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.
This diagnostic study compares unsupervised home self-collected midnasal swabs vs clinician-collected nasopharyngeal swabs for the detection of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2).
The urgent need for massively scaled clinical or surveillance testing for SARS-CoV-2 has necessitated a reconsideration of the methods by which respiratory samples are collected, transported, processed and tested. Conventional testing for SARS-CoV-2 involves collection of a clinical specimen with a nasopharyngeal swab, storage of the swab during transport in universal transport medium (UTM), extraction of RNA, and quantitative reverse transcription PCR (RT-qPCR). As testing has scaled across the world, supply chain challenges have emerged across this entire workflow. Here we sought to evaluate how eliminating the UTM storage and RNA extraction steps would impact the results of molecular testing. Using paired mid-turbinate swabs self-collected by 11 individuals with previously established SARS-CoV-2 positivity, we performed a comparison of conventional (swab → UTM → RNA extraction → RT-qPCR) vs. simplified (direct elution from dry swab → RT-qPCR) protocols. Our results suggest that dry swabs eluted directly into a simple buffered solution (TE) can support molecular detection of SARS-CoV-2 via endpoint RT-qPCR without substantially compromising sensitivity. Although further confirmation with a larger sample size and variation of other parameters is necessary, these results are encouraging for the possibility of a simplified workflow that could support massively scaled testing for COVID-19 control. ResultsBased on prior literature ( 1 , 2 ) and the fact that dry swabs are employed for SARS-CoV-2 testing outside of the United States , we know that swabs collected and transported without transport media are amenable to subsequent nucleic acid detection-based diagnostics. We hypothesized that elution of dry swabs directly into a Tris-EDTA (TE) buffer would be compatible with RT-qPCR, i.e. skipping conventional RNA extraction altogether. TE's lower salt Seattle Flu Study Investigators Principal Investigators:
Introduction. While influenza and other respiratory pathogens cause significant morbidity and mortality, the community-based burden of these infections remains incompletely understood. The development of novel methods to detect respiratory infections is essential for mitigating epidemics and developing pandemic-preparedness infrastructure. Methods. From October 2019 to March 2020, we conducted a home-based cross-sectional study in the greater Seattle area, utilizing electronic consent and data collection instruments. Participants received nasal swab collection kits via rapid delivery within 24 hours of self-reporting respiratory symptoms. Samples were returned to the laboratory and were screened for 26 respiratory pathogens and a housekeeping gene. Participant data were recorded via online survey at the time of sample collection and one week later. Results. Of the 4,572 consented participants, 4,359 (95.3%) received a home swab kit, and 3,648 (83.7%) returned a nasal specimen for respiratory pathogen screening. The 3,638 testable samples had a mean RNase P CRT value of 19.0 (SD: 3.4) and 1,232 (33.9%) samples had positive results for one or more pathogens, including 645 (17.7%) influenza-positive specimens. Among the testable samples, the median time between shipment of the home swab kit and completion of laboratory testing was 8 days [IQR: 7.0-14.0]. A single adverse event occurred and did not cause long-term effects or require medical attention. Discussion. Home-based surveillance using online participant enrollment and specimen self-collection is a safe and feasible method for community-level monitoring of influenza and other respiratory pathogens, which can readily be adapted for use during pandemics.
Background The urgent need for massively scaled clinical testing for SARS-CoV-2, along with global shortages of critical reagents and supplies, has necessitated development of streamlined laboratory testing protocols. Conventional nucleic acid testing for SARS-CoV-2 involves collection of a clinical specimen with a nasopharyngeal swab in transport medium, nucleic acid extraction, and quantitative reverse transcription PCR (RT-qPCR) (1). As testing has scaled across the world, the global supply chain has buckled, rendering testing reagents and materials scarce (2). To address shortages, we developed SwabExpress, an end-to-end protocol developed to employ mass produced anterior nares swabs and bypass the requirement for transport media and nucleic acid extraction. Methods We evaluated anterior nares swabs, transported dry and eluted in low-TE buffer as a direct-to-RT-qPCR alternative to extraction-dependent viral transport media. We validated our protocol of using heat treatment for viral inactivation and added a proteinase K digestion step to reduce amplification interference. We tested this protocol across archived and prospectively collected swab specimens to fine-tune test performance. Results After optimization, SwabExpress has a low limit of detection at 2-4 molecules/uL, 100% sensitivity, and 99.4% specificity when compared side-by-side with a traditional RT-qPCR protocol employing extraction. On real-world specimens, SwabExpress outperforms an automated extraction system while simultaneously reducing cost and hands-on time. Conclusion SwabExpress is a simplified workflow that facilitates scaled testing for COVID-19 without sacrificing test performance. It may serve as a template for the simplification of PCR-based clinical laboratory tests, particularly in times of critical shortages during pandemics.
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