Dehydration my friend will cause darker urine and ejaculate.
The viral infection was likely a separate co-existing event,
however dehydration is the exact opposite of what the body needs when you have an infection.
You really need to stay hydrated all the time, by drinking plently spring water.
When you don't urinate for 3 days, you body is holding on to fluids because of dehydration, but it also makes me suspect
additional urinary/bladder or possibly kidney issues.
If I were you I would see a Urologist or kidney specialist
just to make sure you don't have any serious underlying
problems.
Best wishes,
Niko