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Article ; Online: Understanding the infection severity and epidemiological characteristics of mpox in the UK.

Ward, Thomas / Overton, Christopher E / Paton, Robert S / Christie, Rachel / Cumming, Fergus / Fyles, Martyn

2024 Volume 15, Issue 1, Page(s) 2199

Abstract: In May 2022, individuals infected with the monkeypox virus were detected in the UK without clear travel links to endemic areas. Understanding the clinical characteristics and infection severity of mpox is necessary for effective public health policy. The ...

Abstract	In May 2022, individuals infected with the monkeypox virus were detected in the UK without clear travel links to endemic areas. Understanding the clinical characteristics and infection severity of mpox is necessary for effective public health policy. The study period of this paper, from the 1
MeSH term(s)	Female ; Male ; Humans ; Mpox (monkeypox) ; Hospitalization ; Length of Stay ; Abducens Nerve Diseases ; United Kingdom/epidemiology
Language	English
Publishing date	2024-03-11
Publishing country	England
Document type	Journal Article
ZDB-ID	2553671-0
ISSN	2041-1723 ; 2041-1723
ISSN (online)	2041-1723
ISSN	2041-1723
DOI	10.1038/s41467-024-45110-8
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Article ; Online: Bayesian spatial modelling of localised SARS-CoV-2 transmission through mobility networks across England.

Ward, Thomas / Morris, Mitzi / Gelman, Andrew / Carpenter, Bob / Ferguson, William / Overton, Christopher / Fyles, Martyn

PLoS computational biology

2023 Volume 19, Issue 11, Page(s) e1011580

Abstract: In the early phases of growth, resurgent epidemic waves of SARS-CoV-2 incidence have been characterised by localised outbreaks. Therefore, understanding the geographic dispersion of emerging variants at the start of an outbreak is key for situational ... ...

Abstract	In the early phases of growth, resurgent epidemic waves of SARS-CoV-2 incidence have been characterised by localised outbreaks. Therefore, understanding the geographic dispersion of emerging variants at the start of an outbreak is key for situational public health awareness. Using telecoms data, we derived mobility networks describing the movement patterns between local authorities in England, which we have used to inform the spatial structure of a Bayesian BYM2 model. Surge testing interventions can result in spatio-temporal sampling bias, and we account for this by extending the BYM2 model to include a random effect for each timepoint in a given area. Simulated-scenario modelling and real-world analyses of each variant that became dominant in England were conducted using our BYM2 model at local authority level in England. Simulated datasets were created using a stochastic metapopulation model, with the transmission rates between different areas parameterised using telecoms mobility data. Different scenarios were constructed to reproduce real-world spatial dispersion patterns that could prove challenging to inference, and we used these scenarios to understand the performance characteristics of the BYM2 model. The model performed better than unadjusted test positivity in all the simulation-scenarios, and in particular when sample sizes were small, or data was missing for geographical areas. Through the analyses of emerging variant transmission across England, we found a reduction in the early growth phase geographic clustering of later dominant variants as England became more interconnected from early 2022 and public health interventions were reduced. We have also shown the recent increased geographic spread and dominance of variants with similar mutations in the receptor binding domain, which may be indicative of convergent evolution of SARS-CoV-2 variants.
MeSH term(s)	Humans ; Bayes Theorem ; SARS-CoV-2/genetics ; COVID-19/epidemiology ; England/epidemiology
Language	English
Publishing date	2023-11-13
Publishing country	United States
Document type	Journal Article
ZDB-ID	2193340-6
ISSN	1553-7358 ; 1553-734X
ISSN (online)	1553-7358
ISSN	1553-734X
DOI	10.1371/journal.pcbi.1011580
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Article ; Online: Bayesian spatial modelling of localised SARS-CoV-2 transmission through mobility networks across England.

