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Ali W, Overton CE, Wilkinson RR, Sharkey KJ. Deterministic epidemic models overestimate the basic reproduction number of observed outbreaks. Infect Dis Model 2024; 9:680-688. [PMID: 38638338 PMCID: PMC11024615 DOI: 10.1016/j.idm.2024.02.007] [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] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2023] [Revised: 02/09/2024] [Accepted: 02/13/2024] [Indexed: 04/20/2024] Open
Abstract
The basic reproduction number, R0, is a well-known quantifier of epidemic spread. However, a class of existing methods for estimating R0 from incidence data early in the epidemic can lead to an over-estimation of this quantity. In particular, when fitting deterministic models to estimate the rate of spread, we do not account for the stochastic nature of epidemics and that, given the same system, some outbreaks may lead to epidemics and some may not. Typically, an observed epidemic that we wish to control is a major outbreak. This amounts to implicit selection for major outbreaks which leads to the over-estimation problem. We formally characterised the split between major and minor outbreaks by using Otsu's method which provides us with a working definition. We show that by conditioning a 'deterministic' model on major outbreaks, we can more reliably estimate the basic reproduction number from an observed epidemic trajectory.
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Affiliation(s)
- Wajid Ali
- Department of Mathematical Sciences, University of Liverpool, Peach Street, Liverpool, L69 7ZX, England, United Kingdom
| | - Christopher E. Overton
- Department of Mathematical Sciences, University of Liverpool, Peach Street, Liverpool, L69 7ZX, England, United Kingdom
| | - Robert R. Wilkinson
- Department of Applied Mathematics, Liverpool John Moores University, Byrom Street, Liverpool, L3 5UX, England, United Kingdom
| | - Kieran J. Sharkey
- Department of Mathematical Sciences, University of Liverpool, Peach Street, Liverpool, L69 7ZX, England, United Kingdom
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Ward T, Overton CE, Paton RS, Christie R, Cumming F, Fyles M. Understanding the infection severity and epidemiological characteristics of mpox in the UK. Nat Commun 2024; 15:2199. [PMID: 38467622 PMCID: PMC10928097 DOI: 10.1038/s41467-024-45110-8] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2023] [Accepted: 01/15/2024] [Indexed: 03/13/2024] Open
Abstract
In May 2022, individuals infected with the monkeypox virus were detected in the UK without clear travel links to endemic areas. Understanding the clinical characteristics and infection severity of mpox is necessary for effective public health policy. The study period of this paper, from the 1st June 2022 to 30th September 2022, included 3,375 individuals that tested positive for the monkeypox virus. The posterior mean times from infection to hospital admission and length of hospital stay were 14.89 days (95% Credible Intervals (CrI): 13.60, 16.32) and 7.07 days (95% CrI: 6.07, 8.23), respectively. We estimated the modelled Infection Hospitalisation Risk to be 4.13% (95% CrI: 3.04, 5.02), compared to the overall sample Case Hospitalisation Risk (CHR) of 5.10% (95% CrI: 4.38, 5.86). The overall sample CHR was estimated to be 17.86% (95% CrI: 6.06, 33.11) for females and 4.99% (95% CrI: 4.27, 5.75) for males. A notable difference was observed between the CHRs that were estimated for each sex, which may be indicative of increased infection severity in females or a considerably lower infection ascertainment rate. It was estimated that 74.65% (95% CrI: 55.78, 86.85) of infections with the monkeypox virus in the UK were captured over the outbreak.
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Affiliation(s)
- Thomas Ward
- UK Health Security Agency, Data Analytics & Surveillance, London, UK.
| | - Christopher E Overton
- UK Health Security Agency, Data Analytics & Surveillance, London, UK
- Department of Mathematical Sciences, University of Liverpool, Liverpool, UK
| | - Robert S Paton
- UK Health Security Agency, Data Analytics & Surveillance, London, UK
| | - Rachel Christie
- UK Health Security Agency, Data Analytics & Surveillance, London, UK
| | - Fergus Cumming
- UK Health Security Agency, Data Analytics & Surveillance, London, UK
| | - Martyn Fyles
- UK Health Security Agency, Data Analytics & Surveillance, London, UK
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3
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Overton CE, Abbey R, Baird T, Christie R, Daniel O, Day J, Gittins M, Jones O, Paton R, Tang M, Ward T, Wilkinson J, Woodrow-Hill C, Aldridge T, Chen Y. Identifying employee, workplace and population characteristics associated with COVID-19 outbreaks in the workplace: a population-based study. Occup Environ Med 2024; 81:92-100. [PMID: 38191477 DOI: 10.1136/oemed-2023-109032] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Accepted: 11/15/2023] [Indexed: 01/10/2024]
Abstract
OBJECTIVES To identify risk factors that contribute to outbreaks of COVID-19 in the workplace and quantify their effect on outbreak risk. METHODS We identified outbreaks of COVID-19 cases in the workplace and investigated the characteristics of the individuals, the workplaces, the areas they work and the mode of commute to work, through data linkages based on Middle Layer Super Output Areas in England between 20 June 2021 and 20 February 2022. We estimated population-level associations between potential risk factors and workplace outbreaks, adjusting for plausible confounders identified using a directed acyclic graph. RESULTS For most industries, increased physical proximity in the workplace was associated with increased risk of COVID-19 outbreaks, while increased vaccination was associated with reduced risk. Employee demographic risk factors varied across industry, but for the majority of industries, a higher proportion of black/African/Caribbean ethnicities and living in deprived areas, was associated with increased outbreak risk. A higher proportion of employees in the 60-64 age group was associated with reduced outbreak risk. There were significant associations between gender, work commute modes and staff contract type with outbreak risk, but these were highly variable across industries. CONCLUSIONS This study has used novel national data linkages to identify potential risk factors of workplace COVID-19 outbreaks, including possible protective effects of vaccination and increased physical distance at work. The same methodological approach can be applied to wider occupational and environmental health research.
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Affiliation(s)
- Christopher E Overton
- UK Health Security Agency, London, UK
- Department of Mathematical Sciences, University of Liverpool, Liverpool, UK
| | | | - Tarrion Baird
- UK Health Security Agency, London, UK
- Department of Pathology, University of Cambridge, Cambridge, UK
| | | | | | - Julie Day
- UK Health Security Agency, London, UK
| | - Matthew Gittins
- Centre for Biostatistics, The University of Manchester, Manchester, UK
| | | | | | | | - Tom Ward
- UK Health Security Agency, London, UK
| | - Jack Wilkinson
- Centre for Biostatistics, The University of Manchester, Manchester, UK
| | | | | | - Yiqun Chen
- Science Division, Health and Safety Executive, Buxton, UK
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Mellor J, Christie R, Overton CE, Paton RS, Leslie R, Tang M, Deeny S, Ward T. Author Correction: Forecasting influenza hospital admissions within English sub-regions using hierarchical generalised additive models. Commun Med (Lond) 2024; 4:14. [PMID: 38291099 PMCID: PMC10828412 DOI: 10.1038/s43856-024-00435-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2024] Open
Affiliation(s)
- Jonathon Mellor
- UK Health Security Agency, Data Analytics and Surveillance, 10 South Colonnade, London, UK.
| | - Rachel Christie
- UK Health Security Agency, Data Analytics and Surveillance, 10 South Colonnade, London, UK
| | - Christopher E Overton
- UK Health Security Agency, Data Analytics and Surveillance, 10 South Colonnade, London, UK
- University of Liverpool, Department of Mathematical Sciences, Liverpool, UK
| | - Robert S Paton
- UK Health Security Agency, Data Analytics and Surveillance, 10 South Colonnade, London, UK
| | - Rhianna Leslie
- UK Health Security Agency, Data Analytics and Surveillance, 10 South Colonnade, London, UK
| | - Maria Tang
- UK Health Security Agency, Data Analytics and Surveillance, 10 South Colonnade, London, UK
| | - Sarah Deeny
- UK Health Security Agency, Data Analytics and Surveillance, 10 South Colonnade, London, UK
| | - Thomas Ward
- UK Health Security Agency, Data Analytics and Surveillance, 10 South Colonnade, London, UK
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Mellor J, Christie R, Overton CE, Paton RS, Leslie R, Tang M, Deeny S, Ward T. Forecasting influenza hospital admissions within English sub-regions using hierarchical generalised additive models. Commun Med (Lond) 2023; 3:190. [PMID: 38123630 PMCID: PMC10733380 DOI: 10.1038/s43856-023-00424-4] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2023] [Accepted: 12/06/2023] [Indexed: 12/23/2023] Open
Abstract
BACKGROUND Seasonal influenza places a substantial burden annually on healthcare services. Policies during the COVID-19 pandemic limited the transmission of seasonal influenza, making the timing and magnitude of a potential resurgence difficult to ascertain and its impact important to forecast. METHODS We have developed a hierarchical generalised additive model (GAM) for the short-term forecasting of hospital admissions with a positive test for the influenza virus sub-regionally across England. The model incorporates a multi-level structure of spatio-temporal splines, weekly cycles in admissions, and spatial correlation. Using multiple performance metrics including interval score, coverage, bias, and median absolute error, the predictive performance is evaluated for the 2022-2023 seasonal wave. Performance is measured against autoregressive integrated moving average (ARIMA) and Prophet time series models. RESULTS Across the epidemic phases the hierarchical GAM shows improved performance, at all geographic scales relative to the ARIMA and Prophet models. Temporally, the hierarchical GAM has overall an improved performance at 7 and 14 day time horizons. The performance of the GAM is most sensitive to the flexibility of the smoothing function that measures the national epidemic trend. CONCLUSIONS This study introduces an approach to short-term forecasting of hospital admissions for the influenza virus using hierarchical, spatial, and temporal components. The methodology was designed for the real time forecasting of epidemics. This modelling framework was used across the 2022-2023 winter for healthcare operational planning by the UK Health Security Agency and the National Health Service in England.
