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  1. Article ; Online: Comparing the responses of the UK, Sweden and Denmark to COVID-19 using counterfactual modelling

    Swapnil Mishra / James A. Scott / Daniel J. Laydon / Seth Flaxman / Axel Gandy / Thomas A. Mellan / H. Juliette T. Unwin / Michaela Vollmer / Helen Coupland / Oliver Ratmann / Melodie Monod / Harrison H. Zhu / Anne Cori / Katy A. M. Gaythorpe / Lilith K. Whittles / Charles Whittaker / Christl A. Donnelly / Neil M. Ferguson / Samir Bhatt

    Scientific Reports, Vol 11, Iss 1, Pp 1-

    2021  Volume 9

    Abstract: Abstract The UK and Sweden have among the worst per-capita COVID-19 mortality in Europe. Sweden stands out for its greater reliance on voluntary, rather than mandatory, control measures. We explore how the timing and effectiveness of control measures in ... ...

    Abstract Abstract The UK and Sweden have among the worst per-capita COVID-19 mortality in Europe. Sweden stands out for its greater reliance on voluntary, rather than mandatory, control measures. We explore how the timing and effectiveness of control measures in the UK, Sweden and Denmark shaped COVID-19 mortality in each country, using a counterfactual assessment: what would the impact have been, had each country adopted the others’ policies? Using a Bayesian semi-mechanistic model without prior assumptions on the mechanism or effectiveness of interventions, we estimate the time-varying reproduction number for the UK, Sweden and Denmark from daily mortality data. We use two approaches to evaluate counterfactuals which transpose the transmission profile from one country onto another, in each country’s first wave from 13th March (when stringent interventions began) until 1st July 2020. UK mortality would have approximately doubled had Swedish policy been adopted, while Swedish mortality would have more than halved had Sweden adopted UK or Danish strategies. Danish policies were most effective, although differences between the UK and Denmark were significant for one counterfactual approach only. Our analysis shows that small changes in the timing or effectiveness of interventions have disproportionately large effects on total mortality within a rapidly growing epidemic.
    Keywords Medicine ; R ; Science ; Q
    Subject code 310
    Language English
    Publishing date 2021-08-01T00:00:00Z
    Publisher Nature Portfolio
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  2. Article: Estimating the number of infections and the impact of non-pharmaceutical interventions on COVID-19 in European countries: technical description update

    Seth Flaxman / Swapnil Mishra / Axel Gandy / H Unwin Juliette T / Helen Coupland / Thomas Mellan A / Harrison Zhu / Tresnia Berah / Jeffrey Eaton W / Pablo Guzman N P / Nora Schmit / Lucia Callizo / Imperial Team College COVID-19 Response / Charles Whittaker / Peter Winskill / Xiaoyue Xi / Azra Ghani / Christl Donnelly A. / Steven Riley /
    Lucy Okell C / Michaela Vollmer A C / Neil Ferguson M. / Samir Bhatt

    Abstract: Following the emergence of a novel coronavirus (SARS-CoV-2) and its spread outside of China, Europe has experienced large epidemics. In response, many European countries have implemented unprecedented non-pharmaceutical interventions including case ... ...

    Abstract Following the emergence of a novel coronavirus (SARS-CoV-2) and its spread outside of China, Europe has experienced large epidemics. In response, many European countries have implemented unprecedented non-pharmaceutical interventions including case isolation, the closure of schools and universities, banning of mass gatherings and/or public events, and most recently, wide-scale social distancing including local and national lockdowns. In this technical update, we extend a semi-mechanistic Bayesian hierarchical model that infers the impact of these interventions and estimates the number of infections over time. Our methods assume that changes in the reproductive number - a measure of transmission - are an immediate response to these interventions being implemented rather than broader gradual changes in behaviour. Our model estimates these changes by calculating backwards from temporal data on observed to estimate the number of infections and rate of transmission that occurred several weeks prior, allowing for a probabilistic time lag between infection and death. In this update we extend our original model [Flaxman, Mishra, Gandy et al 2020, Report #13, Imperial College London] to include (a) population saturation effects, (b) prior uncertainty on the infection fatality ratio, (c) a more balanced prior on intervention effects and (d) partial pooling of the lockdown intervention covariate. We also (e) included another 3 countries (Greece, the Netherlands and Portugal). The model code is available at https://github.com/ImperialCollegeLondon/covid19model/ We are now reporting the results of our updated model online at https://mrc-ide.github.io/covid19estimates/ We estimated parameters jointly for all M=14 countries in a single hierarchical model. Inference is performed in the probabilistic programming language Stan using an adaptive Hamiltonian Monte Carlo (HMC) sampler.
    Keywords covid19
    Publisher arxiv
    Document type Article
    Database COVID19

