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. 2020 Dec 3;11(1):6189.
doi: 10.1038/s41467-020-19652-6.

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

H Juliette T Unwin  1 , Swapnil Mishra  2 , Valerie C Bradley  3 , Axel Gandy  4 , Thomas A Mellan  2 , Helen Coupland  2 , Jonathan Ish-Horowicz  4 , Michaela A C Vollmer  2 , Charles Whittaker  2 , Sarah L Filippi  4 , Xiaoyue Xi  4 , Mélodie Monod  4 , Oliver Ratmann  4 , Michael Hutchinson  3 , Fabian Valka, Harrison Zhu  4 , Iwona Hawryluk  2 , Philip Milton  2 , Kylie E C Ainslie  2 , Marc Baguelin  2   5 , Adhiratha Boonyasiri  6 , Nick F Brazeau  2 , Lorenzo Cattarino  2 , Zulma Cucunuba  2 , Gina Cuomo-Dannenburg  2 , Ilaria Dorigatti  2 , Oliver D Eales  2 , Jeffrey W Eaton  7 , Sabine L van Elsland  2 , Richard G FitzJohn  2 , Katy A M Gaythorpe  2 , William Green  2 , Wes Hinsley  2 , Benjamin Jeffrey  2 , Edward Knock  2 , Daniel J Laydon  2 , John Lees  2 , Gemma Nedjati-Gilani  2 , Pierre Nouvellet  2   8 , Lucy Okell  2 , Kris V Parag  2 , Igor Siveroni  2 , Hayley A Thompson  2 , Patrick Walker  2 , Caroline E Walters  2 , Oliver J Watson  2   9 , Lilith K Whittles  2 , Azra C Ghani  2 , Neil M Ferguson  2 , Steven Riley  2 , Christl A Donnelly  2   3 , Samir Bhatt  10 , Seth Flaxman  11
Affiliations

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

H Juliette T Unwin et al. Nat Commun. .

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.

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Conflict of interest statement

The authors declare no competing interests.

Figures

Fig. 1
Fig. 1. Daily estimates of the number of infectious (those still able to transmit) individuals and newly infected individuals.
The light purple band is the 95% credible interval (CI) of the number of infected individuals, dark purple the 50% CI of the number of infected individuals, light blue the 95% CI of the newly infected individuals and dark blue the 50% CI of the newly infected individuals.
Fig. 2
Fig. 2. Estimates of the probability that the time-varying reproduction number Rt is less than one in each state.
This plot shows the certainty that the rate of transmission is under control. These values are an average over the week ending 01 June 2020.
Fig. 3
Fig. 3. Country level covariate effect sizes assuming mobility stopped entirely (100% reduction in average mobility) and residential mobility was increased fully (100% increase in residential mobility).
Average mobility combines “retail & recreation”, “grocery & pharmacy”, “workplaces”. The error bars show 95% credible intervals and the dots show the mean estimate. The sample size n = 105,006 deaths across the 50 states and the District of Columbia up until 1 June and 479,422 cases from 11 May to 1 June.
Fig. 4
Fig. 4. Three-week death forecasts for model fitted up until 01 June 2020.
The coral bars show the reported number of deaths for the 3 weeks after 01 June 2020, and the blue line and ribbon show the mean and 95% CI for our forecast estimates.
See this image and copyright information in PMC

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