ArticleBiology direct2016
Direct next-generation sequencing of virus-human mixed samples without pretreatment is favorable to recover virus genome.
Article in Biology direct, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 10 papers.
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Who cites it
10 citing papers in PubMed.
- VIGA: a one-stop tool for eukaryotic virus identification and genome assembly from next-generation-sequencing data.Briefings in bioinformatics · 2023Article
- Next Generation Sequencing Approaches to Characterize the Respiratory Tract Virome.Microorganisms · 2022Review
- Identification of nsp1 gene as the target of SARS-CoV-2 real-time RT-PCR using nanopore whole-genome sequencing.Journal of medical virology · 2020Article
- Rapid Scanning Electron Microscopy Detection and Sequencing of Severe Acute Respiratory Syndrome Coronavirus 2 and Other Respiratory Viruses.Frontiers in microbiology · 2020Article
- An Optimized Metagenomic Approach for Virome Detection of Clinical Pharyngeal Samples With Respiratory Infection.Frontiers in microbiology · 2020Article
- Article
- Using noninvasive metagenomics to characterize viral communities from wildlife.Molecular ecology resources · 2019Article
- Towards a Universal Molecular Microbiological Test.Journal of clinical microbiology · 2017Review
- Evolution of selective-sequencing approaches for virus discovery and virome analysis.Virus research · 2017Review
- A metagenomics study for the identification of respiratory viruses in mixed clinical specimens: an application of the iterative mapping approach.Archives of virology · 2017Article
Corrections and comments
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Authors and funding
9 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Next-generation sequencing (NGS) enables the recovery of pathogen genomes from clinical samples without the need for culturing. Depletion of host/microbiota components (e.g., ribosomal RNA and poly-A RNA) and whole DNA/cDNA amplification are routine methods to improve recovery results. Using mixtures of human and influenza A virus (H1N1) RNA as a model, we found that background depletion and whole transcriptome amplification introduced biased distributions of read coverage over the H1N1 genome, thereby hampering genome assembly. Influenza serotyping was also affected by pretreatments. We propose that direct sequencing of noncultured samples without pretreatment is a favorable option for pathogen genome recovery applications.
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