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  1. Article ; Online: Is the cure really worse than the disease? The health impacts of lockdowns during COVID-19

    Gavin Yamey / Seth Flaxman / Oliver Ratmann / Samir Bhatt / Swapnil Mishra / Gideon Meyerowitz-Katz / Jan Markus Brauner / Mrinank Sharma / Sören Mindermann / Valerie Bradley / Michaela Vollmer / Lea Merone

    BMJ Global Health, Vol 6, Iss

    2021  Volume 8

    Keywords Medicine (General) ; R5-920 ; Infectious and parasitic diseases ; RC109-216
    Language English
    Publishing date 2021-08-01T00:00:00Z
    Publisher BMJ Publishing Group
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  2. 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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  3. Article ; Online: Changing composition of SARS-CoV-2 lineages and rise of Delta variant in England

    Swapnil Mishra / Sören Mindermann / Mrinank Sharma / Charles Whittaker / Thomas A Mellan / Thomas Wilton / Dimitra Klapsa / Ryan Mate / Martin Fritzsche / Maria Zambon / Janvi Ahuja / Adam Howes / Xenia Miscouridou / Guy P Nason / Oliver Ratmann / Elizaveta Semenova / Gavin Leech / Julia Fabienne Sandkühler / Charlie Rogers-Smith /
    Michaela Vollmer / H Juliette T Unwin / Yarin Gal / Meera Chand / Axel Gandy / Javier Martin / Erik Volz / Neil M Ferguson / Samir Bhatt / Jan M Brauner / Seth Flaxman

    EClinicalMedicine, Vol 39, Iss , Pp 101064- (2021)

    2021  

    Abstract: Background: Since its emergence in Autumn 2020, the SARS-CoV-2 Variant of Concern (VOC) B.1.1.7 (WHO label Alpha) rapidly became the dominant lineage across much of Europe. Simultaneously, several other VOCs were identified globally. Unlike B.1.1.7, some ...

    Abstract Background: Since its emergence in Autumn 2020, the SARS-CoV-2 Variant of Concern (VOC) B.1.1.7 (WHO label Alpha) rapidly became the dominant lineage across much of Europe. Simultaneously, several other VOCs were identified globally. Unlike B.1.1.7, some of these VOCs possess mutations thought to confer partial immune escape. Understanding when and how these additional VOCs pose a threat in settings where B.1.1.7 is currently dominant is vital. Methods: We examine trends in the prevalence of non-B.1.1.7 lineages in London and other English regions using passive-case detection PCR data, cross-sectional community infection surveys, genomic surveillance, and wastewater monitoring. The study period spans from 31st January 2021 to 15th May 2021. Findings: Across data sources, the percentage of non-B.1.1.7 variants has been increasing since late March 2021. This increase was initially driven by a variety of lineages with immune escape. From mid-April, B.1.617.2 (WHO label Delta) spread rapidly, becoming the dominant variant in England by late May. Interpretation: The outcome of competition between variants depends on a wide range of factors such as intrinsic transmissibility, evasion of prior immunity, demographic specificities and interactions with non-pharmaceutical interventions. The presence and rise of non-B.1.1.7 variants in March likely was driven by importations and some community transmission. There was competition between non-B.1.17 variants which resulted in B.1.617.2 becoming dominant in April and May with considerable community transmission. Our results underscore that early detection of new variants requires a diverse array of data sources in community surveillance. Continued real-time information on the highly dynamic composition and trajectory of different SARS-CoV-2 lineages is essential to future control efforts Funding: National Institute for Health Research, Medicines and Healthcare products Regulatory Agency, DeepMind, EPSRC, EA Funds programme, Open Philanthropy, Academy of Medical Sciences ...
    Keywords SARS-CoV-2 ; Variants of concern ; Epidemiology ; Waste water monitoring ; Genomic surveillance ; Public health ; Medicine (General) ; R5-920
    Subject code 360
    Language English
    Publishing date 2021-09-01T00:00:00Z
    Publisher Elsevier
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  4. 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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  5. Article ; Online: Anonymised and aggregated crowd level mobility data from mobile phones suggests that initial compliance with COVID-19 social distancing interventions was high and geographically consistent across the UK [version 1; peer review

