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Analysis of Genomic Characteristics and Transmission Routes of Patients With Confirmed SARS-CoV-2 in Southern California During the Early Stage of the US COVID-19 Pandemic.
JAMA Netw Open. 2020 10 01; 3(10):e2024191.JN

Abstract

Importance

In late December 2019, an outbreak of a novel severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) emerged in Wuhan, China. Data on the routes of transmission to Los Angeles, California, the US West Coast epicenter for coronavirus disease 2019 (COVID-19), and subsequent community spread are limited.

Objective

To determine the transmission routes of SARS-CoV-2 to Southern California and elucidate local community spread within the Los Angeles metropolitan area.

Design, Setting, and Participants

This case series included 192 consecutive patients with reverse transcription-polymerase chain reaction (RT-PCR) test results positive for SARS-CoV-2 who were evaluated at Cedars-Sinai Medical Center in Los Angeles, California, from March 22 to April 15, 2020. Data analysis was performed from April to May 2020.

Main Outcomes and Measures

SARS-CoV-2 viral genomes were sequenced. Los Angeles isolates were compared with genomes from global subsampling and from New York, New York; Washington state; and China to determine potential sources of viral dissemination. Demographic data and outcomes were collected.

Results

The cohort included 192 patients (median [interquartile range] age, 59.5 [43-75] years; 110 [57.3%] men). The genetic characterization of SARS-CoV-2 isolates in the Los Angeles population pinpointed community transmission of 13 patients within a 3.81 km2 radius. Variation landscapes of this case series also revealed a cluster of 10 patients that contained 5 residents at a skilled nursing facility, 1 resident of a nearby skilled nursing facility, 3 health care workers, and a family member of a resident of one of the skilled nursing facilities. Person-to-person transmission was detected in a cluster of 5 patients who shared the same single-nucleotide variation in their SARS-CoV-2 genomes. High viral genomic diversity was identified: 20 Los Angeles isolates (15.0%) resembled SARS-CoV-2 genomes from Asia, while 109 Los Angeles isolates (82.0%) were similar to isolates originating from Europe. Analysis of other common respiratory viral pathogens did not reveal coinfection in the cohort.

Conclusions and Relevance

These findings highlight the precision of detecting person-to-person transmission and accurate contact tracing directly through SARS-CoV-2 genome isolation and sequencing. Development and application of phylogenetic analyses from the Los Angeles population established connections between COVID-19 clusters locally and throughout the US.

Authors+Show Affiliations

Molecular Pathology Laboratory, Department of Pathology and Laboratory Medicine, Cedars-Sinai Medical Center, Los Angeles, California.Molecular Pathology Laboratory, Department of Pathology and Laboratory Medicine, Cedars-Sinai Medical Center, Los Angeles, California.Center for Bioinformatics and Functional Genomics, Department of Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, California. Applied Genomics, Computation and Translational Core, Cedars-Sinai Cancer Center, Los Angeles, California.Center for Bioinformatics and Functional Genomics, Department of Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, California. Applied Genomics, Computation and Translational Core, Cedars-Sinai Cancer Center, Los Angeles, California.Molecular Pathology Laboratory, Department of Pathology and Laboratory Medicine, Cedars-Sinai Medical Center, Los Angeles, California.Molecular Pathology Laboratory, Department of Pathology and Laboratory Medicine, Cedars-Sinai Medical Center, Los Angeles, California.Molecular Pathology Laboratory, Department of Pathology and Laboratory Medicine, Cedars-Sinai Medical Center, Los Angeles, California.Center for Bioinformatics and Functional Genomics, Department of Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, California. Applied Genomics, Computation and Translational Core, Cedars-Sinai Cancer Center, Los Angeles, California.Molecular Pathology Laboratory, Department of Pathology and Laboratory Medicine, Cedars-Sinai Medical Center, Los Angeles, California.

