ArticleJournal of virological methods2015
Comparing viral metagenomics methods using a highly multiplexed human viral pathogens reagent.
Article in Journal of virological methods, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 97 papers.
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Who cites it
97 citing papers in PubMed.
- Optimizing methods for virome analysis based on studies of a synthetic viral community.mSystems · 2026Article
- One health viral metagenomics for pathogen surveillance: robust mNGS workflows for viral detection and genome recovery from swab and tissue specimens.BMC microbiology · 2026Article
- Fecal virome at the human-animal interface: a one health perspective on an uncharted frontier.Animal microbiome · 2026Review
- Viral metagenomic analysis of human bocavirus in pediatric pneumonia: detection pattern and genetic characterization.Frontiers in cellular and infection microbiology · 2026Article
- Optimizing methods for virome analysis based on studies of a synthetic viral community.bioRxiv : the preprint server for biology · 2025Article
- The respiratory tract virome: unravelling the role of viral dark matter in respiratory health and disease.European respiratory review : an official journal of the European Respiratory Society · 2025Review
- Assessing Bias and Reproducibility of Viral Metagenomics Methods for the Combined Detection of Faecal RNA and DNA Viruses.Viruses · 2025Article
- Empirical assessment of the enrichment-based metagenomic methods in identifying diverse respiratory pathogens.Scientific reports · 2024Article
- Comparison of Three Viral Nucleic Acid Preamplification Pipelines for Sewage Viral Metagenomics.Food and environmental virology · 2024Article
- Expanding known viral diversity in plants: virome of 161 species alongside an ancient canal.Environmental microbiome · 2022Article
- Comprehensive Evaluation of RNA and DNA Viromic Methods Based on Species Richness and Abundance Analyses Using Marmot Rectal Samples.mSystems · 2022Article
- Highly diverse ribonucleic acid viruses in the viromes of eukaryotic host species in Yunnan province, China.Frontiers in microbiology · 2022Article
- New Parvoviruses and Picornavirus in Tissues and Feces of Foals with Interstitial Pneumonia.Viruses · 2021Article
- Circovirus in Blood of a Febrile Horse with Hepatitis.Viruses · 2021Article
- ContigExtender: a new approach to improving de novo sequence assembly for viral metagenomics data.BMC bioinformatics · 2021Article
- Norovirus strains in patients with acute gastroenteritis in rural and low-income urban areas in northern Brazil.Archives of virology · 2021Article
- Implementation of next-generation sequencing for virus identification in veterinary diagnostic laboratories.Journal of veterinary diagnostic investigation : official publication of the American Association of Veterinary Laboratory Diagnosticians, Inc · 2021Article
- Deep Impact of Random Amplification and Library Construction Methods on Viral Metagenomics Results.Viruses · 2021Article
- Virome of Bat Guano from Nine Northern California Roosts.Journal of virology · 2021Article
- Astrovirus Outbreak in an Animal Shelter Associated With Feline Vomiting.Frontiers in veterinary science · 2021Article
37 more citing papers are in PubMed but not listed here.
Corrections and comments
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Authors and funding
8 authors.
Funding
Abstract
Unbiased metagenomic sequencing holds significant potential as a diagnostic tool for the simultaneous detection of any previously genetically described viral nucleic acids in clinical samples. Viral genome sequences can also inform on likely phenotypes including drug susceptibility or neutralization serotypes. In this study, different variables of the laboratory methods often used to generate viral metagenomics libraries were compared for their abilities to detect multiple viruses and generate full genome coverage. A biological reagent consisting of 25 different human RNA and DNA viral pathogens was used to estimate the effect of filtration and nuclease digestion, DNA/RNA extraction methods, pre-amplification and the use of different library preparation kits on the detection of viral nucleic acids. Filtration and nuclease treatment led to slight decreases in the percentage of viral sequence reads and number of viruses detected. For nucleic acid extractions silica spin columns improved viral sequence recovery relative to magnetic beads and Trizol extraction. Pre-amplification using random RT-PCR while generating more viral sequence reads resulted in detection of fewer viruses, more overlapping sequences, and lower genome coverage. The ScriptSeq library preparation method retrieved more viruses and a greater fraction of their genomes than the TruSeq and Nextera methods. Viral metagenomics sequencing was able to simultaneously detect up to 22 different viruses in the biological reagent analyzed including all those detected by qPCR. Further optimization will be required for the detection of viruses in biologically more complex samples such as tissues, blood, or feces.
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