Here is an excellent article on ELISA vs IFA tests in cats:
http://www.thecatconnection.com/care/flv.htm it does a good job of explaining the differences in the 2 tests and why you may come up with different results. They test for 2 different components of the virus. IFA is the most conclusive. ELISA shows false positives at times because of the structure of the test.
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Lori McLaughlin
Your veterinarian should ALWAYS be consulted first and foremost when your pet's welfare is at stake.