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
Van Zandvoort K
(2019)
Pneumococcal conjugate vaccine use during humanitarian crises.
in Vaccine
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
Robert A
(2019)
Determinants of Transmission Risk During the Late Stage of the West African Ebola Epidemic.
in American journal of epidemiology
Funk S
(2019)
Assessing the performance of real-time epidemic forecasts: A case study of Ebola in the Western Area region of Sierra Leone, 2014-15.
in PLoS computational biology
Jendrossek M
(2019)
Health care worker vaccination against Ebola: Vaccine acceptance and employment duration in Sierra Leone.
in Vaccine
Jombart T
(2020)
Inferring the number of COVID-19 cases from recently reported deaths.
in Wellcome open research
Eggo RM
(2020)
Feasibility of controlling COVID-19 - Authors' reply.
in The Lancet. Global health
Gibbs H
(2020)
Changing travel patterns in China during the early stages of the COVID-19 pandemic.
in Nature communications
Hellewell J
(2020)
On the fallibility of simulation models in informing pandemic responses - Authors' reply.
in The Lancet. Global health
Scarpino SV
(2020)
Socioeconomic bias in influenza surveillance.
in PLoS computational biology
Endo A
(2020)
Estimating the overdispersion in COVID-19 transmission using outbreak sizes outside China.
in Wellcome open research
Van Zandvoort K
(2020)
Response strategies for COVID-19 epidemics in African settings: a mathematical modelling study.
in BMC medicine
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
Leng T
(2020)
The effectiveness of social bubbles as part of a Covid-19 lockdown exit strategy, a modelling study.
in Wellcome open research
Clark A
(2020)
Global, regional, and national estimates of the population at increased risk of severe COVID-19 due to underlying health conditions in 2020: a modelling study.
in The Lancet. Global health
Dawa J
(2020)
Seasonal influenza vaccination in Kenya: an economic evaluation using dynamic transmission modelling.
in BMC medicine
Kucharski AJ
(2020)
Invisible spread of SARS-CoV-2 - Authors' reply.
in The Lancet. Infectious diseases
Liu Y
(2020)
Secondary attack rate and superspreading events for SARS-CoV-2.
in Lancet (London, England)
Hellewell J
(2020)
Feasibility of controlling COVID-19 outbreaks by isolation of cases and contacts.
in The Lancet. Global health
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
Kucharski AJ
(2020)
Early dynamics of transmission and control of COVID-19: a mathematical modelling study.
in The Lancet. Infectious diseases
Jombart T
(2020)
Inferring the number of COVID-19 cases from recently reported deaths
Davies NG
(2020)
Age-dependent effects in the transmission and control of COVID-19 epidemics.
in Nature 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
Rowan A
(2021)
A comprehensive high cost drugs dataset from the NHS in England - An OpenSAFELY-TPP Short Data Report.
in Wellcome open research
Waterlow NR
(2021)
Competition between RSV and influenza: Limits of modelling inference from surveillance data.
in Epidemics
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
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 |