JOINDER TO THE SECOND AMENDED AND RESTATED STOCKHOLDERS? AGREEMENT

EXHIBIT 4.9

EXECUTION COPY

JOINDER TO THE SECOND AMENDED AND RESTATED

STOCKHOLDERS’ AGREEMENT

THIS JOINDER TO THE SECOND AMENDED AND RESTATED STOCKHOLDERS’ AGREEMENT (the “ Joinder Agreement ”) is entered into as of February 14, 2006 (the “ Effective Date ”) by and among Pharmasset, Inc., a Delaware corporation (the “ Company ”), the Raymond F. Schinazi 2005 Qualified Annuity Trust, a Georgia trust (the “ Trust ”) and Raymond F. Schinazi, Ph.D., individually and as trustee (the “ Trustee ”) of the Trust (“ Schinazi ”).

RECITALS

WHEREAS, Schinazi and the Company and certain other stockholders are parties to the Second Amended and Restated Stockholders’ Agreement dated as of August 4, 2004 and as amended by an amendment dated as of October 26, 2004 (“ Stockholders’ Agreement ”);

WHEREAS, Section 5 of the Stockholders’ Agreement contains certain limitations on the transfer of shares of the Company’s Common Stock, $0.001 par value per share (the “ Common Stock ”);

WHEREAS, pursuant to the Accession Agreement (hereinafter defined), the Company agreed to permit the transfer of 1.0 million shares of Common Stock (the “ Transfer Shares ”) by Schinazi to the Trust under the 1998 Agreement (hereafter defined);

WHEREAS, Schinazi has requested that the Company record the foregoing transfer to the Trust of the Transfer Shares;

WHEREAS, the restrictions to such transfer of the Transfer Shares have been waived in the Waiver Agreement and Second Amendment to the Second Amended and Restated Stockholders’ Agreement by and among the Company and the signatories thereto, dated as of the Effective Date hereof (the “ Waiver ”), by (a) the Majority Investors and (b) Stockholders other than the Investors holding a majority of the Common Shares and Preferred Shares (on an as-if converted basis) owned by such Stockholders (as such terms are defined in the Stockholders’ Agreement) pursuant to the terms of the Stockholders’ Agreement; and

NOW, THEREFORE, in consideration of the mutual promises, representations, warranties, covenants and conditions set forth in this Joinder Agreement, the Company, Schinazi and the Trust (collectively, the “ Parties ”) hereby agree, as follows:

SECTION 1. THE TRANSFER.

1.1 Recording of Transfer . The Company acknowledges receipt of the notice of transfer by Schinazi, and upon surrender to the Company by Schinazi of the certificate (or

certificates, as the case may be) representing the Transfer Shares, the Company shall record the aforesaid transfer of the Transfer Shares to the Trust, and the Trust’s ownership of the Transfer Shares, on its books and records, and shall thereupon take such steps as are necessary promptly to deliver share certificates for the Transfer Shares to the Trust.

1.2 Rights and Obligations under Stockholders’ Agreement . The Company, Schinazi and the Trust each acknowledge, agree and confirm that, as of the Effective Date, by the Trust’s execution of this Joinder Agreement, the Trust will be deemed to be a party to the Stockholders’ Agreement, as amended from time to time, and one of the “Restricted Stockholders” and one of the “Buyers” for all purposes of the Stockholders’ Agreement, as amended from time to time, and shall have all of the rights and obligations of a Restricted Stockholder and of a Buyer thereunder as if it had been an original signatory to the Stockholders’ Agreement and were listed on Schedule A to the Stockholders’ Agreement under the heading “Restricted Stockholders.”

1.3 Trust’s Handling of Transfer Shares . The Trust agrees that, after the aforesaid transfer, (a) the Trust shall not transfer the Transfer Shares except in accordance with the applicable terms of the Stockholders’ Agreement, the Restricted Stock Purchase Agreement of Advisor dated June 19, 1998 (the “ 1998 Agreement ”), the Accession Agreement of the Trust dated as of September 26, 2005 (the “ Accession Agreement ”) and any lock-up agreement to which the Transfer Shares may from time to time be subject and (b) the Trust shall continue to hold such shares for the exclusive benefit of one or more of Schinazi’s spouse, children or grandchildren for estate planning purposes insofar as it is required to do so by the Stockholders’ Agreement and the 1998 Agreement. Nothing in this Joinder Agreement shall preclude the Trust from changing trustees or beneficiaries so long as the Trust is and will at all times be for the exclusive benefit of one or more “Family Member” of Schinazi, or, provided such transfer is made in accordance with the Stockholders’ Agreement, the 1998 Agreement, the Accession Agreement and any lock-up agreement to which the Transfer Shares may from time to time be subject, from further transferring the Transfer Shares.

SECTION 2. REPRESENTATIONS, WARRANTIES AND COVENANTS OF THE COMPANY

The Company hereby represents and warrants to, and covenants and agrees with Schinazi and the Trust, as of the Effective Date,

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T RUST J OINDER TO THE S ECOND A MENDED AND R ESTATED

S TOCKHOLDERS ’ A GREEMENT

SECTION 3. REPRESENTATIONS OF SCHINAZI AND THE TRUST.

Schinazi and the Trust hereby represent and warrant to, and covenant and agree with the Company, as of the Effective Date, that: