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A spokesperson for the ICC said an operational issue at the ground meant the DLS sheets, which contain the target scores at different points of the innings, could not be provided to the teams.
The boat was believed to have left Bangladesh two weeks ago and then broken down at sea, with the UN and rights groups reporting many of the about 90 refugees on board now suffering acute dehydration.
Chasing 231 for victory, Bangladesh came close before being bowled out for 213 with the spin trio of Rahkeem Cornwall (4/105), Brathwaite (3/25) and Jomel Warrican (3/47) claiming all 10 wickets.
West Indies completed the fifth-highest successful run chase in Test history to go one up in the two-match series.
So far, 20.55 lakh Indians have been repatriated through different modes of the Vande Bharat Mission viz. Air India, private and foreign carriers, chartered flights, naval ships and land border crossings.
Shakib was handed a two-year ban, with a one-year suspended sentence, by ICC's Anti-Corruption Unit on October 29 last year, for failing to report multiple corrupt approaches by an Indian bookmaker.
The former fast bowler has served as an assistant coach with the Bangladesh men's team, and subsequently worked on a short term contract with the West Indies women's team, including at the World Cup 2020 held in Australia earlier this year.
Akram Khan, the cricket operations chairman at BCB, said that Bangladesh's tour of Sri Lanka in October and November was the reason for the denial.
The former Bangladesh captain's wife Sumona Haque still remains positive and is under treatment.
Earlier on Saturday, Bangladesh ODI captain Tamim Iqbal's brother Nafees also tested positive for coronavirus.