Improving the efficiency and effectiveness of an industrial SARS-CoV-2 diagnostic facility

Douthwaite, Julie A.; Brown, Christopher; Ferdinand, John R.; Sharma, Rahul; Elliott, Jane; Taylor, Molly A.; Malintan, Nancy T.; Duvoisin, Hannah; Hill, Thomas M.; Delpuech, Oona; Orton, Alexandra L.; Pitt, Haidee; Kuenzi, Fred; Fish, Simon; Nicholls, David J.; Cuthbert, Anna; Richards, Ian; Ratcliffe, Giles S.; Upadhyay, Abhishek; Marklew, Abigail; Hewitt, Craig; Ross‐Thriepland, Douglas; Brankin, Christopher; Chodorge, Matthieu; Browne, Gareth J.; Mander, Palwinder K.; DeWildt, Ruud M.; Weaver, Shane; Smee, Penny A.; Kempen, Joost van; Bartlett, Jon G.; Allen, Paula M.; Koppe, Emma; Ashby, Charlotte A.; Phipps, Julian D.; Mehta, Nalini; Brierley, David; Tew, David G.; Leveridge, Melanie; Baddeley, Stuart M.; Goodfellow, Ian; Green, Clive; Abell, Chris; Neely, Andy; Waddell, Ian D.; Rees, Steve; Maxwell, Patrick H.; Pangalos, Menelas N.; Howes, Rob; Clark, Roger

doi:10.1038/s41598-022-06873-6

“…Faced with the challenge of the SARS-CoV-2 pandemic, laboratories worldwide have been applying a variety of strategies and methods to meet the exceptionally high testing demand (18, 19). For molecular testing, these include rRT-PCR performed directly on crude samples without nucleic acid extraction (20)(21)(22)(23)(24), isothermal ampli cation techniques (25,26) and CRISPR-based nucleic acid detection assays (27)(28)(29). In our approach, we maintained a standard rRT-PCR testing work ow and the associated high detection sensitivity and speci city by combining three pragmatic and straightforward measures to stepwise increase our testing capacity, generating several options to exibly adapt sample throughput according to the current demand.…”

Section: Discussionmentioning

confidence: 99%

Flexible upscaling of laboratory PCR testing capacity at the Robert Koch Institute during the SARS-CoV-2 pandemic

Krause

¹

,

Michel

²

,

Puyskens

³

et al. 2022

Preprint

0

View full text Add to dashboard Cite

Background Over the course of the COVID-19 pandemic, laboratories worldwide have been facing an unprecedented increase in demand for PCR testing because of the high importance of diagnostics for prevention and control of virus spread. Moreover, testing demand has been varying considerably over time, depending on the epidemiological situation, rendering efficient resource allocation difficult. Here, we present a scalable workflow which we implemented in our laboratory to increase PCR testing capacity while maintaining high flexibility regarding the number of samples to be processed. Methods We compared the performance of five automated extraction instruments, using dilutions of SARS-CoV-2 cell culture supernatant as well as clinical samples. To increase PCR throughput, we combined the two duplex PCR reactions of our previously published SARS-CoV-2 PCR assay into one quadruplex reaction and compared their limit of detection as well as their performance on the detection of low viral loads in clinical samples. Furthermore, we developed a sample pooling protocol with either two or four samples per pool, combined with a specifically adapted SARS-CoV-2 quadruplex PCR assay, and compared the diagnostic sensitivity of pooled testing and individual testing. Results All tested automated extraction instruments yielded comparable results regarding the subsequent sensitivity of SARS-CoV-2 detection by PCR. While the limit of detection of the quadruplex SARS-CoV-2 PCR assay (E-Gene assay: 28.7 genome equivalents (ge)/reaction, orf1ab assay: 32.0 ge/reaction) was slightly higher than that of our previously published duplex PCR assays (E-Gene assay: 9.8 ge/reaction, orf1ab assay: 6.6 ge/reaction), the rate of correctly identified positive patient samples was comparable for both assays. Sample pooling with optimized downstream quadruplex PCR showed no loss in diagnostic sensitivity compared to individual testing. Conclusion Specific adaptation of PCR assays can help overcome the potential loss of sensitivity due to higher levels of PCR multiplexing or sample dilution in pooled testing. Combining these adapted PCR assays with different sample processing strategies provides a simple and highly adjustable workflow for resource-efficient SARS-CoV-2 diagnostics. The presented principles can easily be adopted in a variety of laboratory settings as well as be adapted to pathogens other than SARS-CoV-2, making it feasible for any laboratory that conducts PCR diagnostics.

show abstract

“…Alternatively, there has been recent progress on highly automated workflows for PCR diagnostics [61, 62, 63] that require fewer lab technicians. One example is endpoint PCR [64], which uses a waterbath instead of the more common piezoelectric system, for higher-throughput thermal cycling at lower cost.…”

