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Stocks D, Nixon E, Trickey A, Homer M, Brooks-Pollock E. Limited impact of contact tracing in a University setting for COVID-19 due to asymptomatic transmission and social distancing. Epidemics 2023; 45:100716. [PMID: 37690279 DOI: 10.1016/j.epidem.2023.100716] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Revised: 06/21/2023] [Accepted: 08/21/2023] [Indexed: 09/12/2023] Open
Abstract
Contact tracing is an important tool for controlling the spread of infectious diseases, including COVID-19. Here, we investigate the spread of COVID-19 and the effectiveness of contact tracing in a university population, using a data-driven ego-centric network model constructed with social contact data collected during 2020 and similar data collected in 2010. We find that during 2020, university staff and students consistently reported fewer social contacts than in 2010, however those contacts occurred more frequently and were of longer duration. We find that contact tracing in the presence of social distancing is less impactful than without social distancing. By combining multiple data sources, we show that University-aged populations are likely to develop asymptomatic COVID-19 infections. We find that asymptomatic index cases cannot be reliably discovered through contact tracing and consequently transmission in their social network is not significantly reduced through contact tracing. In summary, social distancing restrictions had a large impact on limiting COVID-19 outbreaks in universities; to reduce transmission further contact tracing should be used in conjunction with alternative interventions.
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Affiliation(s)
- Daniel Stocks
- Department of Engineering Mathematics, University of Bristol, Bristol BS8 1TW, United Kingdom.
| | - Emily Nixon
- School of Biological Sciences, University of Bristol, Bristol BS8 1TQ, United Kingdom; Bristol Veterinary School, University of Bristol, Bristol BS40 5DU, United Kingdom
| | - Adam Trickey
- Population Health Sciences, University of Bristol, Bristol BS8 1TW, United Kingdom
| | - Martin Homer
- Department of Engineering Mathematics, University of Bristol, Bristol BS8 1TW, United Kingdom
| | - Ellen Brooks-Pollock
- Bristol Veterinary School, University of Bristol, Bristol BS40 5DU, United Kingdom
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2
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Trickey A, Bivegete S, Duffell E, McNaughton AL, Nerlander L, Walker JG, Fraser H, Hickman M, Vickerman P, Brooks-Pollock E, Christensen H. Estimating hepatitis B virus prevalence among key population groups for European Union and European Economic Area countries and the United Kingdom: a modelling study. BMC Infect Dis 2023; 23:457. [PMID: 37430220 DOI: 10.1186/s12879-023-08433-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2022] [Accepted: 06/29/2023] [Indexed: 07/12/2023] Open
Abstract
BACKGROUND Hepatitis B virus (HBV) epidemiology in Europe differs by region and population risk group, and data are often incomplete. We estimated chronic HBV prevalence as measured by surface antigen (HBsAg) among general and key population groups for each country in the European Union, European Economic Area and the United Kingdom (EU/EEA/UK), including where data are currently unavailable. METHODS We combined data from a 2018 systematic review (updated in 2021), data gathered directly by the European Centre for Disease Control (ECDC) from EU/EEA countries and the UK and further country-level data. We included data on adults from the general population, pregnant women, first time blood donors (FTBD), men who have sex with men (MSM), prisoners, people who inject drugs (PWID), and migrants from 2001 to 2021, with three exceptions made for pre-2001 estimates. Finite Mixture Models (FMM) and Beta regression were used to predict country and population group HBsAg prevalence. A separate multiplier method was used to estimate HBsAg prevalence among the migrant populations within each country, due to biases in the data available. RESULTS There were 595 included studies from 31 countries (N = 41,955,969 people): 66 were among the general population (mean prevalence ([Formula: see text]) 1.3% [range: 0.0-7.6%]), 52 among pregnant women ([Formula: see text]1.1% [0.1-5.3%]), 315 among FTBD ([Formula: see text]0.3% [0.0-6.2%]), 20 among MSM ([Formula: see text]1.7% [0.0-11.2%]), 34 among PWID ([Formula: see text]3.9% [0.0-16.9%]), 24 among prisoners ([Formula: see text]2.9% [0.0-10.7%]), and 84 among migrants ([Formula: see text]7.0% [0.2-37.3%]). The FMM grouped countries into 3 classes. We estimated HBsAg prevalence among the general population to be < 1% in 24/31 countries, although it was higher in 7 Eastern/Southern European countries. HBsAg prevalence among each population group was higher in most Eastern/Southern European than Western/Northern European countries, whilst prevalence among PWID and prisoners was estimated at > 1% for most countries. Portugal had the highest estimated prevalence of HBsAg among migrants (5.0%), with the other highest prevalences mostly seen in Southern Europe. CONCLUSIONS We estimated HBV prevalence for each population group within each EU/EAA country and the UK, with general population HBV prevalence to be < 1% in most countries. Further evidence is required on the HBsAg prevalence of high-risk populations for future evidence synthesis.
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Affiliation(s)
- Adam Trickey
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK.
| | - Sandra Bivegete
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
- Health Protection Research Unit (HPRU) in Behavioural Science and Evaluation, Bristol, UK
| | - Erika Duffell
- European Centre for Disease Control and Prevention (ECDC), Stockholm, Sweden
| | - Anna L McNaughton
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
| | - Lina Nerlander
- European Centre for Disease Control and Prevention (ECDC), Stockholm, Sweden
| | - Josephine G Walker
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
| | - Hannah Fraser
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
- Health Protection Research Unit (HPRU) in Behavioural Science and Evaluation, Bristol, UK
| | - Matthew Hickman
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
- Health Protection Research Unit (HPRU) in Behavioural Science and Evaluation, Bristol, UK
| | - Peter Vickerman
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
- Health Protection Research Unit (HPRU) in Behavioural Science and Evaluation, Bristol, UK
| | - Ellen Brooks-Pollock
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
- Health Protection Research Unit (HPRU) in Behavioural Science and Evaluation, Bristol, UK
| | - Hannah Christensen
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
- Health Protection Research Unit (HPRU) in Behavioural Science and Evaluation, Bristol, UK
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Bivegete S, McNaughton AL, Trickey A, Thornton Z, Scanlan B, Lim AG, Nerlander L, Fraser H, Walker JG, Hickman M, Vickerman P, Johnson H, Duffell E, Brooks-Pollock E, Christensen H. Estimates of hepatitis B virus prevalence among general population and key risk groups in EU/EEA/UK countries: a systematic review. Euro Surveill 2023; 28:2200738. [PMID: 37498533 PMCID: PMC10375838 DOI: 10.2807/1560-7917.es.2023.28.30.2200738] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2022] [Accepted: 03/29/2023] [Indexed: 07/28/2023] Open
Abstract
BackgroundThe burden of chronic hepatitis B virus (HBV) varies across the European Union (EU) and European Economic Area (EEA).AimWe aimed to update the 2017 HBV prevalence estimates in EU/EEA countries and the United Kingdom for 2018 to 2021.MethodsWe undertook a systematic review, adding to HBV prevalence estimates from an existing (2005-2017) database. Databases were searched for original English-language research articles including HBV surface antigen prevalence estimates among the general population, pregnant women, first-time blood donors (FTB), men who have sex with men (MSM), migrants and people in prison. Country experts contributed grey literature data. Risk of bias was assessed using a quality assessment framework.FindingsThe update provided 147 new prevalence estimates across the region (updated total n = 579). Median HBV prevalence in the general population was 0.5% and the highest was 3.8% (Greece). Among FTB, the highest prevalence was 0.8% (Lithuania). Estimates among pregnant women were highest in Romania and Italy (5.1%). Among migrants, the highest estimate was 31.7% (Spain). Relative to 2017 estimates, median prevalence among pregnant women decreased by 0.5% (to 0.3%) and increased by 0.9% (to 5.8%) among migrants. Among MSM, the highest estimate was 3.4% (Croatia). Prevalence among people in prison was highest in Greece (8.3%) and the median prevalence increased by 0.6% (to 2.1%).ConclusionsThe HBV prevalence is low in the general population and confined to risk populations in most European countries with some exceptions. Screening and treatment should be targeted to people in prison and migrants.
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Affiliation(s)
- Sandra Bivegete
- Population Health Sciences, Bristol Medical School, University of Bristol, United Kingdom
- Health Protection Research Unit (HPRU) in Behavioural Science and Evaluation, Bristol, United Kingdom
| | - Anna L McNaughton
- Population Health Sciences, Bristol Medical School, University of Bristol, United Kingdom
| | - Adam Trickey
- Population Health Sciences, Bristol Medical School, University of Bristol, United Kingdom
| | - Zak Thornton
- Population Health Sciences, Bristol Medical School, University of Bristol, United Kingdom
| | - Becky Scanlan
- Population Health Sciences, Bristol Medical School, University of Bristol, United Kingdom
| | - Aaron G Lim
- Population Health Sciences, Bristol Medical School, University of Bristol, United Kingdom
- Health Protection Research Unit (HPRU) in Behavioural Science and Evaluation, Bristol, United Kingdom
| | - Lina Nerlander
- European Centre for Disease Prevention and Control (ECDC), Stockholm, Sweden
| | - Hannah Fraser
- Population Health Sciences, Bristol Medical School, University of Bristol, United Kingdom
- Health Protection Research Unit (HPRU) in Behavioural Science and Evaluation, Bristol, United Kingdom
| | - Josephine G Walker
- Population Health Sciences, Bristol Medical School, University of Bristol, United Kingdom
| | - Matthew Hickman
- Population Health Sciences, Bristol Medical School, University of Bristol, United Kingdom
- Health Protection Research Unit (HPRU) in Behavioural Science and Evaluation, Bristol, United Kingdom
| | - Peter Vickerman
- Population Health Sciences, Bristol Medical School, University of Bristol, United Kingdom
- Health Protection Research Unit (HPRU) in Behavioural Science and Evaluation, Bristol, United Kingdom
| | - Helen Johnson
- European Centre for Disease Prevention and Control (ECDC), Stockholm, Sweden
| | - Erika Duffell
- European Centre for Disease Prevention and Control (ECDC), Stockholm, Sweden
| | - Ellen Brooks-Pollock
- Population Health Sciences, Bristol Medical School, University of Bristol, United Kingdom
- Health Protection Research Unit (HPRU) in Behavioural Science and Evaluation, Bristol, United Kingdom
| | - Hannah Christensen
- Population Health Sciences, Bristol Medical School, University of Bristol, United Kingdom
- Health Protection Research Unit (HPRU) in Behavioural Science and Evaluation, Bristol, United Kingdom
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Brooks-Pollock E, Northstone K, Pellis L, Scarabel F, Thomas A, Nixon E, Matthews DA, Bowyer V, Garcia MP, Steves CJ, Timpson NJ, Danon L. Voluntary risk mitigation behaviour can reduce impact of SARS-CoV-2: a real-time modelling study of the January 2022 Omicron wave in England. BMC Med 2023; 21:25. [PMID: 36658548 PMCID: PMC9851586 DOI: 10.1186/s12916-022-02714-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/16/2022] [Accepted: 12/15/2022] [Indexed: 01/21/2023] Open
Abstract
BACKGROUND Predicting the likely size of future SARS-CoV-2 waves is necessary for public health planning. In England, voluntary "plan B" mitigation measures were introduced in December 2021 including increased home working and face coverings in shops but stopped short of restrictions on social contacts. The impact of voluntary risk mitigation behaviours on future SARS-CoV-2 burden is unknown. METHODS We developed a rapid online survey of risk mitigation behaviours ahead of the winter 2021 festive period and deployed in two longitudinal cohort studies in the UK (Avon Longitudinal Study of Parents and Children (ALSPAC) and TwinsUK/COVID Symptom Study (CSS) Biobank) in December 2021. Using an individual-based, probabilistic model of COVID-19 transmission between social contacts with SARS-CoV-2 Omicron variant parameters and realistic vaccine coverage in England, we predicted the potential impact of the SARS-CoV-2 Omicron wave in England in terms of the effective reproduction number and cumulative infections, hospital admissions and deaths. Using survey results, we estimated in real-time the impact of voluntary risk mitigation behaviours on the Omicron wave in England, if implemented for the entire epidemic wave. RESULTS Over 95% of survey respondents (NALSPAC = 2686 and NTwins = 6155) reported some risk mitigation behaviours, with vaccination and using home testing kits reported most frequently. Less than half of those respondents reported that their behaviour was due to "plan B". We estimate that without risk mitigation behaviours, the Omicron variant is consistent with an effective reproduction number between 2.5 and 3.5. Due to the reduced vaccine effectiveness against infection with the Omicron variant, our modelled estimates suggest that between 55% and 60% of the English population could be infected during the current wave, translating into between 12,000 and 46,000 cumulative deaths, depending on assumptions about severity and vaccine effectiveness. The actual number of deaths was 15,208 (26 November 2021-1 March 2022). We estimate that voluntary risk reduction measures could reduce the effective reproduction number to between 1.8 and 2.2 and reduce the cumulative number of deaths by up to 24%. CONCLUSIONS Predicting future infection burden is affected by uncertainty in disease severity and vaccine effectiveness estimates. In addition to biological uncertainty, we show that voluntary measures substantially reduce the projected impact of the SARS-CoV-2 Omicron variant but that voluntary measures alone would be unlikely to completely control transmission.
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Affiliation(s)
- Ellen Brooks-Pollock
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK.
| | - Kate Northstone
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
| | - Lorenzo Pellis
- Department of Mathematics, University of Manchester, Manchester, UK
- School of Biological Sciences, University of Bristol, Bristol, UK
| | | | - Amy Thomas
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
| | - Emily Nixon
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
- The Alan Turing Institute, London, UK
| | - David A Matthews
- School of Cellular and Molecular Medicine, University of Bristol, Bristol, UK
| | - Vicky Bowyer
- Department of Twin Research & Genetic Epidemiology, King's College London, London, UK
| | - Maria Paz Garcia
- Department of Twin Research & Genetic Epidemiology, King's College London, London, UK
| | - Claire J Steves
- Department of Twin Research & Genetic Epidemiology, King's College London, London, UK
| | - Nicholas J Timpson
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
- MRC Integrative Epidemiology Unit at University of Bristol, Bristol, UK
| | - Leon Danon
- Department of Engineering Mathematics, University of Bristol, Bristol, UK
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5
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Nixon EJ, Brooks-Pollock E, Wall R. Assessing the effectiveness of prophylactic treatment strategies for sheep scab. Vet Parasitol 2022; 312:109822. [DOI: 10.1016/j.vetpar.2022.109822] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2022] [Revised: 10/14/2022] [Accepted: 10/17/2022] [Indexed: 11/29/2022]
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6
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Nixon E, Silvonen T, Barreaux A, Kwiatkowska R, Trickey A, Thomas A, Ali B, Treneman-Evans G, Christensen H, Brooks-Pollock E, Denford S. A mixed methods analysis of participation in a social contact survey. Epidemics 2022; 41:100635. [PMID: 36182804 PMCID: PMC7615368 DOI: 10.1016/j.epidem.2022.100635] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2022] [Revised: 07/28/2022] [Accepted: 09/21/2022] [Indexed: 12/29/2022] Open
Abstract
BACKGROUND Social contact survey data forms a core component of modern epidemic models: however, there has been little assessment of the potential biases in such data. METHODS We conducted focus groups with university students who had (n = 13) and had never (n = 14) completed a social contact survey during the COVID-19 pandemic. Qualitative findings were explored quantitatively by analysing participation data. RESULTS The opportunity to contribute to COVID-19 research, to be heard and feel useful were frequently reported motivators for participating in the contact survey. Reductions in survey engagement following lifting of COVID-19 restrictions may have occurred because the research was perceived to be less critical and/or because the participants were busier and had more contacts. Having a high number of contacts to report, uncertainty around how to report each contact, and concerns around confidentiality were identified as factors leading to inaccurate reporting. Focus groups participants thought that financial incentives or provision of study results would encourage participation. CONCLUSIONS Incentives could improve engagement with social contact surveys. Qualitative research can inform the format, timing, and wording of surveys to optimise completion and accuracy.
