I think if you use your own critical judgement on this you will reach the best solution. The first of the alternatives you mention seems best to me:
"According to X report, 5 of 400 (1.25%) patients recieving CMV prophylaxis developed encephalitis."
Why? Because you can't say (x%) until you have written a of b, and any later in the sentence it is dissociated from the values.
However, perhaps a better solution would be:
"According to X report 1.25% (5 of 400) patients recieving CMV prophylaxis developed encephalitis."
Why? I assume that the primary interest is the overall percentage. The sample size is important, but it's more a qualifier, so it seems more natural to me to place it in parentheses.
Or course, context is important. If X report is being compared to Y report, then the focus might be on different sample sizes, in which case you would put the emphasis there, with something like:
"According to X study of 400 patients, 1.25% recieving CMV prophylaxis developed encephalitis."
So the important thing is not to follow some convention, but to use a sentence structure that conveys the information most clearly (and honestly).