Using genomic epidemiology of SARS-CoV-2 to support contact tracing and public health surveillance in rural Humboldt County, California

Bibliographic Details
Title: Using genomic epidemiology of SARS-CoV-2 to support contact tracing and public health surveillance in rural Humboldt County, California
Authors: Gunnar Stoddard, Allison Black, Patrick Ayscue, Dan Lu, Jack Kamm, Karan Bhatt, Lienna Chan, Amy L Kistler, Joshua Batson, Angela Detweiler, Michelle Tan, Norma Neff, Joseph L DeRisi, Jeremy Corrigan
Source: BMC Public Health, Vol 22, Iss 1, Pp 1-12 (2022)
Publisher Information: BMC, 2022.
Publication Year: 2022
Collection: LCC:Public aspects of medicine
Subject Terms: SARS-CoV-2, Genomic epidemiology, Public health response, Public aspects of medicine, RA1-1270
More Details: Abstract Background During 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. Methods Through 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. Results In 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. Conclusions These 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.
Document Type: article
File Description: electronic resource
Language: English
ISSN: 1471-2458
Relation: https://doaj.org/toc/1471-2458
DOI: 10.1186/s12889-022-12790-0
Access URL: https://doaj.org/article/5fa5a43e5c5c44af83dd47b0bb5ad39b
Accession Number: edsdoj.5fa5a43e5c5c44af83dd47b0bb5ad39b
Database: Directory of Open Access Journals
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More Details
ISSN:14712458
DOI:10.1186/s12889-022-12790-0
Published in:BMC Public Health
Language:English