Thomas Ward / Mitzi Morris / Andrew Gelman / Bob Carpenter / William Ferguson / Christopher Overton / Martyn Fyles

PLoS Computational Biology, Vol 19, Iss 11, p e

2023 Volume 1011580

Abstract	In the early phases of growth, resurgent epidemic waves of SARS-CoV-2 incidence have been characterised by localised outbreaks. Therefore, understanding the geographic dispersion of emerging variants at the start of an outbreak is key for situational public health awareness. Using telecoms data, we derived mobility networks describing the movement patterns between local authorities in England, which we have used to inform the spatial structure of a Bayesian BYM2 model. Surge testing interventions can result in spatio-temporal sampling bias, and we account for this by extending the BYM2 model to include a random effect for each timepoint in a given area. Simulated-scenario modelling and real-world analyses of each variant that became dominant in England were conducted using our BYM2 model at local authority level in England. Simulated datasets were created using a stochastic metapopulation model, with the transmission rates between different areas parameterised using telecoms mobility data. Different scenarios were constructed to reproduce real-world spatial dispersion patterns that could prove challenging to inference, and we used these scenarios to understand the performance characteristics of the BYM2 model. The model performed better than unadjusted test positivity in all the simulation-scenarios, and in particular when sample sizes were small, or data was missing for geographical areas. Through the analyses of emerging variant transmission across England, we found a reduction in the early growth phase geographic clustering of later dominant variants as England became more interconnected from early 2022 and public health interventions were reduced. We have also shown the recent increased geographic spread and dominance of variants with similar mutations in the receptor binding domain, which may be indicative of convergent evolution of SARS-CoV-2 variants.
Keywords	Biology (General) ; QH301-705.5
Subject code	310
Language	English
Publishing date	2023-11-01T00:00:00Z
Publisher	Public Library of Science (PLoS)
Document type	Article ; Online
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Article ; Online: Understanding the leading indicators of hospital admissions from COVID-19 across successive waves in the UK.

Mellor, Jonathon / Overton, Christopher E / Fyles, Martyn / Chawner, Liam / Baxter, James / Baird, Tarrion / Ward, Thomas

Epidemiology and infection

2023 Volume 151, Page(s) e172

Abstract: Following the end of universal testing in the UK, hospital admissions are a key measure of COVID-19 pandemic pressure. Understanding leading indicators of admissions at the National Health Service (NHS) Trust, regional and national geographies help ... ...

Abstract	Following the end of universal testing in the UK, hospital admissions are a key measure of COVID-19 pandemic pressure. Understanding leading indicators of admissions at the National Health Service (NHS) Trust, regional and national geographies help health services plan for ongoing pressures. We explored the spatio-temporal relationships of leading indicators of hospitalisations across SARS-CoV-2 waves in England. This analysis includes an evaluation of internet search volumes from Google Trends, NHS triage calls and online queries, the NHS COVID-19 app, lateral flow devices (LFDs), and the ZOE app. Data sources were analysed for their feasibility as leading indicators using Granger causality, cross-correlation, and dynamic time warping at fine spatial scales. Google Trends and NHS triages consistently temporally led admissions in most locations, with lead times ranging from 5 to 20 days, whereas an inconsistent relationship was found for the ZOE app, NHS COVID-19 app, and LFD testing, which diminished with spatial resolution, showing cross-correlation of leads between -7 and 7 days. The results indicate that novel surveillance sources can be used effectively to understand the expected healthcare burden within hospital administrative areas though the temporal and spatial heterogeneity of these relationships is a key determinant of their operational public health utility.
MeSH term(s)	Humans ; COVID-19/epidemiology ; SARS-CoV-2 ; State Medicine ; Pandemics ; Hospitalization ; England/epidemiology ; Hospitals
Language	English
Publishing date	2023-09-04
Publishing country	England
Document type	Journal Article
ZDB-ID	632982-2
ISSN	1469-4409 ; 0950-2688
ISSN (online)	1469-4409
ISSN	0950-2688
DOI	10.1017/S0950268823001449
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Article ; Online: The role of regular asymptomatic testing in reducing the impact of a COVID-19 wave.

Silva, Miguel E P / Fyles, Martyn / Pi, Li / Panovska-Griffiths, Jasmina / House, Thomas / Jay, Caroline / Fearon, Elizabeth

Epidemics

2023 Volume 44, Page(s) 100699

Abstract: Testing for infection with SARS-CoV-2 is an important intervention in reducing onwards transmission of COVID-19, particularly when combined with the isolation and contact-tracing of positive cases. Many countries with the capacity to do so have made use ... ...

