Altimmune, Inc. 10-Q

Item 1. Financial Statements ALTIMMUNE, INC. CONSOLIDATED BALANCE SHEETS (In thousands, except share and per-share amounts) ​ ​ ​ ​ ​ ​ ​ ​ September 30, ​ December 31, ​ ​ 2025 ​ 2024 ​ ​ (Unaudited) ​ ​ ​ ASSETS ​ ​ ​ Current assets: ​ ​ Cash and cash equivalents ​ $ 61,236 ​ $ 36,926 Restricted cash ​ 42 ​ 42 Total cash, cash equivalents and restricted cash ​ 61,278 ​ 36,968 Short-term investments ​ 149,540 ​ 94,965 Accounts and other receivables ​ 845 ​ 544 Income tax and R&D incentive receivables ​ 547 ​ 2,573 Prepaid expenses and other current assets ​ 4,405 ​ 2,204 Total current assets ​ 216,615 ​ 137,254 Property and equipment, net ​ 337 ​ 413 Other assets ​ 1,495 ​ 1,639 Total assets ​ $ 218,447 ​ $ 139,306 LIABILITIES AND STOCKHOLDERS’ EQUITY ​ ​ Current liabilities: ​ ​ Accounts payable ​ $ 4,804 ​ $ 211 Accrued expenses and other current liabilities ​ 7,802 ​ 10,257 Total current liabilities ​ 12,606 ​ 10,468 Term loan, noncurrent ​ ​ 14,445 ​ — Other noncurrent liabilities ​ 5,795 ​ 5,330 Total liabilities ​ 32,846 ​ 15,798 Commitments and contingencies (Note 10) ​ ​ Stockholders’ equity: ​ ​ Common stock, $ 0.0001 par value; 200,000,000 shares authorized; 95,598,665 and 72,352,701 shares issued and outstanding as of September 30, 2025 and December 31 2024, respectively ​ ​ 10 ​ ​ 7 Additional paid-in capital ​ 812,732 ​ 689,864 Accumulated deficit ​ ( 622,125 ) ​ ( 561,390 ) Accumulated other comprehensive loss, net ​ ( 5,016 ) ​ ( 4,973 ) Total stockholders’ equity ​ 185,601 ​ 123,508 Total liabilities and stockholders’ equity ​ $ 218,447 ​ $ 139,306 ​ The accompanying notes are an integral part of the unaudited consolidated financial statements. ​ 1 Table of Contents ALTIMMUNE, INC. CONSOLIDATED STATEMENTS OF OPERATIONS AND COMPREHENSIVE LOSS (Unaudited) (In thousands, except share and per-share amounts) ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Three Months Ended ​ Nine Months Ended ​ ​ September 30, ​ September 30, ​ ​ 2025 2024 2025 2024 Revenues ​ $ 5 ​ $ 5 ​ $ 15 ​ $ 15 Operating expenses: ​ ​ ​ ​ Research and development ​ 14,960 ​ 19,803 ​ 48,023 ​ 62,445 General and administrative ​ 5,904 ​ 4,969 ​ 17,588 ​ 15,876 Total operating expenses ​ 20,864 ​ 24,772 ​ 65,611 ​ 78,321 Loss from operations ​ ( 20,859 ) ​ ( 24,767 ) ​ ( 65,596 ) ​ ( 78,306 ) Other income (expense): ​ ​ ​ ​ Interest expense ​ ( 495 ) ​ ( 6 ) ​ ( 760 ) ​ ( 8 ) Interest income ​ 2,426 ​ 1,910 ​ 5,103 ​ 6,505 Other income (expense), net ​ ( 86 ) ​ 18 ​ ( 163 ) ​ ( 70 ) Total other income (expense), net ​ 1,845 ​ 1,922 ​ 4,180 ​ 6,427 Net loss before income taxes ​ ( 19,014 ) ​ ( 22,845 ) ​ ( 61,416 ) ​ ( 71,879 ) Income tax expense (benefit) ​ — ​ — ​ ( 681 ) ​ — Net loss ​ ( 19,014 ) ​ ( 22,845 ) ​ ( 60,735 ) ​ ( 71,879 ) Other comprehensive income — unrealized gain (loss) on short-term investments ​ 23 ​ 347 ​ ( 43 ) ​ 159 Comprehensive loss ​ $ ( 18,991 ) ​ $ ( 22,498 ) ​ $ ( 60,778 ) ​ $ ( 71,720 ) Net loss per share, basic and diluted ​ $ ( 0.21 ) ​ $ ( 0.32 ) ​ $ ( 0.74 ) ​ $ ( 1.01 ) Weighted-average common shares outstanding, basic and diluted ​ 89,418,028 ​ 71,084,787 ​ 82,198,581 ​ 70,927,222 ​ The accompanying notes are an integral part of the unaudited consolidated financial statements. ​ ​ 2 Table of Contents ​ ALTIMMUNE, INC. CONSOLIDATED STATEMENTS OF CHANGES IN STOCKHOLDERS’ EQUITY (Unaudited) (In thousands, except share amounts) ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Accumulated ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Additional ​ ​ ​ ​ Other ​ Total ​ Common Stock Paid-In Accumulated Comprehensive Stockholders’ ​ ​ Shares ​ Amount ​ Capital ​ Deficit ​ Loss ​ Equity Balance at December 31, 2024 ​ 72,352,701 ​ $ 7 ​ $ 689,864 ​ $ ( 561,390 ) ​ $ ( 4,973 ) ​ $ 123,508 Stock-based compensation — ​ — ​ 4,015 ​ — ​ — ​ 4,015 Exercise of stock options 1,250 ​ — ​ 4 ​ — ​ — ​ 4 Vesting of restricted stock awards including withholding, net ​ 165,259 ​ ​ — ​ ​ ( 678 ) ​ ​ — ​ ​ — ​ ​ ( 678 ) Issuance of common stock from Employee Stock Purchase Plan 32,872 ​ — ​ 170 ​ — ​ — ​ 170 Issuance of common stock in at-the-market offerings, net 5,273,368 ​ 1 ​ 34,747 ​ ​ — ​ ​ — ​ 34,748 Unrealized (loss) gain on short-term investments — ​ — ​ — ​ — ​ ( 30 ) ​ ( 30 ) Net loss ​ — ​ ​ — ​ ​ — ​ ​ ( 19,575 ) ​ ​ — ​ ​ ( 19,575 ) Balance at March 31, 2025 77,825,450 $ 8 $ 728,122 $ ( 580,965 ) $ ( 5,003 ) $ 142,162 Stock-based compensation — $ — $ 3,566 $ — $ — $ 3,566 Exercise of stock options ​ 1,667 ​ — ​ 4 ​ — ​ — ​ 4 Vesting of restricted stock awards including withholding, net 2,621 ​ — ​ ( 6 ) ​ — ​ — ​ ( 6 ) Issuance of common stock in at-the-market offerings, net ​ 7,246,562 ​ ​ 1 ​ ​ 37,822 ​ ​ — ​ ​ — ​ ​ 37,823 Unrealized (loss) gain on short-term investments — ​ — ​ — ​ — ​ ( 36 ) ​ ( 36 ) Net loss — ​ — ​ — ​ ( 22,146 ) ​ — ​ ( 22,146 ) Balance at June 30, 2025 85,076,300 $ 9 $ 769,508 $ ( 603,111 ) $ ( 5,039 ) $ 161,367 Stock-based compensation — $ — $ 3,554 $ — $ — $ 3,554 Exercise of stock options ​ 11,250 ​ — ​ 33 ​ — ​ — ​ 33 Issuance of common stock from Employee Stock Purchase Plan ​ 38,470 ​ — ​ 121 ​ — ​ — ​ ​ 121 Issuance of common stock in at-the-market offerings, net ​ 10,472,645 ​ 1 ​ 39,516 ​ — ​ — ​ ​ 39,517 