Educated and life experienced readers want plausible science and they will get mad at sloppy names and implausible reasons for scientific happenings.
The flu has to originate somewhere, will be named by scientists, and will eventually be given several popular names, depending on region or social meaning.
1. Give a scientific name first. Find out how the CDC and WHO name viruses. With H1N1 Flu, for example, each letter and number has a meaning.
2. Next, you come up with a name that the media or scientists would give, as with "swine flu", and "Captain Tripps". The generic name can be a location where the flu originated, the name of patient zero, or the scientist who may have created it.
3. Then, If you want to scare the heck out of people, give it a popular name that has supernatural or apocalyptic meaning, as with "The Hand of Satan", "The Mayans Were Right Virus" or "The Zombie Virus"
4. You can also relate the popular name to something horrible that happens when people get the virus.
5. "Captain Tripps" was a really bland name that scared the heck out of me when Stephen King used it.
Here's to good writing!