Time is of the essence: containment of the SARS-CoV-2 epidemic in Switzerland from February to May 2020

  1. Christian L. Althaus
  2. Daniel Probst
  3. Anthony Hauser
  4. Julien Riou

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Abstract

AIM

In late February and early March 2020, Switzerland experienced rapid growth of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infections with 30,243 confirmed cases and 1,860 deaths as of 10 May 2020. The sequential introduction of non-pharmaceutical interventions (NPIs) resulted in successful containment of the epidemic. A better understanding of how the timing of implementing NPIs influences the dynamics and outcome of SARS-CoV-2 epidemics will be crucial for the management of a potential resurgence in Switzerland.

METHODS

We developed a dynamic transmission model that describes infection, hospitalization, recovery and death due to SARS-CoV-2 in Switzerland. Using a maximum likelihood framework, we fitted the model to aggregated daily numbers of hospitalized patients, ICU occupancy and death from 25 February to 10 May 2020. We estimated critical parameters of SARS-CoV-2 transmission in Switzerland and explored counterfactual scenarios of an earlier and later implementation of NPIs.

RESULTS

We estimated the basic reproduction number R 0 = 2.61 (95% compatibility interval, CI: 2.51–2.71) during the early exponential phase of the SARS-CoV-2 epidemic in Switzerland. After the implementation of NPIs, the effective reproduction number approached R e = 0.64 (95% CI: 0.61–0.66). Based on the observed doubling times of the epidemic before and after the implementation of NPIs, we estimated that one week of early exponential spread required 3.1 weeks (95% CI: 2.8–3.3 weeks) of ‘lockdown’ to reduce the number of infections to the same level. Introducing the same sequence of NPIs one week earlier or later would have resulted in substantially lower (399, 95% prediction interval, PI: 347–458) and higher (8,683, 95% PI: 8,038–9,453) numbers of deaths, respectively.

CONCLUSIONS

The introduction of NPIs in March 2020 prevented thousands of SARS-CoV-2-related deaths in Switzerland. Early implementation of NPIs during SARS-CoV-2 outbreaks can reduce the number of deaths and the necessary duration of strict control measures considerably.

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    SciScore for 10.1101/2020.07.21.20158014: (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:
    Our study comes with a number of limitations. First, we did not have access to line lists of patients and used aggregated data of SARS-CoV-2 cases. Compared to the numbers communicated by the Swiss Federal Office of Public Health (FOPH), cantons typically report somewhat higher numbers of hospitalized and deceased patients. For example, FOPH communicated only 1,640 deaths [1], while the cantonal data reported 1,860 deaths by 10 May 2020. The discrepancies may result from missing or delayed patient records that cannot be linked in the line lists at FOPH. Second, we opted for a maximum likelihood framework and fixed a number of model parameters, such as hospitalization periods, to values that were informed by the literature. While our model can accurately describe the changes in hospitalized patients and ICU occupancy, the calculated CIs can be overly narrow for some parameters. Third, we described the SARS-CoV-2 epidemic in Switzerland overall and did not consider cantonal differences in the transmission dynamics as in Lemaitre et al. [11]. We think that this simplification is justified for the purpose of our study but acknowledge that cantonal differences in the epidemic trajectories were arguably important for the timing of the implementation of NPIs at the federal level. Fourth, we did not stratify the population by sex and age and cannot provide age-specific infection attack rates [24]. Fifth, we assumed a fixed IFR of 0.75% [11], which is in the range of estimates for Swi...

    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 10.1101/2020.07.21.20158014v1 on medRxiv