{
  "abstract": "Background Hybrid-capture viral metagenomics improves sensitivity over untargeted metagenomics, but its performance across sequencing platforms and the definition of data-driven analysis cut-offs using real clinical samples have not been systematically evaluated. This study benchmarks the hybrid-capture workflow on mock and clinical specimens across short- and long-read platforms while introducing a new, reproducible approach for setting pathogen-calling cut-offs. Methods The Twist Comprehensive Viral Research Panel was used with both AVITI short-read and Oxford Nanopore Technologies (ONT) long-read sequencing on 12 mock cerebrospinal fluid (CSF) external quality assessment (EQA) panel samples and on 14 CSF and 21 bronchoalveolar lavage (BAL) clinical specimens. Data-driven cut-offs for pathogen calling were derived using Latin hypercube sampling across genome coverage, abundance, and bleed-ratio parameters, then validated on the independent EQA datasets. Results After cut-off application, both platforms detected 22 of 23 expected viral targets in EQA samples (95.7% detection-level sensitivity) with 100% specificity in negative controls. In clinical specimens, AVITI corroborated 26 of 30 (86.7%) and ONT 25 of 30 (83.3%) routine viral detections while maintaining 100% diagnostic specificity. Sensitivity was 100% for CSF but lower in BAL, particularly for low viral load targets, and all detections below a Cq value of 32 were identified by both platforms. Metagenomics also identified a potentially clinically relevant pathogen not tested by routine testing in two CSF samples. Conclusion Hybrid-capture viral metagenomics performed comparably on AVITI and ONT for routine viral targets, with AVITI showing slightly higher genome recovery. In addition, the newly developed data-driven cut-off selection strategy offers a practical, reproducible method other laboratories can apply to their own workflows.",
  "abstract_shown": true,
  "affiliations": [
    "Laboratory of Clinical and Epidemiological Virology, Rega Institute, KU Leuven"
  ],
  "article_type": "PUBLISHAHEADOFPRINT",
  "arxiv": null,
  "author_total": 11,
  "authors": [
    {
      "affs": [
        0
      ],
      "name": "M. Karatas"
    },
    {
      "name": "L. Cuypers"
    },
    {
      "name": "L. Laenen"
    },
    {
      "name": "M. Bloemen"
    },
    {
      "name": "A. Rector"
    },
    {
      "name": "J. Maes"
    },
    {
      "name": "M. Vanrenterghem"
    },
    {
      "name": "M. Van Ranst"
    },
    {
      "name": "E. Wollants"
    },
    {
      "name": "S. Desmet"
    },
    {
      "name": "J. Matthijnssens"
    }
  ],
  "bibtex": "https://research.draconitic.com/paper/6twe7vgd781bh.bib",
  "cited_by": 0,
  "doi": "10.64898/2026.10.27.26366582",
  "fulltext_url": "https://www.medrxiv.org/content/10.64898/2026.10.27.26366582v1.full",
  "id": "6twe7vgd781bh",
  "issns": [],
  "landing_url": "https://www.medrxiv.org/content/10.64898/2026.10.27.26366582v1",
  "language": null,
  "licence": "CC-BY",
  "licence_label": "CC BY",
  "licence_source": "article",
  "licence_url": "https://creativecommons.org/licenses/by/4.0/",
  "metadata_licence": null,
  "native_subjects": [
    [
      "medrxiv",
      "infectious diseases"
    ]
  ],
  "openalex": null,
  "pdf_url": "https://www.medrxiv.org/content/10.64898/2026.10.27.26366582v1.full.pdf",
  "pmcid": null,
  "pmid": null,
  "published": "2026-10-27",
  "publisher": null,
  "ris": "https://research.draconitic.com/paper/6twe7vgd781bh.ris",
  "sources": [
    {
      "first_seen": "2026-10-30T12:22:04Z",
      "native_id": "10.64898/2026.10.27.26366582",
      "source": "medrxiv",
      "url": "https://www.medrxiv.org/content/10.64898/2026.10.27.26366582v1"
    }
  ],
  "subjects": [
    {
      "field": "medicine",
      "origin": "medrxiv:infectious diseases",
      "subfield": "infectious-disease"
    }
  ],
  "title": "Short- and long-read hybrid-capture viral metagenomics reach high sensitivity and specificity with data-driven cut-offs compared with routine diagnostics in CSF and BAL specimens",
  "title_text": "Short- and long-read hybrid-capture viral metagenomics reach high sensitivity and specificity with data-driven cut-offs compared with routine diagnostics in CSF and BAL specimens",
  "type": "preprint",
  "updated_at": "2026-10-31T00:20:38Z",
  "url": "https://research.draconitic.com/paper/6twe7vgd781bh",
  "venue": "medRxiv",
  "versions": []
}