PCR Testing for Bird Flu in Dairy

by Pete Kennedy

It has been about a year since H5N1 virus (bird flu) was “discovered” in dairy cattle; during that time, there hasn’t been a shred of evidence linking any human illness to the consumption of raw milk contaminated with bird flu. Nevertheless, several states are testing raw milk produced for direct consumption for bird flu. The testing has been described as “a solution in search of a problem”; it looks like an attempt to reduce the supply of raw milk—this, at a time when the demand for the product has never been greater. The test that federal and state regulatory agencies use to detect bird flu in a sample of milk is the polymerase chain reaction (PCR) test. PCR detects the presence of RNA from virus cells that have been fragmented in the process so no intact cells remain; therefore, the test itself cannot be used to determine whether the original so-called viral cells were dead and inert or “live” and infective. The detectible presence of viral RNA in a test sample depends on the amount of virus cells (that is, the viral load); the PCR cycle threshold (Ct) indicates the degree of amplification applied to the sample in order to get a result. In order to detect the presence of any viral RNA when the viral load is low, the Ct value will be set higher to run more cycles of amplification; if only a trace amount of viral RNA is present, then more than 35 cycles (Ct 35) might be needed to obtain a positive test result. Even if the result is positive for bird flu, PCR cannot determine whether the viral RNA represents a complete “live” virus capable of infection and replication or merely an inactive fragment of viral RNA that cannot infect. To determine whether there is a supposed intact, infective virus in the sample, a follow-up validation test such as an egg inoculation test is needed to see whether the so-called viral material can be cultured.

There is no consensus on what Ct value is valid for the PCR test. Researchers choose a Ct to distinguish between “presumptive positives” for viral RNA and “negatives” for test samples, but rarely do they provide cultured validation of results (such as, by embryonated egg or tissue inoculations). A Massachusetts Department of Agriculture official stated, “PCR tests are only valuable up to about 30 cycles”—meaning that results from PCR tests run at Ct greater than 30 (Ct>30) are unreliable and may detect only traces of inactive viral fragments. According to reports, the California Department of Food and Agriculture (CDFA) chose to run its PCR tests at Ct set no lower than 35 cycles (Ct>35). The
Maryland Department of Agriculture runs PCR tests set no lower than 40 Ct (Ct>40), as does the USDA National Veterinary Services Laboratory (NVSL) in Ames, Iowa; NVSL is the lab that runs confirmation tests for positive test results from state labs. Finally, the FDA has published a guidance document on testing for bird flu with PCR set at Ct>45.

As far as is known, three states—California, Massachusetts and New York—have required farmers producing raw milk for human consumption to test for bird flu; a fourth state, Maryland, has required farmers producing milk for pet consumption to test for bird flu. California has done the most testing for bird flu so far, and the testing has found H5N1 in well over half the state’s Grade A dairies producing milk for pasteurization that have tested positive for bird flu. If a Grade A dairy cow or milk tests positive for bird flu, then the dairy can continue selling milk and not have to pull the positive cows from the milk line. The position of federal and state governments is that pasteurization inactivates any bird flu virus present in the milk, while known antiviral activity in raw milk is ignored.

So far in California, two dairies producing raw milk for direct consumption (including Raw Farm, the world’s largest raw milk dairy) and a raw milk distributor have had their sales suspended for bird flu due to presumptive positive PCR results of their milk samples. During the suspension, the dairies could still sell raw milk for pasteurization, but the price they received was a fraction of what they get for selling raw milk for human consumption. Raw Farm had its sales suspended for six weeks, costing over one million dollars in sales and causing massive shortages of raw milk in California. Raw Farm accounts for an overwhelming majority of raw milk sales in the state. The CDFA suspended Raw Farm sales solely on the basis of a positive PCR test without running any validation test for infectivity—as mentioned earlier, the PCR test cannot determine whether the virus particles present are live, intact and infective.

There has been tremendous pressure from the federal government on the states to test retail raw milk for bird flu, especially from USDA’s Animal Health Inspection Service (APHIS). A Public Records Act Request from the Weston A. Price Foundation (WAPF) for communications on bird flu between the CDFA and the FDA/USDA was denied by CDFA on the grounds that “. . . based on the facts of this case. . . the public interest served by not disclosing records related to an active investigation and outbreak response clearly outweighs the public interest served by disclosure.”

The bird flu “pandemic” has led to the culling of over 160 million poultry in the U.S. It has led to the shutdown of the country’s largest raw milk producer. The public health threat so far doesn’t come close to justifying the upheaval it has caused with the egg shortages throughout the country and the raw milk shortage in California. The consumer demand for raw milk continues to grow to levels never seen before despite the nonstop fearmongering by the government and media over bird flu. The campaign against bird flu is about reducing the supply of animal protein for the American people, not about public safety.

This update was published in the Spring 2025 edition of Wise Traditions in Food, Farming, and the Healing Arts, the quarterly journal of the Weston A. Price Foundation.