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Article ; Online: Modelling the global spread of diseases: A review of current practice and capability.

Walters, Caroline E / Meslé, Margaux M I / Hall, Ian M

2018 Volume 25, Page(s) 1–8

Abstract: Mathematical models can aid in the understanding of the risks associated with the global spread of infectious diseases. To assess the current state of mathematical models for the global spread of infectious diseases, we reviewed the literature ... ...

Abstract	Mathematical models can aid in the understanding of the risks associated with the global spread of infectious diseases. To assess the current state of mathematical models for the global spread of infectious diseases, we reviewed the literature highlighting common approaches and good practice, and identifying research gaps. We followed a scoping study method and extracted information from 78 records on: modelling approaches; input data (epidemiological, population, and travel) for model parameterization; model validation data. We found that most epidemiological data come from published journal articles, population data come from a wide range of sources, and travel data mainly come from statistics or surveys, or commercial datasets. The use of commercial datasets may benefit the modeller, however makes critical appraisal of their model by other researchers more difficult. We found a minority of records (26) validated their model. We posit that this may be a result of pandemics, or far-reaching epidemics, being relatively rare events compared with other modelled physical phenomena (e.g. climate change). The sparsity of such events, and changes in outbreak recording, may make identifying suitable validation data difficult. We appreciate the challenge of modelling emerging infections given the lack of data for both model parameterisation and validation, and inherent complexity of the approaches used. However, we believe that open access datasets should be used wherever possible to aid model reproducibility and transparency. Further, modellers should validate their models where possible, or explicitly state why validation was not possible.
MeSH term(s)	Communicable Diseases/epidemiology ; Communicable Diseases/transmission ; Disease Outbreaks/statistics & numerical data ; Humans ; Models, Theoretical ; Reproducibility of Results ; Travel
Keywords	covid19
Language	English
Publishing date	2018-05-18
Publishing country	Netherlands
Document type	Journal Article ; Research Support, Non-U.S. Gov't ; Review
ZDB-ID	2467993-8
ISSN	1878-0067 ; 1755-4365
ISSN (online)	1878-0067
ISSN	1755-4365
DOI	10.1016/j.epidem.2018.05.007
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: An SIS model for cultural trait transmission with conformity bias.

Walters, Caroline E / Kendal, Jeremy R

Theoretical population biology

2013 Volume 90, Page(s) 56–63

Abstract: Epidemiological models have been applied to human health-related behaviors that are affected by social interaction. Typically these models have not considered conformity bias, that is, the exaggerated propensity to adopt commonly observed behaviors or ... ...

Abstract	Epidemiological models have been applied to human health-related behaviors that are affected by social interaction. Typically these models have not considered conformity bias, that is, the exaggerated propensity to adopt commonly observed behaviors or opinions, or content biases, where the content of the learned trait affects the probability of adoption. Here we consider an interaction of these two effects, presenting an SIS-type model for the spread and persistence of a behavior which is transmitted via social learning. Uptake is controlled by a nonlinear dependence on the proportion of individuals demonstrating the behavior in a population. Three equilibrium solutions are found, their linear stability is analyzed and the results are compared with a model for unbiased social learning. Our analysis focuses on the effects of the strength of conformity bias and the effects of content biases which alter a conformity threshold frequency of the behavior, above which there is an exaggerated propensity for adoption. The strength of the conformity bias is found to qualitatively alter the predictions regarding whether the trait becomes endemic within the population and the proportion of individuals who display the trait when it is endemic. As the conformity strength increases, the number of feasible equilibrium solutions increases from two to three, leading to a situation where the stable equilibrium attained is dependent upon the initial state. Varying the conformity threshold frequency directionally alters the behavior invasion threshold. Finally we discuss the possible application of this model to binge drinking behavior.
MeSH term(s)	Culture ; Epidemiologic Studies ; Humans ; Models, Theoretical
Language	English
Publishing date	2013-12
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	3948-2
ISSN	1096-0325 ; 0040-5809
ISSN (online)	1096-0325
ISSN	0040-5809
DOI	10.1016/j.tpb.2013.09.010
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Article ; Online: Modelling infectious disease transmission potential as a function of human behaviour

Walters, Caroline E. / Bekker-Nielsen Dunbar, Maria / Weston, Dale / Hall, Ian M.

medRxiv

Abstract: Mathematical modelling is an important public health tool for aiding understanding the spread of respiratory infectious diseases, such as influenza or COVID-19, and for quantifying the effects of behavioural interventions. However, such models rarely ... ...