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Affiliation(s)
- Emily Nixon
- School of Biological Sciences, University of Bristol, Bristol, UK; School of Population Health Sciences, University of Bristol, Bristol, UK; Department of Mathematical Sciences, University of Liverpool, Liverpool, UK.
| | - Taru Silvonen
- School of Population Health Sciences, University of Bristol, Bristol, UK; NIHR Health Protection Research Unit in Behavioural Science and Evaluation, University of Bristol, Bristol, UK
| | - Antoine Barreaux
- Bristol Veterinary School, University of Bristol, Bristol, UK; INTERTRYP (Univ. Montpellier, CIRAD, IRD), Montpellier, France
| | - Rachel Kwiatkowska
- School of Population Health Sciences, University of Bristol, Bristol, UK; NIHR Health Protection Research Unit in Behavioural Science and Evaluation, University of Bristol, Bristol, UK
| | - Adam Trickey
- School of Population Health Sciences, University of Bristol, Bristol, UK
| | - Amy Thomas
- School of Population Health Sciences, University of Bristol, Bristol, UK
| | - Becky Ali
- School of Population Health Sciences, University of Bristol, Bristol, UK; NIHR Health Protection Research Unit in Behavioural Science and Evaluation, University of Bristol, Bristol, UK
| | - Georgia Treneman-Evans
- School of Population Health Sciences, University of Bristol, Bristol, UK; NIHR Health Protection Research Unit in Behavioural Science and Evaluation, University of Bristol, Bristol, UK
| | - Hannah Christensen
- School of Population Health Sciences, University of Bristol, Bristol, UK; NIHR Health Protection Research Unit in Behavioural Science and Evaluation, University of Bristol, Bristol, UK
| | - Ellen Brooks-Pollock
- School of Population Health Sciences, University of Bristol, Bristol, UK; NIHR Health Protection Research Unit in Behavioural Science and Evaluation, University of Bristol, Bristol, UK
| | - Sarah Denford
- School of Population Health Sciences, University of Bristol, Bristol, UK; NIHR Health Protection Research Unit in Behavioural Science and Evaluation, University of Bristol, Bristol, UK
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7
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Challen R, Brooks-Pollock E, Tsaneva-Atanasova K, Danon L. Meta-analysis of the severe acute respiratory syndrome coronavirus 2 serial intervals and the impact of parameter uncertainty on the coronavirus disease 2019 reproduction number. Stat Methods Med Res 2022; 31:1686-1703. [PMID: 34931917 PMCID: PMC9465543 DOI: 10.1177/09622802211065159] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
The serial interval of an infectious disease, commonly interpreted as the time between the onset of symptoms in sequentially infected individuals within a chain of transmission, is a key epidemiological quantity involved in estimating the reproduction number. The serial interval is closely related to other key quantities, including the incubation period, the generation interval (the time between sequential infections), and time delays between infection and the observations associated with monitoring an outbreak such as confirmed cases, hospital admissions, and deaths. Estimates of these quantities are often based on small data sets from early contact tracing and are subject to considerable uncertainty, which is especially true for early coronavirus disease 2019 data. In this paper, we estimate these key quantities in the context of coronavirus disease 2019 for the UK, including a meta-analysis of early estimates of the serial interval. We estimate distributions for the serial interval with a mean of 5.9 (95% CI 5.2; 6.7) and SD 4.1 (95% CI 3.8; 4.7) days (empirical distribution), the generation interval with a mean of 4.9 (95% CI 4.2; 5.5) and SD 2.0 (95% CI 0.5; 3.2) days (fitted gamma distribution), and the incubation period with a mean 5.2 (95% CI 4.9; 5.5) and SD 5.5 (95% CI 5.1; 5.9) days (fitted log-normal distribution). We quantify the impact of the uncertainty surrounding the serial interval, generation interval, incubation period, and time delays, on the subsequent estimation of the reproduction number, when pragmatic and more formal approaches are taken. These estimates place empirical bounds on the estimates of most relevant model parameters and are expected to contribute to modeling coronavirus disease 2019 transmission.
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Affiliation(s)
- Robert Challen
- EPSRC Centre for Predictive Modelling in Healthcare, 3286University of Exeter, UK
- 7852Somerset NHS Foundation Trust, UK
- Joint Universities Pandemic and Epidemiological Research (JUNIPER) consortium, UK
| | - Ellen Brooks-Pollock
- Joint Universities Pandemic and Epidemiological Research (JUNIPER) consortium, UK
- 152331Bristol Medical School, Population Health Sciences, 1980University of Bristol, UK
| | - Krasimira Tsaneva-Atanasova
- EPSRC Centre for Predictive Modelling in Healthcare, 3286University of Exeter, UK
- 522468The Alan Turing Institute, British Library, UK
- Data Science Institute, 151756College of Engineering, Mathematics and Physical Sciences, 3286University of Exeter, UK
| | - Leon Danon
- 152331Bristol Medical School, Population Health Sciences, 1980University of Bristol, UK
- 522468The Alan Turing Institute, British Library, UK
- Data Science Institute, 151756College of Engineering, Mathematics and Physical Sciences, 3286University of Exeter, UK
- Department of Engineering Mathematics, 1980University of Bristol, UK
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8
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Vegvari C, Abbott S, Ball F, Brooks-Pollock E, Challen R, Collyer BS, Dangerfield C, Gog JR, Gostic KM, Heffernan JM, Hollingsworth TD, Isham V, Kenah E, Mollison D, Panovska-Griffiths J, Pellis L, Roberts MG, Scalia Tomba G, Thompson RN, Trapman P. Commentary on the use of the reproduction number R during the COVID-19 pandemic. Stat Methods Med Res 2022; 31:1675-1685. [PMID: 34569883 PMCID: PMC9277711 DOI: 10.1177/09622802211037079] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Since the beginning of the COVID-19 pandemic, the reproduction number [Formula: see text] has become a popular epidemiological metric used to communicate the state of the epidemic. At its most basic, [Formula: see text] is defined as the average number of secondary infections caused by one primary infected individual. [Formula: see text] seems convenient, because the epidemic is expanding if [Formula: see text] and contracting if [Formula: see text]. The magnitude of [Formula: see text] indicates by how much transmission needs to be reduced to control the epidemic. Using [Formula: see text] in a naïve way can cause new problems. The reasons for this are threefold: (1) There is not just one definition of [Formula: see text] but many, and the precise definition of [Formula: see text] affects both its estimated value and how it should be interpreted. (2) Even with a particular clearly defined [Formula: see text], there may be different statistical methods used to estimate its value, and the choice of method will affect the estimate. (3) The availability and type of data used to estimate [Formula: see text] vary, and it is not always clear what data should be included in the estimation. In this review, we discuss when [Formula: see text] is useful, when it may be of use but needs to be interpreted with care, and when it may be an inappropriate indicator of the progress of the epidemic. We also argue that careful definition of [Formula: see text], and the data and methods used to estimate it, can make [Formula: see text] a more useful metric for future management of the epidemic.
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Affiliation(s)
- Carolin Vegvari
- Medical Research Council Centre for Global Infectious Disease Analysis, Department of Infectious Disease Epidemiology, School of Public Health, 4615Imperial College London, London, UK
| | - Sam Abbott
- Center for the Mathematical Modelling of Infectious Diseases, 4906London School of Hygiene & Tropical Medicine, UK
| | - Frank Ball
- School of Mathematical Sciences, 6123University of Nottingham, UK
| | - Ellen Brooks-Pollock
- Bristol Veterinary School, 1980University of Bristol, UK.,NIHR Health Protection Research Unit in Behavioural Science and Evaluation at the University of Bristol, UK
| | - Robert Challen
- EPSRC Centre for Predictive Modelling in Healthcare, 3286University of Exeter, UK.,Somerset NHS Foundation Trust, UK
| | - Benjamin S Collyer
- Medical Research Council Centre for Global Infectious Disease Analysis, Department of Infectious Disease Epidemiology, School of Public Health, 4615Imperial College London, London, UK
| | | | - Julia R Gog
- Department of Applied Mathematics and Theoretical Physics, University of Cambridge, UK
| | - Katelyn M Gostic
- Department of Ecology and Evolution, 2462University of Chicago, USA
| | - Jane M Heffernan
- Centre for Disease Modelling, Mathematics & Statistics, 7991York University, Canada.,COVID Modelling Task-Force, The Fields Institute, Canada
| | - T Déirdre Hollingsworth
- Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, 6396University of Oxford, UK
| | - Valerie Isham
- Department of Statistical Science, 4919University College London, UK
| | - Eben Kenah
- Division of Biostatistics, College of Public Health, 2647The Ohio State University, USA
| | - Denis Mollison
- Department of Actuarial Mathematics and Statistics, Heriot-Watt University, UK
| | - Jasmina Panovska-Griffiths
- The Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, University of Oxford, Oxford, UK.,Wolfson Centre for Mathematical Biology, Mathematical Institute and The Queen's College, University of Oxford, Oxford, UK
| | - Lorenzo Pellis
- Department of Mathematics, 5292The University of Manchester, UK.,The Alan Turing Institute, UK
| | - Michael G Roberts
- School of Natural and Computational Sciences and New Zealand Institute for Advanced Study, Massey University, New Zealand
| | | | - Robin N Thompson
- Mathematics Institute, 2707University of Warwick, Coventry, UK.,Zeeman Institute for Systems Biology and Infectious Disease Epidemiology Research, 2707University of Warwick, Coventry, UK
| | - Pieter Trapman
- Department of Mathematics, 7675Stockholm University, Sweden
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9
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Woodhouse MJ, Aspinall WP, Sparks RSJ, Brooks-Pollock E, Relton C. Alternative COVID-19 mitigation measures in school classrooms: analysis using an agent-based model of SARS-CoV-2 transmission. R Soc Open Sci 2022; 9:211985. [PMID: 35958084 PMCID: PMC9363991 DOI: 10.1098/rsos.211985] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/25/2022] [Accepted: 07/20/2022] [Indexed: 06/15/2023]
Abstract
The SARS-CoV-2 epidemic has impacted children's education, with schools required to implement infection control measures that have led to periods of absence and classroom closures. We developed an agent-based epidemiological model of SARS-CoV-2 transmission in a school classroom that allows us to quantify projected infection patterns within primary school classrooms, and related uncertainties. Our approach is based on a contact model constructed using random networks, informed by structured expert judgement. The effectiveness of mitigation strategies in suppressing infection outbreaks and limiting pupil absence are considered. COVID-19 infections in primary schools in England in autumn 2020 were re-examined and the model was then used to estimate infection levels in autumn 2021, as the Delta variant was emerging and it was thought likely that school transmission would play a major role in an incipient new wave of the epidemic. Our results were in good agreement with available data. These findings indicate that testing-based surveillance is more effective than bubble quarantine, both for reducing transmission and avoiding pupil absence, even accounting for insensitivity of self-administered tests. Bubble quarantine entails large numbers of absences, with only modest impact on classroom infections. However, maintaining reduced contact rates within the classroom can have a major benefit for managing COVID-19 in school settings.
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Affiliation(s)
- M. J. Woodhouse
- School of Earth Sciences, University of Bristol, Wills Memorial Building, Queens Road, Bristol BS8 1RJ, UK
| | - W. P. Aspinall
- School of Earth Sciences, University of Bristol, Wills Memorial Building, Queens Road, Bristol BS8 1RJ, UK
- Aspinall and Associates, Tisbury SP3 6HF, UK
| | - R. S. J. Sparks
- School of Earth Sciences, University of Bristol, Wills Memorial Building, Queens Road, Bristol BS8 1RJ, UK
| | - E. Brooks-Pollock
- Bristol Veterinary School, University of Bristol, Churchill Building, Langford, Bristol BS40 5DU, UK
| | - C. Relton
- Bristol Medical School (PHS), University of Bristol, Oakfield House, Oakfield Grove, Clifton, Bristol BS8 2BN, UK
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10
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French CE, Denford S, Brooks-Pollock E, Wehling H, Hickman M. Low uptake of COVID-19 lateral flow testing among university students: a mixed methods evaluation. Public Health 2022; 204:54-62. [PMID: 35176622 PMCID: PMC8755476 DOI: 10.1016/j.puhe.2022.01.002] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2021] [Revised: 12/21/2021] [Accepted: 01/04/2022] [Indexed: 11/15/2022]
Abstract
OBJECTIVE This study aimed to evaluate COVID-19 lateral flow testing (LFT) among asymptomatic university students. STUDY DESIGN This study was a mixed methods evaluation of LFT among University of Bristol students. METHODS We conducted (1) an analysis of testing uptake and exploration of demographic variations in uptake using logistic regression; (2) an online student survey about views on university testing; and (3) qualitative interviews to explore participants' experiences of testing and subsequent behaviour, analysed using a thematic approach. RESULTS A total of 12,391 LFTs were conducted on 8025 of 36,054 (22.3%) students. Only one in 10 students had the recommended two tests. There were striking demographic disparities in uptake with those from ethnic minority groups having lower uptake (e.g. 3% of Chinese students were tested vs 30.7% of White students) and variations by level and year of study (ranging from 5.3% to 33.7%), place of residence (29.0%-35.6%) and faculty (15.2%-32.8%). Differences persisted in multivariable analyses. A total of 436 students completed the online survey, and 20 in-depth interviews were conducted. Barriers to engagement with testing included a lack of awareness, knowledge and understanding, and concerns about the accuracy and safety. Students understood the limitations of LFTs but requested further information about test accuracy. Tests were used to inform behavioural decisions, often in combination with other information, such as the potential for exposure to the virus and perceptions of vulnerability. CONCLUSIONS The low uptake of testing brings into question the role of mass LFT in university settings. Innovative strategies may be needed to increase LFT uptake among students.
