ArticleGenes2019
Viral Metagenomics in the Clinical Realm: Lessons Learned from a Swiss-Wide Ring Trial.
Article in Genes, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 23 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
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.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
23 citing papers in PubMed.
- Clinical metagenomics for diagnosis and surveillance of viral pathogens.Nature reviews. Microbiology · 2026Review
- teamNGS Balances Sensitivity for Viruses with Comprehensive Microbial Detection in Clinical Specimens.Microorganisms · 2025Article
- Metagenomic Next-Generation Sequencing in Infectious Diseases: Clinical Applications, Translational Challenges, and Future Directions.Diagnostics (Basel, Switzerland) · 2025Review
- Leveraging innovative diagnostics as a tool to contain superbugs.Antonie van Leeuwenhoek · 2025Review
- An interlaboratory proficiency test using metagenomic sequencing as a diagnostic tool for the detection of RNA viruses in swine fecal material.Microbiology spectrum · 2024Article
- MetaAll: integrative bioinformatics workflow for analysing clinical metagenomic data.Briefings in bioinformatics · 2024Article
- Comparison of the performance of two targeted metagenomic virus capture probe-based methods using reference control materials and clinical samples.Journal of clinical microbiology · 2024Article
- Agnostic Sequencing for Detection of Viral Pathogens.Clinical microbiology reviews · 2023Review
- Assessing the impact of meta-genomic tools on current cutting-edge genome engineering and technology.International journal of biochemistry and molecular biology · 2023Review
- One Health surveillance-A cross-sectoral detection, characterization, and notification of foodborne pathogens.Frontiers in public health · 2023Article
- Combination of Whole Genome Sequencing and Metagenomics for Microbiological Diagnostics.International journal of molecular sciences · 2022Review
- Performance of Five Metagenomic Classifiers for Virus Pathogen Detection Using Respiratory Samples from a Clinical Cohort.Pathogens (Basel, Switzerland) · 2022Article
- External Quality Assessment of SARS-CoV-2 Sequencing: an ESGMD-SSM Pilot Trial across 15 European Laboratories.Journal of clinical microbiology · 2022Article
- Metagenomic Pathogen Sequencing in Resource-Scarce Settings: Lessons Learned and the Road Ahead.Frontiers in epidemiology · 2022Article
- Blood virosphere in febrile Tanzanian children.Emerging microbes & infections · 2021Article
- Benchmark of thirteen bioinformatic pipelines for metagenomic virus diagnostics using datasets from clinical samples.Journal of clinical virology : the official publication of the Pan American Society for Clinical Virology · 2021Article
- Article
- 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
- A theoretical and generalized approach for the assessment of the sample-specific limit of detection for clinical metagenomics.Computational and structural biotechnology journal · 2021Article
- Beyond Cytomegalovirus and Epstein-Barr Virus: a Review of Viruses Composing the Blood Virome of Solid Organ Transplant and Hematopoietic Stem Cell Transplant Recipients.Clinical microbiology reviews · 2020Review
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
17 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Shotgun metagenomics using next generation sequencing (NGS) is a promising technique to analyze both DNA and RNA microbial material from patient samples. Mostly used in a research setting, it is now increasingly being used in the clinical realm as well, notably to support diagnosis of viral infections, thereby calling for quality control and the implementation of ring trials (RT) to benchmark pipelines and ensure comparable results. The Swiss NGS clinical virology community therefore decided to conduct a RT in 2018, in order to benchmark current metagenomic workflows used at Swiss clinical virology laboratories, and thereby contribute to the definition of common best practices. The RT consisted of two parts (increments), in order to disentangle the variability arising from the experimental compared to the bioinformatics parts of the laboratory pipeline. In addition, the RT was also designed to assess the impact of databases compared to bioinformatics algorithms on the final results, by asking participants to perform the bioinformatics analysis with a common database, in addition to using their own in-house database. Five laboratories participated in the RT (seven pipelines were tested). We observed that the algorithms had a stronger impact on the overall performance than the choice of the reference database. Our results also suggest that differences in sample preparation can lead to significant differences in the performance, and that laboratories should aim for at least 5-10 Mio reads per sample and use depth of coverage in addition to other interpretation metrics such as the percent of coverage. Performance was generally lower when increasing the number of viruses per sample. The lessons learned from this pilot study will be useful for the development of larger-scale RTs to serve as regular quality control tests for laboratories performing NGS analyses of viruses in a clinical setting.
Indexed as
Identifiers
What OpenQuestion holds
Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.