Roy has one half-century in his last 12 innings and has scored just 33 runs in England's five ODIs this summer.
England were already an unbeatable 2-0 up in the three-match series against South Africa and although Morgan was glad the reverse had come before the Champions Trophy rather than during the tournament, it remains a worry.
However, what Bangladesh showed with this batting innings is that they aren't in this Champions Trophy just to make up the numbers. That is bad news for Bairstow - a player who would walk in to most other ODI sides - but is indicative of a consistency of selection which Morgan believes has been key to England's improvement in limited overs cricket since the 2015 World Cup.
" (Jonny) will miss out unfortunately", he said.
"I think we can expect to see more of what we have been seeing over the past year from South Africa in this tournament - a fearless brand of cricket".
After losing the toss and being asked to bat first on a gorgeous morning at The Oval in London, Bangladesh went about producing a fantastic batting performance, with their experienced heads leading the way. "Indian bowling has improved in the past years so they have been bowling well, in Asian conditions", said Azhar.
"He's a guy we really need in our team if we're going to win the Champions Trophy or be real contenders", said Eoin Morgan. It´s a starting point and it gives me confidence.
"We have guys who can impact a game as much as he can, particularly with the pace we have got".
Hosts England take on Bangladesh in the opener of the eight-team tournament on Thursday.
Laxman said that skipper Virat Kohli will be depending on these two bowlers due to their current form and the pace-friendly conditions in England which will host the Champions Trophy from June 1 to 18.
England captain Eoin Morgan has confirmed Ben Stokes is likely to bowl against Bangladesh in the opening match of the ICC Champions Trophy.
"We have worked on that", said Azhar. Yes, the Australian is quite probably the game's purest current ball-striker, but he is also an global novice.
"Most of all, they are a team that will, with the bat, with the ball and in the field, always take the positive option. Certainly, it's not down to a lack of trying".
Bangladesh were shot out for 84 by Champions Trophy title-holders India at the Oval on Tuesday in a crushing warm-up defeat.
England ended up having issues early. "They appear to be peaking perfectly for this tournament". In this regard, England is well served by Jason Roy, Alex Hales and Joe Root at the top of the order - the recent record-breaking collapse in the third ODI against South Africa notwithstanding.
Bangladesh: Tamim Iqbal, Soumya Sarkar, Sabbir Rahman, Mushfiqur Rahim, Mahmudullah, Shakib Al Hasan, Mosaddek Hossain, Mehedi Hasan, Mashrafe Mortaza (captain), Rubel Hossain, Mustafizur Rahman, Sunzamul Islam, Shafiul Islam, Imrul Kayes, Taskin Ahmed.
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