ArticleScientific reports2016
Contamination-controlled high-throughput whole genome sequencing for influenza A viruses using the MiSeq sequencer.
Article in Scientific reports, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 18 papers.
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Who cites it
18 citing papers in PubMed.
- Descriptive epidemiology and phylogenetic analysis of highly pathogenic avian influenza H5N1 clade 2.3.4.4b in British Columbia (B.C.) and the Yukon, Canada, September 2022 to June 2023.Emerging microbes & infections · 2024Article
- Bioinformatic Methodologies in Assessing Gut Microbiota.Microbiology research · 2024Article
- Recovering high-quality bacterial genomes from cross-contaminated cultures: a case study of marine Vibrio campbellii.BMC genomics · 2024Article
- Improved influenza A whole-genome sequencing protocol.Frontiers in cellular and infection microbiology · 2024Article
- Descriptive Epidemiology and Phylodynamics of the "First Wave" of an Outbreak of Highly Pathogenic Avian Influenza (H5N1 Clade 2.3.4.4b) in British Columbia and the Yukon, Canada, April to September 2022.Transboundary and emerging diseases · 2024Article
- Carryover Contamination-Controlled Amplicon Sequencing Workflow for Accurate Qualitative and Quantitative Detection of Pathogens: a Case Study on SARS-CoV-2.Microbiology spectrum · 2023Article
- Novel Zoonotic Avian Influenza A(H3N8) Virus in Chicken, Hong Kong, China.Emerging infectious diseases · 2022Article
- Method comparison of targeted influenza A virus typing and whole-genome sequencing from respiratory specimens of companion animals.Journal of veterinary diagnostic investigation : official publication of the American Association of Veterinary Laboratory Diagnosticians, Inc · 2021Article
- Contamination Issue in Viral Metagenomics: Problems, Solutions, and Clinical Perspectives.Frontiers in microbiology · 2021Review
- Divergent evolutionary trajectories of influenza B viruses underlie their contemporaneous epidemic activity.Proceedings of the National Academy of Sciences of the United States of America · 2020Article
- Technical Validation of a Hepatitis C Virus Whole Genome Sequencing Assay for Detection of Genotype and Antiviral Resistance in the Clinical Pathway.Frontiers in microbiology · 2020Article
- The difference of detection rate of avian influenza virus in the wild bird surveillance using various methods.Journal of veterinary science · 2019Article
- Improved detection of influenza A virus from blue-winged teals by sequencing directly from swab material.Ecology and evolution · 2019Article
- INSaFLU: an automated open web-based bioinformatics suite "from-reads" for influenza whole-genome-sequencing-based surveillance.Genome medicine · 2018Article
- Sample tracking in microbiome community profiling assays using synthetic 16S rRNA gene spike-in controls.Scientific reports · 2018Article
- Seasonal Genetic Drift of Human Influenza A Virus Quasispecies Revealed by Deep Sequencing.Frontiers in microbiology · 2018Article
- Universal Target Capture of HIV Sequences From NGS Libraries.Frontiers in microbiology · 2018Article
- Increased sequencing depth does not increase captured diversity of arbuscular mycorrhizal fungi.Mycorrhiza · 2017Article
Corrections and comments
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Authors and funding
5 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Accurate full-length genomic sequences are important for viral phylogenetic studies. We developed a targeted high-throughput whole genome sequencing (HT-WGS) method for influenza A viruses, which utilized an enzymatic cleavage-based approach, the Nextera XT DNA library preparation kit, for library preparation. The entire library preparation workflow was adapted for the Sentosa SX101, a liquid handling platform, to automate this labor-intensive step. As the enzymatic cleavage-based approach generates low coverage reads at both ends of the cleaved products, we corrected this loss of sequencing coverage at the termini by introducing modified primers during the targeted amplification step to generate full-length influenza A sequences with even coverage across the whole genome. Another challenge of targeted HTS is the risk of specimen-to-specimen cross-contamination during the library preparation step that results in the calling of false-positive minority variants. We included an in-run, negative system control to capture contamination reads that may be generated during the liquid handling procedures. The upper limits of 99.99% prediction intervals of the contamination rate were adopted as cut-off values of contamination reads. Here, 148 influenza A/H3N2 samples were sequenced using the HTS protocol and were compared against a Sanger-based sequencing method. Our data showed that the rate of specimen-to-specimen cross-contamination was highly significant in HTS.
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