Amendment: SEC Form SCHEDULE 13D/A filed by Assembly Biosciences Inc.

Item 2(c) is amended and restated to read as follows: The principal business of the Reporting Person is to develop and commercialize innovative medicines in areas of unmet medical need and engage in any other activity or business lawfully carried on by a corporation organized under the laws of the State of Delaware. The directors and executive officers of the Reporting Person are set forth on Exhibit 99.1 filed herewith. Exhibit 99.1 sets forth the following information with respect to each such person: (i) name; (ii) business address; (iii) position with the Reporting Person and present principal occupation or employment and, for persons not employed by the Reporting Person, the name, principal business and address of any corporation or other organization in which such employment is conducted; and (iv) citizenship.

Item 2(f) is amended and restated to read as follows: The jurisdiction of organization of the Reporting Person is set forth in subsection (a) above. The citizenship of each of the individuals referred to in Exhibit 99.1 is set forth on Exhibit 99.1.

Item 3 is amended to add the following paragraph immediately following the last paragraph: On August 8, 2025, Gilead entered into a Securities Purchase Agreement with the Issuer (the "2025 Purchase Agreement"), pursuant to which Gilead purchased from the Issuer 2,295,920 shares of Common Stock, a Series A warrant to purchase 1,147,960 shares of Common Stock (the "Series A Warrant"), and a Series B warrant to purchase 1,147,960 shares of Common Stock (the "Series B Warrant"), at a combined purchase price of $19.60 per share of Common Stock and accompanying one half of one Series A Warrant and one half of one Series B Warrant, which purchase closed on August 11, 2025. The total consideration for such purchase was approximately $45 million and such consideration was obtained from the available cash resources of Gilead.

Item 4 is amended to add the following immediately following the last paragraph: 2025 Securities Purchase Agreement and Warrants On August 8, 2025, pursuant to the 2025 Purchase Agreement, Gilead purchased from the Issuer 2,295,920 shares of Common Stock, the Series A Warrant, and the Series B Warrant, at a combined purchase price of $19.60 per share of Common Stock and accompanying one half of one Series A Warrant and one half of one Series B Warrant. The Series A Warrant is exercisable, in whole or in part, immediately at an exercise price of $21.60 per share and expires on the earlier of (i) 5:00 p.m. (New York City time) on August 11, 2030 and (ii) the date that is 30 days after the public announcement (whether by press release, document filed or furnished with the SEC, or other form of public announcement) that the Issuer has completed enrollment (of at least 200 patients total) for its Phase 2 clinical study evaluating ABI-5366 vs. valacyclovir. The Series B Warrant is exercisable, in whole or in part, on or after November 15, 2026 at an exercise price of $21.60 per share and expires on December 31, 2026, provided that the Series B Warrant will automatically terminate in full and be extinguished and shall no longer be exercisable in the event that the Issuer publicly announces prior to November 15, 2026 that it has received at least $75.0 million in the aggregate of non-dilutive capital in connection with a collaboration agreement. Each of the Series A Warrant and the Series B Warrant cannot be exercised by Gilead if, after giving effect thereto, Gilead would beneficially own, as determined in accordance with Section 13(d) of the Securities Exchange Act of 1934, as amended, more than 19.99% of the Issuer's outstanding shares of Common Stock, subject to certain exceptions. The foregoing descriptions of the 2025 Purchase Agreement, the Series A Warrant, and the Series B Warrant are not complete and are subject to and qualified in their entirety by reference to the full text of such documents, which are attached as Exhibits 99.2, 99.3, and 99.4 hereto and incorporated herein by reference.

Item 5(a) of the Schedule 13D is hereby amended and restated to read as follows: Number of shares beneficially owned: Gilead Sciences, Inc. - 4,505,391 Shares Percent of class: Gilead Sciences, Inc. - 29.0% The percent ownership was calculated based upon 15,560,009 shares of Common Stock of the Issuer issued and outstanding upon the closing of the Issuer's most recent public offering, which was completed on August 11, 2025, as disclosed in the Prospectus Supplement.

Item 5(b) of the Schedule 13D is hereby amended and restated to read as follows: (i) Sole power to vote or to direct the vote: Gilead Sciences, Inc. - 4,505,391 shares (ii) Shared power to vote or to direct the vote: Gilead Sciences, Inc. - 0 shares (iii) Sole power to dispose or to direct the disposition of: Gilead Sciences, Inc. - 4,505,391 shares (iv) Shared power to dispose or to direct the disposition of: Gilead Sciences, Inc. - 0 shares To the best knowledge of the Reporting Person, none of the individuals listed on Exhibit 99.1 beneficially owns any of the Issuer's Common Stock. The Reporting Person beneficially owns a warrant to purchase 179,500 shares of Common Stock (the "2024 Warrant") that was acquired from the Issuer on June 17, 2024, the Series A Warrant, and the Series B Warrant (collectively, the "Warrants"). Each of the Warrants is subject to a limitation pursuant to which the Reporting Persons may not exercise such Warrant if such exercise would cause the Reporting Person to beneficially own Common Stock in an amount exceeding the "Beneficial Ownership Limitation" (as defined in such Warrant) then in effect. The Beneficial Ownership Limitation with respect to each Warrant is subject to adjustment upon 61 days' notice by the holder of such Warrant to the Issuer and, as of the date of this Amendment No. 3, was 19.99% of the number of shares of Common Stock outstanding. As a result, none of the aggregate of 2,475,420 shares of Common Stock underlying the Warrants are deemed to be beneficially owned by the Reporting Persons.

Item 5(c) of the Schedule 13D is hereby amended and restated to read as follows: Except as reported in this Amendment No. 3, neither the Reporting Person nor, to the best knowledge of the Reporting Person, any of the individuals listed on Exhibit 99.1 have effected any transactions in the Common Stock during the past sixty (60) days.

Exhibit 99.1 - List of Executive Officers and Directors of Gilead Sciences, Inc. Exhibit 99.2 - Securities Purchase Agreement, dated August 8, 2025, by and between the Company and Gilead Sciences, Inc. (incorporated by reference to Exhibit 10.1 to the Issuer's Current Report on Form 8-K filed with the SEC on August 11, 2025) Exhibit 99.3 - Private Placement Class A Warrant (incorporated by reference to Exhibit 4.4 to the Issuer's Current Report on Form 8-K filed with the SEC on August 11, 2025) Exhibit 99.4 - Private Placement Class B Warrant (incorporated by reference to Exhibit 4.5 to the Issuer's Current Report on Form 8-K filed with the SEC on August 11, 2025)