COVID-19 experts answer questions about Omicron variant – and where it could come from

University of Washington researcher Pavitra Roychoudhury (left) and Fred Hutch Emeritus Director Larry Corey. (Photo UW and Fred Hutch)

Not much is known about the new COVID-19 variant Omicron, but what scientists have seen so far has made them wary.

The variant has dozens of mutations – some suggest that it can spread quickly and undermine protection from vaccines and natural immunity. It is happening in an area in South Africa including Johannesburg, as cases increase, and it was found in specimens from Europe as early as November 19.

Scientists are trying to learn more about it. How well will the vaccine work against Omicron? Do mutants carry a real-world bite? Is it capable of outperforming Delta?

In the coming weeks and months, the answers to such questions will become clear. And researchers in Seattle will have a key role to play in answering them.

Doctor-scientist Fred Hutch said: “The scientific community has really rallied together since the very first posting of this variant. Larry Corey. Researchers in South Africa and Botswana came up with sequences of the variant earlier this month, shortly before the World Health Organization designated it a “variant of concern” last week and named it as “Omicron”.

Corey is the leader COVID-19 Prevention Network, a research consortium that has coordinated large clinical trials for several COVID-19 vaccines and will investigate Omicron. He and his colleagues have a longstanding scientific partnership with the Medical Research Council of South Africa and other groups evaluating Omicron in South Africa, dating back to decades of HIV vaccine research collaboration.

Fred Hutch researchers Jesse Bloom and Trevor Bedford have also spearheaded the sequence analysis of the variant and begun assessing its potential risk. Bedford, who recently won a “genius grant” from MacArthur, co-developers the open source platform Nextstrain, which generates real-time views of the virus’ “family tree”.

GeekWire spoke with Corey and with Pavitra Roychoudhury, who oversees vaccine variant testing efforts at the University of Washington School of Medicine’s virology lab, which handles a large percentage of the state’s COVID-19 tests. We asked why scientists are interested in Omicron, how they plan to assess the variant, and how to know when it has reached Washington. Corey also has an idea of ​​its origin.

Why are scientists interested in Omicrons?

Omicron carries a large number of mutations found in other variants, as well as new variants. Some mutations are associated with reduced response to vaccination or immunity from natural infection, and they may also make monoclonal antibody therapy less effective. Additionally, the variant has some of the same mutations that seem to have made Delta highly infectious, Corey said. “This is a completely novel human-derived variant,” he added.

However, whether the virus is as deadly as it is in its sequence will need to be tested in the lab first. “We have to validate those problems functionally,” he said.

Scientists are also concerned about how the virus behaves in human populations. Corey said the Johannesburg area where the variant is increasing had a major outbreak of the Delta variant five months ago.

“It is known that many people who bought Omicron were infected with Delta before, because they have a registry to confirm COVID cases. So we know it can break through Delta,” and seem to overcome natural immunity, Corey said. “It’s not 100% yet, but the data is highly suggestive.”

Corey and other virologists note that they are just beginning to learn about this variant. It’s still not clear to scientists how all the mutations can interact – sometimes different mutations. can even cancel each other.

“At the end of the day, you have to think together about all the mutations and how it affects the virus,” says Roychoudhury. “I think it remains to be seen what the real impact will be.”

What lab experiments will scientists do to evaluate omicrons?

In key laboratory experiments, the researchers will investigate how well antibodies from vaccinated individuals neutralize the virus. They will test for the whole live virus and its components, such as the “mutant” protein, the part of the virus that the vaccine targets, Corey said. The answers from these lab experiments should give scientists a good idea of ​​how the vaccine will work against the variant. But more precise data would require data on human populations.

How long will the lab experiments take, when will we know more?

“Many labs are starting to do this and hopefully the data coming out will be very consistent and tell us exactly what’s going on,” Corey said. “In my opinion, it will take anywhere from ten days to two weeks to get any information that is actually an accurate result.”

What types of data will be collected on human populations in South Africa?

“Working with the South Africans, who are measuring the outbreak there, is very important,” Corey said. About 30% of the country is vaccinated, mostly with Pfizer/BioNTech and Johnson & Johnson shots, allowing comparisons between vaccinated and unvaccinated populations. Researchers were able to collect data such as hospitalization rates and disease severity in vaccinated and unvaccinated people, Corey said. “All of this information is needed for us to understand the magnitude of this outbreak.”

