An analytical framework for Test, Trace and Isolate in the UK: optimising and targeting deployment alongside other measures.

Lead Research Organisation: London Sch of Hygiene and Trop Medicine
Department Name: Public Health and Policy

Abstract

We will develop a robust analytical framework to guide decisions about the deployment of Test, Trace and Isolate (TTI) to control the SARS CoV2 epidemic over the next 12 months. As the UK eases lockdown and workplaces, leisure venues and schools re-open, refining and targeting TTI is necessary to prevent the return of rapid exponential epidemic growth. This will require quick feedback, assessment and integration with real-time epidemiological, behavioural and operational data. We will develop mathematical models of SARS CoV2 transmission and TTI processes, to assess how TTI could be most effectively refined and targeted in association with other control measures, and to develop metrics to assess TTI performance. We will consider how both the design of the TTI system and environmental factors affect people's behaviour. We will respond to emerging questions but currently prioritise: 1) optimal combinations of TTI, screening and physical distancing measures, both to reduce transmission and to protect vulnerable groups; 2) appraisal of the role of behavioural responses to take up and adhere to TTI policies, including trade-offs and the consequences for how policies are supported; 3) signals to initiate stepped up intervention intensity; 4) assessment of our understanding of transmission patterns.

Technical Summary

We will develop a robust analytical framework to guide decisions about the deployment of Test, Trace and Isolate (TTI) to control the UK SARS CoV2 epidemic over the next 12 months. This framework will be underpinned by branching process models of SARS CoV2 transmission and contact tracing, which are flexible enough to capture factors like households and clusters while being mathematically transparent enough to allow for direct calibration to data and quantification of uncertainty in predictions. We will provide evidence to inform key decisions about optimal combinations of tracing, screening and distancing measures. The inclusion of detailed network structure, settings and heterogeneity in contact patterns enables us to address issues such as: the role of uptake and adherence to TTI; the impact of TTI on transmission; signals to initiate stepped up intervention intensity; and assessment of the consistency of observed contact tracing data with epidemiological hypotheses. The research will take a socio-technical approach, recognizing that to ensure robust decision-support outputs from mathematical models must be situated within an understanding of human behaviour, and that both the technology and the environment in which it is deployed will influence the results obtained. The framework will be informed throughout by a contextual understanding obtained from key stakeholders, including members of the public who test positive, members of the public who are listed as contacts and asked to self-isolate (who do not necessarily test
positive) and people working within the TTI and outbreak teams.

Publications

10 25 50
 
Description Participation and contributions to SPI-M-O, modelling SAGE sub-committee, on control of SARS-CoV-2/COVID-19 (Scientific Advisory Group for Emergencies sub-committee on modelling), October 2020 - present
Geographic Reach National 
Policy Influence Type Participation in a advisory committee
Impact Modelling evidence presented to SPI-M-O influences government policy via SAGE, and via direct interactions and influence on other bodies including NHS Test and Trace, COVID-19 civil service Task Force and the Department for Transport. The topics reflect both commissions from organisations such as NHS Test and Trace, and self-initiated topics. This advice contributes to improved epidemic control of SARS CoV-2 and COVID-19 in the United Kingdom, reducing morbidity and mortality associated with the disease and other health, social and economic harms that have resulted from the epidemic. While we can see where the provision of our evidence and decisions taken align in time, it is difficult for our project to attribute influence directly as we are engaged with the provision of scientific evidence rather than the whole decision-making process.
URL https://www.gov.uk/government/publications/scientific-advisory-group-for-emergencies-sage-coronaviru...
 
Description Presentation of paper on daily testing among contacts of SARS-CoV-2 cases to the Scientific Advisory Group on Emergencies Meeting 68, Nov 16, 2020
Geographic Reach National 
Policy Influence Type Participation in a advisory committee
Impact Our Test, Trace and Isolating modelling project responded to a commission to consider a specific testing and contact tracing strategy in which contacts of a SARS-CoV-2 case test daily with rapid tests (lateral flow assay tests) in lieu of quarantining (with case isolation as per standard policy). Our modelling analysis, which contributed findings that considered the separate contact patterns and processes of within and outside housheold contacts, found that such a strategy could be as or more effective than the existign policy, prompting its consideration for further pilot testing. Our preliminary analysis has been published as part of SAGE papers: https://assets.publishing.service.gov.uk/government/uploads/system/uploads/attachment_data/file/950771/s0897-testing-of-traced-contacts.pdf
URL https://www.gov.uk/government/publications/sage-68-minutes-coronavirus-covid-19-response-16-november...
 
