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#263 Finding COVID – How Good is the Test to Detect it?

What is the chance of obtaining an incorrect result with the polymerase chain reaction (PCR) test for COVID-19?

If the PCR COVID-19 test is positive you have COVID-19 (specificity ~100%). Small Canadian studies suggest the test will detect COVID-19 ~80-90% of the time (sensitivity), although estimates range from ~50%-90%. Collection technique, anatomical sample and timing of collection influence these numbers. The chance of a false negative depends on sensitivity and the pre-test probability the person has COVID-19. Example: someone with abnormal chest x-rays and close COVID-19 positive contacts has a higher risk of false negatives than someone who is asymptomatic.      

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Hospitalized patients in China: 
  • Retrospective study, 1014 patients, COVID-19 symptoms, all underwent both CT chest and PCR.1 
    • Using CT chest and symptoms as the “gold standard”: 
      • PCR sensitivity 68% (601/888). 
    • Using PCR as the “gold standard”: 
      • CT chest sensitivity 97% (580/601). 
  • Samples from various anatomic sites: 
    • 866 samples from 213 inpatients who previously tested positive.2 Sensitivity of swabs collected 0-7 and 8-14 days after symptom onset: 
      • Sputum: 83% (45/54) and 77% (47/61). 
      • Nasal: 72% (158/219) and 58% (130/226). 
      • Throat: 61% (58/95) and 41% (26/63). 
  • 1070 specimens from 205 patients (disease course not reported):3,4 
    • Sensitivity of bronchoalveolar lavage 93%, sputum 72%, nasal/nostril swabs 63%, and pharyngeal swabs (oral or nasopharyngeal) 32%. 
Alberta (30 outpatients) and Toronto (53 inpatients) initial positive nasopharyngeal swab, re-swabbed 10-11 days after symptom onset. Sensitivity:5,6 
  • Nasopharyngeal 90%. 
  • Throat 87%. 
  • Nasal 80%. 
  • Saliva 77%. 
Limitations: studies were of low quality or non-peer reviewed preprints; no gold standard test7 for COVID-19; sampling techniques not always reported.  Context: 
  • Inappropriate specimen collection, storage, and transport are likely the biggest contributors to false negative results.8-10 
  • Chance of false negatives depends on both sensitivity and pre-test probability (the chance of having the disease). 
  • Sensitivities of PCR are between 90% and 50%. 
    • If pre-test probability is ≤10% (example minimally symptomatic patient in community): False negatives from 1% to 5%. 
    • If pre-test probability is ~80% (example hospitalized patient with x-ray findings and known exposure): False negatives from 8% to 40%. 
  • While not a reliable indicator of prevalence, positive rates for COVID-19 testing are persistently below 10% in Canada.11 

Gilbert Bretecher June 6, 2023

PCR test has false negatives

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  • Christina Korownyk MD CCFP
  • James McCormack PharmD

1. Ai T, Yang Z, Hou H, et al. Correlation of Chest CT and RT-PCR Testing in Coronavirus Disease 2019 (COVID-19) in China: A Report of 1014 Cases. Radiology. 2020 Feb 26: 200642. [Epub ahead of print]

2. Yang Y, Yang M, Shen C, et al. Evaluating the accuracy of different respiratory specimens in the laboratory diagnosis and monitoring the viral shedding of 2019-nCoV infections. med Rxiv preprint. Accessed May 13, 2020.

3. Wang W, Xu Y, Gao R, et al. Detection of SARS-CoV-2 in Different Types of Clinical Specimens. JAMA. 2020; 323(18):1843-1844.

4. Carver K, Jones N. Comparative accuracy of oropharyngeal and nasopharyngeal swabs for diagnosis of COVID-19. CEBM. Accessed 13 May 2020.

5. Berenger B, Fonseca K, Schneider A et al. Sensitivity of Nasopharyngeal, Nasal and Throat Swab for the Detection of SARS-CoV-2. Med Rxiv preprint. Accessed May 10, 2020.

6. Jamal A, Mozafarihashjin M, Coomes E, et al. Sensitivity of nasopharyngeal swabs and saliva for the detection of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Med Rxiv preprint.  Accessed May 10,2020.

7. Cheng MP, Papenburg J, Desjardins M, et al. Diagnostic Testing for Severe Acute Respiratory Syndrome-Related Coronavirus-2: A Narrative Review. Ann Intern Med. 2020 Apr 13. doi: 10.7326/M20-1301. [Epub ahead of print]

8. CDC 2019-Novel Coronavirus (2019-nCoV) Real-Time RT-PCR Diagnostic Panel. Accessed 10 May 2020.

9. WHO. Laboratory testing for coronaviruse disease (COVID-19) in suspected human cases. Accessed 10 May 2020.

10. Lippi G, Simundic AM, Plebani M. Potential preanalytical and analytical vulnerabilities in the laboratory diagnosis of coronavirus disease 2019 (COVID-19). Clin Chem Lab Med. 2020 Mar 16. doi: 10.1515/cclm-2020-0285. [Epub ahead of print]

11. Government of Canada. Coronavirus disease (COVID-19): Outbreak update. Accessed May 10,2020. 

Authors do not have any conflicts of interest to declare.

Les auteurs n’ont aucun conflit d’intérêts à déclarer.