Diagnostic performance of the combined nasal and throat swab in patients admitted to hospital with suspected COVID-19

  1. on behalf of the DataLoch COVID-19 Collaboration
  2. Kuan Ken Lee
  3. Dimitrios Doudesis
  4. Daniella A. Ross
  5. Anda Bularga
  6. Claire L. MacKintosh
  7. Oliver Koch
  8. Ingolfur Johannessen
  9. Kate Templeton
  10. Sara Jenks
  11. Andrew R. Chapman
  12. Anoop S. V. Shah
  13. Atul Anand
  14. Meghan R. Perry
  15. Nicholas L. Mills

Reviewed by

Read the full article

Listed in

Log in to save this article

Abstract

Background

Accurate diagnosis in patients with suspected coronavirus disease 2019 (COVID-19) is essential to guide treatment and limit spread of the virus. The combined nasal and throat swab is used widely, but its diagnostic performance is uncertain.

Methods

In a prospective, multi-centre, cohort study conducted in secondary and tertiary care hospitals in Scotland, we evaluated the combined nasal and throat swab with reverse transcriptase-polymerase chain reaction (RT-PCR) for severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) in consecutive patients admitted to hospital with suspected COVID-19. Diagnostic performance of the index and serial tests was evaluated for a primary outcome of confirmed or probable COVID-19, and a secondary outcome of confirmed COVID-19 on serial testing. The diagnosis was adjudicated by a panel, who recorded clinical, laboratory and radiological features blinded to the test results.

Results

We enrolled 1368 consecutive patients (median age 68 [interquartile range, IQR 53–80] years, 47% women) who underwent a total of 3822 tests (median 2 [IQR 1–3] tests per patient). The primary outcome occurred in 36% (496/1368), of whom 65% (323/496) and 35% (173/496) had confirmed and probable COVID-19, respectively. The index test was positive in 255/496 (51%) patients with the primary outcome, giving a sensitivity and specificity of 51.4% (95% confidence interval [CI] 48.8 to 54.1%) and 99.5% (95% CI 99.0 to 99.8%). Sensitivity increased in those undergoing 2, 3 or 4 tests to 60.1% (95% CI 56.7 to 63.4%), 68.3% (95% CI 64.0 to 72.3%) and 77.6% (95% CI 72.7 to 81.9%), respectively. The sensitivity of the index test was 78.9% (95% CI 74.4 to 83.2%) for the secondary outcome of confirmed COVID-19 on serial testing.

Conclusions

In patients admitted to hospital, a single combined nasal and throat swab with RT-PCR for SARS-CoV-2 has excellent specificity, but limited diagnostic sensitivity for COVID-19. Diagnostic performance is significantly improved by repeated testing.

Article activity feed

  1. Version published to 10.1186/s12879-021-05976-1
  2. ScreenIT

    SciScore for 10.1101/2020.10.03.20206243: (What is this?)

    Please note, not all rigor criteria are appropriate for all manuscripts.

    Table 1: Rigor

    Institutional Review Board StatementIRB: The study was performed with approval of the local Research Ethics Committee and delegated Caldicott Guardian for the National Health Service (NHS) Lothian Health Board, in accordance with the Declaration of Helsinki.
    Consent: Individual patient consent was not sought, and only summary data was extracted to minimise the risk of disclosure.
    Randomizationnot detected.
    Blindingnot detected.
    Power AnalysisWe estimated that with 1,000 patients, we will have 80% power to estimate the confidence interval for a sensitivity of 90% with lower and upper intervals of 85% and 95% respectively.
    Sex as a biological variablenot detected.

    Table 2: Resources

    No key resources detected.

    Results from OddPub: We did not detect open data. We also did not detect open code. Researchers are encouraged to share open data when possible (see Nature blog).

    Results from LimitationRecognizer: We detected the following sentences addressing limitations in the study:
    Whilst the diagnosis of COVID-19 is still largely reliant on RT-PCR on material collected on nose and throat swabs, clinicians need to be aware of the strengths and limitations of testing when making decisions on the placement of patients within hospital settings and discharge planning. In our study, the most conservative estimate of diagnostic sensitivity was 51%, where the index test was negative in 1 in 2 patients with the primary outcome of probable or confirmed COVID-19. Our most optimistic estimate of diagnostic sensitivity was 79%, where the index test was negative in 1 in 5 patients with the secondary outcome of confirmed COVID-19. Whilst, the former may underestimate performance, the latter is certainly an overestimate due to circular reasoning, whereby the test under evaluation is an essential component of the reference standard. In this consecutive series of hospitalised patients where testing was performed for symptoms at the discretion of the usual care clinician, our multi-disciplinary panel diagnosed probable COVID-19 in 12.6% of patients. The panel included representation from a broad range of medical specialities involved in the assessment of these patients, and therefore their judgment is likely to be representative of clinical practice. Our approach aims to provide insights into the performance of the test as it is applied in clinical practice. Interestingly patients with probable COVID-19 or confirmed COVID-19 and a negative index test were more likely to ...

    Results from TrialIdentifier: No clinical trial numbers were referenced.

    Results from Barzooka: We did not find any issues relating to the usage of bar graphs.

    Results from JetFighter: We did not find any issues relating to colormaps.

    Results from rtransparent:
    • Thank you for including a conflict of interest statement. Authors are encouraged to include this statement when submitting to a journal.
    • Thank you for including a funding statement. Authors are encouraged to include this statement when submitting to a journal.
    • No protocol registration statement was detected.

    About SciScore

    SciScore is an automated tool that is designed to assist expert reviewers by finding and presenting formulaic information scattered throughout a paper in a standard, easy to digest format. SciScore checks for the presence and correctness of RRIDs (research resource identifiers), and for rigor criteria such as sex and investigator blinding. For details on the theoretical underpinning of rigor criteria and the tools shown here, including references cited, please follow this link.

  3. Version published to 10.1101/2020.10.03.20206243v1 on medRxiv