Section: Implementation Feasibilitymentioning

confidence: 99%

“…Rapidly recruiting skilled technicians when a pandemic is detected is another option, but this would be difficult to do in 1-2 months and only about 1/1000 people are currently employed in the medical diagnostics industry in the US [60]. Alternatively, there has been recent progress on highly automated workflows for PCR diagnostics [61, 62, 63] that require fewer lab technicians. One example is endpoint PCR [64], which uses a waterbath instead of the more common piezoelectric system for higher throughput thermal cycling at lower cost.…”

Section: Appendicesmentioning

confidence: 99%

Enhanced testing can substantially improve defence against several types of respiratory virus pandemic

Petrie,

Hay,

Srimokla

et al. 2024

Preprint

1

0

View full text Add to dashboard Cite

Mass testing to identify and isolate infected individuals is a promising approach for reducing harm from the next acute respiratory virus pandemic, potentially avoiding the need for indiscriminate social distancing measures whilst averting hospitalizations and deaths. To understand scenarios where mass testing might or might not be a viable intervention, here we modelled how effectiveness depends both on characteristics of the pathogen (R0, time to peak viral load) and on the testing strategy (limit of detection, testing frequency, test turnaround time, adherence). We base time-dependent test sensitivity and time-dependent infectiousness on an underlying viral load trajectory model. We show that given moderately high public adherence, achievable frequent testing can prevent as many transmissions as more costly interventions such as school or business closures. With very high adherence and fast, frequent, and more sensitive testing, we show that most respiratory virus pandemics could be controlled with mass testing alone.

show abstract

Flexible upscaling of laboratory PCR testing capacity at the Robert Koch Institute during the SARS-CoV-2 pandemic

Krause

¹

,

Michel

²

,

Puyskens

³

et al. 2023

Virol J

View full text Add to dashboard Cite

Background Over the course of the COVID-19 pandemic, laboratories worldwide have been facing an unprecedented increase in demand for PCR testing because of the high importance of diagnostics for prevention and control of virus spread. Moreover, testing demand has been varying considerably over time, depending on the epidemiological situation, rendering efficient resource allocation difficult. Here, we present a scalable workflow which we implemented in our laboratory to increase PCR testing capacity while maintaining high flexibility regarding the number of samples to be processed. Methods We compared the performance of five automated extraction instruments, using dilutions of SARS-CoV-2 cell culture supernatant as well as clinical samples. To increase PCR throughput, we combined the two duplex PCR reactions of our previously published SARS-CoV-2 PCR assay into one quadruplex reaction and compared their limit of detection as well as their performance on the detection of low viral loads in clinical samples. Furthermore, we developed a sample pooling protocol with either two or four samples per pool, combined with a specifically adapted SARS-CoV-2 quadruplex PCR assay, and compared the diagnostic sensitivity of pooled testing and individual testing. Results All tested automated extraction instruments yielded comparable results regarding the subsequent sensitivity of SARS-CoV-2 detection by PCR. While the limit of detection of the quadruplex SARS-CoV-2 PCR assay (E-Gene assay: 28.7 genome equivalents (ge)/reaction, orf1ab assay: 32.0 ge/reaction) was slightly higher than that of our previously published duplex PCR assays (E-Gene assay: 9.8 ge/reaction, orf1ab assay: 6.6 ge/reaction), the rate of correctly identified positive patient samples was comparable for both assays. Sample pooling with optimized downstream quadruplex PCR showed no loss in diagnostic sensitivity compared to individual testing. Conclusion Specific adaptation of PCR assays can help overcome the potential loss of sensitivity due to higher levels of PCR multiplexing or sample dilution in pooled testing. Combining these adapted PCR assays with different sample processing strategies provides a simple and highly adjustable workflow for resource-efficient SARS-CoV-2 diagnostics. The presented principles can easily be adopted in a variety of laboratory settings as well as be adapted to pathogens other than SARS-CoV-2, making it feasible for any laboratory that conducts PCR diagnostics.

show abstract

Improving the efficiency and effectiveness of an industrial SARS-CoV-2 diagnostic facility

Cited by 4 publications

References 23 publications

Flexible upscaling of laboratory PCR testing capacity at the Robert Koch Institute during the SARS-CoV-2 pandemic

Flexible upscaling of laboratory PCR testing capacity at the Robert Koch Institute during the SARS-CoV-2 pandemic

Enhanced testing can substantially improve defence against several types of respiratory virus pandemic

Flexible upscaling of laboratory PCR testing capacity at the Robert Koch Institute during the SARS-CoV-2 pandemic

Contact Info

Product

Resources

About