Skip to main content

Multiplex Quantitative Polymerase Chain Reaction Test to Identify SARS-CoV-2 Variants

  • Protocol
  • First Online:
Multiplex Biomarker Techniques

Part of the book series: Methods in Molecular Biology ((MIMB,volume 2511))

Abstract

Quantitative polymerase chain reaction (qPCR) is a routinely used method for detection and quantitation of gene expression in real time. This is achieved through the incorporation and measurement of fluorescent reporter probes in the amplified cDNA strands, since the fluorescent signals increase as the reaction progresses. The availability of multiple probes which fluoresce at different wavelengths allows for multiplexing as this gives rise to amplicons with unique fluorescent signatures. Here we describe a method using the Inhibitor-Tolerant RT-qPCR kit, developed by Meridian Bioscience kit which allows simultaneous real-time quantitation of the UK, South Africa, and Brazil SARS-CoV-2 variants.

This is a preview of subscription content, log in via an institution to check access.

Access this chapter

Subscribe and save

Springer+ Basic
$34.99 /Month
  • Get 10 units per month
  • Download Article/Chapter or eBook
  • 1 Unit = 1 Article or 1 Chapter
  • Cancel anytime
Subscribe now

Buy Now

Protocol
USD 49.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD 99.00
Price excludes VAT (USA)
  • Available as EPUB and PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD 129.99
Price excludes VAT (USA)
  • Compact, lightweight edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info
Hardcover Book
USD 199.99
Price excludes VAT (USA)
  • Durable hardcover edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info

Tax calculation will be finalised at checkout

Purchases are for personal use only

Institutional subscriptions

Similar content being viewed by others

References

  1. Elderfield R, Barclay W (2011) Influenza pandemics. Adv Exp Med Biol 719:81–103

    Article  Google Scholar 

  2. Pandey S, Yadav B, Pandey A et al (2020) Lessons from SARS-CoV-2 pandemic: evolution, disease dynamics and future. Biology (Basel) 9(6):141. https://doi.org/10.3390/biology9060141

    Article  CAS  Google Scholar 

  3. https://www.who.int/director-general/speeches/detail/who-director-general-s-opening-remarks-at-the-media-briefing-on-covid-19%2D%2D-11-march-2020

  4. https://www.worldometers.info/coronavirus/

  5. https://ourworldindata.org/covid-vaccinations

  6. https://www.who.int/initiatives/act-accelerator/covax

  7. Hoffmann M, Arora P, Groß R et al (2021) SARS-CoV-2 variants B.1.351 and P.1 escape from neutralizing antibodies. Cell 20:S0092-8674(21)00367-6. https://doi.org/10.1016/j.cell.2021.03.036. Online ahead of print

    Article  CAS  Google Scholar 

  8. Singh J, Samal J, Kumar V et al (2021) Structure-function analyses of new SARS-CoV-2 variants B.1.1.7, B.1.351 and B.1.1.28.1: clinical, diagnostic, therapeutic and public health implications. Viruses 13(3):439. https://doi.org/10.3390/v13030439

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  9. Dejnirattisai W, Zhou D, Supasa P et al (2021) Antibody evasion by the P.1 strain of SARS-CoV-2. Cell 30:S0092-8674(21)00428-1. https://doi.org/10.1016/j.cell.2021.03.055. Online ahead of print

    Article  CAS  Google Scholar 

  10. Leung K, Shum MH, Leung GM et al (2021) Early transmissibility assessment of the N501Y mutant strains of SARS-CoV-2 in the United Kingdom, October to November 2020. Euro Surveill 26(1):2002106. https://doi.org/10.2807/1560-7917.ES.2020.26.1.2002106

    Article  PubMed Central  Google Scholar 

  11. https://www.cdc.gov/coronavirus/2019-ncov/science/science-briefs/scientific-brief-emerging-variants.html

  12. Gu H, Chen Q, Yang G et al (2020) Adaptation of SARS-CoV-2 in BALB/c mice for testing vaccine efficacy. Science 369(6511):1603–1607

    Article  CAS  Google Scholar 

  13. https://www.who.int/csr/don/31-december-2020-sars-cov2-variants/en/

  14. https://www.sciencemediacentre.org/expert-reaction-to-the-south-african-variant/

  15. Callaway E (2021) Could new COVID variants undermine vaccines? Labs scramble to find out. Nature 589(7841):177–178

    Article  CAS  Google Scholar 

  16. Nascimento VAD, Corado ALG, Nascimento FOD et al (2020) Genomic and phylogenetic characterisation of an imported case of SARS-CoV-2 in Amazonas State, Brazil. Mem Inst Oswaldo Cruz 115:e200310. https://doi.org/10.1590/0074-02760200310

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  17. https://www.theguardian.com/world/2021/mar/01/brazil-covid-variant-p1-britain

  18. https://www.theguardian.com/world/2021/mar/01/p1-brazil-variant-found-countries-not-on-uk-travel-red-list

  19. https://virological.org/t/multiplexed-rt-qpcr-to-screen-for-sars-cov-2-b-1-1-7-variants-preliminary-results/588

  20. Glaab WE, Skopek TR (1999) A novel assay for allelic discrimination that combines the fluorogenic 5′ nuclease polymerase chain reaction (TaqMan) and mismatch amplification mutation assay. Mutat Res 430:1–12

    Article  CAS  Google Scholar 

  21. https://www.cdc.gov/coronavirus/2019-ncov/lab/guidelines-clinical-specimens.html

  22. https://www.protocols.io/view/multiplexed-rt-qpcr-to-screen-for-sars-cov-2-b-1-1-br9vm966?step=1

Download references

Conflict of Interest Statement

SFH is an employee of Meridian Bioscience.

Author information

Authors and Affiliations

Authors

Editor information

Editors and Affiliations

Rights and permissions

Reprints and permissions

Copyright information

© 2022 The Author(s), under exclusive license to Springer Science+Business Media, LLC, part of Springer Nature

About this protocol

Check for updates. Verify currency and authenticity via CrossMark

Cite this protocol

Hawkins, S.F.C., Guest, P.C. (2022). Multiplex Quantitative Polymerase Chain Reaction Test to Identify SARS-CoV-2 Variants. In: Guest, P.C. (eds) Multiplex Biomarker Techniques. Methods in Molecular Biology, vol 2511. Humana, New York, NY. https://doi.org/10.1007/978-1-0716-2395-4_5

Download citation

  • DOI: https://doi.org/10.1007/978-1-0716-2395-4_5

  • Published:

  • Publisher Name: Humana, New York, NY

  • Print ISBN: 978-1-0716-2394-7

  • Online ISBN: 978-1-0716-2395-4

  • eBook Packages: Springer Protocols

Publish with us

Policies and ethics