Using genomic epidemiology of SARS-CoV-2 to support contact tracing and public health surveillance in rural Humboldt County, California
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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.
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SciScore for 10.1101/2021.09.21.21258385: (What is this?)
Please note, not all rigor criteria are appropriate for all manuscripts.
Table 1: Rigor
Ethics IRB: Ethics statement: This work was approved by the University of California San Francisco Human Research Protection Program Institutional Review Board (IRB# 21-34522, Reference Number 319235).
Consent: This same IRB also waived consent for specimen collection because collection occurred as part of public health response.
Field Sample Permit: All work was carried out in accordance with relevant regulations and guidelines.Sex as a biological variable not detected. Randomization Briefly, 3 µl of total nucleic acid was used as input for a randomly primed cDNA synthesis reaction. Blinding not detected. Power Analysis not detected. Cell Line Authentication Authentication: Additionally, swabs in both … SciScore for 10.1101/2021.09.21.21258385: (What is this?)
Please note, not all rigor criteria are appropriate for all manuscripts.
Table 1: Rigor
Ethics IRB: Ethics statement: This work was approved by the University of California San Francisco Human Research Protection Program Institutional Review Board (IRB# 21-34522, Reference Number 319235).
Consent: This same IRB also waived consent for specimen collection because collection occurred as part of public health response.
Field Sample Permit: All work was carried out in accordance with relevant regulations and guidelines.Sex as a biological variable not detected. Randomization Briefly, 3 µl of total nucleic acid was used as input for a randomly primed cDNA synthesis reaction. Blinding not detected. Power Analysis not detected. Cell Line Authentication Authentication: Additionally, swabs in both viral transport media and saline transport media were validated for testing. Table 2: Resources
Software and Algorithms Sentences Resources Ethics statement: This work was approved by the University of California San Francisco Human Research Protection Program Institutional Review Board (IRB# 21-34522, Reference Number 319235). Human Research Protection Programsuggested: NoneLow priority samples, such as those collected to provide travel clearance, pre-operative screening, and general population surveillance, were deferred to commercial laboratories such as Quest and LabCorp. Questsuggested: (QUEST, RRID:SCR_005210)Additionally, some extractions were either performed on the Qiagen EZ1 Advanced, eluting samples in 120 µls of elution buffer, or on the KingFisher™ Flex Purification System and the MagMAX™ Viral/Pathogen II Nucleic Acid Isolation Kit (ThermoFisher), which eluted the sample in 100 µls of elution buffer. ThermoFishersuggested: (ThermoFisher; SL 8; Centrifuge, RRID:SCR_020809)We used the Augur pipeline to align the sequences using nextalign v0.1.6, build a maximum likelihood phylogenetic tree with IQTREE v2.0.3 (Minh et al. 2020), and temporally resolve the tree using TreeTime v0.8.1 (Sagulenko, Puller, and Neher 2018). Augursuggested: NoneResults from OddPub: Thank you for sharing your code and data.
Results from LimitationRecognizer: An explicit section about the limitations of the techniques employed in this study was not found. We encourage authors to address study limitations.Results from TrialIdentifier: No clinical trial numbers were referenced.
Results from Barzooka: We did not find any issues relating to the usage of bar graphs.
Results from JetFighter: We did not find any issues relating to colormaps.
Results from rtransparent:- Thank you for including a conflict of interest statement. Authors are encouraged to include this statement when submitting to a journal.
- Thank you for including a funding statement. Authors are encouraged to include this statement when submitting to a journal.
- No protocol registration statement was detected.
Results from scite Reference Check: We found no unreliable references.
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