Abstract	Testing for infection with SARS-CoV-2 is an important intervention in reducing onwards transmission of COVID-19, particularly when combined with the isolation and contact-tracing of positive cases. Many countries with the capacity to do so have made use of lab-processed Polymerase Chain Reaction (PCR) testing targeted at individuals with symptoms and the contacts of confirmed cases. Alternatively, Lateral Flow Tests (LFTs) are able to deliver a result quickly, without lab-processing and at a relatively low cost. Their adoption can support regular mass asymptomatic testing, allowing earlier detection of infection and isolation of infectious individuals. In this paper we extend and apply the agent-based epidemic modelling framework Covasim to explore the impact of regular asymptomatic testing on the peak and total number of infections in an emerging COVID-19 wave. We explore testing with LFTs at different frequency levels within a population with high levels of immunity and with background symptomatic PCR testing, case isolation and contact tracing for testing. The effectiveness of regular asymptomatic testing was compared with 'lockdown' interventions seeking to reduce the number of non-household contacts across the whole population through measures such as mandating working from home and restrictions on gatherings. Since regular asymptomatic testing requires only those with a positive result to reduce contact, while lockdown measures require the whole population to reduce contact, any policy decision that seeks to trade off harms from infection against other harms will not automatically favour one over the other. Our results demonstrate that, where such a trade off is being made, at moderate rates of early exponential growth regular asymptomatic testing has the potential to achieve significant infection control without the wider harms associated with additional lockdown measures.
MeSH term(s)	Humans ; COVID-19/epidemiology ; SARS-CoV-2 ; COVID-19 Testing ; Communicable Disease Control ; Contact Tracing/methods
Language	English
Publishing date	2023-07-18
Publishing country	Netherlands
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2467993-8
ISSN	1878-0067 ; 1755-4365
ISSN (online)	1878-0067
ISSN	1755-4365
DOI	10.1016/j.epidem.2023.100699
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Article ; Online: Using a household-structured branching process to analyse contact tracing in the SARS-CoV-2 pandemic.

Fyles, Martyn / Fearon, Elizabeth / Overton, Christopher / Wingfield, Tom / Medley, Graham F / Hall, Ian / Pellis, Lorenzo / House, Thomas

Philosophical transactions of the Royal Society of London. Series B, Biological sciences

2021 Volume 376, Issue 1829, Page(s) 20200267

Abstract: We explore strategies of contact tracing, case isolation and quarantine of exposed contacts to control the SARS-CoV-2 epidemic using a branching process model with household structure. This structure reflects higher transmission risks among household ... ...

Abstract	We explore strategies of contact tracing, case isolation and quarantine of exposed contacts to control the SARS-CoV-2 epidemic using a branching process model with household structure. This structure reflects higher transmission risks among household members than among non-household members. We explore strategic implementation choices that make use of household structure, and investigate strategies including two-step tracing, backwards tracing, smartphone tracing and tracing upon symptom report rather than test results. The primary model outcome is the effect of contact tracing, in combination with different levels of physical distancing, on the growth rate of the epidemic. Furthermore, we investigate epidemic extinction times to indicate the time period over which interventions must be sustained. We consider effects of non-uptake of isolation/quarantine, non-adherence, and declining recall of contacts over time. Our results find that, compared to self-isolation of cases without contact tracing, a contact tracing strategy designed to take advantage of household structure allows for some relaxation of physical distancing measures but cannot completely control the epidemic absent of other measures. Even assuming no imported cases and sustainment of moderate physical distancing, testing and tracing efforts, the time to bring the epidemic to extinction could be in the order of months to years. This article is part of the theme issue 'Modelling that shaped the early COVID-19 pandemic response in the UK'.
MeSH term(s)	COVID-19/epidemiology ; COVID-19/transmission ; COVID-19/virology ; Contact Tracing/methods ; Family Characteristics ; Humans ; Models, Theoretical ; Pandemics ; Quarantine/methods ; SARS-CoV-2/pathogenicity
Language	English
Publishing date	2021-05-31
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	208382-6
ISSN	1471-2970 ; 0080-4622 ; 0264-3839 ; 0962-8436
ISSN (online)	1471-2970
ISSN	0080-4622 ; 0264-3839 ; 0962-8436
DOI	10.1098/rstb.2020.0267
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Article ; Online: Diversity of symptom phenotypes in SARS-CoV-2 community infections observed in multiple large datasets.