Description Presentation of paper on quarantine and testing strategies for travellers returning from abroad for control of the SARS-CoV-2 epidemic in the UK to the Scientific Advisory Group on Emergencies Meeting 71, Dec 3, 2020 (2020)
Geographic Reach National 
Policy Influence Type Participation in a advisory committee
Impact We presented a modelling paper to SAGE meeting no 71 on quarantine and testing strategies for international arrivals returning to household in the United Kingdom to reduce the number of SARS-CoV-2 cases that might arise from infected travellers. Our model considered the fact that in the UK at the time, returning travellers could be returning to households where household members were not under quarantine. We found simulated epidemics initiated by returning travellers were potentially larger when daily lateral flow testing policies were used in lieu of either a 14 day or 5 day + PCR test-to-release quaratine strategy. We cannot attribute specific policy decisions to this modelling work, but subsequent decisions were in alignment with our findings. Benefits to public health, societal well-being and the economy are realised via improved control of the SARS-CoV-2 epidemic.
URL https://www.gov.uk/government/publications/sage-71-minutes-coronavirus-covid-19-response-3-december-...
 
Description Review of Department for Transport international arrivals SARS-CoV-2 testing policy model
Geographic Reach National 
Policy Influence Type Implementation circular/rapid advice/letter to e.g. Ministry of Health
Impact In late Novermber, early december 2021, concern about the SARS-C0V-2 Omicron variant originating in South Africa meant that the UK government was making decisions about what testing and/or quarantine policies inetrnational arrivals would be subject to in order to limit/delay the establishment of the variant in the UK. At the time there was serious concern as to the effects on increases in cases, and unknown unmpacts on hospital adminssions and deaths. Our review, arranged via the SPI-M (Civil Service secretariat) helped to increase confidence in the findings of the epidemiological model that was being used to support decision-making.
 
Title Household structured branching process model of SARS-CoV-2 infection and contact tracing 
Description Through the course of our Test, Trace and Isolate (TTI) modelling project we have documented and made further developments to our household-structured branching process model of SARS-CoV-2 infection and contact tracing. The model 
Type Of Material Computer model/algorithm 
Year Produced 2021 
Provided To Others? Yes  
Impact This model and adaptations to it has been used in research to provide advice to the UK government on TTI strategies and effectiveness for control of the SARS-CoV-2 epidemic, including research sent to SPI-M, SAGE and in advice given to NHS Test and Trace. 
URL https://github.com/martyn1fyles/HouseholdContactTracing
 
Title Model of SARS-CoV-2 infection and contact tracing: code for investigating trade-offs between quarantine periods, uptake of testing and adherence to isolation and quarantine 
Description This mathematical model has been adapted from that of a previous project to investigate Test, Trace and Isolate (TTI) strategies for SARS CoV-2 epidemic control in the United Kingdom. It uses a population-based branching process of infections and contact tracing to simulate epidemics and estimate the effect of TTI on the probability of a large SARS-CoV-2 outbreak. This model has been utilised throughout this project for research and advice on SARS CoV-2 epidemic control. One application of the model was to investigate trade-offs between quarantine periods, uptake of testing and adherence to isolation and quarantine, documented here. A fuller descripiton of the model is given here: https://www.medrxiv.org/content/10.1101/2020.08.20.20178558v1. 
Type Of Material Computer model/algorithm 
Year Produced 2020 
Provided To Others? Yes  
Impact The findings of research using this model have been presented to SPI-M, the modelling sub-committee of the Scientific Advisory Group on Emergencies since October 2020. The specific analsyes documented here were presented November 11, 2020. https://assets.publishing.service.gov.uk/government/uploads/system/uploads/attachment_data/file/937444/S0877_SAGE67_201111_SPI-M-O_Consensus_Statement.pdf 
URL https://github.com/timcdlucas/ringbp/releases/tag/sevenday1.0
 
