Recommendations for accurate genotyping of SARS-CoV-2 using amplicon-based sequencing of clinical samples.
Fiche publication
Date publication
juillet 2021
Journal
Clinical microbiology and infection : the official publication of the European Society of Clinical Microbiology and Infectious Diseases
Auteurs
Membres identifiés du Cancéropôle Est :
Mr DUFFOURD Yannis
Tous les auteurs :
Kubik S, Marques AC, Xing X, Silvery J, Bertelli C, De Maio F, Pournaras S, Burr T, Duffourd Y, Siemens H, Alloui C, Song L, Wenger Y, Saitta A, Macheret M, Smith EW, Menu P, Brayer M, Steinmetz LM, Si-Mohammed A, Chuisseu J, Stevens R, Constantoulakis P, Sali M, Greub G, Tiemann C, Pelechano V, Willig A, Xu Z
Lien Pubmed
Résumé
Genotyping of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has been instrumental in monitoring viral evolution and transmission during the pandemic. The quality of the sequence data obtained from these genotyping efforts depends on several factors, including the quantity/integrity of the input material, the technology, and laboratory-specific implementation. The current lack of guidelines for SARS-CoV-2 genotyping leads to inclusion of error-containing genome sequences in genomic epidemiology studies. We aimed to establish clear and broadly applicable recommendations for reliable virus genotyping.
Mots clés
Amplicon, Coronavirus, Genome, Genotyping, Guidelines, NGS, Next-generation sequencing, Recommendations, SARS-CoV-2
Référence
Clin Microbiol Infect. 2021 Jul;27(7):1036.e1-1036.e8