{
  "abstract": "In July 2021, the California Code of Regulations Title 17 required all laboratories performing SARS‑CoV‑2 whole genome sequencing (WGS) to report their sequencing results to the California Department of Public Health (CDPH). These viral genomic data and patient metadata were compiled into the Integrated Genomic Epidemiology Database (IGED). Linking anonymized viral sequences with patient‑level information enabled monitoring of infectiousness, pathogenicity, transmission dynamics, evolution, and vaccine evasion among emerging SARS‑CoV‑2 lineages. Laboratories performing SARS-CoV-2 WGS transmitted sequencing results to CDPH through Electronic Laboratory Reporting (ELR) and non-ELR pathways. CDPH applied uniform reporting requirements but allowed flexibility in specific data formats to accommodate diverse data systems. To preserve data quality and interoperability across heterogeneous sources, CDPH implemented standardization, validation, and deduplication protocols. Snowflake, a cloud‑based data storage and analytics platform, and Posit Connect, a cloud deployment and automation platform, supported the management, processing, and integration of data within the IGED. The IGED established links between SARS‑CoV‑2 WGS data and epidemiologic metadata for 801,418 sequences, representing 81.7% of all sequences reported in California. Lineages reported to the IGED showed strong concordance with lineage proportions in GISAID. Sequences reported to the IGED had average turnaround times longer than one month, and the majority of sequencing was performed in Southern California and Los Angeles. The IGED enhanced genomic surveillance through predictive modeling and monitoring concerning evolutionary trends such as recombination and saltations in persistent infections. Development of the IGED highlighted the need for standardized data requirements, sustained funding for sequencing, incentives for data submission, and interdisciplinary collaboration to build an effective genomic surveillance system. This framework for linking genomic and epidemiologic data has not only generated critical insights for SARS‑CoV‑2 but also provided the foundation for CDPH and other public health organizations to develop similar IGED‑like systems for other priority pathogens as genomic surveillance expands. Author summary: In California, the COVID‑19 pandemic generated an unprecedented volume of anonymized viral genomic data, creating a critical need to link sequencing results with patient information for genomic epidemiology. To meet this need, we developed the Integrated Genomic Epidemiology Database (IGED), a comprehensive reso.urce that connects SARS‑CoV‑2 whole‑genome sequencing (WGS) data with corresponding patient records. Using cloud‑based computational infrastructure, we standardized and integrated submissions from numerous laboratories and jurisdictions, each with distinct technical requirements for providing data to CDPH. Of nearly one million records received, we successfully linked 801,418 WGS records to patient data. The IGED supported public reporting of circulating SARS‑CoV‑2 lineages, improved understanding of viral evolutionary dynamics, and served as the foundation for a genomic epidemiology tool used in outbreak investigations. By establishing a robust framework for linking WGS and patient‑level data, we provide a model that can be adapted by other public health agencies for emerging pathogens of concern.",
  "abstract_shown": true,
  "affiliations": [
    "Viral and Rickettsial Disease Laboratory, Center for Laboratory Sciences, California Department of Public Health, Richmond, California, United States of America",
    "Climate Change and Health Equity, California Department of Public Health, Richmond, California, United States of America",
    "Informatics Branch, Center for Infectious Disease, California Department of Public Health, Richmond, California, United States of America",
    "Public Health Reporting Information Exchange, Division of Communicable Disease Control, California Department of Public Health, Richmond, California, United States of America",
    "COVID Control Branch, Center for Infectious Disease, California Department of Public Health, Richmond, California, United States of America",
    "Theiagen Genomics, Highlands Ranch, Colorado, United States of America"
  ],
  "article_type": "Research Article",
  "arxiv": null,
  "author_total": 28,
  "authors": [
    {
      "affs": [
        0
      ],
      "name": "Jesse Elder"
    },
    {
      "affs": [
        1
      ],
      "name": "Rahil Ryder"
    },
    {
      "affs": [
        2
      ],
      "name": "Mayuri Panditrao"
    },
    {
      "affs": [
        3
      ],
      "name": "Kaitlin Grosgebauer"
    },
    {
      "affs": [
        4
      ],
      "name": "Rebecca Katz"