Abstract	Mathematical modelling is an important public health tool for aiding understanding the spread of respiratory infectious diseases, such as influenza or COVID-19, and for quantifying the effects of behavioural interventions. However, such models rarely explicitly appeals to theories of human behaviour to justify model assumptions. Here we propose a novel mathematical model of disease transmission via fomites (luggage trays) at airport security screening during an outbreak. Our model incorporates the self-protective behaviour of using hand sanitiser gel in line with the extended parallel processing model (EPPM) of behaviour. We find that changing model assumptions of human behaviour in line with the EPPM gives qualitatively different results on the optimal placement of hand sanitiser gels within an airport compared to the model with naive behavioural assumptions. Specifically, that it is preferable to place hand sanitiser gels after luggage screening in most scenarios, however in situations where individuals perceive high threat and low efficacy this strategy may need to be reviewed. This model demonstrates how existing behavioural theories can be incorporated into mathematical models of infectious disease.
Keywords	covid19
Language	English
Publishing date	2021-07-20
Publisher	Cold Spring Harbor Laboratory Press
Document type	Article ; Online
DOI	10.1101/2021.07.16.21260521
Database	COVID19

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Article ; Online: Trends in SARS-CoV-2 infection prevalence during England's roadmap out of lockdown, January to July 2021.

Eales, Oliver / Wang, Haowei / Haw, David / Ainslie, Kylie E C / Walters, Caroline E / Atchison, Christina / Cooke, Graham / Barclay, Wendy / Ward, Helen / Darzi, Ara / Ashby, Deborah / Donnelly, Christl A / Elliott, Paul / Riley, Steven

PLoS computational biology

2022 Volume 18, Issue 11, Page(s) e1010724

Abstract: Background: Following rapidly rising COVID-19 case numbers, England entered a national lockdown on 6 January 2021, with staged relaxations of restrictions from 8 March 2021 onwards.: Aim: We characterise how the lockdown and subsequent easing of ... ...

Abstract	Background: Following rapidly rising COVID-19 case numbers, England entered a national lockdown on 6 January 2021, with staged relaxations of restrictions from 8 March 2021 onwards. Aim: We characterise how the lockdown and subsequent easing of restrictions affected trends in SARS-CoV-2 infection prevalence. Methods: On average, risk of infection is proportional to infection prevalence. The REal-time Assessment of Community Transmission-1 (REACT-1) study is a repeat cross-sectional study of over 98,000 people every round (rounds approximately monthly) that estimates infection prevalence in England. We used Bayesian P-splines to estimate prevalence and the time-varying reproduction number (Rt) nationally, regionally and by age group from round 8 (beginning 6 January 2021) to round 13 (ending 12 July 2021) of REACT-1. As a comparator, a separate segmented-exponential model was used to quantify the impact on Rt of each relaxation of restrictions. Results: Following an initial plateau of 1.54% until mid-January, infection prevalence decreased until 13 May when it reached a minimum of 0.09%, before increasing until the end of the study to 0.76%. Following the first easing of restrictions, which included schools reopening, the reproduction number Rt increased by 82% (55%, 108%), but then decreased by 61% (82%, 53%) at the second easing of restrictions, which was timed to match the Easter school holidays. Following further relaxations of restrictions, the observed Rt increased steadily, though the increase due to these restrictions being relaxed was offset by the effects of vaccination and also affected by the rapid rise of Delta. There was a high degree of synchrony in the temporal patterns of prevalence between regions and age groups. Conclusion: High-resolution prevalence data fitted to P-splines allowed us to show that the lockdown was effective at reducing risk of infection with school holidays/closures playing a significant part.
MeSH term(s)	Humans ; COVID-19/epidemiology ; COVID-19/prevention & control ; Cross-Sectional Studies ; Bayes Theorem ; Communicable Disease Control ; SARS-CoV-2
Language	English
Publishing date	2022-11-23
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't ; Research Support, U.S. Gov't, P.H.S.
ZDB-ID	2193340-6
ISSN	1553-7358 ; 1553-734X
ISSN (online)	1553-7358
ISSN	1553-734X
DOI	10.1371/journal.pcbi.1010724
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Article ; Online: Appropriately smoothing prevalence data to inform estimates of growth rate and reproduction number.

