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Research Article
Leonid Kruglyak
University of California, Los Angeles
Corresponding Author
License:
This work is licensed under a CC BY 4.0 License. Read Full License
Background
The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has caused a global disruption to human health and activity. Being able to trace the early outbreak of SARS-CoV-2 within a locality will inform public health measures and provide insights to contain or prevent the viral transmission to save lives. Investigation of the transmission history requires efficient sequencing methods and analytic strategy, which can be generally useful in the study of viral outbreaks.
Methods
Los Angeles (LA) County has sustained a large outbreak of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). To learn about the transmission history, we carried out surveillance viral genome sequencing to determine 142 viral genomes from unique patients seeking care at UCLA Health System. 86 of these genomes are from samples collected before April 19, 2020.
Results
We found that the early outbreak in LA, as in other international air travel hubs, was seeded by multiple introductions of strains from Asia and Europe. We identified a US-specific strain, B.1.43, which has been found predominantly in California and Washington State. While samples from LA County carry the ancestral B.1.43 genome, viral genomes from neighboring counties in California and from counties in Washington State carry additional mutations, suggesting a potential origin of B.1.43 in Southern California. We quantified the transmission rate of SARS-CoV-2 over time, and found evidence that the public health measures put in place in LA County to control the virus were effective at preventing transmission, but may have been undermined by the many introductions of SARS-CoV-2 into the region.
Conclusion
Our work demonstrates that genome sequencing can be a powerful tool for investigating outbreaks and informing the public health response. Our results reinforce the critical need for the U.S. to have coordinated inter-state responses to the pandemic.
Keywords
SARS-CoV-2, human health and activity, viral outbreaks
Figure 1
Figure 2
Figure 3
The full text of this article is available to read as a PDF.
Competing interest reported. JSB consults for and holds equity in Octant Inc.
This is a list of supplementary files associated with this preprint. Click to download.
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CURRENT STATUS: Under Review
Version 1
Posted 10 May, 2021
No community comments so far
Editorial decision: Major revision
On 21 May, 2021
Reviews received
Received 17 May, 2021
Reviewers agreed
On 07 May, 2021
Reviewers invited
Invitations sent on 07 May, 2021
Editor assigned
On 07 May, 2021
Editor invited
On 07 May, 2021
Submission checks complete
On 07 May, 2021
First submitted
On 14 Apr, 2021
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A new preprint design is coming!
We have improved readability, clarity, accessibility, and opportunities for engagement.
This preprint is under consideration at BMC Genomics. A preprint is a preliminary version of a manuscript that has not completed peer review at a journal. Research Square does not conduct peer review prior to posting preprints. The posting of a preprint on this server should not be interpreted as an endorsement of its validity or suitability for dissemination as established information or for guiding clinical practice.
Learn more about In Review
Research Article
Leonid Kruglyak
University of California, Los Angeles
Corresponding Author
Badges
Prescreen
This manuscript passed our Prescreen assessment
Complete author information
Appropriate declaration statements
Potential risks to human health
Prescreen
Peer Review Timeline
CURRENT STATUS: Under Review
Version 1
Posted 10 May, 2021
No community comments so far
Editorial decision: Major revision
On 21 May, 2021
Reviews received
Received 17 May, 2021
Reviewers agreed
On 07 May, 2021
Reviewers invited
Invitations sent on 07 May, 2021
Editor assigned
On 07 May, 2021
Editor invited
On 07 May, 2021
Submission checks complete
On 07 May, 2021
First submitted
On 14 Apr, 2021
Metrics
Comments: 0
PDF Downloads: ...
HTML Views: ...
License:
This work is licensed under a CC BY 4.0 License. Read Full License
Background
The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has caused a global disruption to human health and activity. Being able to trace the early outbreak of SARS-CoV-2 within a locality will inform public health measures and provide insights to contain or prevent the viral transmission to save lives. Investigation of the transmission history requires efficient sequencing methods and analytic strategy, which can be generally useful in the study of viral outbreaks.
Methods
Los Angeles (LA) County has sustained a large outbreak of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). To learn about the transmission history, we carried out surveillance viral genome sequencing to determine 142 viral genomes from unique patients seeking care at UCLA Health System. 86 of these genomes are from samples collected before April 19, 2020.
Results
We found that the early outbreak in LA, as in other international air travel hubs, was seeded by multiple introductions of strains from Asia and Europe. We identified a US-specific strain, B.1.43, which has been found predominantly in California and Washington State. While samples from LA County carry the ancestral B.1.43 genome, viral genomes from neighboring counties in California and from counties in Washington State carry additional mutations, suggesting a potential origin of B.1.43 in Southern California. We quantified the transmission rate of SARS-CoV-2 over time, and found evidence that the public health measures put in place in LA County to control the virus were effective at preventing transmission, but may have been undermined by the many introductions of SARS-CoV-2 into the region.
Conclusion
Our work demonstrates that genome sequencing can be a powerful tool for investigating outbreaks and informing the public health response. Our results reinforce the critical need for the U.S. to have coordinated inter-state responses to the pandemic.
Figure 1
Figure 2
Figure 3
The full text of this article is available to read as a PDF.
Competing interest reported. JSB consults for and holds equity in Octant Inc.
This is a list of supplementary files associated with this preprint. Click to download.
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