    },
    {
      "affs": [
        5
      ],
      "name": "Lawrence Tello"
    },
    {
      "name": "Ellaison Carroll"
    },
    {
      "name": "Deva Borthwick"
    },
    {
      "name": "Chaman Kaur"
    },
    {
      "name": "Romario Smith"
    },
    {
      "name": "Victor Shiau"
    },
    {
      "name": "Will Wheeler"
    },
    {
      "name": "Emilia Reilly"
    },
    {
      "name": "Jennifer Myers"
    },
    {
      "name": "Lauren Nelson"
    },
    {
      "name": "Esther Lim"
    },
    {
      "name": "Phacharee Arunleung"
    },
    {
      "name": "Elizabeth Baylis"
    },
    {
      "name": "Sabrina Gilliam"
    },
    {
      "name": "Tamara Hennessy-Burt"
    },
    {
      "name": "Brooke Bregman"
    },
    {
      "name": "Elana Silver"
    },
    {
      "name": "Curtis Kapsak"
    },
    {
      "name": "Sage Wright"
    },
    {
      "name": "Tomas Leon"
    },
    {
      "name": "John Bell"
    },
    {
      "name": "Christina Morales"
    },
    {
      "name": "Debra A. Wadford"
    }
  ],
  "bibtex": "https://research.draconitic.com/paper/ck25sft4h7r53.bib",
  "cited_by": 0,
  "doi": "10.1371/journal.pdig.0001473",
  "fulltext_url": "https://journals.plos.org/digitalhealth/article?id=10.1371/journal.pdig.0001473",
  "id": "ck25sft4h7r53",
  "issns": [
    "2767-3170"
  ],
  "landing_url": "https://journals.plos.org/digitalhealth/article?id=10.1371/journal.pdig.0001473",
  "language": null,
  "licence": "CC-BY-4.0",
  "licence_label": "CC BY 4.0",
  "licence_source": "journal",
  "licence_url": "https://creativecommons.org/licenses/by/4.0/",
  "metadata_licence": null,
  "native_subjects": [
    [
      "openalex",
      "2725|SARS-CoV-2 and COVID-19 Research"
    ],
    [
      "plos",
      "/Biology and life sciences/Computational biology/Genome analysis/Genomic databases"
    ],
    [
      "plos",
      "/Biology and life sciences/Genetics/Genomics"
    ],
    [
      "plos",
      "/Biology and life sciences/Genetics/Genomics/Genome analysis/Genomic databases"
    ],
    [
      "plos",
      "/Biology and life sciences/Microbiology/Medical microbiology/Microbial pathogens/Viral pathogens/Coronaviruses/SARS coronavirus/SARS CoV 2"
    ],
    [
      "plos",
      "/Biology and life sciences/Organisms/Viruses/RNA viruses/Coronaviruses/SARS coronavirus/SARS CoV 2"
    ],
    [
      "plos",
      "/Biology and life sciences/Organisms/Viruses/Viral pathogens/Coronaviruses/SARS coronavirus/SARS CoV 2"
    ],
    [
      "plos",
      "/Computer and information sciences/Data management"
    ],
    [
      "plos",
      "/Medicine and health sciences/Epidemiology"
    ],
    [
      "plos",
      "/Medicine and health sciences/Medical conditions/Infectious diseases/Viral diseases/COVID 19"
    ],
    [
      "plos",
      "/Medicine and health sciences/Pathology and laboratory medicine/Pathogens/Microbial pathogens/Viral pathogens/Coronaviruses/SARS coronavirus/SARS CoV 2"
    ],
    [
      "plos",
      "/Medicine and health sciences/Public and occupational health"
    ],
    [
      "plos",
      "/People and places/Geographical locations/North America/United States/California"
    ],
    [
      "plos",
      "/Research and analysis methods/Database and informatics methods/Biological databases/Genomic databases"
    ]
  ],
  "openalex": "W7204791581",
  "pdf_url": "https://journals.plos.org/digitalhealth/article/file?id=10.1371/journal.pdig.0001473&type=printable",
  "pmcid": null,
  "pmid": null,
  "published": "2026-08-31",
  "publisher": "Public Library of Science",
  "ris": "https://research.draconitic.com/paper/ck25sft4h7r53.ris",
  "sources": [
    {
      "first_seen": "2026-10-30T12:18:02Z",
      "native_id": "10.1371/journal.pdig.0001473",
      "source": "plos",
      "url": "https://journals.plos.org/digitalhealth/article?id=10.1371/journal.pdig.0001473"
    }
  ],
  "subjects": [
    {
      "field": "biology",
      "origin": "plos:computational biology",
      "subfield": "bioinformatics"
    },
    {
      "field": "biology",
      "origin": "plos:genomics",
      "subfield": "genetics-genomics"
    },
    {
      "field": "medicine",
      "origin": "plos:epidemiology",
      "subfield": "epidemiology-public-health"
    }
  ],
  "title": "The SARS-CoV-2 Integrated Genomic Epidemiology Database (IGED): Linking viral genomes with patient-level metadata to advance statewide genomic surveillance in California",
  "title_text": "The SARS-CoV-2 Integrated Genomic Epidemiology Database (IGED): Linking viral genomes with patient-level metadata to advance statewide genomic surveillance in California",
  "type": "peer-reviewed",
  "updated_at": "2026-10-30T12:18:02Z",
  "url": "https://research.draconitic.com/paper/ck25sft4h7r53",
  "venue": "PLOS Digital Health",
  "versions": []
}