Eales, Oliver / Ainslie, Kylie E C / Walters, Caroline E / Wang, Haowei / Atchison, Christina / Ashby, Deborah / Donnelly, Christl A / Cooke, Graham / Barclay, Wendy / Ward, Helen / Darzi, Ara / Elliott, Paul / Riley, Steven

Epidemics

2022 Volume 40, Page(s) 100604

Abstract: The time-varying reproduction number ( ... ...

Abstract	The time-varying reproduction number (R
MeSH term(s)	Bayes Theorem ; COVID-19/epidemiology ; Communicable Disease Control ; Humans ; Prevalence ; Reproduction ; SARS-CoV-2
Language	English
Publishing date	2022-06-22
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.2022.100604
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Article ; Online: The use of representative community samples to assess SARS-CoV-2 lineage competition: Alpha outcompetes Beta and wild-type in England from January to March 2021.

Microbial genomics

2023 Volume 9, Issue 2

Abstract: Genomic surveillance for SARS-CoV-2 lineages informs our understanding of possible future changes in transmissibility and vaccine efficacy and will be a high priority for public health for the foreseeable future. However, small changes in the frequency ... ...

Abstract	Genomic surveillance for SARS-CoV-2 lineages informs our understanding of possible future changes in transmissibility and vaccine efficacy and will be a high priority for public health for the foreseeable future. However, small changes in the frequency of one lineage over another are often difficult to interpret because surveillance samples are obtained using a variety of methods all of which are known to contain biases. As a case study, using an approach which is largely free of biases, we here describe lineage dynamics and phylogenetic relationships of the Alpha and Beta variant in England during the first 3 months of 2021 using sequences obtained from a random community sample who provided a throat and nose swab for rt-PCR as part of the REal-time Assessment of Community Transmission-1 (REACT-1) study. Overall, diversity decreased during the first quarter of 2021, with the Alpha variant (first identified in Kent) becoming predominant, driven by a reproduction number 0.3 higher than for the prior wild-type. During January, positive samples were more likely to be Alpha in those aged 18 to 54 years old. Although individuals infected with the Alpha variant were no more likely to report one or more classic COVID-19 symptoms compared to those infected with wild-type, they were more likely to be antibody-positive 6 weeks after infection. Further, viral load was higher in those infected with the Alpha variant as measured by cycle threshold (Ct) values. The presence of infections with non-imported Beta variant (first identified in South Africa) during January, but not during February or March, suggests initial establishment in the community followed by fade-out. However, this occurred during a period of stringent social distancing. These results highlight how sequence data from representative community surveys such as REACT-1 can augment routine genomic surveillance during periods of lineage diversity.
MeSH term(s)	Humans ; Adolescent ; Young Adult ; Adult ; Middle Aged ; SARS-CoV-2/genetics ; COVID-19 ; Phylogeny ; England/epidemiology
Language	English
Publishing date	2023-02-06
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2835258-0
ISSN	2057-5858 ; 2057-5858
ISSN (online)	2057-5858
ISSN	2057-5858
DOI	10.1099/mgen.0.000887
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Article ; Online: Primary care coding activity related to the use of online consultation systems or remote consulting: an analysis of 53 million peoples' health records using OpenSAFELY

Fonseca, Martina / MacKenna, Brian / Mehrkar, Amir / The OpenSAFELY Collaborative / Walters, Caroline E / Hickman, George / Fisher, Louis / Pearson, Jonathan / Inglesby, Peter / Bacon, Seb / Davy, Simon / Hulme, William / Goldacre, Ben / Koffman, Ofra / Bakhai, Minal

medRxiv

Abstract: Objective: We aimed to explore general practice coding activity associated with the use of online consultation systems in terms of trends, COVID-19 effect, variation and quality. The pandemic accelerated work by the NHS in England to enable and stimulate ...

