Evaluation of EPISEQ SARS-CoV-2 and a Fully Integrated Application to Identify SARS-CoV-2 Variants from Several Next-Generation Sequencing Approaches
Whole-genome sequencing has become an essential tool for real-time genomic surveillance of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) worldwide. The handling of raw next-generation sequencing (NGS) data is a major challenge for sequencing laboratories. We developed an easy-to-use w...
| Main Authors: | , , , , , , , , , , , , , , , |
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| Format: | Article |
| Language: | English |
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MDPI AG
2022-07-01
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| Series: | Viruses |
| Subjects: | |
| Online Access: | https://www.mdpi.com/1999-4915/14/8/1674 |
| _version_ | 1797431604493156352 |
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| author | Nathalie Mugnier Aurélien Griffon Bruno Simon Maxence Rambaud Hadrien Regue Antonin Bal Gregory Destras Maud Tournoud Magali Jaillard Abel Betraoui Emmanuelle Santiago Valérie Cheynet Alexandre Vignola Véronique Ligeon Laurence Josset Karen Brengel-Pesce |
| author_facet | Nathalie Mugnier Aurélien Griffon Bruno Simon Maxence Rambaud Hadrien Regue Antonin Bal Gregory Destras Maud Tournoud Magali Jaillard Abel Betraoui Emmanuelle Santiago Valérie Cheynet Alexandre Vignola Véronique Ligeon Laurence Josset Karen Brengel-Pesce |
| author_sort | Nathalie Mugnier |
| collection | DOAJ |
| description | Whole-genome sequencing has become an essential tool for real-time genomic surveillance of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) worldwide. The handling of raw next-generation sequencing (NGS) data is a major challenge for sequencing laboratories. We developed an easy-to-use web-based application (EPISEQ SARS-CoV-2) to analyse SARS-CoV-2 NGS data generated on common sequencing platforms using a variety of commercially available reagents. This application performs in one click a quality check, a reference-based genome assembly, and the analysis of the generated consensus sequence as to coverage of the reference genome, mutation screening and variant identification according to the up-to-date Nextstrain clade and Pango lineage. In this study, we validated the EPISEQ SARS-CoV-2 pipeline against a reference pipeline and compared the performance of NGS data generated by different sequencing protocols using EPISEQ SARS-CoV-2. We showed a strong agreement in SARS-CoV-2 clade and lineage identification (>99%) and in spike mutation detection (>99%) between EPISEQ SARS-CoV-2 and the reference pipeline. The comparison of several sequencing approaches using EPISEQ SARS-CoV-2 revealed 100% concordance in clade and lineage classification. It also uncovered reagent-related sequencing issues with a potential impact on SARS-CoV-2 mutation reporting. Altogether, EPISEQ SARS-CoV-2 allows an easy, rapid and reliable analysis of raw NGS data to support the sequencing efforts of laboratories with limited bioinformatics capacity and those willing to accelerate genomic surveillance of SARS-CoV-2. |
| first_indexed | 2024-03-09T09:47:35Z |
| format | Article |
| id | doaj.art-23a95617963e4910a3938072ad3bf43c |
| institution | Directory Open Access Journal |
| issn | 1999-4915 |
| language | English |
| last_indexed | 2024-03-09T09:47:35Z |
| publishDate | 2022-07-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Viruses |
| spelling | doaj.art-23a95617963e4910a3938072ad3bf43c2023-12-02T00:26:22ZengMDPI AGViruses1999-49152022-07-01148167410.3390/v14081674Evaluation of EPISEQ SARS-CoV-2 and a Fully Integrated Application to Identify SARS-CoV-2 Variants from Several Next-Generation Sequencing ApproachesNathalie Mugnier0Aurélien Griffon1Bruno Simon2Maxence Rambaud3Hadrien Regue4Antonin Bal5Gregory Destras6Maud Tournoud7Magali Jaillard8Abel Betraoui9Emmanuelle Santiago10Valérie Cheynet11Alexandre Vignola12Véronique Ligeon13Laurence Josset14Karen Brengel-Pesce15BioMérieux SA, 69280 Marcy-l’Étoile, FranceBioMérieux SA, 69280 Marcy-l’Étoile, FranceGenEPII Sequencing Platform, Institut des Agents Infectieux, Hospices Civils de Lyon, 69004 Lyon, FranceBioMérieux SA, 69280 Marcy-l’Étoile, FranceGenEPII Sequencing Platform, Institut