Genetic Analysis Suggests Multiple Introductions of SARS-CoV-2 in Southern California

Nurse practitioner Alexander Panis awaits his next patient at a mobile COVID-19 testing station in a public school parking area in Compton, California, just south of Los Angeles, on April 28, 2020. – St. John’s Well Child and Family Center is providing COVID-19 testing sites in African-American and Latino communities which have been neglected in terms of testing as compared to wealthier areas of Los Angeles County. (Photo by Robyn Beck / AFP) (Photo by ROBYN BECK/AFP via Getty Images)
SARS-CoV-2 isolates from patients in Los Angeles, California, to isolates that originated from Europe and compared Los Angeles strains with strain distributions found in New York City, Washington state, and China were compared.

An analysis of SARS-CoV-2 genomes from patients in Los Angeles, California, suggested they are predominately related to isolates that originated in Europe, according to study data published in JAMA Network Open. The study found that these isolates are similar to strain distributions found in New York, and highlights the precision of technology currently available to detect transmission and accurate contact tracing via SARS-CoV-2 sequencing.

The SARS-CoV-2 viral genomes were sequenced from a cohort of 192 consecutive patients who tested positive with reverse transcription-polymerase chain reaction. Participants were evaluated at Cedars-Sinai Medical Center in Los Angeles from March 22 through April 15. The isolates were compared with genomes from global subsampling  from New York City, Washington state, and China.

A phylogenetic analysis including 133 of the isolates collected in Los Angeles found 13 patients belonged to one cluster. A community transmission event was observed in a tightly associated cluster containing 5 patients who all shared the same single nucleotide variation. Another cluster of 10 isolates contained 5 patients who were residents of the same skilled nursing facility, 1 patient who lived a block away from the skilled nursing facility, and 3 healthcare workers who likely had contact with patients from the same facility.

The Los Angeles samples were also distributed throughout all clades of the global distribution, indicating multiple introductions to Los Angeles. The analysis showed that 15.0% of the Los Angeles isolates were similar to the Asian lineage and 82.0% were similar to the European lineages. Furthermore, more than half of the Californian isolates were found in a clade containing predominately North American isolates. Phylogenetic analyses with the genomes from New York, Washington state, and China found shared similarities to all subclades derived from these regions.

All of the sampled genomes came from patients hospitalized with COVID-19 and may be a biased sample, according to investigators. Other study limitations include an inability to draw directionality from the data and the potential for misinterpreting multiple introductions from under sampled locations as community spread.

Based on the phylogenetic analysis investigators believe “the large impact of COVID-19 on the Los Angeles community likely originated from independent disseminations of the virus from multiple routes, with some geographical strains having greater prevalence than others.”  

Disclosure: A study author declared affiliations. Please see the original reference for a full list of author’s disclosures.


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.