Analysis and forecasting of global real time RT-PCR primers and probes for SARS-CoV-2

Abstract Rapid tests for active SARS-CoV-2 infections rely on reverse transcription polymerase chain reaction (RT-PCR). RT-PCR uses reverse transcription of RNA into complementary DNA (cDNA) and amplification of specific DNA (primer and probe) targets using polymerase chain reaction (PCR). The techn...

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Autores principales:	Gowri Nayar, Edward E. Seabolt, Mark Kunitomi, Akshay Agarwal, Kristen L. Beck, Vandana Mukherjee, James H. Kaufman
Formato:	article
Lenguaje:	EN
Publicado:	Nature Portfolio 2021
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/b61c34dcf78a47d6ac990fe5517c9373
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spelling	oai:doaj.org-article:b61c34dcf78a47d6ac990fe5517c93732021-12-02T17:39:20ZAnalysis and forecasting of global real time RT-PCR primers and probes for SARS-CoV-210.1038/s41598-021-88532-w2045-2322https://doaj.org/article/b61c34dcf78a47d6ac990fe5517c93732021-04-01T00:00:00Zhttps://doi.org/10.1038/s41598-021-88532-whttps://doaj.org/toc/2045-2322Abstract Rapid tests for active SARS-CoV-2 infections rely on reverse transcription polymerase chain reaction (RT-PCR). RT-PCR uses reverse transcription of RNA into complementary DNA (cDNA) and amplification of specific DNA (primer and probe) targets using polymerase chain reaction (PCR). The technology makes rapid and specific identification of the virus possible based on sequence homology of nucleic acid sequence and is much faster than tissue culture or animal cell models. However the technique can lose sensitivity over time as the virus evolves and the target sequences diverge from the selective primer sequences. Different primer sequences have been adopted in different geographic regions. As we rely on these existing RT-PCR primers to track and manage the spread of the Coronavirus, it is imperative to understand how SARS-CoV-2 mutations, over time and geographically, diverge from existing primers used today. In this study, we analyze the performance of the SARS-CoV-2 primers in use today by measuring the number of mismatches between primer sequence and genome targets over time and spatially. We find that there is a growing number of mismatches, an increase by 2% per month, as well as a high specificity of virus based on geographic location.Gowri NayarEdward E. SeaboltMark KunitomiAkshay AgarwalKristen L. BeckVandana MukherjeeJames H. KaufmanNature PortfolioarticleMedicineRScienceQENScientific Reports, Vol 11, Iss 1, Pp 1-11 (2021)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Gowri Nayar Edward E. Seabolt Mark Kunitomi Akshay Agarwal Kristen L. Beck Vandana Mukherjee James H. Kaufman Analysis and forecasting of global real time RT-PCR primers and probes for SARS-CoV-2
description	Abstract Rapid tests for active SARS-CoV-2 infections rely on reverse transcription polymerase chain reaction (RT-PCR). RT-PCR uses reverse transcription of RNA into complementary DNA (cDNA) and amplification of specific DNA (primer and probe) targets using polymerase chain reaction (PCR). The technology makes rapid and specific identification of the virus possible based on sequence homology of nucleic acid sequence and is much faster than tissue culture or animal cell models. However the technique can lose sensitivity over time as the virus evolves and the target sequences diverge from the selective primer sequences. Different primer sequences have been adopted in different geographic regions. As we rely on these existing RT-PCR primers to track and manage the spread of the Coronavirus, it is imperative to understand how SARS-CoV-2 mutations, over time and geographically, diverge from existing primers used today. In this study, we analyze the performance of the SARS-CoV-2 primers in use today by measuring the number of mismatches between primer sequence and genome targets over time and spatially. We find that there is a growing number of mismatches, an increase by 2% per month, as well as a high specificity of virus based on geographic location.
format	article
author	Gowri Nayar Edward E. Seabolt Mark Kunitomi Akshay Agarwal Kristen L. Beck Vandana Mukherjee James H. Kaufman
author_facet	Gowri Nayar Edward E. Seabolt Mark Kunitomi Akshay Agarwal Kristen L. Beck Vandana Mukherjee James H. Kaufman
author_sort	Gowri Nayar
title	Analysis and forecasting of global real time RT-PCR primers and probes for SARS-CoV-2
title_short	Analysis and forecasting of global real time RT-PCR primers and probes for SARS-CoV-2
title_full	Analysis and forecasting of global real time RT-PCR primers and probes for SARS-CoV-2
title_fullStr	Analysis and forecasting of global real time RT-PCR primers and probes for SARS-CoV-2
title_full_unstemmed	Analysis and forecasting of global real time RT-PCR primers and probes for SARS-CoV-2
title_sort	analysis and forecasting of global real time rt-pcr primers and probes for sars-cov-2
publisher	Nature Portfolio
publishDate	2021
url	https://doaj.org/article/b61c34dcf78a47d6ac990fe5517c9373
work_keys_str_mv	AT gowrinayar analysisandforecastingofglobalrealtimertpcrprimersandprobesforsarscov2 AT edwardeseabolt analysisandforecastingofglobalrealtimertpcrprimersandprobesforsarscov2 AT markkunitomi analysisandforecastingofglobalrealtimertpcrprimersandprobesforsarscov2 AT akshayagarwal analysisandforecastingofglobalrealtimertpcrprimersandprobesforsarscov2 AT kristenlbeck analysisandforecastingofglobalrealtimertpcrprimersandprobesforsarscov2 AT vandanamukherjee analysisandforecastingofglobalrealtimertpcrprimersandprobesforsarscov2 AT jameshkaufman analysisandforecastingofglobalrealtimertpcrprimersandprobesforsarscov2
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Analysis and forecasting of global real time RT-PCR primers and probes for SARS-CoV-2

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