des Agents Infectieux, Hospices Civils de Lyon, 69004 Lyon, FranceGenEPII Sequencing Platform, Institut des Agents Infectieux, Hospices Civils de Lyon, 69004 Lyon, FranceGenEPII Sequencing Platform, Institut des Agents Infectieux, Hospices Civils de Lyon, 69004 Lyon, FranceBioMérieux SA, 69280 Marcy-l’Étoile, FranceBioMérieux SA, 69280 Marcy-l’Étoile, FranceBioMérieux SA, 69280 Marcy-l’Étoile, FranceBioMérieux SA, 69280 Marcy-l’Étoile, FranceBioMérieux SA, 69280 Marcy-l’Étoile, FranceBiogroup-Oriade-Noviale, 38400 Saint-Martin d’Hères, FranceBioMérieux SA, 69280 Marcy-l’Étoile, FranceGenEPII Sequencing Platform, Institut des Agents Infectieux, Hospices Civils de Lyon, 69004 Lyon, FranceBioMérieux SA, 69280 Marcy-l’Étoile, FranceWhole-genome sequencing has become an essential tool for real-time genomic surveillance of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) worldwide. The handling of raw next-generation sequencing (NGS) data is a major challenge for sequencing laboratories. We developed an easy-to-use web-based application (EPISEQ SARS-CoV-2) to analyse SARS-CoV-2 NGS data generated on common sequencing platforms using a variety of commercially available reagents. This application performs in one click a quality check, a reference-based genome assembly, and the analysis of the generated consensus sequence as to coverage of the reference genome, mutation screening and variant identification according to the up-to-date Nextstrain clade and Pango lineage. In this study, we validated the EPISEQ SARS-CoV-2 pipeline against a reference pipeline and compared the performance of NGS data generated by different sequencing protocols using EPISEQ SARS-CoV-2. We showed a strong agreement in SARS-CoV-2 clade and lineage identification (>99%) and in spike mutation detection (>99%) between EPISEQ SARS-CoV-2 and the reference pipeline. The comparison of several sequencing approaches using EPISEQ SARS-CoV-2 revealed 100% concordance in clade and lineage classification. It also uncovered reagent-related sequencing issues with a potential impact on SARS-CoV-2 mutation reporting. Altogether, EPISEQ SARS-CoV-2 allows an easy, rapid and reliable analysis of raw NGS data to support the sequencing efforts of laboratories with limited bioinformatics capacity and those willing to accelerate genomic surveillance of SARS-CoV-2.https://www.mdpi.com/1999-4915/14/8/1674next-generation sequencingSARS-CoV-2variant identificationmutation screeninggenome assemblynextstrain clade |
| spellingShingle | Nathalie Mugnier Aurélien Griffon Bruno Simon Maxence Rambaud Hadrien Regue Antonin Bal Gregory Destras Maud Tournoud Magali Jaillard Abel Betraoui Emmanuelle Santiago Valérie Cheynet Alexandre Vignola Véronique Ligeon Laurence Josset Karen Brengel-Pesce Evaluation of EPISEQ SARS-CoV-2 and a Fully Integrated Application to Identify SARS-CoV-2 Variants from Several Next-Generation Sequencing Approaches Viruses next-generation sequencing SARS-CoV-2 variant identification mutation screening genome assembly nextstrain clade |
| title | Evaluation of EPISEQ SARS-CoV-2 and a Fully Integrated Application to Identify SARS-CoV-2 Variants from Several Next-Generation Sequencing Approaches |
| title_full | Evaluation of EPISEQ SARS-CoV-2 and a Fully Integrated Application to Identify SARS-CoV-2 Variants from Several Next-Generation Sequencing Approaches |
| title_fullStr | Evaluation of EPISEQ SARS-CoV-2 and a Fully Integrated Application to Identify SARS-CoV-2 Variants from Several Next-Generation Sequencing Approaches |
| title_full_unstemmed | Evaluation of EPISEQ SARS-CoV-2 and a Fully Integrated Application to Identify SARS-CoV-2 Variants from Several Next-Generation Sequencing Approaches |
| title_short | Evaluation of EPISEQ SARS-CoV-2 and a Fully Integrated Application to Identify SARS-CoV-2 Variants from Several Next-Generation Sequencing Approaches |
| title_sort | evaluation of episeq sars cov 2 and a fully integrated application to identify sars cov 2 variants from several next generation sequencing approaches |
| topic | next-generation sequencing SARS-CoV-2 variant identification mutation screening genome assembly nextstrain clade |
| url | https://www.mdpi.com/1999-4915/14/8/1674 |
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