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Affiliation(s)
- Jonathon Mellor
- UK Health Security Agency, Data Analytics and Surveillance, 10 South Colonnade, London, United Kingdom.
| | - Rachel Christie
- UK Health Security Agency, Data Analytics and Surveillance, 10 South Colonnade, London, United Kingdom
| | - Christopher E Overton
- UK Health Security Agency, Data Analytics and Surveillance, 10 South Colonnade, London, United Kingdom
- University of Liverpool, Department of Mathematical Sciences, Liverpool, United Kingdom
| | - Robert S Paton
- UK Health Security Agency, Data Analytics and Surveillance, 10 South Colonnade, London, United Kingdom
| | - Rhianna Leslie
- UK Health Security Agency, Data Analytics and Surveillance, 10 South Colonnade, London, United Kingdom
| | - Maria Tang
- UK Health Security Agency, Data Analytics and Surveillance, 10 South Colonnade, London, United Kingdom
| | - Sarah Deeny
- UK Health Security Agency, Data Analytics and Surveillance, 10 South Colonnade, London, United Kingdom
| | - Thomas Ward
- UK Health Security Agency, Data Analytics and Surveillance, 10 South Colonnade, London, United Kingdom
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Mellor J, Overton CE, Fyles M, Chawner L, Baxter J, Baird T, Ward T. Understanding the leading indicators of hospital admissions from COVID-19 across successive waves in the UK. Epidemiol Infect 2023; 151:e172. [PMID: 37664991 PMCID: PMC10600913 DOI: 10.1017/s0950268823001449] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [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: 03/10/2023] [Revised: 07/20/2023] [Accepted: 07/25/2023] [Indexed: 09/05/2023] Open
Abstract
Following the end of universal testing in the UK, hospital admissions are a key measure of COVID-19 pandemic pressure. Understanding leading indicators of admissions at the National Health Service (NHS) Trust, regional and national geographies help health services plan for ongoing pressures. We explored the spatio-temporal relationships of leading indicators of hospitalisations across SARS-CoV-2 waves in England. This analysis includes an evaluation of internet search volumes from Google Trends, NHS triage calls and online queries, the NHS COVID-19 app, lateral flow devices (LFDs), and the ZOE app. Data sources were analysed for their feasibility as leading indicators using Granger causality, cross-correlation, and dynamic time warping at fine spatial scales. Google Trends and NHS triages consistently temporally led admissions in most locations, with lead times ranging from 5 to 20 days, whereas an inconsistent relationship was found for the ZOE app, NHS COVID-19 app, and LFD testing, which diminished with spatial resolution, showing cross-correlation of leads between -7 and 7 days. The results indicate that novel surveillance sources can be used effectively to understand the expected healthcare burden within hospital administrative areas though the temporal and spatial heterogeneity of these relationships is a key determinant of their operational public health utility.
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Affiliation(s)
- Jonathon Mellor
- UK Health Security Agency, Data, Analytics and Surveillance, Nobel House, London, UK
| | - Christopher E Overton
- UK Health Security Agency, Data, Analytics and Surveillance, Nobel House, London, UK
- Department of Mathematical Sciences, University of Liverpool, Liverpool, UK
- Department of Mathematics, University of Manchester, Manchester, UK
| | - Martyn Fyles
- UK Health Security Agency, Data, Analytics and Surveillance, Nobel House, London, UK
- Department of Mathematics, University of Manchester, Manchester, UK
| | - Liam Chawner
- UK Health Security Agency, Data, Analytics and Surveillance, Nobel House, London, UK
| | - James Baxter
- UK Health Security Agency, Data, Analytics and Surveillance, Nobel House, London, UK
| | - Tarrion Baird
- UK Health Security Agency, Data, Analytics and Surveillance, Nobel House, London, UK
- Department of Pathology, University of Cambridge, Cambridge, UK
| | - Thomas Ward
- UK Health Security Agency, Data, Analytics and Surveillance, Nobel House, London, UK
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Overton CE, Abbott S, Christie R, Cumming F, Day J, Jones O, Paton R, Turner C, Ward T. Nowcasting the 2022 mpox outbreak in England. PLoS Comput Biol 2023; 19:e1011463. [PMID: 37721951 PMCID: PMC10538717 DOI: 10.1371/journal.pcbi.1011463] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2023] [Revised: 09/28/2023] [Accepted: 08/25/2023] [Indexed: 09/20/2023] Open
Abstract
In May 2022, a cluster of mpox cases were detected in the UK that could not be traced to recent travel history from an endemic region. Over the coming months, the outbreak grew, with over 3000 total cases reported in the UK, and similar outbreaks occurring worldwide. These outbreaks appeared linked to sexual contact networks between gay, bisexual and other men who have sex with men. Following the COVID-19 pandemic, local health systems were strained, and therefore effective surveillance for mpox was essential for managing public health policy. However, the mpox outbreak in the UK was characterised by substantial delays in the reporting of the symptom onset date and specimen collection date for confirmed positive cases. These delays led to substantial backfilling in the epidemic curve, making it challenging to interpret the epidemic trajectory in real-time. Many nowcasting models exist to tackle this challenge in epidemiological data, but these lacked sufficient flexibility. We have developed a nowcasting model using generalised additive models that makes novel use of individual-level patient data to correct the mpox epidemic curve in England. The aim of this model is to correct for backfilling in the epidemic curve and provide real-time characteristics of the state of the epidemic, including the real-time growth rate. This model benefited from close collaboration with individuals involved in collecting and processing the data, enabling temporal changes in the reporting structure to be built into the model, which improved the robustness of the nowcasts generated. The resulting model accurately captured the true shape of the epidemic curve in real time.
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Affiliation(s)
- Christopher E. Overton
- Department of Mathematical Sciences, University of Liverpool, Liverpool, United Kingdom
- UK Health Security Agency, Data Science and Analytics, London, United Kingdom
- Department of Mathematics, University of Manchester, Manchester, United Kingdom
| | - Sam Abbott
- London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Rachel Christie
- UK Health Security Agency, Data Science and Analytics, London, United Kingdom
| | - Fergus Cumming
- UK Health Security Agency, Data Science and Analytics, London, United Kingdom
| | - Julie Day
- UK Health Security Agency, Data Science and Analytics, London, United Kingdom
| | - Owen Jones
- UK Health Security Agency, Data Science and Analytics, London, United Kingdom
| | - Rob Paton
- UK Health Security Agency, Data Science and Analytics, London, United Kingdom
| | - Charlie Turner
- UK Health Security Agency, Mpox Data, Epi and Analytics Cell, London, United Kingdom
| | - Thomas Ward
- UK Health Security Agency, Data Science and Analytics, London, United Kingdom
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Abstract
OBJECTIVE To analyse the transmission dynamics of the monkeypox outbreak in the UK, declared a Public Health Emergency of International Concern in July 2022. DESIGN Contact tracing study, linking data on case-contact pairs and on probable exposure dates. SETTING Case questionnaires from the UK Health Security Agency (UKHSA), United Kingdom. PARTICIPANTS 2746 people with polymerase chain reaction confirmed monkeypox virus in the UK between 6 May and 1 August 2022. MAIN OUTCOME MEASURES The incubation period and serial interval of a monkeypox infection using two bayesian time delay models-one corrected for interval censoring (ICC-interval censoring corrected) and one corrected for interval censoring, right truncation, and epidemic phase bias (ICRTC-interval censoring right truncation corrected). Growth rates of cases by reporting date, when monkeypox virus was confirmed and reported to UKHSA, were estimated using generalised additive models. RESULTS The mean age of participants was 37.8 years and 95% reported being gay, bisexual, and other men who have sex with men (1160 out of 1213 reporting). The mean incubation period was estimated to be 7.6 days (95% credible interval 6.5 to 9.9) using the ICC model and 7.8 days (6.6 to 9.2) using the ICRTC model. The estimated mean serial interval was 8.0 days (95% credible interval 6.5 to 9.8) using the ICC model and 9.5 days (7.4 to 12.3) using the ICRTC model. Although the mean serial interval was longer than the incubation period for both models, short serial intervals were more common than short incubation periods, with the 25th centile and the median of the serial interval shorter than the incubation period. For the ICC and ICRTC models, the corresponding estimates ranged from 1.8 days (95% credible interval 1.5 to 1.8) to 1.6 days (1.4 to 1.6) shorter at the 25th centile and 1.6 days (1.5 to 1.7) to 0.8 days (0.3 to 1.2) shorter at the median. 10 out of 13 linked patients had documented pre-symptomatic transmission. Doubling times of cases declined from 9.07 days (95% confidence interval 12.63 to 7.08) on the 6 May, when the first case of monkeypox was reported in the UK, to a halving time of 29 days (95% confidence interval 38.02 to 23.44) on 1 August. CONCLUSIONS Analysis of the instantaneous growth rate of monkeypox incidence indicates that the epidemic peaked in the UK as of 9 July and then started to decline. Short serial intervals were more common than short incubation periods suggesting considerable pre-symptomatic transmission, which was validated through linked patient level records. For patients who could be linked through personally identifiable data, four days was the maximum time that transmission was detected before symptoms manifested. An isolation period of 16 to 23 days would be required to detect 95% of people with a potential infection. The 95th centile of the serial interval was between 23 and 41 days, suggesting long infectious periods.
