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


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

BOTTOM LINE
RÉSULTAT FINAL
 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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EVIDENCE
DONNÉES PROBANTES
 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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Author(s)
Auteur(s)
  • 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. https://doi.org/10.1148/radiol.202020064210. [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. http://doi.org/10.1101/2020.02.11.20021493. 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. https://www.cebm.net/covid-19/comparative-accuracy-of-oropharyngeal-and-nasopharyngeal-swabs-for-diagnosis-of-covid-19/ 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.  https://www.medrxiv.org/content/10.1101/2020.05.05.20084889v1.full.pdf 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. https://www.medrxiv.org/content/10.1101/2020.05.01.20081026v1.full.pdf  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. https://www.fda.gov/media/134922/download. Accessed 10 May 2020.

9. WHO. Laboratory testing for coronaviruse disease (COVID-19) in suspected human cases. https://apps.who.int/iris/rest/bitstreams/1272454/retrieve. 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.https://www.canada.ca/en/public-health/services/diseases/2019-novel-coronavirus-infection.html#a1 Accessed May 10,2020. 

Authors do not have any conflicts of interest to declare.

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