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Birrell P, Blake J, van Leeuwen E, Gent N, De Angelis D. Real-time nowcasting and forecasting of COVID-19 dynamics in England: the first wave. Philos Trans R Soc Lond B Biol Sci 2021; 376:20200279. [PMID: 34053254 PMCID: PMC8165585 DOI: 10.1098/rstb.2020.0279] [Citation(s) in RCA: 43] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/12/2021] [Indexed: 01/11/2023] Open
Abstract
England has been heavily affected by the SARS-CoV-2 pandemic, with severe 'lockdown' mitigation measures now gradually being lifted. The real-time pandemic monitoring presented here has contributed to the evidence informing this pandemic management throughout the first wave. Estimates on the 10 May showed lockdown had reduced transmission by 75%, the reproduction number falling from 2.6 to 0.61. This regionally varying impact was largest in London with a reduction of 81% (95% credible interval: 77-84%). Reproduction numbers have since then slowly increased, and on 19 June the probability of the epidemic growing was greater than 5% in two regions, South West and London. By this date, an estimated 8% of the population had been infected, with a higher proportion in London (17%). The infection-to-fatality ratio is 1.1% (0.9-1.4%) overall but 17% (14-22%) among the over-75s. This ongoing work continues to be key to quantifying any widespread resurgence, should accrued immunity and effective contact tracing be insufficient to preclude a second wave. 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)
- Paul Birrell
- Public Health England, National Infection Service, 61 Colindale Avenue, London NW9 5HT, UK
- MRC Biostatistics Unit, University of Cambridge, East Forvie Site Building, Forvie Site, Robinson Way, Cambridge Biomedical Campus, Cambridge CB2 OSR, UK
| | - Joshua Blake
- MRC Biostatistics Unit, University of Cambridge, East Forvie Site Building, Forvie Site, Robinson Way, Cambridge Biomedical Campus, Cambridge CB2 OSR, UK
| | - Edwin van Leeuwen
- Public Health England, National Infection Service, 61 Colindale Avenue, London NW9 5HT, UK
| | - Nick Gent
- Public Health England, Emergency Response Department, Porton Down, SP4 0JG, UK
| | - Daniela De Angelis
- Public Health England, National Infection Service, 61 Colindale Avenue, London NW9 5HT, UK
- MRC Biostatistics Unit, University of Cambridge, East Forvie Site Building, Forvie Site, Robinson Way, Cambridge Biomedical Campus, Cambridge CB2 OSR, UK
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Gu Y, DeDoncker E, VanEnk R, Paul R, Peters S, Stoltman G, Prieto D. Accuracy of State-Level Surveillance during Emerging Outbreaks of Respiratory Viruses: A Model-Based Assessment. Med Decis Making 2021; 41:1004-1016. [PMID: 34269123 PMCID: PMC8488654 DOI: 10.1177/0272989x211022276] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
It is long perceived that the more data collection, the more knowledge emerges about the real disease progression. During emergencies like the H1N1 and the severe acute respiratory syndrome coronavirus 2 pandemics, public health surveillance requested increased testing to address the exacerbated demand. However, it is currently unknown how accurately surveillance portrays disease progression through incidence and confirmed case trends. State surveillance, unlike commercial testing, can process specimens based on the upcoming demand (e.g., with testing restrictions). Hence, proper assessment of accuracy may lead to improvements for a robust infrastructure. Using the H1N1 pandemic experience, we developed a simulation that models the true unobserved influenza incidence trend in the State of Michigan, as well as trends observed at different data collection points of the surveillance system. We calculated the growth rate, or speed at which each trend increases during the pandemic growth phase, and we performed statistical experiments to assess the biases (or differences) between growth rates of unobserved and observed trends. We highlight the following results: 1) emergency-driven high-risk perception increases reporting, which leads to reduction of biases in the growth rates; 2) the best predicted growth rates are those estimated from the trend of specimens submitted to the surveillance point that receives reports from a variety of health care providers; and 3) under several criteria to queue specimens for viral subtyping with limited capacity, the best-performing criterion was to queue first-come, first-serve restricted to specimens with higher hospitalization risk. Under this criterion, the lab released capacity to subtype specimens for each day in the trend, which reduced the growth rate bias the most compared to other queuing criteria. Future research should investigate additional restrictions to the queue.
