Spatial heterogeneity in transmission and the impact of interventions: a mathematical modelling approach
Lead Research Organisation:
UNIVERSITY OF EXETER
Department Name: UNLISTED
Abstract
A new strain of Coronavirus appeared in China at the end of 2019 and is spreading
beyond Chinese borders. The purpose of this project is to minimise the number of serious
cases and deaths caused by the virus, following spread in the United Kingdom. We will
use the latest information about the UK population, the best biological information about
the virus to inform mathematical models that predict where and when the disease will
spread and in what numbers. This information, rapidly communicated to the NHS will
provide the best opportunity to manage care and allocate resources proactively, in
advance of the arrival of new cases of Coronavirus.
beyond Chinese borders. The purpose of this project is to minimise the number of serious
cases and deaths caused by the virus, following spread in the United Kingdom. We will
use the latest information about the UK population, the best biological information about
the virus to inform mathematical models that predict where and when the disease will
spread and in what numbers. This information, rapidly communicated to the NHS will
provide the best opportunity to manage care and allocate resources proactively, in
advance of the arrival of new cases of Coronavirus.
Technical Summary
This COVID-19 Rapid Response award is jointly funded (50:50) between the Medical Research Council and the National Institute for Health Research. The figure displayed is the total award amount of the two funders combined, with each partner contributing equally towards the project.
Predicting the size and duration of potential COVID-19 outbreaks is an essential
component of public-health planning and preparedness. Mathematical models of disease
transmission are potentially powerful tools for predicting the course of an upcoming
epidemic and evaluating control and mitigation strategies. However, standard models of
disease transmission without population structure overestimate the speed of invasion of a
novel pathogen. We have developed a spatial metapopulation transmission model for the
UK that is grounded in demographic data which incorporates regular (commuter-like)
movements of individuals. In previous work, we demonstrated that regular, repeated
movements lead to slower epidemic spread. Adapting this model for COVID-19, we
estimated that an uncontrolled epidemic in England and Wales would peak ~4 months
following sustained person-to-person transmission, but that seasonality in transmission
could substantially alter the timing and magnitude of the peak burden.
Here, we propose to use this model to evaluate control and mitigation strategies for
COVID-19. Guided by the World Health Organization-identified research priorities and
PHE needs, we will estimate the impact of travel restrictions, border screening and
quarantine policies. We will also assess the effects of social distancing measures and
other non-pharmaceutical interventions on peak burden and epidemic timing and rank
measures by effectiveness. The model will also be adapted to assess and rank
pharmaceutical deployment strategies.
Our vision is to make the model adaptable and available to other countries and settings,
both with and without census and commuting data. Key challenges include modelling
commuting patterns, incorporating realistic age structure, adding an observation model to
capture morbidity and mortality and including behaviour change which could substantially
alter dynamics.
Predicting the size and duration of potential COVID-19 outbreaks is an essential
component of public-health planning and preparedness. Mathematical models of disease
transmission are potentially powerful tools for predicting the course of an upcoming
epidemic and evaluating control and mitigation strategies. However, standard models of
disease transmission without population structure overestimate the speed of invasion of a
novel pathogen. We have developed a spatial metapopulation transmission model for the
UK that is grounded in demographic data which incorporates regular (commuter-like)
movements of individuals. In previous work, we demonstrated that regular, repeated
movements lead to slower epidemic spread. Adapting this model for COVID-19, we
estimated that an uncontrolled epidemic in England and Wales would peak ~4 months
following sustained person-to-person transmission, but that seasonality in transmission
could substantially alter the timing and magnitude of the peak burden.
Here, we propose to use this model to evaluate control and mitigation strategies for
COVID-19. Guided by the World Health Organization-identified research priorities and
PHE needs, we will estimate the impact of travel restrictions, border screening and
quarantine policies. We will also assess the effects of social distancing measures and
other non-pharmaceutical interventions on peak burden and epidemic timing and rank
measures by effectiveness. The model will also be adapted to assess and rank
pharmaceutical deployment strategies.
Our vision is to make the model adaptable and available to other countries and settings,
both with and without census and commuting data. Key challenges include modelling
commuting patterns, incorporating realistic age structure, adding an observation model to
capture morbidity and mortality and including behaviour change which could substantially
alter dynamics.
