The fog of COVID-19 data: How many cases aren’t even cases?

By Jon Sanders

Raleigh, NC – On Monday, September 21, I showed that according to Gov. Roy Cooper’s own metrics for reopening, the state should be open. All those metrics (click them for the charts) — COVID-like illnesses (CLI), cases, positive tests as a percentage of total tests, and hospitalizations — had not only been trending down for weeks, but were in fact months past their peaks.

Shortly afterward, on Friday, September 25, Cooper’s Department of Health and Human Services (DHHS), the state bureaucracy providing the state data on COVID-19, announced a major change. They would now be adding “probable cases” from antigen testing, including retroactively, into the state’s count of COVID cases. It provided a one-day increase of 6,142 cases and upended data tracking.

Cooper and media have since acted as if the case count has suddenly spiked without explanation except that people are misbehaving. They act as if cloth face masks are vital and must continue to be forced on healthy people. I’ve documented how the Cooper administration wants to claim that the mask mandate is working while also needing the case counts to stay high to justify all their restrictions. Even the Flying Wallendas couldn’t walk that tightrope.

Testing positive — by going well beyond the scientific consensus on the cycle threshold

Prior to the addition of antigen tests, there already were increasing reasons to question just how many “cases” of COVID-19 in North Carolina were even cases at all. The New York Times sounded the alarm on the tests used predominantly in the U.S. as well as North Carolina; i.e., polymerase chain reaction (PCR) tests. PCR tests tell whether a person has any scrap of viral material, but as currently used, they do not give an indication of how much viral material is present — or even alive.

As reported by the NYT on August 29 in an article titled “Your Coronavirus Test Is Positive. Maybe It Shouldn’t Be“:

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 it could tell them how infectious the patients are.

In three sets of testing data that include cycle thresholds, compiled by officials in Massachusetts, New York and Nevada, up to 90 percent of people testing positive carried barely any virus, a review by The Times found.

Up to 90 percent of “positive cases” barely contained a trace of virus. Virologists contacted by the NYT were “stunned.”

The number of cycles used in PCR tests is very important. As the NYT reports, “Most tests set the cycle limit at 40,” and North Carolina’s state lab sets it at 37. That means “you are positive for the coronavirus if the test process required up to 40 cycles, or 37, to detect the virus.”

That’s far too high, according to virologists (and also research consensus, as you’ll see below):

Tests with thresholds so high may detect not just live virus but also genetic fragments, leftovers from infection that pose no particular risk — akin to finding a hair in a room long after a person has left, Dr. Mina said [Michael Mina, an epidemiologist at the Harvard T.H. Chan School of Public Health].

Any test with a cycle threshold above 35 is too sensitive, agreed Juliet Morrison, a virologist at the University of California, Riverside. …

A more reasonable cutoff would be 30 to 35, she added. Dr. Mina said he would set the figure at 30, or even less. Those changes would mean the amount of genetic material in a patient’s sample would have to be 100-fold to 1,000-fold that of the current standard for the test to return a positive result — at least, one worth acting on. …

The C.D.C.’s own calculations suggest that it is extremely difficult to detect any live virus in a sample above a threshold of 33 cycles.

The NYT had the New York state lab analyze cases according to cutoffs of 35 and 30 cycles rather than the 40 cycles used by NY. “With a cutoff of 35, about 43 percent of those tests would no longer qualify as positive,” the NYT reported. “About 63 percent would no longer be judged positive if the cycles were limited to 30.” Mina said that setting the threshold to 30 in Massachusetts would have eliminated 85–90% of positives there.

Belgium health professionals, in a September 5 open letter to media and authorities, warned about false positives in PCR tests and the lack of actionable information about the viral presence in someone who tests positive:

The PCR test works with cycles of amplification of genetic material – a piece of the genome is amplified each time. Any contamination (e.g. other viruses, debris from old virus genomes) can possibly result in false positives.

The test does not measure how many viruses are present in the sample. A real viral infection means a massive presence of viruses, the so-called virus load. If someone tests positive, this does not mean that that person is actually clinically infected, is ill or is going to become ill.

A paper published on September 28 by the Oxford University Press for the Infectious Diseases Society of America noted that, based on the scientific consensus of more than 100 studies, the cycle threshold should be no more than 30 cycles.

Going further, the researchers tested 3,790 positive tests in which they knew the cycle values. They found they could culture (i.e., they found viable virus in) 70 percent of positive samples at a cycle threshold of 25. That percentage dropped to 20 percent of positive samples at the research consensus of 30 cycles. Above 35 cycles, only 3 percent of positive samples could be cultured.

Given that knowledge, this question becomes inescapable, especially since Cooper continues to restrict people, businesses, outdoor activities, schooling, etc., and more so since he threatens to tighten restrictions at any time:

How many of North Carolina’s “positive” cases would have been negative if the state’s cycle threshold was more in line with research consensus, the CDC’s recommendation, or the best advice from virologists?

The answer would be a fraction of what we’ve been told.