Abstract	Objective: We aimed to explore general practice coding activity associated with the use of online consultation systems in terms of trends, COVID-19 effect, variation and quality. The pandemic accelerated work by the NHS in England to enable and stimulate use of online consultation systems across all practices, for improved access to primary care. Methods: With the approval of NHS England, OpenSAFELY-TPP and OpenSAFELY-EMIS were used to query and analyse in situ records of electronic health record systems of over 53 million patients in over 6,400 practices, mainly in 2019-2020. SNOMED CT codes relevant to online consultation systems and written online consultations were identified. Coded events were described by volumes, practice coverage, trends pre- and post-COVID-19 and inter-practice and sociodemographic variation. Results: 3,550,762 relevant coding events were found in TPP practices, with code eConsultation detected in 84% of practices. Coding activity related to digital forms of interaction increased rapidly from March 2020 at the onset of the COVID-19 pandemic, though we found large variation in coding instance rates among practices in England. Code instances were more commonly found among females, those aged 18-40, those least deprived or white. eConsultation coded activity was more commonly found recorded among patients with a history of asthma or depression. Conclusions: We successfully queried general practice coding activity relevant to the use of online consultation systems, showing increased adoption as well as key areas of variation during the COVID-19 pandemic. The work can be expanded to support monitoring of coding quality and underlying activity. In future, large-scale impact evaluation studies can be implemented within the platform, namely looking at resource utilisation and patient outcomes.
Keywords	covid19
Language	English
Publishing date	2023-01-28
Publisher	Cold Spring Harbor Laboratory Press
Document type	Article ; Online
DOI	10.1101/2023.01.25.23284428
Database	COVID19

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Article ; Online: Health inequalities in SARS-CoV-2 infection during the second wave in England: REACT-1 study

Wang, Haowei / Ainslie, Kylie E. C. / Walters, Caroline E. / Eales, Oliver / Haw, David / Atchison, Christina / Fronterre, Claudio / Diggle, Peter J. / Ashby, Deborah / Cooke, Graham / Barclay, Wendy / Ward, Helen / Darzi, Ara / Donnelly, Christl A. / Riley, Steven / Elliott, Paul

medRxiv

Abstract: Abstract Background The rapid spread of SARS-CoV-2 infection caused high levels of hospitalisation and deaths in late 2020 and early 2021 during the second wave in England. Severe disease during this period was associated with marked health inequalities ... ...

Abstract	Abstract Background The rapid spread of SARS-CoV-2 infection caused high levels of hospitalisation and deaths in late 2020 and early 2021 during the second wave in England. Severe disease during this period was associated with marked health inequalities across ethnic and sociodemographic subgroups. Methods We analysed risk factors for test-positivity for SARS-CoV-2, based on self-administered throat and nose swabs in the community during rounds 5 to 10 of the REal-time Assessment of Community Transmission-1 (REACT-1) study between 18 September 2020 and 30 March 2021. Results Compared to white ethnicity, people of Asian and black ethnicity had a higher risk of infection during rounds 5 to 10, with odds of 1.46 (1.27, 1.69) and 1.35 (1.11, 1.64) respectively. Among ethnic subgroups, the highest and the second-highest odds were found in Bangladeshi and Pakistan participants at 3.29 (2.23, 4.86) and 2.15 (1.73, 2.68) respectively when compared to British whites. People in larger (compared to smaller) households had higher odds of infection. Health care workers with direct patient contact and care home workers showed higher odds of infection compared to other essential/key workers. Additionally, the odds of infection among participants in public-facing activities or settings were greater than among those not working in those activities or settings. Interpretation Planning for future severe waves of respiratory pathogens should include policies to reduce inequality in risk of infection by ethnicity, household size, and occupational activity.
Keywords	covid19
Language	English
Publishing date	2023-08-03
Publisher	Cold Spring Harbor Laboratory Press
Document type	Article ; Online
DOI	10.1101/2023.08.01.23293491
Database	COVID19

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Article ; Online: Health inequalities in SARS-CoV-2 infection during the second wave in England: REACT-1 study

