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State-level tracking of COVID-19 in the United States

As of 1st June 2020, the US Centres for Disease Control and Prevention reported 104,232 confirmed or probable COVID-19-related deaths in the US. This was more than twice the number of deaths reported in the next most severely impacted country. We jointly model the US epidemic at the state-level, usi...

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Autores principales: Unwin, H. Juliette T., Mishra, Swapnil, Bradley, Valerie C., Gandy, Axel, Mellan, Thomas A., Coupland, Helen, Ish-Horowicz, Jonathan, Vollmer, Michaela A. C., Whittaker, Charles, Filippi, Sarah L., Xi, Xiaoyue, Monod, Mélodie, Ratmann, Oliver, Hutchinson, Michael, Valka, Fabian, Zhu, Harrison, Hawryluk, Iwona, Milton, Philip, Ainslie, Kylie E. C., Baguelin, Marc, Boonyasiri, Adhiratha, Brazeau, Nick F., Cattarino, Lorenzo, Cucunuba, Zulma, Cuomo-Dannenburg, Gina, Dorigatti, Ilaria, Eales, Oliver D., Eaton, Jeffrey W., van Elsland, Sabine L., FitzJohn, Richard G., Gaythorpe, Katy A. M., Green, William, Hinsley, Wes, Jeffrey, Benjamin, Knock, Edward, Laydon, Daniel J., Lees, John, Nedjati-Gilani, Gemma, Nouvellet, Pierre, Okell, Lucy, Parag, Kris V., Siveroni, Igor, Thompson, Hayley A., Walker, Patrick, Walters, Caroline E., Watson, Oliver J., Whittles, Lilith K., Ghani, Azra C., Ferguson, Neil M., Riley, Steven, Donnelly, Christl A., Bhatt, Samir, Flaxman, Seth
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Nature Publishing Group UK 2020
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7712910/
https://www.ncbi.nlm.nih.gov/pubmed/33273462
http://dx.doi.org/10.1038/s41467-020-19652-6
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author Unwin, H. Juliette T.
Mishra, Swapnil
Bradley, Valerie C.
Gandy, Axel
Mellan, Thomas A.
Coupland, Helen
Ish-Horowicz, Jonathan
Vollmer, Michaela A. C.
Whittaker, Charles
Filippi, Sarah L.
Xi, Xiaoyue
Monod, Mélodie
Ratmann, Oliver
Hutchinson, Michael
Valka, Fabian
Zhu, Harrison
Hawryluk, Iwona
Milton, Philip
Ainslie, Kylie E. C.
Baguelin, Marc
Boonyasiri, Adhiratha
Brazeau, Nick F.
Cattarino, Lorenzo
Cucunuba, Zulma
Cuomo-Dannenburg, Gina
Dorigatti, Ilaria
Eales, Oliver D.
Eaton, Jeffrey W.
van Elsland, Sabine L.
FitzJohn, Richard G.
Gaythorpe, Katy A. M.
Green, William
Hinsley, Wes
Jeffrey, Benjamin
Knock, Edward
Laydon, Daniel J.
Lees, John
Nedjati-Gilani, Gemma
Nouvellet, Pierre
Okell, Lucy
Parag, Kris V.
Siveroni, Igor
Thompson, Hayley A.
Walker, Patrick
Walters, Caroline E.
Watson, Oliver J.
Whittles, Lilith K.
Ghani, Azra C.
Ferguson, Neil M.
Riley, Steven
Donnelly, Christl A.
Bhatt, Samir
Flaxman, Seth
author_facet Unwin, H. Juliette T.
Mishra, Swapnil
Bradley, Valerie C.
Gandy, Axel
Mellan, Thomas A.
Coupland, Helen
Ish-Horowicz, Jonathan
Vollmer, Michaela A. C.
Whittaker, Charles
Filippi, Sarah L.
Xi, Xiaoyue
Monod, Mélodie
Ratmann, Oliver
Hutchinson, Michael
Valka, Fabian
Zhu, Harrison
Hawryluk, Iwona
Milton, Philip
Ainslie, Kylie E. C.
Baguelin, Marc
Boonyasiri, Adhiratha
Brazeau, Nick F.
Cattarino, Lorenzo
Cucunuba, Zulma
Cuomo-Dannenburg, Gina
Dorigatti, Ilaria
Eales, Oliver D.
Eaton, Jeffrey W.
van Elsland, Sabine L.
FitzJohn, Richard G.
Gaythorpe, Katy A. M.
Green, William
Hinsley, Wes
Jeffrey, Benjamin
Knock, Edward
Laydon, Daniel J.
Lees, John
Nedjati-Gilani, Gemma
Nouvellet, Pierre
Okell, Lucy
Parag, Kris V.
Siveroni, Igor
Thompson, Hayley A.
Walker, Patrick
Walters, Caroline E.
Watson, Oliver J.
Whittles, Lilith K.
Ghani, Azra C.
Ferguson, Neil M.
Riley, Steven
Donnelly, Christl A.
