Using genomic epidemiology of SARS-CoV-2 to support contact tracing and public health surveillance in rural Humboldt County, CaliforniaGunnar Stoddard, Allison Black, Patrick Ayscue, Dan Lu, Jack Kamm, Karan Bhatt, Lienna Cha, Amy L Kistler, Joshua Batson, Angela Detweiler , Michelle Tan , Norma Nef, Joseph L DeRisi. and Jeremy Corrigan
BMC Public Health, 2022Abstract: 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. 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.
