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  1. Book ; Online: ImperialCollegeLondon/covid19model

    Swapnil Mishra / Fabian Valka / Christopher Cave-Ayland / Harrison Zhu / Måns Magnusson / Juliette Unwin / bgoodri / Melodie Monod / Seth Flaxman / Alexandre Payot / hrkulkarMsft

    State-level tracking of COVID-19 in the United States [peer-reviewed]

    2020  

    Abstract: Version 10 Release This is the release related to our usa-paper (soon to be out) and medRxiv paper, where we use mobility data to estimate the situation in all states of the USA. All other code is still the same. To run this code you can directly run the ...

    Abstract Version 10 Release This is the release related to our usa-paper (soon to be out) and medRxiv paper, where we use mobility data to estimate the situation in all states of the USA. All other code is still the same. To run this code you can directly run the base-usa.r file or from the command line after setting the current directory as the repository directory run the following command Rscript base-usa-cases.r The code should be run in full mode to obtain credible results. Not running a full run to estimate anything is not recommended and discouraged. Only a full run should be used to get results. The instructions for European, Italy, Brazil, USA, Nature, IFR, USA age-specific code are the same as earlier (Look at version 3, version 4, version 5, version 6, version 7, version 8, and version 9). This release is specific to [ usa-paper (soon to be out) and medRxiv paper. This release has been checked on macOS Catalina version 10.15.6/7 and Ubuntu version 18.04.2.
    Keywords covid19
    Subject code 005
    Publishing date 2020-10-08
    Publishing country eu
    Document type Book ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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    Inter-library loan at ZB MED

    Your chosen title can be delivered directly to ZB MED Cologne location if you are registered as a user at ZB MED Cologne.

  2. Book ; Online: ImperialCollegeLondon/covid19model

    Swapnil Mishra / Fabian Valka / Christopher Cave-Ayland / Harrison Zhu / Måns Magnusson / bgoodri / Juliette Unwin / Seth Flaxman / Alexandre Payot / hrkulkarMsft / Melodie Monod

    Age groups that sustain resurging COVID-19 epidemics in the United States

    2020  

    Abstract: Version 9 Release This is the release related to report 32 and medRxiv paper, where we use age-specific mobility data to estimate the epidemic in the USA by accounting for age-specific heterogeneity. All other code is still the same for previous releases. ...

    Abstract Version 9 Release This is the release related to report 32 and medRxiv paper, where we use age-specific mobility data to estimate the epidemic in the USA by accounting for age-specific heterogeneity. All other code is still the same for previous releases. To run this code you need to follow the steps listed in the age-specific model here. The code should be run in full mode to obtain credible results. Not running a full run to estimate anything is not recommended and discouraged. Only a full run should be used to get results. The instructions for European, Italy, Brazil, USA, Nature, and IFR code are the same as earlier (Look at version 3, version 4, version 5, version 6, version 7, and version 8). This release is specific to report 32. This release has been checked on macOS Catalina version 10.15.6/7 and Ubuntu version 18.04.2.
    Keywords covid19
    Publishing date 2020-09-30
    Publishing country eu
    Document type Book ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

    Full text online

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    Inter-library loan at ZB MED

    Your chosen title can be delivered directly to ZB MED Cologne location if you are registered as a user at ZB MED Cologne.

  3. Book ; Online: ImperialCollegeLondon/covid19model

    Swapnil Mishra / Fabian Valka / Christopher Cave-Ayland / Harrison Zhu / Måns Magnusson / bgoodri / Juliette Unwin / Melodie Monod / Seth Flaxman / Alexandre Payot / hrkulkarMsft

    Bug Fix

    2020  

    Abstract: Bugfix in post-processing a table that was not in a data.table format and an object that was spelled incorrectly has been corrected. Rest everything remains the same as version 9. ...

    Abstract Bugfix in post-processing a table that was not in a data.table format and an object that was spelled incorrectly has been corrected. Rest everything remains the same as version 9.
    Keywords covid19
    Publishing date 2020-10-01
    Publishing country eu
    Document type Book ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

    Full text online

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    Inter-library loan at ZB MED

    Your chosen title can be delivered directly to ZB MED Cologne location if you are registered as a user at ZB MED Cologne.

  4. 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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    Inter-library loan at ZB MED

    Your chosen title can be delivered directly to ZB MED Cologne location if you are registered as a user at ZB MED Cologne.

  5. Article ; Online: Social contact patterns and implications for infectious disease transmission – a systematic review and meta-analysis of contact surveys

    Andria Mousa / Peter Winskill / Oliver John Watson / Oliver Ratmann / Mélodie Monod / Marco Ajelli / Aldiouma Diallo / Peter J Dodd / Carlos G Grijalva / Moses Chapa Kiti / Anand Krishnan / Rakesh Kumar / Supriya Kumar / Kin O Kwok / Claudio F Lanata / Olivier Le Polain de Waroux / Kathy Leung / Wiriya Mahikul / Alessia Melegaro /
    Carl D Morrow / Joël Mossong / Eleanor FG Neal / D James Nokes / Wirichada Pan-ngum / Gail E Potter / Fiona M Russell / Siddhartha Saha / Jonathan D Sugimoto / Wan In Wei / Robin R Wood / Joseph Wu / Juanjuan Zhang / Patrick Walker / Charles Whittaker

    eLife, Vol

    2021  Volume 10

    Abstract: Background: Transmission of respiratory pathogens such as SARS-CoV-2 depends on patterns of contact and mixing across populations. Understanding this is crucial to predict pathogen spread and the effectiveness of control efforts. Most analyses of contact ...

    Abstract Background: Transmission of respiratory pathogens such as SARS-CoV-2 depends on patterns of contact and mixing across populations. Understanding this is crucial to predict pathogen spread and the effectiveness of control efforts. Most analyses of contact patterns to date have focused on high-income settings. Methods: Here, we conduct a systematic review and individual-participant meta-analysis of surveys carried out in low- and middle-income countries and compare patterns of contact in these settings to surveys previously carried out in high-income countries. Using individual-level data from 28,503 participants and 413,069 contacts across 27 surveys, we explored how contact characteristics (number, location, duration, and whether physical) vary across income settings. Results: Contact rates declined with age in high- and upper-middle-income settings, but not in low-income settings, where adults aged 65+ made similar numbers of contacts as younger individuals and mixed with all age groups. Across all settings, increasing household size was a key determinant of contact frequency and characteristics, with low-income settings characterised by the largest, most intergenerational households. A higher proportion of contacts were made at home in low-income settings, and work/school contacts were more frequent in high-income strata. We also observed contrasting effects of gender across income strata on the frequency, duration, and type of contacts individuals made. Conclusions: These differences in contact patterns between settings have material consequences for both spread of respiratory pathogens and the effectiveness of different non-pharmaceutical interventions. Funding: This work is primarily being funded by joint Centre funding from the UK Medical Research Council and DFID (MR/R015600/1).
    Keywords social contact patterns ; pathogen transmission ; contact surveys ; Medicine ; R ; Science ; Q ; Biology (General) ; QH301-705.5
    Subject code 360
    Language English
    Publishing date 2021-11-01T00:00:00Z
    Publisher eLife Sciences Publications Ltd
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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    Inter-library loan at ZB MED

    Your chosen title can be delivered directly to ZB MED Cologne location if you are registered as a user at ZB MED Cologne.

  6. 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)

    Full text online

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    Inter-library loan at ZB MED

    Your chosen title can be delivered directly to ZB MED Cologne location if you are registered as a user at ZB MED Cologne.

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