ArticleVirus evolution2024
A tale of caution: How endogenous viral elements affect virus discovery in transcriptomic data.
Article in Virus evolution, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 11 papers.
What it found
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Who cites it
11 citing papers in PubMed, 14 citations in OpenAlex.
- RdRpCATCH: a unified resource for RNA virus discovery using viral RNA-dependent RNA polymerase profile Hidden Markov models.NAR genomics and bioinformatics · 2026Article
- Viral metagenome characterization reveals species-specific virome profiles in Triatominae populations from the southern United States.PLoS neglected tropical diseases · 2026Article
- Metaviromic insights into the viral community associated with Dendrobium catenatum.Brazilian journal of microbiology : [publication of the Brazilian Society for Microbiology] · 2026Article
- Complete genome sequence of a novel mitovirus isolated from the fungus Phomopsis asparagi.Archives of virology · 2026Article
- Not an infection: Endogenous circoviral elements underlie BFDV detections in Old World vultures.PloS one · 2026Article
- Unravelling viral identity: avoiding the trap of endogenous sequences for viral surveillance of small ruminant oncogenic retroviruses.Virus evolution · 2026Article
- detectEVE: Fast, Sensitive and Precise Detection of Endogenous Viral Elements in Genomic Data.Molecular ecology resources · 2025Article
- Exploring the potential of tick transcriptomes for virus screening: A data reuse approach for tick-borne virus surveillance.PLoS neglected tropical diseases · 2025Article
- Metagenomic analysis evidences a core virome in Anopheles darlingi from three contrasting Colombian ecoregions.PloS one · 2025Article
- A novel approach to exploring the dark genome and its application to mapping of the vertebrate virus fossil record.Genome biology · 2024Article
- Endogenous viral elements: insights into data availability and accessibility.Virus evolution · 2024Article
Corrections and comments
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Authors and funding
6 authors at 2 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Large-scale metagenomic and -transcriptomic studies have revolutionized our understanding of viral diversity and abundance. In contrast, endogenous viral elements (EVEs), remnants of viral sequences integrated into host genomes, have received limited attention in the context of virus discovery, especially in RNA-Seq data. EVEs resemble their original viruses, a challenge that makes distinguishing between active infections and integrated remnants difficult, affecting virus classification and biases downstream analyses. Here, we systematically assess the effects of EVEs on a prototypical virus discovery pipeline, evaluate their impact on data integrity and classification accuracy, and provide some recommendations for better practices. We examined EVEs and exogenous viral sequences linked to
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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.