ArticlePloS one2011
A sensitive assay for virus discovery in respiratory clinical samples.
Article in PloS one, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 48 papers.
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Who cites it
48 citing papers in PubMed.
- Characterization of the enteric virome of clinically healthy pigs around weaning on commercial farms in the Netherlands using next generation sequencing and qPCR.Porcine health management · 2025Article
- Genome Characterization and Phylogenetic Analysis of Scale Drop Disease Virus Isolated from Asian Seabass (Animals : an open access journal from MDPI · 2024Article
- Unveiling Inter- and Intra-Patient Sequence Variability with a Multi-Sample Coronavirus Target Enrichment Approach.Viruses · 2024Article
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- Agnostic Sequencing for Detection of Viral Pathogens.Clinical microbiology reviews · 2023Review
- Bacterial ribosomal RNA detection in cerebrospinal fluid using a viromics approach.Fluids and barriers of the CNS · 2022Article
- Dynamics of the Enteric Virome in a Swine Herd Affected by Non-PCV2/PRRSV Postweaning Wasting Syndrome.Viruses · 2021Article
- No Evidence Known Viruses Play a Role in the Pathogenesis of Onchocerciasis-Associated Epilepsy. An Explorative Metagenomic Case-Control Study.Pathogens (Basel, Switzerland) · 2021Article
- A Versatile Processing Workflow to Enable Pathogen Detection in Clinical Samples from Organs Using VIDISCA.Diagnostics (Basel, Switzerland) · 2021Article
- High Throughput Sequencing for the Detection and Characterization of RNA Viruses.Frontiers in microbiology · 2021Review
- Review
- Sample descriptors linked to metagenomic sequencing data from human and animal enteric samples from Vietnam.Scientific data · 2019Article
- Absence of accessory genes in a divergent simian T-lymphotropic virus type 1 isolated from a bonnet macaque (Macaca radiata).PLoS neglected tropical diseases · 2019Article
- Viral Metagenomics on Cerebrospinal Fluid.Genes · 2019Article
- Respiratory virus detection and co-infection in children and adults in a large Australian hospital in 2009-2015.Journal of paediatrics and child health · 2018Observational
- Laboratory Methods in Molecular Epidemiology: Viral Infections.Microbiology spectrum · 2018Review
- Genetic diversity and cross-species transmission of kobuviruses in Vietnam.Virus evolution · 2018Article
- Characterization of Posa and Posa-like virus genomes in fecal samples from humans, pigs, rats, and bats collected from a single location in Vietnam.Virus evolution · 2017Article
- Efficient and unbiased metagenomic recovery of RNA virus genomes from human plasma samples.Scientific reports · 2017Article
- Enterovirus D68 in Viet Nam (2009-2015).Wellcome open research · 2017Article
Corrections and comments
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Authors and funding
20 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
In 5-40% of respiratory infections in children, the diagnostics remain negative, suggesting that the patients might be infected with a yet unknown pathogen. Virus discovery cDNA-AFLP (VIDISCA) is a virus discovery method based on recognition of restriction enzyme cleavage sites, ligation of adaptors and subsequent amplification by PCR. However, direct discovery of unknown pathogens in nasopharyngeal swabs is difficult due to the high concentration of ribosomal RNA (rRNA) that acts as competitor. In the current study we optimized VIDISCA by adjusting the reverse transcription enzymes and decreasing rRNA amplification in the reverse transcription, using hexamer oligonucleotides that do not anneal to rRNA. Residual cDNA synthesis on rRNA templates was further reduced with oligonucleotides that anneal to rRNA but can not be extended due to 3'-dideoxy-C6-modification. With these modifications >90% reduction of rRNA amplification was established. Further improvement of the VIDISCA sensitivity was obtained by high throughput sequencing (VIDISCA-454). Eighteen nasopharyngeal swabs were analysed, all containing known respiratory viruses. We could identify the proper virus in the majority of samples tested (11/18). The median load in the VIDISCA-454 positive samples was 7.2 E5 viral genome copies/ml (ranging from 1.4 E3-7.7 E6). Our results show that optimization of VIDISCA and subsequent high-throughput-sequencing enhances sensitivity drastically and provides the opportunity to perform virus discovery directly in patient material.
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