The contagion known as "Yellow Fever", was a scourge particularly in The New World. Many epidemics broke out (in seasons) through South, Central and North America (especially near Port or Harbor communities). The disease caused an eventually "yellowing" of the skin, profuse sweating, high fever, chills and of course, it's characteristic "Black Vomit". Death came within days (no later than a week). Ships that dealt in The Slave Trade in Africa and The Caribbean, were especially susceptible. Poor care and storage of Slaves during their "crossing", hastened the condition and the spread of the contagion (which was passed on to humans from virus-infected mosquitoes). Often a "killer" of ships and responsible for "de-populating" whole Towns, - Ships, Ports and Harbors infected with Yellow Fever, were required to fly a warning flag.
Possibly in 1744, the first use of the term "Yellow Jack", appears. Partly due to the Yellow warming color used and part for the nautical term for shipboard Flag (a Jack). All ships (even Pirate and Privateers), carried the dreaded emblem. Normally, 8 foot x 8 foot, The "Yellow Jack" was flown from the Stern of the ship. The entire field was a bright yellow color, unadorned. In Harbors and Ports, The Quarantine Flag was quartered. The Upper Left and Lower Right Canton's were bright yellow. The Upper Right and Lower Left Cantons were black.