Incubation Period and Other Epidemiological Characteristics of 2019 Novel Coronavirus Infections with Right Truncation: A Statistical Analysis of Publicly Available Case Data

  1. Natalie Linton
  2. Tetsuro Kobayashi
  3. Yichi Yang
  4. Katsuma Hayashi
  5. Andrei Akhmetzhanov
  6. Sung-mok Jung
  7. Baoyin Yuan
  8. Ryo Kinoshita
  9. Hiroshi Nishiura

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Abstract

The geographic spread of 2019 novel coronavirus (COVID-19) infections from the epicenter of Wuhan, China, has provided an opportunity to study the natural history of the recently emerged virus. Using publicly available event-date data from the ongoing epidemic, the present study investigated the incubation period and other time intervals that govern the epidemiological dynamics of COVID-19 infections. Our results show that the incubation period falls within the range of 2–14 days with 95% confidence and has a mean of around 5 days when approximated using the best-fit lognormal distribution. The mean time from illness onset to hospital admission (for treatment and/or isolation) was estimated at 3–4 days without truncation and at 5–9 days when right truncated. Based on the 95th percentile estimate of the incubation period, we recommend that the length of quarantine should be at least 14 days. The median time delay of 13 days from illness onset to death (17 days with right truncation) should be considered when estimating the COVID-19 case fatality risk.

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  1. ScreenIT

    SciScore for 10.1101/2020.01.26.20018754: (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 data were processed using R version 3.6.2 [12], MLE was computed using Julia version 1.3 [13], and the Markov chain Monte Carlo (MCMC) simulations were performed in Stan (cmdStan version 2.22.1 [14]).
    cmdStan
    suggested: None

    Results from OddPub: Thank you for sharing your code.

    Results from LimitationRecognizer: We detected the following sentences addressing limitations in the study:
    Several limitations of the present study exist. First, the dataset relies on publicly available information that is not uniformly distributed (i.e., collected from various sources), and therefore the availability of dates relevant to our analyses is limited to a small, selective sample that is not necessarily generalizable to all confirmed cases. Moreover, given the novelty of the COVID-19 pneumonia, it is possible that illness onset and other event data were handled differently between jurisdictions (e.g., was illness onset the date of fever or date of dyspnea?). Second, our data include very coarse date intervals with some proxy dates used to determine the left and/or right hand dates of some intervals. Third, as the sample size was limited, the variance is likely to be biased. Fourth, we were not able to examine the heterogeneity of estimates by different attributes of cases (e.g., severity of disease) [19]. Lastly, as we only have information on confirmed cases, there is a bias towards more severe disease–particularly for earlier cases. This study presents the estimates of epidemiological characteristics of COVID-19 infections that are key parameter for studies on incidence, case fatality, and epidemic final size, among other possibilities [7, 11]. From the 95th percentile estimate of the incubation period we found that the length of quarantine should be at least 14 days, and we stress that the 17–24-day time delay from illness onset to death must be addressed when estima...

    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 10.3390/jcm9020538
  3. Version published to 10.1101/2020.01.26.20018754 on medRxiv