    Benjamin Jeffrey / Caroline E. Walters / Kylie E. C. Ainslie / Oliver Eales / Constanze Ciavarella / Sangeeta Bhatia / Sarah Hayes / Marc Baguelin / Adhiratha Boonyasiri / Nicholas F. Brazeau / Gina Cuomo-Dannenburg / Richard G. FitzJohn / Katy Gaythorpe / William Green / Natsuko Imai / Thomas A. Mellan / Swapnil Mishra / Pierre Nouvellet / H. Juliette T. Unwin /
    Robert Verity / Michaela Vollmer / Charles Whittaker / Neil M. Ferguson / Christl A. Donnelly / Steven Riley

    Wellcome Open Research, Vol

    2 approved]

    2020  Volume 5

    Abstract: Background: Since early March 2020, the COVID-19 epidemic across the United Kingdom has led to a range of social distancing policies, which have resulted in reduced mobility across different regions. Crowd level data on mobile phone usage can be used as ... ...

    Abstract Background: Since early March 2020, the COVID-19 epidemic across the United Kingdom has led to a range of social distancing policies, which have resulted in reduced mobility across different regions. Crowd level data on mobile phone usage can be used as a proxy for actual population mobility patterns and provide a way of quantifying the impact of social distancing measures on changes in mobility. Methods: Here, we use two mobile phone-based datasets (anonymised and aggregated crowd level data from O2 and from the Facebook app on mobile phones) to assess changes in average mobility, both overall and broken down into high and low population density areas, and changes in the distribution of journey lengths. Results: We show that there was a substantial overall reduction in mobility, with the most rapid decline on the 24th March 2020, the day after the Prime Minister’s announcement of an enforced lockdown. The reduction in mobility was highly synchronized across the UK. Although mobility has remained low since 26th March 2020, we detect a gradual increase since that time. We also show that the two different datasets produce similar trends, albeit with some location-specific differences. We see slightly larger reductions in average mobility in high-density areas than in low-density areas, with greater variation in mobility in the high-density areas: some high-density areas eliminated almost all mobility. Conclusions: These analyses form a baseline from which to observe changes in behaviour in the UK as social distancing is eased and inform policy towards the future control of SARS-CoV-2 in the UK.
    Keywords Medicine ; R ; Science ; Q ; covid19
    Subject code 300
    Language English
    Publishing date 2020-07-01T00:00:00Z
    Publisher Wellcome
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  6. Article ; Online: Evidence of initial success for China exiting COVID-19 social distancing policy after achieving containment [version 2; peer review

    Kylie E. C. Ainslie / Caroline E. Walters / Han Fu / Sangeeta Bhatia / Haowei Wang / Xiaoyue Xi / Marc Baguelin / Samir Bhatt / Adhiratha Boonyasiri / Olivia Boyd / Lorenzo Cattarino / Constanze Ciavarella / Zulma Cucunuba / Gina Cuomo-Dannenburg / Amy Dighe / Ilaria Dorigatti / Sabine L van Elsland / Rich FitzJohn / Katy Gaythorpe /
    Azra C Ghani / Will Green / Arran Hamlet / Wes Hinsley / Natsuko Imai / David Jorgensen / Edward Knock / Daniel Laydon / Gemma Nedjati-Gilani / Lucy C Okell / Igor Siveroni / Hayley A Thompson / H. Juliette T. Unwin / Robert Verity / Michaela Vollmer / Patrick G T Walker / Yuanrong Wang / Oliver J Watson / Charles Whittaker / Peter Winskill / Christl A Donnelly / Neil M Ferguson / Steven Riley

    Wellcome Open Research, Vol

    2 approved]

    2020  Volume 5

    Abstract: Background: The COVID-19 epidemic was declared a Global Pandemic by WHO on 11 March 2020. By 24 March 2020, over 440,000 cases and almost 20,000 deaths had been reported worldwide. In response to the fast-growing epidemic, which began in the Chinese city ...

