivalents and marketable securities.

Income Taxes

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

Results of Operations

Comparison of the Three Months Ended June 30, 2025 and 2024

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


	Three Months Ended June 30,
	2025			2024			Change
	(in thousands)
Operating expenses:
Research and development	$	32,275		$	34,696		$	(2,421	)
General and administrative		9,070			12,220			(3,150	)
Total operating expenses		41,345			46,916			(5,571	)
Loss from operations		(41,345	)		(46,916	)		5,571
Interest income and other, net		4,391			6,637			(2,246	)
Loss before income taxes		(36,954	)		(40,279	)		3,325
Income tax expense		(207	)		(243	)		36
Net loss	$	(37,161	)	$	(40,522	)	$	3,361

Research and Development Expenses

Research and development expenses decreased by $2.4 million from $34.7 million for the three months ended June 30, 2024 to $32.3 million for the three months ended June 30, 2025. The net decrease was primarily driven by substantially lower COVID-19 external spend as a result of our COVID-19 Phase 3 SUNRISE-3 clinical trial being completed in 2024 together with a decrease in internal research and development expenses primarily related to lower stock-based compensation and payroll related expenses in the three months ended June 30, 2025, offset by increased external spend related principally for our HCV Phase 3 clinical development program including the recognition of expense related to the milestone paid to Merck.

General and Administrative Expenses

General and administrative expenses decreased by $3.2 million from $12.2 million for the three months ended June 30, 2024 to $9.1 million for the three months ended June 30, 2025. The net decrease was primarily related to lower stock-based compensation expense partially offset by increased professional fees.

Interest Income and Other, Net

Interest income and other, net, decreased by $2.2 million for the three months ended June 30, 2025 compared to the three months ended June 30, 2024, primarily due to lower investment balances.

Income Taxes

Income tax expense was $0.2 million for the three months ended June 30, 2025 and 2024.

Comparison of the Six Months Ended June 30, 2025 and 2024

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


	Six Months Ended June 30,
	2025		2024		Change
	(in thousands)
Operating expenses:
Research and development	$	61,859	$	92,271	$	(30,412	)
General and administrative		18,527		24,451		(5,924	)
Total operating expenses		80,386		116,722		(36,336	)

Large accelerated filer

Accelerated filer

Non-accelerated filer

Smaller reporting company

Emerging growth company

Atea Pharmaceuticals, Inc. 10-Q