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Affiliation(s)
- Yuwen Gu
- Western Michigan University, Kalamazoo, MI, USA
| | | | | | - Rajib Paul
- University of North Carolina Charlotte College of Health and Human Services, Charlotte, NC, USA
| | - Susan Peters
- Michigan State University College of Human Medicine, East Lansing, MI, USA
| | - Gillian Stoltman
- Western Michigan University Homer Stryker MD School of Medicine, Kalamazoo, MI
| | - Diana Prieto
- Johns Hopkins University Carey Business School, Baltimore, MD, USA
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Fernández-Fontelo A, Moriña D, Cabaña A, Arratia A, Puig P. Estimating the real burden of disease under a pandemic situation: The SARS-CoV2 case. PLoS One 2020; 15:e0242956. [PMID: 33270713 PMCID: PMC7714127 DOI: 10.1371/journal.pone.0242956] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2020] [Accepted: 11/12/2020] [Indexed: 01/01/2023] Open
Abstract
The present paper introduces a new model used to study and analyse the severe acute respiratory syndrome coronavirus 2 (SARS-CoV2) epidemic-reported-data from Spain. This is a Hidden Markov Model whose hidden layer is a regeneration process with Poisson immigration, Po-INAR(1), together with a mechanism that allows the estimation of the under-reporting in non-stationary count time series. A novelty of the model is that the expectation of the unobserved process's innovations is a time-dependent function defined in such a way that information about the spread of an epidemic, as modelled through a Susceptible-Infectious-Removed dynamical system, is incorporated into the model. In addition, the parameter controlling the intensity of the under-reporting is also made to vary with time to adjust to possible seasonality or trend in the data. Maximum likelihood methods are used to estimate the parameters of the model.
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Affiliation(s)
- Amanda Fernández-Fontelo
- Chair of Statistics, School of Business and Economics, Humboldt-Universität zu Berlin, Berlin, Germany
| | - David Moriña
- Departament de Matemàtiques, Barcelona Graduate School of Mathematics (BGSMath), Universitat Autònoma de Barcelona, Barcelona, Spain
- Department of Econometrics, Statistics and Applied Economics, Riskcenter-IREA, Universitat de Barcelona, Barcelona, Spain
- Centre de Recerca Matemàtica (CRM), Barcelona, Spain
| | - Alejandra Cabaña
- Departament de Matemàtiques, Barcelona Graduate School of Mathematics (BGSMath), Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Argimiro Arratia
- Department of Computer Science, Universitat Politècnica de Catalunya, Barcelona, Spain
| | - Pere Puig
- Departament de Matemàtiques, Barcelona Graduate School of Mathematics (BGSMath), Universitat Autònoma de Barcelona, Barcelona, Spain
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Abstract
Background: Like other affected countries around the globe, Malaysia is shocked by the Coronavirus disease 2019, which is also known as COVID-19.Aims: This commentary article discusses the COVID-19 scenario in Malaysia, particularly in relation to the sudden increase in the number of new cases related to an international mass gathering.Findings: Projection through modelling helps the relevant authorities to act quickly and effectively, including enforcement of physical and social distancing. Modelling also assists in understanding the link between the biological processes that underpin transmission events and the population-level dynamics of the disease.Conclusion: There is no one-size-fits-all approach in managing disease outbreak. The fight against COVID-19 very much depends on their attitude during the 14-day Movement Control Order (MCO) which has been extended recently.
