Local scientists eyeing whether COVID-19 vaccines work against emerging strains

COVID-19 vaccine doses at the lab of San Diego biotech Arcturus Therapeutics
Arcturus Therapeutics is testing its COVID-19 vaccine. Chief Executive Joseph Payne believes the vaccine will work against emerging strains of the coronavirus.
(Nelvin C. Cepeda / The San Diego Union-Tribune)

A growing list of new strains of the coronavirus is raising questions around whether COVID-19 vaccines will work against these variants, and if so, how well and for how long.

San Diego County’s bustling life science community is looking into the matter, from the region’s research institutes to local biotechs. While researchers say there’s reason to think current vaccines will provide at least moderate protection against even the most concerning strains, they acknowledge that it’s too early to be certain.

“I don’t think people should panic,” said Dennis Burton, an immunologist at Scripps Research in La Jolla. “But I think it’s worrisome.”

On some level, it’s also predictable. That simply has to do with how viruses work.

When a virus infects a cell, it copies its genetic material over and over again. Some of the copies will have mutations, akin to making a few typos after transcribing the same document 20 times.

Most mutations won’t affect the virus much; they might even hurt it. But given enough time, a virus can mutate in ways that enhance its spread.

“[For] a virus, basically its whole reason to be is to change and adapt so that it continues to be able to be as infectious as possible,” said Kate Broderick, senior vice president of research and development at Inovio Pharmaceuticals in San Diego.

The result: A year ago, we spoke of “the coronavirus.” Now, scientists have identified several fast-spreading variants, including ones first found in the United Kingdom, South Africa and Brazil, as well as the “California variant.”

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

Dr. Eric McDonald, San Diego County’s epidemiology director, announced Jan. 21 that there have been at least 97 confirmed or probable local cases of the U.K. variant. The first case was identified in late December by Kristian Andersen’s lab at Scripps Research in partnership with UC San Diego and the county.

The variant, first detected in September, has at least one mutation thought to help the virus latch more tightly onto a cell’s surface, consistent with reports that the virus may be 70 percent more transmissible than previous strains.

On Jan. 19, Pfizer posted data showing that its vaccine likely works against the mutant. The company tested blood samples from people who had been vaccinated and found that their antibodies — immune proteins that can latch onto the surface of a virus — worked equally in preventing the U.K. strain and the original Wuhan strain from infecting cells in the lab. (The study has not gone through the standard process of scientific peer review.)

A quick rundown of what antibodies can (and can’t) tell us about COVID-19

But Burton, an antibody expert, is concerned by additional mutations found in the Brazil and South Africa variants. For the latter strain, there’s already preliminary evidence that the antibodies of people who have recovered from COVID-19 don’t always block the virus from infecting.

“I think you could be hopeful that you would get at least some level of protection from the vaccines,” Burton said. “But the true answer here is we don’t know for sure.”

His lab is studying antibodies that recognize both the coronavirus SARS-CoV-2 and the coronavirus responsible for the 2002-03 SARS outbreak. The hope is that any antibodies capable of grabbing onto both coronaviruses also would likely work against multiple SARS-CoV-2, making them a useful therapy.

Similar work is happening among local biotechs. Inovio was the world’s second company to conduct a clinical trial of a COVID-19 vaccine, which it designed at its San Diego lab. Broderick said the company’s researchers routinely scour online databases for new coronavirus sequences and use computer modeling to project how certain mutations would alter the virus’ structure.

She added that, if necessary, the company can adjust its vaccine, which uses DNA to teach the body to recognize the coronavirus.

Joseph Payne, chief executive of Arcturus Therapeutics, another local biotech, said the same. Similar to Inovio, the company’s COVID-19 vaccine uses a snippet of the virus’s genetic code, but in the form of a molecule known as messenger RNA. Pfizer’s and Moderna’s vaccines essentially use the same strategy.

All of these vaccines are based on the virus’s genetic code, allowing scientists to quickly tweak their design based on the sequence of a new strain.

“If there’s a different mutation out there, all you have to do is swap out one little element,” Payne said. “It could be very quickly addressed — a matter of weeks, not months.”

But for the moment, retooling vaccines is less pressing than quickly deploying existing doses to as many people as possible. San Diego County officials say the region’s goal is to administer 25,000 doses a day and vaccinate 1.9 million residents by July (each of whom will need two shots to maximize immunity).

Coronavirus statistics from March 2020 to June 14, 2021.

The need for a vaccine to help quell the pandemic was reinforced Jan. 22 when the county reported a single-day record 79 COVID-19 deaths, just two days after the previous record of 65. COVID-19 deaths, which are generally reported by the county days or weeks after they occur, are one of the last metrics to rise after a surge and one of the last to fall. So is intensive care unit capacity. The county reported 437 COVID-19 ICU patients throughout the region’s hospitals Jan. 22, a hair below the single-day total of 438 reported the day before.

The region also recorded 68 new hospitalizations and 2,847 coronavirus cases. That’s an uptick in cases from recent days, but there were plenty of backlogged cases among the 49,000 tests the county received — more than twice the seven-day average.

For information on vaccine eligibility and the regional rollout, visit the county’s website, (click on “COVID-19” and “COVID-19 vaccine”).

— La Jolla Light staff contributed to this report.