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Affiliation(s)
- C E French
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol BS8 1UD, UK; NIHR Health Protection Research Unit in Behavioural Science and Evaluation, University of Bristol, Bristol, UK
| | - S Denford
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol BS8 1UD, UK; NIHR Health Protection Research Unit in Behavioural Science and Evaluation, University of Bristol, Bristol, UK; School of Psychological Science, University of Bristol, Bristol BS8 1TU, UK.
| | - E Brooks-Pollock
- NIHR Health Protection Research Unit in Behavioural Science and Evaluation, University of Bristol, Bristol, UK; Bristol Veterinary School, University of Bristol, Langford BS40 5DU, UK
| | - H Wehling
- NIHR Health Protection Research Unit in Behavioural Science and Evaluation, University of Bristol, Bristol, UK; Behavioural Science & Insights Unit, UK Health Security Agency, Porton Down, Salisbury SP4 0JG, UK
| | - M Hickman
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol BS8 1UD, UK; NIHR Health Protection Research Unit in Behavioural Science and Evaluation, University of Bristol, Bristol, UK
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11
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Abbott S, Christensen H, Brooks-Pollock E. Reassessing the evidence for universal school-age BCG vaccination in England and Wales: re-evaluating and updating a modelling study. BMJ Open 2022; 12:e031573. [PMID: 35017227 PMCID: PMC8753396 DOI: 10.1136/bmjopen-2019-031573] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
OBJECTIVES In 2005, England and Wales switched from universal BCG vaccination against tuberculosis (TB) disease for school-age children to targeted vaccination of neonates. We aimed to recreate and re-evaluate a previously published model, the results of which informed this policy change. DESIGN We recreated an approach for estimating the impact of ending the BCG schools scheme, correcting a methodological flaw in the model, updating the model with parameter uncertainty and improving parameter estimates where possible. We investigated scenarios for the assumed annual decrease in TB incidence rates considered by the UK's Joint Committee on Vaccination and Immunisation and explored alternative scenarios using notification data. SETTING England and Wales. OUTCOME MEASURES The number of vaccines needed to prevent a single notification and the average annual additional notifications caused by ending the policy change. RESULTS The previously published model was found to contain a methodological flaw and to be spuriously precise. It greatly underestimated the impact of ending school-age vaccination compared with our updated, corrected model. The updated model produced predictions with wide CIs when parameter uncertainty was included. Model estimates based on an assumption of an annual decrease in TB incidence rates of 1.9% were closest to those estimated using notification data. Using this assumption, we estimate that 1600 (2.5; 97.5% quantiles: 1300, 2000) vaccines would have been required to prevent a single notification in 2004. CONCLUSIONS The impact of ending the BCG schools scheme was found to be greater than previously thought when notification data were used. Our results highlight the importance of independent evaluations of modelling evidence, including uncertainty, and evaluating multiple scenarios when forecasting the impact of changes in vaccination policy.
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Affiliation(s)
- Sam Abbott
- Bristol Medical School, Population Health Sciences, University of Bristol, Bristol, UK
- Centre for the Mathematical Modelling of Infectious Diseases, London School of Hygiene & Tropical Medicine, London, UK
| | - Hannah Christensen
- Bristol Medical School, Population Health Sciences, University of Bristol, Bristol, UK
| | - Ellen Brooks-Pollock
- Bristol Medical School, Population Health Sciences, University of Bristol, Bristol, UK
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12
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Brooks-Pollock E, Christensen H, Trickey A, Hemani G, Nixon E, Thomas AC, Turner K, Finn A, Hickman M, Relton C, Danon L. High COVID-19 transmission potential associated with re-opening universities can be mitigated with layered interventions. Nat Commun 2021; 12:5017. [PMID: 34404780 PMCID: PMC8371131 DOI: 10.1038/s41467-021-25169-3] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2020] [Accepted: 07/21/2021] [Indexed: 12/17/2022] Open
Abstract
Controlling COVID-19 transmission in universities poses challenges due to the complex social networks and potential for asymptomatic spread. We developed a stochastic transmission model based on realistic mixing patterns and evaluated alternative mitigation strategies. We predict, for plausible model parameters, that if asymptomatic cases are half as infectious as symptomatic cases, then 15% (98% Prediction Interval: 6-35%) of students could be infected during the first term without additional control measures. First year students are the main drivers of transmission with the highest infection rates, largely due to communal residences. In isolation, reducing face-to-face teaching is the most effective intervention considered, however layering multiple interventions could reduce infection rates by 75%. Fortnightly or more frequent mass testing is required to impact transmission and was not the most effective option considered. Our findings suggest that additional outbreak control measures should be considered for university settings.
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Affiliation(s)
- Ellen Brooks-Pollock
- Bristol Veterinary School, University of Bristol, Langford, Bristol, UK.
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK.
| | - Hannah Christensen
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
| | - Adam Trickey
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
| | - Gibran Hemani
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
| | - Emily Nixon
- School of Biological Sciences, University of Bristol, Bristol, Bristol, UK
| | - Amy C Thomas
- Bristol Veterinary School, University of Bristol, Langford, Bristol, UK
| | - Katy Turner
- Bristol Veterinary School, University of Bristol, Langford, Bristol, UK
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
| | - Adam Finn
- Bristol Children's Vaccine Centre, University of Bristol, Bristol, Bristol, UK
| | - Matt Hickman
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
| | - Caroline Relton
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
| | - Leon Danon
- Department of Engineering Mathematics, University of Bristol, Bristol, Bristol, UK
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13
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Enright J, Hill EM, Stage HB, Bolton KJ, Nixon EJ, Fairbanks EL, Tang ML, Brooks-Pollock E, Dyson L, Budd CJ, Hoyle RB, Schewe L, Gog JR, Tildesley MJ. SARS-CoV-2 infection in UK university students: lessons from September-December 2020 and modelling insights for future student return. R Soc Open Sci 2021; 8:210310. [PMID: 34386249 PMCID: PMC8334840 DOI: 10.1098/rsos.210310] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/23/2021] [Accepted: 07/16/2021] [Indexed: 06/06/2023]
Abstract
In this paper, we present work on SARS-CoV-2 transmission in UK higher education settings using multiple approaches to assess the extent of university outbreaks, how much those outbreaks may have led to spillover in the community, and the expected effects of control measures. Firstly, we found that the distribution of outbreaks in universities in late 2020 was consistent with the expected importation of infection from arriving students. Considering outbreaks at one university, larger halls of residence posed higher risks for transmission. The dynamics of transmission from university outbreaks to wider communities is complex, and while sometimes spillover does occur, occasionally even large outbreaks do not give any detectable signal of spillover to the local population. Secondly, we explored proposed control measures for reopening and keeping open universities. We found the proposal of staggering the return of students to university residence is of limited value in terms of reducing transmission. We show that student adherence to testing and self-isolation is likely to be much more important for reducing transmission during term time. Finally, we explored strategies for testing students in the context of a more transmissible variant and found that frequent testing would be necessary to prevent a major outbreak.
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Affiliation(s)
- Jessica Enright
- School of Computing Science, University of Glasgow, Glasgow G12 8QQ, UK
| | - Edward M. Hill
- The Zeeman Institute for Systems Biology and Infectious Disease Epidemiology Research, School of Life Sciences and Mathematics Institute, University of Warwick, Coventry CV4 7AL, UK
- Joint UNIversities Pandemic and Epidemiological Research, UK https://maths.org/juniper/
| | - Helena B. Stage
- Joint UNIversities Pandemic and Epidemiological Research, UK https://maths.org/juniper/
- Department of Mathematics, The University of Manchester, Oxford Road, Manchester, UK
| | - Kirsty J. Bolton
- Centre for Mathematical Medicine and Biology, School of Mathematical Sciences, University of Nottingham, University Park, Nottingham, UK
| | - Emily J. Nixon
- Joint UNIversities Pandemic and Epidemiological Research, UK https://maths.org/juniper/
- Veterinary Public Health, Bristol Veterinary School, University of Bristol, Bristol, UK
| | - Emma L. Fairbanks
- Centre for Mathematical Medicine and Biology, School of Mathematical Sciences, University of Nottingham, University Park, Nottingham, UK
- School of Veterinary Medicine and Science, University of Nottingham, Loughborough, UK
| | - Maria L. Tang
- School of Veterinary Medicine and Science, University of Nottingham, Loughborough, UK
- Department of Applied Mathematics and Theoretical Physics, University of Cambridge, Cambridge, UK
| | - Ellen Brooks-Pollock
- Joint UNIversities Pandemic and Epidemiological Research, UK https://maths.org/juniper/
- Bristol Medical School, Population Health Sciences, University of Bristol, Bristol, UK
| | - Louise Dyson
- The Zeeman Institute for Systems Biology and Infectious Disease Epidemiology Research, School of Life Sciences and Mathematics Institute, University of Warwick, Coventry CV4 7AL, UK
- Joint UNIversities Pandemic and Epidemiological Research, UK https://maths.org/juniper/
| | - Chris J. Budd
- School of Mathematical Sciences, University of Bath, Claverton Down, Bath, UK
| | - Rebecca B. Hoyle
- School of Mathematical Sciences, University of Southampton, Southampton, UK
| | - Lars Schewe
- University of Edinburgh, School of Mathematics, James Clerk Maxwell Building, Peter Guthrie Tait Road, Edinburgh, UK
| | - Julia R. Gog
- Joint UNIversities Pandemic and Epidemiological Research, UK https://maths.org/juniper/
- Department of Applied Mathematics and Theoretical Physics, University of Cambridge, Cambridge, UK
| | - Michael J. Tildesley
- The Zeeman Institute for Systems Biology and Infectious Disease Epidemiology Research, School of Life Sciences and Mathematics Institute, University of Warwick, Coventry CV4 7AL, UK
- Joint UNIversities Pandemic and Epidemiological Research, UK https://maths.org/juniper/
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14
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Brooks-Pollock E, Read JM, House T, Medley GF, Keeling MJ, Danon L. The population attributable fraction of cases due to gatherings and groups with relevance to COVID-19 mitigation strategies. Philos Trans R Soc Lond B Biol Sci 2021; 376:20200273. [PMID: 34053263 PMCID: PMC8165584 DOI: 10.1098/rstb.2020.0273] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/17/2021] [Indexed: 02/06/2023] Open
Abstract
Many countries have banned groups and gatherings as part of their response to the pandemic caused by the coronavirus, SARS-CoV-2. Although there are outbreak reports involving mass gatherings, the contribution to overall transmission is unknown. We used data from a survey of social contact behaviour that specifically asked about contact with groups to estimate the population attributable fraction (PAF) due to groups as the relative change in the basic reproduction number when groups are prevented. Groups of 50+ individuals accounted for 0.5% of reported contact events, and we estimate that the PAF due to groups of 50+ people is 5.4% (95% confidence interval 1.4%, 11.5%). The PAF due to groups of 20+ people is 18.9% (12.7%, 25.7%) and the PAF due to groups of 10+ is 25.2% (19.4%, 31.4%). Under normal circumstances with pre-COVID-19 contact patterns, large groups of individuals have a relatively small epidemiological impact; small- and medium-sized groups between 10 and 50 people have a larger impact on an epidemic. This article is part of the theme issue 'Modelling that shaped the early COVID-19 pandemic response in the UK'.
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Affiliation(s)
- Ellen Brooks-Pollock
- Bristol Veterinary School, University of Bristol, Bristol BS40 5DU, UK
- Population Health Sciences, Bristol Medical School, Bristol, BS8 2BN, UK
| | - Jonathan M. Read
- Lancaster Medical School, Lancaster University, Lancaster LA1 4YW, UK
| | - Thomas House
- Department of Mathematics, University of Manchester, Manchester M13 9PL, UK
| | - Graham F. Medley
- Centre for Mathematical Modelling of Infectious Disease, London School of Hygiene and Tropical Medicine, London WC1H 9SH, UK
| | - Matt J. Keeling
- Mathematics Institute and Department of Life Sciences, University of Warwick, Coventry CV4 7AL, UK
| | - Leon Danon
- Department of Engineering Mathematics, University of Bristol, Bristol BS8 1UB, UK
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15
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Brooks-Pollock E, Read JM, McLean AR, Keeling MJ, Danon L. Mapping social distancing measures to the reproduction number for COVID-19. Philos Trans R Soc Lond B Biol Sci 2021; 376:20200276. [PMID: 34053268 PMCID: PMC8165600 DOI: 10.1098/rstb.2020.0276] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/02/2020] [Indexed: 12/29/2022] Open
Abstract
In the absence of a vaccine, severe acute respiratory syndrome-coronavirus 2 (SARS-CoV-2) transmission has been controlled by preventing person-to-person interactions via social distancing measures. In order to re-open parts of society, policy-makers need to consider how combinations of measures will affect transmission and understand the trade-offs between them. We use age-specific social contact data, together with epidemiological data, to quantify the components of the COVID-19 reproduction number. We estimate the impact of social distancing policies on the reproduction number by turning contacts on and off based on context and age. We focus on the impact of re-opening schools against a background of wider social distancing measures. We demonstrate that pre-collected social contact data can be used to provide a time-varying estimate of the reproduction number (R). We find that following lockdown (when R= 0.7, 95% CI 0.6, 0.8), opening primary schools has a modest impact on transmission (R = 0.89, 95% CI 0.82-0.97) as long as other social interactions are not increased. Opening secondary and primary schools is predicted to have a larger impact (R = 1.22, 95% CI 1.02-1.53). Contact tracing and COVID security can be used to mitigate the impact of increased social mixing to some extent; however, social distancing measures are still required to control transmission. Our approach has been widely used by policy-makers to project the impact of social distancing measures and assess the trade-offs between them. Effective social distancing, contact tracing and COVID security are required if all age groups are to return to school while controlling transmission. This article is part of the theme issue 'Modelling that shaped the early COVID-19 pandemic response in the UK'.
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Affiliation(s)
- Ellen Brooks-Pollock
- Bristol Veterinary School, University of Bristol, Bristol BS40 5DU, UK
- NIHR Health Protection Research Unit in Behavioural Science and Evaluation, Population Health Sciences, Bristol Medical School, University of Bristol, Bristol BS8 2BY, UK
| | - Jonathan M. Read
- Lancaster Medical School, Lancaster University, Lancaster LA1 4YW, UK
| | | | - Matt J. Keeling
- Mathematics Institute, University of Warwick, Warwick CV4 7AL, UK
- School of Life Sciences, University of Warwick, Warwick CV4 7AL, UK
| | - Leon Danon
- NIHR Health Protection Research Unit in Behavioural Science and Evaluation, Population Health Sciences, Bristol Medical School, University of Bristol, Bristol BS8 2BY, UK
- CEMPS, University of Exeter, Exeter, UK
- The Alan Turing Institute, British Library, 96 Euston Road, London NW1 2DB, UK
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16
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Challen R, Tsaneva-Atanasova K, Pitt M, Edwards T, Gompels L, Lacasa L, Brooks-Pollock E, Danon L. Estimates of regional infectivity of COVID-19 in the United Kingdom following imposition of social distancing measures. Philos Trans R Soc Lond B Biol Sci 2021; 376:20200280. [PMID: 34053251 PMCID: PMC8165582 DOI: 10.1098/rstb.2020.0280] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/02/2020] [Indexed: 01/10/2023] Open
Abstract
The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) reproduction number has become an essential parameter for monitoring disease transmission across settings and guiding interventions. The UK published weekly estimates of the reproduction number in the UK starting in May 2020 which are formed from multiple independent estimates. In this paper, we describe methods used to estimate the time-varying SARS-CoV-2 reproduction number for the UK. We used multiple data sources and estimated a serial interval distribution from published studies. We describe regional variability and how estimates evolved during the early phases of the outbreak, until the relaxing of social distancing measures began to be introduced in early July. Our analysis is able to guide localized control and provides a longitudinal example of applying these methods over long timescales. This article is part of the theme issue 'Modelling that shaped the early COVID-19 pandemic response in the UK'.
