Design and in silico validation of polymerase chain reaction primers to detect severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2)

Abstract Accurate designing of polymerase chain reaction (PCR) primers targeting conserved segments in viral genomes is desirable for preventing false-negative results and decreasing the need for standardization across different PCR protocols. In this work, we designed and described a set of primers...

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Autores principales:	Maria Júlia P. Davi, Selma M. B. Jeronimo, João P. M. S. Lima, Daniel C. F. Lanza
Formato:	article
Lenguaje:	EN
Publicado:	Nature Portfolio 2021
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/3fd91cd1abcf4df3853364dcd626ceb5
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spelling	oai:doaj.org-article:3fd91cd1abcf4df3853364dcd626ceb52021-12-02T17:41:26ZDesign and in silico validation of polymerase chain reaction primers to detect severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2)10.1038/s41598-021-91817-92045-2322https://doaj.org/article/3fd91cd1abcf4df3853364dcd626ceb52021-06-01T00:00:00Zhttps://doi.org/10.1038/s41598-021-91817-9https://doaj.org/toc/2045-2322Abstract Accurate designing of polymerase chain reaction (PCR) primers targeting conserved segments in viral genomes is desirable for preventing false-negative results and decreasing the need for standardization across different PCR protocols. In this work, we designed and described a set of primers and probes targeting conserved regions identified from a multiple sequence alignment of 2341 Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) genomes from the Global Initiative on Sharing All Influenza Data (GISAID). We subsequently validated those primers and probes in 211,833 SARS-CoV-2 whole-genome sequences. We obtained nine systems (forward primer + reverse primer + probe) that potentially anneal to highly conserved regions of the virus genome from these analyses. In silico predictions also demonstrated that those primers do not bind to nonspecific targets for human, bacterial, fungal, apicomplexan, and other Betacoronaviruses and less pathogenic sub-strains of coronavirus. The availability of these primer and probe sequences will make it possible to validate more efficient protocols for identifying SARS-CoV-2.Maria Júlia P. DaviSelma M. B. JeronimoJoão P. M. S. LimaDaniel C. F. LanzaNature PortfolioarticleMedicineRScienceQENScientific Reports, Vol 11, Iss 1, Pp 1-10 (2021)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Maria Júlia P. Davi Selma M. B. Jeronimo João P. M. S. Lima Daniel C. F. Lanza Design and in silico validation of polymerase chain reaction primers to detect severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2)
description	Abstract Accurate designing of polymerase chain reaction (PCR) primers targeting conserved segments in viral genomes is desirable for preventing false-negative results and decreasing the need for standardization across different PCR protocols. In this work, we designed and described a set of primers and probes targeting conserved regions identified from a multiple sequence alignment of 2341 Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) genomes from the Global Initiative on Sharing All Influenza Data (GISAID). We subsequently validated those primers and probes in 211,833 SARS-CoV-2 whole-genome sequences. We obtained nine systems (forward primer + reverse primer + probe) that potentially anneal to highly conserved regions of the virus genome from these analyses. In silico predictions also demonstrated that those primers do not bind to nonspecific targets for human, bacterial, fungal, apicomplexan, and other Betacoronaviruses and less pathogenic sub-strains of coronavirus. The availability of these primer and probe sequences will make it possible to validate more efficient protocols for identifying SARS-CoV-2.
format	article
author	Maria Júlia P. Davi Selma M. B. Jeronimo João P. M. S. Lima Daniel C. F. Lanza
author_facet	Maria Júlia P. Davi Selma M. B. Jeronimo João P. M. S. Lima Daniel C. F. Lanza
author_sort	Maria Júlia P. Davi
title	Design and in silico validation of polymerase chain reaction primers to detect severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2)
title_short	Design and in silico validation of polymerase chain reaction primers to detect severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2)
title_full	Design and in silico validation of polymerase chain reaction primers to detect severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2)
title_fullStr	Design and in silico validation of polymerase chain reaction primers to detect severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2)
title_full_unstemmed	Design and in silico validation of polymerase chain reaction primers to detect severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2)
title_sort	design and in silico validation of polymerase chain reaction primers to detect severe acute respiratory syndrome coronavirus 2 (sars-cov-2)
publisher	Nature Portfolio
publishDate	2021
url	https://doaj.org/article/3fd91cd1abcf4df3853364dcd626ceb5
work_keys_str_mv	AT mariajuliapdavi designandinsilicovalidationofpolymerasechainreactionprimerstodetectsevereacuterespiratorysyndromecoronavirus2sarscov2 AT selmambjeronimo designandinsilicovalidationofpolymerasechainreactionprimerstodetectsevereacuterespiratorysyndromecoronavirus2sarscov2 AT joaopmslima designandinsilicovalidationofpolymerasechainreactionprimerstodetectsevereacuterespiratorysyndromecoronavirus2sarscov2 AT danielcflanza designandinsilicovalidationofpolymerasechainreactionprimerstodetectsevereacuterespiratorysyndromecoronavirus2sarscov2
_version_	1718379699118276608

Design and in silico validation of polymerase chain reaction primers to detect severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2)

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