Publications
Brooks-Pollock E
(2021)
Mapping social distancing measures to the reproduction number for COVID-19
in Philosophical Transactions of the Royal Society B: Biological Sciences
Brooks-Pollock E
(2021)
Modelling that shaped the early COVID-19 pandemic response in the UK.
in Philosophical transactions of the Royal Society of London. Series B, Biological sciences
Brooks-Pollock E
(2021)
The population attributable fraction of cases due to gatherings and groups with relevance to COVID-19 mitigation strategies.
in Philosophical transactions of the Royal Society of London. Series B, Biological sciences
Brooks-Pollock E
(2021)
High COVID-19 transmission potential associated with re-opening universities can be mitigated with layered interventions.
in Nature communications
Brooks-Pollock E
(2023)
Voluntary risk mitigation behaviour can reduce impact of SARS-CoV-2: a real-time modelling study of the January 2022 Omicron wave in England.
in BMC medicine
Brooks-Pollock E
(2020)
Mapping social distancing measures to the reproduction number for COVID-19
Challen R
(2022)
Meta-analysis of the severe acute respiratory syndrome coronavirus 2 serial intervals and the impact of parameter uncertainty on the coronavirus disease 2019 reproduction number.
in Statistical methods in medical research
Description | Calculation of R and Medium Term Predictions |
Geographic Reach | National |
Policy Influence Type | Participation in a guidance/advisory committee |
Impact | The reproduction number (R) is a commonly used metric for gauging the spread of the SARS-CoV-2 pandemic in the UK and the impact of control measures. It is generated by combining around 15 estimates (the precise number of estimates varies week-by-week), with the JUNIPER consortium providing 11 out of these 15 estimates. Medium Term Projections are a useful planning tool across government, translating recent behaviour into projections for the next 4-6 weeks. JUNIPER consortium members regularly provide over half of all medium term projections. |
Description | Predictions for Relaxation RoadMap |
Geographic Reach | National |
Policy Influence Type | Participation in a guidance/advisory committee |
Impact | In February, March, June, July and October of 2021, modelling work within the JUNIPER consortium (together with work from Imperial College and LSHTM) was used to provide a predictive underpinning of the government road-map for releasing restrictions. This was extensive work commissioned through SPI-MO (of which 12 members of the JUNIPER consortium are part), with the aim of forecasting the potential impact of relaxing control measures over different time scales. The work was presented to SPI-MO, SAGE by members of JUNIPER and was then communicated to members of government. The June roadmap indicated the considerable uncertainty (at the time) in the dynamics of the Delta variant leading to a postponement of Step 4 from 21st June to 19th July. |
Description | Presentation at the Welsh Government Technical Advisory Group |
Geographic Reach | National |
Policy Influence Type | Participation in a guidance/advisory committee |
Impact | Referenced in Welsh government report: Advice from the Technical Advisory Group and Chief Scientific Advisor for Health: 21 Day Review 13 January 2022 |
URL | https://gov.wales/sites/default/files/publications/2022-01/advice-technical-advisory-cell-and-chief-... |
Description | Social Care Working Group (SCWG) subgroup of SAGE |
Geographic Reach | National |
Policy Influence Type | Implementation circular/rapid advice/letter to e.g. Ministry of Health |
Impact | COVID19 Policy on care home shielding, testing and subsequent interventions were informed by the outputs of the working group. |
Description | COVID-19 Modelling Consortium: quantitative epidemiological predictions in response to an evolving pandemic |
Amount | £3,082,136 (GBP) |
Funding ID | MR/V038613/1 |
Organisation | Medical Research Council (MRC) |
Sector | Public |
Country | United Kingdom |
Start | 11/2020 |
End | 05/2023 |
Title | Metawards mathematical modelling framework for infectious disease |
Description | We developed a modelling framework for the spatial spread of infectious diseases. The package is developed in python with an R interface for widespread use. |
Type Of Material | Computer model/algorithm |
Year Produced | 2020 |
Provided To Others? | Yes |
Impact | It has fed into SPI-M subgroup of SAGE. |
URL | http://metawards.org |
Description | Uncertainty Quantification for Covid UQ4Covid |
Organisation | University of Exeter |
Country | United Kingdom |
Sector | Academic/University |
PI Contribution | I am CO-PI on the UQ4Covid grant with PI Daniel Williamson (EPSRC), based on the modelling framework (metawards) developed as funded by the MRC grant. I wrote the original spatial covid model, and the PI and other COIs are developing the statistical framework for fitting this model. Continuing work is a collaborative effort. |
