PCR tests exaggerating COVID-19 case counts

Your Coronavirus Test Is Positive. Maybe It Shouldn’t Be | New York Times - By Apoorva Mandavilli:

Sept. 8, 2020 - "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. Most of these people are not likely to be contagious, and identifying them may contribute to bottlenecks that prevent those who are contagious from being found in time....

"The most widely used diagnostic test for the new coronavirus, called a PCR test, provides a simple yes-no answer to the question of whether a patient is infected.... 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. On Thursday, the United States recorded 45,604 new coronavirus cases.... 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.

"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. 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. [Michael] Mina [an epidemiologist at the Harvard T.H. Chan School of Public Health] said.

"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 .... 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.... 

"Officials at the Wadsworth Center, New York’s state lab, [have] 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. In Massachusetts, from 85 to 90 percent of people who tested positive in July with a cycle threshold of 40 would have been deemed negative if the threshold were 30 cycles, Dr. Mina said. 'I would say that none of those people should be contact-traced, not one,' he said....

"The F.D.A. noted that people may have a low viral load when they are newly infected. A test with less sensitivity would miss these infections. But that problem is easily solved, Dr. Mina said: 'Test them again, six hours later or 15 hours later or whatever,' he said. A rapid test would find these patients quickly, even if it were less sensitive, because their viral loads would quickly rise....

"Highly sensitive PCR tests seemed like the best option for tracking the coronavirus at the start of the pandemic. But for the outbreaks raging now, he said, what’s needed are coronavirus tests that are fast, cheap and abundant enough to frequently test everyone who needs it — even if the tests are less sensitive. 'It might not catch every last one of the transmitting people, but it sure will catch the most transmissible people, including the superspreaders,' Dr. Mina said. 'That alone would drive epidemics practically to zero.'"

Read more: https://www.nytimes.com/2020/08/29/health/coronavirus-testing.html