In-Depth: San Diego scientists race to help other labs study omicron variant

Virus Outbreak California
Posted at 7:10 PM, Nov 29, 2021
and last updated 2021-11-29 22:46:07-05

SAN DIEGO (KGTV) — Researchers at the La Jolla Institute for Immunology plan to start shipping materials next week to a constellation of laboratories around the world racing to study the omicron coronavirus variant.

It’s one of several local efforts underway to study the concerning variant, which has prompted travel restrictions in countries where the virus has been detected.

The materials, called reagents, are essentially made-made replicas of omicron that are used to measure immune responses. Each reagent is a fragment of the virus, so it is not dangerous.

“We have a network of collaborators around the world, and we are rushing to not only generate this reagent for us but also to ship it to them,” said Dr. Alessandro Sette, a professor at LJI who is helping lead the effort.

LJI has sent reagents for previous variants to nearly 200 laboratories around the world, he said. Within days, they plan to send the materials to South Africa and other countries impacted by omicron to allow scientists there to launch their own experiments on a critical but less scrutinized arm of our defenses: T cells.

Like many scientists, Dr. Sette suspects omicron can evade some number of antibodies produced by our vaccines. Antibodies are Y-shaped molecules designed to stick to invaders like a coat of tar and feathers, preventing them from infecting cells in the first place.

But the vaccines also train white blood cells, called killer T cells, that can swoop in later and kill cells infected by pathogens that slipped past antibodies. Vaccines also train helper T cells, which can summon more defensive troops.

Dr. Sette’s team has started running detailed computer analyses of omicron. He says the early signs appear positive.

“The indication is that the T cells will be impacted a little bit, but not dramatically,” he said, predicting that 50 percent to 75 percent or more of the T cell response should remain intact.

A strong T cell response means an individual might get sick with mild symptoms but not severely ill.

“I do think that we’ll get a good bit of protection from the currently available vaccines and it’s really important for unvaccinated people to get vaccinated and for those who haven’t been boosted to get in there,” said Dr. Robert Schooley, an infectious disease expert at UC San Diego.

There’s no hard evidence yet that omicron causes more severe disease than delta. Early reports from South Africa indicate infections have mainly been mild, although there are signs the hospitalization rate is growing.

What worries scientists is that omicron has a kind of cloaking device in its genetic code, like delta, which allows the virus to hide from the body’s early defenses. Scientists theorize omicron’s cloaking capabilities may be better than delta’s based on its rate of spread in South Africa, and at least in theory, that might make infections with omicron more severe.

“Viruses that do a better job of turning off the immune response early, like this one, tend to cause people, particularly unvaccinated people, to do not as well,” Schooley explained.

UC San Diego is sequencing samples from every student and staff member who test positive, Schooley said. They’re also sampling wastewater daily, looking for signs of omicron.

Both Dr. Schooley and Dr. Sette suspect the variant is already in the United States. The U.S. only sequences about 3.6 percent of all confirmed cases.