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Affiliation(s)
- Thomas Ward
- Data, Analytics and Surveillance, UK Health Security Agency, London SW1P 3JR, UK
| | - Rachel Christie
- Data, Analytics and Surveillance, UK Health Security Agency, London SW1P 3JR, UK
| | - Robert S Paton
- Data, Analytics and Surveillance, UK Health Security Agency, London SW1P 3JR, UK
| | - Fergus Cumming
- Data, Analytics and Surveillance, UK Health Security Agency, London SW1P 3JR, UK
| | - Christopher E Overton
- Data, Analytics and Surveillance, UK Health Security Agency, London SW1P 3JR, UK
- Department of Mathematical Sciences, University of Liverpool, Liverpool, UK
- Department of Mathematics, University of Manchester, Manchester, UK
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Pellis L, Birrell PJ, Blake J, Overton CE, Scarabel F, Stage HB, Brooks‐Pollock E, Danon L, Hall I, House TA, Keeling MJ, Read JM, De Angelis D. Estimation of reproduction numbers in real time: Conceptual and statistical challenges. J R Stat Soc Ser A Stat Soc 2022; 185:S112-S130. [PMID: 37063605 PMCID: PMC10100071 DOI: 10.1111/rssa.12955] [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] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/03/2021] [Accepted: 07/06/2022] [Indexed: 06/19/2023]
Abstract
The reproduction numberR has been a central metric of the COVID-19 pandemic response, published weekly by the UK government and regularly reported in the media. Here, we provide a formal definition and discuss the advantages and most common misconceptions around this quantity. We consider the intuition behind different formulations ofR , the complexities in its estimation (including the unavoidable lags involved), and its value compared to other indicators (e.g. the growth rate) that can be directly observed from aggregate surveillance data and react more promptly to changes in epidemic trend. As models become more sophisticated, with age and/or spatial structure, formulatingR becomes increasingly complicated and inevitably model-dependent. We present some models currently used in the UK pandemic response as examples. Ultimately, limitations in the available data streams, data quality and time constraints force pragmatic choices to be made on a quantity that is an average across time, space, social structure and settings. Effectively communicating these challenges is important but often difficult in an emergency.
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Affiliation(s)
- Lorenzo Pellis
- Department of MathematicsThe University of ManchesterManchesterUK
- Joint UNIversities Pandemic and Epidemiological ResearchUK
- The Alan Turing InstituteLondonUK
| | - Paul J. Birrell
- Joint UNIversities Pandemic and Epidemiological ResearchUK
- MRC Biostatistics Unit, School of Clinical MedicineUniversity of CambridgeCambridgeUK
- Statistics Modelling and Economics DepartmentPublic Health EnglandLondonUK
- Joint Modelling TeamPublic Health EnglandLondonUK
| | - Joshua Blake
- Joint UNIversities Pandemic and Epidemiological ResearchUK
- MRC Biostatistics Unit, School of Clinical MedicineUniversity of CambridgeCambridgeUK
| | - Christopher E. Overton
- Department of MathematicsThe University of ManchesterManchesterUK
- Joint UNIversities Pandemic and Epidemiological ResearchUK
- Manchester University NHS Foundation TrustManchesterUK
| | - Francesca Scarabel
- Department of MathematicsThe University of ManchesterManchesterUK
- Joint UNIversities Pandemic and Epidemiological ResearchUK
| | - Helena B. Stage
- Department of MathematicsThe University of ManchesterManchesterUK
- Joint UNIversities Pandemic and Epidemiological ResearchUK
- Department of PhysicsHumboldt University of BerlinBerlinGermany
- Department of Physics and AstronomyUniversity of PotsdamPotsdamGermany
| | - Ellen Brooks‐Pollock
- Joint UNIversities Pandemic and Epidemiological ResearchUK
- NIHR Health Protection Research Unit (HPRU) in Behavioural Science and Evaluation, Population Health SciencesUniversity of BristolBristolUK
| | - Leon Danon
- Joint UNIversities Pandemic and Epidemiological ResearchUK
- The Alan Turing InstituteLondonUK
- Department of Engineering MathematicsUniversity of BristolBristolUK
| | - Ian Hall
- Department of MathematicsThe University of ManchesterManchesterUK
- Joint UNIversities Pandemic and Epidemiological ResearchUK
- The Alan Turing InstituteLondonUK
- Joint Modelling TeamPublic Health EnglandLondonUK
- School of Health SciencesThe University of ManchesterManchesterUK
| | - Thomas A. House
- Department of MathematicsThe University of ManchesterManchesterUK
- Joint UNIversities Pandemic and Epidemiological ResearchUK
- The Alan Turing InstituteLondonUK
| | - Matt J. Keeling
- Joint UNIversities Pandemic and Epidemiological ResearchUK
- Mathematics Institute and School of Life SciencesUniversity of WarwickCoventryUK
| | - Jonathan M. Read
- Joint UNIversities Pandemic and Epidemiological ResearchUK
- Centre for Health Informatics, Computing and Statistics, Lancaster Medical SchoolLancaster UniversityLancasterUK
| | | | - Daniela De Angelis
- Joint UNIversities Pandemic and Epidemiological ResearchUK
- MRC Biostatistics Unit, School of Clinical MedicineUniversity of CambridgeCambridgeUK
- Statistics Modelling and Economics DepartmentPublic Health EnglandLondonUK
- Joint Modelling TeamPublic Health EnglandLondonUK
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Seaman SR, Nyberg T, Overton CE, Pascall DJ, Presanis AM, De Angelis D. Adjusting for time of infection or positive test when estimating the risk of a post-infection outcome in an epidemic. Stat Methods Med Res 2022; 31:1942-1958. [PMID: 35695245 PMCID: PMC7613654 DOI: 10.1177/09622802221107105] [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: 12/27/2022]
Abstract
When comparing the risk of a post-infection binary outcome, for example, hospitalisation, for two variants of an infectious pathogen, it is important to adjust for calendar time of infection. Typically, the infection time is unknown and positive test time used as a proxy for it. Positive test time may also be used when assessing how risk of the outcome changes over calendar time. We show that if time from infection to positive test is correlated with the outcome, the risk conditional on positive test time is a function of the trajectory of infection incidence. Hence, a risk ratio adjusted for positive test time can be quite different from the risk ratio adjusted for infection time. We propose a simple sensitivity analysis that indicates how risk ratios adjusted for positive test time and infection time may differ. This involves adjusting for a shifted positive test time, shifted to make the difference between it and infection time uncorrelated with the outcome. We illustrate this method by reanalysing published results on the relative risk of hospitalisation following infection with the Alpha versus pre-existing variants of SARS-CoV-2. Results indicate the relative risk adjusted for infection time may be lower than that adjusted for positive test time.