Bhatt, Samir
Flaxman, Seth
author_sort Unwin, H. Juliette T.
collection PubMed
description As of 1st June 2020, the US Centres for Disease Control and Prevention reported 104,232 confirmed or probable COVID-19-related deaths in the US. This was more than twice the number of deaths reported in the next most severely impacted country. We jointly model the US epidemic at the state-level, using publicly available death data within a Bayesian hierarchical semi-mechanistic framework. For each state, we estimate the number of individuals that have been infected, the number of individuals that are currently infectious and the time-varying reproduction number (the average number of secondary infections caused by an infected person). We use changes in mobility to capture the impact that non-pharmaceutical interventions and other behaviour changes have on the rate of transmission of SARS-CoV-2. We estimate that R(t) was only below one in 23 states on 1st June. We also estimate that 3.7% [3.4%–4.0%] of the total population of the US had been infected, with wide variation between states, and approximately 0.01% of the population was infectious. We demonstrate good 3 week model forecasts of deaths with low error and good coverage of our credible intervals.
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spelling pubmed-77129102020-12-07 State-level tracking of COVID-19 in the United States Unwin, H. Juliette T. Mishra, Swapnil Bradley, Valerie C. Gandy, Axel Mellan, Thomas A. Coupland, Helen Ish-Horowicz, Jonathan Vollmer, Michaela A. C. Whittaker, Charles Filippi, Sarah L. Xi, Xiaoyue Monod, Mélodie Ratmann, Oliver Hutchinson, Michael Valka, Fabian Zhu, Harrison Hawryluk, Iwona Milton, Philip Ainslie, Kylie E. C. Baguelin, Marc Boonyasiri, Adhiratha Brazeau, Nick F. Cattarino, Lorenzo Cucunuba, Zulma Cuomo-Dannenburg, Gina Dorigatti, Ilaria Eales, Oliver D. Eaton, Jeffrey W. van Elsland, Sabine L. FitzJohn, Richard G. Gaythorpe, Katy A. M. Green, William Hinsley, Wes Jeffrey, Benjamin Knock, Edward Laydon, Daniel J. Lees, John Nedjati-Gilani, Gemma Nouvellet, Pierre Okell, Lucy Parag, Kris V. Siveroni, Igor Thompson, Hayley A. Walker, Patrick Walters, Caroline E. Watson, Oliver J. Whittles, Lilith K. Ghani, Azra C. Ferguson, Neil M. Riley, Steven Donnelly, Christl A. Bhatt, Samir Flaxman, Seth Nat Commun Article As of 1st June 2020, the US Centres for Disease Control and Prevention reported 104,232 confirmed or probable COVID-19-related deaths in the US. This was more than twice the number of deaths reported in the next most severely impacted country. We jointly model the US epidemic at the state-level, using publicly available death data within a Bayesian hierarchical semi-mechanistic framework. For each state, we estimate the number of individuals that have been infected, the number of individuals that are currently infectious and the time-varying reproduction number (the average number of secondary infections caused by an infected person). We use changes in mobility to capture the impact that non-pharmaceutical interventions and other behaviour changes have on the rate of transmission of SARS-CoV-2. We estimate that R(t) was only below one in 23 states on 1st June. We also estimate that 3.7% [3.4%–4.0%] of the total population of the US had been infected, with wide variation between states, and approximately 0.01% of the population was infectious. We demonstrate good 3 week model forecasts of deaths with low error and good coverage of our credible intervals. Nature Publishing Group UK 2020-12-03 /pmc/articles/PMC7712910/ /pubmed/33273462 http://dx.doi.org/10.1038/s41467-020-19652-6 Text en © The Author(s) 2020 Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/.
spellingShingle Article
Unwin, H. Juliette T.
Mishra, Swapnil
Bradley, Valerie C.
Gandy, Axel
Mellan, Thomas A.
Coupland, Helen
Ish-Horowicz, Jonathan
Vollmer, Michaela A. C.
Whittaker, Charles
Filippi, Sarah L.
Xi, Xiaoyue
Monod, Mélodie
Ratmann, Oliver
Hutchinson, Michael
Valka, Fabian
Zhu, Harrison
Hawryluk, Iwona
Milton, Philip
Ainslie, Kylie E. C.
Baguelin, Marc
Boonyasiri, Adhiratha
Brazeau, Nick F.
Cattarino, Lorenzo
Cucunuba, Zulma
Cuomo-Dannenburg, Gina
Dorigatti, Ilaria
Eales, Oliver D.
Eaton, Jeffrey W.
van Elsland, Sabine L.
FitzJohn, Richard G.
Gaythorpe, Katy A. M.
Green, William
Hinsley, Wes
Jeffrey, Benjamin
Knock, Edward
Laydon, Daniel J.
Lees, John
Nedjati-Gilani, Gemma
Nouvellet, Pierre
Okell, Lucy
Parag, Kris V.
Siveroni, Igor
Thompson, Hayley A.
Walker, Patrick
Walters, Caroline E.
Watson, Oliver J.
Whittles, Lilith K.
Ghani, Azra C.
Ferguson, Neil M.
Riley, Steven
Donnelly, Christl A.
Bhatt, Samir
Flaxman, Seth
State-level tracking of COVID-19 in the United States
title State-level tracking of COVID-19 in the United States
title_full State-level tracking of COVID-19 in the United States
title_fullStr State-level tracking of COVID-19 in the United States
title_full_unstemmed State-level tracking of COVID-19 in the United States
title_short State-level tracking of COVID-19 in the United States
title_sort state-level tracking of covid-19 in the united states
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7712910/
https://www.ncbi.nlm.nih.gov/pubmed/33273462
http://dx.doi.org/10.1038/s41467-020-19652-6
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