Hole in the Sky (2001) by Pete Hautman?
"In 2028, a deadly Flu virus ravages the earth. Only one in two thousand survive the virus, and these "Survivors" are rarely left unaffected. By 2038, only 38 million people remain on Earth. Most of them live in small communities, ever fearful of outsiders who might bring the deadly Flu."Ceej Kane lives with his uncle and his Survivor sister Harryette in an abandoned hotel on the rim of the Grand Canyon. His quiet, boring life suddenly becomes a desperate adventure when Uncle and Harryette disappear. Searching for them, Ceej and his only friend, Tim, are attacked by the Kinka, a renegade band of half-mad Survivors who spread the Flu to make more of their own. Worse yet, it appears that Harryette has joined them.
Fleeing deep into the Canyon, a narrow land of ghosts and ancient secrets, Ceej and Tim meet Bella, a mysterious Hopi girl. She has been searching the canyon for the Sipapuni, a mystical portal that the Hopi believe leads to another world. Tim thinks Bella is crazy, but Ceej is not so sure. Maybe there is a way out of this Flu-ravaged world. But first they must find out what happened to Uncle, and they must save Harryette from the Kinka -- if she wants to be saved.
Found with the Google query
post-apo book virus "mother k" site:goodreads.com/book which popped up this review:
the Kinka, a tribe of Survivors whose mission is to infect people with the Flu virus so those people can prove their fitness to Survive. Mother K infects and kills Hap and Uncle while convincing Harryette to join them.