Optimizing diagnostic strategy for novel coronavirus pneumonia, a multi-center study in Eastern China

  1. Jing-Wen Ai
  2. Hao-Cheng Zhang
  3. Teng Xu
  4. Jing Wu
  5. Mengqi Zhu
  6. Yi-Qi Yu
  7. Han-Yue Zhang
  8. Yang Li
  9. Xian Zhou
  10. Zhongliang Shen
  11. Guo-Qing Zang
  12. Jie Xu
  13. Wen-Jing Chen
  14. Yong-Jun Li
  15. De-Sheng Xie
  16. Ming-Zhe Zhou
  17. Jing-Ying Sun
  18. Jia-Zhen Chen
  19. Wen-Hong Zhang

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Abstract

COVID-19 caused by a novel coronavirus SARS-CoV-2 emerged in Wuhan, Hubei province since December 2019, and caused a rapid outbreak throughout China and globally. Cities outside Hubei are also facing great challenge and require implementing of effective and feasible strategy in precision diagnosing novel coronavirus pneumonia (NCP).

We described a multicenter prospective study on diagnostic strategy of suspected NCP patients from January 22 nd to February 9 th , 2020 in Eastern China cities. Nasopharyngeal swabs were collected from the patients. The epidemiological characteristics, clinical symptoms, laboratory assessments, and computed tomographic (CT) scans were obtained. Pathogen screen were performed including RT-PCR, multiplex PCR, rapid flu antigen tests and mNGS.

We enrolled 53 suspected NCP patients, among whom 20 were laboratory-confirmed. Fourteen (70%) and 3 (15%) patients were positive for the first and second SARS-CoV-2 RT-PCR test, respectively. All NCP patients were positive for mNGS. Chest CT images and the symptoms of early stage NCP patients were similar to other viral pneumonia patients. We identified 11 of 20 co-infections in NCP cases, including regular respiratory virus, fungi and bacteria synchronously. Genomic analysis showed that 8 of 10 cases had no mutation in virus genome, while 2 cases had only one single mutation in N gene.

Our study discovered that a combination of chest CT, SARS-CoV-2 RT-PCR and multi-plex PCR is recommended in regions outside Hubei province. Co-infection of other pathogens with SARS-CoV-2 exists and should be acknowledged. Repeated sampling, change of specimen type or metagenomics sequencing could further facilitate during critical clinical cases.

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  1. ScreenIT

    SciScore for 10.1101/2020.02.13.20022673: (What is this?)

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

    Table 1: Rigor

    Institutional Review Board StatementIRB: Oral consents were obtained from all the patients and the study was approved by the ethics review committee of Huashan Hospital affiliated to Fudan University.
    Randomizationnot detected.
    Blindingnot detected.
    Power Analysisnot detected.
    Sex as a biological variablenot detected.

    Table 2: Resources

    Software and Algorithms
    SentencesResources
    All statistical analyses were performed using SPSS (Statistical Package for the Social Sciences) version 13.0 software (SPSS Inc).
    Statistical Package for the Social Sciences
    suggested: (SPSS, RRID:SCR_002865)
    SPSS
    suggested: (SPSS, RRID:SCR_002865)
    Alignment of multiple sequences was performed with the ClustalW program (MEGA software, version 7.0.14)18.
    ClustalW
    suggested: (ClustalW, RRID:SCR_017277)
    MEGA
    suggested: (Mega BLAST, RRID:SCR_011920)

    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:
    The study has a limitation of a relatively small sample size. More studies are needed to further validate our findings. Also, sputum, lower respiratory tract, serum and fecal samples were not collected for our laboratory-confirmed patients in our study, and collection of the above samples for a larger cohort would help to improve our diagnostic strategy. Our study discovered that, in low epidemic regions outside Hubei province such as Eastern-China region, the current reliable first approach to the unexplained pneumonia should be a combination of chest CT, SARS-COV-2 RT-PCR and multi-plex PCR (rapid influenza antigen tests and RT-PCR could also be used as a substitute). Chest CT alone could not precisely diagnose COVID-2019 due to similar radiological presentations. Co-infection of other pathogens with SARS-COV-2 exists and should be acknowledged. What’s more, different sampling approaches may also affect the results, therefore, in highly suspected cases but with two negative SARS-COV-2 RT-PCR results, repeated sampling or change of sample type could increase the positive rate. Metagenomics sequencing could further facilitate during critical clinical cases and monitor the molecular evolution for SARS-COV-2.

    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 10.1101/2020.02.13.20022673v1 on medRxiv