Coast-to-Coast Spread of SARS-CoV-2 during the Early Epidemic in the United States

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 M. Ott, Joshua Quick, Nicholas J. Loman, Karla M. Neugebauer, Alexander L. GreningerKeith R. Jerome, Pavitra Roychoudhury, Hong Xie, Lasata Shrestha, Meei Li Huang, Virginia E. Pitzer, Akiko Iwasaki, Saad B. Omer, Kamran Khan, Isaac I. Bogoch, Richard A. Martinello, Ellen F. Foxman, Marie L. Landry, Richard A. Neher, Albert I. Ko, Nathan D. Grubaugh

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review

122 Citations (Scopus)

Abstract

Using genomics and air travel information, the spread of SARS-CoV-2 in the United States from coast to coast is shown to be more a consequence of domestic introductions than of international travel.

Original languageEnglish
Pages (from-to)990-996.e5
JournalCell
Volume181
Issue number5
DOIs
Publication statusPublished - 28 May 2020
Externally publishedYes

Bibliographical note

Funding Information:
The authors of this study would like to acknowledge S. Cordey, I. Eckerle, and L. Kaiser from Geneva University Hospital for directly sharing their genome sequence data with our team; everyone who openly shared their genomic data on GenBank and GISAID (authors listed in Data S2 ); D. Ferguson, R. Garner, and J. Criscuolo at the Yale Clinical Virology Laboratory for laboratory support; the staff of the Yale Center for Research Computing for technical support; S. Taylor and P. Jack for enlightening discussions; our friends, families, and the Yale community for support during this difficult time; and all of the health care workers, public health employees, and scientists for efforts in the COVID-19 response. This research was funded with generous support from the Yale Institute for Global Health and the Yale School of Public Health start-up package provided to N.D.G. C.B.F.V. is supported by NWO Rubicon 019.181EN.004 . V.E.P. is funded by NIH/NIAID R01 AI112970 and R01 AI137093 . N.J.L. is funded by a Medical Research Council fellowship as part of the CLIMB project. The ARTIC resources were funded by Wellcome Trust collaborative award project number 206298/A/17/Z . J.Q. is funded by a UKRI Future Leaders fellowship. K.M.N. is funded by NIH R01 GM112766 . I.I.B. is funded by a COVID-2019 grant through the Canadian Institutes of Health Research .

Funding Information:
The authors of this study would like to acknowledge S. Cordey, I. Eckerle, and L. Kaiser from Geneva University Hospital for directly sharing their genome sequence data with our team; everyone who openly shared their genomic data on GenBank and GISAID (authors listed in Data S2); D. Ferguson, R. Garner, and J. Criscuolo at the Yale Clinical Virology Laboratory for laboratory support; the staff of the Yale Center for Research Computing for technical support; S. Taylor and P. Jack for enlightening discussions; our friends, families, and the Yale community for support during this difficult time; and all of the health care workers, public health employees, and scientists for efforts in the COVID-19 response. This research was funded with generous support from the Yale Institute for Global Health and the Yale School of Public Health start-up package provided to N.D.G. C.B.F.V. is supported by NWO Rubicon 019.181EN.004. V.E.P. is funded by NIH/NIAID R01 AI112970 and R01 AI137093. N.J.L. is funded by a Medical Research Council fellowship as part of the CLIMB project. The ARTIC resources were funded by Wellcome Trust collaborative award project number 206298/A/17/Z. J.Q. is funded by a UKRI Future Leaders fellowship. K.M.N. is funded by NIH R01 GM112766. I.I.B. is funded by a COVID-2019 grant through the Canadian Institutes of Health Research. J.R.F. M.E.P. E.B.H. V.E.P. A.I. S.B.O. I.I.B. E.F.F. M.L.L. R.A.N. A.I.K. and N.D.G. designed experiments. A.M. J.R. R.D. N.R.C. R.A.M. E.F.F. M.L.L. and A.I.K. provided clinical samples. C.B.F.V. A.L.W. C.C.K. and I.M.O. performed virus testing and laboratory support. J.R.F. and T.A. performed sequencing. J.Q. N.J.L. and K.M.N. provided sequencing resources and analysis methods. A.L.G. K.R.J. P.R. H.X. L.S. and M.-L.H. provided virus genomic data. A.G.W. K.K. and I.I.B. provided travel data. J.R.F. M.E.P. K.S. H.Y.E. and A.L.W. provided epidemiological data. J.R.F. M.E.P. E.B.H. K.S. H.Y.E. A.G.W. A.F.B. T.A. V.E.P. R.A.N. and N.D.G. analyzed data. J.R.F. M.E.P. and N.D.G. wrote the manuscript. J.R.F. M.E.P. E.B.H. A.F.B. A.L.W. K.M.N. R.A.N. and N.D.G. edited the manuscript. All authors read and approved the final manuscript. A.L.W. is the principal investigator on a research grant from Pfizer to Yale University and has received consulting fees for participation in advisory boards for Pfizer.

Publisher Copyright:
© 2020 Elsevier Inc.

Keywords

  • coronavirus
  • COVID-19
  • genomic epidemiology
  • MinION sequencing
  • phylogenetics
  • SARS-CoV-2
  • travel risk

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