The storm had already claimed the lives of at least two people in China's Hainan and 16 people in the Philippines
England, who had been 22 for three, were 75 for three at the interval with left-handed opener Cook and Bell both 32 not out.
The pair, who both made hundreds in England’s innings and 14-run win in the first Test in Cardiff, had so far put on 53 for the fourth wicket.
Earlier, England saw captain Andrew Strauss (four), Jonathan Trott (two) and Kevin Pietersen (two) all dismised for single figure scores after Sri Lanka skipper Tillakaratne Dilshan defied coventional wisdom by opting to field first in sunny and seemingly ideal batting conditions.
Sri Lanka’s attack had looked less than threatening during the first Test as England took a l-0 lead in this three-match series on Monday.
But left-arm seamer Chanaka Welegedara, recalled with the fit-again Dilhara Fernando in place of the dropped duo of spinner Ajantha Mendis and seamer Thisara Perera, had left-handed opener Strauss lbw, aiming across the line.
Strauss, on his home ground, walked off without asking for a review and England were five for one.
Trott came into this match on the back of 203 in Cardiff and boasting a Test average of 66.67, second only in the all-time standings to that of Australia great Sir Donald Bradman.
But none of that mattered when, aiming legside, he was struck in front by Suranga Lakmal, Sri Lanka’s other new-ball bowler.
Trott called for a review of Billy Doctrove’s lbw decision but replays showed the West Indian umpire had been entirely correct.
His exit brought in Pietersen, who in falling for three to Rangana Herath in Cardiff had been dismissed by a left-arm spinner for the 19th time in Tests.
However Pietersen was out even more cheaply on Friday after loosely steering a Lakmal delivery that cut away to gully, where Dilshan held a diving catch.
England were now 22 for three inside eight overs.
Bell then got off the mark first ball by pulling a short Lakmal delivery for four and he later cover drove him for a boundary. But in between those shots he also edged Lakmal short of the slips.
The storm had already claimed the lives of at least two people in China's Hainan and 16 people in the Philippines
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