Description Evidence for symptom phenotypes of COVID-19 among community based cases across several large studies 
Organisation Evergreen Life Group
Country United Kingdom 
Sector Private 
PI Contribution Our team conceived and led the project, designed the main analysis and developed analysis code, which we shared for partners to adapt.
Collaborator Contribution We have been working with researchers from each partner organisation. We have met regularly and jointly discussed and agreed analysis and write-ups of findings. In some cases, they have conducted analsyes on their own data and in some cases we have run analyses directly.
Impact In 2020 and early 2021 we sent two reports to SPI-M, the modelling sub-committee of the UK's Scientific Advisory Group for Emergencies. We completed a first manuscript draft, and made this and sample code available as a preprint: https://arxiv.org/abs/2111.05728 In eary 2022 we agreed to continue the collaboration with UKHSA to assess the extent to which symptom phenotypes might have changed with the Omicron variant, and more generally over calendar time.
Start Year 2020
 
Description Evidence for symptom phenotypes of COVID-19 among community based cases across several large studies 
Organisation King's College London
Country United Kingdom 
Sector Academic/University 
PI Contribution Our team conceived and led the project, designed the main analysis and developed analysis code, which we shared for partners to adapt.
Collaborator Contribution We have been working with researchers from each partner organisation. We have met regularly and jointly discussed and agreed analysis and write-ups of findings. In some cases, they have conducted analsyes on their own data and in some cases we have run analyses directly.
Impact In 2020 and early 2021 we sent two reports to SPI-M, the modelling sub-committee of the UK's Scientific Advisory Group for Emergencies. We completed a first manuscript draft, and made this and sample code available as a preprint: https://arxiv.org/abs/2111.05728 In eary 2022 we agreed to continue the collaboration with UKHSA to assess the extent to which symptom phenotypes might have changed with the Omicron variant, and more generally over calendar time.
Start Year 2020
 
Description Evidence for symptom phenotypes of COVID-19 among community based cases across several large studies 
Organisation Office for National Statistics
Country United Kingdom 
Sector Private 
PI Contribution Our team conceived and led the project, designed the main analysis and developed analysis code, which we shared for partners to adapt.
Collaborator Contribution We have been working with researchers from each partner organisation. We have met regularly and jointly discussed and agreed analysis and write-ups of findings. In some cases, they have conducted analsyes on their own data and in some cases we have run analyses directly.
Impact In 2020 and early 2021 we sent two reports to SPI-M, the modelling sub-committee of the UK's Scientific Advisory Group for Emergencies. We completed a first manuscript draft, and made this and sample code available as a preprint: https://arxiv.org/abs/2111.05728 In eary 2022 we agreed to continue the collaboration with UKHSA to assess the extent to which symptom phenotypes might have changed with the Omicron variant, and more generally over calendar time.
Start Year 2020
 
Description Evidence for symptom phenotypes of COVID-19 among community based cases across several large studies 
Organisation University of Oxford
Department Nuffield Department of Population Health
Country United Kingdom 
Sector Academic/University 
PI Contribution Our team conceived and led the project, designed the main analysis and developed analysis code, which we shared for partners to adapt.
Collaborator Contribution We have been working with researchers from each partner organisation. We have met regularly and jointly discussed and agreed analysis and write-ups of findings. In some cases, they have conducted analsyes on their own data and in some cases we have run analyses directly.
Impact In 2020 and early 2021 we sent two reports to SPI-M, the modelling sub-committee of the UK's Scientific Advisory Group for Emergencies. We completed a first manuscript draft, and made this and sample code available as a preprint: https://arxiv.org/abs/2111.05728 In eary 2022 we agreed to continue the collaboration with UKHSA to assess the extent to which symptom phenotypes might have changed with the Omicron variant, and more generally over calendar time.
Start Year 2020
 