Fyles, Martyn / Vihta, Karina-Doris / Sudre, Carole H / Long, Harry / Das, Rajenki / Jay, Caroline / Wingfield, Tom / Cumming, Fergus / Green, William / Hadjipantelis, Pantelis / Kirk, Joni / Steves, Claire J / Ourselin, Sebastien / Medley, Graham F / Fearon, Elizabeth / House, Thomas

Scientific reports

2023 Volume 13, Issue 1, Page(s) 21705

Abstract: Variability in case severity and in the range of symptoms experienced has been apparent from the earliest months of the COVID-19 pandemic. From a clinical perspective, symptom variability might indicate various routes/mechanisms by which infection leads ... ...

Abstract	Variability in case severity and in the range of symptoms experienced has been apparent from the earliest months of the COVID-19 pandemic. From a clinical perspective, symptom variability might indicate various routes/mechanisms by which infection leads to disease, with different routes requiring potentially different treatment approaches. For public health and control of transmission, symptoms in community cases were the prompt upon which action such as PCR testing and isolation was taken. However, interpreting symptoms presents challenges, for instance, in balancing the sensitivity and specificity of individual symptoms with the need to maximise case finding, whilst managing demand for limited resources such as testing. For both clinical and transmission control reasons, we require an approach that allows for the possibility of distinct symptom phenotypes, rather than assuming variability along a single dimension. Here we address this problem by bringing together four large and diverse datasets deriving from routine testing, a population-representative household survey and participatory smartphone surveillance in the United Kingdom. Through the use of cutting-edge unsupervised classification techniques from statistics and machine learning, we characterise symptom phenotypes among symptomatic SARS-CoV-2 PCR-positive community cases. We first analyse each dataset in isolation and across age bands, before using methods that allow us to compare multiple datasets. While we observe separation due to the total number of symptoms experienced by cases, we also see a separation of symptoms into gastrointestinal, respiratory and other types, and different symptom co-occurrence patterns at the extremes of age. In this way, we are able to demonstrate the deep structure of symptoms of COVID-19 without usual biases due to study design. This is expected to have implications for the identification and management of community SARS-CoV-2 cases and could be further applied to symptom-based management of other diseases and syndromes.
MeSH term(s)	Humans ; COVID-19/diagnosis ; COVID-19/epidemiology ; SARS-CoV-2/genetics ; Pandemics/prevention & control ; COVID-19 Testing ; Sensitivity and Specificity
Language	English
Publishing date	2023-12-07
Publishing country	England
Document type	Journal Article
ZDB-ID	2615211-3
ISSN	2045-2322 ; 2045-2322
ISSN (online)	2045-2322
ISSN	2045-2322
DOI	10.1038/s41598-023-47488-9
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Book ; Online: The role of regular asymptomatic testing in reducing the impact of a COVID-19 wave

Silva, Miguel E. P. / Fyles, Martyn / Pi, Li / Panovska-Griffiths, Jasmina / Jay, Caroline / House, Thomas / Fearon, Elizabeth

2022

Abstract	Testing for infection with SARS-CoV-2 is an important intervention in reducing onwards transmission of COVID-19, particularly when combined with the isolation and contact-tracing of positive cases. Many countries with the capacity to do so have made use of lab-processed Polymerase Chain Reaction (PCR) testing targeted at individuals with symptoms and the contacts of confirmed cases. Alternatively, Lateral Flow Tests (LFTs) are able to deliver a result quickly, without lab-processing and at a relatively low cost. Their adoption can support regular mass asymptomatic testing, allowing earlier detection of infection and isolation of infectious individuals. In this paper we extend and apply the agent-based epidemic modelling framework Covasim to explore the impact of regular asymptomatic testing on the peak and total number of infections in an emerging COVID-19 wave. We explore testing with LFTs at different frequency levels within a population with high levels of immunity and with background symptomatic PCR testing, case isolation and contact tracing for testing. The effectiveness of regular asymptomatic testing was compared with `lockdown' interventions seeking to reduce the number of non-household contacts across the whole population through measures such as mandating working from home and restrictions on gatherings. Since regular asymptomatic testing requires only those with a positive result to reduce contact, while lockdown measures require the whole population to reduce contact, any policy decision that seeks to trade off harms from infection against other harms will not automatically favour one over the other. Our results demonstrate that, where such a trade off is being made, at moderate rates of early exponential growth regular asymptomatic testing has the potential to achieve significant infection control without the wider harms associated with additional lockdown measures.
Keywords	Quantitative Biology - Populations and Evolution
Subject code	360
Publishing date	2022-07-18
Publishing country	us
Document type	Book ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Diversity of symptom phenotypes in SARS-CoV-2 community infections observed in multiple large datasets

