Practical Diagnostic Accuracy of Nasopharyngeal Swab Testing for Novel Coronavirus Disease 2019 (COVID-19)

Ravindra Gopaul, MD, MBA, MPH; Joshua Davis, MD; Linda Gangai, MSN, RN, CPHQ; Lianna Goetz, MD


Western J Emerg Med. 2020;21(6):1-4. 

In This Article

Abstract and Introduction


Introduction: The novel coronavirus (SARS-CoV-2) is the cause of COVID-19, which has had a devastating international impact. Prior reports of testing have reported low sensitivities of nasopharyngeal polymerase chain reaction (PCR), and reports of viral co-infections have varied from 0–20%. Therefore, we sought to determine the accuracy of nasopharyngeal PCR for COVID-19 and rates of viral co-infection.

Methods: We conducted a retrospective chart review of all patients who received viral testing between March 1, 2020–April 28, 2020. Test results of a complete viral pathogen panel and COVID-19 testing were abstracted. We compared patients with more than one COVID-19 test for diagnostic accuracy against the gold standard of chart review.

Results: We identified 1950 patients, of whom 1024 were tested for COVID-19. There were 221 repeat tests for COVID-19. Among patients with a repeat test, COVID-19 swabs had a sensitivity of 84.6% (95% confidence interval (CI), 69.5–94.4%) and a specificity of 99.5% (95%CI, 97–100%) compared to a clinical and radiographic criterion reference by chart review. We found viral co-infection rates of 2.3% in patients without COVID-19 and 6.1% in patients with COVID-19. Rates of co-infection appeared to be related to base rates of infection in the community and not a specific property of COVID-19.

Conclusion: COVID-19 nasopharyngeal PCR specimens are accurate but have imperfect sensitivity. Repeat testing for high-risk patients should be considered, and presence of an alternative virus should not be used to limit testing for COVID-19 for patients where it would affect treatment or isolation.


Many patients with novel coronavirus disease 2019 (COVID-19) will be asymptomatic;[1] however, a small percentage of patients will become severely ill requiring hospitalization. Overall mortality estimates of COVID-19 vary due to variable access to systematic testing, but the most critically ill requiring intubation have high risk of death.[2,3] The most commonly used initial testing was a nasopharyngeal swab for polymerase chain reaction (PCR), although antibody testing has since become available. PCR is widely used to test for other viral illnesses. Limitations of PCR testing for COVID-19 include unknown risk of transmission from PCR-positive patients and anecdotal reports of lack of sensitivity.[4] Initial reports from China questioned the sensitivity of PCR for COVID-19 and reported it as low as 71%, especially in early illness.[5] Further, PCR tests for the presence of viral RNA, which may or may not be able to transmit infection.

Lack of availability of widespread testing for COVID-19 has been a controversial subject. One method proposed to initially allocate scarce testing resources was to cancel testing patients for COVID-19 if another virus was detected. This was due to initial reports of a 0–4% co-infection rate with influenza and COVID-19.[6,7] However, since then reports of co-infection rates as high as 20% have been reported.[8] Therefore, we sought to examine our viral testing data for the diagnostic accuracy of patients tested more than once for COVID-19, as well as the rate of viral co-infections in patients tested for COVID-19.