{
  "abstract": "Pathogen genomic analysis is central to tracking, understanding and containing outbreaks1–13, but the complexity and cost of state-of-the-art phylogenetic tools limit global access and impact. Here we introduce Delphy, an exact reformulation of Bayesian phylogenetics14–17 designed to transform its speed, scalability and accessibility while retaining Bayesian state-of-the-art accuracy. Delphy’s central data structure, an explicit mutation-annotated tree, takes advantage of the high sequence similarity of large-scale epidemic datasets18–20 for efficient tree exploration and convergence. By reproducing key analyses from recent major epidemics, including Ebola1,21, Zika2, SARS-CoV-2 (ref. 22), mpox3,4 and H5N1 (refs. 23,24), we demonstrate state-of-the-art accuracy with up to 2–3 orders of magnitude improvements in speed. Assessing Delphy’s scalability, we show that a simulated dataset of 100,000 sequences can be analysed within a day. We distribute Delphy as a client-side web application that enables local, interactive analysis of raw data on the user’s machine. Delphy automatically identifies key viral lineages and mutations, as well as their emergence and prevalence through time, with quantified uncertainties grounded in Bayesian theory. Delphy establishes Bayesian phylogenetics as a fast, accessible frontline tool for future outbreak response. Delphy makes near-real-time and scalable Bayesian phylogenetics possible for growing viral outbreaks, enabling public health bodies anywhere to analyse and react to their own data with state-of-the-art accuracy and minimal friction.",
  "abstract_shown": true,
  "affiliations": [
    "Broad Institute of Harvard and MIT, Cambridge, MA, USA. pvarilly@broadinstitute.org",
    "Fathom Information Design, Boston, MA, USA",
    "Broad Institute of Harvard and MIT, Cambridge, MA, USA",
    "Institute for Computational and Mathematical Engineering, School of Engineering, Stanford University, Stanford, CA, USA",
    "The Institute of Genomics and Global Health, Redeemer's University, Ede, Nigeria",
    "Department of Parasitology and Entomology, Nnamdi Azikiwe University, Awka, Nigeria",
    "Institute of Ecology and Evolution, University of Edinburgh, Edinburgh, UK",
    "Department of Organismic and Evolutionary Biology, Faculty of Arts and Sciences, Harvard University, Cambridge, MA, USA",
    "Eric and Wendy Schmidt Center, Broad Institute of Harvard and MIT, Cambridge, MA, USA",
    "FutureHouse, San Francisco, CA, USA",
    "Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA",
    "Scripps Research Translational Institute, La Jolla, CA, USA",
    "Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Harvard University, Boston, MA, USA",
    "Massachusetts Consortium on Pathogen Readiness, Harvard Medical School, Harvard University, Boston, MA, USA",
    "Department of Biological Sciences, Faculty of Natural Sciences, Redeemer's University, Ede, Nigeria",
    "Department of Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA",
    "Department of Pediatrics, Harvard Medical School, Boston, MA, USA",
    "Department of Computer Science, School of Engineering and Applied Sciences, Harvard University, Boston, MA, USA",
    "Broad Institute of Harvard and MIT, Cambridge, MA, USA. pardis@broadinstitute.org",
    "Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Harvard University, Boston, MA, USA. pardis@broadinstitute.org",
    "Department of Organismic and Evolutionary Biology, Faculty of Arts and Sciences, Harvard University, Cambridge, MA, USA. pardis@broadinstitute.org",
    "Howard Hughes Medical Institute, Chevy Chase, MD, USA. pardis@broadinstitute.org",
    "Massachusetts Consortium on Pathogen Readiness, Harvard Medical School, Harvard University, Boston, MA, USA. pardis@broadinstitute.org"
  ],
  "article_type": null,
  "arxiv": null,
  "author_total": 27,
  "authors": [
    {
      "affs": [
        0
      ],
      "name": "Patrick Varilly",
      "orcid": "0000-0003-4619-8174"
    },
    {
      "affs": [
        1
      ],
      "name": "Mark Schifferli",
      "orcid": "0000-0001-7906-6042"
    },
    {
      "affs": [
        1
      ],
      "name": "Katherine Yang"
    },
    {
      "affs": [
        1
      ],
      "name": "Paul Cronan"
    },
    {
      "affs": [
        2,
        3
      ],
      "name": "Ivan Specht",
