Head-to-head comparison of nasal and nasopharyngeal sampling using SARS-CoV-2 rapid antigen testing in Lesotho

  1. Niklaus D. Labhardt
  2. Lucia González Fernández
  3. Bulemba Katende
  4. Josephine Muhairwe
  5. Moniek Bresser
  6. Alain Amstutz
  7. Tracy R. Glass
  8. Morten Ruhwald
  9. Jilian A. Sacks
  10. Camille Escadafal
  11. Mathabo Mareka
  12. Sekhele M. Mooko
  13. Margaretha de Vos
  14. Klaus Reither

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Abstract

To assess the real-world diagnostic performance of nasal and nasopharyngeal swabs for SD Biosensor STANDARD Q COVID-19 Antigen Rapid Diagnostic Test (Ag-RDT).

Methods

Individuals ≥5 years with COVID-19 compatible symptoms or history of exposure to SARS-CoV-2 presenting at hospitals in Lesotho received two nasopharyngeal and one nasal swab. Ag-RDT from nasal and nasopharyngeal swabs were performed as point-of-care on site, the second nasopharyngeal swab used for polymerase chain reaction (PCR) as the reference standard.

Results

Out of 2198 participants enrolled, 2131 had a valid PCR result (61% female, median age 41 years, 8% children), 84.5% were symptomatic. Overall PCR positivity rate was 5.8%. The sensitivity for nasopharyngeal, nasal, and combined nasal and nasopharyngeal Ag-RDT result was 70.2% (95%CI: 61.3–78.0), 67.3% (57.3–76.3) and 74.4% (65.5–82.0), respectively. The respective specificity was 97.9% (97.1–98.4), 97.9% (97.2–98.5) and 97.5% (96.7–98.2). For both sampling modalities, sensitivity was higher in participants with symptom duration ≤ 3days versus ≤ 7days. Agreement between nasal and nasopharyngeal Ag-RDT was 99.4%.

Conclusions

The STANDARD Q Ag-RDT showed high specificity. Sensitivity was, however, below the WHO recommended minimum requirement of ≥ 80%. The high agreement between nasal and nasopharyngeal sampling suggests that for Ag-RDT nasal sampling is a good alternative to nasopharyngeal sampling.

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  1. Version published to 10.1371/journal.pone.0278653
  2. ScreenIT

    SciScore for 10.1101/2021.12.29.21268505: (What is this?)

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

    Table 1: Rigor

    EthicsConsent: Informed consent was obtained after pre-screening.
    IRB: Ethics: This study was approved by the Ethic Committee Switzerland (Ethikkommission Nordwest-und Zentralschweiz (EKNZ) AO_2020-00018) and the National Health and Research and Ethics Committee of Lesotho (NH-REC; ID-107-2020).
    Sex as a biological variableA posterior-anterior chest x-ray was also performed in all adult non-pregnant participants with at least one symptom compatible with COVID-19 (see above), or with clinical signs of tuberculosis or upon specific request by the physician in case of children and pregnant women.
    Randomizationnot detected.
    Blindingnot detected.
    Power Analysisnot 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:
    Limitations are that the study was conducted only at two clinics and that nasal and nasopharyngeal Ag-RDT were read by the same reader by visual inspection without the use of a reading device, which might have allowed for a more standardized test interpretation. Further, the previous nasal swab for Ag-RDT may have influenced the yield of the subsequent two nasopharyngeal swabs in participants with low viral secretions(24). For ethical reasons, we had to exclude critically ill patients, which may have led to a certain spectrum bias by underrepresenting patients with very advanced disease. In conclusion, this prospective study including 2131 not critically ill participants with COVID-19 compatible symptoms or exposure to SARS-CoV-2 in Lesotho showed a rather low overall sensitivity of the STANDARD Q Ag-RDT on nasopharyngeal and nasal sampling of about 70% and 67% whereas the specificity was above 97%. Agreement between nasal and nasopharyngeal sampling for the Ag-RDT was high, suggesting that the more convenient nasal sampling may be sufficient for routine screening and testing in outpatient settings.

    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.

    Results from scite Reference Check: We found no unreliable references.

    About SciScore

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  3. Version published to 10.1101/2021.12.29.21268505v1 on medRxiv