Large-Scale SARS-CoV-2 Testing Utilizing Saliva and Transposition Sample Pooling

Patterson, Joseph R.; Cole-Strauss, Allyson; Kuhn, Nathan C.; Mercier, Carlene; Kochmanski, Joseph; Gerlach, John; LeVeque, Rhiannon M.; Neugebauer, Kerri A.; Conner, Kayla N.; Gomez, Jasper; Hennes, Mark G.; Thompson, Kaje’ne E.; Rytlewski, Destinee L.; Bigwood, Chloe C.; Scharmen, Amy; Simjanovski, Gabriel; Riley, Cassidy; Donaldson, Jessica; Yasin, Dilann; Kouja, Najwa; Contejean, Zaria; Burnett, Michaela; Aminova, Shakhlo; Yawson, Nat Ato; Singh, Simran; Alian, Osama M.; Broeker, Carson D.; Zaluzec, Erin; ONeill, Morgan; Puschner, Birgit; Sousa, Aron; Bix, Laura; Jespersen, Brian; Holzman, Claudia; Mitchell, Jade; Julien, Ryan; Askin, Yesim; Barnes, Danielle; Durshanpalli, Purna; Krum, Doug; Weber, Rett; Patterson, Morgan; Anderson, Becky; Hunt, Ryan; O’Brien, Benjamin; Umstead, Andrew; Beck, John S.; Vega, Irving E.; Sortwell, Caryl E.; Lipton, Jack W.

doi:10.3791/64008

Cited by 4 publications

(4 citation statements)

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“…To facilitate efforts to return to in-person learning, routine screening was proposed to identify infected, asymptomatic individuals and, in combination with other interventions, mitigate the spread of SARS-CoV-2 6 . Many universities developed or implemented screening assays, using a variety of sample types (saliva vs nasal swabs), sample processing (minimal vs RNA extraction), efficiency strategies (pooled vs unpooled), and platforms (qPCR, RT-LAMP, antigen tests), although the majority relied on qPCR [7][8][9][10][11][12][13][14][15][16][17][18][19][20][21][22] . A recent analysis of 1,400 institutions of higher education (IHE) showed that the success of these screening efforts extended to their housed counties, as those with IHEs that conducted widespread testing had fewer hospitalizations and deaths 23 .…”

mentioning

confidence: 99%

A multiplexed, paired-pooled droplet digital PCR assay for detection of SARS-CoV-2 in saliva

Wagner

Fox

Gordon

et al. 2023

Sci Rep

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In response to the SARS-CoV-2 pandemic, we developed a multiplexed, paired-pool droplet digital PCR (MP4) screening assay. Key features of our assay are the use of minimally processed saliva, 8-sample paired pools, and reverse-transcription droplet digital PCR (RT-ddPCR) targeting the SARS-CoV-2 nucleocapsid gene. The limit of detection was determined to be 2 and 12 copies per µl for individual and pooled samples, respectively. Using the MP4 assay, we routinely processed over 1,000 samples a day with a 24-h turnaround time and over the course of 17 months, screened over 250,000 saliva samples. Modeling studies showed that the efficiency of 8-sample pools was reduced with increased viral prevalence and that this could be mitigated by using 4-sample pools. We also present a strategy for, and modeling data supporting, the creation of a third paired pool as an additional strategy to employ under high viral prevalence.

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mentioning

confidence: 99%

A multiplexed, paired-pooled droplet digital PCR assay for detection of SARS-CoV-2 in saliva

Wagner

Fox

Gordon

et al. 2023

Sci Rep

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“…As a result, we were included in the Kent County Health Department’s weekly Community COVID-19 Vaccine Planning meetings as representatives and advocates of the Latino community in West Michigan. At the same time, the Department of Translational Neuroscience at Michigan State University developed a cost-effective COVID-19 test based on self-collections using a nasal swab as well as saliva ( 19 ). This represented an opportunity to validate the new test using samples from the community, which at the same time allowed the COVID-19 test to be available to underserved communities.…”

Section: Resultsmentioning

confidence: 99%

Engaging diverse populations in aging research during the COVID-19 pandemic: Lessons learned from four National Institutes of Health funded-Centers

