Cargando…

Strategy and Performance Evaluation of Low-Frequency Variant Calling for SARS-CoV-2 Using Targeted Deep Illumina Sequencing

The ongoing COVID-19 pandemic, caused by SARS-CoV-2, constitutes a tremendous global health issue. Continuous monitoring of the virus has become a cornerstone to make rational decisions on implementing societal and sanitary measures to curtail the virus spread. Additionally, emerging SARS-CoV-2 vari...

Descripción completa

Detalles Bibliográficos
Autores principales:	Van Poelvoorde, Laura A. E., Delcourt, Thomas, Coucke, Wim, Herman, Philippe, De Keersmaecker, Sigrid C. J., Saelens, Xavier, Roosens, Nancy H. C., Vanneste, Kevin
Formato:	Online Artículo Texto
Lenguaje:	English
Publicado:	Frontiers Media S.A. 2021
Materias:	Microbiology
Acceso en línea:	https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8548777/ https://www.ncbi.nlm.nih.gov/pubmed/34721349 http://dx.doi.org/10.3389/fmicb.2021.747458

Ejemplares similares

A general approach to identify low-frequency variants within influenza samples collected during routine surveillance
por: Van Poelvoorde, Laura A. E., et al.
Publicado: (2022)

Whole-Genome Sequence Approach and Phylogenomic Stratification Improve the Association Analysis of Mutations With Patient Data in Influenza Surveillance
por: Van Poelvoorde, Laura, et al.
Publicado: (2022)

Evaluation of WGS performance for bacterial pathogen characterization with the Illumina technology optimized for time-critical situations
por: Bogaerts, Bert, et al.
Publicado: (2021)

Whole-genome-based phylogenomic analysis of the Belgian 2016–2017 influenza A(H3N2) outbreak season allows improved surveillance
por: Van Poelvoorde, Laura A. E., et al.
Publicado: (2021)

Deepening of In Silico Evaluation of SARS-CoV-2 Detection RT-qPCR Assays in the Context of New Variants
por: Gand, Mathieu, et al.
Publicado: (2021)

NGS for (Hemato-) Oncology in Belgium: Evaluation of Laboratory Performance and Feasibility of a National External Quality Assessment Program
por: Delcourt, Thomas, et al.
Publicado: (2020)

Targeting the 16S rRNA Gene for Bacterial Identification in Complex Mixed Samples: Comparative Evaluation of Second (Illumina) and Third (Oxford Nanopore Technologies) Generation Sequencing Technologies
por: Winand, Raf, et al.
Publicado: (2019)

Evaluation of the added value of viral genomic information for predicting severity of influenza infection
por: Van Goethem, Nina, et al.
Publicado: (2021)

Comparison of 6 DNA extraction methods for isolation of high yield of high molecular weight DNA suitable for shotgun metagenomics Nanopore sequencing to detect bacteria
por: Gand, Mathieu, et al.
Publicado: (2023)

Use of Whole Genome Sequencing Data for a First in Silico Specificity Evaluation of the RT-qPCR Assays Used for SARS-CoV-2 Detection
por: Gand, Mathieu, et al.
Publicado: (2020)

Development of a portable on-site applicable metagenomic data generation workflow for enhanced pathogen and antimicrobial resistance surveillance
por: Bloemen, Bram, et al.
Publicado: (2023)

Development of Digital Droplet PCR Targeting the Influenza H3N2 Oseltamivir-Resistant E119V Mutation and Its Performance through the Use of Reverse Genetics Mutants
por: Van Poelvoorde, Laura A. E., et al.
Publicado: (2023)

Strategy to Develop and Evaluate a Multiplex RT-ddPCR in Response to SARS-CoV-2 Genomic Evolution
por: Van Poelvoorde, Laura A. E., et al.
Publicado: (2021)

Characterization of Genetically Modified Microorganisms Using Short- and Long-Read Whole-Genome Sequencing Reveals Contaminations of Related Origin in Multiple Commercial Food Enzyme Products
por: D’aes, Jolien, et al.
Publicado: (2021)

Using a combination of short- and long-read sequencing to investigate the diversity in plasmid- and chromosomally encoded extended-spectrum beta-lactamases (ESBLs) in clinical Shigella and Salmonella isolates in Belgium
por: Berbers, Bas, et al.
Publicado: (2023)

Shifting national surveillance of Shigella infections toward geno‐serotyping by the development of a tailored Luminex assay and NGS workflow
por: Ventola, Eleonora, et al.
Publicado: (2019)

Development of an NGS-Based Workflow for Improved Monitoring of Circulating Plasmids in Support of Risk Assessment of Antimicrobial Resistance Gene Dissemination
por: Berbers, Bas, et al.
Publicado: (2020)