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Affiliation(s)
- Robert Challen
- EPSRC Centre for Predictive Modelling in Healthcare, University of Exeter, Exeter EX4 4SB, UK
- Taunton and Somerset NHS Foundation Trust, Musgrove Park Hospital, Taunton TA1 5DA, UK
| | - Krasimira Tsaneva-Atanasova
- EPSRC Centre for Predictive Modelling in Healthcare, University of Exeter, Exeter EX4 4SB, UK
- The Alan Turing Institute, British Library, 96 Euston Road, London NW1 2DB, UK
| | - Martin Pitt
- NIHR CLAHRC for the South West Peninsula, University of Exeter Medical School, St Luke's Campus, Exeter, UK
| | - Tom Edwards
- Taunton and Somerset NHS Foundation Trust, Musgrove Park Hospital, Taunton TA1 5DA, UK
| | - Luke Gompels
- Taunton and Somerset NHS Foundation Trust, Musgrove Park Hospital, Taunton TA1 5DA, UK
| | - Lucas Lacasa
- School of Mathematical Sciences, Queen Mary University of London, London E1 4NS, UK
| | - Ellen Brooks-Pollock
- Bristol Medical School, Population Health Sciences, University of Bristol, Bristol, UK
| | - Leon Danon
- Data Science Institute, College of Engineering, Mathematics and Physical Sciences, University of Exeter, Exeter EX4 4SB, UK
- The Alan Turing Institute, British Library, 96 Euston Road, London NW1 2DB, UK
- Bristol Medical School, Population Health Sciences, University of Bristol, Bristol, UK
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17
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Abstract
Infectious disease modelling has played an integral part of the scientific evidence used to guide the response to the COVID-19 pandemic. In the UK, modelling evidence used for policy is reported to the Scientific Advisory Group for Emergencies (SAGE) modelling subgroup, SPI-M-O (Scientific Pandemic Influenza Group on Modelling-Operational). This Special Issue contains 20 articles detailing evidence that underpinned advice to the UK government during the SARS-CoV-2 pandemic in the UK between January 2020 and July 2020. Here, we introduce the UK scientific advisory system and how it operates in practice, and discuss how infectious disease modelling can be useful in policy making. We examine the drawbacks of current publishing practices and academic credit and highlight the importance of transparency and reproducibility during an epidemic emergency. This article is part of the theme issue 'Modelling that shaped the early COVID-19 pandemic response in the UK'.
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Affiliation(s)
- Ellen Brooks-Pollock
- Bristol Veterinary School, University of Bristol, Bristol BS40 5DU, UK.,NIHR Health Protection Research Unit (HPRU) in Behavioural Science and Evaluation, Population Health Sciences, Bristol Medical School, University of Bristol, Bristol BS8 2BN, UK
| | - Leon Danon
- Department of Engineering Mathematics, University of Bristol, Bristol BS8 1TW, UK
| | - Thibaut Jombart
- Centre for Mathematical Modelling of Infectious Diseases, Department of Infectious Disease Epidemiology, London School of Hygiene and Tropical Medicine, London WC1E 7HT, UK.,MRC Centre for Global Infectious Disease Analysis, Department of Infectious Disease Epidemiology, School of Public Health, Imperial College London, UK
| | - Lorenzo Pellis
- Department of Mathematics, University of Manchester, Manchester M13 9PL, UK.,The Alan Turing Institute, London, UK
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18
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Abstract
In the era of social distancing to curb the spread of COVID-19, bubbling is the combining of two or more households to create an exclusive larger group. The impact of bubbling on COVID-19 transmission is challenging to quantify because of the complex social structures involved. We developed a network description of households in the UK, using the configuration model to link households. We explored the impact of bubbling scenarios by joining together households of various sizes. For each bubbling scenario, we calculated the percolation threshold, that is, the number of connections per individual required for a giant component to form, numerically and theoretically. We related the percolation threshold to the household reproduction number. We find that bubbling scenarios in which single-person households join with another household have a minimal impact on network connectivity and transmission potential. Ubiquitous scenarios where all households form a bubble are likely to lead to an extensive transmission that is hard to control. The impact of plausible scenarios, with variable uptake and heterogeneous bubble sizes, can be mitigated with reduced numbers of contacts outside the household. Bubbling of households comes at an increased risk of transmission; however, under certain circumstances risks can be modest and could be balanced by other changes in behaviours. This article is part of the theme issue 'Modelling that shaped the early COVID-19 pandemic response in the UK'.
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Affiliation(s)
- Leon Danon
- Department of Engineering Mathematics, University of Bristol, University Walk, Bristol BS8 1TW, UK
| | - Lucas Lacasa
- School of Mathematical Sciences, Queen Mary University of London, Mile End Road, London E1 4NS, UK
| | - Ellen Brooks-Pollock
- University of Bristol School of Veterinary Sciences, Langford BS40 5DU, UK
- NIHR HPRU in Behaviour Change and Evaluation, Population Health Sciences, Bristol Medical School, University of Bristol, Bristol BS8 2BN, UK
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19
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Nixon EJ, Brooks-Pollock E, Wall R. Sheep scab spatial distribution: the roles of transmission pathways. Parasit Vectors 2021; 14:344. [PMID: 34187531 PMCID: PMC8243883 DOI: 10.1186/s13071-021-04850-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2021] [Accepted: 06/12/2021] [Indexed: 12/02/2022] Open
Abstract
BACKGROUND Ovine psoroptic mange (sheep scab) is a highly pathogenic contagious infection caused by the mite Psoroptes ovis. Following 21 years in which scab was eradicated in the UK, it was inadvertently reintroduced in 1972 and, despite the implementation of a range of control methods, its prevalence increased steadily thereafter. Recent reports of resistance to macrocyclic lactone treatments may further exacerbate control problems. A better understanding of the factors that facilitate its transmission are required to allow improved management of this disease. Transmission of infection occurs within and between contiguous sheep farms via infected sheep-to-sheep or sheep-environment contact and through long-distance movements of infected sheep, such as through markets. METHODS A stochastic metapopulation model was used to investigate the impact of different transmission routes on the spatial pattern of outbreaks. A range of model scenarios were considered following the initial infection of a cluster of highly connected contiguous farms. RESULTS Scab spreads between clusters of neighbouring contiguous farms after introduction but when long-distance movements are excluded, infection then self-limits spatially at boundaries where farm connectivity is low. Inclusion of long-distance movements is required to generate the national patterns of disease spread observed. CONCLUSIONS Preventing the movement of scab infested sheep through sales and markets is essential for any national management programme. If effective movement control can be implemented, regional control in geographic areas where farm densities are high would allow more focussed cost-effective scab management.
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Affiliation(s)
- Emily Joanne Nixon
- School of Biological Sciences, University of Bristol, Bristol, BS8 1TQ, UK.
| | - Ellen Brooks-Pollock
- Veterinary Public Health, Bristol Veterinary School, University of Bristol, Bristol, BS40 5EZ, UK
- NIHR Health Protection Research Unit in Behavioural Science and Evaluation, University of Bristol, Bristol, UK
| | - Richard Wall
- School of Biological Sciences, University of Bristol, Bristol, BS8 1TQ, UK
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20
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Christensen H, Reynolds R, Kwiatkowska R, Brooks-Pollock E, Dominey M, Finn A, Gjini A, Hickman M, Roderick M, Yates J. Influence of commissioned provider type and deprivation score on uptake of the childhood flu immunization. J Public Health (Oxf) 2021; 42:618-624. [PMID: 31188441 DOI: 10.1093/pubmed/fdz060] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2018] [Revised: 04/10/2019] [Indexed: 01/19/2023] Open
Abstract
BACKGROUND Since 2015/16 the UK seasonal influenza immunization programme has included children aged 5 and 6 years. In the South West of England school-based providers, GPs or community pharmacies were commissioned to deliver the vaccine depending on the locality. We aimed to assess variation in vaccine uptake in relation to the type of commissioned provider, and levels of socioeconomic deprivation. METHODS Data from the South West of England (2015-16 season) were analysed using multilevel logistic regression to assess variation in vaccine uptake by type of commissioned provider, allowing for clustering of children within delivery sites. RESULTS Overall uptake in 5 and 6 year olds was 34.3% (37 555/109 404). Vaccine uptake was highest when commissioned through school-based programmes 50.2% (9983/19 867) and lowest when commissioned through pharmacies, 23.1% (4269/18 479). Delivery through schools resulted in less variation by site and equal uptake across age groups, in contrast to GP and pharmacy delivery for which uptake was lower among 6 year olds. Vaccine uptake decreased with increasing levels of deprivation across all types of commissioned provider. CONCLUSION School-based programmes achieve the highest and most consistent rates of childhood influenza vaccination. Interventions are still needed to promote more equitable uptake of the childhood influenza vaccine.
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Affiliation(s)
- Hannah Christensen
- Population Health Sciences, Bristol Medical School, University of Bristol, Canynge Hall, 39 Whatley Road Bristol, UK
| | - Rosy Reynolds
- Population Health Sciences, Bristol Medical School, University of Bristol, Canynge Hall, 39 Whatley Road Bristol, UK.,NIHR Health Protection Research Unit in Evaluation of Interventions, University of Bristol, Oakfield House, Oakfield Grove, Bristol, UK
| | - Rachel Kwiatkowska
- Population Health Sciences, Bristol Medical School, University of Bristol, Canynge Hall, 39 Whatley Road Bristol, UK.,NIHR Health Protection Research Unit in Evaluation of Interventions, University of Bristol, Oakfield House, Oakfield Grove, Bristol, UK.,Field Services, National Infection Service, Public Health England South West, 2 Rivergate Bristol, UK
| | - Ellen Brooks-Pollock
- Population Health Sciences, Bristol Medical School, University of Bristol, Canynge Hall, 39 Whatley Road Bristol, UK.,Bristol Veterinary School, University of Bristol, Langford House, Langford, Bristol, UK
| | - Matthew Dominey
- Screening and Immunisation Team, Public Health England South West, 2 Rivergate Bristol, UK.,NHS England-South (South West), South Plaza, Marlborough Street, Bristol, UK
| | - Adam Finn
- Population Health Sciences, Bristol Medical School, University of Bristol, Canynge Hall, 39 Whatley Road Bristol, UK.,Department of Paediatric Immunology, Bristol Children's Hospital, Upper Maudlin St, Bristol, UK
| | - Ardiana Gjini
- Screening and Immunisation Team, Public Health England South West, 2 Rivergate Bristol, UK.,NHS England-South (South West), South Plaza, Marlborough Street, Bristol, UK
| | - Matthew Hickman
- Population Health Sciences, Bristol Medical School, University of Bristol, Canynge Hall, 39 Whatley Road Bristol, UK.,NIHR Health Protection Research Unit in Evaluation of Interventions, University of Bristol, Oakfield House, Oakfield Grove, Bristol, UK
| | - Marion Roderick
- NHS England-South (South West), South Plaza, Marlborough Street, Bristol, UK
| | - Julie Yates
- Bristol Veterinary School, University of Bristol, Langford House, Langford, Bristol, UK.,Screening and Immunisation Team, Public Health England South West, 2 Rivergate Bristol, UK
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21
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Nixon E, Trickey A, Christensen H, Finn A, Thomas A, Relton C, Montgomery C, Hemani G, Metz J, Walker JG, Turner K, Kwiatkowska R, Sauchelli S, Danon L, Brooks-Pollock E. Contacts and behaviours of university students during the COVID-19 pandemic at the start of the 2020/2021 academic year. Sci Rep 2021; 11:11728. [PMID: 34083593 PMCID: PMC8175593 DOI: 10.1038/s41598-021-91156-9] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2020] [Accepted: 05/21/2021] [Indexed: 11/08/2022] Open
Abstract
University students have unique living, learning and social arrangements which may have implications for infectious disease transmission. To address this data gap, we created CONQUEST (COroNavirus QUESTionnaire), a longitudinal online survey of contacts, behaviour, and COVID-19 symptoms for University of Bristol (UoB) staff/students. Here, we analyse results from 740 students providing 1261 unique records from the start of the 2020/2021 academic year (14/09/2020-01/11/2020), where COVID-19 outbreaks led to the self-isolation of all students in some halls of residences. Although most students reported lower daily contacts than in pre-COVID-19 studies, there was heterogeneity, with some reporting many (median = 2, mean = 6.1, standard deviation = 15.0; 8% had ≥ 20 contacts). Around 40% of students' contacts were with individuals external to the university, indicating potential for transmission to non-students/staff. Only 61% of those reporting cardinal symptoms in the past week self-isolated, although 99% with a positive COVID-19 test during the 2 weeks before survey completion had self-isolated within the last week. Some students who self-isolated had many contacts (mean = 4.3, standard deviation = 10.6). Our results provide context to the COVID-19 outbreaks seen in universities and are available for modelling future outbreaks and informing policy.
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Affiliation(s)
- Emily Nixon
- School of Biological Sciences, University of Bristol, Bristol Life Sciences Building, 24 Tyndall Avenue, Bristol, BS8 1TQ, UK.
- Bristol Veterinary School, University of Bristol, Bristol, UK.
| | - Adam Trickey
- Population Health Sciences, University of Bristol, Bristol, UK
| | - Hannah Christensen
- Population Health Sciences, University of Bristol, Bristol, UK
- NIHR Health Protection Research Unit in Behavioural Science and Evaluation, University of Bristol, Bristol, UK
| | - Adam Finn
- Population Health Sciences, University of Bristol, Bristol, UK
- NIHR Health Protection Research Unit in Behavioural Science and Evaluation, University of Bristol, Bristol, UK
- School of Cellular and Molecular Medicine, University of Bristol, Bristol, UK
| | - Amy Thomas
- Bristol Veterinary School, University of Bristol, Bristol, UK
| | - Caroline Relton
- Population Health Sciences, University of Bristol, Bristol, UK
| | - Clara Montgomery
- School of Biological Sciences, University of Bristol, Bristol Life Sciences Building, 24 Tyndall Avenue, Bristol, BS8 1TQ, UK
| | - Gibran Hemani
- Population Health Sciences, University of Bristol, Bristol, UK
| | - Jane Metz
- Bristol Children's Vaccine Centre, University of Bristol, Bristol, UK
| | | | - Katy Turner
- NIHR Health Protection Research Unit in Behavioural Science and Evaluation, University of Bristol, Bristol, UK
- Bristol Veterinary School, University of Bristol, Bristol, UK
| | | | - Sarah Sauchelli
- National Institute for Health Research Bristol Biomedical Research Centre, University Hospitals of Bristol, Weston NHS Foundation Trust, University of Bristol, Bristol, UK
| | - Leon Danon
- Department of Engineering Mathematics, University of Bristol, Bristol, UK, BS8 1TW
- Alan Turing Institute, British Library, London, UK
| | - Ellen Brooks-Pollock
- NIHR Health Protection Research Unit in Behavioural Science and Evaluation, University of Bristol, Bristol, UK
- Bristol Veterinary School, University of Bristol, Bristol, UK
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22
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Danon L, Brooks-Pollock E, Bailey M, Keeling M. A spatial model of COVID-19 transmission in England and Wales: early spread, peak timing and the impact of seasonality. Philos Trans R Soc Lond B Biol Sci 2021; 376:20200272. [PMID: 34053261 PMCID: PMC8165591 DOI: 10.1098/rstb.2020.0272] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
An outbreak of a novel coronavirus was first reported in China on 31 December 2019. As of 9 February 2020, cases have been reported in 25 countries, including probable human-to-human transmission in England. We adapted an existing national-scale metapopulation model to capture the spread of COVID-19 in England and Wales. We used 2011 census data to inform population sizes and movements, together with parameter estimates from the outbreak in China. We predict that the epidemic will peak 126 to 147 days (approx. 4 months) after the start of person-to-person transmission in the absence of controls. Assuming biological parameters remain unchanged and transmission persists from February, we expect the peak to occur in June. Starting location and model stochasticity have a minimal impact on peak timing. However, realistic parameter uncertainty leads to peak time estimates ranging from 78 to 241 days following sustained transmission. Seasonal changes in transmission rate can substantially impact the timing and size of the epidemic. We provide initial estimates of the epidemic potential of COVID-19. These results can be refined with more precise parameters. Seasonal changes in transmission could shift the timing of the peak into winter, with important implications for healthcare capacity planning. This article is part of the theme issue ‘Modelling that shaped the early COVID-19 pandemic response in the UK.