Vega

Ajrouch

Rorai³

et al. 2023

Front. Public Health

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BackgroundThe COVID-19 pandemic’s impact on our personal and professional lives required a rapid adaptation to the evolving health crisis and accumulating social stresses. Established measures to reduce the spread of infection and potential death had a direct effect on ongoing research that involved older adults and underrepresented racial/ethnic groups. Although important to preserve public health, these measures risk further isolation of vulnerable research participant populations and threatened established community partnerships. To address the social and research challenges evolving from the COVID-19 pandemic, four National Institutes of Health funded-Centers that engage with community members to enhance research and advance the science of aging came together to learn from each other’s efforts, approaches, and communication with community partners.MethodsMonthly meetings served as a venue to discuss the challenges of engagement with research participants and support community partners during the pandemic. The developed learning community also contributed to recognize and address research staff stress and isolation. We describe how these conversations led our Centers to address unprecedented challenges and sustain community engagement within diverse populations, especially Black/African Americans, Latinos, Middle Eastern/Arab Americans and the oldest-old.ResultsThe exchange of information resulted in maintaining long standing community relationships and partnerships in the face of the uncertainties generated by the pandemic. The strategies included adapting education programs to reduce risk of infection, recognizing symptoms, promoting vaccination and understanding of the effect of COVID-19 to the brain. Different strategies were used to address the effects of isolation and maintain community engagement. Although new research participant enrollment was a challenge, telephone and virtual visits allowed research participants to remain active in research. Community members participation in virtual learning events was variable, ranging from a dozen to hundreds of participants. Invitations to organize panels about newly developed topics indicated the need for information from trusted sources.ConclusionIn sum, the COVID-19 pandemic re - directed all four Centers’ commitment to community service led to developing strategies for social support, which will potentially contribute to transforming public perceptions about research and researchers.

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“…To facilitate efforts to return to in-person learning, routine screening was proposed to identify infected, asymptomatic individuals and, in combination with other interventions, mitigate the spread of SARS-CoV-2 6 . Many universities developed or implemented screening assays, using a variety of sample types (saliva vs nasal swabs), sample processing (minimal vs RNA extraction), e ciency strategies (pooled vs unpooled), and platforms (qPCR, RT-LAMP, antigen tests), although the majority relied on qPCR 7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22 . A recent analysis of 1,400 institutions of higher education (IHE) showed that the success of these screening efforts extended to their housed counties, as those with IHEs that conducted widespread testing had fewer hospitalizations and deaths 23 .…”

Section: Introductionmentioning

confidence: 99%

A multiplexed, paired-pooled droplet digital PCR assay for detection of SARS-CoV-2 in saliva

Wagner

Fox

Gordon

et al. 2023

Preprint

View full text Add to dashboard Cite

In response to the SARS-CoV-2 pandemic, we developed a multiplexed, paired-pool droplet digital PCR (MP4) screening assay. Key features of our assay are the use of minimally processed saliva, 8-sample paired pools, and reverse-transcription droplet digital PCR (RT-ddPCR) targeting the SARS-CoV-2 nucleocapsid gene. The limit of detection was determined to be 2 and 12 copies per µl for individual and pooled samples, respectively. Using the MP4 assay, we routinely processed over 1,000 samples a day with a 24-hour turnaround time and over the course of 17 months, screened over 250,000 saliva samples. Modeling studies showed that the efficiency of 8-sample pools was reduced with increased viral prevalence and that this could be mitigated by using 4-sample pools. We also present a strategy for, and modeling data supporting, the creation of a third paired pool as an additional strategy to employ under high viral prevalence.

show abstract

Large-Scale SARS-CoV-2 Testing Utilizing Saliva and Transposition Sample Pooling

Cited by 4 publications

References 0 publications

A multiplexed, paired-pooled droplet digital PCR assay for detection of SARS-CoV-2 in saliva

A multiplexed, paired-pooled droplet digital PCR assay for detection of SARS-CoV-2 in saliva

Engaging diverse populations in aging research during the COVID-19 pandemic: Lessons learned from four National Institutes of Health funded-Centers

A multiplexed, paired-pooled droplet digital PCR assay for detection of SARS-CoV-2 in saliva

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