Real-Time Epidemiology and Acute Care Need Monitoring and Forecasting for COVID-19 via Bayesian Sequential Monte Carlo-Leveraged Transmission Models

Abstract

COVID-19 transmission models have conferred great value in informing public health understanding, planning, and response. However, the pandemic also demonstrated the infeasibility of basing public health decision-making on transmission models with pre-set assumptions. No matter how favourably evidenced when built, a model with fixed assumptions is challenged by numerous factors that are difficult to predict. Ongoing planning associated with rolling back and re-instituting measures, initiating surge planning, and issuing public health advisories can benefit from approaches that allow state estimates for transmission models to be continuously updated in light of unfolding time series. A model being continuously regrounded by empirical data in this way can provide a consistent, integrated depiction of the evolving underlying epidemiology and acute care demand, offer the ability to project forward such a depiction in a fashion suitable for triggering the deployment of acute care surge capacity or public health measures, and support quantitative evaluation of tradeoffs associated with prospective interventions in light of the latest estimates of the underlying epidemiology. We describe here the design, implementation, and multi-year daily use for public health and clinical support decision-making of a particle-filtered COVID-19 compartmental model, which served Canadian federal and provincial governments via regular reporting starting in June 2020. The use of the Bayesian sequential Monte Carlo algorithm of particle filtering allows the model to be regrounded daily and adapt to new trends within daily incoming data—including test volumes and positivity rates, endogenous and travel-related cases, hospital census and admissions flows, daily counts of dose-specific vaccinations administered, measured concentration of SARS-CoV-2 in wastewater, and mortality. Important model outputs include estimates (via sampling) of the count of undiagnosed infectives, the count of individuals at different stages of the natural history of frankly and pauci-symptomatic infection, the current force of infection, effective reproductive number, and current and cumulative infection prevalence. Following a brief description of the model design, we describe how the machine learning algorithm of particle filtering is used to continually reground estimates of the dynamic model state, support a probabilistic model projection of epidemiology and health system capacity utilization and service demand, and probabilistically evaluate tradeoffs between potential intervention scenarios. We further note aspects of model use in practice as an effective reporting tool in a manner that is parameterized by jurisdiction, including the support of a scripting pipeline that permits a fully automated reporting pipeline other than security-restricted new data retrieval, including automated model deployment, data validity checks, and automatic post-scenario scripting and reporting. As demonstrated by this multi-year deployment of the Bayesian machine learning algorithm of particle filtering to provide industrial-strength reporting to inform public health decision-making across Canada, such methods offer strong support for evidence-based public health decision-making informed by ever-current articulated transmission models whose probabilistic state and parameter estimates are continually regrounded by diverse data streams.