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Affiliation(s)
- Leon Danon
- Department of Engineering Mathematics, Population Health Sciences, University of Bristol, Bristol BS8 1QU, UK
| | - Ellen Brooks-Pollock
- Bristol Veterinary School, Population Health Sciences, University of Bristol, Bristol BS8 1QU, UK.,NIHR Health Protection Research Unit (HPRU) in Behavioural Science and Evaluation, Population Health Sciences, University of Bristol, Bristol BS8 1QU, UK
| | - Mick Bailey
- Bristol Veterinary School, Population Health Sciences, University of Bristol, Bristol BS8 1QU, UK
| | - Matt Keeling
- Mathematics Institute, and School of Life Sciences, University of Warwick, Coventry CV4 7AL, UK
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23
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Thomas A, Danon L, Christensen H, Northstone K, Smith D, Nixon E, Trickey A, Hemani G, Sauchelli S, Finn A, Timpson N, Brooks-Pollock E. Limits of lockdown: characterising essential contacts during strict physical distancing. Wellcome Open Res 2021. [DOI: 10.12688/wellcomeopenres.16785.1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Abstract
Background: Coronavirus disease 2019 (COVID-19) has exposed health inequalities within countries and globally. The fundamental determining factor behind an individual’s risk of infection is the number of social contacts they make. In many countries, physical distancing measures have been implemented to control transmission of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), reducing social contacts to a minimum. We characterise social contacts to understand the drivers and inequalities behind differential risks for aiding in planning SARS-CoV-2 mitigation programmes. Methods: We utilised an existing longitudinal birth cohort (n=6807) to explore social contact patterns and behaviours when strict physical distancing measures were in place during the UK’s first lockdown in March-May 2020. We used an online questionnaire to capture information on participant contact patterns, health, SARS-CoV-2 exposure, behaviours and impacts resulting from COVID-19. We quantified daily contacts and examined the association between covariates and numbers of daily total contacts using a negative binomial regression model. Results: A daily average of 3.7 [standard deviation = 10.6] total contacts outside the household were reported. Essential workers, specifically those in healthcare, had 4.5 times as many contacts as non-essential workers [incident rate ratio = 4.42 (95% CI: 3.88–5.04)], whilst essential workers in other sectors, mainly teaching and the police force had three times as many contacts [IRR = 2.84 (2.58–3.13)]. The number of individuals in a household, which largely reflects number of children, increases essential social contacts by 40%. Self-isolation effectively reduces numbers of contacts outside of the home, but not entirely. Conclusions: Contextualising contact patterns has highlighted the health inequalities exposed by COVID-19, as well as potential sources of infection risk and transmission. Together, these findings will aid the interpretation of epidemiological data and impact the design of effective control strategies for SARS-CoV-2, such as vaccination, testing and contact tracing.
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24
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Lacasa L, Challen R, Brooks-Pollock E, Danon L. Correction: A flexible method for optimising sharing of healthcare resources and demand in the context of the COVID-19 pandemic. PLoS One 2021; 16:e0251222. [PMID: 33914845 PMCID: PMC8084216 DOI: 10.1371/journal.pone.0251222] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
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25
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Smith D, Northstone K, Bowring C, Wells N, Crawford M, Pearson RM, Thomas A, Brooks-Pollock E, Lawlor DA, Timpson NJ. The Avon Longitudinal Study of Parents and Children - A resource for COVID-19 research: Generation 2 questionnaire data capture May-July 2020. Wellcome Open Res 2021; 5:278. [PMID: 33791441 PMCID: PMC7968471 DOI: 10.12688/wellcomeopenres.16414.2] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/31/2021] [Indexed: 12/01/2022] Open
Abstract
The Avon Longitudinal Study of Parents and Children (ALSPAC) is a prospective population-based cohort study which recruited pregnant women in 1990-1992 from the Bristol area (UK). ALSPAC has followed these women, their partners (Generation 0; G0) and their offspring (Generation 1; G1) ever since. From 2012, ALSPAC has identified G1 participants who were pregnant (or their partner was) or had become parents, and enrolled them, their partners, and children in the ALSPAC-Generation 2 (ALSPAC-G2) study, providing a unique multi-generational cohort. At present, approximately 1,100 G2 children (excluding those in utero) from 810 G1 participants have been enrolled. In response to the COVID-19 pandemic, ALSPAC rapidly deployed two online questionnaires; one during the initial lockdown phase in 2020 (9 th April-15 th May), and another when national lockdown restrictions were eased (26 th May-5 th July). As part of this second questionnaire, G1 parents completed a questionnaire about each of their G2 children. This covered: parental reports of children's feelings and behaviour since lockdown, school attendance, contact patterns, and health. A total of 289 G1 participants completed this questionnaire on behalf of 411 G2 children. This COVID-19 G2 questionnaire data can be combined with pre-pandemic ALSPAC-G2 data, plus ALSPAC-G1 and -G0 data, to understand how children's health and behaviour has been affected by the pandemic and its management. Data from this questionnaire will be complemented with linkage to health records and results of biological testing as they become available. Prospective studies are necessary to understand the impact of this pandemic on children's health and development, yet few relevant studies exist; this resource will aid these efforts. Data has been released as: 1) a freely-available dataset containing participant responses with key sociodemographic variables; and 2) an ALSPAC-held dataset which can be combined with existing ALSPAC data, enabling bespoke research across all areas supported by the study.
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Affiliation(s)
- Daniel Smith
- ALSPAC, Department of Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, BS8 2BN, UK
- MRC Integrative Epidemiology Unit, University of Bristol, Bristol, UK
| | - Kate Northstone
- ALSPAC, Department of Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, BS8 2BN, UK
| | - Claire Bowring
- ALSPAC, Department of Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, BS8 2BN, UK
| | - Nicholas Wells
- ALSPAC, Department of Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, BS8 2BN, UK
| | - Michael Crawford
- ALSPAC, Department of Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, BS8 2BN, UK
| | - Rebecca M. Pearson
- MRC Integrative Epidemiology Unit, University of Bristol, Bristol, UK
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, BS8 2BN, UK
- NIHR Bristol Biomedical Research Centre, Bristol, UK
| | - Amy Thomas
- Bristol Veterinary School, University of Bristol, Bristol, BS40 5DU, UK
| | - Ellen Brooks-Pollock
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, BS8 2BN, UK
- Bristol Veterinary School, University of Bristol, Bristol, BS40 5DU, UK
| | - Deborah A. Lawlor
- MRC Integrative Epidemiology Unit, University of Bristol, Bristol, UK
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, BS8 2BN, UK
- NIHR Bristol Biomedical Research Centre, Bristol, UK
| | - Nicholas John Timpson
- ALSPAC, Department of Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, BS8 2BN, UK
- MRC Integrative Epidemiology Unit, University of Bristol, Bristol, UK
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26
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Abstract
Psoroptic mange (sheep scab), caused by the parasitic mite, Psoroptes ovis, is an important disease of sheep worldwide. It causes chronic animal welfare issues and economic losses. Eradication of scab has proved impossible in many sheep-rearing areas and recent reports of resistance to macrocyclic lactones, a key class of parasiticide, highlight the importance of improving approaches to scab management. To allow this, the current study aimed to develop a stochastic spatial metapopulation model for sheep scab transmission which can be adapted for use in any geographical region, exhibited here using data for Great Britain. The model uses agricultural survey and sheep movement data to geo-reference farms and capture realistic movement patterns. Reported data on sheep scab outbreaks from 1973 to 1991 were used for model fitting with Sequential Monte Carlo Approximate Bayesian Computation methods. The outbreak incidence predicted by the model was from the same statistical distribution as the reported outbreak data (\documentclass[12pt]{minimal}
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\begin{document}$${\chi }^{2}$$\end{document}χ2 = 115.3, p = 1) and the spatial location of sheep scab outbreaks predicted was positively correlated with the observed outbreak data by county (\documentclass[12pt]{minimal}
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\begin{document}$$\tau$$\end{document}τ = 0.55, p < 0.001), confirming that the model developed is able to accurately capture the number of farms infected in a year, the seasonality of scab incidence and the spatial patterns seen in the data. This model gives insight into the transmission dynamics of sheep scab and will allow the exploration of more effective control strategies.
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Affiliation(s)
- Emily Nixon
- School of Biological Sciences, University of Bristol, 24 Tyndall Avenue, Bristol, BS8 1TQ, UK. .,Bristol Veterinary School, University of Bristol, Langford House, Bristol, BS40 5DU, UK.
| | - Ellen Brooks-Pollock
- Bristol Veterinary School, University of Bristol, Langford House, Bristol, BS40 5DU, UK.,NIHR Health Protection Research Unit in Behavioural Science and Evaluation at University of Bristol, Bristol, UK
| | - Richard Wall
- School of Biological Sciences, University of Bristol, 24 Tyndall Avenue, Bristol, BS8 1TQ, UK
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27
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Hemani G, Thomas AC, Walker JG, Trickey A, Nixon E, Ellis D, Kwiatkowska R, Relton C, Danon L, Christensen H, Brooks-Pollock E. Modelling pooling strategies for SARS-CoV-2 testing in a university setting. Wellcome Open Res 2021. [DOI: 10.12688/wellcomeopenres.16639.1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
Background: Pre-symptomatic and asymptomatic transmission of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) are important elements in the coronavirus disease 2019 (COVID-19) pandemic, and there remains a reliance on testing to manage the spread of the disease. In the UK, many universities opened for blended learning for the 2020-2021 academic year, with a mixture of face to face and online teaching. Methods: In this study we present a simulation framework to evaluate the effectiveness of different mass testing strategies within a university setting, across a range of transmission scenarios. Results: The sensitivity of 5x pooled RT-qPCR tests appears to be higher than testing using the lateral flow device with relatively little loss compared to single RT-qPCR tests, and is improved by pooling by social cluster. The range of strategies that we evaluated give comparable results for estimating prevalence. Conclusions: Pooling tests by known social structures, such as student households can substantially improve the cost effectiveness of RT-qPCR tests. We also note that routine recording of quantitative RT-qPCR results would facilitate future modelling studies.
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28
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Challen R, Brooks-Pollock E, Read JM, Dyson L, Tsaneva-Atanasova K, Danon L. Risk of mortality in patients infected with SARS-CoV-2 variant of concern 202012/1: matched cohort study. BMJ 2021; 372:n579. [PMID: 33687922 PMCID: PMC7941603 DOI: 10.1136/bmj.n579] [Citation(s) in RCA: 459] [Impact Index Per Article: 153.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 02/25/2021] [Indexed: 01/01/2023]
Abstract
OBJECTIVE To establish whether there is any change in mortality from infection with a new variant of SARS-CoV-2, designated a variant of concern (VOC-202012/1) in December 2020, compared with circulating SARS-CoV-2 variants. DESIGN Matched cohort study. SETTING Community based (pillar 2) covid-19 testing centres in the UK using the TaqPath assay (a proxy measure of VOC-202012/1 infection). PARTICIPANTS 54 906 matched pairs of participants who tested positive for SARS-CoV-2 in pillar 2 between 1 October 2020 and 29 January 2021, followed-up until 12 February 2021. Participants were matched on age, sex, ethnicity, index of multiple deprivation, lower tier local authority region, and sample date of positive specimens, and differed only by detectability of the spike protein gene using the TaqPath assay. MAIN OUTCOME MEASURE Death within 28 days of the first positive SARS-CoV-2 test result. RESULTS The mortality hazard ratio associated with infection with VOC-202012/1 compared with infection with previously circulating variants was 1.64 (95% confidence interval 1.32 to 2.04) in patients who tested positive for covid-19 in the community. In this comparatively low risk group, this represents an increase in deaths from 2.5 to 4.1 per 1000 detected cases. CONCLUSIONS The probability that the risk of mortality is increased by infection with VOC-202012/01 is high. If this finding is generalisable to other populations, infection with VOC-202012/1 has the potential to cause substantial additional mortality compared with previously circulating variants. Healthcare capacity planning and national and international control policies are all impacted by this finding, with increased mortality lending weight to the argument that further coordinated and stringent measures are justified to reduce deaths from SARS-CoV-2.