Title Household branching process testing contact model 
Description A household branching process contact model to explore testing and contact tracing approaches for control of infectious disease, developed for assessing policies in the UK during the COVID-19 pandemic. The model was orginally developed by infectious disease modellers and then refactored by research software engineers to enhance usability. The model is written in Python, and freely available. 
Type Of Technology Software 
Year Produced 2021 
Open Source License? Yes  
Impact The model was used to provide government advice as to testing and contact tracing strategies and inetrnational arrivals testing strategies in 2020 and 2021 for COVID-19 control in the UK. 
URL https://zenodo.org/record/5139630#.YijKIN-nzz8
 
Description Advisory panel with public health stakeholders 
Form Of Engagement Activity A formal working group, expert panel or dialogue
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Professional Practitioners
Results and Impact In order to ensure that our modelling of the Test, Trace and Isolate policies for SARS-CoV-2 control in the UK is responding to the primary concerns of stakeholders and reflects key aspects fo the process, we have established an advisory panel of public health professionals. These discussions have fed into our project's considerations of what strategies might improve TTI and would merit further investigation.
Year(s) Of Engagement Activity 2020,2021
 
Description Collaboration with Plus Magazine for an article about lateral flow testing for SARS-CoV-2 
Form Of Engagement Activity A magazine, newsletter or online publication
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Public/other audiences
Results and Impact Our project collaborated with Plus Magazine, a popular science mathematics publication,on an article about the use of lateral flow testing for SARS-CoV-2 for pandemic control. Plus aims to highlight recent news stories with mathematical underpinnings to a non-expert audience, including to schools, students and teachers.

We were interviewed by Plus journalists who then produced a draft which we co-edited and approved.
Year(s) Of Engagement Activity 2021
URL https://plus.maths.org/content/going-flow-are-lateral-flow-tests-useful
 
Description Conference poster presentation at EPIDEMICS 8 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact Poster presentation: Diversity of symptom phenotypes in SARS-CoV-2 infections observed in multiple large datasets, Das R et al, 2021.
Year(s) Of Engagement Activity 2021
URL https://www.elsevier.com/events/conferences/international-conference-on-infectious-disease-dynamics
 
Description Conference poster presentation at EPIDEMICS 8 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact Poster presentation: Considering household structure to improve the effectiveness of testing, tracing and isolation interventions (TTI) interventions in the control of SARS-CoV-2 epidemics
Year(s) Of Engagement Activity 2021
URL https://www.elsevier.com/events/conferences/international-conference-on-infectious-disease-dynamics
 
Description Input into the Events Research Programme 
Form Of Engagement Activity A formal working group, expert panel or dialogue
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Professional Practitioners
Results and Impact Our project provided advice about COVID-19 testing and contact tracing, based on our research, that was relevant to the design of the Events Research Programme convened by government (DHSC, DCMS, BEIS). The ERP aimed to determine how events might be more safely re-established following restrictions in early 2021. We provided advice as part of a consultation with modellers from SPI-M-O, the modelling subcommittee of the Scientific Advisory Group for Emergencies (SAGE). This involved the preparation of a document following discussions, which was then presented ot the ERP Board and discussed.
Year(s) Of Engagement Activity 2021
 
Description Interviewed by journalist about COVID-19 testing strategies 
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 We spoke to a journalist from the Financial Times about lateral flow testing for SARS CoV-2 for an article published in December 2021.
Year(s) Of Engagement Activity 2021
URL https://www.ft.com/content/cbd0fb0a-8c41-4b9b-aa4c-0afa10619383
 
Description Invited conference symposium presentation about the incorporation of household structure into modelling of test, trace and isolate policies 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact Our project PI was invited to speak at a symposium at the British Applied Mathematics Colloquium 2021 about the role of households in the dynamics of SARS CoV-2 transmission, testing and contact tracing.
Year(s) Of Engagement Activity 2021
URL https://sites.google.com/view/bmcbamc2021/abstracts/abstracts-minisymposium
 