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Affiliation(s)
- Shaun R Seaman
- MRC Biostatistics Unit, University of Cambridge, Cambridge, UK
- Shaun Seaman, MRC Biostatistics Unit, University of Cambridge, East Forvie Building, Forvie Site, Robinson Way, Cambridge, CB2 0SR, UK.
| | - Tommy Nyberg
- MRC Biostatistics Unit, University of Cambridge, Cambridge, UK
| | - Christopher E Overton
- Department of Mathematics, University of Manchester, UK
- Clinical Data Science Unit, Manchester University NHS Foundation Trust, UK
- Joint Universities Pandemic and Epidemiological Research (JUNIPER) consortium, Cambridge, UK
| | - David J Pascall
- MRC Biostatistics Unit, University of Cambridge, Cambridge, UK
- Joint Universities Pandemic and Epidemiological Research (JUNIPER) consortium, Cambridge, UK
| | - Anne M Presanis
- MRC Biostatistics Unit, University of Cambridge, Cambridge, UK
| | - Daniela De Angelis
- MRC Biostatistics Unit, University of Cambridge, Cambridge, UK
- Joint Universities Pandemic and Epidemiological Research (JUNIPER) consortium, Cambridge, UK
- Statistics, Modelling and Economics Department, UKHSA, London, UK
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Overton CE, Pellis L, Stage HB, Scarabel F, Burton J, Fraser C, Hall I, House TA, Jewell C, Nurtay A, Pagani F, Lythgoe KA. EpiBeds: Data informed modelling of the COVID-19 hospital burden in England. PLoS Comput Biol 2022; 18:e1010406. [PMID: 36067224 PMCID: PMC9481171 DOI: 10.1371/journal.pcbi.1010406] [Citation(s) in RCA: 0] [Impact Index Per Article: 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: 12/04/2021] [Revised: 09/16/2022] [Accepted: 07/18/2022] [Indexed: 11/24/2022] Open
Abstract
The first year of the COVID-19 pandemic put considerable strain on healthcare systems worldwide. In order to predict the effect of the local epidemic on hospital capacity in England, we used a variety of data streams to inform the construction and parameterisation of a hospital progression model, EpiBeds, which was coupled to a model of the generalised epidemic. In this model, individuals progress through different pathways (e.g. may recover, die, or progress to intensive care and recover or die) and data from a partially complete patient-pathway line-list was used to provide initial estimates of the mean duration that individuals spend in the different hospital compartments. We then fitted EpiBeds using complete data on hospital occupancy and hospital deaths, enabling estimation of the proportion of individuals that follow the different clinical pathways, the reproduction number of the generalised epidemic, and to make short-term predictions of hospital bed demand. The construction of EpiBeds makes it straightforward to adapt to different patient pathways and settings beyond England. As part of the UK response to the pandemic, EpiBeds provided weekly forecasts to the NHS for hospital bed occupancy and admissions in England, Wales, Scotland, and Northern Ireland at national and regional scales. COVID-19, the disease caused by SARS-CoV-2, leads to a high proportion of cases requiring admission to hospital. Coupled with the high burden of infections worldwide, this put substantial pressure on healthcare systems. To enable public health systems to cope with the high levels of demand, forecasting models are vital. These models enable public health managers to plan their workloads accordingly. Here, we developed EpiBeds, which combines an epidemic model with a model for patient flow through hospitals. By fitting this model to data from England, EpiBeds has been used to provide short-term forecasts of hospital admissions and bed demand weekly throughout the COVID-19 pandemic. In this paper, we describe the motivation behind the structure of EpiBeds, how the model is fitted to data, and report the estimates of the key parameters throughout the pandemic. We then evaluate the performance of EpiBeds by comparing generated forecasts to future data points, finding good agreement between the forecasts and data.
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Affiliation(s)
- Christopher E. Overton
- Department of Mathematics, University of Manchester, Manchester United Kingdom
- Clinical Data Science Unit, Manchester University NHS Foundation Trust, Manchester, United Kingdom
- Joint UNIversities Pandemic and Epidemiological Research, https://maths.org/juniper/. Cambridge, United Kingdom
- Infectious Disease Modelling, All Hazards Intelligence, UK Health Security Agency, London, United Kingdom
- * E-mail:
| | - Lorenzo Pellis
- Department of Mathematics, University of Manchester, Manchester United Kingdom
- Joint UNIversities Pandemic and Epidemiological Research, https://maths.org/juniper/. Cambridge, United Kingdom
- Alan Turing Institute, London, United Kingdom
| | - Helena B. Stage
- Department of Mathematics, University of Manchester, Manchester United Kingdom
- The Humboldt University of Berlin, Berlin, Germany
- The University of Potsdam, Potsdam, Germany
| | - Francesca Scarabel
- Department of Mathematics, University of Manchester, Manchester United Kingdom
- Joint UNIversities Pandemic and Epidemiological Research, https://maths.org/juniper/. Cambridge, United Kingdom
| | - Joshua Burton
- Faculty of Biology Medicine and Health, Division of Informatics, Imaging and Data Sciences, University of Manchester, Manchester, United Kingdom
| | - Christophe Fraser
- Big Data Institute, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine, NIHR Biomedical Research Centre, University of Oxford, Oxford, United Kingdom
- Wellcome Sanger Institute, Cambridge, United Kingdom
| | - Ian Hall
- Department of Mathematics, University of Manchester, Manchester United Kingdom
- Clinical Data Science Unit, Manchester University NHS Foundation Trust, Manchester, United Kingdom
- Joint UNIversities Pandemic and Epidemiological Research, https://maths.org/juniper/. Cambridge, United Kingdom
- Alan Turing Institute, London, United Kingdom
- Emergency Preparedness, Health Protection Division, UK Health Security Agency, London, United Kingdom
| | - Thomas A. House
- Department of Mathematics, University of Manchester, Manchester United Kingdom
- Clinical Data Science Unit, Manchester University NHS Foundation Trust, Manchester, United Kingdom
- Joint UNIversities Pandemic and Epidemiological Research, https://maths.org/juniper/. Cambridge, United Kingdom
- Alan Turing Institute, London, United Kingdom
- Faculty of Biology Medicine and Health, Division of Informatics, Imaging and Data Sciences, University of Manchester, Manchester, United Kingdom
- IBM Research, Hartree Centre, Daresbury, United Kingdom
| | - Chris Jewell
- CHICAS, Lancaster Medical School, Lancaster University, Lancaster, United Kingdom
| | - Anel Nurtay
- Big Data Institute, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - Filippo Pagani
- Department of Mathematics, University of Manchester, Manchester United Kingdom
- MRC Biostatistics Unit, University of Cambridge, Cambridge, United Kingdom
| | - Katrina A. Lythgoe
- Big Data Institute, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
- Department of Biology, University of Oxford, Oxford, United Kingdom
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Abstract
The emergence of the B.1.1.529 (Omicron) variant caused international concern due to its rapid spread in Southern Africa. It was unknown whether this variant would replace or co-exist with (either transiently or long-term) the then-dominant Delta variant on its introduction to England. We developed a set of hierarchical logistic growth models to describe changes in the frequency of S gene target failure (SGTF) PCR tests, which was a proxy for Omicron. The doubling time of SGTF cases peaked at 1.56 days (95% CI: 1.49, 1.63) on the 5th of December, while triple positive cases were halving every 5.82 days (95% CI: 5.11, 6.67) going into Christmas 2021. We were unable to characterize the replacement of Delta by Omicron with a single rate. The replacement rate decreased by 53.56% (95% CrI: 45.38, 61.01) between the 14th and 15th of December, meaning the competitive advantage of Omicron approximately halved. Preceding the changepoint, Omicron was replacing Delta 16.24% (95% CrI: 9.72, 23.41) faster in those with two or more vaccine doses, indicative of vaccine escape being a substantial component of the competitive advantage. Despite the slowdown, Delta had almost entirely been replaced in England within a month of the first sequenced domestic case. The synchrony of changepoints across regions at various stages of Omicron epidemics suggests that the growth rate advantage was not attenuated due to biological mechanisms related to strain competition. The step-change in replacement could have resulted from behavioral changes, potentially elicited by public health messaging or policies, that differentially affected Omicron.
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Affiliation(s)
- Robert S Paton
- Data Science and Analytics, UK Health Security Agency, Nobel House, London, UK, SW1P 3JR
| | - Christopher E Overton
- Data Science and Analytics, UK Health Security Agency, Nobel House, London, UK, SW1P 3JR
| | - Thomas Ward
- Data Science and Analytics, UK Health Security Agency, Nobel House, London, UK, SW1P 3JR
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13
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Pattni K, Hungerford D, Adams S, Buchan I, Cheyne CP, García-Fiñana M, Hall I, Hughes DM, Overton CE, Zhang X, Sharkey KJ. Effectiveness of the BNT162b2 (Pfizer-BioNTech) and the ChAdOx1 nCoV-19 (Oxford-AstraZeneca) vaccines for reducing susceptibility to infection with the Delta variant (B.1.617.2) of SARS-CoV-2. BMC Infect Dis 2022; 22:270. [PMID: 35307024 PMCID: PMC8934524 DOI: 10.1186/s12879-022-07239-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2021] [Accepted: 03/03/2022] [Indexed: 12/24/2022] Open
Abstract
Background From January to May 2021 the alpha variant (B.1.1.7) of SARS-CoV-2 was the most commonly detected variant in the UK. Following this, the Delta variant (B.1.617.2) then became the predominant variant. The UK COVID-19 vaccination programme started on 8th December 2020. Prior to the Delta variant, most vaccine effectiveness studies focused on the alpha variant. We therefore aimed to estimate the effectiveness of the BNT162b2 (Pfizer-BioNTech) and the ChAdOx1 nCoV-19 (Oxford-AstraZeneca) vaccines in preventing symptomatic and asymptomatic infection with respect to the Delta variant in a UK setting. Methods We used anonymised public health record data linked to infection data (PCR) using the Combined Intelligence for Population Health Action resource. We then constructed an SIR epidemic model to explain SARS-CoV-2 infection data across the Cheshire and Merseyside region of the UK. Vaccines were assumed to be effective after 21 days for 1 dose and 14 days for 2 doses. Results We determined that the effectiveness of the Oxford-AstraZeneca vaccine in reducing susceptibility to infection is 39% (95% credible interval [34, 43]) and 64% (95% credible interval [61, 67]) for a single dose and a double dose respectively. For the Pfizer-BioNTech vaccine, the effectiveness is 20% (95% credible interval [10, 28]) and 84% (95% credible interval [82, 86]) for a single-dose and a double dose respectively. Conclusion Vaccine effectiveness for reducing susceptibility to SARS-CoV-2 infection shows noticeable improvement after receiving two doses of either vaccine. Findings also suggest that a full course of the Pfizer-BioNTech provides the optimal protection against infection with the Delta variant. This reinforces the need to complete the full course programme to maximise individual protection and reduce transmission. Supplementary Information The online version contains supplementary material available at 10.1186/s12879-022-07239-z.