Pub Type(s)

Journal Article
Research Support, Non-U.S. Gov't

Language

eng

PubMed ID

33026453

Citation

Zhang, Wenjuan, et al. "Analysis of Genomic Characteristics and Transmission Routes of Patients With Confirmed SARS-CoV-2 in Southern California During the Early Stage of the US COVID-19 Pandemic." JAMA Network Open, vol. 3, no. 10, 2020, pp. e2024191.
Zhang W, Govindavari JP, Davis BD, et al. Analysis of Genomic Characteristics and Transmission Routes of Patients With Confirmed SARS-CoV-2 in Southern California During the Early Stage of the US COVID-19 Pandemic. JAMA Netw Open. 2020;3(10):e2024191.
Zhang, W., Govindavari, J. P., Davis, B. D., Chen, S. S., Kim, J. T., Song, J., Lopategui, J., Plummer, J. T., & Vail, E. (2020). Analysis of Genomic Characteristics and Transmission Routes of Patients With Confirmed SARS-CoV-2 in Southern California During the Early Stage of the US COVID-19 Pandemic. JAMA Network Open, 3(10), e2024191. https://doi.org/10.1001/jamanetworkopen.2020.24191
Zhang W, et al. Analysis of Genomic Characteristics and Transmission Routes of Patients With Confirmed SARS-CoV-2 in Southern California During the Early Stage of the US COVID-19 Pandemic. JAMA Netw Open. 2020 10 1;3(10):e2024191. PubMed PMID: 33026453.
* Article titles in AMA citation format should be in sentence-case
TY - JOUR T1 - Analysis of Genomic Characteristics and Transmission Routes of Patients With Confirmed SARS-CoV-2 in Southern California During the Early Stage of the US COVID-19 Pandemic. AU - Zhang,Wenjuan, AU - Govindavari,John Paul, AU - Davis,Brian D, AU - Chen,Stephanie S, AU - Kim,Jong Taek, AU - Song,Jianbo, AU - Lopategui,Jean, AU - Plummer,Jasmine T, AU - Vail,Eric, Y1 - 2020/10/01/ PY - 2020/10/7/entrez PY - 2020/10/8/pubmed PY - 2020/10/21/medline SP - e2024191 EP - e2024191 JF - JAMA network open JO - JAMA Netw Open VL - 3 IS - 10 N2 - Importance: In late December 2019, an outbreak of a novel severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) emerged in Wuhan, China. Data on the routes of transmission to Los Angeles, California, the US West Coast epicenter for coronavirus disease 2019 (COVID-19), and subsequent community spread are limited. Objective: To determine the transmission routes of SARS-CoV-2 to Southern California and elucidate local community spread within the Los Angeles metropolitan area. Design, Setting, and Participants: This case series included 192 consecutive patients with reverse transcription-polymerase chain reaction (RT-PCR) test results positive for SARS-CoV-2 who were evaluated at Cedars-Sinai Medical Center in Los Angeles, California, from March 22 to April 15, 2020. Data analysis was performed from April to May 2020. Main Outcomes and Measures: SARS-CoV-2 viral genomes were sequenced. Los Angeles isolates were compared with genomes from global subsampling and from New York, New York; Washington state; and China to determine potential sources of viral dissemination. Demographic data and outcomes were collected. Results: The cohort included 192 patients (median [interquartile range] age, 59.5 [43-75] years; 110 [57.3%] men). The genetic characterization of SARS-CoV-2 isolates in the Los Angeles population pinpointed community transmission of 13 patients within a 3.81 km2 radius. Variation landscapes of this case series also revealed a cluster of 10 patients that contained 5 residents at a skilled nursing facility, 1 resident of a nearby skilled nursing facility, 3 health care workers, and a family member of a resident of one of the skilled nursing facilities. Person-to-person transmission was detected in a cluster of 5 patients who shared the same single-nucleotide variation in their SARS-CoV-2 genomes. High viral genomic diversity was identified: 20 Los Angeles isolates (15.0%) resembled SARS-CoV-2 genomes from Asia, while 109 Los Angeles isolates (82.0%) were similar to isolates originating from Europe. Analysis of other common respiratory viral pathogens did not reveal coinfection in the cohort. Conclusions and Relevance: These findings highlight the precision of detecting person-to-person transmission and accurate contact tracing directly through SARS-CoV-2 genome isolation and sequencing. Development and application of phylogenetic analyses from the Los Angeles population established connections between COVID-19 clusters locally and throughout the US. SN - 2574-3805 UR - https://www.unboundmedicine.com/medline/citation/33026453/Analysis_of_Genomic_Characteristics_and_Transmission_Routes_of_Patients_With_Confirmed_SARS_CoV_2_in_Southern_California_During_the_Early_Stage_of_the_US_COVID_19_Pandemic_ L2 - https://jamanetwork.com/journals/jamanetworkopen/fullarticle/10.1001/jamanetworkopen.2020.24191 DB - PRIME DP - Unbound Medicine ER -