Unrealized (loss) gain on short-term investments — ​ — ​ — ​ — ​ 23 ​ 23 Net loss — ​ — ​ — ​ ( 19,014 ) ​ — ​ ( 19,014 ) Balance at September 30, 2025 95,598,665 $ 10 $ 812,732 $ ( 622,125 ) $ ( 5,016 ) $ 185,601 ​ The accompanying notes are an integral part of the unaudited consolidated financial statements. ​ 3 Table of Contents ​ ​ ALTIMMUNE, INC. CONSOLIDATED STATEMENTS OF CHANGES IN STOCKHOLDERS’ EQUITY (Unaudited) (In thousands, except share amounts) ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Accumulated ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Additional ​ ​ ​ ​ Other ​ Total ​ Common Stock Paid-In Accumulated Comprehensive Stockholders’ ​ ​ Shares ​ Amount ​ Capital ​ Deficit ​ Loss ​ Equity Balance at December 31, 2023 ​ 70,677,400 ​ $ 7 ​ $ 665,427 ​ $ ( 466,331 ) ​ $ ( 5,004 ) ​ $ 194,099 Stock-based compensation — ​ — ​ 3,650 ​ — ​ — ​ 3,650 Exercise of stock options 1,250 ​ — ​ 9 ​ — ​ — ​ 9 Vesting of restricted stock awards including withholding, net 107,875 ​ ​ — ​ ​ ( 600 ) ​ ​ — ​ ​ — ​ ( 600 ) Issuance of common stock from Employee Stock Purchase Plan 62,609 ​ — ​ 169 ​ — ​ — ​ 169 Issuance of common stock upon exercise of warrants ​ 50,000 ​ ​ — ​ ​ 161 ​ ​ — ​ ​ — ​ ​ 161 Unrealized (loss) gain on short-term investments — ​ — ​ — ​ — ​ ( 157 ) ​ ( 157 ) Net loss ​ — ​ ​ — ​ ​ — ​ ​ ( 24,394 ) ​ ​ — ​ ​ ( 24,394 ) Balance at March 31, 2024 70,899,134 $ 7 $ 668,816 $ ( 490,725 ) $ ( 5,161 ) $ 172,937 Stock-based compensation — $ — $ 4,311 $ — $ — $ 4,311 Exercise of stock options 64,433 ​ — ​ 198 ​ — ​ — ​ 198 Vesting of restricted stock awards including withholding, net 82,700 ​ — ​ ( 244 ) ​ — ​ — ​ ( 244 ) Unrealized (loss) gain on short-term investments — ​ — ​ — ​ — ​ ( 31 ) ​ ( 31 ) Net loss — ​ — ​ — ​ ( 24,640 ) ​ — ​ ( 24,640 ) Balance at June 30, 2024 71,046,267 $ 7 $ 673,081 $ ( 515,365 ) $ ( 5,192 ) $ 152,531 Stock-based compensation — $ — $ 3,078 $ — $ — $ 3,078 Exercise of stock options ​ 52,584 ​ — ​ 139 ​ — ​ — ​ ​ 139 Vesting of restricted stock awards including withholding, net 1,308 ​ — ​ ( 4 ) ​ — ​ — ​ ( 4 ) Issuance of common stock from Employee Stock Purchase Plan 24,248 ​ — ​ 131 ​ — ​ — ​ 131 Unrealized (loss) gain on short-term investments — ​ — ​ — ​ — ​ 347 ​ 347 Net loss ​ — ​ — ​ — ​ ( 22,845 ) ​ — ​ ​ ( 22,845 ) Balance at September 30, 2024 71,124,407 $ 7 $ 676,425 $ ( 538,210 ) $ ( 4,845 ) $ 133,377 ​ The accompanying notes are an integral part of the unaudited consolidated financial statements. ​ ​ 4 Table of Contents ​ ALTIMMUNE, INC. CONSOLIDATED STATEMENTS OF CASH FLOWS (Unaudited) (In thousands) ​ ​ ​ ​ ​ ​ ​ ​ Nine Months Ended ​ ​ September 30, ​ ​ 2025 ​ 2024 CASH FLOWS FROM OPERATING ACTIVITIES: ​ ​ Net loss ​ $ ( 60,735 ) ​ $ ( 71,879 ) Adjustments to reconcile net loss to net cash used in operating activities: ​ ​ ​ Stock-based compensation expense ​ 11,135 ​ 11,039 Depreciation of property and equipment ​ 86 ​ 205 Accretion of discounts on short-term investments ​ ​ ( 1,313 ) ​ ​ ( 3,031 ) Amortization of debt discount and costs ​ ​ 171 ​ ​ — Loss on foreign currency exchange ​ 116 ​ 69 Deferred income tax benefit ​ ​ ( 681 ) ​ ​ — Changes in operating assets and liabilities: ​ ​ ​ ​ Accounts receivable ​ ( 301 ) ​ 683 Prepaid expenses and other assets ​ ( 1,903 ) ​ 3,920 Accounts payable ​ 4,593 ​ ( 937 ) Accrued expenses and other liabilities ​ ( 1,962 ) ​ ( 2,482 ) Income tax and R&D incentive receivables ​ 2,707 ​ 830 Net cash used in operating activities ​ ( 48,087 ) ​ ( 61,583 ) CASH FLOWS FROM INVESTING ACTIVITIES: ​ ​ Proceeds from sales and maturities of short-term investments ​ 143,589 ​ 60,500 Purchases of short-term investments ​ ( 196,894 ) ​ ( 102,518 ) Purchases of property and equipment ​ ( 10 ) ​ — Net cash used in investing activities ​ ( 53,315 ) ​ ( 42,018 ) CASH FLOWS FROM FINANCING ACTIVITIES: ​ ​ Payments of deferred offering costs ​ ​ ( 298 ) ​ ​ — Proceeds from exercises of warrants ​ — ​ 161 Proceeds from term loan ​ ​ 15,000 ​ ​ — Payment for debt issuance costs ​ ​ ( 726 ) ​ ​ — Proceeds from issuance of common stock in at-the-market offerings, net ​ 112,088 ​ — Proceeds from issuance of common stock from Employee Stock Purchase Plan ​ 291 ​ 300 Proceeds from exercises of stock options ​ 41 ​ 346 Payments for tax withholding in share-based compensation ​ ( 684 ) ​ ( 848 ) Net cash provided by (used in) financing activities ​ 125,712 ​ ( 41 ) Net increase (decrease) in cash and cash equivalents and restricted cash ​ 24,310 ​ ( 103,642 ) Cash, cash equivalents and restricted cash at beginning of period ​ 36,968 ​ 135,158 Cash, cash equivalents and restricted cash at end of period ​ $ 61,278 ​ $ 31,516 ​ ​ ​ ​ ​ ​ ​ SUPPLEMENTAL CASH FLOW INFORMATION: ​ ​ Cash paid for interest ​ $ 460 ​ $ — Cash received from income tax refunds ​ $ 1,422 ​ $ — SUPPLEMENTAL NON-CASH ACTIVITIES: ​ ​ ​ ​ Operating lease liability and right-of-use asset addition ​ $ — ​ $ 1,409 ​ The accompanying notes are an integral part of the unaudited consolidated financial statements. ​ 5 Table of Contents ALTIMMUNE, INC. NOTES TO CONSOLIDATED FINANCIAL STATEMENTS (Unaudited) 1. Nature of Business and Basis of Presentation Nature of Business Altimmune, Inc., headquartered in Gaithersburg, Maryland, United