{
  "abstract": "Understanding the selective forces acting upon HIV early in infection is crucial to design prevention strategies. By leveraging deep sequencing and the short diagnostic intervals of the FRESH and RV217 cohorts between the last-negative and first-positive RNA tests (median 4 days), we captured a precise and early snapshot of acute HIV infection. The frequency of multiple transmitted viruses of 37% in these as well as placebo recipients from the AMP trials (NCT02716675 and NCT02568215) was higher than previously published, with the true frequency likely to be higher. The relative abundance of lineages fluctuated substantially over time in two-thirds of the multilineage infections, generating uncertainty in identifying the specific viruses that were transmitted and founding the infection. At the population level, viral populations exhibited limited diversity and selection on the Gag and Env proteins at the earliest times examined, with sites inferred to be undergoing negative selection most evident. These data may help explain vaccination failures and provide new targets for prevention.",
  "abstract_shown": true,
  "affiliations": [
    "Department of Microbiology, University of Washington, Seattle, WA, USA. jmullins@uw.edu",
    "University of Washington",
    "Department of Microbiology, University of Washington, Seattle, WA, USA",
    "Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA, USA",
    "Fred Hutchinson Cancer Center",
    "Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc, Bethesda, MD, USA",
    "U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD, USA",
    "Henry M. Jackson Foundation for the Advancement of Military Medicine,",
    "Santa Fe Institute, Santa Fe, NM, USA",
    "Theoretical Division, Los Alamos National Laboratory, Los Alamos, NM, USA",
    "Los Alamos National Laboratory",
    "Institute of Infectious Diseases and Molecular Medicine, Division of Medical Virology, University of Cape Town, Cape Town, South Africa",
    "Sand Technologies, Cape Town, South Africa",
    "University of Cape Town",
    "Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden",
    "Karolinska Institutet",
    "African Health Research Institute, University of KwaZulu Natal, Durban, South Africa",
    "Division of Infection and Immunity, University College London, London, UK",
    "HIV Pathogenesis Programme, The Doris Duke Medical Research Institute, University of KwaZulu-Natal, Durban, South Africa",
    "Ragon Institute of Mass General Brigham, Massachusetts Institute of Technology and Harvard University, Cambridge, MA, USA",
    "University of KwaZulu Natal",
    "Henry M. Jackson Foundation for the Advancement of Military Medicine",
    "Ragon Institute of Mass General Brigham",
    "Department of Obstetrics and Gynecology, University of Washington, Seattle, WA, USA",
    "Kenya Medical Research Institute",
    "Armed Forces Research Institute of Medical Sciences",
    "Henry M. Jackson Foundation Medical Research International, Nairobi, Kenya",
    "Kenya Medical Research Institute, Walter Reed Army Institute of Research-Africa, Nairobi, Kenya",
    "Armed Forces Research Institute of Medical Sciences, Bangkok, Thailand",
    "Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA",
    "University of North Carolina",
    "University of North Carolina, Chapel Hill, NC, USA",
    "National Health Laboratory Services, Johannesburg, South Africa"
  ],
  "article_type": null,
  "arxiv": null,
  "author_total": 35,
  "authors": [
    {
      "affs": [
        0,
        1
      ],
      "name": "James I. Mullins",
      "orcid": "0000-0002-4461-8158"
    },
    {
      "affs": [
        2,
        3,
        1
      ],
      "name": "Wenjie Deng",
      "orcid": "0000-0001-7567-4489"
    },
    {
      "affs": [
        3,
        4
      ],
      "name": "Elena E. Giorgi",
      "orcid": "0000-0003-2968-1033"
    },
    {
      "affs": [
        3,
        4
      ],
      "name": "Craig A. Magaret",
      "orcid": "0000-0002-5056-2664"
    },
    {
      "affs": [
        5,
        6,
        7
      ],
      "name": "Morgane Rolland",
      "orcid": "0000-0003-3650-8490"
    },
    {
      "affs": [
        8,
        9,
        10
      ],
      "name": "Tanmoy Bhattacharya A",
      "orcid": "0000-0002-1060-652X"
    },
    {
      "affs": [
        2,
        3,
        1
      ],
      "name": "Dylan H. Westfall",
      "orcid": "0000-0002-2434-8525"
    },
    {
      "affs": [
        11,
        12,
        13
      ],
      "name": "Anna Yssel",
      "orcid": "0000-0003-1165-3237"
    },
    {
      "affs": [
        2,
        1
      ],
      "name": "Roger E. Bumgarner",
      "orcid": "0000-0002-8168-6985"
    },
    {
      "affs": [
        14,
        15
      ],
      "name": "Ben Murrell",
      "orcid": "0000-0002-0393-4445"
