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

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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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 /

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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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 /

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 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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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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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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Article ; Online: Factors driving extensive spatial and temporal fluctuations in COVID-19 fatality rates in Brazilian hospitals

Brizzi, Andrea / Whittaker, Charles / Servo, Luciana / Hawryluk, Iwona / Prete, Carlos Augusto / Souza, William Marciel de / Aguiar, Renato / de Araujo, Leonardo / Bastos, Leonardo / Blenkinsop, Alexandra / Bonfirm, Diego / Buss, Lewiss / da Silva Candido, Darlan / Castro, Marcia C. / Costa, Silvia F / Croda, Julio / de Souza Santos, Andreza Aruska / Dye, Christopher / Flaxman, Seth /

medRxiv

Abstract: The SARS-CoV-2 Gamma variant spread rapidly across Brazil, causing substantial infection and death waves. We use individual-level patient records following hospitalisation with suspected or confirmed COVID-19 to document the extensive shocks in hospital ... ...

Abstract	The SARS-CoV-2 Gamma variant spread rapidly across Brazil, causing substantial infection and death waves. We use individual-level patient records following hospitalisation with suspected or confirmed COVID-19 to document the extensive shocks in hospital fatality rates that followed Gamma9s spread across 14 state capitals, and in which more than half of hospitalised patients died over sustained time periods. We show that extensive fluctuations in COVID-19 in-hospital fatality rates also existed prior to Gamma9s detection, and were largely transient after Gamma9s detection, subsiding with hospital demand. Using a Bayesian fatality rate model, we find that the geographic and temporal fluctuations in Brazil9s COVID-19 in-hospital fatality rates are primarily associated with geographic inequities and shortages in healthcare capacity. We project that approximately half of Brazil9s COVID-19 deaths in hospitals could have been avoided without pre-pandemic geographic inequities and without pandemic healthcare pressure. Our results suggest that investments in healthcare resources, healthcare optimization, and pandemic preparedness are critical to minimize population wide mortality and morbidity caused by highly transmissible and deadly pathogens such as SARS-CoV-2, especially in low- and middle-income countries.
Keywords	covid19
Language	English
Publishing date	2021-11-02
Publisher	Cold Spring Harbor Laboratory Press
Document type	Article ; Online
DOI	10.1101/2021.11.01.21265731
Database	COVID19

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

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

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

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Inter-library loan at ZB MED

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

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

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

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Article ; Online: Factors driving extensive spatial and temporal fluctuations in COVID-19 fatality rates in Brazilian hospitals

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Inter-library loan at ZB MED

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

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Inter-library loan at ZB MED