{
  "abstract": "Respiratory viruses are major contributors to global morbidity and mortality. When viral mutations compromise detection by conventional diagnostic assays, identifying cases and tracing transmission becomes challenging. Whole genome sequencing (WGS) improves on conventional diagnostics as it can detect viruses with novel mutations. This study evaluated the performance of the ePlex, a rapid multiplex polymerase chain reaction (PCR) assay (RMPA), an in-house real-time reverse transcription PCR assay (RT-qPCR) and WGS for detecting respiratory virus infections in clinical specimens. Sixty-one sequence libraries were prepared, and bait enriched from nasopharyngeal swabs, collected in 2021, which were negative for SARS-CoV-2 but positive for co-infections of respiratory viruses detected by the ePlex. An in-house bioinformatics pipeline enabled a metagenomic analysis approach to be compared with the ePlex and RT-qPCR. In most swabs, respiratory viruses were detected by WGS (average genome recovery: 85.9%) or RT-qPCR which concurred with the ePlex result, but as single viruses rather than co-infections. WGS recovered respiratory syncytial viruses (80%) and metapneumoviruses (70%) most often. This study demonstrates the power of WGS and bait capture in resolving the genomes of respiratory pathogens from limited clinical material. Detection of a single virus, rather than co-infections, in this instance could highlight the targeted nature of bait capture technology or competition between viruses during bait hybridization. The number of respiratory syncytial viruses detected (16/20) could be due to a spike in activity detected after the alleviation of non-pharmaceutical interventions in the COVID-19 pandemic.",
  "abstract_shown": true,
  "affiliations": [
    "Virus Reference Department, UKHSA",
    "South London Specialist Virology Centre, King’s College Hospital NHS Foundation Trust"
  ],
  "article_type": null,
  "arxiv": null,
  "author_total": 9,
  "authors": [
    {
      "affs": [
        0
      ],
      "name": "Daniel Kelly"
    },
    {
      "affs": [
        0
      ],
      "name": "Ketharani Yogananthan"
    },
    {
      "affs": [
        0
      ],
      "name": "Priya Subramaniam"
    },
    {
      "affs": [
        0
      ],
      "name": "Tiina Talts"
    },
    {
      "affs": [
        0
      ],
      "name": "Carmen F. Manso"
    },
    {
      "affs": [
        0
      ],
      "name": "Beatrix Kele"
    },
    {
      "affs": [
        0
      ],
      "name": "David F. Bibby"
    },
    {
      "affs": [
        1
      ],
      "name": "Mark Zuckerman"
    },
    {
      "affs": [
        0
      ],
      "name": "Jean L. Mbisa"
    }
  ],
  "bibtex": "https://research.draconitic.com/paper/7gvjqcmpqh9th.bib",
  "cited_by": 0,
  "doi": "10.3389/fmicb.2026.1964559",
  "fulltext_url": "https://www.frontiersin.org/articles/10.3389/fmicb.2026.1964559/full",
  "id": "7gvjqcmpqh9th",
  "issns": [
    "1664-302X"
  ],
  "landing_url": "https://www.frontiersin.org/articles/10.3389/fmicb.2026.1964559/full",
  "language": "en",
  "licence": "CC-BY-4.0",
  "licence_label": "CC BY 4.0",
  "licence_source": "article",
  "licence_url": "https://creativecommons.org/licenses/by/4.0/",
  "metadata_licence": null,
  "native_subjects": [
    [
      "lcc",
      "QR1-502"
    ],
    [
      "openalex",
      "2713|Respiratory viral infections research"
    ]
  ],
  "openalex": "W7223269406",
  "pdf_url": "https://www.frontiersin.org/journals/microbiology/articles/10.3389/fmicb.2026.1964559/pdf",
  "pmcid": null,
  "pmid": null,
  "published": "2026-10-23",
  "publisher": "Frontiers Media SA",
  "ris": "https://research.draconitic.com/paper/7gvjqcmpqh9th.ris",
  "sources": [
    {
      "first_seen": "2026-10-30T12:19:12Z",
      "native_id": "10.3389/fmicb.2026.1964559",
      "source": "crossref",
      "url": "https://www.frontiersin.org/articles/10.3389/fmicb.2026.1964559/full"
    },
    {
      "first_seen": "2026-10-30T13:43:48Z",
      "native_id": "c53dd5741da943ceab0c521529ad7b35",
      "source": "doaj",
      "url": "https://doi.org/10.3389/fmicb.2026.1964559"
    }
  ],
  "subjects": [
    {
      "field": "medicine",
      "origin": "openalex:2713|Respiratory viral infections research",
      "subfield": "epidemiology-public-health"
    }
  ],
  "title": "Evaluation of whole genome sequencing protocols and target-capture panels for detection of respiratory viruses in clinical specimens",
  "title_text": "Evaluation of whole genome sequencing protocols and target-capture panels for detection of respiratory viruses in clinical specimens",
  "type": "peer-reviewed",
  "updated_at": "2026-10-30T13:43:48Z",
  "url": "https://research.draconitic.com/paper/7gvjqcmpqh9th",
  "venue": "Frontiers in Microbiology",
  "versions": []
}