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State health departments across country failing to collect critical COVID-19 pandemic data

"Cycle threshold" information for COVID tests remains largely absent from state data.

Updated: December 2, 2020 - 2:46pm

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State health departments across the country are by-and-large failing to collect critical data related to COVID-19 tests, omitting from state data a key metric by which officials and the public might judge the severity of the pandemic in the U.S. 

For months, testing has been viewed by leaders and medical officials worldwide as an indispensable tool for addressing the coronavirus pandemic. COVID-19 tests have been cited as both a way to determine the disease's prevalence in a given region and as a way for individuals who have previously tested positive for the virus to confirm that they are no longer infected. 

The National Institutes of Health in September referred to testing as "the key to getting back to normal," stating that "testing as many people as possible" is a highly important feature of "control[ling] the COVID-19 pandemic."

Yet the broad reliability and/or relevance of those tests has over the course of the pandemic been brought under scrutiny by media reports and comments from health officials and experts. Investigations by both Just the News and the New York Times have revealed that many of the "positive" test results recorded throughout the country may actually denote nothing more than fragments of dead COVID virus picked up by overly sensitive testing equipment. 

The issue hinges on the method by which many COVID-19 tests detect the viral load within a sample taken from a patient. Polymerase chain reaction — or PCR — tests are among the most popular diagnostic tools to detect the COVID-19 virus. They work by amplifying DNA from a viral sample to the point that an antigen can be detected and classified. 

The "cycle threshold" is the number of amplification cycles a PCR test goes through before it determines the presence of a virus. The lower the cycle, the higher the viral load from the original sample; a higher cycle, on the other hand, means that the machine had to work longer and harder to detect a scant amount of virus in the original sample. 

Higher-cycle "positive" tests potentially indicate that a patient is non-infectious and at little health risk from the virus; those results may also indicate that a patient need not subject himself to strict quarantine measures, given the potential lack of infectivity. 

This factor is well-known among infectious disease experts. In July, for instance, Anthony Fauci, the director of the National Institute for Allergy and Infectious Diseases — admitted during a podcast that "if [a patient gets] a cycle threshold of 35 or more ... the chances of it being replication-confident are minuscule." 

"[I]f somebody does come in with 37, 38, even 36, you got to say, you know, it's just dead nucleotides, period," Fauci said during the interview. 

It is not clear to what extent positive COVID-19 tests in the U.S. represent non-infectious cases or mere fragments of coronavirus. The New York Times in its August investigation determined that based on a review of test data from three different states, "up to 90 percent of people testing positive carried barely any virus."

State health departments not tracking cycle threshold numbers

Fauci in that podcast also noted that patients are largely kept in the dark about the cycle threshold levels of their nominally positive tests. "When someone comes in and it's positive, they don't give them the threshold until you go back and ask for it," he said. 

State health departments, meanwhile, are also largely ignorant about those numbers, even as health departments over the last 10 months have largely become clearinghouses for COVID-19 data throughout their respective states. 

Just the News reached out to health departments in every one of the 50 U.S. states to learn whether or not state officials are aware of cycle threshold numbers when reporting positive test results on their websites. 

Overwhelmingly, health officials responded that they are more or less unaware of the cycle thresholds from the vast majority of tests occurring in their states. 

"This information is not tracked by the Kentucky Department for Public Health," said Susan Dunlap, the executive director of the Kentucky Cabinet for Health and Family Services.

Megan Wade-Taxter, a spokeswoman for the Indiana Department of Public Health, told Just the News: "We do not keep this information in our records."

"Idaho does not keep a database or list of Ct values," said Zachary Clark with the Idaho Department of Health.

Maryland Department of Health spokesman Charles Gischlar told Just the News: "The Maryland Department of Health does not report PCR CT values it receives from laboratories."

A representative of the Pennsylvania Department of Health said: "We do not get any cycle thresholds from any laboratories."

Amy Ellis with the North Carolina Department of Health and Human Services responded: "The NC Department of Health and Human Services does not monitor cycle threshold cutoffs for all clinical laboratories reporting results to the State." She added: "The State does not require reporting of cycle thresholds."

An official with the California Department of Health said: "The state does not maintain these values because it does not receive these from reporting labs."

Lora Rae Anderson with Connecticut's Office of the Chief Operating Officer said her state does not receive this information from labs and that "the best way to get this data is to speak directly to labs in the state."

Sara Vetter, a supervisor at the Minnesota Public Health Laboratory, told Just the News: "We are unable to provide a comprehensive list of Ct Values for the state. It is not a required reportable piece of data so the state does not receive that information."

Many of the health officials qualified their responses with caveats about PCR tests and threshold data. Vetter, for instance, argued that cycle thresholds "outside the context of having clinical information such as symptom onset date" are "not valuable and hold little meaning in a clinical context."

Edward Desmond, the administrator at the state laboratory in Hawaii, admitted that the state does not collect cycle threshold values for tests performed in that state. "CT values depend on the chemistry used, the instrument used, and the nucleic acid extraction method used," he argued. "CT values also depend on the quality of the specimen collected. So there are many sources of variability. For this reason, there is limited value to reporting or trying to interpret CT values."

Multiple health officials used similar language to explain the limitations in their data. Arkansas Department of Health spokeswoman Danyelle McNeill said the state's laboratory does not keep track of the cycle thresholds it records because the lab "only uses the Ct value to make a determination of positive/negative."

"It is not something we keep track of because our test is qualitative, not quantitative," McNeill added.

"PCR assays are qualitative not quantitative," the California Department of Health said. Kathryn Beasley with the Delaware state government said her state's laboratory also uses cycle threshold levels "for qualitative detection of SARS-CoV-2, not quantitative."

It is not clear to what extent positive COVID-19 tests in the U.S. represent non-infectious cases or mere fragments of coronavirus. The New York Times, in its August investigation, determined that, upon a review of test data from three different states, "up to 90 percent of people testing positive carried barely any virus."

As with some of the state health officials, other health experts have at times disputed the immediate relevance of cycle threshold numbers. The Association of Public Health Laboratories said in a release last month that "Ct values should not be used to determine how infectious someone is" and that "although Ct may be used as a proxy for viral load, caution must be taken when interpreting in this manner."

"The number of cycles required for detectable amplification of viral RNA is dependent on a long list of variables beyond simply how much viral RNA is present in a patient specimen," the APHL said. "The relative impacts of these variables on the Ct value differs between test platforms and can vary widely."

Still, other health experts have stressed what they say is the critical need for health officials to be more transparent about cycle threshold levels.

Angela Rasmussen, a virologist at Columbia University in New York, told the New York Times in August: "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." Rasmussen said it would be "useful information to know if somebody's positive, whether they have a high viral load or a low viral load."

A preprint paper out of the University of Oxford in September, meanwhile, argued that "infectivity is related to the date of onset of symptoms and cycle threshold level" and that "a binary Yes / No approach to the interpretation of RT-PCR unvalidated against viral culture will result in false positives with possible segregation of large numbers of people who are no longer infectious and hence not a threat to public health."

And in May, researchers with Harvard said in a report that "particularly when testing in the absence of symptoms for COVID-19 ... reporting the Ct value or range could help to better inform clinical decisions."

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