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

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 treatm...

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Autores principales: Portakal, Saygın Hüseyin, Kanat, Beyza, Sayan, Murat, Berber, Burak, Doluca, Osman
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Elsevier B.V. 2021
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8015351/
https://www.ncbi.nlm.nih.gov/pubmed/33812944
http://dx.doi.org/10.1016/j.jviromet.2021.114146
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author Portakal, Saygın Hüseyin
Kanat, Beyza
Sayan, Murat
Berber, Burak
Doluca, Osman
author_facet Portakal, Saygın Hüseyin
Kanat, Beyza
Sayan, Murat
Berber, Burak
Doluca, Osman
author_sort Portakal, Saygın Hüseyin
collection PubMed
description 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.
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spelling pubmed-80153512021-04-01 A novel method for conserved sequence extraction with prospective mutation prediction for SARS-CoV-2 PCR primer design Portakal, Saygın Hüseyin Kanat, Beyza Sayan, Murat Berber, Burak Doluca, Osman J Virol Methods Article 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. Elsevier B.V. 2021-07 2021-04-01 /pmc/articles/PMC8015351/ /pubmed/33812944 http://dx.doi.org/10.1016/j.jviromet.2021.114146 Text en © 2021 Elsevier B.V. All rights reserved. Since January 2020 Elsevier has created a COVID-19 resource centre with free information in English and Mandarin on the novel coronavirus COVID-19. The COVID-19 resource centre is hosted on Elsevier Connect, the company's public news and information website. Elsevier hereby grants permission to make all its COVID-19-related research that is available on the COVID-19 resource centre - including this research content - immediately available in PubMed Central and other publicly funded repositories, such as the WHO COVID database with rights for unrestricted research re-use and analyses in any form or by any means with acknowledgement of the original source. These permissions are granted for free by Elsevier for as long as the COVID-19 resource centre remains active.
spellingShingle Article
Portakal, Saygın Hüseyin
Kanat, Beyza
Sayan, Murat
Berber, Burak
Doluca, Osman
A novel method for conserved sequence extraction with prospective mutation prediction for SARS-CoV-2 PCR primer design
title A novel method for conserved sequence extraction with prospective mutation prediction for SARS-CoV-2 PCR primer design
title_full A novel method for conserved sequence extraction with prospective mutation prediction for SARS-CoV-2 PCR primer design
title_fullStr A novel method for conserved sequence extraction with prospective mutation prediction for SARS-CoV-2 PCR primer design
title_full_unstemmed A novel method for conserved sequence extraction with prospective mutation prediction for SARS-CoV-2 PCR primer design
title_short A novel method for conserved sequence extraction with prospective mutation prediction for SARS-CoV-2 PCR primer design
title_sort novel method for conserved sequence extraction with prospective mutation prediction for sars-cov-2 pcr primer design
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8015351/
https://www.ncbi.nlm.nih.gov/pubmed/33812944
http://dx.doi.org/10.1016/j.jviromet.2021.114146
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