Genomic epidemiology of the Los Angeles COVID-19 outbreak and the early history of the B.1.43 strain in the USA
Abstract Background The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has caused global disruption of human health and activity. Being able to trace the early outbreak of SARS-CoV-2 within a locality can inform public health measures and provide insights to contain or prevent viral tr...
| Main Authors: | , , , , , , , , , , , , , , , , |
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| Format: | Article |
| Language: | English |
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BMC
2022-04-01
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| Series: | BMC Genomics |
| Online Access: | https://doi.org/10.1186/s12864-022-08488-7 |
| _version_ | 1819045694035460096 |
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| author | Longhua Guo James Boocock Evann E. Hilt Sukantha Chandrasekaran Yi Zhang Chetan Munugala Laila Sathe Noah Alexander Valerie A. Arboleda Jonathan Flint Eleazar Eskin Chongyuan Luo Shangxin Yang Omai B. Garner Yi Yin Joshua S. Bloom Leonid Kruglyak |
| author_facet | Longhua Guo James Boocock Evann E. Hilt Sukantha Chandrasekaran Yi Zhang Chetan Munugala Laila Sathe Noah Alexander Valerie A. Arboleda Jonathan Flint Eleazar Eskin Chongyuan Luo Shangxin Yang Omai B. Garner Yi Yin Joshua S. Bloom Leonid Kruglyak |
| author_sort | Longhua Guo |
| collection | DOAJ |
| description | Abstract Background The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has caused global disruption of human health and activity. Being able to trace the early outbreak of SARS-CoV-2 within a locality can inform public health measures and provide insights to contain or prevent viral transmission. Investigation of the transmission history requires efficient sequencing methods and analytic strategies, which can be generally useful in the study of viral outbreaks. Methods The County of Los Angeles (hereafter, LA County) 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 the University of California, Los Angeles (UCLA) Health System. 86 of these genomes were from samples collected before April 19, 2020. Results We found that the early outbreak in LA County, as in other international air travel hubs, was seeded by multiple introductions of strains from Asia and Europe. We identified a USA-specific strain, B.1.43, which was found predominantly in California and Washington State. While samples from LA County carried the ancestral B.1.43 genome, viral genomes from neighboring counties in California and from counties in Washington State carried 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 might 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 USA to have coordinated inter-state responses to the pandemic. |
| first_indexed | 2024-12-21T10:32:38Z |
| format | Article |
| id | doaj.art-438bd4c1e8b94127b57557a01f54b3fc |
| institution | Directory Open Access Journal |
| issn | 1471-2164 |
| language | English |
| last_indexed | 2024-12-21T10:32:38Z |
| publishDate | 2022-04-01 |
| publisher | BMC |
| record_format | Article |
| series | BMC Genomics |
| spelling | doaj.art-438bd4c1e8b94127b57557a01f54b3fc2022-12-21T19:07:10ZengBMCBMC Genomics1471-21642022-04-012311910.1186/s12864-022-08488-7Genomic epidemiology of the Los Angeles COVID-19 outbreak and the early history of the B.1.43 strain in the USALonghua Guo0James Boocock1Evann E. Hilt2Sukantha Chandrasekaran3Yi Zhang4Chetan Munugala5Laila Sathe6Noah Alexander7Valerie A. Arboleda8Jonathan Flint9Eleazar Eskin10Chongyuan Luo11Shangxin Yang12Omai B. Garner13Yi Yin14Joshua S. Bloom15Leonid Kruglyak16Department of Human Genetics, David Geffen School of Medicine, UCLADepartment of Human Genetics, David Geffen School of Medicine, UCLADepartment of Pathology & Laboratory Medicine, David Geffen School of Medicine, UCLADepartment of Pathology & Laboratory Medicine, David Geffen School of Medicine, UCLADepartment of Human Genetics, David Geffen School of Medicine, UCLADepartment of Human Genetics, David Geffen School of Medicine, UCLADepartment of Pathology & Laboratory Medicine, David Geffen School of Medicine, UCLADepartment of Human Genetics, David Geffen School of Medicine, UCLADepartment of Human Genetics, David Geffen School of Medicine, UCLADepartment of Human Genetics, David Geffen School of Medicine, UCLADepartment of Human Genetics, David Geffen School of Medicine, UCLADepartment of Human Genetics, David Geffen School of Medicine, UCLADepartment of Pathology & Laboratory Medicine, David Geffen School of Medicine, UCLADepartment of Pathology & Laboratory Medicine, David Geffen School of Medicine, UCLADepartment of Human Genetics, David Geffen School of Medicine, UCLADepartment of Human Genetics, David Geffen School of Medicine, UCLADepartment of Human Genetics, David Geffen School of Medicine, UCLAAbstract Background The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has caused global disruption of human health and activity. Being able to trace the early outbreak of SARS-CoV-2 within a locality can inform public health measures and provide insights to contain or prevent viral transmission. Investigation of the transmission history requires efficient sequencing methods and analytic strategies, which can be generally useful in the study of viral outbreaks. Methods The County of Los Angeles (hereafter, LA County) 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 the University of California, Los Angeles (UCLA) Health System. 86 of these genomes were from samples collected before April 19, 2020. Results We found that the early outbreak in LA County, as in other international air travel hubs, was seeded by multiple introductions of strains from Asia and Europe. We identified a USA-specific strain, B.1.43, which was found predominantly in California and Washington State. While samples from LA County carried the ancestral B.1.43 genome, viral genomes from neighboring counties in California and from counties in Washington State carried 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 might 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 USA to have coordinated inter-state responses to the pandemic.https://doi.org/10.1186/s12864-022-08488-7 |
| spellingShingle | Longhua Guo James Boocock Evann E. Hilt Sukantha Chandrasekaran Yi Zhang Chetan Munugala Laila Sathe Noah Alexander Valerie A. Arboleda Jonathan Flint Eleazar Eskin Chongyuan Luo Shangxin Yang Omai B. Garner Yi Yin Joshua S. Bloom Leonid Kruglyak Genomic epidemiology of the Los Angeles COVID-19 outbreak and the early history of the B.1.43 strain in the USA BMC Genomics |
| title | Genomic epidemiology of the Los Angeles COVID-19 outbreak and the early history of the B.1.43 strain in the USA |
| title_full | Genomic epidemiology of the Los Angeles COVID-19 outbreak and the early history of the B.1.43 strain in the USA |
| title_fullStr | Genomic epidemiology of the Los Angeles COVID-19 outbreak and the early history of the B.1.43 strain in the USA |
| title_full_unstemmed | Genomic epidemiology of the Los Angeles COVID-19 outbreak and the early history of the B.1.43 strain in the USA |
| title_short | Genomic epidemiology of the Los Angeles COVID-19 outbreak and the early history of the B.1.43 strain in the USA |
| title_sort | genomic epidemiology of the los angeles covid 19 outbreak and the early history of the b 1 43 strain in the usa |
| url | https://doi.org/10.1186/s12864-022-08488-7 |
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