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 SARS-CoV-2 sequences generated here can be found using the NCBI BioProject: (PRJNA614976) and GISAID (EPI_ISL_416416-416424). Sequencing data will be made available via SRA. Data used to create the figures can be found in the supplemental files. The interactive Nextstain page to visualize the genomic data can be found at: https://nextstrain.org/community/grubaughlab/CT-SARS-CoV-2 . The raw data, results, and analyses can be found at: https://github.com/grubaughlab/CT-SARS-CoV-2 . This research was funded by the generous support from the Yale Institute for Global Health and the Yale School of Public Health start-up package provided to NDG. CBFV is supported by NWO Rubicon 019.181EN.004. VEP is funded by NIH/NIAID R01 AI112970 and R01 AI137093. NJL is funded by a Medical Research Council fellowship as part of the CLIMB project. The ARTIC resources were funded by a Wellcome Trust Collaborative Award project number 206298/A/17/Z. JQ is funded by a UKRI Future Leaders Fellowship. KMN is funded by NIH R01 GM112766. IIB is funded by a COVID-2019 grant through the Canadian Institutes of Health Research.