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


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.

SUBMITTER: Unwin HJT 

PROVIDER: S-EPMC7712910 | biostudies-literature | 2020 Dec

REPOSITORIES: biostudies-literature

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

Unwin H Juliette T HJT   Mishra Swapnil S   Bradley Valerie C VC   Gandy Axel A   Mellan Thomas A TA   Coupland Helen H   Ish-Horowicz Jonathan J   Vollmer Michaela A C MAC   Whittaker Charles C   Filippi Sarah L SL   Xi Xiaoyue X   Monod Mélodie M   Ratmann Oliver O   Hutchinson Michael M   Valka Fabian F   Zhu Harrison H   Hawryluk Iwona I   Milton Philip P   Ainslie Kylie E C KEC   Baguelin Marc M   Boonyasiri Adhiratha A   Brazeau Nick F NF   Cattarino Lorenzo L   Cucunuba Zulma Z   Cuomo-Dannenburg Gina G   Dorigatti Ilaria I   Eales Oliver D OD   Eaton Jeffrey W JW   van Elsland Sabine L SL   FitzJohn Richard G RG   Gaythorpe Katy A M KAM   Green William W   Hinsley Wes W   Jeffrey Benjamin B   Knock Edward E   Laydon Daniel J DJ   Lees John J   Nedjati-Gilani Gemma G   Nouvellet Pierre P   Okell Lucy L   Parag Kris V KV   Siveroni Igor I   Thompson Hayley A HA   Walker Patrick P   Walters Caroline E CE   Watson Oliver J OJ   Whittles Lilith K LK   Ghani Azra C AC   Ferguson Neil M NM   Riley Steven S   Donnelly Christl A CA   Bhatt Samir S   Flaxman Seth S  

Nature communications 20201203 1


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 tha  ...[more]

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