Don Pesci: The pesky ‘science’ and politics of COVID-19

Coronavirus seen with electron microscope

VERNON, Conn.
The New York Times, the old gray lady of Eastern Seaboard journalism, published a blockbuster story on Aug. 30, “Your Coronavirus Test Is Positive. Maybe It Shouldn’t Be,” that should be widely reported in other media formats. So far, the substance of the story has remained pretty much on the media shelf.

The Times has discovered that the easily corrected, most often used calibration for Coronavirus testing is not useful for "containing the spread of the virus.” The Coronavirus, of course, causes the disease named COVID-19.

According to The Times, “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.

“On Thursday (8/10/2020), the United States recorded 45,604 new Coronavirus cases, according to a database maintained by The Times. If the rates of contagiousness in Massachusetts and New York were to apply nationwide, then perhaps only 4,500 of those people may actually need to isolate and submit to contact tracing.

The difference between 45,000 and 4,500 is, scientists and reporters may note, not a rounding error.

Leading public-health experts are concerned: “Some of the nation’s leading public-health experts are raising a new concern in the endless debate over Coronavirus testing in the United States: The standard tests are diagnosing huge numbers of people who may be carrying relatively insignificant amounts of the virus,” The Times reported.

To put the matter in terms that non-scientists may understand -- current Coronavirus testing is so over calibrated it cannot discover the four leaf clover in a massive field of clover.

“The most widely used diagnostic test for the new Coronavirus, called a PCR test,” the paper notes, “provides a simple yes-no answer to the question of whether a patient is infected.” However, similar PCR tests for other viruses, “do offer some sense of how contagious an infected patient may be: The results may include a rough estimate of the amount of virus in the patient’s body.”

Dr. Michael Mina, an epidemiologist at the Harvard T.H. Chan School of Public Health, is calling for testing that can find the four leaf clover: “We’ve been using one type of data for everything, and that is just plus or minus — that’s all. We’re using that for clinical diagnostics, for public health, for policy decision-making.’’

But yes-no isn’t good enough, he says, according to The Times story. “It’s the amount of virus that should dictate the infected patient’s next steps. ‘It’s really irresponsible, I think, to forgo the recognition that this is a quantitative issue.’”

The problem is that current PCR tests are imprecisely calibrated. 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.” The cycle threshold -- the “number of amplification cycles needed to find the virus… is never included in the results sent to doctors and Coronavirus patients [emphasis mine], although it could tell them how infectious the patients are.”

The Times story quotes Juliet Morrison, a virologist at the University of California at Riverside: “I’m shocked that people would think that 40 could represent a positive,” And Dr. Mina, who would set the cycle threshold limit at 30 or less, agrees. The change would mean, according to The Times’s story, “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.”

Currently, the cycle threshold limit is set at 40, which means that you are “positive for the Coronavirus if the test process required up to 40 cycles, or 37, to detect the virus.”

However, “’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.”

And the figures deployed by most politicians, in the absence of more useful and predictive figures, are designed to induce in ordinary citizens a posture of compliance to gubernatorial edicts that depend upon medically useless data.   

The Times, not a Trump apologist, quotes another virologist: “It’s just kind of mind-blowing to me that people are not recording the C.T. values from all these tests, that they’re just returning a positive or a negative.”

Not for nothing is Coronavirus called a “novel” virus. There can be no “science” associated with a novel virus. But there are scientists, continuing research, and necessary adjustments in perceptions and medical data. One wonders how many doctors and reporters in Connecticut would be thunderstruck, as were Mina and Morrison, that the “yes and no” figures dangled before them were, to put the best face on it, medically misleading but politically useful.

Don Pesci is a columnist based in Vernon.

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