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  3. Article ; Online: Response to COVID-19 in South Korea and implications for lifting stringent interventions

    Amy Dighe / Lorenzo Cattarino / Gina Cuomo-Dannenburg / Janetta Skarp / Natsuko Imai / Sangeeta Bhatia / Katy A. M. Gaythorpe / Kylie E. C. Ainslie / Marc Baguelin / Samir Bhatt / Adhiratha Boonyasiri / Nicholas F. Brazeau / Laura V. Cooper / Helen Coupland / Zulma Cucunuba / Ilaria Dorigatti / Oliver D. Eales / Sabine L. van Elsland / Richard G. FitzJohn /
    William D. Green / David J. Haw / Wes Hinsley / Edward Knock / Daniel J. Laydon / Thomas Mellan / Swapnil Mishra / Gemma Nedjati-Gilani / Pierre Nouvellet / Margarita Pons-Salort / Hayley A. Thompson / H. Juliette T. Unwin / Robert Verity / Michaela A. C. Vollmer / Caroline E. Walters / Oliver J. Watson / Charles Whittaker / Lilith K. Whittles / Azra C. Ghani / Christl A. Donnelly / Neil M. Ferguson / Steven Riley

    BMC Medicine, Vol 18, Iss 1, Pp 1-

    2020  Volume 12

    Abstract: Abstract Background After experiencing a sharp growth in COVID-19 cases early in the pandemic, South Korea rapidly controlled transmission while implementing less stringent national social distancing measures than countries in Europe and the USA. This ... ...

    Abstract Abstract Background After experiencing a sharp growth in COVID-19 cases early in the pandemic, South Korea rapidly controlled transmission while implementing less stringent national social distancing measures than countries in Europe and the USA. This has led to substantial interest in their “test, trace, isolate” strategy. However, it is important to understand the epidemiological peculiarities of South Korea’s outbreak and characterise their response before attempting to emulate these measures elsewhere. Methods We systematically extracted numbers of suspected cases tested, PCR-confirmed cases, deaths, isolated confirmed cases, and numbers of confirmed cases with an identified epidemiological link from publicly available data. We estimated the time-varying reproduction number, R t , using an established Bayesian framework, and reviewed the package of interventions implemented by South Korea using our extracted data, plus published literature and government sources. Results We estimated that after the initial rapid growth in cases, R t dropped below one in early April before increasing to a maximum of 1.94 (95%CrI, 1.64–2.27) in May following outbreaks in Seoul Metropolitan Region. By mid-June, R t was back below one where it remained until the end of our study (July 13th). Despite less stringent “lockdown” measures, strong social distancing measures were implemented in high-incidence areas and studies measured a considerable national decrease in movement in late February. Testing the capacity was swiftly increased, and protocols were in place to isolate suspected and confirmed cases quickly; however, we could not estimate the delay to isolation using our data. Accounting for just 10% of cases, individual case-based contact tracing picked up a relatively minor proportion of total cases, with cluster investigations accounting for 66%. Conclusions Whilst early adoption of testing and contact tracing is likely to be important for South Korea’s successful outbreak control, other factors including regional ...
    Keywords COVID-19 ; South Korea ; Public health interventions ; Reproduction number ; Contact tracing ; Medicine ; R ; covid19
    Subject code 306
    Language English
    Publishing date 2020-10-01T00:00:00Z
    Publisher BMC
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  4. Article ; Online: Reduction in mobility and COVID-19 transmission