Omicron (red) has a high number of mutations in the region of the ‘mutant’ protein (S1) compared with other variants. (Nextstrain plot)

Will Omicron reach Washington state?

Roychoudhury said it was more likely that there were cases in the state. “And if that’s the case, we’ll eventually catch it [with our testing],” said Roychoudhury. “It’s already reached a few European countries and so we think it’s only a matter of time, based on what we’ve seen of other variants and how long it took for us to detect them. here. There has been a lot of travel in the past few months. “However, it remains unclear whether the variant will be able to compete with Delta, the currently dominant bacterial strain in the US and much of the world.

How are UW researchers looking for variation in Washington?

UW labs do a large percentage of the state’s COVID-19 testing, recently averaging about 10,000 PCR tests per day (PCR testing is a more accurate molecular test that usually takes overnight to get results). fruit). The laboratory also randomly samples positive for the variant type using whole-genome sequencing. Washington state has one of the highest rates of variant testing of any state, testing about 11 percent of samples positive for COVID-19 since the start of the year, Roychoudhury said.

How can UW test data help answer questions about Omicron?

Widespread testing for variants can help researchers understand key questions, such as how quickly a variant spreads and the link between infection and hospital admissions and vaccinations. Roychoudhury. “Is it easier to transmit? Does it cause more serious illness? ” she speaks. “And is it evading current vaccines and making those vaccinated sick? And then putting the vaccinated people in the hospital? ”

“They are heroes, for being so open and helping us.”

How did the omicron emerge?

No one knows for sure how Omicron arose. But Corey has a theory.

One possible way to generate new strains of the virus is by long-term incubation of an immunosuppressed individual. That gives the virus time to evolve and adapt to infect cells more efficiently or to better avoid an immune response.

Corey wrote about the evidence for the evolutionary path of this COVID-19 virus in a recently published with researchers Fred Hutch, Trevor Bedford and other colleagues. “Unfortunately, that might be what happened here,” Corey said.

“It probably came from someone who was immunosuppressed with long-term COVID who developed the disease, and then passed it on in families, then in the community,” he said. “And then we can have a few other transmissions as it adapts a little bit. That’s how these strains come in. ”

Corey added that the rise of the new variant “illustrates the importance of global vaccination policy.” Not only is vaccine supply constrained in some countries, said Corey, but vaccine reluctance in South Africa and other regions is also hindering vaccine adoption.

How do the HIV pandemic and the COVID-19 pandemic intersect?

Corey notes that untreated HIV-positive people can potentially incubate the COVID-19 virus for long periods of time. “The most common immunosuppression in sub-Saharan Africa is untreated HIV infection. So you have two intersecting plagues,” Corey said. “Sub-Saharan Africa has the highest rate of untreated HIV infections in the world. So we need to improve the way HIV is handled, especially treatment, as well as relate the COVID vaccination strategy to the HIV identification and treatment strategy.”

What do your colleagues in South Africa say about the world’s reaction to Omicron? Some countries have implemented travel bans.

“They want to make sure that flights into this country aren’t stopped because they need the scientific equipment and supplies to do the research,” Corey said. “And so we must not treat them like pariahs either.” While the wait time before variants spread can help countries prepare, Corey advocates for increased testing at airports and other measures to detect and contain positive travelers. with COVID-19 due to travel bans.

Corey added: “They are heroes, for being so open and helping us.”

Could vaccine companies need to revise their injections?

Corey has overseen record times to launch and complete clinical trials for Moderna, Johnson & Johnson, and other injections, so he knows how to move quickly. If the vaccine needs to be improved against Omicron or another new variant in the future, how long will that take? “We’ll do it as quickly as we can,” he said.

But until more experiments are completed and more data collected, scientists won’t know how well the current vaccine will protect against Omicron, how widespread the variant is, how much its infection and other important questions.

Meanwhile, the US Centers for Disease Control on Monday urged unvaccinated people to get vaccinated and reinforce its recommendations for COVID-19 shots, says that everyone 18 and older “should” get a booster shot. The CDC has previously said some adults under the age of 50 “may” get booster shots.

Corey added: “Honestly, I can say that strengthening is a very good strategy. You want all the antibodies you can get.”

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