States, together with its subsidiaries (collectively, the “Company” or “Altimmune”) is a late clinical-stage biopharmaceutical company incorporated under the laws of the State of Delaware. The Company is developing novel peptide-based therapeutics for liver and cardiometabolic diseases. The Company’s lead program is pemvidutide (formerly known as ALT-801), a balanced 1:1 glucagon/GLP-1 dual receptor agonist for the treatment of metabolic dysfunction-associated steatohepatitis (“MASH”), alcohol use disorder (“AUD”) and alcohol-associated liver disease (“ALD”). The Company may also pursue additional indications for pemvidutide that leverage its differentiated clinical profile. Since its inception, the Company has devoted substantially all of its efforts to business planning, research and development, recruiting management and technical staff, and raising capital, and has financed its operations through the issuance of common and preferred stock, long-term debt, and proceeds from research grants and government contracts. The Company has not generated any revenues from the sale of any products to date, and there is no assurance of any future revenues from product sales. Basis of Presentation The accompanying unaudited consolidated financial statements are prepared pursuant to the rules and regulations of the U.S. Securities and Exchange Commission (“SEC”) regarding interim financial reporting. Accordingly, they do not include all of the information and disclosures required by accounting principles generally accepted in the United States (“U.S. GAAP”) for complete consolidated financial statements and should be read in conjunction with the audited consolidated financial statements for the year ended December 31, 2024, included in the Annual Report on Form 10-K which was filed with the SEC on February 27, 2025. In the opinion of management, the Company has prepared the accompanying unaudited consolidated financial statements on the same basis as the audited consolidated financial statements, and these consolidated financial statements include all adjustments, consisting only of normal recurring adjustments, necessary for a fair presentation of the results of the interim periods presented. The operating results for the interim periods presented are not necessarily indicative of the results expected for the full year 2025 or any future years or periods. The accompanying unaudited consolidated financial statements include the accounts of the Company and its wholly owned subsidiaries. All significant intercompany accounts and transactions have been eliminated in consolidation. The accompanying unaudited consolidated financial statements have been prepared on the basis of continuity of operations, realization of assets, and the satisfaction of liabilities in the ordinary course of business. The financial statements do not include any adjustments relating to the recoverability and classification of recorded assets and liabilities that might be necessary should the Company be unable to continue as a going concern. 2. Summary of Significant Accounting Policies During the nine months ended September 30, 2025, there have been no significant changes to the Company’s summary of significant accounting policies contained in the Company’s Annual Report on Form 10-K for the year ended December 31, 2024, as filed with the SEC on February 27, 2025. Use of Estimates The preparation of financial statements in conformity with U.S. GAAP requires management to make estimates and assumptions that affect the amounts reported in the financial statements and accompanying notes. Significant estimates 6 Table of Contents and assumptions made in the accompanying condensed consolidated financial statements include, but are not limited to, the valuation of share-based awards, income taxes, prepaids, and accruals for research and development activities. The Company bases its estimates on historical experience and on various other assumptions that are believed to be reasonable. However, actual results could differ from those estimates. Income Taxes During the nine months ended September 30, 2025, the Company has recorded a discrete tax benefit of approximately $ 0.7 million, related to a portion of carryback claims with the State of Maryland of which the Company previously held an uncertain tax position against. Other than the discrete tax benefit discussed above, due to a full valuation allowance, the Company did no t record an income tax expense (benefit) for either of the three and nine months ended September 30, 2025 and 2024. The Company calculates its quarterly income tax provision based on estimated, annual effective tax rates applied to ordinary income (or loss) and other known items computed and recognized as they occur. The Company’s total provision is based on the United States statutory rate, increased by state and foreign taxes and reduced by a full valuation allowance on the Company’s deferred tax assets. On July 4, 2025, the One Big Beautiful Bill Act (“OBBBA”) was enacted in the U.S. The OBBBA includes significant provisions, such as the permanent extension of certain expiring provisions of the Tax Cuts and Jobs Act, modifications to the international tax framework and the restoration of favorable tax treatment for