ArticleBMC public health2022
Using genomic epidemiology of SARS-CoV-2 to support contact tracing and public health surveillance in rural Humboldt County, California.
Article in BMC public health, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 14 papers.
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Who cites it
14 citing papers in PubMed.
- The SARS-CoV-2 Integrated Genomic Epidemiology Database (IGED): Linking viral genomes with patient-level metadata to advance statewide genomic surveillance in California.PLOS digital health · 2026Article
- Use of integrated genomic surveillance by local public health authorities: Recommendations based on a mixed-methods study of current adoption, applications and success factors, Germany, 2023.Euro surveillance : bulletin Europeen sur les maladies transmissibles = European communicable disease bulletin · 2025Article
- SARS-CoV-2 introductions to the island of Ireland: a phylogenetic and geospatiotemporal study of infection dynamics.Genome medicine · 2024Article
- Dimensionality reduction distills complex evolutionary relationships in seasonal influenza and SARS-CoV-2.bioRxiv : the preprint server for biology · 2024Article
- A response playbook for early detection and population surveillance of new SARS-CoV-2 variants in a regional public health laboratory.BMC public health · 2024Article
- Dimensionality reduction distills complex evolutionary relationships in seasonal influenza and SARS-CoV-2.Virus evolution · 2024Article
- Genomic surveillance of SARS-CoV-2 reveals highest severity and mortality of delta over other variants: evidence from Cameroon.Scientific reports · 2023Article
- Case Investigation and Contact Tracing in US State and Local Public Health Agencies: Sustaining Capacities and Applying Lessons Learned From the COVID-19 Pandemic and 2022 Mpox Outbreak.Health security · 2023Article
- Web Resources for SARS-CoV-2 Genomic Database, Annotation, Analysis and Variant Tracking.Viruses · 2023Review
- Comparative Analysis of Library Preparation Approaches for SARS-CoV-2 Genome Sequencing on the Illumina MiSeq Platform.International journal of molecular sciences · 2023Article
- Implementation of California COVIDNet - a multi-sector collaboration for statewide SARS-CoV-2 genomic surveillance.Frontiers in public health · 2023Article
- Rural populations facilitated early SARS-CoV-2 evolution and transmission in Missouri, USA.Npj viruses · 2023Article
- SARS-CoV-2 Delta variant in Cartagena de Indias, Colombia, August 2021.Health science reports · 2022Article
- Methods for sequencing the pandemic: benefits of rapid or high-throughput processing.F1000Research · 2021Article
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Authors and funding
14 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundDuring the COVID-19 pandemic within the United States, much of the responsibility for diagnostic testing and epidemiologic response has relied on the action of county-level departments of public health. Here we describe the integration of genomic surveillance into epidemiologic response within Humboldt County, a rural county in northwest California.
methodsThrough a collaborative effort, 853 whole SARS-CoV-2 genomes were generated, representing ~58% of the 1,449 SARS-CoV-2-positive cases detected in Humboldt County as of March 12, 2021. Phylogenetic analysis of these data was used to develop a comprehensive understanding of SARS-CoV-2 introductions to the county and to support contact tracing and epidemiologic investigations of all large outbreaks in the county.
resultsIn the case of an outbreak on a commercial farm, viral genomic data were used to validate reported epidemiologic links and link additional cases within the community who did not report a farm exposure to the outbreak. During a separate outbreak within a skilled nursing facility, genomic surveillance data were used to rule out the putative index case, detect the emergence of an independent Spike:N501Y substitution, and verify that the outbreak had been brought under control.
conclusionsThese use cases demonstrate how developing genomic surveillance capacity within local public health departments can support timely and responsive deployment of genomic epidemiology for surveillance and outbreak response based on local needs and priorities.
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