Whole-Genome Sequencing of SARS-CoV-2: Assessment of the Ion Torrent AmpliSeq Panel and Comparison with the Illumina MiSeq ARTIC Protocol.
ARTIC
AmpliSeq
Ion Torrent
MiSeq
SARS-CoV-2
whole-genome sequencing
Journal
Journal of clinical microbiology
ISSN: 1098-660X
Titre abrégé: J Clin Microbiol
Pays: United States
ID NLM: 7505564
Informations de publication
Date de publication:
18 11 2021
18 11 2021
Historique:
pubmed:
23
9
2021
medline:
24
11
2021
entrez:
22
9
2021
Statut:
ppublish
Résumé
Fast and effective methods are needed for sequencing of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) genome to track genetic mutations and to identify new and emerging variants during the ongoing pandemic. The objectives were to assess the performance of the SARS-CoV-2 AmpliSeq research panel and S5 plug-in analysis tools for whole-genome sequencing analysis of SARS-CoV-2 and to compare the results with those obtained with the MiSeq-based ARTIC analysis pipeline, using metrics such as depth, coverage, and concordance of single-nucleotide variant (SNV) calls. A total of 191 clinical specimens and a single cultured isolate were extracted and sequenced with AmpliSeq technology and analysis tools. Of the 191 clinical specimens, 83 (with threshold cycle [
Identifiants
pubmed: 34550806
doi: 10.1128/JCM.00649-21
pmc: PMC8601232
doi:
Types de publication
Journal Article
Research Support, Non-U.S. Gov't
Research Support, U.S. Gov't, P.H.S.
Langues
eng
Sous-ensembles de citation
IM
Pagination
e0064921Subventions
Organisme : Association of Public Health Laboratories (APHL)
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