Contagion by Teri Terry

Callie is missing.

Her brother Kai is losing hope of ever seeing her again. Then he meets Shay, a girl who saw Callie the day she disappeared, and his hope is reignited.

Their search leads them to the heart of a terrifying epidemic that is raging through the country.

Can Kai and Shay escape death and find Callie? -Goodreads