PHLOX: I inoculated the entire crew to prevent an outbreak. Would you mind rolling up your sleeve? (puts a cuff over Archer's wrist and shows his bloodstream on the monitor)
The vaccine contained millions of genetically altered microbes. Most of them are still in your bloodstream. They typically survive for, oh, at least several weeks. (does the same for the body)
Every one of the alien microbes in this body is dead.