ArticleJournal of virological methods2023
Evaluation of extraction and enrichment methods for recovery of respiratory RNA viruses in a metagenomics approach.
Article in Journal of virological methods, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 12 papers.
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Who cites it
12 citing papers in PubMed, 22 citations in OpenAlex.
- One health viral metagenomics for pathogen surveillance: robust mNGS workflows for viral detection and genome recovery from swab and tissue specimens.BMC microbiology · 2026Article
- Article
- The Human Respiratory Virome in Health and Disease: Interactions, Dysbiosis, and Methodological Challenges.Advanced genetics (Hoboken, N.J.) · 2025Review
- Viral Metagenomic Next-Generation Sequencing for One Health Discovery and Surveillance of (Re)Emerging Viruses: A Deep Review.International journal of molecular sciences · 2025Review
- Anellovirus abundance as an indicator for viral metagenomic classifier utility in plasma samples.Virology journal · 2025Article
- A ribodepletion and tagging protocol to multiplex samples for RNA-seq based virus detection: application to the cassava virome.Virology journal · 2025Article
- Viral metagenomic analysis of fecal samples fromFrontiers in cellular and infection microbiology · 2025Article
- Evaluating metagenomics and targeted approaches for diagnosis and surveillance of viruses.Genome medicine · 2024Article
- Non-Targeted RNA Sequencing: Towards the Development of Universal Clinical Diagnosis Methods for Human and Veterinary Infectious Diseases.Veterinary sciences · 2024Review
- Enhancing Clinical Utility: Utilization of International Standards and Guidelines for Metagenomic Sequencing in Infectious Disease Diagnosis.International journal of molecular sciences · 2024Review
- Expanding diversity of bunyaviruses identified in mosquitoes.Scientific reports · 2023Article
- Bioinformatic Tools for NGS-Based Metagenomics to Improve the Clinical Diagnosis of Emerging, Re-Emerging and New Viruses.Viruses · 2023Review
Corrections and comments
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Authors and funding
3 authors at 2 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Viral metagenomics is increasingly applied in viral detection and virome characterization. Different extraction and enrichment techniques may be adopted, however, reports on their effective influence on viral recovery is often conflicting. Using a three step enrichment steps, the effect of three extraction kits and the influence of DNase treatment with or without rRNA removal for respiratory RNA virus recovery from nasopharyngeal swab samples was evaluated. The viral cocktail containing six different RNA viruses pooled in equal volume were subjected to the different extraction and enrichment methods, sequenced using the Illumina MiSeq, and analysed using Genome Detective. The PureLink® Viral RNA/DNA Mini Kit (PureLink) was highly efficient with better recovery of all the viral agents in the cocktail. The use of rRNA treatment resulted in increased viral recovery with PureLink and QIAamp® Viral RNA Mini kit, while having comparable recovery rate as DNase only with the QIAamp® MinElute Virus Spin Kit. The observed low reads and genome coverage of some of the viruses could be attributed to their low abundance. Depending on sample matrix, extraction choice and enrichment strategy may influence recovery of respiratory RNA virus in metagenomics studies, therefore individual evaluation and adoption may be necessary for a robust result.
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