Journal Article

A real-time regional model for COVID-19: Probabilistic situational awareness and forecasting

Rø, Gunnar, Kristoffersen, Anja Bråthen, Frigessi, Arnoldo, de Blasio, Birgitte Freiesleben, Di Ruscio, Francesco, Engø-Monsen, Kenth, Diz-Lois Palomares, Alfonso, Midtbø, Jørgen Eriksson, Kamineni, Meghana, White, Richard, Hin Chan, Louis Yat, Dale, Ørjan, Engebretsen, Solveig, Lindstrøm, Jonas Christoffer, Stenerud, Kristian Lindalen

2023

Overview

The COVID-19 pandemic is challenging nations with devastating health and economic consequences. The spread of the disease has revealed major geographical heterogeneity because of regionally varying individual behaviour and mobility patterns, unequal meteorological conditions, diverse viral variants, and locally implemented non-pharmaceutical interventions and vaccination roll-out. To support national and regional authorities in surveilling and controlling the pandemic in real-time as it unfolds, we here develop a new regional mathematical and statistical model. The model, which has been in use in Norway during the first two years of the pandemic, is informed by real-time mobility estimates from mobile phone data and laboratory-confirmed case and hospitalisation incidence. To estimate regional and time-varying transmissibility, case detection probabilities, and missed imported cases, we developed a novel sequential Approximate Bayesian Computation method allowing inference in useful time, despite the high parametric dimension. We test our approach on Norway and find that three-week-ahead predictions are precise and well-calibrated, enabling policy-relevant situational awareness at a local scale. By comparing the reproduction numbers before and after lockdowns, we identify spatially heterogeneous patterns in their effect on the transmissibility, with a stronger effect in the most populated regions compared to the national reduction estimated to be 85% (95% CI 78%-89%). Our approach is the first regional changepoint stochastic metapopulation model capable of real time spatially refined surveillance and forecasting during emergencies.

• Publisher: Public Library of Science,Public Library of Science (PLoS)
• Subject: Awareness / Bayes Theorem / Bayesian analysis / Bayesian statistical decision theory / Biology and Life Sciences / Cellular telephones / Communicable Disease Control / Contact tracing / Coronaviruses / COVID-19 / COVID-19 - epidemiology / COVID-19 - prevention & control / COVID-19 vaccines / Datasets / Disease transmission / Epidemics / Forecasting / Forecasts and trends / Geography / Heterogeneity / Hospitals / Humans / Immunization / Infectious diseases / Intensive care / Laboratories / Mathematical models / Medicine and Health Sciences / Metapopulations / Methods / Mobility / Norway / Pandemics / People and Places / Real time / Regional development / Sentinel health events / Severe acute respiratory syndrome coronavirus 2 / Situational awareness / Statistical analysis / Statistical models / Statistics / Stochasticity / Telecommunications towers / Vaccination / Viral diseases