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Affiliation(s)
- Halimatus Sakdiah Minhat
- Department of Community Health, Faculty of Medicine and Health Sciences, Universiti Putra Malaysia, Serdang, Malaysia
| | - Hayati Kadir Shahar
- Department of Community Health, Faculty of Medicine and Health Sciences, Universiti Putra Malaysia, Serdang, Malaysia
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Forecasting the 2017/2018 seasonal influenza epidemic in England using multiple dynamic transmission models: a case study. BMC Public Health 2020; 20:486. [PMID: 32293372 PMCID: PMC7158152 DOI: 10.1186/s12889-020-8455-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2019] [Accepted: 03/04/2020] [Indexed: 01/13/2023] Open
Abstract
Background Since the 2009 A/H1N1 pandemic, Public Health England have developed a suite of real-time statistical models utilising enhanced pandemic surveillance data to nowcast and forecast a future pandemic. Their ability to track seasonal influenza and predict heightened winter healthcare burden in the light of high activity in Australia in 2017 was untested. Methods Four transmission models were used in forecasting the 2017/2018 seasonal influenza epidemic in England: a stratified primary care model using daily, region-specific, counts and virological swab positivity of influenza-like illness consultations in general practice (GP); a strain-specific (SS) model using weekly, national GP ILI and virological data; an intensive care model (ICU) using reports of ICU influenza admissions; and a synthesis model that included all data sources. For the first 12 weeks of 2018, each model was applied to the latest data to provide estimates of epidemic parameters and short-term influenza forecasts. The added value of pre-season population susceptibility data was explored. Results The combined results provided valuable nowcasts of the state of the epidemic. Short-term predictions of burden on primary and secondary health services were initially highly variable before reaching consensus beyond the observed peaks in activity between weeks 3–4 of 2018. Estimates for R0 were consistent over time for three of the four models until week 12 of 2018, and there was consistency in the estimation of R0 across the SPC and SS models, and in the ICU attack rates estimated by the ICU and the synthesis model. Estimation and predictions varied according to the assumed levels of pre-season immunity. Conclusions This exercise successfully applied a range of pandemic models to seasonal influenza. Forecasting early in the season remains challenging but represents a crucially important activity to inform planning. Improved knowledge of pre-existing levels of immunity would be valuable.
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Simpson CR, Beever D, Challen K, De Angelis D, Fragaszy E, Goodacre S, Hayward A, Lim WS, Rubin GJ, Semple MG, Knight M. The UK's pandemic influenza research portfolio: a model for future research on emerging infections. THE LANCET. INFECTIOUS DISEASES 2019; 19:e295-e300. [PMID: 31006605 DOI: 10.1016/s1473-3099(18)30786-2] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/08/2018] [Revised: 11/30/2018] [Accepted: 12/11/2018] [Indexed: 12/15/2022]
Abstract
The 2009 influenza A H1N1 pandemic was responsible for considerable global morbidity and mortality. In 2009, several research studies in the UK were rapidly funded and activated for clinical and public health actions. However, some studies were too late for their results to have an early and substantial effect on clinical care, because of the time required to call for research proposals, assess, fund, and set up the projects. In recognition of these inherent delays, a portfolio of projects was funded by the National Institute for Health Research in 2012. These studies have now been set up (ie, with relevant permissions and arrangements made for data collection) and pilot tested where relevant. All studies are now on standby awaiting activation in the event of a pandemic being declared. In this Personal View, we describe the projects that were set up, the challenges of putting these projects into a maintenance-only state, and ongoing activities to maintain readiness for activation, and discuss how to plan research for a range of major incidents.
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Affiliation(s)
- Colin R Simpson
- School of Health, Faculty of Health, Victoria University of Wellington, Wellington, New Zealand; Usher Institute, The University of Edinburgh, Edinburgh, UK.
| | - Dan Beever
- Clinical Trials Research Unit, School of Health and Related Research, University of Sheffield, UK
| | - Kirsty Challen
- Lancashire Teaching Hospitals National Health Service Trust, Preston, UK
| | - Daniela De Angelis
- Medical Research Council Biostatistics Unit, University of Cambridge, Cambridge, UK
| | - Ellen Fragaszy
- Centre for Public Health Data Science, Institute of Health Informatics, University College London, London, UK; Department of Infectious Disease Epidemiology, London School of Hygiene and Tropical Medicine, London, UK
| | - Steve Goodacre
- Clinical Trials Research Unit, School of Health and Related Research, University of Sheffield, UK
| | - Andrew Hayward
- Centre for Public Health Data Science, Institute of Health Informatics, University College London, London, UK; Institute of Epidemiology and Health Care, University College London, London, UK
| | - Wei Shen Lim
- Nottingham University Hospitals NHS Trust, Nottingham, UK
| | - G James Rubin
- Department of Psychological Medicine, Weston Education Centre, King's College London, London, UK
| | - Malcolm G Semple
- Institute of Translational Medicine, University of Liverpool, UK
| | - Marian Knight
- National Perinatal Epidemiology Unit, University of Oxford, Oxford, UK
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