COVID boosters aim just at omicron. This lab is going after coronaviruses not seen yet

PHILADELPHIA — Her gloved fingers working quickly yet carefully, Garima Dwivedi filled row after row of little wells on a plastic laboratory plate, pushing a button to squirt drops of clear fluid she had extracted from the blood of mice.

The mice had been vaccinated against a coronavirus infection. Like so many other scientists throughout the COVID-19 pandemic, Dwivedi wanted to see if the animals had responded by making antibodies.

But not just for this coronavirus. This new vaccine, in the University of Pennsylvania lab of Drew Weissman, is designed to protect the world against multiple coronaviruses — including those we don’t know about yet.

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At the University of Pennsylvania, Garima Dwivedi analyzes serum from mice that have been vaccinated against multiple coronaviruses.

Weissman’s research on messenger RNA helped pave the way for the original COVID-19 vaccines, as well as the new boosters tailored to the omicron variant. Yet even before the FDA cleared the initial shots from Pfizer and Moderna, in late 2020, the Penn scientist was worrying about the next pandemic.

In less than 20 years, at least three dangerous coronaviruses have jumped from animals to humans. Before the COVID-19 virus emerged in late 2019, there were SARS and MERS, each of which sickened thousands of people worldwide. A fourth new coronavirus, little known outside China, has so far been found only in pigs. But it’s a grim one, having killed thousands of animals since 2016.

More than a dozen teams of scientists worldwide are now racing to stay ahead of the next one by developing what’s known as pan-coronavirus vaccines. Weissman, 63, is involved with four of them.

Some are designed to guard against all future variants of the COVID-19 virus, as well as the older SARS and MERS. Others might also protect against less closely related coronaviruses that so far have been found only in bats. Some might even work against ones that cause the common cold.

For years, other scientists have tried to make a similarly broad, one-and-done vaccine against the flu, with limited success. But early evidence from Weissman’s lab and others suggests that with coronaviruses, the challenge may be more surmountable. He says we can’t afford not to try.

“Coronaviruses have caused three epidemics in the past 20 years,” he said. “We have to assume there will be more.”

Tyger Williams/The Philadelphia Inquirer

In Drew Weissman's lab at Penn, Benjamin Davis is testing the proteins in a new type of vaccine that would protect against multiple coronaviruses.

The first COVID-19 vaccines taught the immune system to recognize, and make antibodies against, the coronavirus spikes — the dozens of little proteins that stick out from the surface of each virus particle.

That made sense. The virus uses these spikes like a lock pick, breaking through the membranes of cells in humans and other animals. But in someone who’s been vaccinated, antibodies latch onto this lock pick so that it no longer fits a certain receptor on the cell’s exterior — the equivalent of a keyhole.

In the early rush to develop a vaccine, scientists reasoned that was enough. No need to teach the immune system about the rest of the virus if the spike can’t get through the front door.

Then came the delta variant, followed by omicron. The spike picked up a series of shape-shifting mutations that somehow allowed it pull off a double stunt: avoiding recognition by the antibodies, yet still fitting the lock well enough to open the door.

That’s where the next-generation vaccines come in.

In Weissman’s lab at Penn, Dwivedi was testing mice for their response to one of them: a viruslike particle that contains both the spike and other structural proteins.

The idea is that while the spike can change its shape and retain the ability to penetrate a cell, the other proteins appear to be similar across multiple COVID-19 variants — and even across multiple types of coronaviruses. Teach the immune system to recognize these shared proteins, or so the theory goes, and it will be prepared to ward off a variety of threats.

But first, it has to work in mice.

“It’s important to see the response in the animals before you even think about injecting the vaccine in humans,” Dwivedi said.

Nearby, colleague Benjamin Davis was analyzing the viruslike particles to make sure they contained the correct proteins. Magnified many thousands of times on an electron microscope, each particle looked like a child’s drawing of the sun — a blank circle with little rays all around the edge.

Basically, it’s a coronavirus with nothing inside — festooned with enough different proteins to give the immune system a chance to develop an array of defenses, yet lacking the internal machinery it would need to cause a real infection.

“It’s like an empty shell,” Davis said.

Predicting the next pandemic

But how real is the threat?

Using a combination of demographic and antibody data, one recent study suggests that coronaviruses are jumping from bats to humans far more often than is commonly appreciated — likely thousands of times a year.

In most cases, these spillovers appear to fizzle out, says Ken Field, a Bucknell University biologist who studies the immune system of bats. The virus may have picked up the ability to jump from animal to human, but not the ability to make copies of itself inside the person — nor the ability to be transmitted from that person to the next.

Still, if viruses jump from animals to humans thousands of times a year, every so often it’s going to be a bad one.

Weissman, the Penn scientist, likens it to rolling the dice.

“In most cases, they just burn out,” he said. “But every so often, you get a bad roll.”

Not that bats have a lock on transmitting viruses to humans. The flu originally came from birds. Other viruses come from rodents, foxes or raccoons. The key is to exercise caution when interacting with wild animals of all kinds, Field said.

But with continued clearing of forests, industrial farming, and air and rail service connecting formerly isolated areas, risky exposures may be on the rise.

“We’re making further and further incursions into what used to be wild areas,” he said. “The animals leave those areas and come out.”