Coast-to-coast spread of SARS-CoV-2 in the United States revealed by genomic epidemiology

Joseph R Fauver; Mary E. Petrone; Emma B Hodcroft; Kayoko Shioda; Hanna Y Ehrlich; Alexander G. Watts; Chantal B.F. Vogels; Anderson F. Brito; Tara Alpert; Anthony Muyombwe; Jafar Razeq; Randy Downing; Nagarjuna R. Cheemarla; Anne L Wyllie; Chaney C. Kalinich; Isabel Ott; Josh Quick; Nicholas J. Loman; Karla M. Neugebauer; Alexander L. Greninger; Keith R. Jerome; Pavitra Roychoundhury; Hong Xie; Lasata Shrestha; Meei-Li Huang; Virginia E. Pitzer; Akiko Iwasaki; Saad B. Omer; Kamran Khan; Isaac Bogoch; Richard A. Martinello; Ellen F. Foxman; Marie-Louise Landry; Richard A Neher; Albert I Ko; Nathan D. Grubaugh

We assumed a constant ascertainment period of d =5 days between symptom onset and testing (Ferguson et al., 2020) . Because of the evidence of pre-symptomatic transmission (Tindale et al., 2020), we also assumed that cases become infectious one day before symptom onset. To account for substantial uncertainty around reporting rates, we assigned different reporting rates to individual locations based on the testing criteria enacted in that location (Niehus et al., 2020) . For each country and state, we first extracted testing criteria from the department or ministry of health website. We assumed that countries or states with similar testing criteria policies captured similar proportions of true infections. Using the respective testing criteria, we categorized countries or states as having narrow, moderate, or broad testing levels. We then assigned reporting rates to each testing level by using the mean and 95% confidence interval of the reporting rate estimated by Nishiura et al. (Nishiura et al., 2020) : 0.092 (95% CI= 0.05-0.20). The reporting rate for the broadest testing level, ρ=0.20, also corresponded to the reporting rate in Mainland China (Chinazzi et al., 2020) . We thus assigned Iran, Florida, Washington, and Illinois to a "narrow" testing level (ρ=0.05); Spain, Italy, and Louisiana to a "moderate'' testing level (ρ=0.092); and China, Germany, and California to a "broad" testing level (ρ=0.20, Data S2 , "testing-criteria" ).