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Affiliation(s)
- Robert Challen
- College of Engineering, Mathematics and Physical Sciences, University of Exeter, Exeter, UK
- Somerset NHS Foundation Trust, Taunton, UK
- Joint Universities Pandemic and Epidemiological Research (JUNIPER consortium)
| | - Ellen Brooks-Pollock
- Joint Universities Pandemic and Epidemiological Research (JUNIPER consortium)
- University of Bristol, Bristol Veterinary School, Langford, Bristol, UK
- Bristol Medical School, Population Health Sciences, University of Bristol, Bristol, UK
| | - Jonathan M Read
- Joint Universities Pandemic and Epidemiological Research (JUNIPER consortium)
- Lancaster Medical School, Lancaster University, Bailrigg, Lancaster, UK
| | - Louise Dyson
- Joint Universities Pandemic and Epidemiological Research (JUNIPER consortium)
- The Zeeman Institute for Systems Biology and Infectious Disease Epidemiology Research, School of Life Sciences and Mathematics Institute, University of Warwick, Coventry, UK
| | - Krasimira Tsaneva-Atanasova
- College of Engineering, Mathematics and Physical Sciences, University of Exeter, Exeter, UK
- The Alan Turing Institute, British Library, London, UK
| | - Leon Danon
- Joint Universities Pandemic and Epidemiological Research (JUNIPER consortium)
- Bristol Medical School, Population Health Sciences, University of Bristol, Bristol, UK
- The Alan Turing Institute, British Library, London, UK
- Department of Engineering Mathematics, University of Bristol, Bristol, UK
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29
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Booton RD, MacGregor L, Vass L, Looker KJ, Hyams C, Bright PD, Harding I, Lazarus R, Hamilton F, Lawson D, Danon L, Pratt A, Wood R, Brooks-Pollock E, Turner KME. Estimating the COVID-19 epidemic trajectory and hospital capacity requirements in South West England: a mathematical modelling framework. BMJ Open 2021; 11:e041536. [PMID: 33414147 PMCID: PMC7797241 DOI: 10.1136/bmjopen-2020-041536] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/10/2020] [Revised: 09/16/2020] [Accepted: 11/06/2020] [Indexed: 01/01/2023] Open
Abstract
OBJECTIVES To develop a regional model of COVID-19 dynamics for use in estimating the number of infections, deaths and required acute and intensive care (IC) beds using the South West England (SW) as an example case. DESIGN Open-source age-structured variant of a susceptible-exposed-infectious-recovered compartmental mathematical model. Latin hypercube sampling and maximum likelihood estimation were used to calibrate to cumulative cases and cumulative deaths. SETTING SW at a time considered early in the pandemic, where National Health Service authorities required evidence to guide localised planning and support decision-making. PARTICIPANTS Publicly available data on patients with COVID-19. PRIMARY AND SECONDARY OUTCOME MEASURES The expected numbers of infected cases, deaths due to COVID-19 infection, patient occupancy of acute and IC beds and the reproduction ('R') number over time. RESULTS SW model projections indicate that, as of 11 May 2020 (when 'lockdown' measures were eased), 5793 (95% credible interval (CrI) 2003 to 12 051) individuals were still infectious (0.10% of the total SW population, 95% CrI 0.04% to 0.22%), and a total of 189 048 (95% CrI 141 580 to 277 955) had been infected with the virus (either asymptomatically or symptomatically), but recovered, which is 3.4% (95% CrI 2.5% to 5.0%) of the SW population. The total number of patients in acute and IC beds in the SW on 11 May 2020 was predicted to be 701 (95% CrI 169 to 1543) and 110 (95% CrI 8 to 464), respectively. The R value in SW was predicted to be 2.6 (95% CrI 2.0 to 3.2) prior to any interventions, with social distancing reducing this to 2.3 (95% CrI 1.8 to 2.9) and lockdown/school closures further reducing the R value to 0.6 (95% CrI 0.5 to 0.7). CONCLUSIONS The developed model has proved a valuable asset for regional healthcare services. The model will be used further in the SW as the pandemic evolves, and-as open-source software-is portable to healthcare systems in other geographies.
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Affiliation(s)
- Ross D Booton
- School of Veterinary Sciences, University of Bristol, Bristol, UK
| | - Louis MacGregor
- Population Health Science Institute, University of Bristol Medical School, Bristol, UK
- NIHR Health Protection Research Unit in Behavioural Science and Evaluation, Bristol, UK
| | - Lucy Vass
- School of Veterinary Sciences, University of Bristol, Bristol, UK
- Population Health Science Institute, University of Bristol Medical School, Bristol, UK
| | - Katharine J Looker
- Population Health Science Institute, University of Bristol Medical School, Bristol, UK
- NIHR Health Protection Research Unit in Behavioural Science and Evaluation, Bristol, UK
| | | | - Philip D Bright
- Immunology, Pathology Sciences, North Bristol NHS Trust, Bristol, UK
| | - Irasha Harding
- Consultant in Microbiology, University Hospitals Bristol, Bristol, UK
| | - Rajeka Lazarus
- Consultant in Microbiology and Infectious Diseases, University Hospitals Bristol, Bristol, UK
| | - Fergus Hamilton
- Infection Science, Southmead Hospital, North Bristol NHS Trust, Bristol, UK
| | - Daniel Lawson
- School of Mathematics, University of Bristol, Bristol, UK
| | - Leon Danon
- Population Health Science Institute, University of Bristol Medical School, Bristol, UK
- Department of Engineering Mathematics, University of Bristol, Bristol, UK
- Alan Turing Institute, London, UK
- Health Data Research UK South-West of England Partnership, Bristol, UK
| | - Adrian Pratt
- Modelling and Analytics Team, NHS Bristol, North Somerset and South Gloucestershire CCG, Bristol, UK
| | - Richard Wood
- Health Data Research UK South-West of England Partnership, Bristol, UK
- Modelling and Analytics Team, NHS Bristol, North Somerset and South Gloucestershire CCG, Bristol, UK
| | - Ellen Brooks-Pollock
- School of Veterinary Sciences, University of Bristol, Bristol, UK
- Population Health Science Institute, University of Bristol Medical School, Bristol, UK
- NIHR Health Protection Research Unit in Behavioural Science and Evaluation, Bristol, UK
| | - Katherine M E Turner
- School of Veterinary Sciences, University of Bristol, Bristol, UK
- Population Health Science Institute, University of Bristol Medical School, Bristol, UK
- NIHR Health Protection Research Unit in Behavioural Science and Evaluation, Bristol, UK
- Health Data Research UK South-West of England Partnership, Bristol, UK
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30
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Sparks RSJ, Aspinall WP, Brooks-Pollock E, Cooke RM, Danon L, Barclay J, Scarrow JH, Cox J. A novel approach for evaluating contact patterns and risk mitigation strategies for COVID-19 in English primary schools with application of structured expert judgement. R Soc Open Sci 2021; 8:201566. [PMID: 33614088 PMCID: PMC7890480 DOI: 10.1098/rsos.201566] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/31/2020] [Accepted: 01/13/2021] [Indexed: 06/12/2023]
Abstract
Personal contacts drive COVID-19 infections. After being closed (23 March 2020) UK primary schools partially re-opened on 1 June 2020 with social distancing and new risk mitigation strategies. We conducted a structured expert elicitation of teachers to quantify primary school contact patterns and how contact rates changed upon re-opening with risk mitigation measures in place. These rates, with uncertainties, were determined using a performance-based algorithm. We report mean number of contacts per day for four cohorts within schools, with associated 90% confidence ranges. Prior to lockdown, younger children (Reception and Year 1) made 15 contacts per day [range 8.35] within school, older children (Year 6) 18 contacts [range 5.55], teaching staff 25 contacts [range 4.55] and non-classroom staff 11 contacts [range 2.27]. After re-opening, the mean number of contacts was reduced by 53% for young children, 62% for older children, 60% for classroom staff and 64% for other staff. Contacts between teaching and non-teaching staff reduced by 80%. The distributions of contacts per person are asymmetric with heavy tail reflecting a few individuals with high contact numbers. Questions on risk mitigation and supplementary structured interviews elucidated how new measures reduced daily contacts in-school and contribute to infection risk reduction.
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Affiliation(s)
- R. S. J. Sparks
- School of Earth Sciences, University of Bristol, Bristol BS8 1RJ, UK
| | - W. P. Aspinall
- School of Earth Sciences, University of Bristol, Bristol BS8 1RJ, UK
- Aspinall and Associates, Tisbury SP3 6HF, UK
| | - E. Brooks-Pollock
- School of Veterinary Sciences, University of Bristol, Office OF24, Churchill Building, Langford, Bristol BS40 5DU, UK
| | - R. M. Cooke
- Resources for the Future, 1616 P St NW, Washington, DC 20036, USA
| | - L. Danon
- Department of Engineering Mathematics, University of Bristol, Ada Lovelace Building, University Walk, Bristol BS8 1TW, UK
| | - J. Barclay
- School of Environmental Sciences, University of East Anglia, Norwich Research Park, Norwich NR4 7TJ, UK
| | - J. H. Scarrow
- Departamento de Mineralogía y Petrología, Facultad de Ciencias, Universidad de Granada, 18071 Granada, Spain
| | - J. Cox
- The Royal Society, 6–9 Carlton House Terrace, London SW7 5QR, UK
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Smith D, Northstone K, Bowring C, Wells N, Crawford M, Pearson RM, Thomas A, Brooks-Pollock E, Lawlor DA, Timpson NJ. The Avon Longitudinal Study of Parents and Children - A resource for COVID-19 research: Generation 2 questionnaire data capture May-July 2020. Wellcome Open Res 2020; 5:278. [PMID: 33791441 PMCID: PMC7968471 DOI: 10.12688/wellcomeopenres.16414.1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/12/2020] [Indexed: 11/20/2022] Open
Abstract
The Avon Longitudinal Study of Parents and Children (ALSPAC) is a prospective population-based cohort study which recruited pregnant women in 1990-1992 from the Bristol area (UK). ALSPAC has followed these women, their partners (Generation 0; G0) and their offspring (Generation 1; G1) ever since. From 2012, ALSPAC has identified G1 participants who were pregnant (or their partner was) or had become parents, and enrolled them, their partners, and children in the ALSPAC-Generation 2 (ALSPAC-G2) study, providing a unique multi-generational cohort. At present, approximately 1,100 G2 children (excluding those in utero) from 810 G1 participants have been enrolled. In response to the COVID-19 pandemic, ALSPAC rapidly deployed two online questionnaires; one during the initial lockdown phase in 2020 (9 th April-15 th May), and another when national lockdown restrictions were eased (26 th May-5 th July). As part of this second questionnaire, G1 parents completed a questionnaire about each of their G2 children. This covered: parental reports of children's feelings and behaviour since lockdown, school attendance, contact patterns, and health. A total of 289 G1 participants completed this questionnaire on behalf of 411 G2 children. This COVID-19 G2 questionnaire data can be combined with pre-pandemic ALSPAC-G2 data, plus ALSPAC-G1 and -G0 data, to understand how children's health and behaviour has been affected by the pandemic and its management. Data from this questionnaire will be complemented with linkage to health records and results of biological testing as they become available. Prospective studies are necessary to understand the impact of this pandemic on children's health and development, yet few relevant studies exist; this resource will aid these efforts. Data has been released as: 1) a freely-available dataset containing participant responses with key sociodemographic variables; and 2) an ALSPAC-held dataset which can be combined with existing ALSPAC data, enabling bespoke research across all areas supported by the study.
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Affiliation(s)
- Daniel Smith
- ALSPAC, Department of Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, BS8 2BN, UK
- MRC Integrative Epidemiology Unit, University of Bristol, Bristol, UK
| | - Kate Northstone
- ALSPAC, Department of Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, BS8 2BN, UK
| | - Claire Bowring
- ALSPAC, Department of Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, BS8 2BN, UK
| | - Nicholas Wells
- ALSPAC, Department of Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, BS8 2BN, UK
| | - Michael Crawford
- ALSPAC, Department of Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, BS8 2BN, UK
| | - Rebecca M. Pearson
- MRC Integrative Epidemiology Unit, University of Bristol, Bristol, UK
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, BS8 2BN, UK
- NIHR Bristol Biomedical Research Centre, Bristol, UK
| | - Amy Thomas
- Bristol Veterinary School, University of Bristol, Bristol, BS40 5DU, UK
| | - Ellen Brooks-Pollock
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, BS8 2BN, UK
- Bristol Veterinary School, University of Bristol, Bristol, BS40 5DU, UK
| | - Deborah A. Lawlor
- MRC Integrative Epidemiology Unit, University of Bristol, Bristol, UK
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, BS8 2BN, UK
- NIHR Bristol Biomedical Research Centre, Bristol, UK
| | - Nicholas John Timpson
- ALSPAC, Department of Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, BS8 2BN, UK
- MRC Integrative Epidemiology Unit, University of Bristol, Bristol, UK
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Lacasa L, Challen R, Brooks-Pollock E, Danon L. A flexible method for optimising sharing of healthcare resources and demand in the context of the COVID-19 pandemic. PLoS One 2020; 15:e0241027. [PMID: 33085729 PMCID: PMC7577502 DOI: 10.1371/journal.pone.0241027] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2020] [Accepted: 09/22/2020] [Indexed: 11/22/2022] Open
Abstract
As the number of cases of COVID-19 continues to grow, local health services are at risk of being overwhelmed with patients requiring intensive care. We develop and implement an algorithm to provide optimal re-routing strategies to either transfer patients requiring Intensive Care Units (ICU) or ventilators, constrained by feasibility of transfer. We validate our approach with realistic data from the United Kingdom and Spain. In the UK, we consider the National Health Service at the level of trusts and define a 4-regular geometric graph which indicates the four nearest neighbours of any given trust. In Spain we coarse-grain the healthcare system at the level of autonomous communities, and extract similar contact networks. Through random search optimisation we identify the best load sharing strategy, where the cost function to minimise is based on the total number of ICU units above capacity. Our framework is general and flexible allowing for additional criteria, alternative cost functions, and can be extended to other resources beyond ICU units or ventilators. Assuming a uniform ICU demand, we show that it is possible to enable access to ICU for up to 1000 additional cases in the UK in a single step of the algorithm. Under a more realistic and heterogeneous demand, our method is able to balance about 600 beds per step in the Spanish system only using local sharing, and over 1300 using countrywide sharing, potentially saving a large percentage of these lives that would otherwise not have access to ICU.
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Affiliation(s)
- Lucas Lacasa
- School of Mathematical Sciences, Queen Mary University of London, London, United Kingdom
- Institute for Cross-Disciplinary Physics and Complex Systems IFISC (UIB-CSIC), Palma de Mallorca, Spain
| | - Robert Challen
- EPSRC Centre for Predictive Modelling in Healthcare, University of Exeter, Exeter, Devon, United Kingdom
- Taunton and Somerset NHS Foundation Trust, Taunton, Somerset, United Kingdom
| | - Ellen Brooks-Pollock
- Bristol Medical School: Population Health Sciences, University of Bristol, Bristol, United Kingdom
| | - Leon Danon
- Data Science Institute, College of Engineering, Mathematics and Physical Sciences, University of Exeter, Exeter, United Kingdom
- The Alan Turing Institute, British Library, London, United Kingdom
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Thompson RN, Brooks-Pollock E. Preface to theme issue 'Modelling infectious disease outbreaks in humans, animals and plants: epidemic forecasting and control'. Philos Trans R Soc Lond B Biol Sci 2020; 374:20190375. [PMID: 31104610 DOI: 10.1098/rstb.2019.0375] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
This preface forms part of the theme issue 'Modelling infectious disease outbreaks in humans, animals and plants: epidemic forecasting and control'. This theme issue is linked with the earlier issue 'Modelling infectious disease outbreaks in humans, animals and plants: approaches and important themes'.