Metagenomic Characterization of Multiple Genetically Modified Bacillus Contaminations in Commercial Microbial Fermentation Products
por: D’aes, Jolien, et al.
Publicado: (2022)

Reliable variant calling during runtime of Illumina sequencing
por: Loka, Tobias P., et al.
Publicado: (2019)

Targeted High-Throughput Sequencing Enables the Detection of Single Nucleotide Variations in CRISPR/Cas9 Gene-Edited Organisms
por: Fraiture, Marie-Alice, et al.
Publicado: (2023)

Nanopore sequencing technology: a new route for the fast detection of unauthorized GMO
por: Fraiture, Marie-Alice, et al.
Publicado: (2018)

Identification of an unauthorized genetically modified bacteria in food enzyme through whole-genome sequencing
por: Fraiture, Marie-Alice, et al.
Publicado: (2020)

Development of a Droplet Digital PCR to Monitor SARS-CoV-2 Omicron Variant BA.2 in Wastewater Samples
por: Van Poelvoorde, Laura A. E., et al.
Publicado: (2023)

Detection and identification of authorized and unauthorized GMOs using high-throughput sequencing with the support of a sequence-based GMO database
por: Saltykova, Assia, et al.
Publicado: (2022)

Impact of DNA extraction on whole genome sequencing analysis for characterization and relatedness of Shiga toxin-producing Escherichia coli isolates
por: Nouws, Stéphanie, et al.
Publicado: (2020)

Whole Genome Sequencing Provides an Added Value to the Investigation of Staphylococcal Food Poisoning Outbreaks
por: Nouws, Stéphanie, et al.
Publicado: (2021)

A Bioinformatics Whole-Genome Sequencing Workflow for Clinical Mycobacterium tuberculosis Complex Isolate Analysis, Validated Using a Reference Collection Extensively Characterized with Conventional Methods and In Silico Approaches
por: Bogaerts, Bert, et al.
Publicado: (2021)

Development and performance assessment of a luminex xMAP(®) direct hybridization assay for the detection and identification of indoor air fungal contamination
por: Libert, Xavier, et al.
Publicado: (2017)

Discrimination of three genetically close Aspergillus species by using high resolution melting analysis applied to indoor air as case study
por: Libert, Xavier, et al.
Publicado: (2017)

A Practical Method to Implement Strain-Level Metagenomics-Based Foodborne Outbreak Investigation and Source Tracking in Routine
por: Buytaers, Florence E., et al.
Publicado: (2020)

Towards Real-Time and Affordable Strain-Level Metagenomics-Based Foodborne Outbreak Investigations Using Oxford Nanopore Sequencing Technologies
por: Buytaers, Florence E., et al.
Publicado: (2021)

Coverage of the national surveillance system for human Salmonella infections, Belgium, 2016-2020
por: Van Goethem, Nina, et al.
Publicado: (2021)

Case Report: Multidrug Resistant Raoultella ornithinolytica in a Septicemic Calf
por: Pas, Mathilde L., et al.
Publicado: (2021)

Phylogenomic Investigation of Increasing Fluoroquinolone Resistance among Belgian Cases of Shigellosis between 2013 and 2018 Indicates Both Travel-Related Imports and Domestic Circulation
por: Bogaerts, Bert, et al.
Publicado: (2021)

Metagenomics to Detect and Characterize Viruses in Food Samples at Genome Level? Lessons Learnt from a Norovirus Study
por: Buytaers, Florence E., et al.
Publicado: (2022)

Transforming Shiga toxin-producing Escherichia coli surveillance through whole genome sequencing in food safety practices
por: Nouws, Stéphanie, et al.
Publicado: (2023)

Development of a real-time PCR method for the genoserotyping of Salmonella Paratyphi B variant Java
por: Gand, Mathieu, et al.
Publicado: (2019)

Combining short and long read sequencing to characterize antimicrobial resistance genes on plasmids applied to an unauthorized genetically modified Bacillus
por: Berbers, Bas, et al.
Publicado: (2020)

Retrospective surveillance of viable Bacillus cereus group contaminations in commercial food and feed vitamin B(2) products sold on the Belgian market using whole-genome sequencing
por: Bogaerts, Bert, et al.
Publicado: (2023)

Exploiting the Advantages of Molecular Tools for the Monitoring of Fungal Indoor Air Contamination: First Detection of Exophiala jeanselmei in Indoor Air of Air-Conditioned Offices
por: Libert, Xavier, et al.
Publicado: (2019)

Cannot write session to /tmp/vufind_sessions/sess_mre4o7t3cn1s9h5nqbssqm4u6l