Cryptic transmission of SARS-CoV-2 in Washington State
Alexander L. Greninger,
Lea M Starita,
Truong N Nguyen,
Peter D Han,
Chris D. Frazar,
Thomas R. Sibley,
Caitlin R Wolf,
Deborah A Nickerson,
Mark J. Rieder,
Janet A Englund,
the Seattle Flu Study Investigators,
Emma B Hodcroft,
Louise H Moncla,
Nicola Felix Müller,
Richard A Neher,
Gregory L. Armstrong,
Geoffrey S. Baird,
Helen Y Chu,
Keith R Jerome
Posted 06 Apr 2020
medRxiv DOI: 10.1101/2020.04.02.20051417
Posted 06 Apr 2020
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.
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