A novel method for conserved sequence extraction with prospective mutation prediction for SARS-CoV-2 PCR primer design.
COVID-19
Conserved sequence
Evolution
Mutation prediction
Phylogenetics
Primer design
Probe design
SARS-CoV-2
Journal
Journal of virological methods
ISSN: 1879-0984
Titre abrégé: J Virol Methods
Pays: Netherlands
ID NLM: 8005839
Informations de publication
Date de publication:
07 2021
07 2021
Historique:
received:
10
07
2020
revised:
29
03
2021
accepted:
30
03
2021
pubmed:
5
4
2021
medline:
5
6
2021
entrez:
4
4
2021
Statut:
ppublish
Résumé
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.
Identifiants
pubmed: 33812944
pii: S0166-0934(21)00085-9
doi: 10.1016/j.jviromet.2021.114146
pmc: PMC8015351
pii:
doi:
Substances chimiques
DNA Primers
0
Types de publication
Journal Article
Langues
eng
Sous-ensembles de citation
IM
Pagination
114146Informations de copyright
Copyright © 2021 Elsevier B.V. All rights reserved.
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