Does circadian rhythm affect accuracy of PCR tests for SARS-CoV-2?

By Candace D. McNaughton,Carl Hirschie Johnson, Michael J. Ward, Jonathan E. Schmitz AND Thomas A. Lasko

Accurate detection of the virus that causes COVID-19 is a vital component in all containment and mitigation strategies for the current global pandemic crisis. Polymerase chain reaction (PCR) tests are commonly used in hospital and clinic settings because they are highly specific, but false-negative tests are common, up to 30% and particularly in early infection. Some patients report symptoms such as fever and body aches are worse in the late afternoon, which led us to ask whether viral shedding might also vary by time of day; if true, this in turn could also influence the accuracy of PCR tests by time of day, which would have important implications for testing strategies as well as for measures used to stop viral spread.

To explore whether SARS-CoV-2 viral shedding might vary by time of day, we examined the results of >86,000 PCR tests for SARS-CoV-2 collected from > 68,000 patients in a healthcare system in the southeastern U.S. between March and August 2020. We found that the proportion of positive test results varied by the time of day, with a higher positivity rate during the day than at night. When we examined the proportion of positive tests by location, i.e., outpatient clinic, hospital, emergency department, we found that the pattern of variation by time of day with a peak in the afternoon was identified for samples collected in outpatient clinics and in the hospital; among patients in the emergency department, there was less variation by time of day.

In addition, among ~2,000 tests for which cycle time thresholds were available, we found that the amount of viral genetic material detected was dramatically lower across patients at night compared to during the daytime (i.e., levels peaked in the early afternoon), even after adjusting for age, sex, race, testing location, month, and day of the week.

We used data from samples that were collected during routine clinical care, so it was not possible to determine exactly which patients were symptomatic at the time of sample collection, nor was it possible to determine how far along in their clinical course patients were. This data was also collected in the U.S. before the delta variant was dominant.

These findings are, however, crucial for two reasons. First, for most sensitive determination of whether a person is infected, testing in the middle of the day appears to be the most accurate. Second, our results suggest that there is a daily rhythm of SARS-CoV-2 viral shedding, possibly related to circadian regulation of the human immune system. This suggests that, as is the case in other viral infections such as influenza, people may be more susceptible to infection at certain times of the day, they may be more contagious at certain times of the day, vaccination effectiveness may vary by time of day, and response to treatment may also vary by time of day. Given the significant and ongoing burden of morbidity and mortality, each of these questions warrants its own focus in future work.

Article details

Diurnal Variation in SARS-CoV-2 PCR Test Results: Test Accuracy May Vary by Time of Day
Candace D. McNaughton,Carl Hirschie Johnson, Michael J. Ward, Jonathan E. Schmitz and Thomas A. Lasko
First Published: October 26, 2021
DOI: 10.1177/07487304211051841
Journal of Biological Rhythms

About the Authors

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Carl Hirschie Johnson is the Cornelius Vanderbilt Professor of Biological Sciences at Vanderbilt University. He researches “all things circadian” in organisms from bacteria to humans, and served as president of the international Society for Research on Biological Rhythms (“SRBR”) in 2012-2014. He received his Ph.D. from Stanford University and, after postdoctoral research at Harvard University, joined the faculty at Vanderbilt University in 1987.

Candace D. McNaughton is an emergency physician and clinician scientist at Sunnybrook Health Sciences Centre, and an associate professor at University of Toronto. She has a special interest in diagnostic tests and leveraging emergency care to improve public health. She received her M.D. from Washington University in St. Louis and then completed emergency medicine residency at Vanderbilt University Medical Center, followed by a masters of public health and Ph.D. in epidemiology from Vanderbilt University.