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Article

Evaluation of EPISEQ SARS-CoV-2 and a Fully Integrated Application to Identify SARS-CoV-2 Variants from Several Next-Generation Sequencing Approaches

1
BioMérieux SA, 69280 Marcy-l’Étoile, France
2
GenEPII Sequencing Platform, Institut des Agents Infectieux, Hospices Civils de Lyon, 69004 Lyon, France
3
Joint Research Unit Hospices Civils de Lyon-bioMerieux, Centre Hospitalier Lyon Sud, 69310 Pierre-Benite, France
4
Biogroup-Oriade-Noviale, 38400 Saint-Martin d’Hères, France
*
Author to whom correspondence should be addressed.
These authors contributed equally to this work.
Academic Editors: Yohei Kurosaki, Danyelly Bruneska Gondim Martins and José Luiz Lima Filho
Viruses 2022, 14(8), 1674; https://doi.org/10.3390/v14081674
Received: 31 May 2022 / Revised: 22 July 2022 / Accepted: 27 July 2022 / Published: 29 July 2022
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. View Full-Text
Keywords: next-generation sequencing; SARS-CoV-2; variant identification; mutation screening; genome assembly; nextstrain clade; pango lineage; bioinformatics next-generation sequencing; SARS-CoV-2; variant identification; mutation screening; genome assembly; nextstrain clade; pango lineage; bioinformatics
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MDPI and ACS Style

Mugnier, N.; Griffon, A.; Simon, B.; Rambaud, M.; Regue, H.; Bal, A.; Destras, G.; Tournoud, M.; Jaillard, M.; Betraoui, A.; Santiago, E.; Cheynet, V.; Vignola, A.; Ligeon, V.; Josset, L.; Brengel-Pesce, K. Evaluation of EPISEQ SARS-CoV-2 and a Fully Integrated Application to Identify SARS-CoV-2 Variants from Several Next-Generation Sequencing Approaches. Viruses 2022, 14, 1674. https://doi.org/10.3390/v14081674

AMA Style

Mugnier N, Griffon A, Simon B, Rambaud M, Regue H, Bal A, Destras G, Tournoud M, Jaillard M, Betraoui A, Santiago E, Cheynet V, Vignola A, Ligeon V, Josset L, Brengel-Pesce K. Evaluation of EPISEQ SARS-CoV-2 and a Fully Integrated Application to Identify SARS-CoV-2 Variants from Several Next-Generation Sequencing Approaches. Viruses. 2022; 14(8):1674. https://doi.org/10.3390/v14081674

Chicago/Turabian Style

Mugnier, Nathalie, 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, and Karen Brengel-Pesce. 2022. "Evaluation of EPISEQ SARS-CoV-2 and a Fully Integrated Application to Identify SARS-CoV-2 Variants from Several Next-Generation Sequencing Approaches" Viruses 14, no. 8: 1674. https://doi.org/10.3390/v14081674

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