Martyn Fyles / Karina-Doris Vihta / Carole H Sudre / Harry Long / Rajenki Das / Caroline Jay / Tom Wingfield / Fergus Cumming / William Green / Pantelis Hadjipantelis / Joni Kirk / Claire J Steves / Sebastien Ourselin / Graham F Medley / Elizabeth Fearon / Thomas House

Scientific Reports, Vol 13, Iss 1, Pp 1-

2023 Volume 19

Abstract: Abstract Variability in case severity and in the range of symptoms experienced has been apparent from the earliest months of the COVID-19 pandemic. From a clinical perspective, symptom variability might indicate various routes/mechanisms by which ... ...

Abstract	Abstract Variability in case severity and in the range of symptoms experienced has been apparent from the earliest months of the COVID-19 pandemic. From a clinical perspective, symptom variability might indicate various routes/mechanisms by which infection leads to disease, with different routes requiring potentially different treatment approaches. For public health and control of transmission, symptoms in community cases were the prompt upon which action such as PCR testing and isolation was taken. However, interpreting symptoms presents challenges, for instance, in balancing the sensitivity and specificity of individual symptoms with the need to maximise case finding, whilst managing demand for limited resources such as testing. For both clinical and transmission control reasons, we require an approach that allows for the possibility of distinct symptom phenotypes, rather than assuming variability along a single dimension. Here we address this problem by bringing together four large and diverse datasets deriving from routine testing, a population-representative household survey and participatory smartphone surveillance in the United Kingdom. Through the use of cutting-edge unsupervised classification techniques from statistics and machine learning, we characterise symptom phenotypes among symptomatic SARS-CoV-2 PCR-positive community cases. We first analyse each dataset in isolation and across age bands, before using methods that allow us to compare multiple datasets. While we observe separation due to the total number of symptoms experienced by cases, we also see a separation of symptoms into gastrointestinal, respiratory and other types, and different symptom co-occurrence patterns at the extremes of age. In this way, we are able to demonstrate the deep structure of symptoms of COVID-19 without usual biases due to study design. This is expected to have implications for the identification and management of community SARS-CoV-2 cases and could be further applied to symptom-based management of other diseases ...
Keywords	Medicine ; R ; Science ; Q
Subject code	310
Language	English
Publishing date	2023-12-01T00:00:00Z
Publisher	Nature Portfolio
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: SARS-CoV-2 antigen testing: weighing the false positives against the costs of failing to control transmission.

Fearon, Elizabeth / Buchan, Iain E / Das, Rajenki / Davis, Emma L / Fyles, Martyn / Hall, Ian / Hollingsworth, T Deirdre / House, Thomas / Jay, Caroline / Medley, Graham F / Pellis, Lorenzo / Quilty, Billy J / Silva, Miguel E P / Stage, Helena B / Wingfield, Tom

The Lancet. Respiratory medicine

2021 Volume 9, Issue 7, Page(s) 685–687

MeSH term(s)	Antigens, Viral/blood ; COVID-19/blood ; COVID-19/diagnosis ; COVID-19/prevention & control ; COVID-19/transmission ; COVID-19 Testing ; False Positive Reactions ; Humans ; SARS-CoV-2/immunology
Chemical Substances	Antigens, Viral
Language	English
Publishing date	2021-06-14
Publishing country	England
Document type	Journal Article
ZDB-ID	2686754-0
ISSN	2213-2619 ; 2213-2600
ISSN (online)	2213-2619
ISSN	2213-2600
DOI	10.1016/S2213-2600(21)00234-4
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