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Article ; Online: Shut and re-open: the role of schools in the spread of COVID-19 in Europe.

Stage, Helena B / Shingleton, Joseph / Ghosh, Sanmitra / Scarabel, Francesca / Pellis, Lorenzo / Finnie, Thomas

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

2021 Volume 376, Issue 1829, Page(s) 20200277

Abstract: We investigate the effect of school closure and subsequent reopening on the transmission of COVID-19, by considering Denmark, Norway, Sweden and German states as case studies. By comparing the growth rates in daily hospitalizations or confirmed cases ... ...

Abstract	We investigate the effect of school closure and subsequent reopening on the transmission of COVID-19, by considering Denmark, Norway, Sweden and German states as case studies. By comparing the growth rates in daily hospitalizations or confirmed cases under different interventions, we provide evidence that school closures contribute to a reduction in the growth rate approximately 7 days after implementation. Limited school attendance, such as older students sitting exams or the partial return of younger year groups, does not appear to significantly affect community transmission. In countries where community transmission is generally low, such as Denmark or Norway, a large-scale reopening of schools while controlling or suppressing the epidemic appears feasible. However, school reopening can contribute to statistically significant increases in the growth rate in countries like Germany, where community transmission is relatively high. In all regions, a combination of low classroom occupancy and robust test-and-trace measures were in place. Our findings underscore the need for a cautious evaluation of reopening strategies. This article is part of the theme issue 'Modelling that shaped the early COVID-19 pandemic response in the UK'.
MeSH term(s)	Adolescent ; COVID-19/epidemiology ; COVID-19/transmission ; COVID-19/virology ; Denmark/epidemiology ; Europe/epidemiology ; Germany/epidemiology ; Humans ; Norway/epidemiology ; Pandemics ; SARS-CoV-2/pathogenicity ; Schools/trends ; Sweden/epidemiology
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.2020.0277
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article: Estimation of reproduction numbers in real time: Conceptual and statistical challenges.

Pellis, Lorenzo / Birrell, Paul J / Blake, Joshua / Overton, Christopher E / Scarabel, Francesca / Stage, Helena B / Brooks-Pollock, Ellen / Danon, Leon / Hall, Ian / House, Thomas A / Keeling, Matt J / Read, Jonathan M / De Angelis, Daniela

Journal of the Royal Statistical Society. Series A, (Statistics in Society)

2022 Volume 185, Issue Suppl 1, Page(s) S112–S130

Abstract: The reproduction ... ...

Abstract	The reproduction number
Language	English
Publishing date	2022-11-22
Publishing country	England
Document type	Journal Article
ZDB-ID	1490715-X
ISSN	1467-985X ; 0964-1998 ; 0035-9238
ISSN (online)	1467-985X
ISSN	0964-1998 ; 0035-9238
DOI	10.1111/rssa.12955
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article: Superinfection and the evolution of an initial asymptomatic stage.

Saad-Roy, Chadi M / Grenfell, Bryan T / Levin, Simon A / Pellis, Lorenzo / Stage, Helena B / van den Driessche, P / Wingreen, Ned S

Royal Society open science

2021 Volume 8, Issue 1, Page(s) 202212

Abstract: ... still partially or fully asymptomatic. During this initial stage of infection, it is possible ... we study the effect of superinfection during the first stage of an infection on the evolutionary dynamics ... of the degree to which the host is asymptomatic (host latency) in that same stage. We find that superinfection ...

Abstract	Pathogens have evolved a variety of life-history strategies. An important strategy consists of successful transmission by an infected host before the appearance of symptoms, that is, while the host is still partially or fully asymptomatic. During this initial stage of infection, it is possible for another pathogen to superinfect an already infected host and replace the previously infecting pathogen. Here, we study the effect of superinfection during the first stage of an infection on the evolutionary dynamics of the degree to which the host is asymptomatic (host latency) in that same stage. We find that superinfection can lead to major differences in evolutionary behaviour. Most strikingly, the duration of immunity following infection can significantly influence pathogen evolutionary dynamics, whereas without superinfection the outcomes are independent of host immunity. For example, changes in host immunity can drive evolutionary transitions from a fully symptomatic to a fully asymptomatic first infection stage. Additionally, if superinfection relative to susceptible infection is strong enough, evolution can lead to a unique strategy of latency that corresponds to a local fitness minimum, and is therefore invasible by nearby mutants. Thus, this strategy is a branching point, and can lead to coexistence of pathogens with different latencies. Furthermore, in this new framework with superinfection, we also find that there can exist two interior singular strategies. Overall, new evolutionary outcomes can cascade from superinfection.
Language	English
Publishing date	2021-01-27
Publishing country	England
Document type	Journal Article
ZDB-ID	2787755-3
ISSN	2054-5703
ISSN	2054-5703
DOI	10.1098/rsos.202212
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: Challenges for modelling interventions for future pandemics.

