Novel methods in data science to quantify viral and environmental triggers of chronic disease exacerbations
Lead Research Organisation:
London School of Hygiene & Tropical Medicine
Department Name: Epidemiology and Population Health
Abstract
People living with chronic diseases are at risk of early death, and suffer significant illness due to these diseases. Worsening periods of health, or "exacerbations" of asthma, chronic obstructive pulmonary disease, and coronary heart disease are costly and are bad for patients. Infection by a virus (like a cold, or 'flu) is known to trigger exacerbations, but there are other factors, like air pollution, and low or high temperatures that can also trigger them.
Despite knowing the importance of viruses, there is not good understanding of how circulation of viruses in the general population affects the timing of exacerbations at the level of a city or town. This also makes it hard to estimate the effect of other triggers, like air pollution, which is urgently needed.
This study will analyse the patterns of exacerbations, including respiratory virus circulation in the general population as well as non-infectious triggers, such as air pollution.
Despite knowing the importance of viruses, there is not good understanding of how circulation of viruses in the general population affects the timing of exacerbations at the level of a city or town. This also makes it hard to estimate the effect of other triggers, like air pollution, which is urgently needed.
This study will analyse the patterns of exacerbations, including respiratory virus circulation in the general population as well as non-infectious triggers, such as air pollution.
Technical Summary
This project focuses on exacerbations (periods of worsening) of three major diseases in the UK: asthma, chronic obstructive pulmonary disease, and coronary heart disease. People with these chronic diseases are at risk of early death, and suffer significant morbidity as a result of their conditions. Viral infections are known to trigger exacerbations from individual-level studies, but there is limited understanding of how circulation of triggering viruses impacts population-level patterns of exacerbations. A key tool for interrogating infectious disease dynamics - infectious disease modelling - has not been used to understand the role of infections in population-level patterns of chronic disease exacerbations. Current methods either inaccurately include infectious variables, or use statistical smoothing to remove their effect, leading to unreliable estimation of other triggers. Reliable estimation of the effect of risk factors is crucial for policymakers, and for patients. The accepted best tool for understanding infectious disease dynamics is transmission modelling. I aim to close this gap in our knowledge by using state of the art transmission modelling techniques to better quantify the burden of infectious disease on chronic conditions. By bringing together two disciplines and using novel methods, this project will strengthen the evidence base for possible interventions, such as vaccinations, preventive care, risk awareness, and treatment options.
Publications
Wong AY
(2022)
Association between oral anticoagulants and COVID-19-related outcomes: a population-based cohort study.
in The British journal of general practice : the journal of the Royal College of General Practitioners
Wing K
(2022)
Association between household composition and severe COVID-19 outcomes in older people by ethnicity: an observational cohort study using the OpenSAFELY platform.
in International journal of epidemiology
Williamson EJ
(2021)
Risks of covid-19 hospital admission and death for people with learning disability: population based cohort study using the OpenSAFELY platform.
in BMJ (Clinical research ed.)
Waterlow NR
(2021)
Competition between RSV and influenza: Limits of modelling inference from surveillance data.
in Epidemics
Waterlow NR
(2022)
Evidence for influenza and RSV interaction from 10 years of enhanced surveillance in Nha Trang, Vietnam, a modelling study.
in PLoS computational biology
Walker JL
(2021)
UK prevalence of underlying conditions which increase the risk of severe COVID-19 disease: a point prevalence study using electronic health records.
in BMC public health
Walker AJ
(2021)
Clinical coding of long COVID in English primary care: a federated analysis of 58 million patient records in situ using OpenSAFELY.
in The British journal of general practice : the journal of the Royal College of General Practitioners
Van Zandvoort K
(2019)
Pneumococcal conjugate vaccine use during humanitarian crises.
in Vaccine
Van Zandvoort K
(2020)
Response strategies for COVID-19 epidemics in African settings: a mathematical modelling study.
