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Cryptic transmission of SARS-CoV-2 in Washington State

2020; Cold Spring Harbor Laboratory; Linguagem: Inglês

10.1101/2020.04.02.20051417

Trevor Bedford, Alexander L. Greninger, Pavitra Roychoudhury, Lea M. Starita, Michael Famulare, Meei‐Li Huang, Arun Kumar Nalla, Gregory Pepper, Adam Reinhardt, Hong Xie, Lasata Shrestha, Truong N. Nguyen, Amanda Adler, Elisabeth Brandstetter, Shari Cho, Danielle Giroux, Peter D. Han, Kairsten Fay, Chris Frazar, Misja Ilcisin, Kirsten Lacombe, Jover Lee, Anahita Kiavand, M Richardson, Thomas R. Sibley, Melissa Truong, Caitlin R. Wolf, Deborah A. Nickerson, Mark J. Rieder, Janet A. Englund, James Hadfield, Emma B. Hodcroft, John Huddleston, Louise H. Moncla, Nicola F. Müller, Richard A. Neher, Xianding Deng, Wei Gu, Scot Federman, Charles Y. Chiu, Jeff Duchin, Romesh Gautom, Geoff Melly, Brian Hiatt, Philip Dykema, Scott Lindquist, Krista Queen, Ying Tao, Anna Uehara, Suxiang Tong, Duncan MacCannell, Gregory L. Armstrong, Geoffrey S. Baird, Helen Y. Chu, Jay Shendure, Keith R. Jerome,

SARS-CoV-2 detection and testing

Abstract Following 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.