Gunathilaka, 27, was suspended on Sunday by Sri Lanka Cricket over a "misconduct" charge after a close associate of his was arrested for allegedly raping a Norwegian woman in the team hotel in Colombo.
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The Sri Lanka board had said Gunathilaka, who was allegedly in the room at the same time but was not arrested, will remain suspended pending a disciplinary inquiry. It was unclear, however, when the inquiry will begin.
His suspension is a blow to Sri Lanka as Gunathilaka was the side's second-highest-scoring batsman in the 2-0 Test series whitewash completed on Monday.
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The ODI series begins on Sunday at Dambulla and ends on August 12 in Colombo. A one-off Twenty20 is due to be played in Colombo on August 14.
All-rounder Shehan Jayasuriya, 26, is expected to replace Gunathilaka, while uncapped Prabath Jayasuriya was brought in to the squad.
Sri Lanka ODI squad: Angelo Mathews (Captain), Dasun Shanaka, Kusal Perera, Dhananjaya de Silva, Upul Tharanga, Kusal Mendis, Thisara Perera, Niroshan Dickwella, Suranga Lakmal, Lahiru Kumara, Kasun Rajitha, Akila Dananjaya, Prabath Jayasuriya, Lakshan Sandakan, and Shehan Jayasuriya.
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