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Related Concept Videos

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RNA sequencing, or RNA-Seq, is a high-throughput sequencing technology used to study the transcriptome of a cell. Transcriptomics helps to interpret the functional elements of a genome and identify the molecular constituents of an organism. Additionally, it also helps in understanding the development of an organism and the occurrence of diseases. 
Before the discovery of RNA-seq, microarray-based methods and Sanger sequencing were used for transcriptome analysis. However, while...
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Enriched Long-Read Sequencing of Co-circulating Viruses in Complex Samples.

Mariana Meneguzzi1, Jonathan Bravo2, Tara N Gaire3

  • 1Department of Veterinary Population Medicine, College of Veterinary Medicine, University of Minnesota, 1333 Gortner Avenue, St. Paul, MN 55108, USA.

Molecular Biology and Evolution
|October 15, 2025
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Summary
This summary is machine-generated.

A new workflow, TELSVirus, enables rapid detection and genomic analysis of multiple viruses in single samples using long-read sequencing. This method improves upon traditional techniques for viral surveillance and characterization.

Keywords:
long-readminionprobe-capturetarget enrichmentviruses

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Area of Science:

  • Virology
  • Genomics
  • Bioinformatics

Background:

  • Current workflows lack efficiency for simultaneous identification and analysis of diverse viral genomes in complex samples, especially with long-read sequencing.
  • Accurate viral identification is crucial for diagnostics, surveillance, and understanding viral ecosystems.

Purpose of the Study:

  • To develop and validate a novel workflow, TELSVirus, for rapid, accurate, and comprehensive identification and genomic analysis of multiple viruses in single samples.
  • To assess the performance of TELSVirus compared to traditional methods like real-time reverse transcription polymerase chain reaction (rRT-PCR) and shotgun metagenomics.

Main Methods:

  • Developed TELSVirus by combining targeted enrichment with long-read, real-time sequencing using a probe panel for 16,069 viral genomes.
  • Validated the workflow on complex swine sample matrices, including serial dilutions, and compared results with rRT-PCR and shotgun metagenomics.
  • Applied TELSVirus to 144 field-collected swine oral fluid samples for viral surveillance.

Main Results:

  • TELSVirus successfully generated viral reads for dilutions up to 10⁻⁹, demonstrating high sensitivity.
  • The workflow detected viral targets missed by shotgun metagenomics and when rRT-PCR results were undetermined.
  • Analysis of swine oral fluids revealed high prevalence of understudied co-circulating viruses, with TELSVirus providing ultra-deep genome coverage.

Conclusions:

  • TELSVirus offers a significant advancement for rapid detection and genomic characterization of multiple low-abundance viruses from single samples using long-read sequencing.
  • The workflow shows promise for viral surveillance and epidemiological investigations, though bioinformatic analysis methods require further development.
  • TELSVirus enhances the ability to study complex viral communities and discover novel or understudied viruses.