Buildout and integration of an automated high-throughput CLIA laboratory for SARS-CoV-2 testing on a large urban campus

Landaverde, Lena; McIntyre, David; Robson, James; Fu, Dany; Ortiz, Luis; Chen, Rita; Oliveira, Samuel M. D.; Fan, Andy; Barrett, Amy; Burgay, Stephen P.; Choate, Stephen; Corbett, David; Doucette‐Stamm, Lynn; Gonzales, Kevin Andrew Uy; Hamer, Davidson H.; Huang, Lilly; Huval, Shari; Knight, Christopher; Landa, Carrie; Lindquist, Diane; Lockard, Kelly; Macdowell, Trevor L; Mauro, Elizabeth; McGinty, Colleen; Miller, Candice; Monahan, Maura; Moore, Randall; Platt, Judy; Rolles, Lloyd; Roy, Jeffrey; Schroeder, Tracey; Tolan, Dean R.; Zaia, Ann M.; Brown, Robert A.; Waters, Gloria; Densmore, Douglas; Klapperich, Catherine M.

doi:10.1016/j.slast.2022.06.003

Cited by 13 publications

(11 citation statements)

References 23 publications

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“…Our LOD is lower than that reported for SalivaDirect (6-12 SARS-CoV-2 copies per µL) 28 , which has a similar sample work ow, but relies on the less sensitive RT-qPCR platform 41 . Most other screening assays report LODs within this range as well (0.5-10.6 copies per µl) 16,17,18,19,20,21,22 . For pooled samples our LOD was 12 copies per µl, which is in line with at least one other report 20 and considered an acceptable trade-off for screening assays in which frequency and turnaround time rather than sensitivity are more important for mitigation of viral spread 42 .…”

Section: Discussionmentioning

confidence: 88%

“…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%

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

Wagner

Fox

Gordon

et al. 2023

Preprint

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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-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.

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Section: Discussionmentioning

confidence: 88%

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

show abstract

“…Our LOD is lower than that reported for SalivaDirect (6-12 SARS-CoV-2 copies per µL) 24 , which has a similar sample work ow, but relies on the less sensitive RT-qPCR platform 37 . Most other screening assays report LODs within this range as well (0.5-10.6 copies per µl) 12,13,14,15,16,17,18 . For pooled samples our LOD was 12 copies per µl, which is in line with at least one other report 16 and considered an acceptable trade-off for screening assays in which frequency and turnaround time rather than sensitivity are more important for mitigation of viral spread 38 .…”

Section: Discussionmentioning

confidence: 89%

“…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 2 . 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 3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18 . 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 19 .…”

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. 2022

Preprint

View full text Add to dashboard Cite

show abstract

“…Evaluations of testing programmes conducted on university settings commonly focus on test performance [ 11 ], number of tests performed, disease transmission and infections detected, or the technical, logistical, and regulatory processes that enabled the scale-up of testing onsite [ 12 , 13 , 14 , 15 , 16 , 17 , 18 , 19 , 20 , 21 , 22 , 23 , 24 , 25 ]. Some studies include surveys which are primarily focused on student transmissibility or symptom reporting [ 23 , 26 ].…”

Section: Introductionmentioning

confidence: 99%

A Qualitative Evaluation of the Barriers and Enablers for Implementation of an Asymptomatic SARS-CoV-2 Testing Service at the University of Nottingham: A Multi-Site Higher Education Setting in England

Blake

Somerset

Mahmood

et al. 2022

IJERPH

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Asymptomatic testing for SARS-CoV-2 RNA has been used to prevent and manage COVID-19 outbreaks in university settings, but few studies have explored their implementation. The aim of the study was to evaluate how an accredited asymptomatic SARS-CoV-2 testing service (ATS) was implemented at the University of Nottingham, a multi-campus university in England, to identify barriers and enablers of implementation and to draw out lessons for implementing pandemic response initiatives in higher education settings. A qualitative interview study was conducted with 25 ATS personnel between May and July 2022. Interviews were conducted online, audio-recorded, and transcribed. Participants were asked about their experience of the ATS, barriers and enablers of implementation. Transcripts were thematically analysed. There were four overarching themes: (1) social responsibility and innovation, (2) when, how and why people accessed testing, (3) impact of the ATS on the spread of COVID-19, and (4) lessons learned for the future. In establishing the service, the institution was seen to be valuing its community and socially responsible. The service was viewed to be broadly successful as a COVID-19 mitigation approach. Challenges to service implementation were the rapidly changing pandemic situation and government advice, delays in service accreditation and rollout to staff, ambivalence towards testing and isolating in the target population, and an inability to provide follow-up support for positive cases within the service. Facilitators included service visibility, reduction in organisational bureaucracy and red tape, inclusive leadership, collaborative working with regular feedback on service status, flexibility in service delivery approaches and simplicity of saliva testing. The ATS instilled a perception of early ‘return to normality’ and impacted positively on staff feelings of safety and wellbeing, with wider benefits for healthcare services and local communities. In conclusion, we identified common themes that have facilitated or hindered the implementation of a SARS-CoV-2 testing service at a university in England. Lessons learned from ATS implementation will inform future pandemic response interventions in higher education settings.

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Buildout and integration of an automated high-throughput CLIA laboratory for SARS-CoV-2 testing on a large urban campus

Cited by 13 publications

References 23 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

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

A Qualitative Evaluation of the Barriers and Enablers for Implementation of an Asymptomatic SARS-CoV-2 Testing Service at the University of Nottingham: A Multi-Site Higher Education Setting in England

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