The second game of the group saw Rwanda beat Equatorial Guinea by the same scoreline.
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Both Nigeria and Rwanda struggled to make their dominance count against opponents happy to cautiously take chances when they presented themselves.
Libya beat Equatorial Guinea in its first match and now remains with three points from one win and one loss.
Next up is the final Group 3 match against Rwanda, which the Mediterranean Knights need to win if they want to qualify for the quarterfinals of CHAN.