Innoviva, Inc. 10-K/A

10-K/A UNITED STATES SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549 FORM 10-K/A (Amendment No. 1) (Mark One) ☒ ANNUAL REPORT PURSUANT TO SECTION 13 OR 15(d) OF THE SECURITIES EXCHANGE ACT OF 1934 For the fiscal year ended December 31 , 2024 or ☐ TRANSITION REPORT PURSUANT TO SECTION 13 OR 15(d) OF THE SECURITIES EXCHANGE ACT OF 1934 For the transition period from to Commission File No. 000-30319 INNOVIVA, INC. (Exact name of registrant as specified in its charter) Delaware (State or other jurisdiction of incorporation or organization) 94-3265960 (I.R.S. Employer Identification No.) 1350 Old Bayshore Highway, Suite 400 Burlingame , CA (Address of principal executive offices) 94010 (Zip Code) Registrant’s telephone number, including area code: ( 650 ) 238-9600 Title of Each Class Trading Symbol(s) Name of Each Exchange On Which Registered Common Stock $0.01 Par Value INVA The Nasdaq Stock Market LLC SECURITIES REGISTERED PURSUANT TO SECTION 12(g) OF THE ACT: NONE Indicate by check mark if the registrant is a well‑known seasoned issuer, as defined in Rule 405 of the Securities Act. Yes ☒ No ☐ Indicate by check mark if the registrant is not required to file reports pursuant to Section 13 or Section 15(d) of the Act. Yes ☐ No ☒ 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 registrant is a large accelerated filer, an accelerated filer or a non-accelerated filer. See definition of “accelerated filer and large accelerated filer” in Rule 12b-2 of the Exchange Act (Check One): Large accelerated filer ☒ Accelerated filer ☐ Non‑accelerated filer ☐ Smaller reporting company ☐ Emerging growth company ☐ 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 has filed a report on and attestation to its management’s assessment of the effectiveness of its internal control over financial reporting under Section 404(b) of the Sarbanes-Oxley Act (15 U.S.C. 7262(b)) by the registered public accounting firm that prepared or issued its audit report. ☒ If securities are registered pursuant to Section 12(b) of the Act, indicate by check mark whether the financial statements of the registrant included in the filing reflect the correction of an error to previously issued financial statements. ☐ Indicate by check mark whether any of those error corrections are restatements that required a recovery analysis of incentive-based compensation received by any of the registrant’s executive officers during the relevant recovery period pursuant to §240.10D-1(b). ☐ Indicate by check mark whether the registrant is a shell company (as defined in Rule 12b‑2 of the Exchange Act). Yes ☐ No ☒ The aggregate market value of the voting and non-voting common equity held by non-affiliates of the registrant based upon the closing price of the registrant’s Common Stock on The Nasdaq Global Select Market on June 30, 2024 was $ 899,110,517 . This calculation does not reflect a determination that persons are affiliates for any other purpose. On February 14, 2025, there were 62,675,545 shares of the registrant’s Common Stock outstanding. DOCUMENTS INCORPORATED BY REFERENCE Specified portions of the registrant’s definitive Proxy Statement to be issued in conjunction with the registrant’s 2025 Annual Meeting of Stockholders, which is expected to be filed not later than 120 days after the registrant’s fiscal year ended December 31, 2024 , are incorporated by reference into Part III of this Annual Report. Except as expressly incorporated by reference, the registrant’s Proxy Statement shall not be deemed to be a part of this Annual Report on Form 10-K/A. EXPLANATORY NOTE This Amendment No. 1 on Form 10-K/A (the “Amendment”) amends the Annual Report on Form 10-K of Innoviva, Inc. (the “Company”) for the year ended December 31, 2024, originally filed on February 26, 2025 (the “Original Filing”), is being filed pursuant to and in compliance with the time requirements of Rule 3-09 of Regulation S-X, to amend Item 15, Exhibits and Financial Statement Schedules, to include the Audited Consolidated Financial Statements of