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Article ; Online: Epidemiological drivers of transmissibility and severity of SARS-CoV-2 in England

Pablo N. Perez-Guzman / Edward Knock / Natsuko Imai / Thomas Rawson / Yasin Elmaci / Joana Alcada / Lilith K. Whittles / Divya Thekke Kanapram / Raphael Sonabend / Katy A. M. Gaythorpe / Wes Hinsley / Richard G. FitzJohn / Erik Volz / Robert Verity / Neil M. Ferguson / Anne Cori / Marc Baguelin

Nature Communications, Vol 14, Iss 1, Pp 1-

2023 Volume 9

Abstract: Abstract As the SARS-CoV-2 pandemic progressed, distinct variants emerged and dominated in England. These variants, Wildtype, Alpha, Delta, and Omicron were characterized by variations in transmissibility and severity. We used a robust mathematical model ...

Abstract	Abstract As the SARS-CoV-2 pandemic progressed, distinct variants emerged and dominated in England. These variants, Wildtype, Alpha, Delta, and Omicron were characterized by variations in transmissibility and severity. We used a robust mathematical model and Bayesian inference framework to analyse epidemiological surveillance data from England. We quantified the impact of non-pharmaceutical interventions (NPIs), therapeutics, and vaccination on virus transmission and severity. Each successive variant had a higher intrinsic transmissibility. Omicron (BA.1) had the highest basic reproduction number at 8.4 (95% credible interval (CrI) 7.8-9.1). Varying levels of NPIs were crucial in controlling virus transmission until population immunity accumulated. Immune escape properties of Omicron decreased effective levels of immunity in the population by a third. Furthermore, in contrast to previous studies, we found Alpha had the highest basic infection fatality ratio (3.0%, 95% CrI 2.8-3.2), followed by Delta (2.1%, 95% CrI 1.9–2.4), Wildtype (1.2%, 95% CrI 1.1–1.2), and Omicron (0.7%, 95% CrI 0.6-0.8). Our findings highlight the importance of continued surveillance. Long-term strategies for monitoring and maintaining effective immunity against SARS-CoV-2 are critical to inform the role of NPIs to effectively manage future variants with potentially higher intrinsic transmissibility and severe outcomes.
Keywords	Science ; Q
Subject code	360
Language	English
Publishing date	2023-07-01T00:00:00Z
Publisher	Nature Portfolio
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Author Correction

Nature Communications, Vol 14, Iss 1, Pp 1-

Epidemiological drivers of transmissibility and severity of SARS-CoV-2 in England

2023 Volume 4

Keywords	Science ; Q
Language	English
Publishing date	2023-12-01T00:00:00Z
Publisher	Nature Portfolio
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: 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 ; 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: Response to COVID-19 in South Korea and implications for lifting stringent interventions

Amy Dighe / Lorenzo Cattarino / Gina Cuomo-Dannenburg / Janetta Skarp / Natsuko Imai / Sangeeta Bhatia / Katy A. M. Gaythorpe / Kylie E. C. Ainslie / Marc Baguelin / Samir Bhatt / Adhiratha Boonyasiri / Nicholas F. Brazeau / Laura V. Cooper / Helen Coupland / Zulma Cucunuba / Ilaria Dorigatti / Oliver D. Eales / Sabine L. van Elsland / Richard G. FitzJohn /

BMC Medicine, Vol 18, Iss 1, Pp 1-

2020 Volume 12

Abstract: Abstract Background After experiencing a sharp growth in COVID-19 cases early in the pandemic, South Korea rapidly controlled transmission while implementing less stringent national social distancing measures than countries in Europe and the USA. This ... ...

