Many are celebrating Monday’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 a group of researchers at UC San Diego, Scripps Research and other respected institutions warned Tuesday that the coming dominance of a new viral variant first spotted in the United Kingdom makes this precisely the wrong moment to take any action that could increase the community’s collective amount of social contact.
Standing before the San Diego County Board of Supervisors, 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 spotted 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 it is necessary to vaccinate a large percentage of the human population — many estimate it will be about 70 percent — to achieve a level of herd immunity capable of keeping infections from spreading rapidly person-to-person.
Martin’s presentation before the board Tuesday 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.
Simply because it is capable of spreading more quickly than other variants it is competing with, B.1.1.7, Martin noted, is expected to quickly become the dominant variant in circulation. 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 change over, she said, is inevitable. It has already happened in the United Kingdom, Portugal and Ireland.
Increased amounts of gathering, especially if done sans masks, means that San Diego, and California in general, is “potentially looking at a scenario with 7,000 cases per day.”
That would be significantly more than the previous record of 4,550 set on Jan. 7.
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.”
It’s quite a shot across the bow for a situation that has been looking gradually better for 10 days straight.
Tuesday’s county COVID-19 report lists 1,434 new cases with still-high but declining numbers of patients in hospital beds with confirmed coronavirus infections. The report lists 46 additional deaths, but, while tragic, deaths tend to come long after infections. Increases in deaths, then, reflect infection activity that happened weeks ago.
The state, as indicated in briefings Monday and Tuesday, has continued to see declining infection rates, leading to the cancelation 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 has recently estimated to have 0 percent ICU capacity available, is expected to improve to 33 percent by Feb. 21.
It was not clear Tuesday whether the state’s models are accounting for the predicted dominance of the more transmissible B.1.1.7 variant.
An email, sent Tuesday afternoon by officials in the communications office at the California Department of Public Health, said that the “modeling used in projecting ICU capacity takes into account current conditions, including recently observed transmission rates.”
That sentence seems to indicate that the data used to make the decision to remove the stay-at-home order, for the most part, used current trends in the infection rate to predict where things will go in the future rather than trying to predict how a dominant UK variant would change things.
The state agency seemed to confirm that interpretation Tuesday evening, stating in a follow-up email: “if conditions on the ground change, like more widespread transmission, that’s included in the model.”
It is clear, however, that the UK variant currently looks like a San Diego problem, rather than a California problem.
Monday’s coronavirus update included an update on B.1.1.7, indicating that there have been only 90 cases confirmed statewide so far, 87 of them in San Diego County.
Does this mean that the UK variant is just a San Diego problem, 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 UCSD, 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 just two of three genetic targets positive serve as a smoke signal that the UK 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 smoke 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 that San Diego does, meaning that many of the positive tests results coming back daily in San Diego and everywhere else are caused by the variant.
“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.”
As to the seemingly opposite predictions, with the local research consortium predicting an explosion of new cases and the state predicting declines, especially in intensive care admissions, both, Andersen notes, could be true.
After all, 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,” he 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.”
While still small, he said, the frequency of UK variant cases popping up in test results is “doubling roughly every week.”
Of course, vaccination is the other major variable in every coronavirus prediction algorithm.
The scenarios tested by UCSD/Scripps model assume that 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 becoming immune after a second dose.
However, it appeared Tuesday that the region is already starting to exceed those vaccination estimates.
Nick Macchione, director of the county’s health and 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 “super site” vaccination locations, including one in East County that is to be run by Sharp HealthCare and two more in North County, one operated collaboratively by Palomar Health, Tri-City Medical Center, UC San Diego and the county health department. Another, serving coastal North County, is to be run by Scripps Health.
“We hope to reach 70 percent of our population well before July 1,” Macchione said.
The county health department is set to take additional questions about coronavirus Wednesday during its regular weekly COVID-19 media briefing.
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UK variant, UCSD researcher warns, looks like a COVID-19 time bomb - The San Diego Union-Tribune
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