The Ancients' device scanned every member of the Atlantean team and revealed that Sheppard was carrying Ancient Blood. However, since the gene modification (inaccurately called 'gene therapy', the molecular correction of genetic disorders) was done, McKay should also have been marked as Ancient.
At around 27:26, a crew member walks behind McKay after making it clear that only he and a local villager are in the catacombs of the derelict Ancient city.