certain business provisions. The legislation has multiple effective dates, with certain provisions effective in 2025 and others implemented through 2027. The Company is currently assessing its impact on our consolidated financial statements and will continue to evaluate the full impact of these legislative changes as additional guidance becomes available; however, it does not expect the OBBBA to have a material impact on our estimated annual effective tax rate in 2025. Debt discount and issuance costs The Company accounts for fees paid to lenders, as compensation for services beyond their role as a creditor, and third parties whose costs are directly related to issuing debt as debt issuance cost. Amounts paid to the lender as a reduction in the proceeds received are considered a discount on the issuance. Debt issuance costs and discounts related to term loans are reported as a direct deduction from the outstanding debt and amortized over the term of the loan using the effective interest method as an additional interest expense. 3. Fair Value Measurements The Company’s assets measured at fair value on a recurring basis as of September 30, 2025 consisted of the following (in thousands): ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Fair Value Measurement at September 30, 2025 ​ Total Level 1 Level 2 Level 3 Assets: ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Cash equivalents - money market funds ​ $ 16,640 ​ $ 16,640 ​ $ — ​ $ — Cash equivalents - agency debt securities ​ ​ 1,990 ​ ​ — ​ ​ 1,990 ​ ​ — Cash equivalents - commercial paper ​ ​ 11,621 ​ ​ — ​ ​ 11,621 ​ ​ — Cash equivalents - US treasury ​ ​ 5,964 ​ ​ — ​ ​ 5,964 ​ ​ — Short-term investments ​ 149,540 ​ — ​ 149,540 ​ — Total ​ $ 185,755 ​ $ 16,640 ​ $ 169,115 ​ $ — 7 Table of Contents ​ The Company’s assets measured at fair value on a recurring basis as of December 31, 2024 consisted of the following (in thousands): ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Fair Value Measurement at December 31, 2024 ​ Total Level 1 Level 2 Level 3 Assets: ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Cash equivalents - money market funds ​ $ 27,279 ​ $ 27,279 ​ $ — ​ $ — Short-term investments ​ 94,965 ​ — ​ 94,965 ​ — Total ​ $ 122,244 ​ $ 27,279 ​ $ 94,965 ​ $ — ​ ​ Short-term investments have been initially valued at the transaction price and subsequently valued at the end of each reporting period utilizing third party pricing services or other market observable data (Level 2). The pricing services utilize industry standard valuation models, including both income and market-based approaches and observable market inputs to determine value. The Company’s short-term investments have a maturity date of one year or less. Short-term investments with quoted prices as of September 30, 2025 as shown below (in thousands): ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ September 30, 2025 ​ ​ ​ ​ Unrealized Gain ​ Unrealized Gain ​ ​ ​ ​ Amortized Cost ​ Unrealized (Loss) Gain ​ Credit loss ​ Market Value United States treasury securities $ 49,233 $ 7 $ — $ 49,240 Commercial paper and corporate debt securities ​ ​ 86,356 ​ ​ 8 ​ ​ — ​ ​ 86,364 Asset backed securities ​ 8,001 ​ 5 ​ — ​ 8,006 Agency debt securities ​ ​ 5,927 ​ ​ 3 ​ ​ — ​ ​ 5,930 Total ​ $ 149,517 ​ $ 23 ​ $ — ​ $ 149,540 ​ Short-term investments with quoted prices as of December 31, 2024 as shown below (in thousands): ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ December 31, 2024 ​ ​ ​ ​ Unrealized Gain ​ Unrealized Gain ​ ​ ​ ​ ​ Amortized Cost ​ Unrealized (Loss) Gain ​ Credit Loss ​ Market Value United States treasury securities $ 21,375 $ 16 $ — $ 21,391 Commercial paper and corporate debt securities ​ ​ 52,641 ​ ​ 15 ​ ​ — ​ ​ 52,656 Asset backed securities ​ 5,951 ​ 14 ​ — ​ 5,965 Agency debt securities ​ ​ 14,931 ​ ​ 22 ​ ​ — ​ ​ 14,953 Total ​ $ 94,898 ​ $ 67 ​ $ — ​ $ 94,965 ​ During the nine months ended September 30, 2025, the Company recognized approximately $ 0.1 million realized net loss from the sales of available-for-sale debt securities that were classified as short-term investments. These investments had an insignificant amount of unrealized net loss that was reclassified out of other comprehensive income. As of September 30, 2025 and December 31, 2024, none of the unrealized losses on the Company’s short-term investments were a result of credit loss; therefore, any unrealized losses were recognized in other comprehensive income. As of September 30, 2025 and December 31, 2024, the Company had $ 0.7 million and $ 0.4 million, respectively, accrued interest on short-term investments included in “Accounts and other receivables” on the accompanying Consolidated Balance Sheets. The carrying amounts of the Company’s debt approximate fair value because the rates are floating rates based on the prime lending rate, which approximates market rates (see Note 5) and represents a Level 2 fair value measurement. 