Skip to main content
bioRxiv
  • Home
  • About
  • Submit
  • ALERTS / RSS
Advanced Search
New Results

INSIGHT: a population scale COVID-19 testing strategy combining point-of-care diagnosis with centralised high-throughput sequencing

Qianxin Wu, View ORCID ProfileChenqu Suo, View ORCID ProfileTom Brown, View ORCID ProfileTengyao Wang, View ORCID ProfileSarah A. Teichmann, View ORCID ProfileAndrew R. Bassett
doi: https://doi.org/10.1101/2020.06.01.127019
Qianxin Wu
1Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Chenqu Suo
1Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK
2Department of Paediatrics, Cambridge University Hospitals, Hills Road, Cambridge CB2 0QQ, UK
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • ORCID record for Chenqu Suo
Tom Brown
3Department of Chemistry, University of Oxford, Chemistry Research Laboratory, 12 Mansfield Road, Oxford OX1 3TA, UK
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • ORCID record for Tom Brown
Tengyao Wang
4Department of Statistical Science, University College London, 1-19 Torrington Place, London WC1E 7HB, UK
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • ORCID record for Tengyao Wang
Sarah A. Teichmann
1Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK
5Department of Physics/Cavendish Laboratory, University of Cambridge, JJ Thomson Ave, Cambridge CB3 0HE, UK
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • ORCID record for Sarah A. Teichmann
  • For correspondence: st9@sanger.ac.uk ab42@sanger.ac.uk
Andrew R. Bassett
1Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • ORCID record for Andrew R. Bassett
  • For correspondence: st9@sanger.ac.uk ab42@sanger.ac.uk
  • Abstract
  • Full Text
  • Info/History
  • Metrics
  • Preview PDF
Loading

Abstract

We present INSIGHT (Isothermal NASBA-Sequencing-based hIGH-througput Test): a two-stage COVID-19 testing strategy, using a barcoded isothermal NASBA reaction that combines point-of-care diagnosis with next generation sequencing, aiming to achieve population-scale COVID-19 testing. INSIGHT combines the advantages of near-patient with centralised testing. Stage 1 allows a quick decentralised readout for early isolation of pre-symptomatic or asymptomatic patients. The same reaction products can then be used in a highly multiplexed sequencing-based assay in Stage 2, confirming the near-patient testing results and facilitating centralised data collection. Based on experiments using commercially acquired human saliva with spiked-in viral RNA as input, the INSIGHT platform gives Stage 1 results within one to two hours, using either fluorescence detection or a lateral flow (dipstick) readout, whilst simultaneously incorporating sample-specific barcodes into the amplification product. INSIGHT Stage 2 can be performed by directly pooling and sequencing all post-amplification barcoded Stage 1 products from hundreds of thousands of samples with minimal sample preparation steps. The 95% limit of detection (LoD-95) for INSIGHT is estimated to be below 50 copies of viral RNA per 20 μl of reaction. Our two-stage testing strategy is suitable for further development into a rapid home-based and point-of-care assay, and is potentially scalable to the population level.

Competing Interest Statement

Q.W., C.S., S.A.T. and A.R.B. are inventors on a patent application (GB2007724.4) submitted by Genome Research Limited, with the aim of making this technology freely available for research and deployment. In the past three years, S.A.T. has consulted for Genentech and Roche, and sits on Scientific Advisory Boards for Foresite Labs, Biogen and GlaxoSmithKline. T.B. is a consultant at ATDBio.

Footnotes

  • *** IMPORTANT: This protocol has not been validated on patient samples and should not be used for clinical diagnosis without further validation and certification. ***

  • *** This is ongoing research to develop a testing strategy for the SARS-CoV-2 virus. The Wellcome Sanger Institute is not in a position to develop this into a commercial product, but would be open to discussions with third parties about how they could develop this further to achieve the societal benefits of this work. ***

  • Methods and Results sections updated details on dipstick readout and sequencing

  • 2 Molecular beacons were synthesised in the ATDBio laboratory using a K&A H-8 SE DNA Synthesiser, and purified by reversed-phase HPLC.

  • 3 Molecular beacon is reconstituted with annealing buffer (10 mM Tris pH 8 with 10 μM MgCl2) to the final concentration of 10 μM. Beacon is then annealed by incubation at 85 °C for 5 min, then gradual cooling to 4 °C by 0.1 °C/s before the NASBA reaction.

Copyright 
The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-NC-ND 4.0 International license.
Back to top
PreviousNext
Posted August 16, 2020.
Download PDF
Email

Thank you for your interest in spreading the word about bioRxiv.

NOTE: Your email address is requested solely to identify you as the sender of this article.

Enter multiple addresses on separate lines or separate them with commas.
INSIGHT: a population scale COVID-19 testing strategy combining point-of-care diagnosis with centralised high-throughput sequencing
(Your Name) has forwarded a page to you from bioRxiv
(Your Name) thought you would like to see this page from the bioRxiv website.
CAPTCHA
This question is for testing whether or not you are a human visitor and to prevent automated spam submissions.
Share
INSIGHT: a population scale COVID-19 testing strategy combining point-of-care diagnosis with centralised high-throughput sequencing
Qianxin Wu, Chenqu Suo, Tom Brown, Tengyao Wang, Sarah A. Teichmann, Andrew R. Bassett
bioRxiv 2020.06.01.127019; doi: https://doi.org/10.1101/2020.06.01.127019
Digg logo Reddit logo Twitter logo Facebook logo Google logo LinkedIn logo Mendeley logo
Citation Tools
INSIGHT: a population scale COVID-19 testing strategy combining point-of-care diagnosis with centralised high-throughput sequencing
Qianxin Wu, Chenqu Suo, Tom Brown, Tengyao Wang, Sarah A. Teichmann, Andrew R. Bassett
bioRxiv 2020.06.01.127019; doi: https://doi.org/10.1101/2020.06.01.127019

Citation Manager Formats

  • BibTeX
  • Bookends
  • EasyBib
  • EndNote (tagged)
  • EndNote 8 (xml)
  • Medlars
  • Mendeley
  • Papers
  • RefWorks Tagged
  • Ref Manager
  • RIS
  • Zotero
  • Tweet Widget
  • Facebook Like
  • Google Plus One

Subject Area

  • Molecular Biology
Subject Areas
All Articles
  • Animal Behavior and Cognition (3484)
  • Biochemistry (7336)
  • Bioengineering (5308)
  • Bioinformatics (20225)
  • Biophysics (9991)
  • Cancer Biology (7717)
  • Cell Biology (11280)
  • Clinical Trials (138)
  • Developmental Biology (6426)
  • Ecology (9930)
  • Epidemiology (2065)
  • Evolutionary Biology (13298)
  • Genetics (9354)
  • Genomics (12566)
  • Immunology (7687)
  • Microbiology (18979)
  • Molecular Biology (7428)
  • Neuroscience (40944)
  • Paleontology (300)
  • Pathology (1226)
  • Pharmacology and Toxicology (2132)
  • Physiology (3146)
  • Plant Biology (6850)
  • Scientific Communication and Education (1272)
  • Synthetic Biology (1893)
  • Systems Biology (5306)
  • Zoology (1087)