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

The combined results of our genomic epidemiology and travel pattern analyses suggest that domestic spread recently became a significant source of new SARS-CoV-2 infections in the U.S. We find strong evidence that outbreaks on the East Coast (Connecticut) are linked to outbreaks on the West Coast (Washington), demonstrating that trans-continental spread has already occured. As of March 25, there are >1000 SARS-CoV-2 genomes sequenced from around the world, including >350 from the U.S. ( https://nextstrain.org/ncov ); however most of the latter were obtained from a small number of U.S. states. Therefore, we cannot yet determine the exact origins of the viral introductions into Connecticut. Recent domestic travel history of the nine reported cases was not available, but it is unlikely that all of the infections originated in Washington state. Furthermore, due to low genetic diversity between these early sequences from Connecticut and Washington, we cannot yet determine how often the virus may be spreading between the U.S. coasts or whether an introduction from a common source is responsible for phylogenetic grouping. As testing capacity increases and more viral genome sequences become available from new locations, more granular reconstructions of virus spread throughout the U.S. will be possible (Grubaugh et al., 2019a) . Specifically, elucidating the phylogenetic relationship of viral genomes collected in Connecticut to those collected in neighboring states, especially those with a high burden of disease like New York, will improve our understanding of critical interstate dynamics.