Armata Pharmaceuticals, Inc. (“Armata”) at December 31, 2024 and 2023 and for the years then ended and the Consent of Ernst & Young LLP Independent Registered Public Accounting Firm of Armata as Exhibit 99.1 and Exhibit 23.3, respectively. These exhibits were not available at the time of the Original Filing. Additional information on the Audited Consolidated Financial Statements of Armata for the year ended December 31, 2022 can be found in the Company ’ s Amendment No. 2 on Form 10-K/A for the year ended December 31, 2023, filed on March 22, 2024, and is incorporated herein by reference. In accordance with applicable Securities and Exchange Commission (“SEC”) rules and as required by Rule 12b-15 under the Securities Exchange Act of 1934, as amended, this Amendment includes new certifications from the Company’s Principal Executive Officer and Principal Financial Officer dated as of the date of filing of this Amendment. This Amendment consists solely of the preceding cover page, this explanatory note, Part IV., Item 15., “Exhibits and Financial Statement Schedules,” in its entirety, the Exhibits, the signature page and the new certifications of the Company’s Principal Executive Officer and Principal Financial Officer. This Amendment does not reflect events occurring after the date of the Original Filing and does not amend or update in any way the disclosures made in the Original Filing, except as described above. In particular, the information included in this Amendment under Part II, Item 8 is identical in all respects to the information included under such caption in the Original Filing. This Amendment should be read in conjunction with the Original Filing and with the Company’s subsequent filings with the SEC. 3 PART IV ITEM 15. EXHIBITS AND FINANCIAL STATEMENT SCHEDULES (a) The following documents are filed as part of this Amendment No. 1 on Form 10‑K/A: 1. Financial Statements: The following financial statements, supplementary data and reports of independent public accountants appear in Part II, Item 8 of the Original Filing and are incorporated herein by reference: Consolidated Balance Sheets as of December 31, 2024 and 2023 Consolidated Statements of Income for each of the three years in the period ended December 31, 2024 Consolidated Statements of Comprehensive Income for each of the three years in the period ended December 31, 2024 Consolidated Statements of Stockholders’ Equity for each of the three years in the period ended December 31, 2024 Consolidated Statements of Cash Flows for each of the three years in the period ended December 31, 2024 Notes to the Consolidated Financial Statements Report of Independent Registered Public Accounting Firm, Deloitte & Touche LLP , San Jose, CA (PCAOB ID 34 ) 2. Financial Statement Schedules: All schedules have been omitted because of the absence of conditions under which they are required or because the required information, where material, is shown in the financial statements, financial notes or supplementary financial information. (b) Exhibits required by Item 601 of Regulation S‑K: The information required by this Item is set forth on the exhibit index that follows the signature page of this report. 4 Exhibits Incorporated by Reference Filed Herewith Exhibit Number Description Form Exhibit Filing Date/Period End Date 2.1 Agreement and Plan of Merger, dated as of May 23, 2022, by and among Innoviva, Inc., Innoviva Merger Sub, Inc. and Entasis Therapeutics 8-K 2.1 5/24/2022 2.2 Agreement and Plan of Merger, dated as of July 10, 2022, by and among Innoviva, Inc., Innoviva Acquisition Sub, Inc. and La Jolla Pharmaceutical Company 8-K 2.1 7/11/2022 3.1 Amended and Restated Certificate of Incorporation 8‑K 99.2 4/28/2016 3.2 Amended and Restated Bylaws, amended and restated as of January 1, 2023 8‑K 3.1 1/4/2023 4.1 Specimen certificate representing the common stock of the registrant 10‑K 4.1 12/31/2006 4.2 Indenture, dated as of January 24, 2013 by and between Theravance, Inc. and The Bank of New York Mellon Trust Company, N.A., as trustee 8‑K 4.1 1/25/2013 