{
  "abstract": "Predicting viral evolution and function remains a central challenge in biology, hindered by high sequence divergence and limited knowledge compared to cellular organisms. Here, we introduce LucaVirus, a multi-modal foundation model for viruses, trained on 25.4 billion nucleotide and amino acid tokens covering a vast majority of catalogued viral diversity. LucaVirus learns biologically meaningful representations that reflect relationships between sequences, protein/gene homology, and evolutionary divergence. Using these embeddings, we developed downstream models that address key virology tasks: identifying hidden viruses in genomic 'dark matter', annotating enzymatic activities of uncharacterized proteins, predicting viral evolvability, and identifying antibody candidates for emerging viruses. LucaVirus demonstrates competitive performance in three tasks and matches leading models in the fourth with one-third the parameters. Together, these findings demonstrate the utility of a unified foundation model in analyzing viral sequence data and establish LucaVirus as an efficient and versatile platform for AI-driven virology, from virus discovery to functional and therapeutic predictions.",
  "abstract_shown": true,
  "affiliations": [
    "National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, School of Medicine, Shenzhen Campus of Sun Yat-sen University, Sun Yat-sen University , Shenzhen 518107 ,",
    "State Key Laboratory for Biocontrol, School of Medicine, Shenzhen Campus of Sun Yat-sen University, Sun Yat-sen University , Shenzhen 518107 ,",
    "State Key Laboratory of Wetland Conservation and Restoration, National Observations and Research Station for Wetland Ecosystems of the Yangtze Estuary, Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, and Institute of Eco-Chongming, School of Life Sciences, Fudan University , Shanghai 200433 ,",
    "Apsara Lab, Alibaba Cloud Intelligence, Alibaba Group , Hangzhou 310030 ,",
    "BGI Research , Hangzhou 310030 ,",
    "HIM-BGI Omics Center, Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences , Hangzhou 310000 ,",
    "Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences , Hangzhou 310024 ,",
    "Zhejiang Lab , Hangzhou 311121 ,",
    "State Key Laboratory of Biocontrol, School of Life Science, Sun Yat-sen University , Guangzhou 510275 ,",
    "School of Public Health (Shenzhen), Shenzhen Campus of Sun Yat-sen University, Sun Yat-sen University , Shenzhen 518107 ,",
    "BGI Research , Sanya 572025 ,",
    "College of Pharmaceutical Sciences, Zhejiang University , Hangzhou 310058, Zhejiang ,",
    "School of Marine Sciences, Sun Yat-sen University State Key Laboratory of Biocontrol/Southern Laboratory of Ocean Science and Engineering (Guangdong, Zhuhai ), ; Guangzhou 510275 ,",
    "School of Medical Sciences, The University of Sydney , Sydney, NSW 2006 ,",
    "State Key Laboratory for Vegetation Structure, Functions and Construction (VegLab), Ministry of Education Key Laboratory for Transboundary Ecosecurity of Southwest China, Institute of Biodiversity, School of Ecology and Environmental Science, and Southwest United Graduate School, Yunnan University , Kunming 650500 ,",
    "Guangdong Provincial Center for Disease Control and Prevention , Guangzhou 511430 ,"
  ],
  "article_type": null,
  "arxiv": null,
  "author_total": 19,
  "authors": [
    {
      "affs": [
        0,
        1,
        2
      ],
      "name": "Yuanfei Pan",
      "orcid": "0000-0001-7450-9334"
    },
    {
      "affs": [
        3
      ],
      "name": "Yong He",
      "orcid": "0000-0001-9112-4663"
    },
    {
      "affs": [
        4,
        5,
        6,
        7
      ],
      "name": "Yu-Qi Liu"
    },
    {
      "affs": [
        8,
        7
      ],
      "name": "Yongtao Shan",
      "orcid": "0009-0001-6457-4658"
    },
    {
      "affs": [
        9
      ],
      "name": "Shuning Liu",
      "orcid": "0000-0003-4473-8237"
    },
    {
      "affs": [
        0,
        1
      ],
      "name": "Jia-Hao Ma"
    },
    {
      "affs": [
        0
      ],
      "name": "Xue Liu",
      "orcid": "0000-0001-9195-5408"
    },
    {
      "affs": [
        2
      ],
      "name": "Xiaoyun Pan",
      "orcid": "0000-0001-6462-7767"
    },
    {
      "affs": [
        10
      ],
      "name": "Yinqi Bai",
      "orcid": "0000-0003-1017-5712"
    },
    {
      "affs": [
        3
      ],
      "name": "Zan Xu"
    },
    {
      "affs": [
        11
      ],
      "name": "Tingjun Hou",
      "orcid": "0000-0001-7227-2580"
    },
    {
      "affs": [
        3
      ],
      "name": "Zheng Wang",
      "orcid": "0000-0001-5107-0322"
    },
    {
      "affs": [
        3
      ],
      "name": "Jieping Ye",
      "orcid": "0000-0001-8662-5818"
    },
    {
      "affs": [
        12,
        8
      ],
      "name": "Jianguo He"
    },
    {
      "affs": [
        13
      ],
      "name": "Edward Charles Holmes",
      "orcid": "0000-0001-9596-3552"
    },
    {
      "affs": [
        14,
        2
      ],
      "name": "Bo Li",
      "orcid": "0000-0002-0439-5666"
    },
    {
      "affs": [
        9
      ],
      "name": "Yao-Qing Chen",
      "orcid": "0000-0002-4659-1550"
    },
    {
      "affs": [
        3,
        7
      ],
      "name": "Zhaorong Li",
      "orcid": "0000-0002-2047-6191"
    },
    {
      "affs": [
        15,
        0,
        1
      ],
      "name": "Mǎng Shī",
      "orcid": "0000-0002-6154-4437"
    }
  ],
  "bibtex": "https://research.draconitic.com/paper/7t4qdrwsbfq11.bib",
  "cited_by": 9,
  "doi": "10.1093/nsr/nwag376",
  "fulltext_url": null,
  "id": "7t4qdrwsbfq11",
  "issns": [
    "2053-714X",
    "2095-5138"
  ],
  "landing_url": "https://doi.org/10.1093/nsr/nwag376",
  "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": [
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      "1312|Genomics and Phylogenetic Studies"
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  "openalex": "W4411484089",
  "pdf_url": null,
  "pmcid": "PMC13397533",
  "pmid": "42500742",
  "published": "2026-06-16",
  "publisher": "Oxford University Press",
  "ris": "https://research.draconitic.com/paper/7t4qdrwsbfq11.ris",
  "sources": [
    {
      "first_seen": "2026-10-30T13:26:48Z",
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      "url": "https://doi.org/10.1093/nsr/nwag376"
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  "subjects": [
    {
      "field": "biochemistry",
      "origin": "openalex:1312|Genomics and Phylogenetic Studies",
      "subfield": "molecular-biology"
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  ],
  "title": "Predicting the evolutionary and functional landscapes of viruses with a unified nucleotide-protein language model: LucaVirus",
  "title_text": "Predicting the evolutionary and functional landscapes of viruses with a unified nucleotide-protein language model: LucaVirus",
  "type": "peer-reviewed",
  "updated_at": "2026-11-08T13:20:43Z",
  "url": "https://research.draconitic.com/paper/7t4qdrwsbfq11",
  "venue": "National Science Review",
  "versions": []
}