Association Between rRT-PCR Test Results Upon Admission and Outcome in Hospitalized Chest CT-Positive COVID-19 Patients: A Provincial Retrospective Cohort with Active Follow-up

  1. Saeed Nemati
  2. Hamid Reza Najari
  3. Anita Eftekharzadeh
  4. Amir Mohammad Kazemifar
  5. Ali Qandian
  6. Pedram Fattahi
  7. Sepideh Abdi
  8. Elnaz Saeedi
  9. Maedeh Zokaei Nikoo
  10. Mohammad Reza Rouhollahi

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Abstract

Background: The coronavirus disease 2019 (COVID-19) pandemic imposed the most devastating challenge on healthcare systems worldwide. Iran was among the first countries that had to confront serious shortages in reverse-transcriptase-polymerase chain reaction (RT-PCR) testing for severe acute respiratory syndrome Coronavirus 2 (SARS-CoV-2) and ventilators availabilities throughout the COVID-19 outbreak. Objectives: This study aimed to investigate the clinical course of hospitalized COVID-19 patients with different real-time RT-PCR test results during the first three weeks of the outbreak in Qazvin province, Iran. Methods: In this retrospective cohort study, patients with a positive chest computed tomography (CT) scan for COVID-19 who were admitted to all 12 hospitals across Qazvin province, Iran, between February 20 and March 11, 2020, were included and followed up until March 27, 2020. A multivariate logistic regression model was applied to compare the independent associates of death among COVID-19 patients. Then, patients were categorized into six groups based on admission to the intensive care unit (ICU) and rRT-PCR test status (positive, negative, or no test). Also, multilevel logistic regression was used to compare the odds of surviving in each group against the reference group (PCR negative patients not-received ICU) to show if the rational allocation of ICU occurred while its capacity is limited. Results: In this study, we included 998 patients (57% male; median age: 54 years) with positive chest CT scan changes. Among them, 558 patients were examined with rRT-PCR test and 73.8% tested positive. Case fatality rate (CFR) was 20.68 and 7.53% among hospitalized patients with positive and negative tests, respectively. While only 5.2% of patients were admitted to the ICU, CFR outside ICU was 17.70 and 4.65% in patients with positive and negative results not admitted to the ICU, respectively. Conclusions: Total CFR in all hospitalized COVID-19 patients in Qazvin province during the first three weeks of the pandemic was 11.7%. Also, according to the results, the main risk factors included a positive rRT-PCR test, age more than 70 years, and having two or more comorbidities or just immunodeficiency disorders. Hence, the ICU admission criteria or prioritized ICU beds allocation should be considered with more emphasis on rRT-PCR results when the capacity of ICU beds is low.

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  1. Version published to 10.5812/archcid.111866
  2. ScreenIT

    SciScore for 10.1101/2020.04.21.20074641: (What is this?)

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

    Table 1: Rigor

    Institutional Review Board StatementIRB: This study was approved by the Research Ethic Committee of Qazvin University of Medical Sciences (QUMS-EC).
    Randomizationnot detected.
    Blindingnot detected.
    Power Analysisnot detected.
    Sex as a biological variablenot detected.

    Table 2: Resources

    Software and Algorithms
    SentencesResources
    Statistical analysis was performed using the Stata statistical software package (StataCorp. 2014. Stata Statistical
    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:
    However, the findings on the clinical pattern and outcome of the patients need to be interpreted in the context of our limitations. Among them, we need to emphasize on the low availability of PCR testing in Iran. Also we did not have access to data on the patients’ laboratory results, their smoking status, or the medications they received. The applied diagnosis and treatment flowchart as was first proposed by the INIGCDT(3) merits further explanation. The guidance which had originally adapted the related World Health Organization (WHO) guidance,(7, 8) proposed chest imaging as the first diagnostic step to screen patients who require prompt hospitalization amid shortages in RT-PCR test kits in Iran. As a result, all hospital-admitted patients with suggestive SARS-CoV-2 symptoms - with or without comorbidities - underwent chest imaging (specifically chest CT-scan) in the province of Qazvin hospitals. From among them, 59·3% were tested with RT-PCR and 24·9% had negative results. The proportion of the negative test results is in line with previous findings. While there has been a significant correlation between throat swab and sputum sample viral loads,(9) one study examining the bio-distribution of SARS-CoV-2 in different body tissues, reported positive RT-PCR rates only in 72% of sputum specimens.(10) Examining the concordance between chest CT-scan and PCR test results, a previous study from Wuhan, China, reported that chest CT sensitivity was 97% in RT-PCR-positive patients. O...

    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.

  3. ScreenIT

    SciScore for 10.1101/2020.04.21.20074641: (What is this?)

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

    Table 1: Rigor

    Institutional Review Board StatementThis study was approved by the Research Ethic Committee of Qazvin University of Medical Sciences (QUMS-EC). 4 Criteria and definitions Patients were admitted with a primary diagnosis of COVID-19 based on INIGCDT.Randomizationnot detected.Blindingnot detected.Power Analysisnot detected.Sex as a biological variableA total of 998 patients ( 57 % male ) with a median ( IQR 25-75 ) age of 54 ( 25 ) years were analyzed.

    Table 2: Resources

    Software and Algorithms
    SentencesResources
    Statistical analysis was performed using the Stata statistical software package (StataCorp. 2014. Stata Statistical
    StataCorp
    suggested: (Stata, SCR_012763)

    Results from OddPub: We did not find a statement about open data. We also did not find a statement about open code. Researchers are encouraged to share open data when possible (see Nature blog).

    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, please follow this link.

  4. Version published to 10.1101/2020.04.21.20074641v1 on medRxiv