Collaborator Contribution | The PI and CO-I have contributed to the continued development of the metawards modelling framework, especially the model fitting, but also the importation of data. |
Impact | N/A |
Start Year | 2020 |
Title | MetaWards: A flexible metapopulation framework for modelling disease spread |
Description | Understanding how disease spreads through populations is important when designing and implementing control measures. MetaWards implements a stochastic metapopulation model of disease transmission that enables geographical modelling of disease spread that can scale all the way from modelling local transmission up to full national-or international-scale outbreaks. It is built in Python and has a flexible plugin architecture to support complex scenario modelling. This enables the code to be adapted to model new situations and new control measures as they arise, e.g. emergence of new variants of disease, enaction of different types of movement restrictions, availability of different types of vaccines etc. It implements a userdefinable compartmental transmission model, such as an SIR model, that can be extended multi-dimensionally via multiple demographics or sub-populations, and multiple geographical regions. Models can be constructed from the various sources of movement and demographic data that are available, and are accelerated via Cython (Behnel et al., 2020), OpenMP, Scoop (Hold & Gagnon, 2019) and MPI4Py (Dalcin & Fang, 2021) to scale efficiently from running on personal laptops to large supercomputers. Python, R and command line interfaces and a complete set of tutorials empower researchers to adapt their models to a variety of scenarios. |
Type Of Technology | Software |
Year Produced | 2020 |
Open Source License? | Yes |
Impact | MetaWards has been downloaded over 100,000 times and forked 15 times. It is the main model being used for the EPSRC funded project 'UQ4Covid', EP/V051555/1. |
URL | https://gtr.ukri.org/projects?ref=EP%2FV051555%2F1 |
Description | BBC News Channel interviews |
Form Of Engagement Activity | A press release, press conference or response to a media enquiry/interview |
Part Of Official Scheme? | No |
Geographic Reach | National |
Primary Audience | Media (as a channel to the public) |
Results and Impact | BBC News Channel Interview on three separate occasions, commenting on COVID-19: Omicron variant, hospitalisations and testing. |
Year(s) Of Engagement Activity | 2022 |
Description | BBC News article |
Form Of Engagement Activity | A press release, press conference or response to a media enquiry/interview |
Part Of Official Scheme? | No |
Geographic Reach | International |
Primary Audience | Public/other audiences |
Results and Impact | BBC News article on household bubbles |
Year(s) Of Engagement Activity | 2020 |
URL | https://www.bbc.co.uk/news/uk-55372743 |
Description | Media coverage of B.1.1.7 Variant mortality paper |
Form Of Engagement Activity | A press release, press conference or response to a media enquiry/interview |
Part Of Official Scheme? | No |
Geographic Reach | International |
Primary Audience | Media (as a channel to the public) |
Results and Impact | Press release accompanied our paper published in the BMJ, which was picked up by over 500 media outlets. Dr Robert Challen (postdoc) and Dr Leon Danon (PI) appeared on national and international radio and TV. |
Year(s) Of Engagement Activity | 2021 |
URL | https://www.bristol.ac.uk/research/impact/coronavirus/media-coverage/#March-2021 |
Description | Podcast with +Plus Magazine |
Form Of Engagement Activity | Engagement focused website, blog or social media channel |
Part Of Official Scheme? | No |
Geographic Reach | International |
Primary Audience | Public/other audiences |
Results and Impact | +Plus magazine podcast |
Year(s) Of Engagement Activity | 2021 |
URL | https://plus.maths.org/content/mathematical-frontline-ellen-brooks-pollock-and-leon-danon |
Description | Radio 4 Today interview. |
Form Of Engagement Activity | A press release, press conference or response to a media enquiry/interview |
Part Of Official Scheme? | No |
Geographic Reach | National |
Primary Audience | Media (as a channel to the public) |
Results and Impact | Expert scientist, commenting on various aspects of the COVID-19 pandemic on three separate occasions. |
Year(s) Of Engagement Activity | 2020,2021 |
Description | Spanish TV interview |
Form Of Engagement Activity | A press release, press conference or response to a media enquiry/interview |
Part Of Official Scheme? | No |
Geographic Reach | National |
Primary Audience | Media (as a channel to the public) |
Results and Impact | Wide ranging interview on Spanish TV: 'laSexta con Ana Pastor' on COVID-19 spread and mitigation strategies. |
Year(s) Of Engagement Activity | 2020 |
URL | https://www.entornointeligente.com/el-objetivo-en-lasexta-ana-pastor-entrevista-esta-noche-a-la-mini... |