Application and optimization of RT-PCR in diagnosis of SARS-CoV-2 infection

  1. Xiaoshuai Ren
  2. Yan Liu
  3. Hongtao Chen
  4. Wei Liu
  5. Zhaowang Guo
  6. Yaqin Zhang
  7. Chaoqun Chen
  8. Jianhui Zhou
  9. Qiang Xiao
  10. Guanmin Jiang
  11. Hong Shan

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Abstract

Background

Coronavirus Disease 2019 (COVID-19) caused by Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has become a global threat to public health. Aiming to construct an efficient screening pattern, we comprehensively evaluated the performances of RT-PCR and chest CT in diagnosing COVID-19.

Methods

The records including demographics, RT-PCR, and CT from 87 confirmed COVID-19 cases and 481 exclusion cases were collected. The diagnostic accuracy of the pharyngeal swab RT-PCR, CT, combination with the second pharyngeal swab RT-PCR or with CT were evaluated individually. Besides, all the stool RT-PCR results were plotted by time to explore the value of stool RT-PCR.

Findings

Combination of RT-PCR and CT has the higher sensitivity (91.9%,79/86) than RT-PCR alone (78.2%,68/87) or CT alone (66.7%, 54 of 81) or combination of two RT-PCR tests (86.2%,75/87). There was good agreement between RT-PCR and CT (kappa-value, 0.430). In 34 COVID-19 cases with inconsistent results, 94.1% (n=32) are mild infection, 62.5% of which (20/32) showed positive RT-PCR. 46.7% (35/75) COVID-19 patients had at least one positive stool during the course. Two cases had positive stool earlier than the pharyngeal swabs. Importantly, one patient had consecutive positive stool but negative pharyngeal swabs.

Interpretation

Combination of RT-PCR and CT with the highest sensitivity is an optimal pattern to screen COVID-19. RT-PCR is superior to CT in diagnosing mild infections. Stool RT-PCR should be considered as an item for improving discovery rate and hospital discharge. This study shed light for optimizing scheme of screening and monitoring of SARS-CoV-2 infection.

Funding

This work was supported by the National Natural Science Foundation of China (No. 81502104), National Program on Key Basic Research Project (No. 2018YFC0910600),the Nature Science Foundation of Guangdong Province, China (Grant No: 2017A030313771 and 2020A151501001) and the Young Teachers Nurturing Program of Sun Yat-Sen University (Grant No:17ykpy62)

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  1. ScreenIT

    SciScore for 10.1101/2020.02.25.20027755: (What is this?)

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

    Table 1: Rigor

    Institutional Review Board StatementIRB: The study was approved by The Fifth Affiliated Hospital of Sun Yat-sen University Ethics Committee and written informed consent was obtained from patients involved before enrolment when data were collected retrospectively.
    Consent: The study was approved by The Fifth Affiliated Hospital of Sun Yat-sen University Ethics Committee and written informed consent was obtained from patients involved before enrolment when data were collected retrospectively.
    Randomizationnot detected.
    Blindingnot detected.
    Power Analysisnot detected.
    Sex as a biological variablenot detected.

    Table 2: Resources

    Software and Algorithms
    SentencesResources
    RNA was extracted and tested by real-time RT-PCR with SARS-Cov-2 specific primers and probes according to instruction of Kit.
    SARS-Cov-2
    suggested: (SARS-CoV-2-Sequences, RRID:SCR_018319)

    Results from OddPub: Thank you for sharing your data.

    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.

    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.

  2. Version published to 10.1101/2020.02.25.20027755 on medRxiv