University of California San Francisco researchers believe at least seven different COVID-19 lineages made their way into California.

Genome detectives using a method called “Genomic epidemiology,” tracked the virus evolution and spread in Northern California from late January to mid-March 2020.

Samples from 36 patients spanning nine counties and the Grand Princess cruise ship were tested.

Researchers just published a paper with their findings.

Swab Samples Screened

Scientists screened 62 respiratory swab samples from 54 COVID-19 patients available from hospitals and clinics at UCSF, the California Department of Public Health (CDPH), and eight county public health departments in Northern California.

The patient samples included:

• 11 samples from the Grand Princess cruise ship, during its two voyages from San Francisco to Mexico and Hawaii in February and March 2020
• 3 samples from a Solano County cluster that included the first reported case of community transmission in the U.S. with subsequent spread to two healthcare workers
• 7 samples from Santa Clara County from a cluster associated with workspace transmission
• 3 samples from patients who contracted the infection from a sick contacts
• 5 samples related to domestic or international travel
• 7 samples from additional cases of community transmission

COVID-19: Dispersed Across the Evolutionary Tree

Here is how the genomes from the samples broke down:

• 14 in the Washington State lineage
• 10 in a lineage associated with the Santa Clara County outbreak cluster
• 3 from a Solano County cluster of 3 individuals
• 5 related to lineages circulating in Europe and New York
• 4 related to early lineages from Wuhan or other regions of China (including 2 patients from San Benito County with identical genomes)

Grand Princess Cruise Ship

A large outbreak was associated with the Grand Princess (with at least 78 confirmed positive cases out of 469 tested) as of March 26.

The chronology of the cruise ship outbreak suggested that the virus likely came from Washington state, although the cases may also have originated from a different region in which the original strain is circulating.

Santa Clara County Outbreak

UCSF researchers also studied seven genomes from individuals who were part of a local outbreak of COVID-19 at a large workplace facility with multiple employers, large areas of shared space, and heavy pedestrian traffic.

Four employees had dates of symptom onset within two weeks of each other, although they did not know each other.

It’s noted in the report that genomes from a Solano county resident and a San Mateo couple were also placed in the Santa Clara County outbreak cluster, suggesting possible spread to different counties. But, further investigation found the Solano County resident had visited a merchant in Santa Clara, during which he likely became infected.

Washington Outbreak

The study’s authors write there is growing evidence the Washington outbreak has lineage spread across the United States.

Washington lineage viruses have been identified in COVID-19 cases from many states including Minnesota, Connecticut, Utah, Virginia, and New York.

A copy of the entire article is below.