      "orcid": "0000-0003-2834-8191"
    },
    {
      "affs": [
        1
      ],
      "name": "Timothy Burcham",
      "orcid": "0009-0009-6246-1367"
    },
    {
      "affs": [
        1
      ],
      "name": "Olivia Glennon",
      "orcid": "0009-0009-4157-9913"
    },
    {
      "affs": [
        1
      ],
      "name": "Olivia Jacks"
    },
    {
      "affs": [
        1
      ],
      "name": "Ellory Laning"
    },
    {
      "affs": [
        1
      ],
      "name": "Libby Marrs"
    },
    {
      "affs": [
        1
      ],
      "name": "Kyle Oba",
      "orcid": "0000-0001-6879-9013"
    },
    {
      "affs": [
        1
      ],
      "name": "Shannon Yeung"
    },
    {
      "affs": [
        1
      ],
      "name": "Karlie Wenran Zhao"
    },
    {
      "affs": [
        4
      ],
      "name": "Edyth Parker",
      "orcid": "0000-0001-8312-1446"
    },
    {
      "affs": [
        5,
        6
      ],
      "name": "Ifeanyi F. Omah",
      "orcid": "0000-0002-9044-3096"
    },
    {
      "affs": [
        6
      ],
      "name": "Jonathan E. Pekar",
      "orcid": "0000-0003-0977-2886"
    },
    {
      "affs": [
        7,
        8,
        9
      ],
      "name": "Laura Luebbert",
      "orcid": "0000-0003-1379-2927"
    },
    {
      "affs": [
        10,
        11
      ],
      "name": "Kristian G. Andersen",
      "orcid": "0000-0001-6431-5982"
    },
    {
      "affs": [
        2
      ],
      "name": "Daniel J. Park",
      "orcid": "0000-0001-7226-7781"
    },
    {
      "affs": [
        2,
        12
      ],
      "name": "Stephen F. Schaffner",
      "orcid": "0000-0001-6699-3568"
    },
    {
      "affs": [
        2,
        12,
        13
      ],
      "name": "Bronwyn L. MacInnis",
      "orcid": "0000-0003-0082-968X"
    },
    {
      "affs": [
        14,
        12,
        4
      ],
      "name": "Christian Tientcha Happi",
      "orcid": "0000-0002-3056-6705"
    },
    {
      "affs": [
        2,
        15
      ],
      "name": "Jacob E. Lemieux",
      "orcid": "0000-0002-2758-4005"
    },
    {
      "affs": [
        2,
        16
      ],
      "name": "Al Ozonoff",
      "orcid": "0000-0003-4233-5899"
    },
    {
      "affs": [
        17
      ],
      "name": "Michael Mitzenmacher",
      "orcid": "0000-0001-5430-5457"
    },
    {
      "affs": [
        1
      ],
      "name": "Ben Fry",
      "orcid": "0000-0002-6414-5570"
    },
    {
      "affs": [
        18,
        19,
        20,
        21,
        22
      ],
      "name": "Pardis Christine Sabeti",
      "orcid": "0000-0002-9843-1890"
    }
  ],
  "bibtex": "https://research.draconitic.com/paper/35pa3a9jeb8xj.bib",
  "cited_by": 10,
  "doi": "10.1038/s41586-026-11012-6",
  "fulltext_url": null,
  "id": "35pa3a9jeb8xj",
  "issns": [
    "0028-0836",
    "1476-4687"
  ],
  "landing_url": "https://doi.org/10.1038/s41586-026-11012-6",
  "language": "en",
  "licence": "CC-BY-NC-ND",
  "licence_label": "CC BY-NC-ND",
  "licence_source": "journal",
  "licence_url": "https://creativecommons.org/licenses/by-nc-nd/4.0/",
  "metadata_licence": null,
  "native_subjects": [
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      "1312|Genomics and Phylogenetic Studies"
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  "openalex": "W7213428392",
  "pdf_url": "https://www.nature.com/articles/s41586-026-11012-6.pdf",
  "pmcid": "PMC13668698",
  "pmid": "42749814",
  "published": "2026-09-16",
  "publisher": "Nature Portfolio",
  "ris": "https://research.draconitic.com/paper/35pa3a9jeb8xj.ris",
  "sources": [
    {
      "first_seen": "2026-11-04T13:21:07Z",
      "native_id": "W7213428392",
      "source": "openalex",
      "url": "https://doi.org/10.1038/s41586-026-11012-6"
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  "subjects": [
    {
      "field": "biochemistry",
      "origin": "openalex:1312|Genomics and Phylogenetic Studies",
      "subfield": "molecular-biology"
    }
  ],
  "title": "Scalable near-real-time Bayesian phylogenetics for outbreaks with Delphy",
  "title_text": "Scalable near-real-time Bayesian phylogenetics for outbreaks with Delphy",
  "type": "peer-reviewed",
  "updated_at": "2026-11-09T13:21:07Z",
  "url": "https://research.draconitic.com/paper/35pa3a9jeb8xj",
  "venue": "Nature",
  "versions": []
}