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Appears in Collections:Aquaculture Journal Articles
Peer Review Status: Refereed
Title: Efficient Screening of Long Oligonucleotides Against Hundred Thousands of SARS-CoV-2 Genome Sequences
Author(s): Weidmann, Manfred
Graf, Elena
Lichterfeld, Daniel
Abd El Wahed, Ahmed
Bekaert, Michaël
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Keywords: recombinase polymerase amplification
sequence mutation screening
SARS-CoV-2 genomes
screening of oligonucleotides
mutations in oligonucleotides
Issue Date: 2022
Date Deposited: 4-Apr-2022
Citation: Weidmann M, Graf E, Lichterfeld D, Abd El Wahed A & Bekaert M (2022) Efficient Screening of Long Oligonucleotides Against Hundred Thousands of SARS-CoV-2 Genome Sequences. Frontiers in Virology, 2, Art. No.: 835707.
Abstract: An unprecedented use of high-throughput sequencing for routine monitoring of SARS-CoV-2 viruses in patient samples has created a dataset of over 6 million SARS-CoV-2 genomes. To monitor genomes, deposited in the GISAID database, and to track the continuous sequence evolution of molecular assay oligonucleotide target sequences. A simple pipeline tool for non-experts was developed to mine this database for nucleotide changes in oligonucleotides and tested with the long oligonucleotides of a Recombinase polymerase amplification (RPA) assay targeting the RNA-dependent RNA polymerase (RdRP) gene of the SARS-CoV-2. Results indicate the emergence of a single nucleotide change in the reverse oligonucleotide from 0.03 to 26.23% (January to May 2021) in Alpha variant genomes, which however reduced to 17.64% by September after which the Alpha variant was completely displaced by the Delta variant. For all other variants, no relevant nucleotide changes were observed. The oligonucleotide screening pipeline allows efficient screening of nucleotide changes in oligonucleotides of all sizes in minutes.
DOI Link: 10.3389/fviro.2022.835707
Rights: © 2022 Weidmann, Graf, Lichterfeld, Abd El Wahed and Bekaert. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY - The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms
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