Cryptic transmission of SARS-CoV-2 in Washington State
Source code
github.com/blab/ncov-cryptic-transmission
Contributors
trvrb
joverlee521
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Cryptic transmission of SARS-CoV-2 in Washington State

Trevor Bedford1,2,3, Alexander L. Greninger1,3, Pavitra Roychoudhury1,3, Lea M. Starita2,3, Michael Famulare4, Meei-Li Huang3, Arun Nalla3, Gregory Pepper3, Adam Reinhardt3, Hong Xie3, Lasata Shrestha3, Truong N Nguyen3, Amanda Adler5, Elisabeth Brandstetter3, Shari Cho3, Danielle Giroux3, Peter D. Han3, Kairsten Fay1, Chris D. Frazar3, Misja Ilcisin1, Kirsten Lacombe5, Jover Lee1, Anahita Kiavand3, Matthew Richardson3, Thomas R. Sibley1, Melissa Truong3, Caitlin R. Wolf3, Deborah A. Nickerson2,3, Mark J. Rieder2,3, Janet A. Englund3,5, the Seattle Flu Study Investigators, James Hadfield1, Emma B. Hodcroft6, John Huddleston1,3, Louise H. Moncla1, Nicola F. Müller1, Richard A. Neher6, Xianding Deng7, Wei Gu7, Scot Federman7, Charles Chiu7, Jeff Duchin3,8, Romesh Gautom9, Geoff Melly9, Brian Hiatt9, Philip Dykema9, Scott Lindquist9, Krista Queen10, Ying Tao10, Anna Uehara10, Suxiang Tong10, Duncan MacCannell10, Gregory L. Armstrong10, Geoffrey S. Baird3, Helen Y. Chu2,3, Jay Shendure2,3,11, Keith R. Jerome1,3

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. On March 11, 2020, the World Health Organization declared Coronavirus Disease 2019 (COVID-19) a pandemic. 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, strongly suggesting cryptic spread of COVID-19 during the months of January and February 2020, 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 introductions and spread and the power of pathogen genomics to inform epidemiological understanding.

Organization

  • data: Contains consensus SARS-CoV-2 genomes in FASTA format alongside metadata for WA genomes sequenced up to 25 March 2020.
  • augur-build: Contains consensus SARS-CoV-2 genomes in data/ and a reproducible Nextstrain phylogenetic pipeline focusing on the WA1 clade. Results of this pipeline are viewable at nextstrain.org/community/blab/ncov-cryptic-transmission/wa1-clade (Figure 1a).
  • beast: Contains XML with genome data, BEAST output and a Mathematica analysis notebook (Figure 1b)
  • forward-sim: Contains MatLab code to conduct forward simulation (Figure 3)
  • Figure 2 and Supp Figure 1 are generated from the Nextstrain ncov build run on 25 March 2020 available at nextstrain.org/ncov/2020-03-25. The code to reproduce these figures is available at commit 3ac03a9a.

Citation

Bedford T, Greninger AL, Roychoudhury P, Lea M Starita, Famulare M, Huang M, Nalla A, Pepper G, Reinhardt A, Xie H, Shrestha L, Nguyen TN, Adler A, Brandstetter E, Cho S, Giroux D, Peter D Han, 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, Hadfield J, Hodcroft EB, Huddleston J, Moncla LH, Müller NF, Neher RA, Deng X, Gu W, Federman S, Chiu C, Duchin J, 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, Jerome KR. 2020. Cryptic transmission of SARS-CoV-2 in Washington State. medRxiv: 2020.04.02.20051417.

All code (files ending in .py) is licensed under an MIT License.