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14
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Kretzschmar ME, Ashby B, Fearon E, Overton CE, Panovska-Griffiths J, Pellis L, Quaife M, Rozhnova G, Scarabel F, Stage HB, Swallow B, Thompson RN, Tildesley MJ, Villela D. Challenges for modelling interventions for future pandemics. Epidemics 2022; 38:100546. [PMID: 35183834 PMCID: PMC8830929 DOI: 10.1016/j.epidem.2022.100546] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [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: 07/05/2021] [Revised: 02/04/2022] [Accepted: 02/09/2022] [Indexed: 12/16/2022] Open
Abstract
Mathematical modelling and statistical inference provide a framework to evaluate different non-pharmaceutical and pharmaceutical interventions for the control of epidemics that has been widely used during the COVID-19 pandemic. In this paper, lessons learned from this and previous epidemics are used to highlight the challenges for future pandemic control. We consider the availability and use of data, as well as the need for correct parameterisation and calibration for different model frameworks. We discuss challenges that arise in describing and distinguishing between different interventions, within different modelling structures, and allowing both within and between host dynamics. We also highlight challenges in modelling the health economic and political aspects of interventions. Given the diversity of these challenges, a broad variety of interdisciplinary expertise is needed to address them, combining mathematical knowledge with biological and social insights, and including health economics and communication skills. Addressing these challenges for the future requires strong cross-disciplinary collaboration together with close communication between scientists and policy makers.
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Affiliation(s)
- Mirjam E Kretzschmar
- Julius Center for Health Sciences and Primary Care, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands.
| | - Ben Ashby
- Department of Mathematical Sciences, University of Bath, Bath BA2 7AY, UK
| | - Elizabeth Fearon
- Department of Global Health and Development, London School of Hygiene and Tropical Medicine, London, UK; Centre for the Mathematical Modelling of Infectious Diseases, London School of Hygiene and Tropical Medicine, UK
| | - Christopher E Overton
- Department of Mathematics, University of Manchester, UK; Joint UNIversities Pandemic and Epidemiological Research, UK; Clinical Data Science Unit, Manchester University NHS Foundation Trust, UK
| | - Jasmina Panovska-Griffiths
- The Big Data Institute, Nuffield Department of Medicine, University of Oxford, Oxford, UK; The Queen's College, University of Oxford, Oxford, UK
| | - Lorenzo Pellis
- Department of Mathematics, University of Manchester, UK; Joint UNIversities Pandemic and Epidemiological Research, UK; The Alan Turing Institute, London, UK
| | - Matthew Quaife
- TB Modelling Group, Faculty of Epidemiology and Population Health, London School of Hygiene and Tropical Medicine, UK
| | - Ganna Rozhnova
- Julius Center for Health Sciences and Primary Care, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands; BioISI-Biosystems & Integrative Sciences Institute, Faculdade de Ciências, Universidade de Lisboa, Lisbon, Portugal
| | - Francesca Scarabel
- Department of Mathematics, University of Manchester, UK; Joint UNIversities Pandemic and Epidemiological Research, UK; CDLab - Computational Dynamics Laboratory, Department of Mathematics, Computer Science and Physics, University of Udine, Italy
| | - Helena B Stage
- Department of Mathematics, University of Manchester, UK; Joint UNIversities Pandemic and Epidemiological Research, UK; University of Potsdam, Germany; Humboldt University of Berlin, Germany
| | - Ben Swallow
- School of Mathematics and Statistics, University of Glasgow, Glasgow, UK; Scottish Covid-19 Response Consortium, UK
| | - Robin N Thompson
- Joint UNIversities Pandemic and Epidemiological Research, UK; Mathematics Institute, University of Warwick, Coventry CV4 7AL, UK; Zeeman Institute for Systems Biology and Infectious Disease Epidemiology Research, University of Warwick, Coventry CV4 7AL, UK
| | - Michael J Tildesley
- Joint UNIversities Pandemic and Epidemiological Research, UK; Mathematics Institute, University of Warwick, Coventry CV4 7AL, UK; Zeeman Institute for Systems Biology and Infectious Disease Epidemiology Research, University of Warwick, Coventry CV4 7AL, UK
| | - Daniel Villela
- Program of Scientific Computing, Oswaldo Cruz Foundation, Rio de Janeiro, Brazil
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15
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Swallow B, Birrell P, Blake J, Burgman M, Challenor P, Coffeng LE, Dawid P, De Angelis D, Goldstein M, Hemming V, Marion G, McKinley TJ, Overton CE, Panovska-Griffiths J, Pellis L, Probert W, Shea K, Villela D, Vernon I. Challenges in estimation, uncertainty quantification and elicitation for pandemic modelling. Epidemics 2022; 38:100547. [PMID: 35180542 PMCID: PMC7612598 DOI: 10.1016/j.epidem.2022.100547] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2021] [Revised: 12/22/2021] [Accepted: 02/09/2022] [Indexed: 12/15/2022] Open
Affiliation(s)
- Ben Swallow
- School of Mathematics and Statistics, University of Glasgow, Glasgow, UK; Scottish COVID-19 Response Consortium, UK.
