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High Throughput SARS-CoV-2 Genome Sequencing from 384 Respiratory Samples Using the Illumina COVIDSeq Protocol

The emergence of the Coronavirus Disease 2019 (COVID-19) pandemic has fostered the use of high-throughput techniques to sequence the entire severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) genome and track its evolution. The present study proposes a rapid and relatively less expensive se...

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Autores principales: Papa Mze, Nasserdine, Kacel, Idir, Beye, Mamadou, Tola, Raphael, Sarr, Mariéma, Basco, Leonardo, Bogreau, Hervé, Colson, Philippe, Fournier, Pierre-Edouard
Formato: Online Artículo Texto
Lenguaje:English
Publicado: MDPI 2023
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10048438/
https://www.ncbi.nlm.nih.gov/pubmed/36980953
http://dx.doi.org/10.3390/genes14030681
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author Papa Mze, Nasserdine
Kacel, Idir
Beye, Mamadou
Tola, Raphael
Sarr, Mariéma
Basco, Leonardo
Bogreau, Hervé
Colson, Philippe
Fournier, Pierre-Edouard
author_facet Papa Mze, Nasserdine
Kacel, Idir
Beye, Mamadou
Tola, Raphael
Sarr, Mariéma
Basco, Leonardo
Bogreau, Hervé
Colson, Philippe
Fournier, Pierre-Edouard
author_sort Papa Mze, Nasserdine
collection PubMed
description The emergence of the Coronavirus Disease 2019 (COVID-19) pandemic has fostered the use of high-throughput techniques to sequence the entire severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) genome and track its evolution. The present study proposes a rapid and relatively less expensive sequencing protocol for 384 samples by adapting the use of an Illumina NovaSeq library to an Illumina MiSeq flow cell instrument. The SARS-CoV-2 genome sequences obtained with Illumina NovaSeq and those obtained using MiSeq instruments were compared with the objective to validate the new, modified protocol. A total of 356 (94.6%) samples yielded interpretable sequences using the modified Illumina COVIDSeq protocol, with an average coverage of 91.6%. By comparison, 357 (94.9%) samples yielded interpretable sequences with the standard COVIDSeq protocol, with an average coverage of 95.6%. Our modified COVIDSeq protocol could save 14,155 euros per run and yield results from 384 samples in 53.5 h, compared to four times 55.5 h with the standard Illumina MiSeq protocol. The modified COVIDSeq protocol thus provides high quality results comparable to those obtained with the standard COVIDSeq protocol, four times faster, while saving money.
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spelling pubmed-100484382023-03-29 High Throughput SARS-CoV-2 Genome Sequencing from 384 Respiratory Samples Using the Illumina COVIDSeq Protocol Papa Mze, Nasserdine Kacel, Idir Beye, Mamadou Tola, Raphael Sarr, Mariéma Basco, Leonardo Bogreau, Hervé Colson, Philippe Fournier, Pierre-Edouard Genes (Basel) Article The emergence of the Coronavirus Disease 2019 (COVID-19) pandemic has fostered the use of high-throughput techniques to sequence the entire severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) genome and track its evolution. The present study proposes a rapid and relatively less expensive sequencing protocol for 384 samples by adapting the use of an Illumina NovaSeq library to an Illumina MiSeq flow cell instrument. The SARS-CoV-2 genome sequences obtained with Illumina NovaSeq and those obtained using MiSeq instruments were compared with the objective to validate the new, modified protocol. A total of 356 (94.6%) samples yielded interpretable sequences using the modified Illumina COVIDSeq protocol, with an average coverage of 91.6%. By comparison, 357 (94.9%) samples yielded interpretable sequences with the standard COVIDSeq protocol, with an average coverage of 95.6%. Our modified COVIDSeq protocol could save 14,155 euros per run and yield results from 384 samples in 53.5 h, compared to four times 55.5 h with the standard Illumina MiSeq protocol. The modified COVIDSeq protocol thus provides high quality results comparable to those obtained with the standard COVIDSeq protocol, four times faster, while saving money. MDPI 2023-03-09 /pmc/articles/PMC10048438/ /pubmed/36980953 http://dx.doi.org/10.3390/genes14030681 Text en © 2023 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
Papa Mze, Nasserdine
Kacel, Idir
Beye, Mamadou
Tola, Raphael
Sarr, Mariéma
Basco, Leonardo
Bogreau, Hervé
Colson, Philippe
Fournier, Pierre-Edouard
High Throughput SARS-CoV-2 Genome Sequencing from 384 Respiratory Samples Using the Illumina COVIDSeq Protocol
title High Throughput SARS-CoV-2 Genome Sequencing from 384 Respiratory Samples Using the Illumina COVIDSeq Protocol
title_full High Throughput SARS-CoV-2 Genome Sequencing from 384 Respiratory Samples Using the Illumina COVIDSeq Protocol
title_fullStr High Throughput SARS-CoV-2 Genome Sequencing from 384 Respiratory Samples Using the Illumina COVIDSeq Protocol
title_full_unstemmed High Throughput SARS-CoV-2 Genome Sequencing from 384 Respiratory Samples Using the Illumina COVIDSeq Protocol
title_short High Throughput SARS-CoV-2 Genome Sequencing from 384 Respiratory Samples Using the Illumina COVIDSeq Protocol
title_sort high throughput sars-cov-2 genome sequencing from 384 respiratory samples using the illumina covidseq protocol
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10048438/
https://www.ncbi.nlm.nih.gov/pubmed/36980953
http://dx.doi.org/10.3390/genes14030681
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