8 Table of Contents Separate disclosure is required for assets and liabilities measured at fair value on a recurring basis from those measured at fair value on a non-recurring basis. Assets recorded at fair value on a non-recurring basis, such as property and equipment and intangible assets are recognized at fair value when they are impaired. During the nine months ended September 30, 2025 and year ended December 31, 2024, the Company had no assets or liabilities that were measured at fair value on a non-recurring basis. ​ 4. Accrued Expenses Accrued expenses and other current liabilities consist of the following (in thousands): ​ ​ ​ ​ ​ ​ ​ ​ ​ September 30, 2025 ​ December 31, 2024 Accrued professional services $ 403 ​ $ 401 Accrued payroll and employee benefits ​ 2,411 ​ 3,079 Accrued research and development ​ 4,564 ​ 6,443 Lease obligation, current portion ​ 247 ​ ​ 279 Accrued interest and other ​ 177 ​ 55 Total accrued expenses and other current liabilities ​ $ 7,802 ​ $ 10,257 ​ ​ 5. Term Loan On May 13, 2025 (“Closing Date”), the Company and certain of its subsidiaries entered into a Loan and Security Agreement (“Loan Agreement”) with Hercules Capital, Inc. (“Hercules”) and the lenders party thereto, pursuant to which the lenders will make available up to four tranches of term loans in an aggregate principal amount of $ 100.0 million (the “Term Loan”), subject to certain terms and conditions. Under the terms of the Loan Agreement, the first Term Loan tranche was drawn down on the Closing Date in an aggregate principal amount of $ 15.0 million. Upon the achievement of certain milestones and subject to other terms and conditions set out in the Loan Agreement, (i) the second Term Loan tranche will be made available in an aggregate principal amount of up to $ 25.0 million and (ii) the third Term Loan tranche will be made available in an aggregate principal amount of up to $ 15.0 million. The fourth Term Loan tranche will be made available in an aggregate principal amount of up to $ 45.0 million subject to the approval of the lenders. The Term Loan will mature on January 1, 2029 (the “Maturity Date”). The Term Loan bears interest equal to the greater of (a) the prime rate as reported in The Wall Street Journal plus 2.45 % and (b) (i) 9.95 % until December 31, 2025, and (ii) 9.45 % thereafter (the “Interest Rate”). The Company may make payments of interest only through June 1, 2027, which will be extended to December 1, 2027, June 1, 2028, or December 1, 2028, if certain conditions described in the Loan Agreement are met. Thereafter, the Company is obligated to make payments that will include installments of principal and interest through the Maturity Date. The Loan Agreement includes customary representations and warranties and covenants associated with the Term Loan. Such terms include (1) covenants concerning financial and other reporting obligations, and (2) certain limitations on indebtedness, liens, investments, distributions (including dividends), collateral, transfers, mergers or acquisitions, taxes, corporate changes, and deposit accounts. Compliance with the financial covenant will be conditionally waived pursuant to the terms of the Loan Agreement when the Company’s market capitalization exceeds $ 800 million. The Loan Agreement includes customary events of default, including payment defaults, breaches of representations and warranties, breaches of covenants following any applicable cure period and the occurrence of certain events that could reasonably be expected to have a “material adverse effect” as set forth in the Loan Agreement. As of September 30, 2025, the Company was in compliance with the covenants under the Loan Agreement. The obligation under the Loan Agreement is secured by a security interest in substantially all of the Company’s assets and the assets of its subsidiaries that are co-borrowers or guarantors. Upon the occurrence of an event of default, Hercules will be entitled to exercise remedies, including acceleration of the Term Loan obligations and foreclosure on collateral. 9 Table of Contents The Loan Agreement provides for a prepayment charge equal to 3.0 % of the outstanding principal balance of the Term Loan if prepayment is made within the twelve months after closing, 2.0 % if within the twenty-four months after closing, 1.0 % if within the thirty-six months after closing and 0.0 % thereafter. The Loan Agreement provides for an end of term charge of 6.25 % of the funded loan amount, due at the earlier of prepayment or maturity. Pro-rata payment of any earned end of term charge will be due upon any partial prepayment (the “End of Term Charge”). In addition, the Loan Agreement requires the Company to pay a facility charge of 1.0 % of the Term Loan funded due at the Closing Date and of each subsequent Term Loan tranche at the time such tranche is funded. The Company accounted for the End of Term Charge, Facility Charge, and other direct costs incurred in connection with the Loan Agreement as a debt discount and issuance costs, and they are being amortized over the term of the loan using the effective interest method. The effective interest rate on the Term Loan is 14.4 %. The Company incurred interest expense on the Term Loan, including debt discount and issuance costs amortization, of $ 0.5 million and $ 0.8 million during the three and nine months ended September 30, 2025, respectively. The Term Loan consists of the following (in thousands): ​ ​ ​ ​ ​ ​ ​ ​ ​ September 30, 2025 ​ December 31, 2024 Term loan principal amount $ 15,000 $ — End of term charge ​ ​ 937 ​ ​ — Unamortized discount and issuance costs ​ ​ ( 1,492 ) ​ ​ — Total term loan ​ ​ 14,445 ​ ​ — Less: current portion of term loan ​ — ​ — Total term loan, net of current portion ​ $ 14,445 ​ $ — ​ Future principal loan payments on the currently outstanding Term Loan as of September 30, 2025 are as follows (in thousands): ​ ​ ​ ​ 2025 - remainder of the year ​ $ — 2026 ​ — 2027 ​ 4,449 2028 ​ 7,266 2029 ​ ​ 3,285 Total future principal payments ​ 15,000 Add: End of term charge ​ ​ 937 Less: Unamortized discount and issuance costs ​ ( 1,492 ) Less: Current portion of term loan ​ ​ — Total term loan, net of current portion ​ $ 14,445 ​ ​ ​ 6. Other Noncurrent Liabilities The Company’s other noncurrent liabilities are summarized as follows (in thousands): ​ ​ ​ ​ ​ ​ ​ ​ ​ September 30, 2025 ​ December 31, 2024 Research and development incentive credit ​ $ 4,416 ​ $ 3,746 Lease obligation, long-term portion ​ 1,213 ​ ​ 1,402 Conditional economic incentive grants ​ 160 ​ 160 Other ​ 6 ​ 22 Total other noncurrent liabilities ​ $ 5,795 ​ $ 5,330 ​ ​ ​ ​ 10 Table of Contents 7. Stockholders’ Equity The Amended and Restated Certificate of Incorporation, as amended (“Charter”), authorized the Company to issue 200,000,000 shares of common stock, par value $ 0.0001 per share. As of September 30, 2025, the Company had 95,598,665 shares of common stock issued and outstanding . Each share of common stock entitles the holder to one vote on all matters submitted to a vote of the Company’s stockholders. Common stockholders are not entitled to receive dividends, unless declared by the board of directors. The Charter also authorized the Company to issue 1,000,000 shares of preferred stock, par value $ 0.0001 per share. As of September 30, 2025, the Company had no shares of preferred stock issued and outstanding . At-the-Market Offerings On February 27, 2025, the Company entered into an Equity Distribution Agreement (the “2025 Agreement”) with Leerink Partners LLC, Piper Sandler & Co. and Stifel, Nicolaus & Company, Incorporated, serving as sales agents (the “2025 Sales Agents”) with respect to an at-the-market offerings program under which the Company may offer and sell, from time to time at its sole discretion, shares of its common stock, having an aggregate offering price of up to $ 150.0 million (the “2025 Shares”) through the 2025 Sales Agents (the “2025 Offering”). All Shares offered and sold in the 2025 Offering will be issued pursuant to the Company’s Registration Statement on Form S-3 filed with the SEC on February 27, 2025, which was declared effective on March 13, 2025, and the prospectus supplements related to the 2025 Offering that form a part of the Registration Statement. The Company capitalized approximately $ 0.3 million of other offering costs which will offset the proceeds received from the shares sold under the 2025 Agreement. During the nine months ended September 30, 2025, the Company has sold 18,524,709 shares of common stock under the 2025 Agreement resulting in approximately $ 81.9 million in proceeds, net of $ 2.7 million commission and other offering costs, and as of September 30, 2025, $ 65.4 million remained available to be sold under the 2025 Agreement. As of September 30, 2025, there was $ 0.1 million deferred offering costs included in prepaid expenses and other current assets on the accompanying consolidated balance sheets. On February 28, 2023, the Company entered into an Equity Distribution Agreement (the “2023 Agreement”) with Evercore Group L.L.C., JMP Securities LLC and B. Riley Securities, Inc., serving as sales agents (the “2023 Sales Agents”), with respect to an at-the-market offerings program under which the Company offered and sold shares of its common stock, having an aggregate offering price of up to $ 150.0 million (the “2023 Shares”) through the 2023 Sales Agents (the “2023 Offering”). All 2023 Shares offered and sold in the 2023 Offering were issued pursuant to the Company’s Registration Statement on Form S-3 filed with the SEC on February 28, 2023. During the nine months ended September 30, 2025, the Company has sold 4,467,866 shares of common stock under the 2023 Agreement resulting in approximately $ 30.2 million in proceeds, net of $ 1.0 million commission and other offering costs. Since inception through the expiration of the 2023 Agreement in February 2025, the Company sold 26,129,903 shares of common stock under the 2023 Agreement, resulting in approximately $ 126.8 million in proceeds, As of September 30, 2025, there were no remaining shares available under the 2023 Agreement as the 2023 Agreement was terminated. ​ 8. Stock-Based Compensation 2017 Omnibus Incentive Plan (Omnibus Plan) The Company’s Omnibus Plan provides for an annual increase on January 1 of each year, commencing in 2019 and ending on and including January 1, 2027, up to an amount equal to the lowest of (i) 4 % of the total number of shares of common stock outstanding on a fully diluted basis as of December 31 of the immediately preceding calendar year, and (ii) such number of shares of common stock, if any, determined by the Company’s board of directors. Accordingly, on January 1, 2025, the number of shares of Common Stock reserved and available for issuance under the Omnibus Plan increased by 3,193,659 shares of common stock. 