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Detecting SARS-CoV-2 and its variant strains with a full genome tiling array
Coronavirus disease 2019 pandemic is the most damaging pandemic in recent human history. Rapid detection of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and variant strains is paramount for recovery from this pandemic. Conventional SARS-CoV-2 tests interrogate only limited regions of...
Autores principales: | , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
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Oxford University Press
2021
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8344516/ https://www.ncbi.nlm.nih.gov/pubmed/34097003 http://dx.doi.org/10.1093/bib/bbab213 |
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author | Jiang, Limin Guo, Yan Yu, Hui Hoff, Kendal Ding, Xun Zhou, Wei Edwards, Jeremy |
author_facet | Jiang, Limin Guo, Yan Yu, Hui Hoff, Kendal Ding, Xun Zhou, Wei Edwards, Jeremy |
author_sort | Jiang, Limin |
collection | PubMed |
description | Coronavirus disease 2019 pandemic is the most damaging pandemic in recent human history. Rapid detection of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and variant strains is paramount for recovery from this pandemic. Conventional SARS-CoV-2 tests interrogate only limited regions of the whole SARS-CoV-2 genome, which are subjected to low specificity and miss the opportunity of detecting variant strains. In this work, we developed the first SARS-CoV-2 tiling array that captures the entire SARS-CoV-2 genome at single nucleotide resolution and offers the opportunity to detect point mutations. A thorough bioinformatics protocol of two base calling methods has been developed to accompany this array. To demonstrate the effectiveness of the tiling array, we genotyped all genomic positions of eight SARS-CoV-2 samples. Using high-throughput sequencing as the benchmark, we show that the tiling array had a genome-wide accuracy of at least 99.5%. From the tiling array analysis results, we identified the D614G mutation in the spike protein in four of the eight samples, suggesting the widespread distribution of this variant at the early stage of the outbreak in the United States. Two additional nonsynonymous mutations were identified in one sample in the nucleocapsid protein (P13L and S197L), which may complicate future vaccine development. With around $5 per array, supreme accuracy, and an ultrafast bioinformatics protocol, the SARS-CoV-2 tiling array makes an invaluable toolkit for combating current and future pandemics. Our SARS-CoV-2 tilting array is currently utilized by Molecular Vision, a CLIA-certified lab for SARS-CoV-2 diagnosis. |
format | Online Article Text |
id | pubmed-8344516 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2021 |
publisher | Oxford University Press |
record_format | MEDLINE/PubMed |
spelling | pubmed-83445162021-08-10 Detecting SARS-CoV-2 and its variant strains with a full genome tiling array Jiang, Limin Guo, Yan Yu, Hui Hoff, Kendal Ding, Xun Zhou, Wei Edwards, Jeremy Brief Bioinform Problem Solving Protocol Coronavirus disease 2019 pandemic is the most damaging pandemic in recent human history. Rapid detection of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and variant strains is paramount for recovery from this pandemic. Conventional SARS-CoV-2 tests interrogate only limited regions of the whole SARS-CoV-2 genome, which are subjected to low specificity and miss the opportunity of detecting variant strains. In this work, we developed the first SARS-CoV-2 tiling array that captures the entire SARS-CoV-2 genome at single nucleotide resolution and offers the opportunity to detect point mutations. A thorough bioinformatics protocol of two base calling methods has been developed to accompany this array. To demonstrate the effectiveness of the tiling array, we genotyped all genomic positions of eight SARS-CoV-2 samples. Using high-throughput sequencing as the benchmark, we show that the tiling array had a genome-wide accuracy of at least 99.5%. From the tiling array analysis results, we identified the D614G mutation in the spike protein in four of the eight samples, suggesting the widespread distribution of this variant at the early stage of the outbreak in the United States. Two additional nonsynonymous mutations were identified in one sample in the nucleocapsid protein (P13L and S197L), which may complicate future vaccine development. With around $5 per array, supreme accuracy, and an ultrafast bioinformatics protocol, the SARS-CoV-2 tiling array makes an invaluable toolkit for combating current and future pandemics. Our SARS-CoV-2 tilting array is currently utilized by Molecular Vision, a CLIA-certified lab for SARS-CoV-2 diagnosis. Oxford University Press 2021-06-07 /pmc/articles/PMC8344516/ /pubmed/34097003 http://dx.doi.org/10.1093/bib/bbab213 Text en © The Author(s) 2021. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com https://academic.oup.com/journals/pages/open_access/funder_policies/chorus/standard_publication_modelThis article is published and distributed under the terms of the Oxford University Press, Standard Journals Publication Model (https://academic.oup.com/journals/pages/open_access/funder_policies/chorus/standard_publication_model) |
spellingShingle | Problem Solving Protocol Jiang, Limin Guo, Yan Yu, Hui Hoff, Kendal Ding, Xun Zhou, Wei Edwards, Jeremy Detecting SARS-CoV-2 and its variant strains with a full genome tiling array |
title | Detecting SARS-CoV-2 and its variant strains with a full genome tiling array |
title_full | Detecting SARS-CoV-2 and its variant strains with a full genome tiling array |
title_fullStr | Detecting SARS-CoV-2 and its variant strains with a full genome tiling array |
title_full_unstemmed | Detecting SARS-CoV-2 and its variant strains with a full genome tiling array |
title_short | Detecting SARS-CoV-2 and its variant strains with a full genome tiling array |
title_sort | detecting sars-cov-2 and its variant strains with a full genome tiling array |
topic | Problem Solving Protocol |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8344516/ https://www.ncbi.nlm.nih.gov/pubmed/34097003 http://dx.doi.org/10.1093/bib/bbab213 |
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