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Structure-Based Primer Design Minimizes the Risk of PCR Failure Caused by SARS-CoV-2 Mutations

The coronavirus disease 2019 (COVID-19) has caused and is still causing tremendous damage to the global economy and human health. Qualitative reverse transcription-PCR (RT-qPCR) is the golden standard for COVID-19 test. However, the SARS-CoV-2 variants may not only make vaccine less effective but al...

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Autores principales: Dong, Hongjie, Wang, Shuai, Zhang, Junmei, Zhang, Kundi, Zhang, Fengyu, Wang, Hongwei, Xie, Shiling, Hu, Wei, Gu, Lichuan
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Frontiers Media S.A. 2021
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8573093/
https://www.ncbi.nlm.nih.gov/pubmed/34760717
http://dx.doi.org/10.3389/fcimb.2021.741147
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author Dong, Hongjie
Wang, Shuai
Zhang, Junmei
Zhang, Kundi
Zhang, Fengyu
Wang, Hongwei
Xie, Shiling
Hu, Wei
Gu, Lichuan
author_facet Dong, Hongjie
Wang, Shuai
Zhang, Junmei
Zhang, Kundi
Zhang, Fengyu
Wang, Hongwei
Xie, Shiling
Hu, Wei
Gu, Lichuan
author_sort Dong, Hongjie
collection PubMed
description The coronavirus disease 2019 (COVID-19) has caused and is still causing tremendous damage to the global economy and human health. Qualitative reverse transcription-PCR (RT-qPCR) is the golden standard for COVID-19 test. However, the SARS-CoV-2 variants may not only make vaccine less effective but also evade RT-qPCR test. Here we suggest an innovative primer design strategy for the RT-qPCR test of SARS-CoV-2. The principle is that the primers should be designed based on both the nucleic acid sequence and the structure of the protein encoded. The three nucleotides closest to the 3′ end of the primer should be the codon which encodes the tryptophan in the structure core. Based on this principle, we designed a pair of primers targeting the nucleocapsid (N) gene. Since tryptophan is encoded by only one codon, any mutation that occurs at this position would change the amino acid residue, resulting in an unstable N protein. This means that this kind of SARS-CoV-2 variant could not survive. In addition, both our data and previous reports all indicate that the mutations occurring at other places in the primers do not significantly affect the RT-qPCR result. Consequently, no SARS-CoV-2 variant can escape detection by the RT-qPCR kit containing the primers designed based on our strategy.
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spelling pubmed-85730932021-11-09 Structure-Based Primer Design Minimizes the Risk of PCR Failure Caused by SARS-CoV-2 Mutations Dong, Hongjie Wang, Shuai Zhang, Junmei Zhang, Kundi Zhang, Fengyu Wang, Hongwei Xie, Shiling Hu, Wei Gu, Lichuan Front Cell Infect Microbiol Cellular and Infection Microbiology The coronavirus disease 2019 (COVID-19) has caused and is still causing tremendous damage to the global economy and human health. Qualitative reverse transcription-PCR (RT-qPCR) is the golden standard for COVID-19 test. However, the SARS-CoV-2 variants may not only make vaccine less effective but also evade RT-qPCR test. Here we suggest an innovative primer design strategy for the RT-qPCR test of SARS-CoV-2. The principle is that the primers should be designed based on both the nucleic acid sequence and the structure of the protein encoded. The three nucleotides closest to the 3′ end of the primer should be the codon which encodes the tryptophan in the structure core. Based on this principle, we designed a pair of primers targeting the nucleocapsid (N) gene. Since tryptophan is encoded by only one codon, any mutation that occurs at this position would change the amino acid residue, resulting in an unstable N protein. This means that this kind of SARS-CoV-2 variant could not survive. In addition, both our data and previous reports all indicate that the mutations occurring at other places in the primers do not significantly affect the RT-qPCR result. Consequently, no SARS-CoV-2 variant can escape detection by the RT-qPCR kit containing the primers designed based on our strategy. Frontiers Media S.A. 2021-10-25 /pmc/articles/PMC8573093/ /pubmed/34760717 http://dx.doi.org/10.3389/fcimb.2021.741147 Text en Copyright © 2021 Dong, Wang, Zhang, Zhang, Zhang, Wang, Xie, Hu and Gu https://creativecommons.org/licenses/by/4.0/This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.
spellingShingle Cellular and Infection Microbiology
Dong, Hongjie
Wang, Shuai
Zhang, Junmei
Zhang, Kundi
Zhang, Fengyu
Wang, Hongwei
Xie, Shiling
Hu, Wei
Gu, Lichuan
Structure-Based Primer Design Minimizes the Risk of PCR Failure Caused by SARS-CoV-2 Mutations
title Structure-Based Primer Design Minimizes the Risk of PCR Failure Caused by SARS-CoV-2 Mutations
title_full Structure-Based Primer Design Minimizes the Risk of PCR Failure Caused by SARS-CoV-2 Mutations
title_fullStr Structure-Based Primer Design Minimizes the Risk of PCR Failure Caused by SARS-CoV-2 Mutations
title_full_unstemmed Structure-Based Primer Design Minimizes the Risk of PCR Failure Caused by SARS-CoV-2 Mutations
title_short Structure-Based Primer Design Minimizes the Risk of PCR Failure Caused by SARS-CoV-2 Mutations
title_sort structure-based primer design minimizes the risk of pcr failure caused by sars-cov-2 mutations
topic Cellular and Infection Microbiology
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8573093/
https://www.ncbi.nlm.nih.gov/pubmed/34760717
http://dx.doi.org/10.3389/fcimb.2021.741147
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