11 Table of Contents Stock Options The Company’s stock option awards generally vest over four years and typically have a contractual life of ten years . As of September 30, 2025, there was $ 20.2 million of unrecognized compensation cost related to stock options, which is expected to be recognized over a weighted-average period of 2.6 years. During the nine months ended September 30, 2025, the Company granted 2,672,150 stock options with a weighted average exercise price of $ 5.86 and per share weighted average grant date fair value of $ 4.74 . Information related to stock options outstanding as of September 30, 2025 is as follows (in thousands, except share, exercise price, and contractual term): ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Weighted-Average ​ ​ ​ ​ ​ ​ Weighted- ​ Remaining ​ ​ ​ ​ ​ Number of ​ Average ​ Contractual Term ​ Aggregate Intrinsic ​ ​ Stock Options ​ Exercise Price ​ (Years) ​ Value Outstanding, December 31, 2024 6,630,477 ​ $ 9.32 6.0 ​ $ 5,839 Granted 2,672,150 ​ $ 5.86 ​ Exercised ( 14,167 ) ​ $ 2.91 ​ Forfeited or expired ( 627,103 ) ​ $ 9.56 ​ Outstanding, September 30, 2025 8,661,357 ​ $ 8.24 5.9 ​ $ 1,076 Exercisable, September 30, 2025 4,502,219 ​ $ 9.23 5.9 ​ $ 1,036 Vested and expected to vest, September 30, 2025 8,287,035 ​ $ 8.29 5.9 ​ $ 1,072 ​ Restricted Stock Units (RSUs) During the nine months ended September 30, 2025, the Company granted 577,700 shares of RSUs with a weighted average grant date fair value of $ 6.31 which vest over four years . As of September 30, 2025, the Company had unvested RSUs of 1,135,950 shares with total unrecognized compensation expense of $ 6.3 million, which the Company expects to recognize over a weighted average period of approximately 2.7 years. During the nine months ended September 30, 2025, the Company issued 167,880 shares of unrestricted common stock as a result of the vesting of 267,903 RSUs net of 100,023 shares of common stock withheld to satisfy tax withholding obligations. 2019 Employee Stock Purchase Plan (“ESPP”) Under the ESPP, employees purchased 71,342 shares of the Company’s common stock for $ 0.3 million during the nine months ended September 30, 2025. Stock-based Compensation Expense Stock-based compensation expense is classified in the unaudited consolidated Statements of Operations and Comprehensive Loss for the three and nine months ended September 30, 2025 and 2024 as follows (in thousands): ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Three Months Ended Nine Months Ended ​ ​ September 30, ​ September 30, ​ ​ 2025 2024 ​ 2025 2024 Research and development ​ $ 1,522 ​ $ 1,545 ​ $ 4,851 ​ $ 4,794 General and administrative ​ 2,032 ​ 1,533 ​ 6,284 ​ 6,245 Total ​ $ 3,554 ​ $ 3,078 ​ $ 11,135 ​ $ 11,039 ​ ​ ​ 9. Net Loss Per Share Because the Company has reported net loss attributable to common stockholders for the three and nine months ended September 30, 2025 and 2024, basic and diluted net loss per share attributable to common stockholders in each period are the same. 12 Table of Contents Basic net loss per share attributable to common stockholders is computed by dividing the net loss attributable to common stockholders by the weighted average numbers of shares of common stock outstanding for the period. Diluted net loss per share is calculated by adjusting weighted average shares outstanding for the dilutive effect of common stock equivalents outstanding for the period. As such, all unvested RSUs and stock options have been excluded from the computation of diluted weighted average shares outstanding because such securities would have an anti-dilutive impact for all periods presented. Potential common shares, issuable upon conversion, vesting, or exercise of unvested RSUs and stock options, that are excluded from the computation of diluted weighted-average shares outstanding, as they are anti-dilutive, are as follows: ​ ​ ​ ​ ​ ​ ​ Three and Nine Months Ended ​ ​ September 30, ​ ​ 2025 ​ 2024 Common stock options 8,725,956 6,435,016 Restricted stock units 1,135,950 ​ 784,227 ​ ​ ​ 10. Commitments and Contingencies Spitfire Acquisition In July 2019, the Company entered into the Spitfire merger agreement to acquire all of the equity interests of Spitfire Pharma, Inc. (“Spitfire”). Spitfire was a privately held, preclinical pharmaceutical company developing novel peptide products for pharmaceutical indications, including pemvidutide for the treatment of MASH. As part of the agreement, the Company is obligated to make payments of up to $ 80.0 million upon the achievement of specified worldwide net sales of all products developed using the technology acquired from Spitfire Pharma, Inc. (the “Sales Milestone”) within ten years following the approval of a new drug application filed with the U. S. Food and Drug Administration (the “FDA”). The contingent payments related to the Sales Milestones are predominately cash-based payments accounted for under FASB Accounting Standards Codification Topic 450, Contingencies. Accordingly, the Company will recognize the Sales Milestones when the contingency is probable and the amount can be reasonably estimated. Litigation On August 5, 2025, a class action complaint was filed in federal district court in