A computational framework for modelling infectious disease policy based on age and household structure with applications to the COVID-19 pandemic

• Published in: PLoS computational biology 2022-09, Vol.18 (9), p.e1010390
• Main Authors: Hilton, Joe, Riley, Heather, Pellis, Lorenzo, Aziza, Rabia, Brand, Samuel P C, K Kombe, Ivy, Ojal, John, Parisi, Andrea, Keeling, Matt J, Nokes, D James, Manson-Sawko, Robert, House, Thomas
• Format: Article
• Language: English
• Subjects: Age; Age composition; Age groups; Analysis; Biology and Life Sciences; Calibration; Communicable Disease Control - methods; Communicable Diseases; Computer applications; Computer simulation; Computer-generated environments; Coronaviruses; COVID-19; COVID-19 - epidemiology; COVID-19 - prevention & control; COVID-19 vaccines; Demography; Differential equations; Disease transmission; Epidemics; Households; Humans; Immunization; Infections; Infectious diseases; Influenza; Mathematical models; Medicine and Health Sciences; Methods; Ordinary differential equations; Pandemics; Pandemics - prevention & control; Policy; Public health; Risk assessment; SARS-CoV-2; Severe acute respiratory syndrome coronavirus 2; Simulation; Social conditions; Viral diseases
• ISSN: 1553-7358; 1553-734X; 1553-7358
• DOI: 10.1371/journal.pcbi.1010390

The widespread, and in many countries unprecedented, use of non-pharmaceutical interventions (NPIs) during the COVID-19 pandemic has highlighted the need for mathematical models which can estimate the impact of these measures while accounting for the highly heterogeneous risk profile of COVID-19. Models accounting either for age structure or the household structure necessary to explicitly model many NPIs are commonly used in infectious disease modelling, but models incorporating both levels of structure present substantial computational and mathematical challenges due to their high dimensionality. Here we present a modelling framework for the spread of an epidemic that includes explicit representation of age structure and household structure. Our model is formulated in terms of tractable systems of ordinary differential equations for which we provide an open-source Python implementation. Such tractability leads to significant benefits for model calibration, exhaustive evaluation of possible parameter values, and interpretability of results. We demonstrate the flexibility of our model through four policy case studies, where we quantify the likely benefits of the following measures which were either considered or implemented in the UK during the current COVID-19 pandemic: control of within- and between-household mixing through NPIs; formation of support bubbles during lockdown periods; out-of-household isolation (OOHI); and temporary relaxation of NPIs during holiday periods. Our ordinary differential equation formulation and associated analysis demonstrate that multiple dimensions of risk stratification and social structure can be incorporated into infectious disease models without sacrificing mathematical tractability. This model and its software implementation expand the range of tools available to infectious disease policy analysts.