First-half goals from Johnny Evans and Chris Brunt gave the Irish their fifth successive win in the group, all with clean sheets. Evans headed past Tomas Vaclik in the 28th minute and Brunt curled in a free kick four minutes before halftime.
Northern Ireland have 19 points in Group C with two games each to play, nine clear of third-placed Azerbaijan and five behind leaders Germany. Fourth-placed Czech are out of the running with nine points.
The winners of the nine European groups qualify directly for Russia next year and the eight best runners-up go into a playoff round for four more places
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