ReviewFrontiers in microbiology2021
Contamination Issue in Viral Metagenomics: Problems, Solutions, and Clinical Perspectives.
Review in Frontiers in microbiology, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 52 papers.
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Who cites it
52 citing papers in PubMed.
- Article
- Interpreting Viral Associations in Neurodegenerative Diseases.International journal of molecular sciences · 2026Review
- Optimizing methods for virome analysis based on studies of a synthetic viral community.mSystems · 2026Article
- Comparison of short nasal swab and deep nasopharyngeal swab sampling methods to describe BRD-associated viruses and bacteria detected using a metagenomics approach optimized for virus recovery in fall-placed beef calves shortly after feedlot arrival.Veterinary and animal science · 2026Article
- Gut virome-microbiome interactions across hosts and environments.NPJ biofilms and microbiomes · 2026Article
- First detection and characterization of Bovine parvovirus 2 and Bopivirus A in a neonatal calf with diarrhea in Iran through metagenomic RNA-seq.Virus genes · 2026Article
- Unveiling pathogens and contaminants: refining metagenomics for clinical diagnostics.Frontiers in microbiology · 2026Article
- Combined NGS and proteomics improves viral diagnostics in wildlife: coronaviruses confirmed in hedgehogs.Frontiers in cellular and infection microbiology · 2026Article
- Diagnostic sensitivity and specificity of metagenomic sequencing and qPCR for detection of viruses associated with bovine respiratory disease estimated using Bayesian latent class models.Frontiers in veterinary science · 2026Article
- Development of a multiplex ddPCR assay for simultaneous absolute quantification of bacterial, fungal, and human DNA.PloS one · 2026Article
- Mitigation and detection of putative microbial contaminant reads from long-read metagenomic datasets.Microbial genomics · 2026Article
- Viral metagenomic analysis of human bocavirus in pediatric pneumonia: detection pattern and genetic characterization.Frontiers in cellular and infection microbiology · 2026Article
- Acute Respiratory Infections (ARIs): Current Etiological Perspectives and Advances in Viral Metagenomics-A Review.Viruses · 2025Review
- Next-Generation Sequencing for Bloodstream Infections: Shaping the Future of Rapid Diagnostics and Precision Medicine.Diagnostics (Basel, Switzerland) · 2025Review
- Contamination of fungal genomes of Onygenaceae (Phylum Ascomycota) in public databases: incidence, detection, and impact.BMC genomics · 2025Article
- Article
- Viral Metagenomic Next-Generation Sequencing for One Health Discovery and Surveillance of (Re)Emerging Viruses: A Deep Review.International journal of molecular sciences · 2025Review
- vPro-MS enables identification of human-pathogenic viruses from patient samples by untargeted proteomics.Nature communications · 2025Article
- Negativeome characterization and decontamination in early-life virome studies.Nature communications · 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
Corrections and comments
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Authors and funding
3 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
We describe the most common internal and external sources and types of contamination encountered in viral metagenomic studies and discuss their negative impact on sequencing results, particularly for low-biomass samples and clinical applications. We also propose some basic recommendations for reducing the background noise in viral shotgun metagenomic (SM) studies, which would limit the bias introduced by various classes of contaminants. Regardless of the specific viral SM protocol, contamination cannot be totally avoided; in particular, the issue of reagent contamination should always be addressed with high priority. There is an urgent need for the development and validation of standards for viral metagenomic studies especially if viral SM protocols will be more widely applied in diagnostics.
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