Estimating underdiagnosis of COVID-19 with nowcasting and machine learning

  1. Leandro Pereira Garcia
  2. André Vinícius Gonçalves
  3. Matheus Pacheco Andrade
  4. Lucas Alexandre Pedebôs
  5. Ana Cristina Vidor
  6. Roberto Zaina
  7. Ana Luiza Curi Hallal
  8. Graziela de Luca Canto
  9. Jefferson Traebert
  10. Gustavo Medeiros de Araújo
  11. Fernanda Vargas Amaral

Reviewed by

Read the full article

Listed in

Log in to save this article

Abstract

ABSTRACT: Objective: To analyze the underdiagnosis of COVID-19 through nowcasting with machine learning in a Southern Brazilian capital city. Methods: Observational ecological design and data from 3916 notified cases of COVID-19 from April 14th to June 2nd, 2020 in Florianópolis, Brazil. A machine-learning algorithm was used to classify cases that had no diagnosis, producing the nowcast. To analyze the underdiagnosis, the difference between data without nowcasting and the median of the nowcasted projections for the entire period and for the six days from the date of onset of symptoms were compared. Results: The number of new cases throughout the entire period without nowcasting was 389. With nowcasting, it was 694 (95%CI 496–897). During the six-day period, the number without nowcasting was 19 and 104 (95%CI 60–142) with nowcasting. The underdiagnosis was 37.29% in the entire period and 81.73% in the six-day period. The underdiagnosis was more critical in the six days from the date of onset of symptoms to diagnosis before the data collection than in the entire period. Conclusion: The use of nowcasting with machine learning techniques can help to estimate the number of new disease cases.

Article activity feed

  1. Version published to 10.1590/1980-549720210047
  2. ScreenIT

    SciScore for 10.1101/2020.07.01.20144402: (What is this?)

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

    Table 1: Rigor

    Institutional Review Board Statementnot detected.
    Randomizationnot detected.
    Blindingnot detected.
    Power Analysisnot detected.
    Sex as a biological variableThe proportion of male people, people aged 60 years old or over, people with non-white race and people with 10 or less schooling time, was calculated as possible indicators of vulnerability.

    Table 2: Resources

    No key resources detected.

    Results from OddPub: Thank you for sharing your code.

    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.

  3. Version published to 10.1101/2020.07.01.20144402v1 on medRxiv