"Bird fly outbreaks may go unnoticed in humans", a news piece in the 26 February, 2005 issue of New Scientist, reports that human cases of Avian Flu (H5N1) may be misdiagnosed. Several patients in SE Asia have presented with symptoms unusual for the flu, and only after death did they test positive for the virus. The piece also reports that the WHO is "analysing blood samples from people in areas affected by h5N1 to see how many carry antibodies against the virus".
The difficulty here is that it can take up to several weeks (say, one to three, depending on the etiology of the bug) for the adaptive immune response to produce antibodies against a pathogen. It appears that people are dying within that time frame, which means that testing for antibodies is unlikely to be a useful diagnostic tool, at least given standard assay sensitivities. Using reverse-transcriptase PCR (RT-PCR), it may be possible to detect the RNA genome of the bug, but clinical PCR is a true art. It is often quite difficult to see anything via PCR in a clinical sample, unless you can really clean it up via purification. That purification, however, particularly in the case of RNA, tends to reduce the sensitivity of the assay by removing or destroying the target nucleic acids before the amplification step.