Following its emergence in Wuhan, China, in late November or early December 2019, the SARS-CoV-2 virus has rapidly spread globally. Genome sequencing of SARS-CoV-2 allows reconstruction of its transmission history, although this is contingent on sampling. We have analyzed 453 SARS-CoV-2 genomes collected between 20 February and 15 March 2020 from infected patients in Washington State, USA. 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.

Following its emergence in Wuhan,

Summary and statement of need The analysis of human pathogens requires a diverse collection of bioinformatics tools. These tools include standard genomic and phylogenetic software and custom software developed to handle the relatively numerous and short genomes of viruses and bacteria. Researchers increasingly depend on the outputs of these tools to infer transmission dynamics of human diseases and make actionable recommendations to public health officials ( Black et al., 2020 ; Gardy et al., 2015 ). In order to enable real-time analyses of pathogen evolution, bioinformatics tools must scale rapidly with the number of samples and be flexible enough to adapt to a variety of questions and organisms. To meet these needs, we developed Augur, a bioinformatics toolkit designed for phylogenetic analyses of human pathogens.

We describe projections for the burden of infections and deaths in King and Snohomish Counties through April 7, as projections further out are strongly sensitive to assumptions about the scale of the local outbreak and importation dynamics from other regions that are not yet known. For the projections, we considered four scenarios for the increasingly effective impact of social distancing on COVID-19 incidence: • A baseline scenario assuming no change since January 15. • Scenarios with 25, 50, and 75 percent reductions in the rate of transmission assumed to take place starting March 10. The scenarios describe the generalized impacts of social distancing policies but do not currently speak to specific policy recommendations on issues like school closures, event cancellation, and work policies. We estimate that in the baseline scenario, on average across multiple simulations, there will have been roughly 25,000 people infected by April 7. Assuming mortality statistics will be like those seen in China, we expect that roughly 80 deaths will have occurred by April 7 and that roughly 400 total deaths will have been destined but not yet occurred. Effective social distancing slows the growth rate of the epidemic, and very effective interventions may stop the continued exponential growth. The table below illustrates the reductions in infections and deaths we expect with social distancing interventions. Social distancing intervention Estimated infections Destined deaths Business as usual 25,000 400 25% reduction 9,700 160 50% reduction 4,800 100 75% reduction 1,700 30 We do not yet know which scenario best represents current conditions in King and Snohomish counties, but previous experience in the region with weather-related social distancing and in other countries suggests to us that current efforts will likely land between baseline and 25% reduction scenarios. While we are not yet confident in our ability to estimate when the volume of new infections will overwhelm the health system, we discuss the issue below and believe it will be a critically important issue to address in the weeks to come. Thus, we believe more comprehensive non-pharmaceutical intervention policies in the region as soon as possible will be necessary to slow the onslaught of the disease, and we hope these are accompanied by policies to mitigate the broader societal impacts on the healthcare workforce and vulnerable populations.

Congregate living situations, such as homeless shelters, are high-risk settings for transmission of SARS-CoV-2 among residents and staff. This article describes findings from a study using active surveillance for SARS-CoV-2 that took place in 14 homeless shelters in King County, Washington, between 1 January and 24 April 2020.