epidemiological modeling in the context of covid-19 · ispn university of bern. testing: •are...
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Epidemiological modeling in the context of COVID-19
Dr. Caroline BuckeeAssociate Professor of Epidemiology, Associate Director of the Centre for Communicable Disease Dynamics, Harvard TH Chan School of Public [email protected], @Caroline_OF_B
CarolineOB
DATA SCIENCE ZOOMPOSIUM APRIL 2nd
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Early stage of the epidemic• Estimation of R0 (simple growth rate estimate or mechanistic model) • Establish basic parameters: incubation period, latent period, duration
of infection, CFR
And then… • Evaluate interventions, scenario planning• Forecasting for particular places and issues (hospital bed capacity)• Thinking through the endgame
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Goal: Establish R0
Zhao et al (2020) biorxiv
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ISPN University of Bern
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TESTING:
• Are there enough testing kits? • What are the testing criteria?• What is the clinical spectrum?
Implications for modeling:
*Difficult to assess the number of infected people in your model (where are we on the epidemic curve?)
*Model structure uncertainty: what fraction of infections are asymptomatic and how do they contribute to transmission?
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Wu et al (2020) Nature Med
Goal: Establish fatality rates
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Ian Miller, Alex Becker, Bryan Grenfell, and Jess Metcalf of Princeton University.
Goal: Understand demographic and health system risk profiles for COVID-19
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S(E)IR model basics
S I R
Probability of infectious contact: contact rate k
Probability of transmission given contact: b
Recovery rate: r
R0 = bk/r
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The premise of flattening the curve through social distancingis to reduce k
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Peak et al (2017) PNAS
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Hellewell et al (2020) Lancet Global Health
Think through what interventions might work
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Peak et al (2020) MedRxiv
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Ferreti et al (2020) Science
Goal: understand transmission routes, implications for contact tracing
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Prem et al. (2020) Lancet
Asymptomatic
Mechanistic models for scenario planning
Kucharski et al. (2020) Lancet Inf Dis
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Ferreti et al (2020) Science
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Prem et al. (2020) Lancet
Goal: scenario planning
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Ferguson et al (March 16 2020) Imperial College COVID-19 Response Team
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Prem et al. (2020) Lancet
How to parameterize contact rates?
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How to parameterize contact rates?
Courtesy of Jessica Metcalf (age structures from POLYMOD study)
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Ainslie, Walters, Fu et al (March 24 2020) Imperial College COVID-19 Response Team Report
What impact is social distancing having?
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Goal: thinking through the endgame - how long will this last?
Kissler et al (2020)
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• Forecasting very challenging because of testing heterogeneities and difficulty understanding contact rate changes under social distancing• Models useful for understanding what interventions might work
under different assumptions• Scenario planning useful for thinking through qualitative dynamics of
this pandemic• Models highlight data gaps and identify key uncertainties (measures
of social distancing, need for serology to establish asymptomatics)• Important to use context-specific parameters and consider indirect
effects of interventions
Summary