COVID Counterpunch

PCR Testing Protocols Spark COVID Case Count Controversy

Photo by Mika Baumeister

New guidance from the CDC for testing breakthrough cases of COVID is reigniting controversies about PCR testing standards.

PCR tests— or polymerase chain reaction — extract a small amount of viral genetic code found in a sample (in this case, a respiratory swab) and replicate it until there are many millions of copies. The replications then make it possible for the viral molecules to be detected by an instrument called a thermal cycler. The number of replications it takes to detect a virus is called the cycle threshold.

Positive tests, however, don’t necessarily indicate a “case” of COVID (or anything else). They merely indicate that viral molecules were detected. The more replications, the more likely they are to detect something.

Put another way, a positive test at 25 cycles indicates a person who is likely sick and infectious, whereas a positive test at 35 cycles indicates a person who only has remnants of a previously recovered virus in their system or an extremely low viral load.

The reason this is important is obvious:  when virus particles are found at higher testing thresholds, the results are likely false positives.

In an August 29, 2020 article titled “Your Coronavirus Test Is Positive. Maybe It Shouldn’t Be, The New York Times sounded the alarm that COVID case counts might be artificially elevated due to too-high testing thresholds.

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.

Tests with thresholds so high may detect not just live virus but also genetic fragments, leftovers from infection that pose no particular risk…

The Times goes on:

Officials at the Wadsworth Center, New York’s state lab, have access to C.T. values from tests they have processed, and analyzed their numbers at The Times’s request. In July, the lab identified 872 positive tests, based on a threshold of 40 cycles.

With a cutoff of 35, about 43 percent of those tests would no longer qualify as positive. About 63 percent would no longer be judged positive if the cycles were limited to 30.

— The New York Times (August 29, 2020)

Saint Anthony Fauci acknowledged the problem in July 2020 when he said that a cycle threshold higher than 35 was just picking up dead viral nucleotides.

“What is now sort of evolving into a bit of a standard that if you get a cycle threshold of 35 or more that the chances of it being replication competent are minuscule…You almost never can culture virus from a 37 threshold cycle, so I think if somebody does come in with 37, 38 — even 36 — you gotta say, you know, it’s just dead nucleotides, period.” 

— Anthony Fauci, This Week in Virology podcast (July 16, 2020)

To our credit, at least some labs in New Mexico have reported using a lower threshold. KOB reported in December 2020 that while some states’ COVID test threshold values go up to 40, “most labs in New Mexico go below 29.

The New Mexico Department of Health claimed that cycle thresholds are 29, but that’s only at state-run labs. 

Sandia National Laboratories reported on January 29, 2021, by contrast, that it sets a cycle threshold of 38 for COVID PCR tests.

If the experts know that the cycle threshold shouldn’t be so high, and millions of tests were performed at these cycles anyway, why is anyone taking the official numbers seriously?

Which brings us back to the CDC.

The CDC’s website doesn’t appear to have published any official guidance for testing thresholds previous to May 1, 2021, indicating per The New York Times that testing thresholds as high as 40 have been regularly used by laboratories across the U.S. throughout the pandemic.

It wasn’t until May 1, 2021 that the CDC issued specific guidance for vaccinated individuals being tested for breakthrough cases of COVID. The CDC now only accepts specimens from positive tests with a cycle threshold of…28.

For cases with a known RT-PCR cycle threshold (Ct) value, submit only specimens with Ct value ≤28 to CDC for sequencing.

COVID-19 Vaccine Breakthrough Case Investigation and Reporting

Someone once said, “There are no conspiracies, but there are no coincidences.”

It seems fair to ask why the CDC is now so concerned about improving the accuracy cycle thresholds, and thus lowering case counts in people who are vaccinated, when it still has not provided guidance for the unvaccinated.

I’ll leave you to draw your own conclusions.

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