Using genomic epidemiology of SARS-CoV-2 to support contact tracing and public health surveillance in rural Humboldt County, California.
Genomic epidemiology
Public health response
SARS-CoV-2
Journal
BMC public health
ISSN: 1471-2458
Titre abrégé: BMC Public Health
Pays: England
ID NLM: 100968562
Informations de publication
Date de publication:
07 03 2022
07 03 2022
Historique:
received:
25
06
2021
accepted:
03
01
2022
entrez:
8
3
2022
pubmed:
9
3
2022
medline:
11
3
2022
Statut:
epublish
Résumé
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. 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. 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.
Sections du résumé
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.
Identifiants
pubmed: 35255849
doi: 10.1186/s12889-022-12790-0
pii: 10.1186/s12889-022-12790-0
pmc: PMC8900115
doi:
Types de publication
Journal Article
Langues
eng
Sous-ensembles de citation
IM
Pagination
456Informations de copyright
© 2022. The Author(s).
Références
Emerg Infect Dis. 2020 Dec;26(12):2854-2862
pubmed: 33219646
Nature. 2021 Apr;592(7854):438-443
pubmed: 33690265
Biosaf Health. 2021 Apr;3(2):124-127
pubmed: 33558859
Science. 2021 Apr 9;372(6538):
pubmed: 33658326
Cell. 2020 Sep 3;182(5):1295-1310.e20
pubmed: 32841599
Cell. 2020 May 28;181(5):990-996.e5
pubmed: 32386545
Mol Biol Evol. 2020 May 1;37(5):1530-1534
pubmed: 32011700
Nat Med. 2020 Jun;26(6):832-841
pubmed: 32528156
MMWR Morb Mortal Wkly Rep. 2020 Apr 17;69(15):446-450
pubmed: 32298246
Science. 2020 Oct 30;370(6516):571-575
pubmed: 32913002
PLoS Comput Biol. 2009 Sep;5(9):e1000520
pubmed: 19779555
Nat Commun. 2021 Jan 19;12(1):434
pubmed: 33469026
Virus Evol. 2018 Jan 08;4(1):vex042
pubmed: 29340210
Bioinformatics. 2018 Dec 1;34(23):4121-4123
pubmed: 29790939
N Engl J Med. 2019 Dec 26;381(26):2569-2580
pubmed: 31881145
Euro Surveill. 2017 Mar 30;22(13):
pubmed: 28382917
Lancet. 2021 Feb 6;397(10273):452-455
pubmed: 33515491
Clin Infect Dis. 2022 Jan 7;74(1):32-39
pubmed: 33788923
Virus Evol. 2021 Jul 30;7(2):veab064
pubmed: 34527285
Glob Chall. 2017 Jan 10;1(1):33-46
pubmed: 31565258
Nucleic Acids Res. 2016 Jan 4;44(D1):D67-72
pubmed: 26590407