    },
    {
      "affs": [
        16,
        17,
        18,
        19,
        20
      ],
      "name": "Thumbi Ndung’u",
      "orcid": "0000-0003-2962-3992"
    },
    {
      "affs": [
        5,
        21
      ],
      "name": "Merlin Lee Robb",
      "orcid": "0000-0003-3949-9649"
    },
    {
      "affs": [
        3,
        4
      ],
      "name": "Raabya Rossenkhan",
      "orcid": "0009-0005-5907-8325"
    },
    {
      "affs": [
        3,
        4
      ],
      "name": "Paul T. Edlefsen",
      "orcid": "0000-0002-8393-8103"
    },
    {
      "affs": [
        19,
        22
      ],
      "name": "Krista L. Dong",
      "orcid": "0000-0002-2038-3518"
    },
    {
      "affs": [
        2,
        1
      ],
      "name": "Lennie Chen"
    },
    {
      "affs": [
        11,
        13
      ],
      "name": "Asanda Gwashu-Nyangiri"
    },
    {
      "affs": [
        2,
        23,
        1
      ],
      "name": "Hong Zhao",
      "orcid": "0000-0003-1325-2701"
    },
    {
      "affs": [
        11,
        13
      ],
      "name": "Ruwayhida Thebus"
    },
    {
      "affs": [
        11,
        24
      ],
      "name": "Nonkululeko Ndabambi"
    },
    {
      "affs": [
        11,
        25
      ],
      "name": "Bruna Galvão",
      "orcid": "0009-0007-9189-1521"
    },
    {
      "affs": [
        26,
        27,
        13
      ],
      "name": "Fredrick Sawe"
    },
    {
      "affs": [
        28,
        13
      ],
      "name": "Sorachai Nitayaphan",
      "orcid": "0000-0001-6935-1405"
    },
    {
      "affs": [
        11,
        13
      ],
      "name": "Talita York",
      "orcid": "0000-0003-2884-3010"
    },
    {
      "affs": [
        11,
        1
      ],
      "name": "David Matten",
      "orcid": "0000-0003-1085-4344"
    },
    {
      "affs": [
        11,
        4
      ],
      "name": "Hugh Murrell",
      "orcid": "0000-0002-6185-9885"
    },
    {
      "affs": [
        29,
        2,
        4
      ],
      "name": "Alec P. Pankow",
      "orcid": "0000-0001-9108-1683"
    },
    {
      "affs": [
        3,
        4
      ],
      "name": "Michal Juraska",
      "orcid": "0000-0002-0920-2915"
    },
    {
      "affs": [
        3,
        30
      ],
      "name": "James Ludwig",
      "orcid": "0000-0003-3500-3490"
    },
    {
      "affs": [
        3,
        4
      ],
      "name": "John Hural",
      "orcid": "0000-0002-5382-9774"
    },
    {
      "affs": [
        31,
        4
      ],
      "name": "Myron S. Cohen",
      "orcid": "0000-0001-5917-9664"
    },
    {
      "affs": [
        3,
        4
      ],
      "name": "Lawrence Corey",
      "orcid": "0000-0002-2179-2436"
    },
    {
      "affs": [
        3,
        13
      ],
      "name": "M. Juliana McElrath",
      "orcid": "0000-0003-2276-7117"
    },
    {
      "affs": [
        3
      ],
      "name": "Peter B. Gilbert",
      "orcid": "0000-0002-2662-9427"
    },
    {
      "affs": [
        11,
        32
      ],
      "name": "Carolyn E. Williamson",
      "orcid": "0000-0003-0125-1226"
    }
  ],
  "bibtex": "https://research.draconitic.com/paper/40xwbqnh6hg3f.bib",
  "cited_by": 7,
  "doi": "10.1038/s41467-026-73496-0",
  "fulltext_url": null,
  "id": "40xwbqnh6hg3f",
  "issns": [
    "2041-1723"
  ],
  "landing_url": "https://doi.org/10.1038/s41467-026-73496-0",
  "language": "en",
  "licence": "CC-BY",
  "licence_label": "CC BY",
  "licence_source": "journal",
  "licence_url": "https://creativecommons.org/licenses/by/4.0/",
  "metadata_licence": null,
  "native_subjects": [
    [
      "openalex",
      "2406|HIV Research and Treatment"
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  ],
  "openalex": "W4415235220",
  "pdf_url": "https://www.nature.com/articles/s41467-026-73496-0_reference.pdf",
  "pmcid": "PMC12632927",
  "pmid": "41279611",
  "published": "2026-05-25",
  "publisher": "Nature Portfolio",
  "ris": "https://research.draconitic.com/paper/40xwbqnh6hg3f.ris",
  "sources": [
    {
      "first_seen": "2026-10-30T13:26:51Z",
      "native_id": "W4415235220",
      "source": "openalex",
      "url": "https://doi.org/10.1038/s41467-026-73496-0"
    }
  ],
  "subjects": [
    {
      "field": "biology",
      "origin": "openalex:2406|HIV Research and Treatment",
      "subfield": "microbiology"
    }
  ],
  "title": "Long-read deep sequencing reveals high rates of multilineage transmission and rapid viral population changes in acute HIV infection",
  "title_text": "Long-read deep sequencing reveals high rates of multilineage transmission and rapid viral population changes in acute HIV infection",
  "type": "peer-reviewed",
  "updated_at": "2026-11-09T13:21:11Z",
  "url": "https://research.draconitic.com/paper/40xwbqnh6hg3f",
  "venue": "Nature Communications",
  "versions": []
}