Kretzschmar, Mirjam E / Ashby, Ben / Fearon, Elizabeth / Overton, Christopher E / Panovska-Griffiths, Jasmina / Pellis, Lorenzo / Quaife, Matthew / Rozhnova, Ganna / Scarabel, Francesca / Stage, Helena B / Swallow, Ben / Thompson, Robin N / Tildesley, Michael J / Villela, Daniel

Epidemics

2022 Volume 38, Page(s) 100546

Abstract: Mathematical modelling and statistical inference provide a framework to evaluate different non-pharmaceutical and pharmaceutical interventions for the control of epidemics that has been widely used during the COVID-19 pandemic. In this paper, lessons ... ...

Abstract	Mathematical modelling and statistical inference provide a framework to evaluate different non-pharmaceutical and pharmaceutical interventions for the control of epidemics that has been widely used during the COVID-19 pandemic. In this paper, lessons learned from this and previous epidemics are used to highlight the challenges for future pandemic control. We consider the availability and use of data, as well as the need for correct parameterisation and calibration for different model frameworks. We discuss challenges that arise in describing and distinguishing between different interventions, within different modelling structures, and allowing both within and between host dynamics. We also highlight challenges in modelling the health economic and political aspects of interventions. Given the diversity of these challenges, a broad variety of interdisciplinary expertise is needed to address them, combining mathematical knowledge with biological and social insights, and including health economics and communication skills. Addressing these challenges for the future requires strong cross-disciplinary collaboration together with close communication between scientists and policy makers.
MeSH term(s)	COVID-19/epidemiology ; Humans ; Pandemics ; SARS-CoV-2
Language	English
Publishing date	2022-02-11
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.2022.100546
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: EpiBeds: Data informed modelling of the COVID-19 hospital burden in England.

Overton, Christopher E / Pellis, Lorenzo / Stage, Helena B / Scarabel, Francesca / Burton, Joshua / Fraser, Christophe / Hall, Ian / House, Thomas A / Jewell, Chris / Nurtay, Anel / Pagani, Filippo / Lythgoe, Katrina A

PLoS computational biology

2022 Volume 18, Issue 9, Page(s) e1010406

Abstract: The first year of the COVID-19 pandemic put considerable strain on healthcare systems worldwide. In order to predict the effect of the local epidemic on hospital capacity in England, we used a variety of data streams to inform the construction and ... ...

Abstract	The first year of the COVID-19 pandemic put considerable strain on healthcare systems worldwide. In order to predict the effect of the local epidemic on hospital capacity in England, we used a variety of data streams to inform the construction and parameterisation of a hospital progression model, EpiBeds, which was coupled to a model of the generalised epidemic. In this model, individuals progress through different pathways (e.g. may recover, die, or progress to intensive care and recover or die) and data from a partially complete patient-pathway line-list was used to provide initial estimates of the mean duration that individuals spend in the different hospital compartments. We then fitted EpiBeds using complete data on hospital occupancy and hospital deaths, enabling estimation of the proportion of individuals that follow the different clinical pathways, the reproduction number of the generalised epidemic, and to make short-term predictions of hospital bed demand. The construction of EpiBeds makes it straightforward to adapt to different patient pathways and settings beyond England. As part of the UK response to the pandemic, EpiBeds provided weekly forecasts to the NHS for hospital bed occupancy and admissions in England, Wales, Scotland, and Northern Ireland at national and regional scales.
MeSH term(s)	COVID-19/epidemiology ; England/epidemiology ; Hospitalization ; Hospitals ; Humans ; Pandemics
Language	English
Publishing date	2022-09-06
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2193340-6
ISSN	1553-7358 ; 1553-734X
ISSN (online)	1553-7358
ISSN	1553-734X
DOI	10.1371/journal.pcbi.1010406
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Article ; Online: Shut and re-open: the role of schools in the spread of COVID-19 in Europe

Stage, Helena B / Shingleton, Joseph / Ghosh, Sanmitra / Scarabel, Francesca / Pellis, Lorenzo / Finnie, Thomas

medRxiv

Abstract: We investigate the effect of school closure and subsequent reopening on the transmission of COVID-19, by considering Denmark, Norway, Sweden, and German states as case studies. By comparing the growth rates in daily hospitalisations or confirmed cases ... ...

Abstract	We investigate the effect of school closure and subsequent reopening on the transmission of COVID-19, by considering Denmark, Norway, Sweden, and German states as case studies. By comparing the growth rates in daily hospitalisations or confirmed cases under different interventions, we provide evidence that the effect of school closure is visible as a reduction in the growth rate approximately 9 days after implementation. Limited school attendance, such as older students sitting exams or the partial return of younger year groups, does not appear to significantly affect community transmission. A large-scale reopening of schools while controlling or suppressing the epidemic appears feasible in countries such as Denmark or Norway, where community transmission is generally low. However, school reopening can contribute to significant increases in the growth rate in countries like Germany, where community transmission is relatively high. Our findings underscore the need for a cautious evaluation of reopening strategies that ensure low classroom occupancy and a solid infrastructure to quickly identify and isolate new infections.
Keywords	covid19
Language	English
Publishing date	2020-06-26
Publisher	Cold Spring Harbor Laboratory Press
Document type	Article ; Online
DOI	10.1101/2020.06.24.20139634
Database	COVID19

