What factors affect sensitivity and specificity of the COVID-19 nasal swab?

Posted on April 17, 2020 by Raymond Cho

Summary

  • NP swabs must have proper technique and reach the nasopharynx for adequate collection.
  • Swabs performed closer to the onset of symptoms are generally more accurate.
  • Heat may affect test accuracy so samples must be stored properly before shipping to the lab.
  • CT Chest has been shown to be more sensitive than RT-PCR and other tests are on the horizon.

I.   EVIDENCE FOR COVID-19 NASOPHARYNGEAL SWAB

  • While the nasopharyngeal swabs have high specificity, recent low-quality evidence suggests potentially low sensitivity (71-97%), resulting in high rates of false negative tests.
    • Xie et. al. evaluated 167 patients treated for COVID-19 and found that 5/167 had initially negative RT-PCR (97% sensitivity) but positive CT Chest (1).
    • Fang et. al. studied 51 patients and showed that RT-PCR had a sensitivity of 71% (36/51) (2).
    • Finally, Luo et. al. similarly reported that the initial sensitivity of oropharyngeal swabs in close contacts  was 71.3% in the first PCR test (92.2% in the second) (3).
  • In summary, the COVID-19 RT-PCR is very specific but recent evidence from China suggests that sensitivity may be limited to ~71%.

II.   FACTORS AFFECTING ACCURACY

    • Swab technique/modality (0-7 days after symptom onset) (4,5)
      • Bronchoalveolar lavage fluid: 88.5% of patients tested positive for COVID-19.
      • Sputum: 82.2% of patients with mild symptoms and 88.9% with severe tested positive.
      • NP: 72.1% with mild symptoms and 73.3% with severe tested positive (you must swab the nasopharynx to obtain an acceptable sample) (6).
      • OP: 61.3% with mild symptoms and 60.0% with severe tested positive.

 

  • Recommendation: although sputum is more sensitive, NP swabs are more accessible and accurate than OP swabs, making it the better choice for outpatient primary care.
  • Timing of swab relative to onset of symptoms

 

      • Using NP swabs, Yang et. al. showed that patients with severe symptoms had a 73.3% positive test rate 0-7 days after symptom onset, 72.3% at 8-14 days and 50.0% at 15+ days. They also showed that patients with mild symptoms had a 72.1% positive test rate at 0-7 days, 53.6% at 8-14 days and 54.5% at 15+ days (4).
      • Wikramaratna et. al. analyzed publically available data to show that the probability of a positive test decreases through time as the infection progresses (7).

 

  • Recommendation: NP swabs should be performed as early as possible to reduce the probability of false negative testing for COVID-19.
  • Storage and transportation

 

      • Pan et. al. showed that 7/15 weakly-positive viral samples to be RT-PCR negative after thermal incubation (56°C water bath for 30 min) (8).

 

  • Recommendation: according to the CDC, NP swabs should be stored in viral media tubes at 2-8°C for up to 72 hours. If delays are expected, store samples at -70°C or below (9).
  • Multiple tests

 

    • There is some evidence to suggest that 2 NP swabs for RT-PCR 24 hours apart can increase sensitivity to 92.2% but given the lack of resources in BC, this is not common practice (3).

III.   OTHER TESTS

  • CT Chest: Ai et. al. suggests that CT chest has a sensitivity of 97% but this is likely an overestimation as it uses RT-PCR as the standard for comparison, which itself is not an entirely reliable testing modality (10).
  • COVID-19 Antibody Tests: this detects the presence of COVID-19 antibodies in blood. Recent reports suggest that antibody testing has a sensitivity of 93.8% and a specificity of 96.4% (11). However, there have been a number of reports of faulty test supplies and lower-than-expected antibody production in some patients. The test is also limited in that it shows only previous exposures to COVID-19, not necessarily an active infection. Commercial antibody testing is still under development (12).

Questions? Comments? Does this need to be updated? Do you have valuable points to add ? Please email ask.reakt@ubc.ca.

