Relapses can occur after treatment ends if the virus has not been eliminated, which can be caused by insufficient uptake of antiviral into some lesions, viral resistance to the antiviral, or treatment of insufficient length or dosage.  

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When relapses occur, the cat may not show the same symptoms as at the original diagnosis.  For example, cats who had effusions may not show any signs of such upon relapse.  A common pattern is for relapses to manifest with ocular or neurological symptoms even if the cat had not previously shown symptoms of ocular or neurological involvement.  Neurological and ocular symptoms can sometimes be subtle, and may have been missed during the original diagnosis, or may not be visibly manifesting yet -- in which case too low a dose may have been selected, merely suppressing the virus.   In other cases, the virus may have escaped to the eyes or brain during treatment.

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The relapse rate seems quite low for cats who have successfully (and accurately) completed a full treatment (with high-quality preparations of the anti-viral.)  For cats treated with GS-441524, anecdotally this seems to be less than 10% of cats that complete treatment.  For other protocols less data is available, but from available data seems similarly low.

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Cats with neurological and ocular involvement are more likely to relapse, due to the extra difficulty in overcoming the blood/brain and blood/eye barriers.  This can also be exacerbated by viral resistance to the antiviral.

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The most likely time for a cat to relapse is within the first few weeks after treatment. There have been a very small number of reported cases where a treated cat has again been diagnosed with FIP after more than 3 months post treatment -- it is unclear whether these are a true relapse or a re-infection/re-mutation of FIP. 

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Treating a Relapse

Relapses should be retreated for at least 8 weeks at a higher starting daily dosage than the previous round of treatment using the guidelines for dosage increases used when there is poor response to treatment.

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In some cases, particularly when the dosages are relatively high (for example above 15 mg/kg for GS-441524) or where there has been a previous relapse, it may be wise to consider switching to a different antiviral, as these factors are likely a sign that resistance to the original antiviral has developed.