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

Our estimates of domestic importation risk are likely conservative despite some important limitations in our air travel analysis. Because we do not have access to current airline data, we could not exactly quantify the impact of government restrictions on international travel. In addition, even without explicit government restrictions, general social distancing and work-from-home guidelines are reducing all airline travel. We did not account for these decreases in either our international or domestic travel data. While such variations may lower our domestic risk estimates, we also did not account for the large volumes of regional automobile and rail travel, especially along the corridor that connects Massachusetts, New York, New Jersey, Pennsylvania, and Washington D.C. to Connecticut. As such, the interconnectedness and large volumes of daily travel within the U.S. indicate that domestic spread of SARS-CoV-2 has become and will likely continue to be the primary source of new infections.