Scripps Research and UCSD win $2.5 million CDC contract to track coronavirus spread across San Diego

A simulated view of the coronavirus that causes COVID-19.
A simulated view of the coronavirus that causes COVID-19, showing the surface spike proteins the virus uses to slip inside human cells.
(Lorenzo Casalino, Amaro Lab, UC San Diego)

Scientists are studying the virus’ sequence to understand how it’s moving through communities.

La Jolla’s Scripps Research and UC San Diego have been awarded a $2.5 million contract from the Centers for Disease Control and Prevention to use genomics to track the spread of the COVID-19 coronavirus in San Diego County.

There’s a lot of virus to track these days. The county posted a single-day record of 661 new cases Nov. 12 as residents braced for a new round of closures and other restrictions that started this weekend because of the county’s surging case rate. The record jumped to 736 new cases Nov. 14.

La Jolla restaurants, retailers, gyms and other businesses are adapting their plans and hoping to weather the latest round of restrictions as San Diego County moves into the state’s most restrictive COVID-19 tier.

According to researchers’ estimates, 80 percent of coronavirus cases result from “superspreading” events in which a single person infects an unusually large number of people.

SDSU investigation illustrates how patterns of transmission can emerge

Superspreading events can be deadly. They’re also detectable, said Kristian Andersen, whose lab at Scripps Research has used genomic sequencing to track viruses for more than a decade, from Ebola in West Africa to Zika in the Americas. He first approached San Diego County in January to discuss using genomics to track the virus that causes COVID-19.

Here’s the idea: As a virus spreads, it makes copies of itself. Over time, those copies pick up mutations. By looking at the genetic sequence of viral samples, researchers can map how closely they are related.

“You can think of these as family trees,” Andersen said. “We can say things like, ‘Well, this is a child of that one, this is a sister of that one, this is a cousin of that one.’”

If sequences from people who attend a single event are nearly identical, it is likely a superspreading event.

Andersen, colleagues at UCSD and county officials have worked together to use sequencing to investigate outbreaks at universities, skilled nursing facilities and other locations.

The information from these studies can shed light on which public health policies successfully contain the virus and which ones don’t.

Lately, it hasn’t been looking good.

“Really early on, San Diego was characterized by a lot of individual transmission changes, none of them very successful. These are examples of the virus coming in, stuttering a little bit in the community and then dying out,” Andersen said. “Now we’re seeing much more evidence of stuff that could be superspreading.”

The good news? Researchers know how to reduce the risk of these events: Wear a mask and avoid large indoor gatherings.

Andersen’s team processes a few hundred samples a week. He said the CDC contract will enable the team to scale that up to 1,000 to 2,000.

— Jonathan Wosen writes for The San Diego Union-Tribune. U-T staff writer Paul Sisson and La Jolla Light staff contributed to this report.