Optimization of magnetic bead-based nucleic acid extraction for SARS-CoV-2 testing using readily available reagents

Simon Haile; Aidan M Nikiforuk; Pawan K Pandoh; David D W Twa; Duane E Smailus; Jason Nguyen; Stephen Pleasance; Angus Wong; Yongjun Zhao; Diane Eisler; Michelle Moksa; Qi Cao; Marcus Wong; Edmund Su; Martin Krzywinski; Jessica Nelson; Andrew J Mungall; Frankie Tsang; Leah M Prentice; Agatha Jassem; Amee R Manges; Steven J M Jones; Robin J Coope; Natalie Prystajecky; Marco A Marra; Mel Krajden; Martin Hirst

doi:10.1016/j.jviromet.2021.114339

Optimization of magnetic bead-based nucleic acid extraction for SARS-CoV-2 testing using readily available reagents

J Virol Methods. 2022 Jan:299:114339. doi: 10.1016/j.jviromet.2021.114339. Epub 2021 Oct 20.

Authors

Simon Haile¹, Aidan M Nikiforuk², Pawan K Pandoh¹, David D W Twa³, Duane E Smailus¹, Jason Nguyen⁴, Stephen Pleasance¹, Angus Wong¹, Yongjun Zhao¹, Diane Eisler⁴, Michelle Moksa⁵, Qi Cao⁵, Marcus Wong⁵, Edmund Su⁵, Martin Krzywinski¹, Jessica Nelson¹, Andrew J Mungall¹, Frankie Tsang⁴, Leah M Prentice⁶, Agatha Jassem⁷, Amee R Manges⁸, Steven J M Jones⁹, Robin J Coope¹, Natalie Prystajecky⁷, Marco A Marra⁹, Mel Krajden⁷, Martin Hirst¹⁰

Affiliations

¹ Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, British Columbia, Canada.
² School of Population and Public Health, University of British Columbia, Vancouver, British Columbia, Canada.
³ BC Cancer Research Centre, BC Cancer, Vancouver, British Columbia, Canada.
⁴ British Columbia Centre for Disease Control Public Health Laboratory, Vancouver, Canada.
⁵ Department of Microbiology and Immunology, Michael Smith Laboratories, University of British Columbia, Vancouver, British Columbia, Canada.
⁶ Provincial Laboratory Medicine Services, Provincial Health Services Authority, Vancouver, British Columbia, Canada.
⁷ British Columbia Centre for Disease Control Public Health Laboratory, Vancouver, Canada; Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, British Columbia, Canada.
⁸ School of Population and Public Health, University of British Columbia, Vancouver, British Columbia, Canada; British Columbia Centre for Disease Control Public Health Laboratory, Vancouver, Canada.
⁹ Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, British Columbia, Canada; Department of Medical Genetics, University of British Columbia, Vancouver, British Columbia, Canada.
¹⁰ Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, British Columbia, Canada; Department of Microbiology and Immunology, Michael Smith Laboratories, University of British Columbia, Vancouver, British Columbia, Canada. Electronic address: hirstm@mail.ubc.ca.

Abstract

The COVID-19 pandemic has highlighted the need for generic reagents and flexible systems in diagnostic testing. Magnetic bead-based nucleic acid extraction protocols using 96-well plates on open liquid handlers are readily amenable to meet this need. Here, one such approach is rigorously optimized to minimize cross-well contamination while maintaining sensitivity.

Keywords: COVID-19; Contamination; Cross-well; Hamilton NIMBUS; Magnetic beads; Nucleic acid extraction; RNA; SARS-CoV-2.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

COVID-19 Testing
COVID-19*
Humans
Indicators and Reagents
Magnetic Phenomena
Nucleic Acids*
Pandemics
RNA, Viral / genetics
SARS-CoV-2
Sensitivity and Specificity

Substances

Indicators and Reagents
Nucleic Acids
RNA, Viral