Dr. Donnica..so sorry about your son! (I/we can sympathize with your anguish so well!)
According to my doc (and I'm both paraphrasing - a MOST unscientific thing to do! - AND reaching into my limited memory bank!)...one of the reasons that Enteroviruses, for example, survive for so long is that they do not KILL their host cells! Our own cells actually protect them from the attack of our immune response.
It's possible, from the start of the virus infection, the immune system failed to kill off the infected cells. Afterwards, the immune systems efforts are futile in destroying the virus and unintentionally continue the flu-like symptoms.
Periodicaly, the virus loads in cells will decrease as the result of an immune response. You feel "better" for awhile - since the immune response subsides. Then... the virus grows back - the immune system reacts again... and so on and so on!
Re:.your sons terrible G.I. problems (again, my Docs explanation for my recurring distress).....the viruses in the respiratory tract are swallowed into the stomach - then travel to the intestinal tract where more infections occur. The symptoms of upper/lower G.I.tract can occur when the immune system reacts to viruses growing in the intestinal cells (virus protein has been found in muscle layers of the small intestine and colon).
This may be responsible for motility problems and explain the gastro symptoms. Decrease the viruses in the cells - you feel better.
Re: brain fog/cognitive function/memory, headaches, dizziness....once again, problems may be the result of immune response against virus-infected cells in brain (enteroviruses esp. are known to spread to many regions of the brain).
Re: the time lag (sometimes many years!) Sometimes after the acute infection resolves - the symptoms continue at low levels or even disappear - resulting in less "clues" to trace back to the ACUTE infection.
Other times people already had an episode of the same symptoms years ago! When the immune system is unbalanced, the viral infection recurs causing severe symptoms. All about the shift from TH1 to TH2 (immune responses).
Since many infections (not just enteros - although there are over 100 of those!) behave this way...some Doctors suggest Immune Boosters and/or Anti-virals be taken for long periods of time.
Thanks so much, and good luck with the show! .........jackie