Estimating the generation interval for coronavirus disease (COVID-19) based on symptom onset data, March 2020

  1. Tapiwa Ganyani
  2. Cécile Kremer
  3. Dongxuan Chen
  4. Andrea Torneri
  5. Christel Faes
  6. Jacco Wallinga
  7. Niel Hens

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Abstract

Estimating key infectious disease parameters from the coronavirus disease (COVID-19) outbreak is essential for modelling studies and guiding intervention strategies.

Aim

We estimate the generation interval, serial interval, proportion of pre-symptomatic transmission and effective reproduction number of COVID-19. We illustrate that reproduction numbers calculated based on serial interval estimates can be biased.

Methods

We used outbreak data from clusters in Singapore and Tianjin, China to estimate the generation interval from symptom onset data while acknowledging uncertainty about the incubation period distribution and the underlying transmission network. From those estimates, we obtained the serial interval, proportions of pre-symptomatic transmission and reproduction numbers.

Results

The mean generation interval was 5.20 days (95% credible interval (CrI): 3.78–6.78) for Singapore and 3.95 days (95% CrI: 3.01–4.91) for Tianjin. The proportion of pre-symptomatic transmission was 48% (95% CrI: 32–67) for Singapore and 62% (95% CrI: 50–76) for Tianjin. Reproduction number estimates based on the generation interval distribution were slightly higher than those based on the serial interval distribution. Sensitivity analyses showed that estimating these quantities from outbreak data requires detailed contact tracing information.

Conclusion

High estimates of the proportion of pre-symptomatic transmission imply that case finding and contact tracing need to be supplemented by physical distancing measures in order to control the COVID-19 outbreak. Notably, quarantine and other containment measures were already in place at the time of data collection, which may inflate the proportion of infections from pre-symptomatic individuals.

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  1. ScreenIT

    SciScore for 10.1101/2020.03.05.20031815: (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

    No key resources detected.

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

    Results from LimitationRecognizer: We detected the following sentences addressing limitations in the study:
    This study does have some limitations. First, we rely on previous estimates for the incubation period. However, sensitivity analyses show that changing the incubation period distribution does not have a big impact on our estimates of the generation interval distribution. Second, we do not account for incomplete or possible changes in reporting over the course of the epidemic. Third, we do not acknowledge changes in contact processes and thus behavioral change, which could shape realised generation interval distributions as well as serial interval distributions (unpublished work). Fourth, we do not account for contraction of the generation interval because of depletion of susceptibles. Future work should take into account these shortcomings. Infection control for the COVID-19 epidemic relies on case-based measures such as finding cases and tracing contacts. A variable that determines how effective these case-based measures are is the proportion of pre-symptomatic transmission. Our estimates of this proportion are high, ranging from 0.48 to 0.77. This implies that the effectiveness of case finding and contact tracing in preventing COVID-19 infections will be considerably smaller compared to the effectiveness in preventing SARS or MERS infections, where pre-symptomatic transmission did not play an important role (see e.g. [15]). It is unlikely that these measures alone will suffice to control the COVID-19 epidemic. Additional measures, such as social distancing, are required.

    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 10.2807/1560-7917.es.2020.25.17.2000257
  3. Version published to 10.1101/2020.03.05.20031815v1 on medRxiv