The Bayesian Susceptible-Exposed-Infected-Recovered model for the outbreak of COVID-19 on the Diamond Princess Cruise Ship

  1. Chao-Chih Lai
  2. Chen-Yang Hsu
  3. Hsiao-Hsuan Jen
  4. Amy Ming-Fang Yen
  5. Chang-Chuan Chan
  6. Hsiu-Hsi Chen

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Abstract

The outbreak of COVID-19 on the Diamond Princess Cruise Ship provides an unprecedented opportunity to estimate its original transmissibility with basic reproductive number (R 0 ) and the effectiveness of containment measures. We developed an ordinary differential equation-based Susceptible-Exposed-Infected-Recovery (SEIR) model with Bayesian underpinning to estimate the main parameter of R 0 determined by transmission coefficients, incubation period, and the recovery rate. Bayesian Markov Chain Monte Carlo (MCMC) estimation method was used to tackle the parameters of uncertainty resulting from the outbreak of COVID-19 given a small cohort of the cruise ship. The extended stratified SEIR model was also proposed to elucidate the heterogeneity of transmission route by the level of deck with passengers and crews. With the application of the overall model, R 0 was estimated as high as 5.70 (95% credible interval: 4.23–7.79). The entire epidemic period without containment measurements was approximately 47 days and reached the peak one month later after the index case. The partial containment measure reduced 63% (95% credible interval: 60–66%) infected passengers. With the deck-specific SEIR model, the heterogeneity of R 0 estimates by each deck was noted. The estimated R 0 figures were 5.18 for passengers (5–14 deck), mainly from the within-deck transmission, and 2.46 for crews (2–4 deck), mainly from the between-deck transmission. Modelling the dynamic of COVID-19 on the cruise ship not only provides an insight into timely evacuation and early isolation and quarantine but also elucidates the relative contributions of different transmission modes on the cruise ship though the deck-stratified SEIR model.

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  1. Version published to 10.1007/s00477-020-01968-w
  2. ScreenIT

    SciScore for 10.1101/2020.06.21.20136465: (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 variablenot detected.

    Table 2: Resources

    No key resources detected.

    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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  3. Version published to 10.1101/2020.06.21.20136465v1 on medRxiv