{
  "abstract": "Influenza A viruses (IAV) remain a persistent One Health threat, and whole-genome sequencing from wastewater offers a promising surveillance tool. However, IAV is at low abundance in wastewater, making it difficult to sequence. We benchmark four targeted enrichment methods suited for multi-subtype whole-genome IAV sequencing including custom and off-the-shelf methods. Our custom HA tiled-amplicon panel is sensitive, fast, and cost-effective, making it suitable for monitoring low-abundance seasonal variants of known subtypes, although its reliance on conserved and intact primer-binding sites limits primer design to fewer subtypes. A published universal amplicon method targets all IAV subtypes but performs poorly in wastewater due to its reliance on intact genome segments. Meanwhile, probe-capture methods are resilient to RNA degradation. In real wastewater samples, our custom probe panel recovers whole-genome signals from circulating H1N1, H3N2, H5N1, including validated H5N1 2.3.4.4b reads in samples where dPCR detection is limited. However, probe-capture is generally more costly and labor-intensive than amplicon methods. Across all four sequencing methods, two wastewater matrices, and most spike-in and endogenous virus targets, ultrafiltration-based virus concentration consistently outperforms large-volume direct extraction. Together, these benchmarking comparisons and custom panels provide needed information for implementing IAV genomic sequencing in routine wastewater surveillance.",
  "abstract_shown": true,
  "affiliations": [],
  "article_type": null,
  "arxiv": null,
  "author_total": 6,
  "authors": [
    {
      "name": "Minxi Jiang",
      "orcid": "0000-0002-0796-2590"
    },
    {
      "name": "Audrey L. W. Wang"
    },
    {
      "name": "James B. Thissen"
    },
    {
      "name": "Kara L. Nelson"
    },
    {
      "name": "Lenore Pipes"
    },
    {
      "name": "Rose S. Kantor",
      "orcid": "0000-0002-5402-8979"
    }
  ],
  "bibtex": "https://research.draconitic.com/paper/8s34g4aj4c1xc.bib",
  "cited_by": 0,
  "doi": "10.1038/s41467-026-78683-7",
  "fulltext_url": null,
  "id": "8s34g4aj4c1xc",
  "issns": [
    "2041-1723"
  ],
  "landing_url": "https://www.nature.com/articles/s41467-026-78683-7",
  "language": null,
  "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": [
    [
      "openalex",
      "2713|Influenza Virus Research Studies"
    ]
  ],
  "openalex": "W7222818749",
  "pdf_url": "https://www.nature.com/articles/s41467-026-78683-7_reference.pdf",
  "pmcid": null,
  "pmid": null,
  "published": "2026-10-17",
  "publisher": "Springer Science and Business Media LLC",
  "ris": "https://research.draconitic.com/paper/8s34g4aj4c1xc.ris",
  "sources": [
    {
      "first_seen": "2026-10-30T12:17:39Z",
      "native_id": "10.1038/s41467-026-78683-7",
      "source": "crossref",
      "url": "https://www.nature.com/articles/s41467-026-78683-7"
    }
  ],
  "subjects": [
    {
      "field": "medicine",
      "origin": "openalex:2713|Influenza Virus Research Studies",
      "subfield": "epidemiology-public-health"
    }
  ],
  "title": "Developing and benchmarking one health genomic surveillance tools for influenza A virus in wastewater",
  "title_text": "Developing and benchmarking one health genomic surveillance tools for influenza A virus in wastewater",
  "type": "peer-reviewed",
  "updated_at": "2026-10-30T12:17:39Z",
  "url": "https://research.draconitic.com/paper/8s34g4aj4c1xc",
  "venue": "Nature Communications",
  "versions": []
}