    Pierre Nouvellet / Sangeeta Bhatia / Anne Cori / Kylie E. C. Ainslie / Marc Baguelin / Samir Bhatt / Adhiratha Boonyasiri / Nicholas F. Brazeau / Lorenzo Cattarino / Laura V. Cooper / Helen Coupland / Zulma M. Cucunuba / Gina Cuomo-Dannenburg / Amy Dighe / Bimandra A. Djaafara / Ilaria Dorigatti / Oliver D. Eales / Sabine L. van Elsland / Fabricia F. Nascimento /
    Richard G. FitzJohn / Katy A. M. Gaythorpe / Lily Geidelberg / William D. Green / Arran Hamlet / Katharina Hauck / Wes Hinsley / Natsuko Imai / Benjamin Jeffrey / Edward Knock / Daniel J. Laydon / John A. Lees / Tara Mangal / Thomas A. Mellan / Gemma Nedjati-Gilani / Kris V. Parag / Margarita Pons-Salort / Manon Ragonnet-Cronin / Steven Riley / H. Juliette T. Unwin / Robert Verity / Michaela A. C. Vollmer / Erik Volz / Patrick G. T. Walker / Caroline E. Walters / Haowei Wang / Oliver J. Watson / Charles Whittaker / Lilith K. Whittles / Xiaoyue Xi / Neil M. Ferguson

    Nature Communications, Vol 12, Iss 1, Pp 1-

    2021  Volume 9

    Abstract: Social distancing policies aiming to reduce COVID-19 transmission have been reflected in reductions in human mobility. Here, the authors show that reduced mobility is correlated with decreased transmission, but that this relationship weakened over time ... ...

    Abstract Social distancing policies aiming to reduce COVID-19 transmission have been reflected in reductions in human mobility. Here, the authors show that reduced mobility is correlated with decreased transmission, but that this relationship weakened over time as social distancing measures were relaxed.
    Keywords Science ; Q
    Language English
    Publishing date 2021-02-01T00:00:00Z
    Publisher Nature Portfolio
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  5. Article ; Online: State-level tracking of COVID-19 in the United States

    H. Juliette T. Unwin / Swapnil Mishra / Valerie C. Bradley / Axel Gandy / Thomas A. Mellan / Helen Coupland / Jonathan Ish-Horowicz / Michaela A. C. Vollmer / Charles Whittaker / Sarah L. Filippi / Xiaoyue Xi / Mélodie Monod / Oliver Ratmann / Michael Hutchinson / Fabian Valka / Harrison Zhu / Iwona Hawryluk / Philip Milton / Kylie E. C. Ainslie /
    Marc Baguelin / Adhiratha Boonyasiri / Nick F. Brazeau / Lorenzo Cattarino / Zulma Cucunuba / Gina Cuomo-Dannenburg / Ilaria Dorigatti / Oliver D. Eales / Jeffrey W. Eaton / Sabine L. van Elsland / Richard G. FitzJohn / Katy A. M. Gaythorpe / William Green / Wes Hinsley / Benjamin Jeffrey / Edward Knock / Daniel J. Laydon / John Lees / Gemma Nedjati-Gilani / Pierre Nouvellet / Lucy Okell / Kris V. Parag / Igor Siveroni / Hayley A. Thompson / Patrick Walker / Caroline E. Walters / Oliver J. Watson / Lilith K. Whittles / Azra C. Ghani / Neil M. Ferguson / Steven Riley / Christl A. Donnelly / Samir Bhatt / Seth Flaxman

    Nature Communications, Vol 11, Iss 1, Pp 1-

    2020  Volume 9

    Abstract: High numbers of COVID-19-related deaths have been reported in the United States, but estimation of the true numbers of infections is challenging. Here, the authors estimate that on 1 June 2020, 3.7% of the US population was infected with SARS-CoV-2, and ... ...

