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. 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 () and Seth Flaxman ()
Additional contact information
H. Juliette T. Unwin: Abdul Latif Jameel Institute for Disease and Emergency Analytics (J-IDEA), Imperial College
Swapnil Mishra: Abdul Latif Jameel Institute for Disease and Emergency Analytics (J-IDEA), Imperial College
Valerie C. Bradley: University of Oxford
Axel Gandy: Imperial College
Thomas A. Mellan: Abdul Latif Jameel Institute for Disease and Emergency Analytics (J-IDEA), Imperial College
Helen Coupland: Abdul Latif Jameel Institute for Disease and Emergency Analytics (J-IDEA), Imperial College
Jonathan Ish-Horowicz: Imperial College
Michaela A. C. Vollmer: Abdul Latif Jameel Institute for Disease and Emergency Analytics (J-IDEA), Imperial College
Charles Whittaker: Abdul Latif Jameel Institute for Disease and Emergency Analytics (J-IDEA), Imperial College
Sarah L. Filippi: Imperial College
Xiaoyue Xi: Imperial College
Mélodie Monod: Imperial College
Oliver Ratmann: Imperial College
Michael Hutchinson: University of Oxford
Harrison Zhu: Imperial College
Iwona Hawryluk: Abdul Latif Jameel Institute for Disease and Emergency Analytics (J-IDEA), Imperial College
Philip Milton: Abdul Latif Jameel Institute for Disease and Emergency Analytics (J-IDEA), Imperial College
Kylie E. C. Ainslie: Abdul Latif Jameel Institute for Disease and Emergency Analytics (J-IDEA), Imperial College
Marc Baguelin: Abdul Latif Jameel Institute for Disease and Emergency Analytics (J-IDEA), Imperial College
Adhiratha Boonyasiri: Imperial College London
Nick F. Brazeau: Abdul Latif Jameel Institute for Disease and Emergency Analytics (J-IDEA), Imperial College
Lorenzo Cattarino: Abdul Latif Jameel Institute for Disease and Emergency Analytics (J-IDEA), Imperial College
Zulma Cucunuba: Abdul Latif Jameel Institute for Disease and Emergency Analytics (J-IDEA), Imperial College
Gina Cuomo-Dannenburg: Abdul Latif Jameel Institute for Disease and Emergency Analytics (J-IDEA), Imperial College
Ilaria Dorigatti: Abdul Latif Jameel Institute for Disease and Emergency Analytics (J-IDEA), Imperial College
Oliver D. Eales: Abdul Latif Jameel Institute for Disease and Emergency Analytics (J-IDEA), Imperial College
Jeffrey W. Eaton: Imperial College
Sabine L. Elsland: Abdul Latif Jameel Institute for Disease and Emergency Analytics (J-IDEA), Imperial College
Richard G. FitzJohn: Abdul Latif Jameel Institute for Disease and Emergency Analytics (J-IDEA), Imperial College
Katy A. M. Gaythorpe: Abdul Latif Jameel Institute for Disease and Emergency Analytics (J-IDEA), Imperial College
William Green: Abdul Latif Jameel Institute for Disease and Emergency Analytics (J-IDEA), Imperial College
Wes Hinsley: Abdul Latif Jameel Institute for Disease and Emergency Analytics (J-IDEA), Imperial College
Benjamin Jeffrey: Abdul Latif Jameel Institute for Disease and Emergency Analytics (J-IDEA), Imperial College
Edward Knock: Abdul Latif Jameel Institute for Disease and Emergency Analytics (J-IDEA), Imperial College
Daniel J. Laydon: Abdul Latif Jameel Institute for Disease and Emergency Analytics (J-IDEA), Imperial College
John Lees: Abdul Latif Jameel Institute for Disease and Emergency Analytics (J-IDEA), Imperial College
Gemma Nedjati-Gilani: Abdul Latif Jameel Institute for Disease and Emergency Analytics (J-IDEA), Imperial College
Pierre Nouvellet: Abdul Latif Jameel Institute for Disease and Emergency Analytics (J-IDEA), Imperial College
Lucy Okell: Abdul Latif Jameel Institute for Disease and Emergency Analytics (J-IDEA), Imperial College
Kris V. Parag: Abdul Latif Jameel Institute for Disease and Emergency Analytics (J-IDEA), Imperial College
Igor Siveroni: Abdul Latif Jameel Institute for Disease and Emergency Analytics (J-IDEA), Imperial College
Hayley A. Thompson: Abdul Latif Jameel Institute for Disease and Emergency Analytics (J-IDEA), Imperial College
Patrick Walker: Abdul Latif Jameel Institute for Disease and Emergency Analytics (J-IDEA), Imperial College
Caroline E. Walters: Abdul Latif Jameel Institute for Disease and Emergency Analytics (J-IDEA), Imperial College
Oliver J. Watson: Abdul Latif Jameel Institute for Disease and Emergency Analytics (J-IDEA), Imperial College
Lilith K. Whittles: Abdul Latif Jameel Institute for Disease and Emergency Analytics (J-IDEA), Imperial College
Azra C. Ghani: Abdul Latif Jameel Institute for Disease and Emergency Analytics (J-IDEA), Imperial College
Neil M. Ferguson: Abdul Latif Jameel Institute for Disease and Emergency Analytics (J-IDEA), Imperial College
Steven Riley: Abdul Latif Jameel Institute for Disease and Emergency Analytics (J-IDEA), Imperial College
Christl A. Donnelly: Abdul Latif Jameel Institute for Disease and Emergency Analytics (J-IDEA), Imperial College
Samir Bhatt: Abdul Latif Jameel Institute for Disease and Emergency Analytics (J-IDEA), Imperial College
Seth Flaxman: Imperial College

Nature Communications, 2020, vol. 11, issue 1, 1-9

Abstract: Abstract 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 Rt 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.

Date: 2020
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Persistent link: https://EconPapers.repec.org/RePEc:nat:natcom:v:11:y:2020:i:1:d:10.1038_s41467-020-19652-6

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DOI: 10.1038/s41467-020-19652-6

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