4.3 Form of 2.125% Convertible Subordinated Note Due 2023 (included in Exhibit 4.4 ) 8-K 4.1 1/25/2013 4.4 Indenture (including form of Note) with respect to Innoviva’s 2.50% Convertible Senior Notes due 2025, dated as of August 7, 2017, between Innoviva and The Bank of New York Mellon Trust Company, N.A., as trustee 8‑K 4.1 8/7/2017 4.5 Description of Registrant’s Securities Registered Pursuant to Section 12 of the Securities Exchange Act of 1934 10-K 4.9 2/19/2020 4.6 Indenture (including form of Note) with respect to Innoviva's 2.125% Convertible Senior Notes due 2028, dated as of March 7, 2022, between Innoviva, Inc. and The Bank of New York Mellon Trust Company, N.A., as trustee 8-K 4.1 3/8/2022 10.2 Collaboration Agreement between the registrant and Glaxo Group Limited, dated as of November 14, 2002 10‑Q 10.1 6/30/2014 10.3 Amended and Restated Investors’ Rights Agreement by and among the registrant and the parties listed therein, dated as of May 11, 2004 S‑1 10.13 6/10/2004 10.4* Strategic Alliance Agreement between the registrant and Glaxo Group Limited, dated as of March 30, 2004 10‑K 10.13 12/31/2013 10.5+ Description of Cash Bonus Program, as amended 10‑K 10.22 12/31/2009 10.6+ Amendment to Change in Control Severance Plan effective December 16, 2009 10‑K 10.47 12/31/2009 10.7+ 2009 Change in Control Severance Plan adopted December 16, 2009 10‑K 10.48 12/31/2009 10.8 Second Amendment to Amended and Restated Governance Agreement among the registrant, Glaxo Group Limited, GlaxoSmithKline plc and GlaxoSmithKline LLC, dated as of November 29, 2010 8‑K 10.2 11/29/2010 10.9 Amendment to Strategic Alliance Agreement, dated October 3, 2011 10‑K 10.34 12/31/2011 10.10+ 2012 Equity Incentive Plan, as approved by the board of directors February 8, 2012 and approved by stockholders May 16, 2012 and forms of equity award 10‑Q 10.38 6/30/2012 10.11 Base Capped Call Transaction, dated January 17, 2013 8‑K 10.1 1/23/2013 10.12 Additional Capped Call Transaction, dated January 18, 2013 8‑K 10.2 1/23/2013 10.13 Master Agreement by and among Theravance, Inc., Theravance Biopharma, Inc. and Glaxo Group Limited, dated March 3, 2014 8‑K/A 10.1 3/6/2014 10.14* Collaboration Agreement Amendment by and between Theravance, Inc. and Glaxo Group Limited, dated March 3, 2014 8‑K/A 10.2 3/6/2014 10.15* Strategic Alliance Agreement Amendment by and between Theravance, Inc. and Glaxo Group Limited, dated March 3, 2014 8‑K/A 10.3 3/6/2014 10.16 Transition Services Agreement between Theravance and Theravance Biopharma, dated June 2, 2014 8‑K 10.2 6/5/2014 10.17 Tax Matters Agreement between Theravance and Theravance Biopharma, dated June 2, 2014 8‑K 10.3 6/5/2014 5 10.18 Employee Matters Agreement between Theravance and Theravance Biopharma, dated June 1, 2014 8‑K 10.4 6/5/2014 10.19 Theravance Respiratory Company, LLC Limited Liability Company Agreement between Theravance and Theravance Biopharma, dated May 31, 2014 8‑K 10.5 6/5/2014 10.20 Amendment/Clarification to Transition Services Agreement between Theravance and Theravance Biopharma, dated March 2, 2015 10‑Q 10.64 3/31/2015 10.21+ First Amendment to 2009 Change In Control Severance Plan (Renamed 2009 Severance Plan) 8‑K 10.2 7/29/2015 10.22 Form of Notice of Performance‑Based Restricted Stock Award and Restricted Stock Award Agreement under 2012 Equity Incentive Plan (director form) 10‑K 10.76 2/23/2018 10.23+ Second Amendment to 2009 Severance Plan 10‑Q 10.81 7/26/2018 10.24+ Offer Letter with Marianne Zhen, dated September 7, 2018 8‑K 10.1 9/11/2018 10.25+ Offer Letter between Innoviva, Inc. and Pavel Raifeld, dated May 20, 2020 8‑K 10.1 5/26/2020 10.26+ Offer Letter between Innoviva, Inc. and Pavel Raifeld, dated April 29, 2022 8-K 10.1 5/2/2022 10.27 Strategic Advisory Agreement, dated as of December 11, 2020, by and between Sarissa Capital Management LP and Innoviva, Inc. 8‑K 10.1 12/14/2020 10.28 Amended and Restated Limited Partnership Agreement of ISP Fund LP, dated as of December 11, 2020, by and among ISP Fund LP, Sarissa Capital Fund GP LP, Innoviva