Wang, Haowei / Ainslie, Kylie E. C. / Eales, Oliver / Walters, Caroline E. / Haw, David / Atchinson, Christina / Fronterre, Claudio / Diggle, Peter J. / Ashby, Deborah / Cooke, Graham / Barclay, Wendy / Ward, Helen / Darzi, Ara / Donnelly, Christl A / Elliott, Paul / Riley, Steven

medRxiv

Abstract	Abstract Background The rapid spread of SARS-CoV-2 infection caused high levels of hospitalisation and deaths in late 2020 and early 2021 during the second wave in England. Severe disease during this period was associated with marked health inequalities across ethnic and sociodemographic subgroups. Methods We analysed risk factors for test-positivity for SARS-CoV-2, based on self-administered throat and nose swabs in the community during rounds 5 to 10 of the REal-time Assessment of Community Transmission-1 (REACT-1) study between 18 September 2020 and 30 March 2021. Results Compared to white ethnicity, people of Asian and black ethnicity had a higher risk of infection during rounds 5 to 10, with odds of 1.46 (1.27, 1.69) and 1.35 (1.11, 1.64) respectively. Among ethnic subgroups, the highest and the second-highest odds were found in Bangladeshi and Pakistan participants at 3.29 (2.23, 4.86) and 2.15 (1.73, 2.68) respectively when compared to British whites. People in larger (compared to smaller) households had higher odds of infection. Health care workers with direct patient contact and care home workers showed higher odds of infection compared to other essential/key workers. Additionally, the odds of infection among participants in public-facing activities or settings were greater than among those not working in those activities or settings. Interpretation Planning for future severe waves of respiratory pathogens should include policies to reduce inequality in risk of infection by ethnicity, household size, and occupational activity.
Keywords	covid19
Language	English
Publishing date	2023-08-03
Publisher	Cold Spring Harbor Laboratory Press
Document type	Article ; Online
DOI	10.1101/2023.08.01.23293491
Database	COVID19

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Article ; Online: Trends in SARS-CoV-2 infection prevalence during England's roadmap out of lockdown, January to July 2021

Eales, Oliver / Wang, Haowei / Haw, David / Ainslie, Kylie E.C. / Walters, Caroline E. / Atchison, Christina / Cooke, Graham / Barclay, Wendy / Ward, Helen / Darzi, Ara / Ashby, Deborah / Donnelly, Christl A / Elliott, Paul / Riley, Steven

medRxiv

Abstract: Background: Following rapidly rising COVID-19 case numbers, England entered a national lockdown on 6 January 2021, with staged relaxations of restrictions from 8 March 2021 onwards. Aim: We characterise how the lockdown and subsequent easing of ... ...

Abstract	Background: Following rapidly rising COVID-19 case numbers, England entered a national lockdown on 6 January 2021, with staged relaxations of restrictions from 8 March 2021 onwards. Aim: We characterise how the lockdown and subsequent easing of restrictions affected trends in SARS-CoV-2 infection prevalence. Methods: On average, risk of infection is proportional to infection prevalence. The REal-time Assessment of Community Transmission-1 (REACT-1) study is a repeat cross-sectional study of over 98,000 people every round (rounds approximately monthly) that estimates infection prevalence in England. We used Bayesian P-splines to estimate prevalence and the time-varying reproduction number (Rt) nationally, regionally and by age group from round 8 (beginning 6 January 2021) to round 13 (ending 12 July 2021) of REACT-1. As a comparator, a separate segmented-exponential model was used to quantify the impact on Rt of each relaxation of restrictions. Results: Following an initial plateau of 1.54% until mid-January, infection prevalence decreased until 13 May when it reached a minimum of 0.09%, before increasing until the end of the study to 0.76%. Following the first easing of restrictions, which included schools reopening, the reproduction number Rt increased by 82% (55%, 108%), but then decreased by 61% (82%, 53%) at the second easing of restrictions, which was timed to match the Easter school holidays. Following further relaxations of restrictions, the observed Rt increased steadily, though the increase due to these restrictions being relaxed was masked by the effects of vaccination and the rapid rise of Delta. There was a high degree of synchrony in the temporal patterns of prevalence between regions and age groups. Conclusion: High-resolution prevalence data fitted to P-splines allowed us to show that the lockdown was highly effective at reducing risk of infection with school holidays/closures playing a significant part.
Keywords	covid19
Language	English
Publishing date	2022-06-02
Publisher	Cold Spring Harbor Laboratory Press
Document type	Article ; Online
DOI	10.1101/2022.06.02.22275900
Database	COVID19

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