Incidence, clinical outcomes, and transmission dynamics of hospitalized 2019 coronavirus disease among 9,596,321 individuals residing in California and Washington, United States: a prospective cohort study

Joseph A Lewnard; Vincent X Liu; Michael L Jackson; Mark A Schmidt; Britta L Jewell; Jean P Flores; Chris Jentz; Graham R Northrup; Ayesha Mahmud; Arthur L Reingold; Maya Petersen; Nicholas P Jewell; Scott Young; Jim Bellows

Our estimates suggest RE declined to a range near 1 amid the implementation of social distancing interventions, in line with declining increases in the incidence rate of new COVID-19 inpatient admissions. These reductions precede large-scale implementation of social distancing in the study regions. It should be noted that our daily RE(t) estimates describe transmission resulting from infections acquired each day t, rather than those transmitting on each day t. Because most individuals begin transmitting >4 days after acquiring infection, declines in RE values are expected to precede dates of implementation of interventions that would affect transmission during individuals' infectious periods. Individuals may have also taken precautionary measures to limit risk of acquiring or transmitting infection prior to implementation of stay-at-home orders. Similar observations have been reported in a study of transmission dynamics in King County, Washington. 28 As our method propagates uncertainty in cumulative infection estimates based on time to hospitalization as well as the proportion of infected individuals experiencing symptoms, our approach does not aim to provide precise estimates of changes in RE associated with interventions implemented on particular dates.