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.
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.
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