Preprint Article Version 1 Preserved in Portico This version is not peer-reviewed

Rapid Design of a Bait Capture Platform for Culture- and Amplification-Free Next-Generation Sequencing of SARS-CoV-2

Jalees A. Nasir
ORCID logo ,
David J. Speicher
ORCID logo ,
Robert A. Kozak
,
Hendrik N. Poinar
,
Matthew S. Miller
ORCID logo ,
Andrew G. McArthur
*
Version 1 : Received: 25 February 2020 / Approved: 26 February 2020 / Online: 26 February 2020 (02:27:21 CET)

How to cite: Nasir, J.A.; Speicher, D.J.; Kozak, R.A.; Poinar, H.N.; Miller, M.S.; McArthur, A.G. Rapid Design of a Bait Capture Platform for Culture- and Amplification-Free Next-Generation Sequencing of SARS-CoV-2. Preprints 2020, 2020020385. https://doi.org/10.20944/preprints202002.0385.v1 Nasir, J.A.; Speicher, D.J.; Kozak, R.A.; Poinar, H.N.; Miller, M.S.; McArthur, A.G. Rapid Design of a Bait Capture Platform for Culture- and Amplification-Free Next-Generation Sequencing of SARS-CoV-2. Preprints 2020, 2020020385. https://doi.org/10.20944/preprints202002.0385.v1

Abstract

SARS-CoV-2 is a novel betacoronavirus and the aetiological agent of the current COVID-19 outbreak that originated in Hubei Province, China. While polymerase chain reaction is the front-line tool for SARS-CoV-2 surveillance, application of amplification-free and culture-free methods for isolation of SARS-CoV-2 RNA, partnered with next-generation sequencing, would provide a useful tool for both surveillance and research of SARS-CoV-2. We here release into the public domain a set of bait capture hybridization probe sequences for enrichment of SARS-CoV-2 RNA from complex biological samples. These probe sequences have been designed using rigorous bioinformatics methods to provide sensitivity, accuracy, and minimal off-target hybridization. Probe design was based on existing, validated approaches for detecting antimicrobial resistance genes in complex samples and it is our hope that this SARS-CoV-2 bait capture platform, once validated by those with samples in hand, will be of aid in combating the current outbreak.

Supplementary and Associated Material

https://github.com/jaleezyy/covid-19-baits: Software and Sequence Files

Keywords

Coronavirus; SARS-CoV-2; enrichment; next-generation sequencing

Subject

Biology and Life Sciences, Virology

Copyright: This is an open access article distributed under the Creative Commons Attribution License which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

Download PDF

Comments (0)

We encourage comments and feedback from a broad range of readers. See criteria for comments and our Diversity statement.

Leave a public comment
Send a private comment to the author(s)
* All users must log in before leaving a comment
Views 0
Downloads 0
Comments 0
Metrics 0
Get PDF Cite Share 0
Bookmark BibSonomy Mendeley Reddit Delicious
×
Alerts
Notify me about updates to this article or when a peer-reviewed version is published.
We use cookies on our website to ensure you get the best experience.
Read more about our cookies here.