ArticleJournal of clinical microbiology2018
Detection of Viruses in Clinical Samples by Use of Metagenomic Sequencing and Targeted Sequence Capture.
Article in Journal of clinical microbiology, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 29 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
29 citing papers in PubMed, 59 citations in OpenAlex.
- Association of the eukaryotic vaginal virome with prophylactic antibiotic exposure and reproductive outcomes in a subfertile population undergoing in vitro fertilisation: a prospective exploratory study.BJOG : an international journal of obstetrics and gynaecology · 2020Trial
- One health viral metagenomics for pathogen surveillance: robust mNGS workflows for viral detection and genome recovery from swab and tissue specimens.BMC microbiology · 2026Article
- teamNGS Balances Sensitivity for Viruses with Comprehensive Microbial Detection in Clinical Specimens.Microorganisms · 2025Article
- Methods, applications, and computational challenges in bait capture enrichment.Cell reports methods · 2025Review
- Complete genomic characterization of global pathogens respiratory syntical virus and human norovirus using probe based capture enrichment.Scientific reports · 2025Article
- Empirical assessment of the enrichment-based metagenomic methods in identifying diverse respiratory pathogens.Scientific reports · 2024Article
- MetaAll: integrative bioinformatics workflow for analysing clinical metagenomic data.Briefings in bioinformatics · 2024Article
- Evaluating metagenomics and targeted approaches for diagnosis and surveillance of viruses.Genome medicine · 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
- Metagenomic Analysis of DNA Viruses with Targeted Sequence Capture of Canine Lobular Orbital Adenomas and Normal Conjunctiva.Microorganisms · 2023Article
- Virome Analysis and Association of Positive Coxsackievirus B Serology during Pregnancy with Congenital Heart Disease.Microorganisms · 2023Article
- The plasma virome in longitudinal samples from pregnant patients.Frontiers in cellular and infection microbiology · 2023Article
- Article
- A Case of Persistent Human Pegivirus Infection in Two Separate Pregnancies of a Woman.Microorganisms · 2022Article
- Assessment of Rapid MinION Nanopore DNA Virus Meta-Genomics Using Calves Experimentally Infected with Bovine Herpes Virus-1.Viruses · 2022Article
- Progress in COVID research and developments during pandemic.View (Beijing, China) · 2022Review
- Novel Biorecognition Elements against Pathogens in the Design of State-of-the-Art Diagnostics.Biosensors · 2021Review
- ViroMatch: A Computational Pipeline for the Detection of Viral Sequences from Complex Metagenomic Data.Microbiology resource announcements · 2021Article
- Contamination Issue in Viral Metagenomics: Problems, Solutions, and Clinical Perspectives.Frontiers in microbiology · 2021Review
- Assessment of Viral Targeted Sequence Capture Using Nanopore Sequencing Directly from Clinical Samples.Viruses · 2020Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
6 authors at 2 institutions in 1 country.
Funding
Abstract
Metagenomic shotgun sequencing (MSS) is a revolutionary approach to viral diagnostic testing that allows simultaneous detection of a broad range of viruses, detailed taxonomic assignment, and detection of mutations associated with antiviral drug resistance. To enhance sensitivity for virus detection, we previously developed ViroCap, a targeted sequence capture panel designed to enrich nucleic acid from a comprehensive set of eukaryotic viruses prior to sequencing. To demonstrate the utility of MSS with targeted sequence capture for detecting clinically important viruses and characterizing clinically important viral features, we used ViroCap to analyze clinical samples from a diagnostic virology laboratory containing a broad range of medically relevant viruses. From 26 samples, MSS with ViroCap detected all of the expected viruses and 30 additional viruses. Comparing sequencing after capture enrichment with standard MSS, we detected 13 viruses only with capture enrichment and observed a consistent increase in the number and percentage of viral sequence reads as well as the breadth and depth of coverage of the viral genomes. Compared with clinical testing, MSS enhanced taxonomic assignment for 15 viruses, and codons associated with antiviral drug resistance in influenza A virus, herpes simplex virus (HSV), human immunodeficiency virus (HIV), and hepatitis C virus (HCV) could be analyzed. Overall, in clinical samples, MSS with targeted sequence capture provides enhanced virus detection and information of clinical and epidemiologic relevance compared with clinical testing and MSS without targeted sequence capture.
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.