in BMC medicine
Van Zandvoort K
(2022)
Social contacts and other risk factors for respiratory infections among internally displaced people in Somaliland.
in Epidemics
Schultze A
(2022)
Mortality among Care Home Residents in England during the first and second waves of the COVID-19 pandemic: an observational study of 4.3 million adults over the age of 65.
in The Lancet regional health. Europe
Scarpino SV
(2020)
Socioeconomic bias in influenza surveillance.
in PLoS computational biology
Rowan A
(2021)
A comprehensive high cost drugs dataset from the NHS in England - An OpenSAFELY-TPP Short Data Report.
in Wellcome open research
Robert A
(2019)
Determinants of Transmission Risk During the Late Stage of the West African Ebola Epidemic.
in American journal of epidemiology
Quilty BJ
(2020)
The effect of travel restrictions on the geographical spread of COVID-19 between large cities in China: a modelling study.
in BMC medicine
Quilty BJ
(2020)
Effectiveness of airport screening at detecting travellers infected with novel coronavirus (2019-nCoV).
in Euro surveillance : bulletin Europeen sur les maladies transmissibles = European communicable disease bulletin
Prem K
(2020)
The effect of control strategies to reduce social mixing on outcomes of the COVID-19 epidemic in Wuhan, China: a modelling study.
in The Lancet. Public health
Polonsky JA
(2019)
Outbreak analytics: a developing data science for informing the response to emerging pathogens.
in Philosophical transactions of the Royal Society of London. Series B, Biological sciences
Pearson CAB
(2022)
Potential test-negative design study bias in outbreak settings: application to Ebola vaccination in Democratic Republic of Congo.
in International journal of epidemiology
Patel RS
(2022)
Reproducible disease phenotyping at scale: Example of coronary artery disease in UK Biobank.
in PloS one
OpenSAFELY Collaborative
(2021)
OpenSAFELY: impact of national guidance on switching anticoagulant therapy during COVID-19 pandemic.
in Open heart
OpenSAFELY Collaborative
(2022)
Potentially inappropriate prescribing of DOACs to people with mechanical heart valves: A federated analysis of 57.9 million patients' primary care records in situ using OpenSAFELY.
in Thrombosis research
OpenSAFELY Collaborative
(2022)
Comparison of methods for predicting COVID-19-related death in the general population using the OpenSAFELY platform.
in Diagnostic and prognostic research
OpenSAFELY Collaborative
(2022)
Describing the population experiencing COVID-19 vaccine breakthrough following second vaccination in England: a cohort study from OpenSAFELY.
in BMC medicine
OpenSAFELY Collaborative
(2021)
Association between warfarin and COVID-19-related outcomes compared with direct oral anticoagulants: population-based cohort study.
in Journal of hematology & oncology
Munday JD
(2021)
Estimating the impact of reopening schools on the reproduction number of SARS-CoV-2 in England, using weekly contact survey data.
in BMC medicine
Munday JD
(2021)
Implications of the school-household network structure on SARS-CoV-2 transmission under school reopening strategies in England.
in Nature communications
Mburu CN
(2021)
The importance of supplementary immunisation activities to prevent measles outbreaks during the COVID-19 pandemic in Kenya.
in BMC medicine
MacKenna B
(2022)
Risk of severe COVID-19 outcomes associated with immune-mediated inflammatory diseases and immune-modifying therapies: a nationwide cohort study in the OpenSAFELY platform.
in The Lancet. Rheumatology
Liu Y
(2022)
Optimising health and economic impacts of COVID-19 vaccine prioritisation strategies in the WHO European Region: a mathematical modelling study.
in The Lancet regional health. Europe
Liu Y
(2022)
Dosing interval strategies for two-dose COVID-19 vaccination in 13 middle-income countries of Europe: Health impact modelling and benefit-risk analysis.
in The Lancet regional health. Europe
Liu Y
(2021)
The impact of non-pharmaceutical interventions on SARS-CoV-2 transmission across 130 countries and territories.