References

  1. Xie X, Zhong Z, Zhao W, Zheng C, Wang F, Liu J. Chest CT for Typical 2019-nCoV Pneumonia: Relationship to Negative RT-PCR Testing. Radiology [Internet]. 2020 [cited 17 April 2020];. Available from: https://pubs.rsna.org/doi/10.1148/radiol.2020200343
  2. Fang Y, Zhang H, Xie J, Lin M, Ying L, Pang P et al. Sensitivity of Chest CT for COVID-19: Comparison to RT-PCR. Radiology [Internet]. 2020 [cited 17 April 2020];. Available from: https://pubs.rsna.org/doi/10.1148/radiol.2020200432
  3. Luo L, Liu D, Liao X, Wu X, Jing Q, Zheng J et al. Modes of Contact and Risk of Transmission in COVID-19: A Prospective Cohort Study 4950 Close Contact Persons in Guangzhou of China. SSRN Electronic Journal [Internet]. 2020 [cited 17 April 2020];. Available from: https://www.medrxiv.org/content/10.1101/2020.03.24.20042606v1
  4. Yang Y, Yang M, Shen C, Wang F, Yuan J, Li J. Evaluating the accuracy of different respiratory specimens in the laboratory diagnosis and monitoring the viral shedding of 2019-nCoV infections. [Internet]. 2020 [cited 17 April 2020];. Available from: https://www.medrxiv.org/content/10.1101/2020.02.11.20021493v2.full.pdf
  5. Wang W, Xu Y, Gao R, Lu R, Han K, Wu G et al. Detection of SARS-CoV-2 in Different Types of Clinical Specimens. JAMA [Internet]. 2020 [cited 17 April 2020];. Available from: https://jamanetwork.com/journals/jama/fullarticle/2762997
  6. How to collect a Nasopharyngeal (NP) swab [Internet]. Ottawa Public Health. 2020 [cited 17 April 2020]. Available from: https://www.ottawapublichealth.ca/en/professionals-and-partners/how-to-collect-a-nasopharyngeal–np–swab.aspx
  7. Wikramaratna P, Paton R, Ghafari M, Lourenco J. Estimating false-negative detection rate of SARS-CoV-2 by RT-PCR. [Internet]. 2020 [cited 17 April 2020];. Available from: https://www.medrxiv.org/content/medrxiv/early/2020/04/07/2020.04.05.20053355.full.pdf
  8. Pan Y, Long L, Zhang D, Yan T, Cui S, Yang P et al. Potential false-negative nucleic acid testing results for Severe Acute Respiratory Syndrome Coronavirus 2 from thermal inactivation of samples with low viral loads. Clinical Chemistry [Internet]. 2020 [cited 17 April 2020];. Available from: https://academic.oup.com/clinchem/article/doi/10.1093/clinchem/hvaa091/5815979
  9. Coronavirus Disease 2019 (COVID-19) [Internet]. Centers for Disease Control and Prevention. 2020 [cited 17 April 2020]. Available from: https://www.cdc.gov/coronavirus/2019-ncov/lab/guidelines-clinical-specimens.html
  10. Ai T, Yang Z, Hou H, Zhan C, Chen C, Lv W et al. Correlation of Chest CT and RT-PCR Testing in Coronavirus Disease 2019 (COVID-19) in China: A Report of 1014 Cases. Radiology [Internet]. 2020 [cited 17 April 2020];. Available from: https://pubs.rsna.org/doi/10.1148/radiol.2020200642
  11. Cellex. Cellex qSARS-CoV-2 IgG/IgM Rapid test [Internet]. FDA. 2020 [cited 17 April 2020]. Available from: https://www.fda.gov/media/136625/download
  12. Laboratory testing for 2019 novel coronavirus (2019-nCoV) in suspected human cases [Internet]. World Health Organization. 2020 [cited 17 April 2020]. Available from: https://www.who.int/publications-detail/laboratory-testing-for-2019-novel-coronavirus-in-suspected-human-cases-20200117

Disclaimer

The above is intended to serve as a rapidly-created, accessible source of information curated by medical students and healthcare professionals. It is for educational purposes only and is not a complete reference resource. It is not professional medical advice, and is not a substitute for the discretion, judgment, and duties of healthcare professionals. You are solely responsible for evaluating the information above.