Cryptic transmission of SARS-CoV-2 in Washington state.
Bedford T., Greninger AL., Roychoudhury P., Starita LM., Famulare M., Huang M-L., Nalla A., Pepper G., Reinhardt A., Xie H., Shrestha L., Nguyen TN., Adler A., Brandstetter E., Cho S., Giroux D., Han PD., Fay K., Frazar CD., Ilcisin M., Lacombe K., Lee J., Kiavand A., Richardson M., Sibley TR., Truong M., Wolf CR., Nickerson DA., Rieder MJ., Englund JA., Seattle Flu Study Investigators None., Hadfield J., Hodcroft EB., Huddleston J., Moncla LH., Müller NF., Neher RA., Deng X., Gu W., Federman S., Chiu C., Duchin JS., Gautom R., Melly G., Hiatt B., Dykema P., Lindquist S., Queen K., Tao Y., Uehara A., Tong S., MacCannell D., Armstrong GL., Baird GS., Chu HY., Shendure J., Jerome KR.
After its emergence in Wuhan, China, in late November or early December 2019, the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) virus rapidly spread globally. Genome sequencing of SARS-CoV-2 allows the reconstruction of its transmission history, although this is contingent on sampling. We analyzed 453 SARS-CoV-2 genomes collected between 20 February and 15 March 2020 from infected patients in Washington state in the United States. We find that most SARS-CoV-2 infections sampled during this time derive from a single introduction in late January or early February 2020, which subsequently spread locally before active community surveillance was implemented.