Epidemic modelling and statistical support for policy: sub-populations, forecasting, and long-term planning
Lead Research Organisation:
University of Manchester
Department Name: Mathematics
Abstract
The ongoing COVID-19 epidemic requires careful monitoring as a variety of measures such as lockdown and social distancing are introduced and subsequently relaxed, leading to varying levels of demand for and capacity within the healthcare system. The disease has varying expected outcomes depending on the age, sex, and underlying comorbidities of cases. Epidemic dynamics, particularly in the presence of changing control policies, will shift the dominant modes of transmission and hence the distribution of disease. We will develop models to integrate the diverse but often noisy and incomplete datasets available, providing real-time policy support together with quantification of uncertainty. We will address three particular challenges. (1) Understanding spread in closely connected sub-populations in which there are close, repeated contacts capable of spreading disease such as households, hospitals, prisons, and care homes. Data from these contexts allow epidemiological parameters relating to infection risk conditional on contact to be identified in statistical work, and they are also important foci for policies. (2) Making short- and medium-term predictions of the epidemic trajectory and healthcare demand with appropriate uncertainty quantification. (3) Modelling long-term prospects for the epidemic, including the likelihood of eventual endemicity, the consequences of different virological assumptions about SARS-CoV-2, and how the different scenarios in this context will interact with long-term societal and health consequences of the pandemic. The project will use mathematical methodology, integrated with interdisciplinary expertise from social science, biology, clinical medicine, and epidemiology.
Publications
Curran-Sebastian J
(2024)
Calculation of Epidemic First Passage and Peak Time Probability Distributions
in SIAM/ASA Journal on Uncertainty Quantification
Ghafari M
(2024)
Prevalence of persistent SARS-CoV-2 in a large community surveillance study.
in Nature
Cahuantzi R
(2024)
Unsupervised identification of significant lineages of SARS-CoV-2 through scalable machine learning methods.
in Proceedings of the National Academy of Sciences of the United States of America
Lythgoe K
(2023)
Lineage replacement and evolution captured by 3 years of the United Kingdom Coronavirus (COVID-19) Infection Survey
in Proceedings of the Royal Society B: Biological Sciences
Brand SPC
(2023)
The role of vaccination and public awareness in forecasts of Mpox incidence in the United Kingdom.
in Nature communications
Whitfield CA
(2023)
Modelling the impact of non-pharmaceutical interventions on workplace transmission of SARS-CoV-2 in the home-delivery sector.
in PloS one
Wisniowski A
(2023)
The economic impact of the COVID-19 pandemic on ethnic minorities in Manchester: lessons from the early stage of the pandemic.
in Frontiers in sociology
Fyles M
(2023)
Diversity of symptom phenotypes in SARS-CoV-2 community infections observed in multiple large datasets.
in Scientific reports
Silva M
(2023)
Tracking the structure and sentiment of vaccination discussions on Mumsnet
in Social Network Analysis and Mining
Vihta KD
(2022)
Omicron-associated changes in SARS-CoV-2 symptoms in the United Kingdom.
in Clinical infectious diseases : an official publication of the Infectious Diseases Society of America
Pellis L
(2022)
Authors' Reply to the Discussion of 'Estimation of Reproduction Numbers in Real Time: Conceptual and Statistical Challenges' by Pellis et al. in Session 3 of The Royal Statistical Society's Special Topic Meeting on COVID-19 Transmission: 11 June 2021
in Journal of the Royal Statistical Society Series A: Statistics in Society
Vihta KD
(2022)
Symptoms and Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) Positivity in the General Population in the United Kingdom.
in Clinical infectious diseases : an official publication of the Infectious Diseases Society of America
Fong K
(2022)
Understanding Waiting Lists Pressures
Overton CE
(2022)
EpiBeds: Data informed modelling of the COVID-19 hospital burden in England.
in PLoS computational biology
House T
(2022)
Inferring risks of coronavirus transmission from community household data.
in Statistical methods in medical research
Wei J
(2022)
Antibody responses and correlates of protection in the general population after two doses of the ChAdOx1 or BNT162b2 vaccines.
in Nature medicine
Hilton J
(2022)
A computational framework for modelling infectious disease policy based on age and household structure with applications to the COVID-19 pandemic
in PLOS Computational Biology
De Angelis D
(2022)
Editorial.
in Statistical methods in medical research
Pritchard E
(2022)
Monitoring populations at increased risk for SARS-CoV-2 infection in the community using population-level demographic and behavioural surveillance.
in The Lancet regional health. Europe
Description | We have made important discoveries about: - Transmission of SARS-CoV2 in close contact populations like households and care homes, and how these interact with other parts of the population - Trade-offs in policy, particularly modelling of test and trace - Hospital capacity modelling - Consideration of longer-term prognosis for pandemic - Application of machine learning methods to statistical data |
Exploitation Route | The work *is* currently being used by: the Government, through the SPI-M sub-committee of SAGE as well as other sub-committees the PI and CoIs attend; by the Office for National Statistics as part of its running the Coronavirus Infection Survey; and the NHS in the North West and more widely which is using this in planning; and the UKHSA who have found the work important enough to fund a significant fraction of the PI's time. |
Sectors | Communities and Social Services/Policy Healthcare Government Democracy and Justice |
URL | https://personalpages.manchester.ac.uk/staff/thomas.house |
Description | The work is currently being used in at least the following contexts: (1) The Government through the SPI-MO sub-committee of SAGE as well as other sub-committees the PI and CoIs attended during the pandemic. The work also continues to feed in to SPI-M running as an advisory committee for DHSC (2) The Office for National Statistics as part of its running the Coronavirus Infection Survey. Household code is routinely run as part of the survey, and now this is being paused, will be expected to be further developed and documented for future use and retrospective analysis. (3) The NHS in the North West and more widely is using outputs from this project in planning. This is being developed as a more general tool for use in hospital planning. (4) UKHSA who have found the work important enough to fund a significant fraction of the PI's time as Joint Chief Data Scientist, a 30% secondment to their Data Science division. (5) The WHO is currently negotiating to fund the PI to roll out household analysis and code across its European region. |
First Year Of Impact | 2020 |
Sector | Communities and Social Services/Policy,Healthcare,Government, Democracy and Justice |
Impact Types | Societal Economic Policy & public services |