Diagnosis of BVD
Do your cows have BVD?
Types of Samples
Ear notch sampleearnotcher
An ear notch sample is a suitable method for submitting samples because persistently infected (PI) animals contain lots of virus in any haired skin. You can use a medium pig ear notcher and take a sample from the ventrolateral edge of the ear.  The ear notch can then be put in formalin if you want to submit the sample for immunohistochemistry.  It can be frozen if you want to store it for longer or if you want to submit it for tests like ELISA or PCR.  You should clean and rinse the ear notcher in disinfectant to prevent contamination of samples.  If the sample is allowed to dry out, you risk finding false negative results.
Other samples
Blood, serum and other tissues also contain enough virus to detect, but they are less practical to collect on a herd scale.  You can send serum for virus neutralization.  If you are using blood in animals less than 12 weeks of age, PCR is the better test because maternal antibodies can interfere with virus isolation and ELISA.

Samples from dead animalshttp://www.biotracking.com/tailbleed.php
If you want to test a dead animal, you can send multiple sections of intestines, spleen, Peyers patches, mesenteric lymph nodes or erosions in the forestomach for testing.  Gross lesions are more likely to be seen in animals over 6 months of age.  These samples should be shipped frozen so that PCR or isolation can be done.  For an aborted fetus, you can send in lungs, liver, spleen, thymus, thyroid, placenta and fetal fluid for testing.  You can use PCR to examine these tissues or do ELISA on an ear notch.

Types of Tests
Virus isolation
Virus isolation involves growing the virus for two passages in a cell culture (bovine spleen) and then the lab uses immunofluorescence to identify noncytopathic BVDV.  Samples should not be frozen, but sent on ice packs.  If the sample is less than 12 weeks, you should send 20 mL of EDTA blood, but if the sample is older than 12 weeks, you should send 10 mL of clotted blood.  The benefit of this test is that the lab can also look for other viruses and it is also quite sensitive, as you can use it to identify acute and persistently infected animals.  This test costs $10.75 - $11.75 per sample and takes between 2 and 3 weeks.  This is the best test method to look for virus in an aborted fetus.

Polymerase Chain Reaction (PCR)
PCR is a very sensitive test which means that it is the most likely to be cross contaminated.  It detects genetic material in the virus which makes it very sensitive, but it is too expensive to use on each animal in a herd setting.  It is a more practical method to use for individual cases when other methods are not feasible.  It can be used to identify acute and persistently infected animals.  This test costs $29/sample.  You can use RT-PCR to determine whether it is type 1 or 2 but you can not tell if the virus is the cytopathic or non cytopathic type (you must use isolation to determine this).

Serology tests
You can use virus neutralization tests using the serum in order to look for antibodies to type 1a, 1b and 2.  An animal that has type 2 BVD will have higher titres in the type 2 assay.  The best way to use serological tests is by submitting paired sera that were taken 2-4 weeks apart.  A single sample is used if you only want to detect previous exposure.

Immunohistochemistry (IHC)
IHC involves fixing the tissue in formalin and then submitting it to a lab where they detect viral antigen.  It is a very sensitive test (very unlikely to miss a PI animal), assuming the samples are collected in a correct manner.  Lab technicians can also make an educated guess as to whether the animal has an acute infection or is persistently infected, although this is not 100% accurate.  If the skin sample dries out before it is put in formalin or if the sample has sat in formalin for longer than 2 weeks, this test has less accurate results.  It takes a bit longer than the other methods because the lab must trim the sample, process it, stain the slide and then examine it.  It is an ideal method for pre-sale testing, herd scale testing or if you only have formalin fixed tissue from the animal in question.

IDEXX Antigen Capture ELISA (Enzyme-Linked Immunosorbent Assay)  elisa
An ACE test involves soaking the sample in phosphate buffered saline.  Then the supernatant is tested for viral antigen.  It is sensitive and specific, plus it is good for large scale testing.  It takes a few days for the lab to conduct this test and costs $10.75 – $11.75.  This test is not as ideal for acute animals.  If you suspect an acute infection, you should send blood, serum or plasma for PCR or EDTA blood for isolation
Pooling samples
Pooling samples is controversial, but is still done because PI calves have a low prevalence so it is one of the only ways of economically detecting them.  Pooling means that you dilute the few positive samples with potentially many negative samples which means that you must use a sensitive test.  One way of pooling is by combining the ear notch fluid from multiple animals and then conducting PCR or ACE on the combined sample.  If the pooled sample tests positive, then you conduct individual tests for each animal in the pool.  Labs will pool samples from 20-50 animals.  A well stirred bulk tank milk sample can be used because some PI animals may live longer than 2 years.  You should submit a chilled 200 mL sample.  If the sample tests positive, you should re-test in 3 weeks to determine whether it was an acute infection.  If the second test was also positive, you should probably do individual tests for all animals that contributed to that bulk milk tank sample.

Herd screening
The herd should only be screened once tests prove that the virus is in the herd.  One method of screening is to test offspring because if a calf tests negative, you know that its mother must be negative too.  This also works because PI cows always have PI calves.  You can also take a bulk milk sample and use PCR.  In order to determine whether an animal is actually persistently infected, you need to re-test positives 3 weeks after their first test because an acutely infected animal will recover and test negative.

http://www.pdsinc.ca/Portals/0/Perspectives%20-%20February%202008.pdf (Prairie Diagnostic Services)
http://www.uoguelph.ca/labserv/units/ahl/documents/LabNote01-BVD.pdf (University of Guelph Laboratory Services)