in BMC medicine
Liu Y
(2020)
Secondary attack rate and superspreading events for SARS-CoV-2.
in Lancet (London, England)
Leng T
(2020)
The effectiveness of social bubbles as part of a Covid-19 lockdown exit strategy, a modelling study.
in Wellcome open research
Leclerc QJ
(2021)
Importance of patient bed pathways and length of stay differences in predicting COVID-19 hospital bed occupancy in England.
in BMC health services research
Description | Conference on Infectious Disease Dynamics |
Geographic Reach | National |
Policy Influence Type | Influenced training of practitioners or researchers |
Impact | I started a conference (with 2 others) in 2017. After the pilot conference in 2017, the conference ran again in September 2018 during the award. It will run again in 2019 (also during the award). 105 scientists attended in 2018, to give presentations on research topics on infectious disease transmission dynamics and data scientific techniques in infectious disease research. The conference website is available at IDDconf.org, and the twitter account has nearly 500 followers: https://twitter.com/IDDconf through which increases engagement beyond attendees. For 2019 the conference is expanding to include 2 workshop training sessions for researchers and PhD students. |
URL | http://IDDconf.org |
Description | House of Lords Science and Technology Committee - Gave evidence on COVID-19 |
Geographic Reach | National |
Policy Influence Type | Contribution to a national consultation/review |
URL | https://www.parliament.uk/business/lords/media-centre/house-of-lords-media-notices/2020/may-20/what-... |
Description | Member of SAGE Ethnicity subgroup |
Geographic Reach | National |
Policy Influence Type | Membership of a guideline committee |
URL | https://www.gov.uk/government/publications/scientific-advisory-group-for-emergencies-sage-coronaviru... |
Description | Member of SPI-M |
Geographic Reach | National |
Policy Influence Type | Membership of a guideline committee |
URL | https://www.gov.uk/government/publications/scientific-advisory-group-for-emergencies-sage-coronaviru... |
Description | Member of WHO TAG on Educational Establishments and COVID-19 |
Geographic Reach | Multiple continents/international |
Policy Influence Type | Membership of a guideline committee |
URL | https://www.who.int/groups/technical-advisory-group-of-experts-on-educational-institutions-and-covid... |
Description | Membership of the Children's Task and Finish Group |
Geographic Reach | National |
Policy Influence Type | Membership of a guideline committee |
URL | https://www.gov.uk/government/publications/scientific-advisory-group-for-emergencies-sage-coronaviru... |
Description | New short training course for postgraduate/professional |
Geographic Reach | National |
Policy Influence Type | Influenced training of practitioners or researchers |
Impact | This is a new short training course called "Modern Techniques in Modelling" that will run in 2019. The course development was started in 2018 during the award. I am developing this course with 2 other members of staff at LSHTM. We will first run it internally in June 2019 for research degree students at our university, and then externally for research degree students and professional practitioners in November 2019. The course is 3 days on computational methods in infectious disease modelling and data science. |
Description | Presented work at SPI-M |
Geographic Reach | National |
Policy Influence Type | Participation in a guidance/advisory committee |
Impact | I presented work on the COVID epidemic at the SPI-M committee meeting on March 2 2020. |
Description | Presented work on a WHO technical call |
Geographic Reach | Multiple continents/international |
Policy Influence Type | Participation in a guidance/advisory committee |
Impact | I presented work on COVID control strategies to the WHO technical advisory group on modelling about COVID. 10th Feb 2020 |
Description | The effect of social distance measures on deaths and peak demand for hospital services in England, 3 March 2020 |
Geographic Reach | National |
Policy Influence Type | Citation in other policy documents |
