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Evaluation of EPISEQ SARS-CoV-2 and a Fully Integrated Application to Identify SARS-CoV-2 Variants from Several Next-Generation Sequencing Approaches.
Mugnier, Nathalie; Griffon, Aurélien; Simon, Bruno; Rambaud, Maxence; Regue, Hadrien; Bal, Antonin; Destras, Gregory; Tournoud, Maud; Jaillard, Magali; Betraoui, Abel; Santiago, Emmanuelle; Cheynet, Valérie; Vignola, Alexandre; Ligeon, Véronique; Josset, Laurence; Brengel-Pesce, Karen.
  • Mugnier N; BioMérieux SA, 69280 Marcy-l'Étoile, France.
  • Griffon A; BioMérieux SA, 69280 Marcy-l'Étoile, France.
  • Simon B; GenEPII Sequencing Platform, Institut des Agents Infectieux, Hospices Civils de Lyon, 69004 Lyon, France.
  • Rambaud M; BioMérieux SA, 69280 Marcy-l'Étoile, France.
  • Regue H; GenEPII Sequencing Platform, Institut des Agents Infectieux, Hospices Civils de Lyon, 69004 Lyon, France.
  • Bal A; GenEPII Sequencing Platform, Institut des Agents Infectieux, Hospices Civils de Lyon, 69004 Lyon, France.
  • Destras G; GenEPII Sequencing Platform, Institut des Agents Infectieux, Hospices Civils de Lyon, 69004 Lyon, France.
  • Tournoud M; BioMérieux SA, 69280 Marcy-l'Étoile, France.
  • Jaillard M; BioMérieux SA, 69280 Marcy-l'Étoile, France.
  • Betraoui A; BioMérieux SA, 69280 Marcy-l'Étoile, France.
  • Santiago E; BioMérieux SA, 69280 Marcy-l'Étoile, France.
  • Cheynet V; BioMérieux SA, 69280 Marcy-l'Étoile, France.
  • Vignola A; Joint Research Unit Hospices Civils de Lyon-bioMerieux, Centre Hospitalier Lyon Sud, 69310 Pierre-Benite, France.
  • Ligeon V; Biogroup-Oriade-Noviale, 38400 Saint-Martin d'Hères, France.
  • Josset L; BioMérieux SA, 69280 Marcy-l'Étoile, France.
  • Brengel-Pesce K; GenEPII Sequencing Platform, Institut des Agents Infectieux, Hospices Civils de Lyon, 69004 Lyon, France.
Viruses ; 14(8)2022 07 29.
Article in English | MEDLINE | ID: covidwho-1969505
ABSTRACT
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.
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Full text: Available Collection: International databases Database: MEDLINE Main subject: SARS-CoV-2 / COVID-19 Type of study: Diagnostic study / Experimental Studies / Prognostic study Topics: Variants Limits: Humans Language: English Year: 2022 Document Type: Article Affiliation country: V14081674

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Full text: Available Collection: International databases Database: MEDLINE Main subject: SARS-CoV-2 / COVID-19 Type of study: Diagnostic study / Experimental Studies / Prognostic study Topics: Variants Limits: Humans Language: English Year: 2022 Document Type: Article Affiliation country: V14081674