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High-Integrity Sequencing of Spike Gene for SARS-CoV-2 Variant Determination
For tiling of the SARS-CoV-2 genome, the ARTIC Network provided a V4 protocol using 99 pairs of primers for amplicon production and is currently the widely used amplicon-based approach. However, this technique has regions of low sequence coverage and is labour-, time-, and cost-intensive. Moreover,...
Autores principales: | , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
MDPI
2022
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8954144/ https://www.ncbi.nlm.nih.gov/pubmed/35328676 http://dx.doi.org/10.3390/ijms23063257 |
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author | Liao, Yu-Chieh Chen, Feng-Jui Chuang, Min-Chieh Wu, Han-Chieh Ji, Wan-Chen Yu, Guann-Yi Huang, Tsi-Shu |
author_facet | Liao, Yu-Chieh Chen, Feng-Jui Chuang, Min-Chieh Wu, Han-Chieh Ji, Wan-Chen Yu, Guann-Yi Huang, Tsi-Shu |
author_sort | Liao, Yu-Chieh |
collection | PubMed |
description | For tiling of the SARS-CoV-2 genome, the ARTIC Network provided a V4 protocol using 99 pairs of primers for amplicon production and is currently the widely used amplicon-based approach. However, this technique has regions of low sequence coverage and is labour-, time-, and cost-intensive. Moreover, it requires 14 pairs of primers in two separate PCRs to obtain spike gene sequences. To overcome these disadvantages, we proposed a single PCR to efficiently detect spike gene mutations. We proposed a bioinformatic protocol that can process FASTQ reads into spike gene consensus sequences to accurately call spike protein variants from sequenced samples or to fairly express the cases of missing amplicons. We evaluated the in silico detection rate of primer sets that yield amplicon sizes of 400, 1200, and 2500 bp for spike gene sequencing of SARS-CoV-2 to be 59.49, 76.19, and 92.20%, respectively. The in silico detection rate of our proposed single PCR primers was 97.07%. We demonstrated the robustness of our analytical protocol against 3000 Oxford Nanopore sequencing runs of distinct datasets, thus ensuring high-integrity sequencing of spike genes for variant SARS-CoV-2 determination. Our protocol works well with the data yielded from versatile primer designs, making it easy to determine spike protein variants. |
format | Online Article Text |
id | pubmed-8954144 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2022 |
publisher | MDPI |
record_format | MEDLINE/PubMed |
spelling | pubmed-89541442022-03-26 High-Integrity Sequencing of Spike Gene for SARS-CoV-2 Variant Determination Liao, Yu-Chieh Chen, Feng-Jui Chuang, Min-Chieh Wu, Han-Chieh Ji, Wan-Chen Yu, Guann-Yi Huang, Tsi-Shu Int J Mol Sci Article For tiling of the SARS-CoV-2 genome, the ARTIC Network provided a V4 protocol using 99 pairs of primers for amplicon production and is currently the widely used amplicon-based approach. However, this technique has regions of low sequence coverage and is labour-, time-, and cost-intensive. Moreover, it requires 14 pairs of primers in two separate PCRs to obtain spike gene sequences. To overcome these disadvantages, we proposed a single PCR to efficiently detect spike gene mutations. We proposed a bioinformatic protocol that can process FASTQ reads into spike gene consensus sequences to accurately call spike protein variants from sequenced samples or to fairly express the cases of missing amplicons. We evaluated the in silico detection rate of primer sets that yield amplicon sizes of 400, 1200, and 2500 bp for spike gene sequencing of SARS-CoV-2 to be 59.49, 76.19, and 92.20%, respectively. The in silico detection rate of our proposed single PCR primers was 97.07%. We demonstrated the robustness of our analytical protocol against 3000 Oxford Nanopore sequencing runs of distinct datasets, thus ensuring high-integrity sequencing of spike genes for variant SARS-CoV-2 determination. Our protocol works well with the data yielded from versatile primer designs, making it easy to determine spike protein variants. MDPI 2022-03-17 /pmc/articles/PMC8954144/ /pubmed/35328676 http://dx.doi.org/10.3390/ijms23063257 Text en © 2022 by the authors. https://creativecommons.org/licenses/by/4.0/Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (https://creativecommons.org/licenses/by/4.0/). |
spellingShingle | Article Liao, Yu-Chieh Chen, Feng-Jui Chuang, Min-Chieh Wu, Han-Chieh Ji, Wan-Chen Yu, Guann-Yi Huang, Tsi-Shu High-Integrity Sequencing of Spike Gene for SARS-CoV-2 Variant Determination |
title | High-Integrity Sequencing of Spike Gene for SARS-CoV-2 Variant Determination |
title_full | High-Integrity Sequencing of Spike Gene for SARS-CoV-2 Variant Determination |
title_fullStr | High-Integrity Sequencing of Spike Gene for SARS-CoV-2 Variant Determination |
title_full_unstemmed | High-Integrity Sequencing of Spike Gene for SARS-CoV-2 Variant Determination |
title_short | High-Integrity Sequencing of Spike Gene for SARS-CoV-2 Variant Determination |
title_sort | high-integrity sequencing of spike gene for sars-cov-2 variant determination |
topic | Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8954144/ https://www.ncbi.nlm.nih.gov/pubmed/35328676 http://dx.doi.org/10.3390/ijms23063257 |
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