ArticleJournal of clinical microbiology2011
Evaluation of high-throughput sequencing for identifying known and unknown viruses in biological samples.
Article in Journal of clinical microbiology, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 73 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
73 citing papers in PubMed, 162 citations in OpenAlex.
- Exploring viral diversity and metagenomics in livestock: insights into disease emergence and spillover risks in cattle.Veterinary research communications · 2024Review
- Host influence on the eukaryotic virome of sympatric mosquitoes and abundance of diverse viruses with a broad host range.PloS one · 2024Article
- Human Anelloviruses: Influence of Demographic Factors, Recombination, and Worldwide Diversity.Microbiology spectrum · 2023Article
- Agnostic Sequencing for Detection of Viral Pathogens.Clinical microbiology reviews · 2023Review
- Spatial scale influences the distribution of viral diversity in the eukaryotic virome of the mosquitoVirus evolution · 2023Article
- Metagenomic analysis reveals presence of different animal viruses in commercial fetal bovine serum and trypsin.Zoological research · 2022Article
- Virome Characterization in Commercial Bovine Serum Batches-A Potentially Needed Testing Strategy for Biological Products.Viruses · 2021Article
- Explorative assessment of coronavirus-like short sequences from host-associated and environmental metagenomes.The Science of the total environment · 2021Article
- Deep viral blood metagenomics reveals extensive anellovirus diversity in healthy humans.Scientific reports · 2021Article
- Deep Impact of Random Amplification and Library Construction Methods on Viral Metagenomics Results.Viruses · 2021Article
- Clinical metagenomics for infectious corneal ulcers: Rags to riches?The ocular surface · 2020Article
- Article
- Sensitivity and specificity of metatranscriptomics as an arbovirus surveillance tool.Scientific reports · 2019Article
- Evaluation of Direct Metagenomics and Target Enriched Approaches for High-throughput Sequencing of Field Rabies Viruses.Journal of veterinary research · 2019Article
- Universal human papillomavirus typing by whole genome sequencing following target enrichment: evaluation of assay reproducibility and limit of detection.BMC genomics · 2019Article
- The utility and perspectives of NGS-based methods in BSL-3 and BSL-4 laboratory - sequencing and analysis strategies.Briefings in functional genomics · 2018Review
- Metagenomic analysis of viral nucleic acid extraction methods in respiratory clinical samples.BMC genomics · 2018Article
- Review
- Coinfections identified from metagenomic analysis of cervical lymph nodes from tularemia patients.BMC infectious diseases · 2018Article
- Limited Correlation of Shotgun Metagenomics Following Host Depletion and Routine Diagnostics for Viruses and Bacteria in Low Concentrated Surrogate and Clinical Samples.Frontiers in cellular and infection microbiology · 2018Article
13 more citing papers are in PubMed but not listed here.
Corrections and comments
- Commented on by
Authors and funding
18 authors at 2 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
High-throughput sequencing furnishes a large number of short sequence reads from uncloned DNA and has rapidly become a major tool for identifying viruses in biological samples, and in particular when the target sequence is undefined. In this study, we assessed the analytical sensitivity of a pipeline for detection of viruses in biological samples based on either the Roche-454 genome sequencer or Illumina genome analyzer platforms. We sequenced biological samples artificially spiked with a wide range of viruses with genomes composed of single or double-stranded DNA or RNA, including linear or circular single-stranded DNA. Viruses were added at a very low concentration most often corresponding to 3 or 0.8 times the validated level of detection of quantitative reverse transcriptase PCRs (RT-PCRs). For the viruses represented, or resembling those represented, in public nucleotide sequence databases, we show that the higher output of Illumina is associated with a much greater sensitivity, approaching that of optimized quantitative (RT-)PCRs. In this blind study, identification of viruses was achieved without incorrect identification. Nevertheless, at these low concentrations, the number of reads generated by the Illumina platform was too small to facilitate assembly of contigs without the use of a reference sequence, thus precluding detection of unknown viruses. When the virus load was sufficiently high, de novo assembly permitted the generation of long contigs corresponding to nearly full-length genomes and thus should facilitate the identification of novel viruses.
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.