Nine Bangladesh players resumed individual training at four venues under strict safety measures.
Tamim Iqbal opted out of the upcoming India tour, as his wife is expecting their second child.
The inclusion of Soumya and Kayes came after Bangladesh were bowled out for a meagre 173 runs in their first Super Four game against India.
Disappointed with umpire's decision, Shakib Al Hasan got furious and even uttered few cuss words.
Virat Kohli and Murali Vijay led India to a commanding position on Day 1 of the one-off Test against Bangladesh in Hyderabad as they finished on 356/3 in 90 overs.
Imrul Kayes was a key batsman for Bangladesh but will not play the Test match against India due to an injury.
Tom Latham calmly went about his work at the Basin Reserve on Saturday, Bangladesh removed senior batsmen Kane Williamson and Ross Taylor after declaring early in the day at an imposing 595-8
Kane Williamson was left unbeaten on 95 while Neil Broom fell just before the close for 97 as New Zealand overhauled Bangladesh's 236 for the loss of only two wickets to sweep the series 3-0
Imrul Kayes replaces Tamim Iqbal, who is on a break due to the birth of his first child, in Bangladesh's squad for the Asia Cup Twenty20 tournament.
Comilla Victorians, led by Bangladesh skipper Mashrafe Mortaza, won the 2015 edition of the Bangladesh Premier League after a tense last-ball win over Barisal Bulls in the final.