He will become the ninth captain for Sri Lanka in the shortest format of the game. He has so far 42 T20Is.
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Situation changed after the World XI series in September, in which Pakistan Cricket Board ensured safety of the all the cricketers.
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The 18-year-old all rounder Perera was also a part of the touring World XI side and played an important role in winning the 2nd T20I.
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However, it is still not clear whether Tharanga will make to the squad of 15 or not.
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It all started when as many as 40 centrally contracted Sri Lanka cricketers signed a petition depicting their unwillingness in traveling to Pakistan for the third and final T20I.
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The players were in favour of a change in venue as it was the Sri Lankan team bus that became a subject to a deadly terror attack in 2009. Since then barring Zimbabwe, no side has toured Pakistan.
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The SLC, since then has been able to convince 15 among 40 of those cricketers to travel to Pakistan and Perera was the most prominent one among them.
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The decision came after regular captain Upul Tharanga pulled out from the third T20I slated to be played in Lahore.
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The decision to name Perera the captain also means Tharanga will not lead Sri Lanka even in the first two matches in UAE.
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Taking a strong stance on its cricketing ties with Pakistan, the Sri Lanka Cricket Board has named all-rounder Thisara Perera the captain for the upcoming three-match T20I series against its neighbours.