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

  1. H. Juliette T. Unwin
  2. Swapnil Mishra
  3. Valerie C. Bradley
  4. Axel Gandy
  5. Thomas A. Mellan
  6. Helen Coupland
  7. Jonathan Ish-Horowicz
  8. Michaela A. C. Vollmer
  9. Charles Whittaker
  10. Sarah L. Filippi
  11. Xiaoyue Xi
  12. Mélodie Monod
  13. Oliver Ratmann
  14. Michael Hutchinson
  15. Fabian Valka
  16. Harrison Zhu
  17. Iwona Hawryluk
  18. Philip Milton
  19. Kylie E. C. Ainslie
  20. Marc Baguelin
  21. Adhiratha Boonyasiri
  22. Nick F. Brazeau
  23. Lorenzo Cattarino
  24. Zulma Cucunuba
  25. Gina Cuomo-Dannenburg
  26. Ilaria Dorigatti
  27. Oliver D. Eales
  28. Jeffrey W. Eaton
  29. Sabine L. van Elsland
  30. Richard G. FitzJohn
  31. Katy A. M. Gaythorpe
  32. William Green
  33. Wes Hinsley
  34. Benjamin Jeffrey
  35. Edward Knock
  36. Daniel J. Laydon
  37. John Lees
  38. Gemma Nedjati-Gilani
  39. Pierre Nouvellet
  40. Lucy Okell
  41. Kris V. Parag
  42. Igor Siveroni
  43. Hayley A. Thompson
  44. Patrick Walker
  45. Caroline E. Walters
  46. Oliver J. Watson
  47. Lilith K. Whittles
  48. Azra C. Ghani
  49. Neil M. Ferguson
  50. Steven Riley
  51. Christl A. Donnelly
  52. Samir Bhatt
  53. Seth Flaxman

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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 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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  1. Version published to 10.1038/s41467-020-19652-6
  2. Version published to 10.1101/2020.07.13.20152355v2 on medRxiv
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  4. Version published to 10.1101/2020.07.13.20152355v1 on medRxiv