the District of Maryland, Southern Division, naming as defendants the Company and two of the Company’s executive officers, which is now captioned In re Altimmune, Inc. Securities Litigation , Case No. 8:25-cv-02581 (D. Md.) (the “Securities Class Action”). The Securities Class Action alleges that the defendants violated Sections 10(b) and 20(a) of the Securities Exchange Act of 1934, as amended, and Rule 10b-5 thereunder, by making false and misleading statements and omissions of material fact to the investing public including the plaintiff and class members, who purchased or otherwise acquired the Company’s common stock between August 10, 2023 and June 25, 2025, including relating to pemvidutide and our IMPACT Phase 2b trial of pemvidutide in MASH. The plaintiff and class members seek, among other things, to have the action maintained as a class action under Rule 23 of the Federal Rules of Civil Procedure and for the defendants to pay damages, interest, and an award of costs, including attorneys’ fees. On October 16, 2025, the court appointed lead plaintiffs for the litigation. On October 29, 2025, the court entered an order requiring lead plaintiffs to file an amended complaint by November 26, 2025, and for defendants to file an answer or notice of intent to file a motion to dismiss such amended complaint by December 10, 2025. The Company intends to defend vigorously against this litigation. On September 29, 2025, a shareholder derivative complaint was filed in federal district court in the District of Maryland, purportedly on behalf of the Company, naming as defendants two of the Company’s then-executive officers and eight of the Company’s current and former board members, captioned Alaraidah v. Altimmune, Inc., et al ., No. 8:25-cv-03223 (D. Md.) (the “Derivative Action”). The complaint is based upon allegations that are similar to those alleged in a class action complaint previously filed against us in the Securities Class Action and alleges claims for violations of 13 Table of Contents Section 14(a) of the Securities Exchange Act of 1934, breaches of fiduciary duty, unjust enrichment, abuse of control, gross mismanagement, waste of corporate assets, and contribution under Sections 10(b) and 21D of the Securities Exchange Act of 1934 based on the defendants purportedly making or causing to be made false and misleading statements and omissions of material fact between August 10, 2023 and June 25, 2025. The complaint seeks unspecified monetary relief, restitution, costs, and equitable relief. The Company intends to defend vigorously against this litigation. The Company is a party to various contracts that are subject to potential disputes, litigation, and claims arising in the ordinary course of business, none of which are currently reasonably possible or probable of material loss. ​ 11. Segment Information The Company is a late clinical-stage biopharmaceutical company developing novel peptide-based therapeutics for liver and cardiometabolic diseases. The Company’s lead program is pemvidutide, a balanced 1:1 glucagon/GLP-1 dual receptor agonist for the treatment of MASH, AUD and ALD. To date, the Company has not generated any revenue from the sale of any products. The chief operating decision maker assesses the performance of the Company and decides how to allocate resources based solely on net (loss) income, which is also reported on the consolidated statements of operations and consolidated loss as net (loss) income. The measure of segment assets is reported on the consolidated balance sheet as total assets. ​ 12. Subsequent Events The Company evaluated subsequent events through the issuance date of the financial statements on this quarterly report on Form 10-Q. During October 2025 and through the date of the issuance of the financial statements, the Company raised $ 33.8 million in net proceeds through the issuance of 8,743,720 shares of common stock pursuant to the 2025 Offering. On November 5, 2025, (the “Amendment Closing”), the Company entered into an amendment to the Loan Agreement with Hercules and the lenders party thereto, pursuant to which the lenders will, subject to certain terms and conditions, increase the availability under the Term Loan from an aggregate principal amount of $ 100.0 million to $ 125.0 million. The Term Loan, as amended, is structured in four tranches. As disclosed in Note 5, the first Term Loan tranche was drawn down on the Closing Date in an aggregate principal amount of $ 15.0 million. The second Term Loan tranche was drawn down on the Amendment Closing in an aggregate principal amount of $ 20.0 million. Upon the achievement of certain milestones and subject to other terms and conditions set out in the Loan Agreement, as amended, the third Term Loan tranche will be made available in an aggregate principal amount of up to $ 10.0 million. The fourth Term Loan tranche will be made available in an aggregate principal amount of up to $ 80.0 million subject to the approval of the lenders. The Term Loan, as amended, bears interest equal to the greater of (a) 9.70 % per annum and (b) the prime rate as reported in The Wall Street Journal plus 2.45 % per annum. The interest-only period has been extended to 30 months from May 13, 2025. ​ ​ 14 Table of Contents