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  1. Article ; Online: Understanding the risks for post-disaster infectious disease outbreaks

    Ilan Kelman / Gina E C Charnley / Katy Gaythorpe / Kris Murray

    BMJ Open, Vol 10, Iss

    a systematic review protocol

    2020  Volume 9

    Keywords Medicine ; R
    Language English
    Publishing date 2020-09-01T00:00:00Z
    Publisher BMJ Publishing Group
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  2. Article ; Online: Chainchecker

    Katy Gaythorpe / Aaron Morris / Natsuko Imai / Miles Stewart / Jeffrey Freeman / Mary Choi

    PLoS ONE, Vol 16, Iss 2, p e

    An application to visualise and explore transmission chains for Ebola virus disease.

    2021  Volume 0247002

    Abstract: 2020 saw the continuation of the second largest outbreak of Ebola virus disease (EVD) in history. Determining epidemiological links between cases is a key part of outbreak control. However, due to the large quantity of data and subsequent data entry ... ...

    Abstract 2020 saw the continuation of the second largest outbreak of Ebola virus disease (EVD) in history. Determining epidemiological links between cases is a key part of outbreak control. However, due to the large quantity of data and subsequent data entry errors, inconsistencies in potential epidemiological links are difficult to identify. We present chainchecker, an online and offline shiny application which visualises, curates and verifies transmission chain data. The application includes the calculation of exposure windows for individual cases of EVD based on user defined incubation periods and user specified symptom profiles. It has an upload function for viral hemorrhagic fever data and utility for additional entries. This data may then be visualised as a transmission tree with inconsistent links highlighted. Finally, there is utility for cluster analysis and the ability to highlight nosocomial transmission. chainchecker is a R shiny application which has an offline version for use with VHF (viral hemorrhagic fever) databases or linelists. The software is available at https://shiny.dide.imperial.ac.uk/chainchecker which is a web-based application that links to the desktop application available for download and the github repository, https://github.com/imperialebola2018/chainchecker.
    Keywords Medicine ; R ; Science ; Q
    Language English
    Publishing date 2021-01-01T00:00:00Z
    Publisher Public Library of Science (PLoS)
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  3. Article ; Online: Estimating the number of undetected COVID-19 cases among travellers from mainland China [version 2; peer review

    Sangeeta Bhatia / Natsuko Imai / Gina Cuomo-Dannenburg / Marc Baguelin / Adhiratha Boonyasiri / Anne Cori / Zulma Cucunubá / Ilaria Dorigatti / Rich FitzJohn / Han Fu / Katy Gaythorpe / Azra Ghani / Arran Hamlet / Wes Hinsley / Daniel Laydon / Gemma Nedjati-Gilani / Lucy Okell / Steven Riley / Hayley Thompson /
    Sabine van Elsland / Erik Volz / Haowei Wang / Yuanrong Wang / Charles Whittaker / Xiaoyue Xi / Christl A. Donnelly / Neil M. Ferguson

    Wellcome Open Research, Vol

    1 approved, 2 approved with reservations]

    2021  Volume 5

    Abstract: Background: As of August 2021, every region of the world has been affected by the COVID-19 pandemic, with more than 196,000,000 cases worldwide. Methods: We analysed COVID-19 cases among travellers from mainland China to different regions and countries, ... ...

    Abstract Background: As of August 2021, every region of the world has been affected by the COVID-19 pandemic, with more than 196,000,000 cases worldwide. Methods: We analysed COVID-19 cases among travellers from mainland China to different regions and countries, comparing the region- and country-specific rates of detected and confirmed cases per flight volume to estimate the relative sensitivity of surveillance in different regions and countries. Results: Although travel restrictions from Wuhan City and other cities across China may have reduced the absolute number of travellers to and from China, we estimated that up to 70% (95% CI: 54% - 80%) of imported cases could remain undetected relative to the sensitivity of surveillance in Singapore. The percentage of undetected imported cases rises to 75% (95% CI 66% - 82%) when comparing to the surveillance sensitivity in multiple countries. Conclusions: Our analysis shows that a large number of COVID-19 cases remain undetected across the world. These undetected cases potentially resulted in multiple chains of human-to-human transmission outside mainland China.
    Keywords Medicine ; R ; Science ; Q
    Subject code 950
    Language English
    Publishing date 2021-09-01T00:00:00Z
    Publisher Wellcome
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  4. 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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    Inter-library loan at ZB MED

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  5. 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)

    Full text online

    More links

    Kategorien

    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: 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)

    Full text online

    More links

    Kategorien

    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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