    Abstract High numbers of COVID-19-related deaths have been reported in the United States, but estimation of the true numbers of infections is challenging. Here, the authors estimate that on 1 June 2020, 3.7% of the US population was infected with SARS-CoV-2, and 0.01% was infectious, with wide variation by state.
    Keywords Science ; Q
    Language English
    Publishing date 2020-12-01T00:00:00Z
    Publisher Nature Portfolio
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  6. Article ; Online: Potential impact of the COVID-19 pandemic on HIV, tuberculosis, and malaria in low-income and middle-income countries

    Alexandra B Hogan, PhD / Britta L Jewell, PhD / Ellie Sherrard-Smith, PhD / Juan F Vesga, PhD / Oliver J Watson, PhD / Charles Whittaker, MSc / Arran Hamlet, PhD / Jennifer A Smith, DPhil / Peter Winskill, PhD / Robert Verity, PhD / Marc Baguelin, PhD / John A Lees, PhD / Lilith K Whittles, PhD / Kylie E C Ainslie, PhD / Samir Bhatt, DPhil / Adhiratha Boonyasiri, MD / Nicholas F Brazeau, PhD / Lorenzo Cattarino, PhD / Laura V Cooper, MPhil /
    Helen Coupland, MRes / Gina Cuomo-Dannenburg, MMath / Amy Dighe, MRes / Bimandra A Djaafara, MRes / Christl A Donnelly, ProfScD / Jeff W Eaton, PhD / Sabine L van Elsland, PhD / Richard G FitzJohn, PhD / Han Fu, PhD / Katy A M Gaythorpe, PhD / William Green, MRes / David J Haw, PhD / Sarah Hayes, MSc / Wes Hinsley, PhD / Natsuko Imai, PhD / Daniel J Laydon, PhD / Tara D Mangal, PhD / Thomas A Mellan, PhD / Swapnil Mishra, PhD / Gemma Nedjati-Gilani, PhD / Kris V Parag, PhD / Hayley A Thompson, MPH / H Juliette T Unwin, PhD / Michaela A C Vollmer, PhD / Caroline E Walters, PhD / Haowei Wang, MSc / Yuanrong Wang / Xiaoyue Xi, MSc / Neil M Ferguson, ProfDPhil / Lucy C Okell, PhD / Thomas S Churcher, PhD

    The Lancet Global Health, Vol 8, Iss 9, Pp e1132-e

    a modelling study

    2020  Volume 1141

    Abstract: Summary: Background: COVID-19 has the potential to cause substantial disruptions to health services, due to cases overburdening the health system or response measures limiting usual programmatic activities. We aimed to quantify the extent to which ... ...

    Abstract Summary: Background: COVID-19 has the potential to cause substantial disruptions to health services, due to cases overburdening the health system or response measures limiting usual programmatic activities. We aimed to quantify the extent to which disruptions to services for HIV, tuberculosis, and malaria in low-income and middle-income countries with high burdens of these diseases could lead to additional loss of life over the next 5 years. Methods: Assuming a basic reproduction number of 3·0, we constructed four scenarios for possible responses to the COVID-19 pandemic: no action, mitigation for 6 months, suppression for 2 months, or suppression for 1 year. We used established transmission models of HIV, tuberculosis, and malaria to estimate the additional impact on health that could be caused in selected settings, either due to COVID-19 interventions limiting activities, or due to the high demand on the health system due to the COVID-19 pandemic. Findings: In high-burden settings, deaths due to HIV, tuberculosis, and malaria over 5 years could increase by up to 10%, 20%, and 36%, respectively, compared with if there was no COVID-19 pandemic. The greatest impact on HIV was estimated to be from interruption to antiretroviral therapy, which could occur during a period of high health system demand. For tuberculosis, the greatest impact would be from reductions in timely diagnosis and treatment of new cases, which could result from any prolonged period of COVID-19 suppression interventions. The greatest impact on malaria burden could be as a result of interruption of planned net campaigns. These disruptions could lead to a loss of life-years over 5 years that is of the same order of magnitude as the direct impact from COVID-19 in places with a high burden of malaria and large HIV and tuberculosis epidemics. Interpretation: Maintaining the most critical prevention activities and health-care services for HIV, tuberculosis, and malaria could substantially reduce the overall impact of the COVID-19 pandemic. Funding: ...
    Keywords Public aspects of medicine ; RA1-1270 ; covid19
    Subject code 306
    Language English
    Publishing date 2020-09-01T00:00:00Z
    Publisher Elsevier
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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