Viral shedding dynamics reveals sputum as a reliable and cost-saving specimen for SARS-CoV-2 diagnosis within the first 10 days since symptom onset: A prospective cohort study

  1. Jorge Levican
  2. Leonardo I. Almonacid
  3. Gonzalo Valenzuela
  4. Tamara García-Salum
  5. Luis Rojas
  6. Eileen Serrano
  7. Catalina Pardo-Roa
  8. Erick Salinas
  9. María José Avendaño
  10. Fabiola Perazzo
  11. Luis Antonio Díaz
  12. Sebastián Valderrama
  13. Marcos Ortega
  14. Adriana Toro
  15. Viviana Montecinos
  16. Arnoldo Riquelme
  17. Rafael A. Medina

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Abstract

Background

Coronavirus disease 2019 (COVID-19) caused by the severe acute respiratory syndrome virus (SARS-CoV-2) is challenging global public health, due to an increasing demand for testing and the shortage of diagnostic supplies. Nasopharyngeal swab (NPS) is considered the optimal sample for SARS-CoV2 diagnosis and sputum (SPT) has been proposed as an economic alternative. However, the temporal concordance of diagnosis in NPS and SPT has not been addressed.

Methods

Through a longitudinal study we compared the shedding dynamics of SARS-CoV-2 RNA evaluated by RT-qPCR in serially collected SPT and NPS obtained from 82 ambulatory and hospitalized patients during acute infection and convalescence. The concordance during the follow-up and cost analysis between both collected specimens was evaluated.

Findings

We analyzed 379 samples, 177 NPS and 202 SPT. The highest proportion of positive samples was detected within the first 15 days after the symptoms onset. The median time of positivity was higher for NPS (median= 25 days) than SPT (median= 21 days). There was no significant difference in the median RT-qPCR C T values between both sample types. The temporal categorization of matched-paired samples indicated substantial correlation (r=0·6023) and substantial agreement (87·23%) during the first ten days since symptoms onset (kappa = 0·697). A cost analysis demonstrated a significant saving when the SPT specimen was used.

Interpretation

Sputum is a feasible and cost-saving alternative to NPS, providing an equivalent value for the detection and follow-up of SARS-CoV-2 RNA.

Funding

Agencia Nacional de Investigación y Desarrollo (ANID) of Chile, NIH-NIAID USA.

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  1. ScreenIT

    SciScore for 10.1101/2020.08.30.20183889: (What is this?)

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

    Table 1: Rigor

    Institutional Review Board StatementConsent: Written informed consent was obtained under protocol 16·066, which was reviewed and approved by the Scientific Ethics Committee at Pontificia Universidad Católica de Chile (PUC).
    IRB: Written informed consent was obtained under protocol 16·066, which was reviewed and approved by the Scientific Ethics Committee at Pontificia Universidad Católica de Chile (PUC).
    Randomizationnot detected.
    Blindingnot detected.
    Power Analysisnot detected.
    Sex as a biological variablenot detected.

    Table 2: Resources

    Software and Algorithms
    SentencesResources
    Statistical analyses were conducted using PRISM 8·0 (v8-4·2).
    PRISM
    suggested: (PRISM, RRID:SCR_005375)

    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: An explicit section about the limitations of the techniques employed in this study was not found. We encourage authors to address study limitations.

    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.

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  2. Version published to 10.1101/2020.08.30.20183889v1 on medRxiv