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 F 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.
- Downloaded 10,005 times
- Download rankings, all-time:
- Site-wide: 1,349
- In epidemiology: 179
- Year to date:
- Site-wide: 29,056
- Since beginning of last month:
- Site-wide: 25,296
Downloads over time
Distribution of downloads per paper, site-wide
- 27 Nov 2020: The website and API now include results pulled from medRxiv as well as bioRxiv.
- 18 Dec 2019: We're pleased to announce PanLingua, a new tool that enables you to search for machine-translated bioRxiv preprints using more than 100 different languages.
- 21 May 2019: PLOS Biology has published a community page about Rxivist.org and its design.
- 10 May 2019: The paper analyzing the Rxivist dataset has been published at eLife.
- 1 Mar 2019: We now have summary statistics about bioRxiv downloads and submissions.
- 8 Feb 2019: Data from Altmetric is now available on the Rxivist details page for every preprint. Look for the "donut" under the download metrics.
- 30 Jan 2019: preLights has featured the Rxivist preprint and written about our findings.
- 22 Jan 2019: Nature just published an article about Rxivist and our data.
- 13 Jan 2019: The Rxivist preprint is live!