Abby refers to the 'pertussis virus'. Pertussis (whooping cough) is caused by a bacterium, Bordetella pertussis, not a virus.
Ducky, Gibbs and the other agents don't figure out the dead body, Seaman Balfour, wasn't a captain until after McGee checked his fingerprints in the database. However it should have been immediately apparent that something was off just by seeing how young the victim was; Balfour was only 22, far too young to be a captain. Not counting rare/wartime exceptions, officers are at least 22 years old when they graduate from the Naval Academy as an ensign, and an officer has to have a minimum of 18 years of service to be promoted to the rank of captain; most captains are promoted around 20-23 years. Which means an officer would be at least 40 before being eligible for promotion to captain and Balfour clearly didn't appear to be in his early 40's or even late 30's.