| | - Paul Birrell
- Analytics & Data Science, UKHSA, UK; MRC Biostatistics Unit, University of Cambridge, Cambridge, UK
| | - Joshua Blake
- MRC Biostatistics Unit, University of Cambridge, Cambridge, UK
| | - Mark Burgman
- Centre for Environmental Policy, Imperial College London, London, UK
| | - Peter Challenor
- The Alan Turing Institute, London, UK; College of Engineering, Mathematics and Physical Sciences, University of Exeter, Exeter, UK
| | - Luc E Coffeng
- Department of Public Health, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Philip Dawid
- Statistical Laboratory, University of Cambridge, Cambridge, UK
| | - Daniela De Angelis
- MRC Biostatistics Unit, University of Cambridge, Cambridge, UK; Joint UNIversities Pandemic and Epidemiological Research, UK
| | - Michael Goldstein
- Department of Mathematical Sciences, Durham University, Stockton Road, Durham, UK
| | - Victoria Hemming
- Department of Forest and Conservation Sciences, University of British Columbia, Vancouver, Canada
| | - Glenn Marion
- Scottish COVID-19 Response Consortium, UK; Biomathematics and Statistics Scotland, Edinburgh, UK
| | - Trevelyan J McKinley
- College of Medicine and Health, University of Exeter, Exeter, UK; Joint UNIversities Pandemic and Epidemiological Research, UK
| | - Christopher E Overton
- Department of Mathematics, University of Manchester, Manchester, UK; Clinical Data Science Unit, Manchester University NHS Foundation Trust, Manchester, UK; Joint UNIversities Pandemic and Epidemiological Research, UK
| | - Jasmina Panovska-Griffiths
- The Big Data Institute, University of Oxford, Oxford, UK; The Queen's College, University of Oxford, Oxford, UK
| | - Lorenzo Pellis
- Department of Mathematics, University of Manchester, Manchester, UK; Joint UNIversities Pandemic and Epidemiological Research, UK; The Alan Turing Institute, London, UK
| | - Will Probert
- The Big Data Institute, University of Oxford, Oxford, UK
| | - Katriona Shea
- Department of Biology and Centre for Infectious Disease Dynamics, The Pennsylvania State University, PA 16802, USA
| | - Daniel Villela
- Program of Scientific Computing, Fundação Oswaldo Cruz, Rio de Janeiro, Brazil
| | - Ian Vernon
- Department of Mathematical Sciences, Durham University, Stockton Road, Durham, UK
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16
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Pellis L, Scarabel F, Stage HB, Overton CE, Chappell LHK, Fearon E, Bennett E, Lythgoe KA, House TA, Hall I. Challenges in control of COVID-19: short doubling time and long delay to effect of interventions. Philos Trans R Soc Lond B Biol Sci 2021; 376:20200264. [PMID: 34053267 PMCID: PMC8165602 DOI: 10.1098/rstb.2020.0264] [Citation(s) in RCA: 65] [Impact Index Per Article: 21.7] [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: 04/21/2021] [Indexed: 12/20/2022] Open
Abstract
Early assessments of the growth rate of COVID-19 were subject to significant uncertainty, as expected with limited data and difficulties in case ascertainment, but as cases were recorded in multiple countries, more robust inferences could be made. Using multiple countries, data streams and methods, we estimated that, when unconstrained, European COVID-19 confirmed cases doubled on average every 3 days (range 2.2-4.3 days) and Italian hospital and intensive care unit admissions every 2-3 days; values that are significantly lower than the 5-7 days dominating the early published literature. Furthermore, we showed that the impact of physical distancing interventions was typically not seen until at least 9 days after implementation, during which time confirmed cases could grow eightfold. We argue that such temporal patterns are more critical than precise estimates of the time-insensitive basic reproduction number R0 for initiating interventions, and that the combination of fast growth and long detection delays explains the struggle in countries' outbreak response better than large values of R0 alone. One year on from first reporting these results, reproduction numbers continue to dominate the media and public discourse, but robust estimates of unconstrained growth remain essential for planning worst-case scenarios, and detection delays are still key in informing the relaxation and re-implementation of interventions. 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)
- Lorenzo Pellis
- Department of Mathematics, The University of Manchester, Manchester, UK
- Joint UNIversities Pandemic and Epidemiological Research, UK
- The Alan Turing Institute, London, UK
| | - Francesca Scarabel
- Department of Mathematics, The University of Manchester, Manchester, UK
- Joint UNIversities Pandemic and Epidemiological Research, UK
- LIAM - Laboratory of Industrial and Applied Mathematics, Department of Mathematics and Statistics, York University, Toronto, Ontario, Canada
- CDLab - Computational Dynamics Laboratory, Department of Mathematics, Computer Science and Physics, University of Udine, Italy
| | - Helena B. Stage
- Department of Mathematics, The University of Manchester, Manchester, UK
- Joint UNIversities Pandemic and Epidemiological Research, UK
| | - Christopher E. Overton
- Department of Mathematics, The University of Manchester, Manchester, UK
- Clinical Data Science Unit, Manchester University NHS Foundation Trust, Manchester, UK
- Joint UNIversities Pandemic and Epidemiological Research, UK
| | | | - Elizabeth Fearon
- Department of Global Health and Development, London School of Hygiene and Tropical Medicine, UK
- CMMID - Centre for the Mathematical Modelling of Infectious Disease, London School of Hygiene and Tropical Medicine, UK
| | - Emma Bennett
- Emergency Response Department, Public Health England, UK
| | - Katrina A. Lythgoe
- Big Data Institute, University of Oxford, UK
- Department of Zoology, University of Oxford, UK
| | - Thomas A. House
- Department of Mathematics, The University of Manchester, Manchester, UK
- Joint UNIversities Pandemic and Epidemiological Research, UK
- The Alan Turing Institute, London, UK
- IBM Research, Hartree Centre, SciTech Daresbury, Warrington, UK
| | - Ian Hall
- Department of Mathematics, The University of Manchester, Manchester, UK
- Joint UNIversities Pandemic and Epidemiological Research, UK
- The Alan Turing Institute, London, UK
- Emergency Response Department, Public Health England, UK
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17
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Overton CE, Sharkey KJ. Evolutionary bet-hedging in structured populations. J Math Biol 2021; 82:43. [PMID: 33796960 PMCID: PMC8016807 DOI: 10.1007/s00285-021-01597-z] [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] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2020] [Revised: 03/08/2021] [Accepted: 03/16/2021] [Indexed: 11/21/2022]
Abstract
As ecosystems evolve, species can become extinct due to fluctuations in the environment. This leads to the evolutionary adaption known as bet-hedging, where species hedge against these fluctuations to reduce their likelihood of extinction. Environmental variation can be either within or between generations. Previous work has shown that selection for bet-hedging against within-generational variation should not occur in large populations. However, this work has been limited by assumptions of well-mixed populations, whereas real populations usually have some degree of structure. Using the framework of evolutionary graph theory, we show that through adding competition structure to the population, within-generational variation can have a significant impact on the evolutionary process for any population size. This complements research using subdivided populations, which suggests that within-generational variation is important when local population sizes are small. Together, these conclusions provide evidence to support observations by some ecologists that are contrary to the widely held view that only between-generational environmental variation has an impact on natural selection. This provides theoretical justification for further empirical study into this largely unexplored area.
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18
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Pattni K, Overton CE, Sharkey KJ. Evolutionary graph theory derived from eco-evolutionary dynamics. J Theor Biol 2021; 519:110648. [PMID: 33636202 DOI: 10.1016/j.jtbi.2021.110648] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2020] [Revised: 02/15/2021] [Accepted: 02/18/2021] [Indexed: 11/28/2022]
Abstract
A biologically motivated individual-based framework for evolution in network-structured populations is developed that can accommodate eco-evolutionary dynamics. This framework is used to construct a network birth and death model. The evolutionary graph theory model, which considers evolutionary dynamics only, is derived as a special case, highlighting additional assumptions that diverge from real biological processes. This is achieved by introducing a negative ecological feedback loop that suppresses ecological dynamics by forcing births and deaths to be coupled. We also investigate how fitness, a measure of reproductive success used in evolutionary graph theory, is related to the life-history of individuals in terms of their birth and death rates. In simple networks, these ecologically motivated dynamics are used to provide new insight into the spread of adaptive mutations, both with and without clonal interference. For example, the star network, which is known to be an amplifier of selection in evolutionary graph theory, can inhibit the spread of adaptive mutations when individuals can die naturally.
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Affiliation(s)
- Karan Pattni
- Department of Mathematical Sciences, University of Liverpool, United Kingdom.
| | | | - Kieran J Sharkey
- Department of Mathematical Sciences, University of Liverpool, United Kingdom.
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19
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Overton CE, Stage HB, Ahmad S, Curran-Sebastian J, Dark P, Das R, Fearon E, Felton T, Fyles M, Gent N, Hall I, House T, Lewkowicz H, Pang X, Pellis L, Sawko R, Ustianowski A, Vekaria B, Webb L. Using statistics and mathematical modelling to understand infectious disease outbreaks: COVID-19 as an example. Infect Dis Model 2020; 5:409-441. [PMID: 32691015 PMCID: PMC7334973 DOI: 10.1016/j.idm.2020.06.008] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [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] [Received: 05/21/2020] [Revised: 06/30/2020] [Accepted: 06/30/2020] [Indexed: 01/12/2023] Open
Abstract
During an infectious disease outbreak, biases in the data and complexities of the underlying dynamics pose significant challenges in mathematically modelling the outbreak and designing policy. Motivated by the ongoing response to COVID-19, we provide a toolkit of statistical and mathematical models beyond the simple SIR-type differential equation models for analysing the early stages of an outbreak and assessing interventions. In particular, we focus on parameter estimation in the presence of known biases in the data, and the effect of non-pharmaceutical interventions in enclosed subpopulations, such as households and care homes. We illustrate these methods by applying them to the COVID-19 pandemic.