Strategic Partners LLC and the other parties named therein 8‑K 10.2 12/14/2020 10.29 Share Repurchase Agreement, dated as of May 2021, by and between Innoviva, Inc. and Glaxo Group Limited 8-K 10.1 5/20/2021 10.30 Letter Agreement, dated as of May 20, 2021, by and among Innoviva Strategic Partners LLC, ISP Fund LP and Sarissa Capital Fung GP LP 8-K 10.2 5/20/2021 10.31 Capped Call Confirmation dated March 2, 2022, by and among Innoviva, Inc., Bank of America, N.A., Goldman Sachs & Co. LLC and Deutsche Bank AG, London Branch 8-K 10.1 3/8/2022 10.32 Amendment No. 1 to the Investor Rights Agreement, dated May 23, 2022, by and among Innoviva, Inc. and Entasis Therapeutics Holdings Inc. 8-K 10.1 5/24/2022 10.33 Support Agreement, dated July 10, 2022, by and among Innoviva, Inc., Innoviva Acquisition Sub, Inc., Tang Capital Partners, LP and Kevin C. Tang Foundation 8-K 10.1 7/11/2022 10.34 Equity Purchase Agreement, dated July 13, 2022, by and among Innoviva, Inc., Innoviva TRC Holdings LLC and Royalty Pharma Investments 2019 ICAV 8-K 10.1 7/13/2022 10.35 Third Amendment to Collaboration Agreement, dated July 13, 2022, by and among Innoviva, Inc., Glaxo Group Limited, and Theravance Respiratory Company, LLC. 8-K 10.2 7/13/2022 10.36+ Transition Agreement between Larry Edwards and Innoviva Specialty Therapeutics, Inc., dated February 23, 2023, and Release of Claims form signed by Larry Edwards, dated April 5, 2023 10-Q 10.1 5/9/2023 10.37 2023 Employee Stock Purchase Plan DEF 14A 4/28/2023 10.38+ Offer Letter between Innoviva, Inc. and Stephen Basso dated July 28, 2023 8-K 10.1 8/25/2023 19 Amended and Restated Insider Trading Policy and Guidelines with Respect to Certain Transactions in Securities (effective as of March 15, 2023) X** 21.1 List of Subsidiaries X** 23.1 Consent of Deloitte & Touche LLP, Independent Registered Public Accounting Firm X** 23.3 Consent of Ernst & Young LLP, Independent Registered Public Accounting Firm of Armata Pharmaceuticals, Inc. X 6 24.1 Power of Attorney (see signature page to this Annual Report on Form 10‑K) X** 31.1 Certification of Principal Executive Officer Pursuant to Rule 13a‑14 under the Securities Exchange Act of 1934 X 31.2 Certification of Principal Financial Officer Pursuant to Rule 13a‑14 under the Securities Exchange Act of 1934 X 32# Certifications Pursuant to 18 U.S.C. Section 1350 97 Innoviva Clawback Policy (effective as of October 2, 2023) 10-K 97 2/29/2024 99.1 Audited Consolidated Financial Statements of Armata Pharmaceuticals, Inc. at December 31, 2024 and 2023 and for the two years ended December 31, 2024 X 101.INS Inline XBRL Instance Document - the instance document does not appear in the Interactive Data File because its XBRL tags are embedded within the Inline XBRL document. X** 101.SCH Inline XBRL Taxonomy Extension Schema Document X** 101.CAL Inline XBRL Taxonomy Extension Calculation Linkbase Document X** 101.DEF Inline XBRL Taxonomy Extension Definition Linkbase Document X** 101.LAB Inline XBRL Taxonomy Extension Label Linkbase Document X** 101.PRE Inline XBRL Taxonomy Extension Presentation Linkbase Document X** 104 Cover Page Interactive Data File (embedded within the Inline XBRL document) X** + Management contract or compensatory plan or arrangement required to be filed pursuant to Item 15(b) of Form 10‑K. * Confidential treatment has been granted for certain portions which are omitted in the copy of the exhibit electronically filed with the Securities and Exchange Commission. The omitted information has been filed separately with the Securities and Exchange Commission pursuant to Innoviva, Inc.’s application for confidential treatment. ** Previously filed with the Original Filing on February 26, 2025. # Furnished herewith. 7 SIGNATURES Pursuant to the requirements of Section 13 or 15(d) of the Securities Exchange Act of 1934, the Registrant has duly caused this report to be signed on its behalf by the undersigned, thereunto duly authorized. INNOVIVA, INC. Date: March 24, 2025 By: /s/ PAVEL RAIFELD Pavel Raifeld Chief Executive Officer 8