Comparative performance of four nucleic acid amplification tests for SARS-CoV-2 virus

  1. Yujuan Xiong
  2. Zhen-Zhen Li
  3. Qi-Zhen Zhuang
  4. Yan Chao
  5. Fei Li
  6. Yi-Yuan Ge
  7. Yi Wang
  8. Pei-Feng Ke
  9. Xian-Zhang Huang

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Abstract

Coronavirus disease 2019 (COVID-19) can be screened and diagnosed through the detection of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) by real-time reverse transcription polymerase chain reaction. SARS-CoV-2 nucleic acid amplification tests (NAATs) have been rapidly developed and quickly applied to clinical testing during the pandemic. However, studies evaluating the performance of these NAAT assays are limited. We evaluated the performance of four NAATs, which were marked by the Conformité Européenne and widely used in China during the pandemic. Results showed that the analytical sensitivity of the four assays was significantly lower than that claimed by the NAAT manufacturers. The limit of detection (LOD) of Daan, Sansure, and Hybribio NAATs was 3000 copies/mL, whereas the LOD of Bioperfectus NAATs was 4000 copies/mL. The results of the consistency test using 46 samples showed that Daan, Sansure, and Hybribio NAATs could detect the samples with a specificity of 100% (30/30) and a sensitivity of 100% (16 /16), whereas Bioperfectus NAAT detected the samples with a specificity of 100% (30/30) and a sensitivity 81.25% (13/16). The sensitivity of Bioperfectus NAAT was lower than that of the three other NAATs; this finding was consistent with the result that Bioperfectus NAAT had a higher LOD than the three other kinds of NAATs. The four above mentioned reagents presented high specificity; however, for the detection of the samples with low virus concentration, Bioperfectus reagent had the risk of missing detection. Therefore, the LOD should be considered in the selection of SARS-CoV-2 NAATs.

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  1. ScreenIT

    SciScore for 10.1101/2020.03.26.010975: (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 Ethics Committees from the Guangdong Provincial Hospital of Chinese Medicine (ZE2020-027-01).
    Randomizationnot detected.
    Blindingnot detected.
    Power Analysisnot detected.
    Sex as a biological variablenot detected.
    Cell Line AuthenticationContamination: Analytical specificity: Eighteen pseudovirus samples of analytical specificity reference materials from the performance verification reference material kit were used to determine the analytical specificity of four NAATs, including human coronavirus HCoV-OC43, HCoV-HKU1 RNA, HCoV-229E RNA, HCoV-NL63 RNA, SARS RNA, Middle East respiratory syndrome (MERS) RNA, influenza A HIN1 virus, influenza B INFB virus, respiratory syncytial virus type A and type B, human parainfluenza virus, adenovirus, enterovirus, mycoplasma pneumoniae, Epstein–Barr (EB) virus, human cytomegalovirus, Mycobacterium tuberculosis, and two samples with human genome DNA.

    Table 2: Resources

    Software and Algorithms
    SentencesResources
    Statistical analysis: The significance of the difference in sensitivity between the NAATs was assessed by using Fisher’s exact test in GraphPad Prism (5.0).
    GraphPad
    suggested: (GraphPad Prism, RRID:SCR_002798)
    The 95% confidence intervals (CIs) for specificity and sensitivity were calculated by using the Wilson–Score method in GraphPad Prism.
    GraphPad Prism
    suggested: (GraphPad Prism, RRID:SCR_002798)

    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:
    • No conflict of interest statement was detected. If there are no conflicts, we encourage authors to explicit state so.
    • No funding statement was detected.
    • 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 10.1101/2020.03.26.010975 on bioRxiv