No member of the 26-man England squad which includes Leeds United's Kalvin Phillips, Sheffield United's Aaron Ramsdale and Yorkshire-born Harry Maguire, John Stones, Kyle Walker and Dominic Calvert-Lewin have failed a Covid-19 test since the teams met at Wembley, nor has any member of the support staff.
Nor have any of Gilmour's team-mates, but his absence is a major to their hopes of qualifying for the knockout stages on Tuesday.
The Chelsea midfielder was in many people's eyes the best player on the pitch during the 0-0 draw despite it being the 20-year-old's first international start. Steve Clarke also changed Scott McTominay's role to accommodate him, moving the Manchester United midfielder into a back three.
If McTominay returns to the role he played in the opening game, Leeds United's Liam Cooper will compete with Jack Hendry to come into the side. If not, Sheffield United's John Fleck is an option in midfield.
Fleck tested positive for coronavirus in the build-up to the tournament.
A Scottish win against Croatia at Hampden Park on Tuesday is likely to see them qualify as one of the four best third-placed teams. Gilmour would miss the last-16 tie as he will have to isolate for 10 days.
Only an England win over Czech Republic would see them top their group and stay at Wembley for a last-16 tie against the runners up in Group F, which features world champions France, European champions Portugal and Germany.
They will finish second in the grup if they draw or Croatia beat Scotland.
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