ArticleViruses2021
Deep Impact of Random Amplification and Library Construction Methods on Viral Metagenomics Results.
Article in Viruses, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. It is linked to trial NCT05388968 (Pathogen Detection by Metatranscriptomic Next Generation Sequencing in the Trophoblast Collected in Women Carrying a Fetus With Increasing Nuchal Translucency in the First Trimester of Pregnancy), which is not on this map. Cited by 15 papers.
What it found
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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.
Pathogen Detection by Metatranscriptomic Next Generation Sequencing in the Trophoblast Collected in Women Carrying a Fetus With Increasing Nuchal Translucency in the First Trimester of Pregnancy
Who cites it
15 citing papers in PubMed, 28 citations in OpenAlex.
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- Highly Virulent Newcastle Disease Virus in Eurasian Collared Doves in the North of Portugal.Animals : an open access journal from MDPI · 2025Article
- Wastewater Metavirome Diversity: Exploring Replicate Inconsistencies and Bioinformatic Tool Disparities.International journal of environmental research and public health · 2025Article
- Broad range molecular detection methods identify onlyOne health (Amsterdam, Netherlands) · 2024Article
- Comparison of Three Viral Nucleic Acid Preamplification Pipelines for Sewage Viral Metagenomics.Food and environmental virology · 2024Article
- Metagenomic Analysis of Viromes ofViruses · 2024Article
- A primer-independent DNA polymerase-based method for competent whole-genome amplification of intermediate to high GC sequences.NAR genomics and bioinformatics · 2023Article
- Circovirus Hepatitis Infection in Heart-Lung Transplant Patient, France.Emerging infectious diseases · 2023Article
- Detection of Hepatitis E Virus Genotype 3 in Feces of Capybaras (Hydrochoeris hydrochaeris) in Brazil.Viruses · 2023Article
- The Emerging Role of the Gut Virome in Health and Inflammatory Bowel Disease: Challenges, Covariates and a Viral Imbalance.Viruses · 2023Review
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- RdRp-scan: A bioinformatic resource to identify and annotate divergent RNA viruses in metagenomic sequence data.Virus evolution · 2022Article
- NGSocomial Infections: High-Resolution Views of Hospital-Acquired Infections Through Genomic Epidemiology.Journal of the Pediatric Infectious Diseases Society · 2021Review
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 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Clinical metagenomics is a broad-range agnostic detection method of pathogens, including novel microorganisms. A major limit is the low pathogen load compared to the high background of host nucleic acids. To overcome this issue, several solutions exist, such as applying a very high depth of sequencing, or performing a relative enrichment of viral genomes associated with capsids. At the end, the quantity of total nucleic acids is often below the concentrations recommended by the manufacturers of library kits, which necessitates to random amplify nucleic acids. Using a pool of 26 viruses representative of viral diversity, we observed a deep impact of the nature of sample (total nucleic acids versus RNA only), the reverse transcription, the random amplification and library construction method on virus recovery. We further optimized the two most promising methods and assessed their performance with fully characterized reference virus stocks. Good genome coverage and limit of detection lower than 100 or 1000 genome copies per mL of plasma, depending on the genome viral type, were obtained from a three million reads dataset. Our study reveals that optimized random amplification is a technique of choice when insufficient amounts of nucleic acid are available for direct libraries constructions.
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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.