Author:
Bedford Trevor,Greninger Alexander L.,Roychoudhury Pavitra,Starita Lea M.,Famulare Michael,Huang Meei-Li,Nalla Arun,Pepper Gregory,Reinhardt Adam,Xie Hong,Shrestha Lasata,Nguyen Truong N,Adler Amanda,Brandstetter Elisabeth,Cho Shari,Giroux Danielle,Han Peter D.,Fay Kairsten,Frazar Chris D.,Ilcisin Misja,Lacombe Kirsten,Lee Jover,Kiavand Anahita,Richardson Matthew,Sibley Thomas R.,Truong Melissa,Wolf Caitlin R.,Nickerson Deborah A.,Rieder Mark J.,Englund Janet A.,Hadfield James,Hodcroft Emma B.,Huddleston John,Moncla Louise H.,Müller Nicola F.,Neher Richard A.,Deng Xianding,Gu Wei,Federman Scot,Chiu Charles,Duchin Jeff,Gautom Romesh,Melly Geoff,Hiatt Brian,Dykema Philip,Lindquist Scott,Queen Krista,Tao Ying,Uehara Anna,Tong Suxiang,MacCannell Duncan,Armstrong Gregory L.,Baird Geoffrey S.,Chu Helen Y.,Shendure Jay,Jerome Keith R.,
Abstract
AbstractFollowing its emergence in Wuhan, China, in late November or early December 2019, the SARS-CoV-2 virus has rapidly spread throughout the world. Genome sequencing of SARS-CoV-2 strains allows for the reconstruction of transmission history connecting these infections. Here, we analyze 346 SARS-CoV-2 genomes from samples collected between 20 February and 15 March 2020 from infected patients in Washington State, USA. We found that the large majority of SARS-CoV-2 infections sampled during this time frame appeared to have derived from a single introduction event into the state in late January or early February 2020 and subsequent local spread, indicating cryptic spread of COVID-19 before active community surveillance was implemented. We estimate a common ancestor of this outbreak clade as occurring between 18 January and 9 February 2020. From genomic data, we estimate an exponential doubling between 2.4 and 5.1 days. These results highlight the need for large-scale community surveillance for SARS-CoV-2 and the power of pathogen genomics to inform epidemiological understanding.
Publisher
Cold Spring Harbor Laboratory
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