I'm going to post this reply in 3 logical parts. Part one explains why ANY test could result in a false result, due to the nature of the viruses. Part two explains the operator error aspect of the procedure. Part three actually talks about the studied nature of false testing results on various types of tests, the IDEXX SNAP being one of the ones included in the study.
 
1. From the IDEXX website (the people that make the SNAP test):
 

FIV Testing

Antibodies can be detected in the blood about 60 days post-exposure to FIV, although it may be much later. Antibody ELISA is the most common method for FIV testing, with two tests available: the in-house IDEXX SNAP® FIV/FeLV Combo Test and the laboratory IDEXX PetChek® assay. The Western blot is the confirmatory test for FIV; however, in a recent study, the sensitivity and specificity of the IDEXX SNAP® FIV/FeLV Combo Test and IDEXX PetChek® for FIV were 100% and Western blot was 98% when compared to virus isolation.4 A small number of cats infected with FIV do not produce detectable antibody and will have a false-negative test on both ELISA and Western blot. Unfortunately, screening for FIV antigen is not possible because of the low level of circulating virus after acute infection.

FeLV Testing

The in-house IDEXX SNAP® FIV/FeLV Combo Test and laboratory IDEXX PetChek® assay test for the p27 core antigen of FeLV.

Cats will test positive around 30 days post-exposure on both of the IDEXX ELISA tests. The pathogenesis of FeLV can take one of three paths. Cats can be transiently infected and then clear the virus around 12–16 weeks after exposure. They can also develop a latent infection, in which case both the IDEXX SNAP® FIV/FeLV Combo Test and IFA test will be negative. Latently infected cats can harbor the virus in their bone marrow for years with no clinical signs. Most latently infected cats can eventually clear the infection, but in a small percentage, the virus can reactivate and clinical FeLV can occur later in life. This reactivation of latent virus explains why a nine-year-old cat that has tested negative and lived indoors alone may suddenly become ill and test positive for FeLV. Cats can also be persistently infected, clinical or nonclinical, but these cats may be shedding virus. Kittens can become infected transplacentally from infected queens, but are more likely to become infected during grooming. As with FIV, not all kittens in a litter may be become infected with FeLV from infected queens, so pooling of sera in a litter or only testing one kitten or an infected queen is not recommended. Kittens infected with FeLV have a poorer prognosis for long-term survival than adult cats, which can live for years with the virus.
 
 
2. In additon, lots of false results are directly in relation to bad testing kit usage, in other words, not following the instructions fully. As you can read on this UK IDEXX website, the instructions are complex. The kits come with solution, the right bottle of solution must be used with the right kit (from the same batch), the test kit must be stored at a certain temperature (this includes during the shipping to the vet's office), the blood must be a certain tempature. The test kit must be room temperature before using (but has to be stored cold) and the website says wait 30 minutes after removing from refridgerator (how many times have you had to wait 30 minutes in the exam room for the test kit to warm to room temperature?)... it goes on and on. Operator error alone creates a vast number of false results. http://www.idexx.com/animalhealth/testkits/fivfelv/060148205.pdf 
 
 
3. http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=545975 on the subject of IDEXX SNAP FIV tests kits:
Most available FIV diagnostic tests detect serum, plasma, or whole blood antibodies to FIV. An enzyme-linked immunosorbent assay (ELISA) consisting of labeled antigens that are immobilized on either a membrane or a plastic well, and bind to antibodies, is the only available FIV test for commercial or in-practice laboratories in North America. The test comes in kit format for in-practice use (SNAP FIV Antibody/FeLV Antigen Combo Test; IDEXX, Westbrook, Maine, USA), or in a microwell format for laboratory use (PetChek FIV Antibody Test Kit; IDEXX). This ELISA is based on detection of antibodies against a core viral protein, p24, and a positive or negative result depends on color development relative to a positive control (8). Other available serological tests include a Western blot and an immunofluorescent antibody (IFA) test (9). Advantages of the Western blot are that antibodies reactive with a range of viral proteins, derived from nondomestic cat FIV, are detectable; however, it is technically more demanding and more costly. Immunofluorescent antibody tests are not commonly used to diagnose FIV infection, and little is known regarding their performance. The microwell ELISA used in veterinary laboratories has been described as having high sensitivity and specificity (9). False negative results are rare and due mostly to acute infection prior to the generation of specific antibodies. False positive results have been attributed to poor technique and nonspecific reactivity against tissue culture components following vaccination (10). Similar information is not available for the in-practice ELISA kit; however, up to 20% of in-practice positive samples submitted for Western blot confirmation were identified as false positives (10). This discrepancy has been attributed to more frequent operator error in veterinary practices as opposed to veterinary laboratories (10). Based on these test characteristics, it was recommended that a positive in-practice ELISA in a healthy cat be confirmed with a Western blot.
 
Results

The veterinary diagnostic laboratories reported results as “FIV-positive” or “FIV-negative,” the research laboratory reported results as “positive,” “negative,” or “equivocal.” An “equivocal” result referred to a distinct PCR product that differed by 100 bp or less from the predicted size.

Ten cats categorized as “FIV-positive” were all confirmed as positive by KELA. The ELISA results from the veterinary diagnostic laboratory agreed with the KELA result in all 10 FIV positive samples (Table 1). The PCR results from laboratories X, Y, and Z were in concordance with the infection category and KELA result in 100%, 80%, and 50% of cases, respectively. There was no consistency in the identification of false negative samples by PCR between the 2 different laboratories.

Sequence analysis of the PCR products from the research laboratory identified FIV-subtypes A, B, and C (Table 1). The sequences clearly clustered with established FIV subtypes (Figure 1).

Among 14 cats categorized as “FIV-negative,” 10 confirmatory negative KELA results and 4 discordant or equivocal results were obtained. The ELISA result agreed with the negative KELA result for 9 of these 10 samples. Among the cats with concordant FIV category and KELA result, the PCR results from labs X, Y, and Z agreed in 100%, 90%, and 70% of cases, respectively (Table 1). There was no apparent correlation between the false positive results obtained by either of the 2 diagnostic laboratories.

Four samples were categorized as “FIV-negative,” according to criteria described previously, but yielded positive or equivocal KELA results (Table 1). Among these discordant samples, 1 was categorized as “FIVnegative,” yielded a positive KELA result, and tested negative in 2 PCR assays and the ELISA. The Western blot was equivocal in this case. Three other samples categorized as “FIV-negative” yielded equivocal KELA results, and 2 could not be resolved by Western blot testing either. One sample with an equivocal KELA result yielded a positive Western blot interpretation. The PCR and ELISA results were variable for these 4 cases (Table 1). The FIV infection status could not be resolved for these 4 cats through these tests, and they were therefore considered “discordant.”

Blood samples from the dogs yielded negative KELA results in all 3 cases, 1 positive ELISA result, and a range of positive, negative, or equivocal PCR results (Table 1). The sequence of the 2 “equivocal” PCR products from 1 cat and 1 dog obtained in the research laboratory had a similar sequence but no homology with retroviral sequences in GenBank. Each had short stretches (25 to 40 bp) of homology with feline major histocompatibility (MHC) class II genes and canine sequences of unidentified origin.

(it's a huge study paper, go read it all, it says a LOT on the topic of various testing types and results, and the false negatives and positives.)
 

Phaewryn
 
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