The Kill Order by James Dashner (The Maze Runner #4)

 When sun flares hit the Earth, intense heat, toxic radiation and flooding followed, wiping out much of the human race. Those who survived live in basic communities in the mountains, hunting for food. For Mark and his friends, surviving is difficult, and then an enemy arrives, infecting people with a highly contagious virus. Thousands die, and the virus is spreading. Worse, it's mutating, and people are going crazy. It's up to Mark and his friends to find the enemy - and a cure - before the Flare infects them all ...