SARS-CoV-2 Epidemiology on a Public University Campus in Washington State

Weil, Ana A.; Sohlberg, Sarah L; O’Hanlon, Jessica; Casto, Amanda M.; Emanuels, Anne; Lo, Natalie; Greismer, Emily P.; Magedson, Ariana; Wilcox, Naomi; Kim, Ashley E.; Back, Lewis; Frazar, Christian D.; Pelle, Ben; Sibley, Thomas H.; Ilcisin, Misja; Lee, Jover; Ryke, Erica; Craft, Jenna; Schwabe‐Fry, Kristen; Fay, Kairsten; Cho, Shari; Han, Peter D.; Heidl, Sarah; Pfau, Brian; Truong, Melissa; Zhong, Weizhi; Srivatsan, Sanjay; Harb, Katia; Gottlieb, Geoffrey S.; Nickerson, Deborah A.; Lockwood, Christina M.; Bedford, Trevor; Shendure, Jay

doi:10.1101/2021.03.15.21253227

Cited by 8 publications

(19 citation statements)

References 18 publications

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“…Importantly, we gained efficiency without sacrificing accuracy; our results suggest that the simplified SwabExpress protocol (direct elution from dry swab into low-TE + proteinase K → RT-qPCR) is as sensitive as the conventional PCR protocol (swab → UTM → RNA extraction → RT-qPCR). SwabExpress has supported scaled testing in our lab with over 72,000 tests performed to date and allowed us to support large testing endeavors such as the Husky Coronavirus Testing Program for the University of Washington (26).…”

Section: Discussionmentioning

confidence: 99%

“…Participants placed one swab in a tube with UTM (Becton Dickinson PN 220220) and the other in an empty, dry 15 mL conical tube for transport. For all other studies, anterior nares (US Cotton #3, distributed by Steripack) swabs were collected by the Seattle Flu Study, Husky Coronavirus Testing Program (HCT) (26) or the Seattle Coronavirus Assessment Network (SCAN) (28). Anterior Nares swabs were transported in a sterile, empty conical tube directly to the lab by HCT technicians.…”

Section: Methodsmentioning

confidence: 99%

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SwabExpress: An end-to-end protocol for extraction-free COVID-19 testing

Srivatsan

Heidl

Pfau

et al. 2020

Preprint

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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:

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Section: Discussionmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

SwabExpress: An end-to-end protocol for extraction-free COVID-19 testing

Srivatsan

Heidl

Pfau

et al. 2020

Preprint

Self Cite

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“…Importantly, we gained efficiency without sacrificing accuracy; our results suggest that the simplified SwabExpress protocol (direct elution from dry swab into low-TE + proteinase K → RT–qPCR) is as sensitive as the conventional PCR protocol (swab → UTM → RNA extraction → RT–qPCR). SwabExpress has supported scaled testing in our laboratory with over 91 000 tests performed to date and allowed us to support large testing endeavors such as thHusky Coronavirus Testing Program for the University of Washington ( 17 ).…”

Section: Discussionmentioning

confidence: 99%

“…Participants placed one swab in a tube with UTM (Becton Dickinson PN 220220) and the other in an empty, dry 15-mL conical tube for transport. For all other studies, AN (US Cotton #3, distributed by Steripack) swabs were collected by the Seattle Flu Study, Husky Coronavirus Testing Program (HCT) ( 17 ) or the Seattle Coronavirus Assessment Network (SCAN) ( 18 ). Anterior nares swabs were transported in a sterile, empty conical tube directly to the laboratory by HCT technicians.…”

Section: Methodsmentioning

confidence: 99%

SwabExpress: An End-to-End Protocol for Extraction-Free COVID-19 Testing

et al. 2021

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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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“…Institutions of higher education (IHE), such as colleges and universities, have been associated with high incidence of COVID-19 in the United States (Andersen et al, 2021;Leidner, 2021;Vang, 2021). Congregate settings, such as on-campus housing and off-campus social gatherings, have led to large outbreaks of COVID-19 despite mitigation efforts (Currie et al, 2021;Fox, 2021;Weil et al, 2021;Wilson, 2020). It is essential to gain a better understanding of SARS-CoV-2 transmission dynamics surrounding IHE to inform infection prevention strategies (Bradley et al, 2020;Paltiel et al, 2020;Yamey and Walensky, 2020), especially as more contagious variants continue to circulate.…”

Section: Introductionmentioning

confidence: 99%

SARS-CoV-2 Genomic Surveillance Reveals Little Spread Between a Large University Campus and the Surrounding Community

Valesano

Fitzsimmons

Blair

et al. 2021

Preprint

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COVID-19 has had high incidence at institutions of higher education (IHE) in the United States, but the transmission dynamics in these settings are not well understood. It remains unclear to what extent IHE-associated outbreaks have contributed to transmission in nearby communities. We implemented high-density prospective genomic surveillance to investigate these dynamics at the University of Michigan-Ann Arbor and the surrounding community during the Fall 2020 semester (August 16th through November 24th). We sequenced complete SARS-CoV-2 genomes from 1659 individuals, including 468 students, representing 20% of cases in students and 25% of total confirmed cases in Washtenaw County over the study interval. Phylogenetic analysis identified over 200 introductions into the student population, most of which were not related to other student cases. There were two prolonged transmission clusters among students that spanned across multiple on-campus residences. However, there were very few genetic descendants of student clusters among non-students during a subsequent November wave of infections in the community. We conclude that outbreaks at the University of Michigan did not significantly contribute to the rise in Washtenaw County COVID-19 incidence during November 2020. These results provide valuable insights into the distinct transmission dynamics of SARS- CoV-2 among IHE populations and surrounding communities.

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SARS-CoV-2 Epidemiology on a Public University Campus in Washington State

Cited by 8 publications

References 18 publications

SwabExpress: An end-to-end protocol for extraction-free COVID-19 testing

SwabExpress: An end-to-end protocol for extraction-free COVID-19 testing

SwabExpress: An End-to-End Protocol for Extraction-Free COVID-19 Testing

SARS-CoV-2 Genomic Surveillance Reveals Little Spread Between a Large University Campus and the Surrounding Community

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