Impact | Presented to SAGE on COVID-19 pandemic |
URL | https://www.gov.uk/government/publications/the-effect-of-social-distance-measures-on-deaths-and-peak... |
Description | The impact of adding school closure to other social distance measures, 17 March 2020 |
Geographic Reach | National |
Policy Influence Type | Citation in other policy documents |
Impact | Evidence presented to SAGE on COVID-19 pandemic |
URL | https://www.gov.uk/government/publications/the-impact-of-adding-school-closure-to-other-social-dista... |
Description | The impact of aggressively managing peak incidence, 11 March 2020 |
Geographic Reach | National |
Policy Influence Type | Citation in other policy documents |
Impact | Evidence presented to SAGE on COVID-19 pandemic |
URL | https://www.gov.uk/government/publications/the-impact-of-aggressively-managing-peak-incidence-11-mar... |
Description | The impact of banning sporting events and other leisure activities on the COVID-19 epidemic, 11 March 2020 |
Geographic Reach | National |
Policy Influence Type | Citation in other policy documents |
Impact | Evidence presented to SAGE on COVID-19 pandemic |
URL | https://www.gov.uk/government/publications/the-impact-of-banning-sporting-events-and-other-leisure-a... |
Description | The impact of relaxing lockdown measures: 2, 1 April 2020 |
Geographic Reach | National |
Policy Influence Type | Citation in other policy documents |
Impact | Evidence presented to SAGE on COVID-19 pandemic |
URL | https://www.gov.uk/government/publications/the-impact-of-relaxing-lockdown-measures-2-1-april-2020 |
Description | Emerging Leaders Prize 1st Place Winner |
Amount | £103,442 (GBP) |
Funding ID | MRF-160-0019-ELP-EGGO-C0911 |
Organisation | Medical Research Council (MRC) |
Department | Medical Research Foundation |
Sector | Charity/Non Profit |
Country | United Kingdom |
Start | 11/2021 |
End | 02/2024 |
Description | Urgent research and surveillance on Covid-19 using the new OpenSAFELY secure platform across 55 million patients' full linked primary care records |
Amount | £1,306,409 (GBP) |
Funding ID | MR/V015737/1 |
Organisation | Medical Research Council (MRC) |
Sector | Public |
Country | United Kingdom |
Start | 05/2020 |
End | 11/2021 |
Description | Al Jazeera English 9pm Newshour - 20-1-20 |
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 | Coronavirus epidemiology and outbreak information for TV. |
Year(s) Of Engagement Activity | 2020 |
Description | Article in the New Yorker |
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 | Interviewed about a research study in the New Yorker. |
Year(s) Of Engagement Activity | 2020 |
URL | https://www.newyorker.com/news/news-desk/what-it-means-to-contain-and-mitigate-the-coronavirus |
Description | BBC Explainer video - 24-1-20 |
Form Of Engagement Activity | A broadcast e.g. TV/radio/film/podcast (other than news/press) |
Part Of Official Scheme? | No |
Geographic Reach | International |
Primary Audience | Media (as a channel to the public) |
Results and Impact | This was an "explainer" educational video about epidemics and pandemics recorded by the BBC. It was used widely across their platforms on Twitter, Instagram, and on the front page of BBC news. It got hundreds of thousands of views. It was also embedded in many news articles about the coronavirus outbreak and epidemic. |
Year(s) Of Engagement Activity | 2020 |
URL | https://www.bbc.co.uk/news/av/health-51224894/coronavirus-what-s-the-difference-between-pandemic-and... |
Description | Channel 4 News - 10-3-20 |
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 | Coronavirus epidemiology and outbreak information for TV. |
Year(s) Of Engagement Activity | 2020 |
URL | https://www.channel4.com/news/deciding-when-to-put-extra-measures-in-place-a-really-difficult-decisi... |
Description | Channel 4 News - 25-2-20 |
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 | Channel 4 news interview about coronavirus and the outbreak. |
Year(s) Of Engagement Activity | 2020 |
URL | https://www.channel4.com/news/so-far-in-uk-cases-weve-seen-have-been-brought-in-from-other-places-dr... |