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Book ; Online: Shut and re-open

Stage, Helena B. / Shingleton, Joseph / Ghosh, Sanmitra / Scarabel, Francesca / Pellis, Lorenzo / Finnie, Thomas

the role of schools in the spread of COVID-19 in Europe

2020

Abstract	We investigate the effect of school closure and subsequent reopening on the transmission of COVID-19, by considering Denmark, Norway, Sweden, and German states as case studies. By comparing the growth rates in daily hospitalisations or confirmed cases under different interventions, we provide evidence that the effect of school closure is visible as a reduction in the growth rate approximately 9 days after implementation. Limited school attendance, such as older students sitting exams or the partial return of younger year groups, does not appear to significantly affect community transmission. A large-scale reopening of schools while controlling or suppressing the epidemic appears feasible in countries such as Denmark or Norway, where community transmission is generally low. However, school reopening can contribute to significant increases in the growth rate in countries like Germany, where community transmission is relatively high. Our findings underscore the need for a cautious evaluation of reopening strategies that ensure low classroom occupancy and a solid infrastructure to quickly identify and isolate new infections.
Keywords	Quantitative Biology - Populations and Evolution ; Physics - Physics and Society
Subject code	370
Publishing date	2020-06-24
Publishing country	us
Document type	Book ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Challenges in control of COVID-19: short doubling time and long delay to effect of interventions.

Pellis, Lorenzo / Scarabel, Francesca / Stage, Helena B / Overton, Christopher E / Chappell, Lauren H K / Fearon, Elizabeth / Bennett, Emma / Lythgoe, Katrina A / House, Thomas A / Hall, Ian

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

2021 Volume 376, Issue 1829, Page(s) 20200264

Abstract: Early assessments of the growth rate of COVID-19 were subject to significant uncertainty, as expected with limited data and difficulties in case ascertainment, but as cases were recorded in multiple countries, more robust inferences could be made. Using ... ...

Abstract	Early assessments of the growth rate of COVID-19 were subject to significant uncertainty, as expected with limited data and difficulties in case ascertainment, but as cases were recorded in multiple countries, more robust inferences could be made. Using multiple countries, data streams and methods, we estimated that, when unconstrained, European COVID-19 confirmed cases doubled on average every 3 days (range 2.2-4.3 days) and Italian hospital and intensive care unit admissions every 2-3 days; values that are significantly lower than the 5-7 days dominating the early published literature. Furthermore, we showed that the impact of physical distancing interventions was typically not seen until at least 9 days after implementation, during which time confirmed cases could grow eightfold. We argue that such temporal patterns are more critical than precise estimates of the time-insensitive basic reproduction number
MeSH term(s)	COVID-19/epidemiology ; COVID-19/virology ; Humans ; Italy/epidemiology ; Models, Theoretical ; Pandemics ; Physical Distancing ; SARS-CoV-2
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.2020.0264
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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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Article ; Online: Superinfection and the evolution of an initial asymptomatic stage

Chadi M. Saad-Roy / Bryan T. Grenfell / Simon A. Levin / Lorenzo Pellis / Helena B. Stage / P. van den Driessche / Ned S. Wingreen

Royal Society Open Science, Vol 8, Iss

2021 Volume 1

Abstract	Pathogens have evolved a variety of life-history strategies. An important strategy consists of successful transmission by an infected host before the appearance of symptoms, that is, while the host is still partially or fully asymptomatic. During this initial stage of infection, it is possible for another pathogen to superinfect an already infected host and replace the previously infecting pathogen. Here, we study the effect of superinfection during the first stage of an infection on the evolutionary dynamics of the degree to which the host is asymptomatic (host latency) in that same stage. We find that superinfection can lead to major differences in evolutionary behaviour. Most strikingly, the duration of immunity following infection can significantly influence pathogen evolutionary dynamics, whereas without superinfection the outcomes are independent of host immunity. For example, changes in host immunity can drive evolutionary transitions from a fully symptomatic to a fully asymptomatic first infection stage. Additionally, if superinfection relative to susceptible infection is strong enough, evolution can lead to a unique strategy of latency that corresponds to a local fitness minimum, and is therefore invasible by nearby mutants. Thus, this strategy is a branching point, and can lead to coexistence of pathogens with different latencies. Furthermore, in this new framework with superinfection, we also find that there can exist two interior singular strategies. Overall, new evolutionary outcomes can cascade from superinfection.
Keywords	superinfection ; asymptomatic infectious stage ; pathogen evolutionary dynamics ; life histories of pathogens ; Science ; Q
Subject code	501
Language	English
Publishing date	2021-01-01T00:00:00Z
Publisher	The Royal Society
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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