Predicting the evolution of SARS-Covid-2 in Portugal using an adapted SIR Model previously used in South Korea for the MERS outbreak

  1. Pedro Teles

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Abstract

The covid-19 has spread very quickly worldwide, leading the World Health Organization (WHO) to declare a state of pandemic. Moreover, the WHO has announced that the European continent is now the main centre of the pandemic.

One of the questions many governments are asking is how the spread is going to evolve in time. In this study, an adapted SIR model previously used in South Korea to model the MERS outbreak was applied to estimate the evolution of the curve of active cases in the case of the Portuguese situation. As some of the parameters were unknown, and the data for Portugal is still scarce, given that the outbreak started later (first case on the 2nd of March) I used Italian data (first reported case in Italy on the 31st of January) to predict them. I then construct five different scenarios for the evolution of covid-19 in Portugal, considering both the effectiveness of the mitigation measurements implemented by the government, and the self-protective measures taken by the population, as explained in the South Korean model.

In the out of control scenario, the number of active cases could reach as much as 40,000 people by the beginning of April. In the best-case-scenario considered, the active cases could reach circa 7,000 people. The actual figure probably lies between the interval (7,000-13,000) and the peak will be reached between 9th and the 20th of April 2020.

Without control and self-protective measures, this model predicts that the figures of active cases of SARS-covid-2 would reach a staggering 40,000 people It shows the importance of control and self-protecting measure to bring down the number of affected people by following the recommendations of the WHO and health authorities. With the appropriate measures, this number can be brought down to 7,000-13,000 people

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    SciScore for 10.1101/2020.03.18.20038612: (What is this?)

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

    Table 1: Rigor

    NIH rigor criteria are not applicable to paper type.

    Table 2: Resources

    Software and Algorithms
    SentencesResources
    H, the number of hospitalized cases; R, the number of removed cases, and finally N, the total population of Portugal. β1 is the transmission coefficient of the asymptomatic infected cases, β2 is the transmission coefficient of the symptomatic infected cases (mild infected person and severe patients) to the susceptible, β3 is the transmission coefficient of the hospitalized cases to the susceptible, σ−1 is the mean incubation period, λ−1 is the mean time between symptom onset to hospitalization, k1-1 is the mean infectious period of asymptomatic infected person for survivors, k2-1 is the mean duration for hospitalized cases for survivors, δ−1 is the mean time from hospitalization to death, γ is the clinical outbreak rate in all the infected cases.
    Portugal.
    suggested: None
    The solving of the system of differential equations was performed using the Mathematica code [17], using the function “NonLinearModelFit”[18].
    Mathematica
    suggested: (Wolfram Mathematica, RRID:SCR_014448)

    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:
    • 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.

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  2. Version published to 10.1101/2020.03.18.20038612v3 on medRxiv
  3. Version published to 10.1101/2020.03.18.20038612v2 on medRxiv
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