Description | Channel 4 News - 29-1-20 |
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 | Coronavirus epidemiology and outbreak information for TV. |
Year(s) Of Engagement Activity | 2020 |
Description | Guardian Science Podcast 24-1-20 |
Form Of Engagement Activity | A broadcast e.g. TV/radio/film/podcast (other than news/press) |
Part Of Official Scheme? | No |
Geographic Reach | International |
Primary Audience | Media (as a channel to the public) |
Results and Impact | Guardian Science podcast about the coronavirus outbreak |
Year(s) Of Engagement Activity | 2020 |
URL | https://twitter.com/guardianaudio/status/1220624660477300736?s=20 |
Description | Guardian reports on work |
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 | Research reported on by the Guardian Newspaper. |
Year(s) Of Engagement Activity | 2020 |
URL | https://www.theguardian.com/world/live/2020/jan/30/coronavirus-live-updates-china-death-toll-wuhan-e... |
Description | NPR segment on work |
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 | I was interviewed by NPR for a special on models and modelling. Radio and online article. It was part of "Morning Edition" which averages 14.9m listeners: https://www.npr.org/about-npr/597590072/npr-maintains-highest-ratings-ever |
Year(s) Of Engagement Activity | 2020 |
URL | https://www.npr.org/sections/health-shots/2020/03/04/811146915/how-computer-modeling-of-covid-19s-sp... |
Description | Outreach to Royal College of Nursing |
Form Of Engagement Activity | Participation in an activity, workshop or similar |
Part Of Official Scheme? | No |
Geographic Reach | Local |
Primary Audience | Professional Practitioners |
Results and Impact | A presentation/public engagement event was run at an outreach event at the Royal College of Nursing. The event was https://www.eventbrite.co.uk/e/rcn-late-beat-the-bugs-london-tickets-44405220209# Unfortunately I could not attend the event (not available that day), but the presenters used a website that I made (with 2 others) and support the maintenance and development of: https://rozeggo.shinyapps.io/hpru_day/ as a key part of their outreach activities. This aims to explain modelling methods, and also demonstrate impact of indirect effect of vaccination, using an example of influenza. The event aimed to engage people in disease transmission processes, infectious diseases more broadly, and in the effect of vaccination. |
Year(s) Of Engagement Activity | 2018 |
URL | https://rozeggo.shinyapps.io/hpru_day/ |
Description | Participation in Royal Institution Christmas Lectures |
Form Of Engagement Activity | A broadcast e.g. TV/radio/film/podcast (other than news/press) |
Part Of Official Scheme? | No |
Geographic Reach | International |
Primary Audience | Public/other audiences |
Results and Impact | I participated in Lecture 1 of Hannah Fry's Royal Institution Christmas Lectures in 2019. https://www.rigb.org/christmas-lectures/watch/2019/secrets-and-lies I described modelling of infectious diseases and how herd immunity works. The RI said they usually reach 3m people. |
Year(s) Of Engagement Activity | 2019 |
URL | https://www.rigb.org/christmas-lectures/watch/2019/secrets-and-lies |
Description | Speaking at TEDxThessaloniki |
Form Of Engagement Activity | A talk or presentation |
Part Of Official Scheme? | No |
Geographic Reach | International |
Primary Audience | Public/other audiences |
Results and Impact | https://www.tedxthessaloniki.com/tedx_speaker/rosalind-eggo/ https://www.youtube.com/watch?v=GkLlqobr3PY I was invited to give a public talk at a TEDx Event in Greece. It was a ticketed event with hundreds of participants. Also generated a YouTube video, which I will use for outreach in the future. This talk was about modelling in general, which is part of my project, but I did not talk about the work in the fellowship itself during the talk. This is because: i) at that time there were not results yet, ii) it was not in the requested title. But the methods from the fellowship are relevant to this talk, so it falls under engagement with modelling methods. |
Year(s) Of Engagement Activity | 2018 |