Covid Confusion On PCR Testing: Maybe Most Of Those Positives Are Negatives.

Photo: CDC. Handling viruses requires the use of a great deal of protective equipment.
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In a shocking report the New York Times suggests that the usual diagnostic tests, called PCR may simply be too sensitive and too slow to contain the spread of the Covid-19 virus.

This follows up a concern raised in a letter to the British Medical Journal (BMJ) on May 12th, 2020 in which doctors in Wales raised similar concerns.

Polymerase chain reaction (PCR) is a method widely used to rapidly make millions to billions of copies of a specific DNA sample, allowing scientists to take a very small sample of DNA and amplify it to a large enough amount to study in detail.

But now leading scientists say that standard tests are diagnosing as positive huge numbers of people who may be carrying relatively insignificant amounts of the virus.

Most of these people are not likely to be contagious, and identifying them as positive may just increase confusion all around.  But researchers say the solution is not to test less, or to skip testing people without symptoms, as recently suggested by the Centers for Disease Control and Prevention in a not untypical about-face on testing.

“The decision not to test asymptomatic people is just really backward,” Dr. Michael Mina, an epidemiologist at the Harvard T.H. Chan School of Public Health told the New York Times, referring to the C.D.C. recommendation.

The PCR test, provides a simple yes/no answer to the question of whether a patient is infected.

Similar PCR tests for other viruses nearly always offer some measure of the amount of virus. But yes/no isn’t good enough, Mina added. “It’s the amount of virus that should dictate the infected patient’s next steps. “It’s really irresponsible, I think, to [ignore this]” Dr. Mina said, of how contagious an infected patient may be.

“We’ve been using one type of data for everything,” Mina said. “for [diagnosing patients], for public health, and for policy decision-making.”

The PCR test amplifies genetic matter from the virus in cycles; the fewer cycles required, the greater the amount of virus, or viral load, in the sample. The greater the viral load, the more likely the patient is to be contagious.

This number of amplification cycles needed to find the virus, called the cycle threshold, is never included in the results sent to doctors and coronavirus patients, although if it was, it could give them an idea of how infectious the patients are.

One solution would be to adjust the cycle threshold used now to decide that a patient is infected. Most tests set the limit at 40, a few at 37. This means that you are positive for the coronavirus if the test process required up to 40 cycles, or 37, to detect the virus.

FDA Says “We Dunno.”

The Food and Drug Administration said in an emailed statement to the New York Times that it does not specify the cycle threshold ranges used to determine who is positive, and that “commercial manufacturers and laboratories set their own.”

The FDA noted that people may have a low viral load when newly infected and a test with less sensitivity would miss these infections.

Mina says that those people can be tested again if that’s the case.

Any test with a cycle threshold above 35 is too sensitive, Juliet Morrison, a virologist at the University of California, Riverside told the New York Times. “I’m shocked that people would think that 40 could represent a positive,” she said.

A more reasonable cutoff would be 30 to 35, she added. Dr. Mina said he would set the figure at 30, or even less.

Another solution, researchers agree, is to use even more widespread use of Rapid Diagnostic Tests (RDTs) which are much less sensitive and more likely to identify only patients with high levels of virus who are a transmission risk.

RDTs can be done in a few minutes using a drop of blood, saliva samples, or nasal swabs and cost about $5 each wholesale. The Trump administration recently ordered 150 million of these quick tests, so perhaps that is the direction of the future.

The Centers for Disease Control and Prevention said it is examining the issue.

The U.S. Centers for Disease Control and Prevention’s shift in guidance on Covid-19 testing away from asymptomatic individuals this week alarmed many public-health experts who say it’s a wrong turn that could restrict how many tests are performed.

But Brett Giroir, a top Trump administration official overseeing coronavirus testing, fired back on the criticism with an even more confusing explanation during a Wednesday briefing, telling reporters that the change is intended to clarify to the public the limitations of such screenings, not to reduce how many tests are conducted. (Thanks for that, Brett!)

At press time it is not clear what cycle threshold number labs in countries outside of the US are using, or whether discrepancies in testing numbers between nations could be based on how they are applying the tests, or on manipulation.




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