The Utility of rRT-PCR in Diagnosis and Assessment of Case-fatality rates of COVID-19 In the Iranian Population – Positive Test Results are a Marker for Illness Severity

  1. Ghasem Janbabaei
  2. Eric J. Brandt
  3. Reza Golpira
  4. Alireza Raeisi
  5. Jafar Sadegh Tabrizi
  6. Hamid Reza Safikhani
  7. Mohammad Taghi Talebian
  8. Siamak Mirab Samiee
  9. Alireza Biglar
  10. Reza Malekzadeh
  11. Arya Mani

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Abstract

The utility of PCR-based testing in characterizing patients with COVID-19 and the severity of their disease remains unknown. We performed an observational study among patients presenting to hospitals in Iran who were tested for 2019-nCoV viral RNA by rRT-PCR between the fourth week of February 2020 to the fourth week of March 2020. Frequency of symptoms, comorbidities, intubation, and mortality rates were compared between COVID-19 positive vs. negative patients. 96103 patients were tested from 879 hospitals. 18754 (19.5%) tested positive for COVID-19. Positive testing was more frequent in those 50 years or older. The prevalence of cough (54.5% vs. 49.7%), fever (49.5% vs. 44.7%), and respiratory distress (43.0% vs. 39.0%) but not hypoxia (46.9% vs. 56.7%) was higher in COVID-19 positive vs. negative patients (p<0.001 for all). More patients had cardiovascular diseases (10.6% vs. 9.5%, p<0.001) and type 2 diabetes mellitus (10.8% vs. 8.7%, p<0.001) among COVID-19 positive vs. negative patients. There were fewer patients with cancer (1.1%, vs. 1.4%, p<0.001), asthma (1.9% vs. 2.5%, p<0.001), or pregnant (0.4% vs. 0.6%, =0.001) in COVID-19 positive vs. negative groups. COVID-19 positive vs. negative patients required more intubation (7.7% vs. 5.2%, p<0.001) and had higher mortality (14.6% vs. 6.3%, p<0.001). Odds ratios for death of positive vs negative patients range from 2.01 to 3.10 across all age groups. In conclusion, COVID-19 test-positive vs. test-negative patients had more severe symptoms and comorbidities, required higher intubation, and had higher mortality. rRT-PCR positive result provided diagnosis and a marker of disease severity in Iranians.

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  1. ScreenIT

    SciScore for 10.1101/2020.04.29.20085233: (What is this?)

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

    Table 1: Rigor

    Institutional Review Board StatementIRB: Study oversight: The study was initiated by The Deputy for Health and Curative affairs at the Iranian Ministry of Health and Medical Education (MOHME) and approved by the institutional review boards of the participating hospitals (http://ethics.research.ac.ir/IndexEn.php).
    Randomizationnot detected.
    Blindingnot detected.
    Power Analysisnot detected.
    Sex as a biological variableThose deemed as high risk for acquiring the disease, including those with T2D and hypertension, obesity, immunodeficiency, malignant disorders undergoing immune suppressive therapy, and pregnant women were prioritized.

    Table 2: Resources

    Software and Algorithms
    SentencesResources
    Data were analyzed using Excel v16.35
    Excel
    suggested: None
    5 (Microsoft) and Stata 16 (StataCorp, LLC).
    StataCorp
    suggested: (Stata, RRID:SCR_012763)

    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:
    Our study has limitations that confines interpretation. Our data does not include the chest CT-scan results of patients with acute respiratory illness. Access to this data given the probability of false negative PCR results is particularly important. Additionally, the data analyzed in our study were aggregated and hence adjustment for multiple covariates due to lack of access to patient level data could not be carried out. Nevertheless, the higher rate of mortality in patients tested positive vs. those tested negatives suggests that the PCR-based testing has been a relatively suitable method for the screening of high-risk patients.

    Results from TrialIdentifier: No clinical trial numbers were referenced.

    Results from Barzooka: We found bar graphs of continuous data. We recommend replacing bar graphs with more informative graphics, as many different datasets can lead to the same bar graph. The actual data may suggest different conclusions from the summary statistics. For more information, please see Weissgerber et al (2015).

    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. ScreenIT

    SciScore for 10.1101/2020.04.29.20085233: (What is this?)

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

    Table 1: Rigor

    Institutional Review Board StatementStudy oversight The study was initiated by The Deputy for Health and Curative affairs at the Iranian Ministry of Health and Medical Education ( MOHME ) and approved by the institutional review boards of the participating hospital ( http://ethics.research.ac.ir/IndexEn.php).Randomizationnot detected.Blindingnot detected.Power Analysisnot detected.Sex as a biological variableThose deemed as high risk for acquiring the disease, including those with T2D and hypertension, obesity, immunodeficiency, malignant disorders undergoing immune suppressive therapy, and pregnant women were prioritized.

    Table 2: Resources

    Software and Algorithms
    SentencesResources
    ( Microsoft ) and Stata 16 ( StataCorp , LLC) .
    StataCorp
    suggested: (Stata, SCR_012763)

    Results from Barzooka: We also found bar graphs of continuous data. We recommend replacing bar graphs with more informative graphics, as many different datasets can lead to the same bar graph. The actual data may suggest different conclusions from the summary statistics. For more information, please see Weissgerber et al (2015).

    Results from OddPub: Thank you for sharing your data.

    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 is not a substitute for expert review. SciScore checks for the presence and correctness of RRIDs (research resource identifiers) in the manuscript, and detects sentences that appear to be missing RRIDs. SciScore also checks to make sure that rigor criteria are addressed by authors. It does this by detecting sentences that discuss criteria such as blinding or power analysis. SciScore does not guarantee that the rigor criteria that it detects are appropriate for the particular study. Instead it assists authors, editors, and reviewers by drawing attention to sections of the manuscript that contain or should contain various rigor criteria and key resources. For details on the results shown here, including references cited, please follow this link.

  3. Version published to 10.1101/2020.04.29.20085233v1 on medRxiv