Description Invited talk on modelling of test, trace and isolate strategies in the UK 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Professional Practitioners
Results and Impact We were invited to present at a JUNIPER Consortium (Joint UNIversities Pandemic and Epidemiological Research group) seminar (24/11/2021) about our work on modelling asymptomatic and symptomatic testing strategies for control of COVID-19 over the Winter 2021/22 period, and about work on inferring the relationship between viral load and transmissability.
Year(s) Of Engagement Activity 2021
 
Description Oral presentation at EPIDEMICS 8 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact Oral conference presentation: Inferring the relaitonship between viral load and infectiousness using contact tracing data. Fyles M et al. 2021.
Year(s) Of Engagement Activity 2021
 
Description Presentation to the Office for National Statistics COVID-19 Infection Survey working group 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Professional Practitioners
Results and Impact Members of our project were invited to present at the ONS Covid Infection Survey working group seminar series about our work on discerning Covid-19 symptom phenotypes among cases in the community (21 February, 2022).
Year(s) Of Engagement Activity 2022
 
Description Presentation to the Office for National Statistics Research Accreditation Panel meeting 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Professional Practitioners
Results and Impact Members of our projected presented to the Office for National Statistics Research Accreditation Panel meeting (Dec 8, 2021) about our use of the ONS Secure Research Service in conducting rapid response research to provide UK government advice during the COVID-19 pandemic.

As well as giving examples of the work done, we were able to feedback on what worked well and what challenges were experienced in providing this kind of emergency response work, so that structures and procedures might be improved upon in future.
Year(s) Of Engagement Activity 2021
 
Description Talk on Test, Trace and Isolate methods for Virtual Forum for Knowledge Exchange in the Mathematical Sciences Covid-19 Safety for Large Events study programme 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Professional Practitioners
Results and Impact We gave a presentation on COVID-19 testing and contact tracing considerations in relation to holding large events (July 2021) for a Virtual Forum for Knowledge Exchange in the Mathematical Sciences Covid-19 Safety for Large Events study programme. The study programme aimed to engage mathematicians with events convenors (large indoor and outdoor events, arts and sports) to help develop strategies to more safely hold events during the COVID-19 pandemic.
Year(s) Of Engagement Activity 2021
URL https://ktn-uk.org/news/covid-19-safety-in-large-events-using-mathematical-sciences/
 
Description Workshop on Test, Trace and Isolate learnings and future recommendations 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Professional Practitioners
Results and Impact We organised a vitrual afternoon workshop on Test, trace and isolate: learnings from the past 18 months, considerations for Winter 2021/22 and a framework for considering recommendations for future pandemics.

The workshop was organised in conjunction with the JUNIPER consortium providing research to guide the UK pandemic response, and the International Centre for Mathematical Sciences (ICMS).

The workshop, for which we had an applicaiton process, had approximately 15-20 speakers and attendees from: academic research, including those involved in providing pandemic response advice to the govenrment; UKHSA; the UK government's civil service Covid Task Force; and postgraduate students.

A write-up of the workshop is in progress, assisted with funding from ICMS.
Year(s) Of Engagement Activity 2021
URL https://www.icms.org.uk/events/2021/test-trace-and-isolate-epidemic-control-lessons-learnt-covid-19-...
 
Description Workshop with epidemic modellers to assess the implications of findings from interviews with members of the public about their engagement with TTI interventions in the UK 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Professional Practitioners
Results and Impact We conducted inetrviews with members of the public in England in summer 2021 about their perceptions of and inetractions with COVID-19 testing, contact tracing and isolaiton (TTI) policies during the pandemic. We thematically analysed the findings and presented them to a workshop of infectious disease modellers who had been engaged with researching and providing evidence to UK the government (primarily via SPI-M, modelling SAGE sub-committee both project memebrs and non-project members), about COVID-19 testing and contact tracing policies. We then facilitated a discussion about what these findings meant for the assumptions made in mathematical models, and how/whether different types of models might be required for answering various quesitons about TTI policies. We then co-edited a paper presenting findings and summarising these discussions.
Year(s) Of Engagement Activity 2021
URL https://www.medrxiv.org/content/10.1101/2022.01.31.22269871v1