Lyric discussion by Bearded 

Cover art for Cue lyrics by Scott Walker

Seoul has been subjected to the outbreak of the Seoul Virus, Sudan and Ivory Coast to that of the Ebola Virus, both viruses being hemorrhagic fevers. They're transmitted from animals to men, and between men by physical contacts and body fluids.

A flugelman is probably a flugelhorn player, a flugelhorn being heard extensively in the song playing a recurring theme.

Now if anyone can explain what "jigger raps pits" means that would be most helpful.

@Bearded The explanation that the first line could be a reference to the Seoul virus (SEOV) and Sudan virus (SUDV, a strain of the Ebola virus) makes even more sense if you consider the second line: 'both start with an S'. In several interviews, Scott Walker said that a friend of his has a large library, and that he (Walker) enjoys spending his time there, browsing through the books. It is possible that he came across the two viruses right there, in some kind of medical encyclopedia.