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  1. Book ; Online: mrc-ide/china-exit-covid-19

    Rich FitzJohn / Kylie Ainslie

    Second release

    2020  

    Abstract: This release includes supplemental material from the manuscript. ...

    Abstract This release includes supplemental material from the manuscript.
    Keywords covid19
    Publishing date 2020-04-14
    Publishing country eu
    Document type Book ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  2. Book ; Online: mrc-ide/china-exit-covid-19

    Rich FitzJohn / Kylie Ainslie

    china-exit-covid-19

    2020  

    Abstract: First release of data and code that accompany the manuscript "Evidence of initial success for China exiting COVID-19 social distancing policy after achieving containment" ...

    Abstract First release of data and code that accompany the manuscript "Evidence of initial success for China exiting COVID-19 social distancing policy after achieving containment"
    Keywords covid19
    Publishing date 2020-04-09
    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

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  3. Book ; Online: mrc-ide/squire

    OJ Watson / cwhittaker1000 / Peter Winskill / Giovanni / Nicholas Brazeau / Rich FitzJohn / patrickgtwalker / Darío Hereñú

    v0.4.34

    2020  

    Abstract: SEIR transmission model of COVID-19. Documentation at: ...

    Abstract SEIR transmission model of COVID-19. Documentation at:
    Keywords covid19
    Publishing date 2020-09-11
    Publishing country eu
    Document type Book ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  4. Article ; Online: outbreaker2

    Finlay Campbell / Xavier Didelot / Rich Fitzjohn / Neil Ferguson / Anne Cori / Thibaut Jombart

    BMC Bioinformatics, Vol 19, Iss S11, Pp 1-

    a modular platform for outbreak reconstruction

    2018  Volume 8

    Abstract: Abstract Background Reconstructing individual transmission events in an infectious disease outbreak can provide valuable information and help inform infection control policy. Recent years have seen considerable progress in the development of ... ...

    Abstract Abstract Background Reconstructing individual transmission events in an infectious disease outbreak can provide valuable information and help inform infection control policy. Recent years have seen considerable progress in the development of methodologies for reconstructing transmission chains using both epidemiological and genetic data. However, only a few of these methods have been implemented in software packages, and with little consideration for customisability and interoperability. Users are therefore limited to a small number of alternatives, incompatible tools with fixed functionality, or forced to develop their own algorithms at considerable personal effort. Results Here we present outbreaker2, a flexible framework for outbreak reconstruction. This R package re-implements and extends the original model introduced with outbreaker, but most importantly also provides a modular platform allowing users to specify custom models within an optimised inferential framework. As a proof of concept, we implement the within-host evolutionary model introduced with TransPhylo, which is very distinct from the original genetic model in outbreaker, and demonstrate how even complex model results can be successfully included with minimal effort. Conclusions outbreaker2 provides a valuable starting point for future outbreak reconstruction tools, and represents a unifying platform that promotes customisability and interoperability. Implemented in the R software, outbreaker2 joins a growing body of tools for outbreak analysis.
    Keywords Transmission ; Epidemics ; Chain ; Tree ; Genomics ; Software ; Computer applications to medicine. Medical informatics ; R858-859.7 ; Biology (General) ; QH301-705.5
    Subject code 006
    Language English
    Publishing date 2018-10-01T00:00:00Z
    Publisher BMC
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  5. 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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  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)

    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.

  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)

    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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