Superspreading in early transmissions of COVID-19 in Indonesia

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Abstract

This paper presents a study of early epidemiological assessment of COVID-19 transmission dynamics in Indonesia. The aim is to quantify heterogeneity in the numbers of secondary infections. To this end, we estimate the basic reproduction number $$\mathscr {R}_0$$ R 0 and the overdispersion parameter $$\mathscr {K}$$ K at two regions in Indonesia: Jakarta–Depok and Batam. The method to estimate $$\mathscr {R}_0$$ R 0 is based on a sequential Bayesian method, while the parameter $$\mathscr {K}$$ K is estimated by fitting the secondary case data with a negative binomial distribution. Based on the first 1288 confirmed cases collected from both regions, we find a high degree of individual-level variation in the transmission. The basic reproduction number $$\mathscr {R}_0$$ R 0 is estimated at 6.79 and 2.47, while the overdispersion parameter $$\mathscr {K}$$ K of a negative-binomial distribution is estimated at 0.06 and 0.2 for Jakarta–Depok and Batam, respectively. This suggests that superspreading events played a key role in the early stage of the outbreak, i.e., a small number of infected individuals are responsible for large numbers of COVID-19 transmission. This finding can be used to determine effective public measures, such as rapid isolation and identification, which are critical since delay of diagnosis is the most common cause of superspreading events.

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  1. SciScore for 10.1101/2020.06.28.20142133: (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
    The num b erofsecond arycases byonep erson xc anb eexpress edi nterm so ftheover dis persi onparametera ndthep roba bili typ,

    We use aMATLA B®fun ct ion n bi nfittoe st imatet heo verdi sper s io npa r am e te r.

    MATLAB®
    suggested: (MATLAB, RRID:SCR_001622)

    Results from OddPub: Thank you for sharing your code and data.


    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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