    Abstract Background: The COVID-19 epidemic was declared a Global Pandemic by WHO on 11 March 2020. By 24 March 2020, over 440,000 cases and almost 20,000 deaths had been reported worldwide. In response to the fast-growing epidemic, which began in the Chinese city of Wuhan, Hubei, China imposed strict social distancing in Wuhan on 23 January 2020 followed closely by similar measures in other provinces. These interventions have impacted economic productivity in China, and the ability of the Chinese economy to resume without restarting the epidemic was not clear. Methods: Using daily reported cases from mainland China and Hong Kong SAR, we estimated transmissibility over time and compared it to daily within-city movement, as a proxy for economic activity. Results: Initially, within-city movement and transmission were very strongly correlated in the five mainland provinces most affected by the epidemic and Beijing. However, that correlation decreased rapidly after the initial sharp fall in transmissibility. In general, towards the end of the study period, the correlation was no longer apparent, despite substantial increases in within-city movement. A similar analysis for Hong Kong shows that intermediate levels of local activity were maintained while avoiding a large outbreak. At the very end of the study period, when China began to experience the re-introduction of a small number of cases from Europe and the United States, there is an apparent up-tick in transmission. Conclusions: Although these results do not preclude future substantial increases in incidence, they suggest that after very intense social distancing (which resulted in containment), China successfully exited its lockdown to some degree. Elsewhere, movement data are being used as proxies for economic activity to assess the impact of interventions. The results presented here illustrate how the eventual decorrelation between transmission and movement is likely a key feature of successful COVID-19 exit strategies.
    Keywords Medicine ; R ; Science ; Q ; covid19
    Subject code 950
    Language English
    Publishing date 2020-10-01T00:00:00Z
    Publisher Wellcome
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  7. Article ; Online: Evidence of initial success for China exiting COVID-19 social distancing policy after achieving containment [version 1; peer review

    Kylie E C Ainslie / Caroline E. Walters / Han Fu / Sangeeta Bhatia / Haowei Wang / Xiaoyue Xi / Marc Baguelin / Samir Bhatt / Adhiratha Boonyasiri / Olivia Boyd / Lorenzo Cattarino / Constanze Ciavarella / Zulma Cucunuba / Gina Cuomo-Dannenburg / Amy Dighe / Ilaria Dorigatti / Sabine L van Elsland / Rich FitzJohn / Katy Gaythorpe /
    Azra C Ghani / Will Green / Arran Hamlet / Wes Hinsley / Natsuko Imai / David Jorgensen / Edward Knock / Daniel Laydon / Gemma Nedjati-Gilani / Lucy C Okell / Igor Siveroni / Hayley A Thompson / H Juliette T Unwin / Robert Verity / Michaela Vollmer / Patrick G T Walker / Yuanrong Wang / Oliver J Watson / Charles Whittaker / Peter Winskill / Christl A Donnelly / Neil M Ferguson / Steven Riley

    Wellcome Open Research, Vol

    2 approved]

    2020  Volume 5

    Abstract: Background: The COVID-19 epidemic was declared a Global Pandemic by WHO on 11 March 2020. By 24 March 2020, over 440,000 cases and almost 20,000 deaths had been reported worldwide. In response to the fast-growing epidemic, which began in the Chinese city ...

    Abstract Background: The COVID-19 epidemic was declared a Global Pandemic by WHO on 11 March 2020. By 24 March 2020, over 440,000 cases and almost 20,000 deaths had been reported worldwide. In response to the fast-growing epidemic, which began in the Chinese city of Wuhan, Hubei, China imposed strict social distancing in Wuhan on 23 January 2020 followed closely by similar measures in other provinces. These interventions have impacted economic productivity in China, and the ability of the Chinese economy to resume without restarting the epidemic was not clear. Methods: Using daily reported cases from mainland China and Hong Kong SAR, we estimated transmissibility over time and compared it to daily within-city movement, as a proxy for economic activity. Results: Initially, within-city movement and transmission were very strongly correlated in the five mainland provinces most affected by the epidemic and Beijing. However, that correlation decreased rapidly after the initial sharp fall in transmissibility. In general, towards the end of the study period, the correlation was no longer apparent, despite substantial increases in within-city movement. A similar analysis for Hong Kong shows that intermediate levels of local activity were maintained while avoiding a large outbreak. At the very end of the study period, when China began to experience the re-introduction of a small number of cases from Europe and the United States, there is an apparent up-tick in transmission. Conclusions: Although these results do not preclude future substantial increases in incidence, they suggest that after very intense social distancing (which resulted in containment), China successfully exited its lockdown to some degree. Elsewhere, movement data are being used as proxies for economic activity to assess the impact of interventions. The results presented here illustrate how the eventual decorrelation between transmission and movement is likely a key feature of successful COVID-19 exit strategies.
    Keywords Medicine ; R ; Science ; Q
    Subject code 950
    Language English
    Publishing date 2020-04-01T00:00:00Z
    Publisher Wellcome
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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