Researchers in La Jolla sound alarm about U.K. coronavirus variant and new reopenings

Brenda Alva helps her daughter Natalia, 8, put her face shield back on after taking a coronavirus test.
Brenda Alva helps her daughter Natalia, 8, put her face shield back on after taking a coronavirus test at a San Diego County testing center.
(Sam Hodgson / The San Diego Union-Tribune)

An increase in social contact, a UCSD modeler warns, could be just the thing to cause infection rates to explode as the strain achieves dominance.


Many are celebrating this week’s lifting of California’s regional stay-at-home order and the increase in opportunities for outdoor dining, youth sports competition and other social gatherings.

But researchers at UC San Diego and Scripps Research in La Jolla, as well as other institutions, warned that the coming dominance of a new viral variant first spotted in the United Kingdom makes this the wrong moment to take any action that could increase the community’s collective amount of social contact.

Newsom says dropping infection rates influenced his canceling of the weeks-long order, which allows hair and nail salons to reopen and restaurants to resume outdoor dining.

Standing before the San Diego County Board of Supervisors on Jan. 26, Natasha Martin, a university infectious-disease modeler with a doctorate in mathematical biology from Oxford University, noted that B.1.1.7, the variant first seen in San Diego County on Dec. 30, is estimated to be 50 percent to 70 percent more transmissible than initial versions that swept across the globe after popping up in China.

Things are much different today than they were in late 2019 and early 2020, with vaccines now increasingly available and significant indications that they will be effective against the new variant, at least to some extent. But experts say it is necessary to vaccinate a large percentage of the population — many estimate 70 percent — to achieve a level of herd immunity capable of keeping infections from spreading rapidly from person to person.

A new study led by scientists at the La Jolla Institute for Immunology suggests that T cells try to fight SARS-CoV-2, the coronavirus that causes COVID-19, by targeting a broad range of sites on the virus.

Martin’s presentation before the board made the case that, while vaccination is ramping up significantly, a surge in the amount of social contact, combined with B.1.1.7’s significantly greater ability to spread, could cause a surge in infections that outpaces the vaccination effort.

“In a scenario where contact rates increase, in two weeks’ time, due to reopening activities, a substantial surge would occur, exceeding our health care capacity, in all of the scenarios, even with vaccination,” Martin said.

Because it is capable of spreading more quickly than other variants it is competing with, B.1.1.7, is expected to quickly become the dominant variant in circulation, Martin said. The speed at which that transition occurs, she said, is in proportion to the number of people in the population sharing space, and air, especially if they’re not wearing masks.

The changeover, she said, is inevitable. It has already happened in the United Kingdom, Portugal and Ireland.

The new variant has been showing up throughout the state, including San Diego County.

Increased amounts of gathering, especially if done without masks, means that San Diego County is “potentially looking at a scenario with 7,000 cases per day.”

That would be significantly more than the record of 4,550 set earlier this month.

So, while many are celebrating the opportunity to get out and about more now that the stay-at-home order is back on the shelf, experts are advising just the opposite.

“I can’t stress this enough; with the emergence of B.1.1.7 and other strains which may be more transmissible and potentially more lethal, now is the time to double down on reducing transmission and expanding vaccination,” Martin said.

“We need to be extremely cautious about reopening and monitoring the situation closely.”

The county’s COVID-19 report Jan. 26 listed 1,434 new cases with still-high but declining numbers of patients in hospital beds with confirmed coronavirus infections. The report listed 46 additional deaths, though increases in deaths reflect infection activity that happened weeks ago.

The state has continued to see declining infection rates, leading to the cancellation of the stay-at-home order.

Fewer infections, officials said, caused models to show significantly decreasing numbers of intensive care admissions into February. Southern California, for example, which the state recently estimated to have 0 percent ICU capacity available, is expected to improve to 33 percent by Feb. 21.

It wasn’t clear whether the state’s models accounted for the expected dominance of the more transmissible B.1.1.7 variant.

It is clear, however, that the U.K. variant currently looks like a San Diego problem rather than a California problem.

The coronavirus update Jan. 25 included an update on B.1.1.7, indicating there had been 90 cases confirmed statewide — 87 of them in San Diego County.

Does that mean the U.K. variant is a localized situation not likely to grow as quickly elsewhere?

Probably not, said Scripps Research immunologist and molecular biologist Kristian Andersen, whose lab, working with positive tests provided by UC San Diego, was the first to confirm the new variant’s presence in San Diego County.

Detecting the presence of B.1.1.7 requires extra work. Tests, only those from certain manufacturers, that come back with two of three genetic targets positive serve as a smoke signal that the U.K. variant may be involved, but additional genetic analysis is necessary for a confirmation.

That means that, in order to detect the variant’s presence, local labs must happen to be using the kinds of tests that have a serendipitous and completely unintentional sensitivity to a deletion in the variant’s genetic code, and local researchers must be looking for those subtle signals and also must be willing to follow up with proper genetic analysis.

Few health departments, Andersen said, have all of those components in place in the way San Diego does.

“It’s certainly not localized to San Diego, although it’s possible that it’s more prevalent in San Diego than most other places,” Andersen said. “Unfortunately, [it’s] impossible to say because of lack of surveillance in most other places.”

With the local research consortium projecting an explosion of new cases and the state predicting declines, especially in intensive care admissions, both could be true, Andersen said. It usually takes weeks for today’s new infections to worsen to the point where a small percentage require intensive care admissions.

“I expect we’ll see ICU admissions go down — probably quite a lot — and plausibly also cases over the next few weeks,” Andersen said.

Such a decrease, he added, will probably be enough to “lull us into a false sense of security that we have turned it around, only to come back up, first gradually, but then rapidly as B.1.1.7 takes over.”

Though still small, he said, the frequency of U.K. variant cases popping up in test results is “doubling roughly every week.”

Vaccination is the other major variable in every coronavirus prediction algorithm.

The scenarios tested by the UCSD/Scripps model assume the region will vaccinate about 6,000 people per day through January and about 20,000 per day in February, with about 50 percent gaining protection from their first dose and 95 percent becoming immune after a second dose.

However, it appeared Jan. 26 that the region is already starting to exceed those vaccination estimates.

Nick Macchione, director of the county’s Health & Human Services Agency and co-chair of its testing, tracing and treatment effort, estimated that county vaccination sites are now delivering about 12,000 vaccines per day. He said he expects the inoculation effort to ramp up quickly to 25,000 doses per day with the opening of additional “supersite” vaccination locations.

“We hope to reach 70 percent of our population well before July 1,” Macchione said.

— Paul Sisson is a reporter for The San Diego Union-Tribune