The SARS-CoV-2 Integrated Genomic Epidemiology Database (IGED): Linking viral genomes with patient-level metadata to advance statewide genomic surveillance in California

@article{elder2026sarscov2,
  title = {{The SARS-CoV-2 Integrated Genomic Epidemiology Database (IGED): Linking viral genomes with patient-level metadata to advance statewide genomic surveillance in California}},
  author = {Jesse Elder and Rahil Ryder and Mayuri Panditrao and Kaitlin Grosgebauer and Rebecca Katz and Lawrence Tello and Ellaison Carroll and Deva Borthwick and Chaman Kaur and Romario Smith and Victor Shiau and Will Wheeler and Emilia Reilly and Jennifer Myers and Lauren Nelson and Esther Lim and Phacharee Arunleung and Elizabeth Baylis and Sabrina Gilliam and Tamara Hennessy-Burt and Brooke Bregman and Elana Silver and Curtis Kapsak and Sage Wright and Tomas Leon and John Bell and Christina Morales and Debra A. Wadford},
  journal = {PLOS Digital Health},
  year = {2026},
  month = aug,
  doi = {10.1371/journal.pdig.0001473},
  url = {https://journals.plos.org/digitalhealth/article?id=10.1371/journal.pdig.0001473},
  note = {CC BY 4.0},
}

TY  - JOUR
TI  - The SARS-CoV-2 Integrated Genomic Epidemiology Database (IGED): Linking viral genomes with patient-level metadata to advance statewide genomic surveillance in California
AU  - Jesse Elder
AU  - Rahil Ryder
AU  - Mayuri Panditrao
AU  - Kaitlin Grosgebauer
AU  - Rebecca Katz
AU  - Lawrence Tello
AU  - Ellaison Carroll
AU  - Deva Borthwick
AU  - Chaman Kaur
AU  - Romario Smith
AU  - Victor Shiau
AU  - Will Wheeler
AU  - Emilia Reilly
AU  - Jennifer Myers
AU  - Lauren Nelson
AU  - Esther Lim
AU  - Phacharee Arunleung
AU  - Elizabeth Baylis
AU  - Sabrina Gilliam
AU  - Tamara Hennessy-Burt
AU  - Brooke Bregman
AU  - Elana Silver
AU  - Curtis Kapsak
AU  - Sage Wright
AU  - Tomas Leon
AU  - John Bell
AU  - Christina Morales
AU  - Debra A. Wadford
PY  - 2026
DA  - 2026/08/31
JO  - PLOS Digital Health
DO  - 10.1371/journal.pdig.0001473
UR  - https://journals.plos.org/digitalhealth/article?id=10.1371/journal.pdig.0001473
AB  - 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.
SN  - 2767-3170
ER  -