A novel method for conserved sequence extraction with prospective mutation prediction for SARS-CoV-2 PCR primer design

[Display omitted] •An algorithm was tested for prediction of mutation resistant regions of COVID19 genome, and can be adopted to other viruses.•This algorithm may be used to improve the sensitivity of the PCR primer and probes.•The algorithm can score each nucleotide based on its risk of mutation.•U...

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Bibliographic Details
Published in:Journal of virological methods 2021-07, Vol.293, p.114146-114146, Article 114146
Main Authors: Portakal, Saygın Hüseyin, Kanat, Beyza, Sayan, Murat, Berber, Burak, Doluca, Osman
Format: Article
Language:English
Subjects:
Algorithms
Conserved sequence
COVID-19
COVID-19 - diagnosis
COVID-19 Nucleic Acid Testing - methods
DNA Primers
Evolution
Humans
Mutation
Mutation prediction
Phylogenetics
Primer design
Probe design
Prospective Studies
SARS-CoV-2
SARS-CoV-2 - genetics
Sequence Alignment
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Summary:[Display omitted] •An algorithm was tested for prediction of mutation resistant regions of COVID19 genome, and can be adopted to other viruses.•This algorithm may be used to improve the sensitivity of the PCR primer and probes.•The algorithm can score each nucleotide based on its risk of mutation.•Using a threshold of 1.0 around %60 of prospective mutations were able to be filtered out.•The mutation prediction power is high even at the early stages of the pandemic. While the whole genomic sequence of SARS-CoV-2 had been revealed, it was also demonstrated that the genome of SARS-CoV-2 exhibits identity with the genome of SARS-CoV and MERS-CoV with ratios of 80 % and 50 % respectively. In the light of SARS-CoV-2 infection and mortality data, diagnosis and treatment of COVID-19 came into prominence around the world. As such many RT-PCR kits have been developed by biotechnology scientists. However viruses are fast mutating organisms and in order to increase accuracy, feasibility in long term and avoid the off target results of RT-PCR assays, regions of viral genome with low mutation rate and designing of primers targeting these regions are quite important. In this scope, we are presenting a novel algorithm that could be used for finding low mutation rate regions of SARS-CoV-2 and primers that were designed according to findings from our algorithm in this study.
ISSN:0166-0934
1879-0984
DOI:10.1016/j.jviromet.2021.114146