Root, an ever-present in England squads in all formats of recent times and winner of the Compton-Miller Medal as man of the series in this summer's Ashes, is rested both from a 13-man squad for next Monday's one-off NatWest Twenty20 international in Cardiff and from a 14-man squad for the five Royal London one-day internationals which follow.
Essex left-arm seamer Topley is included in the Twenty20 squad only.
Eoin Morgan will captain both, having led England in their unsuccessful World Cup campaign last winter but also then to success in a thrilling ODI series victory at home to New Zealand.
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Morgan has been rested for several matches by Middlesex after losing his form with the bat, but will be back in international colours as expected.
Three Yorkshire players still feature, however, in Adil Rashid, Liam Plunkett and new signing David Willey.
National Selector, James Whitaker, said: “We have made some significant progress in our limited overs cricket this summer and the next six games allow these players to continue testing themselves against one of the very best sides in the world.
“This is primarily a young group of players and the next three weeks will provide them with valuable experience as we continue to identify players who can take our limited overs cricket forward over the next four years.
“On behalf of the selectors I would like to wish Eoin Morgan and Trevor Bayliss all the very best for what I’m sure will be a very competitive and entertaining series.”