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Affiliation(s)
- Christopher E Overton
- Department of Mathematics, University of Manchester, UK
- Department of Mathematical Sciences, University of Liverpool, UK
| | | | - Shazaad Ahmad
- Department of Virology, Manchester Medical Microbiology Partnership, Manchester Foundation Trust, UK
- Manchester Academic Health Sciences Centre, UK
| | | | - Paul Dark
- Division of Infection, Immunity and Respiratory Medicine, NIHR Biomedical Research Centre, University of Manchester, UK
- Critical Care Unit, Salford Royal Hospital, Northern Care Alliance NHS Group, UK
| | - Rajenki Das
- Department of Mathematics, University of Manchester, UK
| | - Elizabeth Fearon
- Department of Global Health and Development, London School of Hygiene and Tropical Medicine, UK
| | - Timothy Felton
- Division of Infection, Immunity and Respiratory Medicine, NIHR Biomedical Research Centre, University of Manchester, UK
- Intensive Care Unit, Wythenshawe Hospital, Manchester University NHS Foundation Trust, UK
| | - Martyn Fyles
- Department of Mathematics, University of Manchester, UK
- The Alan Turing Institute, UK
| | - Nick Gent
- Emergency Response Department, Public Health England, UK
| | - Ian Hall
- Department of Mathematics, University of Manchester, UK
- Emergency Response Department, Public Health England, UK
| | - Thomas House
- Department of Mathematics, University of Manchester, UK
- IBM Research, Hartree Centre, SciTech Daresbury, UK
| | - Hugo Lewkowicz
- Department of Health Sciences, University of Manchester, UK
- Department of Mathematics, University of Manchester, UK
| | - Xiaoxi Pang
- Department of Mathematics, University of Manchester, UK
| | | | - Robert Sawko
- IBM Research, Hartree Centre, SciTech Daresbury, UK
| | - Andrew Ustianowski
- Regional Infectious Diseases Unit, North Manchester General Hospital, UK
- School of Medical Sciences, University of Manchester, UK
| | - Bindu Vekaria
- Department of Mathematics, University of Manchester, UK
| | - Luke Webb
- Department of Mathematics, University of Manchester, UK
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20
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Okeke Ogwulu CB, Goranitis I, Devall AJ, Cheed V, Gallos ID, Middleton LJ, Harb HM, Williams HM, Eapen A, Daniels JP, Ahmed A, Bender-Atik R, Bhatia K, Bottomley C, Brewin J, Choudhary M, Deb S, Duncan WC, Ewer AK, Hinshaw K, Holland T, Izzat F, Johns J, Lumsden M, Manda P, Norman JE, Nunes N, Overton CE, Kriedt K, Quenby S, Rao S, Ross J, Shahid A, Underwood M, Vaithilingham N, Watkins L, Wykes C, Horne AW, Jurkovic D, Coomarasamy A, Roberts TE. The cost-effectiveness of progesterone in preventing miscarriages in women with early pregnancy bleeding: an economic evaluation based on the PRISM trial. BJOG 2020; 127:757-767. [PMID: 32003141 PMCID: PMC7187468 DOI: 10.1111/1471-0528.16068] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [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] [Accepted: 12/12/2019] [Indexed: 11/27/2022]
Abstract
OBJECTIVES To assess the cost-effectiveness of progesterone compared with placebo in preventing pregnancy loss in women with early pregnancy vaginal bleeding. DESIGN Economic evaluation alongside a large multi-centre randomised placebo-controlled trial. SETTING Forty-eight UK NHS early pregnancy units. POPULATION Four thousand one hundred and fifty-three women aged 16-39 years with bleeding in early pregnancy and ultrasound evidence of an intrauterine sac. METHODS An incremental cost-effectiveness analysis was performed from National Health Service (NHS) and NHS and Personal Social Services perspectives. Subgroup analyses were carried out on women with one or more and three or more previous miscarriages. MAIN OUTCOME MEASURES Cost per additional live birth at ≥34 weeks of gestation. RESULTS Progesterone intervention led to an effect difference of 0.022 (95% CI -0.004 to 0.050) in the trial. The mean cost per woman in the progesterone group was £76 (95% CI -£559 to £711) more than the mean cost in the placebo group. The incremental cost-effectiveness ratio for progesterone compared with placebo was £3305 per additional live birth. For women with at least one previous miscarriage, progesterone was more effective than placebo with an effect difference of 0.055 (95% CI 0.014-0.096) and this was associated with a cost saving of £322 (95% CI -£1318 to £673). CONCLUSIONS The results suggest that progesterone is associated with a small positive impact and a small additional cost. Both subgroup analyses were more favourable, especially for women who had one or more previous miscarriages. Given available evidence, progesterone is likely to be a cost-effective intervention, particularly for women with previous miscarriage(s). TWEETABLE ABSTRACT Progesterone treatment is likely to be cost-effective in women with early pregnancy bleeding and a history of miscarriage.
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Affiliation(s)
- C B Okeke Ogwulu
- Health Economics Unit, College of Medical and Dental Sciences, Institute of Applied Health Research, University of Birmingham, Birmingham, UK
| | - I Goranitis
- Health Economics Unit, College of Medical and Dental Sciences, Institute of Applied Health Research, University of Birmingham, Birmingham, UK.,Health Economics Unit, Centre for Health Policy, Melbourne School of Population and Global Health, The University of Melbourne, Melbourne, Vic., Australia
| | - A J Devall
- College of Medical and Dental Sciences, Institute of Metabolism and Systems Research, University of Birmingham, Birmingham, UK
| | - V Cheed
- College of Medical and Dental Sciences, Institute of Applied Health Research, University of Birmingham, Birmingham, UK
| | - I D Gallos
- College of Medical and Dental Sciences, Institute of Metabolism and Systems Research, University of Birmingham, Birmingham, UK
| | - L J Middleton
- College of Medical and Dental Sciences, Institute of Applied Health Research, University of Birmingham, Birmingham, UK
| | - H M Harb
- College of Medical and Dental Sciences, Institute of Metabolism and Systems Research, University of Birmingham, Birmingham, UK
| | - H M Williams
- College of Medical and Dental Sciences, Institute of Metabolism and Systems Research, University of Birmingham, Birmingham, UK
| | - A Eapen
- Carver College of Medicine, University of Iowa Health Care, Iowa City, IA, USA
| | - J P Daniels
- Faculty of Medicine & Health Sciences, Queen's Medical Centre, University of Nottingham, Nottingham, UK
| | - A Ahmed
- Sunderland Royal Hospital, City Hospitals Sunderland NHS Foundation Trust, Sunderland, UK
| | | | - K Bhatia
- Burnley General Hospital, East Lancashire Hospitals NHS Trust, Burnley, UK
| | - C Bottomley
- University College Hospital, University College London Hospitals NHS Foundation Trust, London, UK
| | | | - M Choudhary
- Royal Victoria Infirmary, Newcastle upon Tyne Hospitals NHS Foundation Trust, Newcastle upon Tyne, UK
| | - S Deb
- Queen's Medical Centre, Nottingham University Hospitals NHS Trust, Nottingham, UK
| | - W C Duncan
- MRC Centre for Reproductive Health, the Queen's Medical Research Institute, University of Edinburgh, Edinburgh, UK
| | - A K Ewer
- College of Medical and Dental Sciences, Institute of Metabolism and Systems Research, University of Birmingham, Birmingham, UK
| | - K Hinshaw
- Sunderland Royal Hospital, City Hospitals Sunderland NHS Foundation Trust, Sunderland, UK
| | - T Holland
- Guy's and St Thomas' Hospital, Guy's and St Thomas' NHS Foundation Trust, London, UK
| | - F Izzat
- University Hospital Coventry, University Hospitals Coventry and Warwickshire NHS Trust, Coventry, UK
| | - J Johns
- Kings College Hospital, King's College Hospital NHS Foundation Trust, London, UK
| | - M Lumsden
- Academic Unit of Reproductive and Maternal Medicine, University of Glasgow, Glasgow, UK
| | - P Manda
- James Cook University Hospital, South Tees Hospitals NHS Foundation Trust, Middlesbrough, UK
| | - J E Norman
- Faculty of Health Sciences, University of Bristol, Bristol, UK
| | - N Nunes
- West Middlesex University Hospital, Chelsea and Westminster Hospital NHS Foundation Trust, Isleworth, UK
| | - C E Overton
- St Michael's Hospital, University Hospitals Bristol NHS Foundation Trust, Bristol, UK
| | - K Kriedt
- University College Hospital, University College London Hospitals NHS Foundation Trust, London, UK
| | - S Quenby
- Biomedical Research Unit in Reproductive Health, University of Warwick, Warwick, UK
| | - S Rao
- Whiston Hospital, St Helen's and Knowsley Teaching Hospitals NHS Trust, Whiston, Prescot, UK
| | - J Ross
- Academic Unit of Reproductive and Maternal Medicine, University of Glasgow, Glasgow, UK
| | - A Shahid
- Whipps Cross Hospital, Barts Health NHS Trust, Leytonstone, London, UK
| | - M Underwood
- Princess Royal Hospital, Shrewsbury and Telford Hospital NHS Trust, Apley, Telford, UK
| | - N Vaithilingham
- Portsmouth Hospitals NHS Trust, Queen Alexandra Hospital, Cosham, Portsmouth, UK
| | - L Watkins
- Liverpool Women's Hospital, Liverpool Women's NHS Foundation Trust, Liverpool Women's Hospital, Liverpool, UK
| | - C Wykes
- East Surrey Hospital, Surrey and Sussex Healthcare NHS Trust, Redhill, UK
| | - A W Horne
- MRC Centre for Reproductive Health, the Queen's Medical Research Institute, University of Edinburgh, Edinburgh, UK
| | - D Jurkovic
- University College Hospital, University College London Hospitals NHS Foundation Trust, London, UK
| | - A Coomarasamy
- College of Medical and Dental Sciences, Institute of Metabolism and Systems Research, University of Birmingham, Birmingham, UK
| | - T E Roberts
- Health Economics Unit, College of Medical and Dental Sciences, Institute of Applied Health Research, University of Birmingham, Birmingham, UK
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Overton CE, Broom M, Hadjichrysanthou C, Sharkey KJ. Methods for approximating stochastic evolutionary dynamics on graphs. J Theor Biol 2019; 468:45-59. [PMID: 30772340 DOI: 10.1016/j.jtbi.2019.02.009] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [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: 05/20/2018] [Revised: 02/07/2019] [Accepted: 02/13/2019] [Indexed: 10/27/2022]
Abstract
Population structure can have a significant effect on evolution. For some systems with sufficient symmetry, analytic results can be derived within the mathematical framework of evolutionary graph theory which relate to the outcome of the evolutionary process. However, for more complicated heterogeneous structures, computationally intensive methods are required such as individual-based stochastic simulations. By adapting methods from statistical physics, including moment closure techniques, we first show how to derive existing homogenised pair approximation models and the exact neutral drift model. We then develop node-level approximations to stochastic evolutionary processes on arbitrarily complex structured populations represented by finite graphs, which can capture the different dynamics for individual nodes in the population. Using these approximations, we evaluate the fixation probability of invading mutants for given initial conditions, where the dynamics follow standard evolutionary processes such as the invasion process. Comparisons with the output of stochastic simulations reveal the effectiveness of our approximations in describing the stochastic processes and in predicting the probability of fixation of mutants on a wide range of graphs. Construction of these models facilitates a systematic analysis and is valuable for a greater understanding of the influence of population structure on evolutionary processes.
