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Modern Molecular Taxonomy01:29

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Advancements in molecular biology have revolutionized the identification and characterization of bacteria, with multiple methods leveraging DNA sequencing for enhanced precision. As sequencing technologies improve and costs decline, these approaches are increasingly used in clinical, environmental, and evolutionary studies.Multilocus Sequence Typing (MLST) examines several housekeeping genes, essential chromosomal genes encoding cellular functions, to distinguish strains. Approximately...
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teamNGS Balances Sensitivity for Viruses with Comprehensive Microbial Detection in Clinical Specimens.

Julie Yamaguchi1,2, Gregory S Orf1,2, Jenna Malinauskas1,2

  • 1Infectious Disease Research, Abbott Laboratories, Abbott Park, IL 60064, USA.

Microorganisms
|December 31, 2025
PubMed
Summary

Target enrichment for viral metagenomic next-generation sequencing (mNGS) significantly boosts sensitivity and genome coverage. Combining target enrichment (teNGS) with mNGS into teamNGS streamlines workflows and improves viral and non-viral microbe recovery.

Keywords:
metagenomicsnext-generation sequencingtarget enrichmentvirus discovery

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Area of Science:

  • Virology
  • Genomics
  • Bioinformatics

Background:

  • Metagenomic next-generation sequencing (mNGS) faces challenges with host background interference and low viral detection sensitivity.
  • Probe-based capture offers a promising solution for enriching target nucleic acids in complex samples.

Purpose of the Study:

  • To develop and evaluate a highly sensitive and cost-effective method for viral detection in clinical specimens using mNGS.
  • To optimize target enrichment (teNGS) protocols and integrate them with standard mNGS workflows.

Main Methods:

  • Generated mNGS libraries using random priming and Nextera XT tagmentation from global clinical specimens.
  • Performed target enrichment (teNGS) using the Comprehensive Viral Research Panel (CVRP) probes.
  • Optimized capture pool sizes and sequencing depth, then combined teNGS and mNGS libraries into a single sequencing run (teamNGS).

Main Results:

  • teNGS achieved 100-10,000× increased depth and >50% genome coverage for viruses with titers ≥ 1000 cp/mL, using only 3-4% of standard mNGS reads.
  • teamNGS demonstrated improved genome recovery, maintaining viral sensitivity and coverage while ensuring comprehensive recovery of non-viral microbes.
  • The method detected diverse viral families and established a minimum 65% nucleotide identity for hybridization.

Conclusions:

  • teamNGS significantly enhances viral detection sensitivity and genome recovery in clinical samples.
  • This streamlined approach improves efficiency and has the potential to optimize patient management by reducing unnecessary testing and antibiotic use.