Proficiency testing for SARS-CoV-2 whole genome sequencing.
SARS-CoV-2
bioinformatics analysis
proficiency testing
whole genome sequencing
Journal
Pathology
ISSN: 1465-3931
Titre abrégé: Pathology
Pays: England
ID NLM: 0175411
Informations de publication
Date de publication:
Aug 2022
Aug 2022
Historique:
received:
09
12
2021
revised:
12
04
2022
accepted:
20
04
2022
pubmed:
2
7
2022
medline:
17
8
2022
entrez:
1
7
2022
Statut:
ppublish
Résumé
Extensive studies and analyses into the molecular features of severe acute respiratory syndrome related coronavirus 2 (SARS-CoV-2) have enhanced the surveillance and investigation of its clusters and transmission worldwide. The whole genome sequencing (WGS) approach is crucial in identifying the source of infection and transmission routes by monitoring the emergence of variants over time and through communities. Varying SARS-CoV-2 genomics capacity and capability levels have been established in public health laboratories across different Australian states and territories. Therefore, laboratories performing SARS-CoV-2 WGS for public health purposes are recommended to participate in an external proficiency testing program (PTP). This study describes the development of a SARS-CoV-2 WGS PTP. The PTP assessed the performance of laboratories while providing valuable insight into the current state of SARS-CoV-2 genomics in public health across Australia. Part 1 of the PTP contained eight simulated SARS-CoV-2 positive and negative specimens to assess laboratories' wet and dry laboratory capacity. Part 2 involved the analysis of a genomic dataset that consisted of a multi-FASTA file of 70 consensus genomes of SARS-CoV-2. Participating laboratories were required to (1) submit raw data for independent bioinformatics analysis, (2) analyse the data with their processes, and (3) answer relevant questions about the data. The performance of the laboratories was commendable, despite some variation in the reported results due to the different sequencing and bioinformatics approaches used by laboratories. The overall outcome is positive and demonstrates the critical role of the PTP in supporting the implementation and validation of SARS-CoV-2 WGS processes. The data derived from this PTP will contribute to the development of SARS-CoV-2 bioinformatic quality control (QC) and performance benchmarking for accreditation.
Identifiants
pubmed: 35778290
pii: S0031-3025(22)00172-6
doi: 10.1016/j.pathol.2022.04.002
pmc: PMC9239710
pii:
doi:
Types de publication
Journal Article
Langues
eng
Sous-ensembles de citation
IM
Pagination
615-622Informations de copyright
Copyright © 2022 Royal College of Pathologists of Australasia. Published by Elsevier B.V. All rights reserved.
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