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

traveling by air from five international (China, Italy, Iran, Spain, and Germany) and five U.S. locations (Washington, California, Florida, Illinois, and Louisiana) to airports that are commonly used by Connecticutians: Bradley International Airport (BDL, Hartford, Connecticut; ranked 53rd in U.S. in yearly passenger volume; https://www.faa.gov/airports/planning_capacity/passenger_allcargo_stats/passenger/ ), General Edward Lawrence Logan International Airport (BOS, Boston, Massachusetts; ranked 16th), and John F. Kennedy International Airport (JFK, New York, New York; ranked 6th). Air passenger data from 2020 is not currently available; thus, we used data from January to March 2019 to represent general trends in passenger volumes, as done previously (Bogoch et al., 2020) . We took the average of the 3-month passenger volumes to estimate the daily number of travelers entering each airport from the specified origin. To account for passenger reductions following U.S. government alerts and restrictions (Taylor, 2020) , we modeled two scenarios: a 40% reduction in passenger volume and a 90% reduction in passenger volume. These thresholds were determined based on previously reported estimates and assumptions around travel restrictions (Chinazzi et al., 2020) .