Novel methods in data science to quantify viral and environmental triggers of chronic disease exacerbations

Lead Research Organisation: London Sch of Hygiene and Trop 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.

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

10 25 50

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Liu Y (2020) Secondary attack rate and superspreading events for SARS-CoV-2. in Lancet (London, England)

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Polonsky J (2019) Outbreak analytics: a developing data science for informing the response to emerging pathogens in Philosophical Transactions of the Royal Society B: Biological Sciences

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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

 
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 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 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 advisory committee
Impact I presented work on COVID control strategies to the WHO technical advisory group on modelling about COVID. 10th Feb 2020
 
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