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Affiliation(s)
- R N Thompson
- 1 Mathematical Institute, University of Oxford , Andrew Wiles Building, Radcliffe Observatory Quarter, Woodstock Road, Oxford OX2 6GG , UK.,2 Department of Zoology, University of Oxford , Peter Medawar Building, South Parks Road, Oxford OX1 3SY , UK.,3 Christ Church, University of Oxford , St Aldates, Oxford OX1 1DP , UK
| | - Ellen Brooks-Pollock
- 4 Bristol Veterinary School, University of Bristol , Langford BS40 5DU , UK.,5 National Institute for Health Research, Health Protection Research Unit in Evaluation of Interventions, Bristol Medical School , Bristol BS8 2BN , UK
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Thompson RN, Brooks-Pollock E. Detection, forecasting and control of infectious disease epidemics: modelling outbreaks in humans, animals and plants. Philos Trans R Soc Lond B Biol Sci 2020; 374:20190038. [PMID: 31056051 DOI: 10.1098/rstb.2019.0038] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
The 1918 influenza pandemic is one of the most devastating infectious disease epidemics on record, having caused approximately 50 million deaths worldwide. Control measures, including prohibiting non-essential gatherings as well as closing cinemas and music halls, were applied with varying success and limited knowledge of transmission dynamics. One hundred years later, following developments in the field of mathematical epidemiology, models are increasingly used to guide decision-making and devise appropriate interventions that mitigate the impacts of epidemics. Epidemiological models have been used as decision-making tools during outbreaks in human, animal and plant populations. However, as the subject has developed, human, animal and plant disease modelling have diverged. Approaches have been developed independently for pathogens of each host type, often despite similarities between the models used in these complementary fields. With the increased importance of a One Health approach that unifies human, animal and plant health, we argue that more inter-disciplinary collaboration would enhance each of the related disciplines. This pair of theme issues presents research articles written by human, animal and plant disease modellers. In this introductory article, we compare the questions pertinent to, and approaches used by, epidemiological modellers of human, animal and plant pathogens, and summarize the articles in these theme issues. We encourage future collaboration that transcends disciplinary boundaries and links the closely related areas of human, animal and plant disease epidemic modelling. This article is part of the theme issue 'Modelling infectious disease outbreaks in humans, animals and plants: approaches and important themes'. This issue is linked with the subsequent theme issue 'Modelling infectious disease outbreaks in humans, animals and plants: epidemic forecasting and control'.
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Affiliation(s)
- Robin N Thompson
- 1 Mathematical Institute, University of Oxford , Andrew Wiles Building, Radcliffe Observatory Quarter, Woodstock Road, Oxford OX2 6GG , UK.,2 Department of Zoology, University of Oxford , Peter Medawar Building, South Parks Road, Oxford OX1 3SY , UK.,3 Christ Church, University of Oxford , St Aldates, Oxford OX1 1DP , UK
| | - Ellen Brooks-Pollock
- 4 Bristol Veterinary School, University of Bristol , Langford BS40 5DU , UK.,5 National Institute for Health Research, Health Protection Research Unit in Evaluation of Interventions, Bristol Medical School , Bristol BS8 2BN , UK
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Brooks-Pollock E, Danon L, Korthals Altes H, Davidson JA, Pollock AMT, van Soolingen D, Campbell C, Lalor MK. A model of tuberculosis clustering in low incidence countries reveals more transmission in the United Kingdom than the Netherlands between 2010 and 2015. PLoS Comput Biol 2020; 16:e1007687. [PMID: 32218567 PMCID: PMC7141699 DOI: 10.1371/journal.pcbi.1007687] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2019] [Revised: 04/08/2020] [Accepted: 01/16/2020] [Indexed: 11/18/2022] Open
Abstract
Tuberculosis (TB) remains a public health threat in low TB incidence countries, through a combination of reactivated disease and onward transmission. Using surveillance data from the United Kingdom (UK) and the Netherlands (NL), we demonstrate a simple and predictable relationship between the probability of observing a cluster and its size (the number of cases with a single genotype). We demonstrate that the full range of observed cluster sizes can be described using a modified branching process model with the individual reproduction number following a Poisson lognormal distribution. We estimate that, on average, between 2010 and 2015, a TB case generated 0.41 (95% CrI 0.30,0.60) secondary cases in the UK, and 0.24 (0.14,0.48) secondary cases in the NL. A majority of cases did not generate any secondary cases. Recent transmission accounted for 39% (26%,60%) of UK cases and 23%(13%,37%) of NL cases. We predict that reducing UK transmission rates to those observed in the NL would result in 538(266,818) fewer cases annually in the UK. In conclusion, while TB in low incidence countries is strongly associated with reactivated infections, we demonstrate that recent transmission remains sufficient to warrant policies aimed at limiting local TB spread.
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Affiliation(s)
- Ellen Brooks-Pollock
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, United Kingdom
- Bristol Veterinary School, University of Bristol, Bristol, United Kingdom
- * E-mail:
| | - Leon Danon
- College of Engineering and Mathematical Sciences, University of Exeter, Exeter, United Kingdom
- The Alan Turing Institute, London, United Kingdom
| | - Hester Korthals Altes
- Centre for Infectious Disease Control, National Institute for Public Health and the Environment, Bilthoven, the Netherlands
| | | | | | - Dick van Soolingen
- Centre for Infectious Disease Control, National Institute for Public Health and the Environment, Bilthoven, the Netherlands
- Departments of Clinical Microbiology and Pulmonary Diseases, Radboud University Nijmegen Medical Center, Nijmegen, The Netherlands
| | - Colin Campbell
- TB Section, Public Health England, London, United Kingdom
| | - Maeve K. Lalor
- TB Section, Public Health England, London, United Kingdom
- Institute for Global Health, University College London, London, United Kingdom
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Abstract
Background In 2005 in England, universal Bacillus Calmette–Guérin (BCG) vaccination of school-age children was replaced by targeted BCG vaccination of high-risk neonates. Aim Estimate the impact of the 2005 change in BCG policy on tuberculosis (TB) incidence rates in England. Methods We conducted an observational study by combining notifications from the Enhanced Tuberculosis Surveillance system, with demographic data from the Labour Force Survey to construct retrospective cohorts relevant to both the universal and targeted vaccination between 1 January 2000 and 31 December 2010. We then estimated incidence rates over a 5-year follow-up period and used regression modelling to estimate the impact of the change in policy on TB. Results In the non-United Kingdom (UK) born, we found evidence for an association between a reduction in incidence rates and the change in BCG policy (school-age incidence rate ratio (IRR): 0.74; 95% credible interval (CrI): 0.61 to 0.88 and neonatal IRR: 0.62; 95%CrI: 0.44 to 0.88). We found some evidence that the change in policy was associated with an increase in incidence rates in the UK born school-age population (IRR: 1.08; 95%CrI: 0.97 to 1.19) and weaker evidence of an association with a reduction in incidence rates in UK born neonates (IRR: 0.96; 95%CrI: 0.82 to 1.14). Overall, we found that the change in policy was associated with directly preventing 385 (95%CrI: −105 to 881) cases. Conclusions Withdrawing universal vaccination at school age and targeting vaccination towards high-risk neonates was associated with reduced incidence of TB. This was largely driven by reductions in the non-UK born with cases increasing in the UK born.
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Affiliation(s)
- Sam Abbott
- Bristol Medical School: Population Health Sciences, University of Bristol, Bristol, United Kingdom
| | - Hannah Christensen
- Bristol Medical School: Population Health Sciences, University of Bristol, Bristol, United Kingdom
| | - Nicky J Welton
- Bristol Medical School: Population Health Sciences, University of Bristol, Bristol, United Kingdom
| | - Ellen Brooks-Pollock
- Bristol Medical School: Population Health Sciences, University of Bristol, Bristol, United Kingdom
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Abbott S, Christensen H, Lalor MK, Zenner D, Campbell C, Ramsay ME, Brooks-Pollock E. Exploring the effects of BCG vaccination in patients diagnosed with tuberculosis: Observational study using the Enhanced Tuberculosis Surveillance system. Vaccine 2019; 37:5067-5072. [PMID: 31296375 DOI: 10.1016/j.vaccine.2019.06.056] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2018] [Revised: 05/28/2019] [Accepted: 06/18/2019] [Indexed: 11/16/2022]
Abstract
BACKGROUND Bacillus Calmette-Guérin (BCG) is one of the most widely-used vaccines worldwide. BCG primarily reduces the progression from infection to disease, however there is evidence that BCG may provide additional benefits. We aimed to investigate whether there is evidence in routinely-collected surveillance data that BCG vaccination impacts outcomes for tuberculosis (TB) cases in England. METHODS We obtained all TB notifications for 2009-2015 in England from the Enhanced Tuberculosis surveillance system. We considered five outcomes: All-cause mortality, death due to TB (in those who died), recurrent TB, pulmonary disease, and sputum smear status. We used logistic regression, with complete case analysis, to investigate each outcome with BCG vaccination, years since vaccination and age at vaccination, adjusting for potential confounders. All analyses were repeated using multiply imputed data. RESULTS We found evidence of an association between BCG vaccination and reduced all-cause mortality (aOR:0.76 (95%CI 0.64-0.89), P:0.001) and weak evidence of an association with reduced recurrent TB (aOR:0.90 (95%CI 0.81-1.00), P:0.056). Analyses using multiple imputation suggested that the benefits of vaccination for all-cause mortality were reduced after 10 years. CONCLUSIONS We found that BCG vaccination was associated with reduced all-cause mortality in people with TB although this benefit was less pronounced more than 10 years after vaccination. There was weak evidence of an association with reduced recurrent TB.
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Affiliation(s)
- Sam Abbott
- Bristol Medical School: Population Health Sciences, University of Bristol, Bristol, UK.
| | - Hannah Christensen
- Bristol Medical School: Population Health Sciences, University of Bristol, Bristol, UK
| | - Maeve K Lalor
- TB Unit, T.A.R.G.E.T, National Infection Service (NIS), Public Health England, London, UK
| | - Dominik Zenner
- Institute for Global Health, University College London, London, UK
| | - Colin Campbell
- TB Unit, T.A.R.G.E.T, National Infection Service (NIS), Public Health England, London, UK
| | - Mary E Ramsay
- Immunisation, Hepatitis and Blood Safety Department, Public Health England, London, UK
| | - Ellen Brooks-Pollock
- Bristol Medical School: Population Health Sciences, University of Bristol, Bristol, UK
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Packer S, Green C, Brooks-Pollock E, Chaintarli K, Harrison S, Beck CR. Social network analysis and whole genome sequencing in a cohort study to investigate TB transmission in an educational setting. BMC Infect Dis 2019; 19:154. [PMID: 30760211 PMCID: PMC6375175 DOI: 10.1186/s12879-019-3734-8] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2018] [Accepted: 01/18/2019] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND TB outbreaks in educational institutions can result in significant transmission and pose a considerable threat to TB control. Investigation using traditional microbiological and epidemiological tools can lead to imprecise screening strategies due to difficulties characterising complex transmission networks. Application of whole genome sequencing (WGS) and social network analysis can provide additional information that may facilitate rapid directed public health action. We report the utility of these methods in combination with traditional approaches for the first time to investigate a TB outbreak in an educational setting. METHODS Latent tuberculosis infection (LTBI) cases were screenees with a positive T-SPOT®.TB test. Active TB cases were defined through laboratory confirmation of M. tuberculosis on culture or through clinical or radiological findings consistent with infection. Epidemiological data were collected from institutional records and screenees. Samples were cultured and analysed using traditional M. tuberculosis typing and WGS. We undertook multivariable multinomial regression and social network analysis to identify exposures associated with case status and risk communities. RESULTS We identified 189 LTBI cases (13.7% positivity rate) and nine active TB cases from 1377 persons screened. The LTBI positivity rate was 39.1% (99/253) among persons who shared a course with an infectious case (odds ratio 7.3, 95% confidence interval [CI] 5.2 to 10.3). The community structure analysis divided the students into five communities based on connectivity, as opposed to the 11 shared courses. Social network analysis identified that the community including the suspected index case was at significantly elevated risk of active disease (odds ratio 7.5, 95% CI 1.3 to 44.0) and contained eight persons who were lost to follow-up. Five sputum samples underwent WGS, four had zero single nucleotide polymorphism (SNP) differences and one had a single SNP difference. CONCLUSION This study demonstrates the public health impact an undiagnosed case of active TB disease can have in an educational setting within a low incidence area. Social network analysis and whole genome sequencing provided greater insight to evolution of the transmission network and identification of communities of risk. These tools provide further information over traditional epidemiological and microbiological approaches to direct public health action in this setting.
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Affiliation(s)
- Simon Packer
- Field Epidemiology Service, Public Health England, Bristol, UK
| | - Claire Green
- Heart and Lung Unit, Torbay and South Devon NHS Foundation Trust, Torbay, UK
| | - Ellen Brooks-Pollock
- NIHR Health Protection Research Unit in Evaluation of Interventions at the University of Bristol, Bristol, UK
| | | | | | - Charles R Beck
- Field Epidemiology Service, Public Health England, Bristol, UK. .,NIHR Health Protection Research Unit in Evaluation of Interventions at the University of Bristol, Bristol, UK. .,School of Social and Community Medicine, University of Bristol, Bristol, UK.
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Abstract
Background The population attributable fraction (PAF) is used to quantify the contribution of a risk group to disease burden. For infectious diseases, high-risk individuals may increase disease risk for the wider population in addition to themselves; therefore methods are required to estimate the PAF for infectious diseases. Methods A mathematical model of disease transmission in a population with a high-risk group was used to compare existing approaches for calculating the PAF. We quantify when existing methods are consistent and when estimates diverge. We introduce a new method, based on the basic reproduction number, for calculating the PAF, which bridges the gap between existing methods and addresses shortcomings. We illustrate the methods with two examples of the contribution of badgers to bovine tuberculosis in cattle and the role of commercial sex in an HIV epidemic. Results We demonstrate that current methods result in irreconcilable PAF estimates, depending on how chains of transmission are categorized. Using two novel simple formulae for emerging and endemic diseases, we demonstrate that the largest differences occur when transmission in the general population is not self-sustaining. Crucially, some existing methods are not able to discriminate between multiple risk groups. We show that compared with traditional estimates, assortative mixing leads to a decreased PAF, whereas disassortative mixing increases PAF. Conclusions Recent methods for calculating the population attributable fraction (PAF) are not consistent with traditional approaches. Policy makers and users of PAF statistics should be aware of these differences. Our approach offers a straightforward and parsimonious method for calculating the PAF for infectious diseases.