Abstract	Abstract Background After experiencing a sharp growth in COVID-19 cases early in the pandemic, South Korea rapidly controlled transmission while implementing less stringent national social distancing measures than countries in Europe and the USA. This has led to substantial interest in their “test, trace, isolate” strategy. However, it is important to understand the epidemiological peculiarities of South Korea’s outbreak and characterise their response before attempting to emulate these measures elsewhere. Methods We systematically extracted numbers of suspected cases tested, PCR-confirmed cases, deaths, isolated confirmed cases, and numbers of confirmed cases with an identified epidemiological link from publicly available data. We estimated the time-varying reproduction number, R t , using an established Bayesian framework, and reviewed the package of interventions implemented by South Korea using our extracted data, plus published literature and government sources. Results We estimated that after the initial rapid growth in cases, R t dropped below one in early April before increasing to a maximum of 1.94 (95%CrI, 1.64–2.27) in May following outbreaks in Seoul Metropolitan Region. By mid-June, R t was back below one where it remained until the end of our study (July 13th). Despite less stringent “lockdown” measures, strong social distancing measures were implemented in high-incidence areas and studies measured a considerable national decrease in movement in late February. Testing the capacity was swiftly increased, and protocols were in place to isolate suspected and confirmed cases quickly; however, we could not estimate the delay to isolation using our data. Accounting for just 10% of cases, individual case-based contact tracing picked up a relatively minor proportion of total cases, with cluster investigations accounting for 66%. Conclusions Whilst early adoption of testing and contact tracing is likely to be important for South Korea’s successful outbreak control, other factors including regional ...
Keywords	COVID-19 ; South Korea ; Public health interventions ; Reproduction number ; Contact tracing ; Medicine ; R ; covid19
Subject code	306
Language	English
Publishing date	2020-10-01T00:00:00Z
Publisher	BMC
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: Reducing Plasmodium falciparum malaria transmission in Africa

Jamie T Griffin / T Deirdre Hollingsworth / Lucy C Okell / Thomas S Churcher / Michael White / Wes Hinsley / Teun Bousema / Chris J Drakeley / Neil M Ferguson / María-Gloria Basáñez / Azra C Ghani

PLoS Medicine, Vol 7, Iss 8, p e

a model-based evaluation of intervention strategies.

2010 Volume 1000324

Abstract: Over the past decade malaria intervention coverage has been scaled up across Africa. However, it remains unclear what overall reduction in transmission is achievable using currently available tools. We developed an individual-based simulation model for ... ...

Abstract	Over the past decade malaria intervention coverage has been scaled up across Africa. However, it remains unclear what overall reduction in transmission is achievable using currently available tools. We developed an individual-based simulation model for Plasmodium falciparum transmission in an African context incorporating the three major vector species (Anopheles gambiae s.s., An. arabiensis, and An. funestus) with parameters obtained by fitting to parasite prevalence data from 34 transmission settings across Africa. We incorporated the effect of the switch to artemisinin-combination therapy (ACT) and increasing coverage of long-lasting insecticide treated nets (LLINs) from the year 2000 onwards. We then explored the impact on transmission of continued roll-out of LLINs, additional rounds of indoor residual spraying (IRS), mass screening and treatment (MSAT), and a future RTS,S/AS01 vaccine in six representative settings with varying transmission intensity (as summarized by the annual entomological inoculation rate, EIR: 1 setting with low, 3 with moderate, and 2 with high EIRs), vector-species combinations, and patterns of seasonality. In all settings we considered a realistic target of 80% coverage of interventions. In the low-transmission setting (EIR approximately 3 ibppy [infectious bites per person per year]), LLINs have the potential to reduce malaria transmission to low levels (<1% parasite prevalence in all age-groups) provided usage levels are high and sustained. In two of the moderate-transmission settings (EIR approximately 43 and 81 ibppy), additional rounds of IRS with DDT coupled with MSAT could drive parasite prevalence below a 1% threshold. However, in the third (EIR = 46) with An. arabiensis prevailing, these interventions are insufficient to reach this threshold. In both high-transmission settings (EIR approximately 586 and 675 ibppy), either unrealistically high coverage levels (>90%) or novel tools and/or substantial social improvements will be required, although considerable ...
Keywords	Medicine ; R
Subject code	535
Language	English
Publishing date	2010-08-01T00:00:00Z
Publisher	Public Library of Science (PLoS)
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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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: 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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