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Affiliation(s)
- Christopher E Overton
- Department of Mathematical Sciences, University of Liverpool, Mathematical Sciences Building, Liverpool L69 7ZL, UK.
| | - Mark Broom
- Department of Mathematics, City, University of London, Northampton Square, London EC1V 0HB, UK
| | - Christoforos Hadjichrysanthou
- Department of Infectious Disease Epidemiology, School of Public Health, Imperial College London, St Mary's Campus, Norfolk Place, London W2 1PG, UK
| | - Kieran J Sharkey
- Department of Mathematical Sciences, University of Liverpool, Mathematical Sciences Building, Liverpool L69 7ZL, UK
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Overton CE, Warren RC. Surviving twins delivered at 29 weeks' gestation following abortion of one triplet at 15 weeks and rescue cervical cerclage. J OBSTET GYNAECOL 2004; 19:202-3. [PMID: 15512274 DOI: 10.1080/01443619965642] [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] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/16/2022]
Affiliation(s)
- C E Overton
- Department of Obstetrics and Gynaecology, Norfolk and Norwich Distric Hospital, UK
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MacDougall J, Davies MC, Overton CE, Gulekli B, Hall M, Bounds W, Jacobs HS, Guillebaud JG. Bone density in a population of long term oral contraceptive pill users does not differ from that in menstruating women. Br J Fam Plann 1999; 25:96-100. [PMID: 10567058] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 02/14/2023]
Abstract
Prevention of osteoporosis is a major public health issue. Amenorrhoeic women have lower bone density than normally menstruating women, which is related to the duration of amenorrhoea and the severity of oestrogen deficiency. Bone mineral density (BMD) in amenorrhoeic women can be improved by oestrogen replacement in the form of the combined oral contraceptive pill (COCP), so increased BMD might be an important non-contraceptive benefit of the COCP in menstruating women. Previous studies have been variably reported, but have used different methodologies for measurement of BMD. We measured BMD using the DEXA technique in long term COCP users and compared this with menstruating women who had never used the COCP. No differences in bone density were found, suggesting that the COCP does not improve bone mass in menstruating women who are adequately oestrogenised by their own ovaries.
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Affiliation(s)
- J MacDougall
- Department of Reproductive Endocrinology, The Middlesex Hospital, London, UK
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Overton CE, Fernàndez-Shaw S, Hicks B, Barlow DH, Starkey P. In vitro culture of endometrial stromal and gland cells as a model for endometriosis: the effect of peritoneal fluid on proliferation. Fertil Steril 1997; 67:51-6. [PMID: 8986683 DOI: 10.1016/s0015-0282(97)81855-9] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
OBJECTIVE To test the hypothesis that the cell-free fraction of PF from women with endometriosis affects the proliferation of endometrial epithelial and stromal cells in vitro. DESIGN A cell biologic and immunohistochemical study. SETTING University teaching hospital. PATIENT(S) Premenopausal women undergoing laparoscopy and women with histologically normal endometrium undergoing hysterectomy were selected. INTERVENTION(S) Peritoneal fluid (PF) and serum were collected at laparoscopy. Endometrial epithelial and stromal cells were obtained by enzymic dissociation of tissue, and epithelium was separated from stromal cells by sieving. Epithelial and stromal cell populations were purified by removal of contaminating cells using Thy-1-and CD-45-labeled immunomagnetic beads. Isolated endometrial gland and stromal cells were cultured in the presence of PF or serum from women with and without endometriosis. MAIN OUTCOME MEASURE(S) Cell proliferation was assessed by measurement of incorporation of 3[H]thymidine after 48 hours in culture. RESULT(S) Isolated endometrial gland and stromal cells were able to proliferate in vitro. The proliferative effect of PF or sera from women with endometriosis did not differ significantly from normal controls. CONCLUSION(S) We conclude that PF from women with endometriosis does not have an additional mitogenic effect compared with women without endometriosis. It may be postulated that the endometrium from women with endometriosis responds differently to the effects of PF.
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Affiliation(s)
- C E Overton
- Nuffield Department of Obstetrics and Gynaecology, John Radcliffe Hospital, Maternity Department, Headington, Oxford, United Kingdom.
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25
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Affiliation(s)
- C E Overton
- Department of Obstetrics and Gynaecology, Norfolk and Norwich District Hospital, UK
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Overton CE, Lindsay PC, Johal B, Collins SA, Siddle NC, Shaw RW, Barlow DH. A randomized, double-blind, placebo-controlled study of luteal phase dydrogesterone (Duphaston) in women with minimal to mild endometriosis. Fertil Steril 1994; 62:701-7. [PMID: 7926076 DOI: 10.1016/s0015-0282(16)56991-x] [Citation(s) in RCA: 78] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
OBJECTIVE To compare dydrogesterone with placebos in the treatment of minimal to mild endometriosis. DESIGN Prospective, double-blind, randomized study. SETTING Three Obstetrics and Gynaecology Departments in the United Kingdom. PATIENTS Sixty-two premenopausal women with complaints of pain (n = 12) and infertility with or without pain (n = 50) with minimal to mild endometriosis diagnosed at laparoscopy. Thirty-nine women had a laparoscopy after treatment and 56 women were followed up 12 months after treatment. INTERVENTIONS Two high doses of dydrogesterone (either 40 or 60 mg) or a placebo, which was given for 12 days, beginning 2 days after the LH surge for a treatment period of 6 months. MAIN OUTCOME MEASURES Change between before and after treatment endometriosis scores, pregnancy rates (PRs), and pain. RESULTS Treatment with dydrogesterone did not alter the natural history of endometriosis or PRs when compared with placebo. Pain was reduced significantly during treatment with 60 mg dydrogesterone and this improvement still was evident at 12-month follow-up. CONCLUSION Luteal phase dydrogesterone reduces pain associated with endometriosis.
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Affiliation(s)
- C E Overton
- John Radcliffe Hospital, Oxford, United Kingdom
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Overton CE, Kennedy SH, Egan DE, Barlow DH. The effect of nafarelin on human plasma adrenocorticotrophic hormone and cortisol concentrations. Hum Reprod 1993; 8:1593-7. [PMID: 8300812 DOI: 10.1093/oxfordjournals.humrep.a137897] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023] Open
Abstract
This study assessed the effects on plasma adrenocorticotrophic hormone (ACTH) and cortisol concentrations of 3 months' treatment with intranasal nafarelin 200 micrograms b.d. in 11 women (aged 26-43 years) for the treatment of endometriosis (n = 9), fibroids (n = 1) and pre-menstrual syndrome (n = 1). Serial blood samples were taken over 5 h, before and after nafarelin administration on the first day of treatment, and after 1 and 3 months' treatment. Control samples were taken before and after intranasal placebo administration on the day before nafarelin was commenced. The area under the curve (AUC) for mean ACTH concentrations at each time point from 0 to 240 min was calculated. There were no statistically significant changes in total secretion of either ACTH or cortisol. There was a transient rise in ACTH 30-60 min after nafarelin administration on the first day of treatment in seven out of 11 women. The rise did not exceed the normal range. Seven women with ovarian suppression (oestradiol concentration < 175 pmol/l by day 28) had consistently lower mean ACTH concentrations at all time points than the four remaining women who had oestradiol concentrations 222-880 pmol/l by day 28. Cortisol concentrations were unaffected by nafarelin. We conclude from the results of this study that 3 months' treatment with nafarelin has no effects on adrenal function, as assessed by ACTH and cortisol concentrations.
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Affiliation(s)
- C E Overton
- Nuffield Department of Obstetrics & Gynaecology, University of Oxford, John Radcliffe Hospital, UK
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