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

To estimate RE for new infections acquired each day in each cohort, we applied the method of Wallinga and Teunis 12 to our reconstructed estimates of daily new infections, using the distribution of the serial interval to assign the probability of a transmission link between any two infections on differing days. Similar to the analysis described for incubation periods, we sampled from serial interval estimates from previous studies 13, [19] [20] [21] according to the number of subjects for whom data were available, and fitted a Weibull distribution to the sampled data by maximum likelihood. To correct for right censoring of transmission pairs, we divided estimates of RE for infections acquired each day t by the cumulative distribution function of the serial interval evaluated over the period from day t to the end of the study.