Genetic analysis IDs 8 viral lineages
Study concludes pathogen came from all over, so domestic and global travel ban may be needed
Where did the Bay Area’s COVID-19 virus come from? All over.
There is no single smoking gun. No lone Patient Zero. No one case ignited an epidemic that now has infected more than 13,000 and killed more than 300 Californians.
A new UC San Francisco genetic analysis detected at least eight different viral lineages in 29 patients in February and early March, suggesting multiple independent introductions of the pathogen into our state during the earliest days of the pandemic.
By now, “there are almost certainly many, many more,” said Dr. Charles Chiu, a professor of laboratory medicine at UC San Francisco, who directed the 23-member project.
Comparing viral genomes in nine Bay Area counties, “it’s like sparks entering California, from different sources, causing multiple wildfires,” he said.
The finding has implications for the state’s public health policy, revealing that the Bay Area is vulnerable to new introductions in the months ahead, even as we diligently shelter in place to contain outbreaks.
If the virus keeps crossing borders, “then the suspension of nonessential domestic and international long-range travel may be necessary to prevent further importation of new cases in California and other states,” the study concludes.
But it’s reassuring that no single lineage is tearing through the region, said Chiu, whose team included universities, county health departments and the U.S. Centers for Disease Control and Prevention.
Like us, the virus’ lineages are diverse, as opposed to a single variant spreading widely from person to person. Several arrived here from Europe; of these, one can be linked to a business meeting in New York. Others came directly from China.
Many are close relatives to the virus in Washington state, the site of America’s presumed first case and inadvertently delivered here by cruise ship passengers.
Even in one single location — an undisclosed large facility somewhere in Santa Clara County — three workers were infected by viruses with genetically different fingerprints. The three sick people didn’t share employers, worked in different areas of the facility and had no known social contact with one another.
The UCSF project has since been expanded and deepened to explore relationships among 120 early cases in Santa Clara County.
The microbes got here the same way so many of us did — via international and interstate travel, by boat and by plane. Then they spread by car.
They’re responsible for several outbreaks of illness in Bay Area homes, workplaces and social gatherings. Several of these early clusters were small and quickly extinguished, due to a quick response from county health officials.
For instance, a San Benito couple, infected in China, never spread the virus beyond their home. A Solano County cluster did not grow beyond the sick patient and her health care workers. Others were larger and may be continuing still.
Epidemiologists said the lab’s discovery reflects the Bay Area’s close and tangled relationship to the rest of the globe.
“It doesn’t surprise me at all, given the extensive contact with academics and techies in the region and Asia, especially China, as well as major capitals throughout the world,” said Dr. Mark R. Cullen, director of the Center for Population Health Sciences at Stanford University’s School of Medicine.
For the same reason, Cullen said, “it’s also not surprising that the largest number of early cases were in Silicon Valley.”
“It makes sense that there would be multiple seeding events,” said biomedical data specialist John Ioannidis at Stanford University’s School of Medicine. “This made containment difficult in the early stages.”
The near-simultaneous introductions may help explain the sudden early acceleration of the illness in the Bay Area.
“We’re beginning to understand that with each introduction, a ‘hotspot’ is created,” said Dr. John Swartzberg, clinical professor emeritus of infectious diseases and vaccinology at UC Berkeley’s School of Public Health.
“Some of these will smolder, some burn out, and some result in a wildfire,” he said. That’s how the virus “got its foothold, and more.”
Similar research efforts are underway elsewhere, with teams conducting genetic analyses in New York City, Connecticut, Washington state and other viral hotspots.
New York, like California, has experienced multiple introductions from around the globe, they’ve found.
In Washington state, there’s one main lineage, believed to trace its roots to China, according to Trevor Bedford, an associate professor at the Fred Hutchinson Cancer Research Center and the University of Washington.
Mysteriously, the virus found in Connecticut looks nearly identical to Washington’s variety.
The UCSF study is a microcosm of what happened over two to three weeks in late February and early March. At that time, more than 50% of the state’s cases were travel-associated.
The research is a viral version of Ancestry.com, where side-by-side comparisons of tiny mutations in genomes from diverse populations and nations can reveal close relationships.
Of the 29 Northern California cases it studied, the UCSF-led team lumped together near-identical viruses into clusters. These clusters shared real-world relationships.
They include: a husband and wife in San Mateo County, infected by someone from China; a San Franciscan infected during a business meeting in New York with European participants; a Solano County resident infected by a Santa Clara County resident, who went on to inadvertently infect two Solano County health care workers; and a San Mateo County resident infected by a traveler from Switzerland.
Nine passengers aboard the Grand Princess cruise ship were sickened by a virus nearly identical to one found in Washington.
Presumably introduced on an earlier cruise, this virus went home with these passengers to San Francisco, Sonoma, Santa Clara and other counties.
The UCSF findings point to the role that interstate travel restrictions can play in protecting places where the virus has not yet gained a foothold — particularly because there is no nationwide shelter in place policy, said Chiu.
Last week, for instance, Kentucky Gov. Andy Beshear forbid residents from traveling to other states.
Such travel restrictions needs to be considered in light of the huge economic and social impact they create, Chiu said.
“There’s no good way to stamp it out if you constantly have more sparks coming in,” he said.
“The airlines are still flying to New York, Chicago, Europe. There is no way we can screen all passengers going back and forth. There’s such a large movement of people.”