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Genomic surveillance reveals multiple introductions of SARS-CoV-2 into Northern California

Our take —

This study describes sequencing and phylogenetic analysis of SARS-CoV-2 from cases in northern California and two voyages of the Grand Princess cruise. The authors identify multiple independent introductions of the virus into the region, with limited evidence for a dominant circulating lineage. They find that the virus on the Grand Princess cruise likely originated in Washington state, and find evidence of transmission of the virus between two different cruise voyages. Travel histories from several patients allowed the authors to support a previous hypothesis that the outbreak in New York was seeded by travelers from Europe. This study shows the value of analyzing sequence data in the context of epidemiological information, and the authors point out that minimizing transmission of the virus is essential to keeping numbers low enough that contact trancing and epidemiological tracing remains possible.

Study design


Study population and setting

This study generated and analyzed 36 SARS-CoV-2 virus sequences collected from COVID-19 cases diagnosed from January 29 to March 20, 2020, in 9 counties in northern California. Samples came from hospitals and clinics at the University of California, San Francisco, the California Department of Public Health, and 8 county public health departments in Northern California. The study population also included 11 samples from two voyages of the Grand Princess cruise ship in February and March 2020.

Summary of Main Findings

The authors used two laboratory methods to sequence the virus contained in 62 respiratory swab samples from 54 COVID-19 patients and generated 36 SARS-CoV-2 sequences from 36 unique patients. They found evidence for multiple unrelated introductions of the virus into northern California, and did not identify a single predominant lineage. They incorporate detailed epidemiological information about patient contacts and travel histories, and found that the virus on the Grand Princess cruise ship was closely related to the strain responsible for the first reported case in Washington state. The virus sequences from two travelers from New York to California were similar to sequences from Europe, supporting previous evidence that the New York outbreak that began in March 2020 was seeded from Europe.

Study Strengths

Analyzing the viral genomes in the context of epidemiological information such as patient contacts and travel histories greatly strengthens the conclusions in this study. Travel histories in particular allow the authors to epidemiologically confirm connections suggested by their sequence data and those from previous studies.


Due to small sample sizes, the authors are not able to make definitive conclusions about viral transmission routes.

Value added

This paper clearly highlights the importance of analyzing genomic data in the context of epidemiological information. Although the conclusions presented are epidemiologically supported with appropriate caveats, their findings about SARS-CoV-2 transmission are not particularly new or surprising given the large number of viral sequences and many other analyses currently available.

This review was posted on: 15 July 2020