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Affiliation(s)
- Ellen Brooks-Pollock
- National Institute for Health Research Health Protection Research Unit (NIHR HPRU) in Evaluation of Interventions, School of Social and Community Medicine
| | - Leon Danon
- School of Social and Community Medicine, University of Bristol, Bristol, UK
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Brooks-Pollock E, Jacobson KR. Rethinking tuberculosis control by targeting previously treated individuals. Lancet Glob Health 2018; 6:e361-e362. [PMID: 29472017 DOI: 10.1016/s2214-109x(18)30068-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/06/2018] [Accepted: 02/07/2018] [Indexed: 10/18/2022]
Affiliation(s)
- Ellen Brooks-Pollock
- Bristol Veterinary School, University of Bristol, BS40 5DU, UK; Population Health Sciences, Bristol Medical School, University of Bristol, UK.
| | - Karen R Jacobson
- Section of Infectious Diseases, Boston University School of Medicine and Boston Medical Center, Boston, MA, USA
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Altice FL, Azbel L, Stone J, Brooks-Pollock E, Smyrnov P, Dvoriak S, Taxman FS, El-Bassel N, Martin NK, Booth R, Stöver H, Dolan K, Vickerman P. The perfect storm: incarceration and the high-risk environment perpetuating transmission of HIV, hepatitis C virus, and tuberculosis in Eastern Europe and Central Asia. Lancet 2016; 388:1228-48. [PMID: 27427455 PMCID: PMC5087988 DOI: 10.1016/s0140-6736(16)30856-x] [Citation(s) in RCA: 172] [Impact Index Per Article: 21.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Despite global reductions in HIV incidence and mortality, the 15 UNAIDS-designated countries of Eastern Europe and Central Asia (EECA) that gained independence from the Soviet Union in 1991 constitute the only region where both continue to rise. HIV transmission in EECA is fuelled primarily by injection of opioids, with harsh criminalisation of drug use that has resulted in extraordinarily high levels of incarceration. Consequently, people who inject drugs, including those with HIV, hepatitis C virus, and tuberculosis, are concentrated within prisons. Evidence-based primary and secondary prevention of HIV using opioid agonist therapies such as methadone and buprenorphine is available in prisons in only a handful of EECA countries (methadone or buprenorphine in five countries and needle and syringe programmes in three countries), with none of them meeting recommended coverage levels. Similarly, antiretroviral therapy coverage, especially among people who inject drugs, is markedly under-scaled. Russia completely bans opioid agonist therapies and does not support needle and syringe programmes-with neither available in prisons-despite the country's high incarceration rate and having the largest burden of people with HIV who inject drugs in the region. Mathematical modelling for Ukraine suggests that high levels of incarceration in EECA countries facilitate HIV transmission among people who inject drugs, with 28-55% of all new HIV infections over the next 15 years predicted to be attributable to heightened HIV transmission risk among currently or previously incarcerated people who inject drugs. Scaling up of opioid agonist therapies within prisons and maintaining treatment after release would yield the greatest HIV transmission reduction in people who inject drugs. Additional analyses also suggest that at least 6% of all incident tuberculosis cases, and 75% of incident tuberculosis cases in people who inject drugs are due to incarceration. Interventions that reduce incarceration itself and effectively intervene with prisoners to screen, diagnose, and treat addiction and HIV, hepatitis C virus, and tuberculosis are urgently needed to stem the multiple overlapping epidemics concentrated in prisons.
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Affiliation(s)
- Frederick L Altice
- School of Medicine and School Public Health, Yale University, New Haven, CT, USA.
| | - Lyuba Azbel
- Public Health and Policy, London School of Hygiene & Tropical Medicine, London, UK
| | - Jack Stone
- School of Social and Community Medicine, Bristol University, Bristol, UK
| | | | - Pavlo Smyrnov
- ICF International Alliance for Public Health, Kiev, Ukraine
| | - Sergii Dvoriak
- Ukrainian Institute on Public Health Policy, Kiev, Ukraine
| | - Faye S Taxman
- Department of Criminology, Law and Society, George Mason University, Fairfax, VA, USA
| | | | - Natasha K Martin
- School of Social and Community Medicine, Bristol University, Bristol, UK; Division of Global Public Health, University of California San Diego, San Diego, CA, USA
| | - Robert Booth
- Department of Psychiatry, University of Colorado, Denver, CO, USA
| | - Heino Stöver
- Institute of Addiction Research, Frankfurt University of Applied Sciences, Frankfurt, Germany
| | - Kate Dolan
- National Drug and Alcohol Research Centre, University of New South Wales, Sydney, NSW, Australia
| | - Peter Vickerman
- School of Social and Community Medicine, Bristol University, Bristol, UK
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Danon L, Brooks-Pollock E. The need for data science in epidemic modelling. Phys Life Rev 2016; 18:102-104. [DOI: 10.1016/j.plrev.2016.08.011] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2016] [Accepted: 08/19/2016] [Indexed: 11/28/2022]
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Abstract
‘Big-data’ epidemic models are being increasingly used to influence government policy to help with control and eradication of infectious diseases. In the case of livestock, detailed movement records have been used to parametrize realistic transmission models. While livestock movement data are readily available in the UK and other countries in the EU, in many countries around the world, such detailed data are not available. By using a comprehensive database of the UK cattle trade network, we implement various sampling strategies to determine the quantity of network data required to give accurate epidemiological predictions. It is found that by targeting nodes with the highest number of movements, accurate predictions on the size and spatial spread of epidemics can be made. This work has implications for countries such as the USA, where access to data is limited, and developing countries that may lack the resources to collect a full dataset on livestock movements.
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Affiliation(s)
- Peter M Dawson
- Centre for Complexity Science, University of Warwick, Coventry CV4 7AL, UK
| | - Marleen Werkman
- School of Veterinary Medicine and Science, University of Nottingham, Sutton Bonington LE12 5RD, UK Central Veterinary Institute, Wageningen UR (CVI), PO Box 65, 8200 AB Lelystad, The Netherlands
| | - Ellen Brooks-Pollock
- School of Social and Community Medicine, University of Bristol, Bristol BS8 2BN, UK
| | - Michael J Tildesley
- School of Veterinary Medicine and Science, University of Nottingham, Sutton Bonington LE12 5RD, UK Fogarty International Center, US National Institute of Health, Bethesda, MD 20892, USA
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Abstract
Bovine tuberculosis (BTB) is a multi-species infection that commonly affects cattle and badgers in Great Britain. Despite years of study, the impact of badgers on BTB incidence in cattle is poorly understood. Using a two-host transmission model of BTB in cattle and badgers, we find that published data and parameter estimates are most consistent with a system at the threshold of control. The most consistent explanation for data obtained from cattle and badger populations includes within-host reproduction numbers close to 1 and between-host reproduction numbers of approximately 0.05. In terms of controlling infection in cattle, reducing cattle-to-cattle transmission is essential. In some regions, even large reductions in badger prevalence can have a modest impact on cattle infection and a multi-stranded approach is necessary that also targets badger-to-cattle transmission directly. The new perspective highlighted by this two-host approach provides insight into the control of BTB in Great Britain.
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Affiliation(s)
- Ellen Brooks-Pollock
- Disease Dynamics Unit, Department of Veterinary Medicine, University of Cambridge, Madingley Road, Cambridge CB3 0ES, UK School of Social and Community Medicine, University of Bristol, Oakfield House, Oakfield Grove, Bristol BS8 2BN, UK
| | - James L N Wood
- Disease Dynamics Unit, Department of Veterinary Medicine, University of Cambridge, Madingley Road, Cambridge CB3 0ES, UK
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Brooks-Pollock E, Conlan AJK, Mitchell AP, Blackwell R, McKinley TJ, Wood JLN. Age-dependent patterns of bovine tuberculosis in cattle. Vet Res 2013; 44:97. [PMID: 24131703 PMCID: PMC3853322 DOI: 10.1186/1297-9716-44-97] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2013] [Accepted: 09/30/2013] [Indexed: 11/10/2022] Open
Abstract
Bovine tuberculosis (BTB) is an important livestock disease, seriously impacting cattle industries in both industrialised and pre-industrialised countries. Like TB in other mammals, infection is life long and, if undiagnosed, may progress to disease years after exposure. The risk of disease in humans is highly age-dependent, however in cattle, age-dependent risks have yet to be quantified, largely due to insufficient data and limited diagnostics. Here, we estimate age-specific reactor rates in Great Britain by combining herd-level testing data with spatial movement data from the Cattle Tracing System (CTS). Using a catalytic model, we find strong age dependencies in infection risk and that the probability of detecting infection increases with age. Between 2004 and 2009, infection incidence in cattle fluctuated around 1%. Age-specific incidence increased monotonically until 24-36 months, with cattle aged between 12 and 36 months experiencing the highest rates of infection. Beef and dairy cattle under 24 months experienced similar infection risks, however major differences occurred in older ages. The average reproductive number in cattle was greater than 1 for the years 2004-2009. These methods reveal a consistent pattern of BTB rates with age, across different population structures and testing patterns. The results provide practical insights into BTB epidemiology and control, suggesting that targeting a mass control programme at cattle between 12 and 36 months could be beneficial.
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Affiliation(s)
- Ellen Brooks-Pollock
- Disease Dynamics Unit, Department of Veterinary Medicine, University of Cambridge, Madingley Road, Cambridge, CB3 0ES, UK.
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46
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Amos W, Brooks-Pollock E, Blackwell R, Driscoll E, Nelson-Flower M, Conlan AJK. Genetic predisposition to pass the standard SICCT test for bovine tuberculosis in British cattle. PLoS One 2013; 8:e58245. [PMID: 23554880 PMCID: PMC3605902 DOI: 10.1371/journal.pone.0058245] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2012] [Accepted: 02/05/2013] [Indexed: 11/18/2022] Open
Abstract
Bovine tuberculosis (bTB) imposes an important financial burden on the British cattle industry, yet despite intense efforts to control its spread, incidence is currently rising. Surveillance for bTB is based on a skin test that measures an immunological response to tuberculin. Cattle that fail the test are classified as "reactors" and slaughtered. Recent studies have identified genetic markers associated with the reaction of cattle to the tuberculin test. At marker INRA111 a relatively common '22' genotype occurs significantly more frequently in non-reactor cattle. Here we test the possibility that the putative protective '22' genotype does not confer resistance but instead causes cattle that carry it to react less strongly to the prescribed test, and hence avoid slaughter, potentially even though they are infected. We show that, after controlling for age and breed, '22' cattle react less strongly to the immunological challenge and may therefore be less likely to be classified as a reactor. These results highlight the potential discrepancy between infection and test status and imply that the effectiveness of the test-and-slaughter policy may be being compromised by selection for cattle that are genetically predisposed to react less strongly to tuberculin.
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Affiliation(s)
- William Amos
- Department of Zoology, Cambridge University, Cambridge, Cambridgeshire, United Kingdom.
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Eames KTD, Tilston NL, Brooks-Pollock E, Edmunds WJ. Measured dynamic social contact patterns explain the spread of H1N1v influenza. PLoS Comput Biol 2012; 8:e1002425. [PMID: 22412366 PMCID: PMC3297563 DOI: 10.1371/journal.pcbi.1002425] [Citation(s) in RCA: 137] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2011] [Accepted: 01/27/2012] [Indexed: 11/18/2022] Open
Abstract
Patterns of social mixing are key determinants of epidemic spread. Here we present the results of an internet-based social contact survey completed by a cohort of participants over 9,000 times between July 2009 and March 2010, during the 2009 H1N1v influenza epidemic. We quantify the changes in social contact patterns over time, finding that school children make 40% fewer contacts during holiday periods than during term time. We use these dynamically varying contact patterns to parameterise an age-structured model of influenza spread, capturing well the observed patterns of incidence; the changing contact patterns resulted in a fall of approximately 35% in the reproduction number of influenza during the holidays. This work illustrates the importance of including changing mixing patterns in epidemic models. We conclude that changes in contact patterns explain changes in disease incidence, and that the timing of school terms drove the 2009 H1N1v epidemic in the UK. Changes in social mixing patterns can be usefully measured through simple internet-based surveys. Changes in patterns of social mixing can result in changes in epidemic behaviour; this was observed during the 2009 influenza pandemic, in which the epidemic declined during school holidays and grew during term time. Until now, little information has been available to quantify how people's mixing patterns change over time. Here, we present the results of an internet-based survey of social mixing patterns that was carried out in the UK throughout the 2009 pandemic. We show that school holidays resulted in a substantial drop in the number of social contacts made each day, particularly between children. To test whether these measured patterns of social mixing could explain the observed epidemic, we used our mixing data in a simple mathematical model of influenza spread. We found that changing social contact behaviour could explain levels of infection in the community, and conclude that the timing of school terms was responsible for the shape of the influenza epidemic.
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Affiliation(s)
- Ken T D Eames
- Department of Infectious Disease Epidemiology, London School of Hygiene and Tropical Medicine, London, United Kingdom.
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Brooks-Pollock E, Becerra MC, Goldstein E, Cohen T, Murray MB. Epidemiologic inference from the distribution of tuberculosis cases in households in Lima, Peru. J Infect Dis 2011; 203:1582-9. [PMID: 21592987 DOI: 10.1093/infdis/jir162] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
BACKGROUND Tuberculosis (TB) often occurs among household contacts of people with active TB. It is unclear whether clustering of cases represents household transmission or shared household risk factors for TB. METHODS We used cross-sectional data from 764 households in Lima, Peru, to estimate the relative contributions of household and community transmission, the average time between cases, and the immunity afforded by a previous TB infection. RESULTS The distribution of cases per household suggests that almost 7 of 10 nonindex household cases were infected in the community rather than in the household. The average interval between household cases was 3.5 years. We observed a saturation effect in the number of cases per household and estimated that protective immunity conferred up to 35% reduction in the risk of disease. CONCLUSIONS Cross-sectional household data can elucidate the natural history and transmission dynamics of TB. In this high-incidence setting, we found that the majority of cases were attributable to community transmission and that household contacts of case patients derive some immunity from household exposures. Screening of household contacts may be an effective method of detecting new TB cases if carried out over several years.
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Affiliation(s)
- Ellen Brooks-Pollock
- Department of Epidemiology, Harvard School of Public Health, Brigham and Women's Hospital, Massachusetts General Hospital, Boston, USA.
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Brooks-Pollock E, Tilston N, Edmunds WJ, Eames KTD. Using an online survey of healthcare-seeking behaviour to estimate the magnitude and severity of the 2009 H1N1v influenza epidemic in England. BMC Infect Dis 2011; 11:68. [PMID: 21410965 PMCID: PMC3073914 DOI: 10.1186/1471-2334-11-68] [Citation(s) in RCA: 79] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2010] [Accepted: 03/16/2011] [Indexed: 12/24/2022] Open
Abstract
Background During the 2009 H1N1v influenza epidemic, the total number of symptomatic cases was estimated by combining influenza-like illness (ILI) consultations, virological surveillance and assumptions about healthcare-seeking behaviour. Changes in healthcare-seeking behaviour due to changing scientific information, media coverage and public anxiety, were not included in case estimates. The purpose of the study was to improve estimates of the number of symptomatic H1N1v cases and the case fatality rate (CFR) in England by quantifying healthcare-seeking behaviour using an internet-based survey carried out during the course of the 2009 H1N1v influenza epidemic. Methods We used an online survey that ran continuously from July 2009 to March 2010 to estimate the proportion of ILI cases that sought healthcare during the 2009 H1N1v influenza epidemic. We used dynamic age- and gender-dependent measures of healthcare-seeking behaviour to re-interpret consultation numbers and estimate the true number of cases of symptomatic ILI in 2009 and the case fatality rate (CFR). Results There were significant differences between age groups in healthcare usage. From the start to the end of the epidemic, the percentage of individuals with influenza-like symptoms who sought medical attention decreased from 43% to 32% (p < 0.0001). Adjusting official numbers accordingly, we estimate that there were 1.1 million symptomatic cases in England, over 320,000 (40%) more cases than previously estimated and that the autumn epidemic wave was 45% bigger than previously thought. Combining symptomatic case numbers with reported deaths leads to a reduced overall CFR estimate of 17 deaths per 100,000 cases, with the largest reduction in adults. Conclusions Active surveillance of healthcare-seeking behaviour, which can be achieved using novel data collection methods, is vital for providing accurate real-time estimates of epidemic size and disease severity. The differences in healthcare-seeking between different population groups and changes over time have significant implications for estimates of total case numbers and the case fatality rate.
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Affiliation(s)
- Ellen Brooks-Pollock
- Centre for Mathematical Modelling of Infectious Diseases, London School of Hygiene and Tropical Medicine, London, UK.
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