What we need to understand about the Omicron variant
How worrisome is Omicron? There are three key questions that help scientists understand how consequential any variant might be.
The first question is whether the variant is more transmissible than the current, prevalent Delta strain? Second, does it cause more severe disease? And third, will it render our immune defenses — from vaccines and prior infections — less effective (a phenomenon known as immune escape)?
On transmissibility, the data, while early, look worrisome. This new variant appears to have taken off very quickly in South Africa, with early national data suggesting the variant already makes up the majority of sequenced cases in the country. It’s possible that this early data will be revised as epidemiologists look closer at factors other than transmissibility, such as whether an early Omicron superspreader event led to the variant appearing more highly contagious than it really is. While this is possible, the more likely scenario is that Omicron does spread more easily than Delta.
Because the variant is so new, scientists simply do not have adequate data yet to assess whether the new variant causes more severe disease. Answering this question will require careful case tracking in hospitals along with expanded viral sequencing efforts, both in South Africa and elsewhere. A key part of this analysis is ensuring that countries are doing adequate testing of a broad sample of people. It will likely take weeks to sort this out. [Continue reading…]
Scientists can’t predict how different mutations will behave when combined, but of particular worry to scientists is that the virus has some 32 mutations in its spike protein, which is what vaccines teach our immune system to recognize and target.
The variant “has a very high number of mutations with a concern for predictive immune evasion and transmissibility,” said Tulio de Oliveira, director of the Centre for Epidemic Response and Innovation, who helped identify the variant in South Africa.
If the spike protein changes, the antibodies elicited by vaccines or an earlier infection can’t recognize it as well. The more changes, the more foreign that spike starts to look to the immune system.
Vaccines generate what’s called a polyclonal response, with lots of antibodies that recognize different pieces of the spike protein. Other variants have had mutations that caused changes in a particular spot on the protein — called an antigenic site — and might have thrown off those corresponding antibodies, but there were plenty of other antibodies that still could recognize the virus.
But with the new variant, “it has so many changes across spike that nearly all the antigenic sites we know about are changed on this virus,” said Wendy Barclay, who leads a U.K. group studying new variants of the SARS-CoV-2 coronavirus. That suggests, Barclay said, that the ability of antibodies “will be compromised in their ability to neutralize the virus” — though she cautioned that scientists need to study that question to confirm it. [Continue reading…]
Theodora Hatziioannou, a virologist at Rockefeller University in New York, said that Omicron’s distinctive mutations raise the possibility that it first evolved inside the body of someone with H.I.V., whose immune systems may have been too weak to quickly fight it off. “Your responses are just not as good,” Dr. Hatziioannou said.
Instead of getting cleared away in a matter of days, the virus may have lingered in that person for months, spending the time gaining the ability to evade antibodies. “This virus has seen a lot of antibodies,” Dr. Hatziioannou said.
Dr. Hatziioannou and her colleagues have been able to produce mutant spike proteins in their laboratory that make viruses highly resistant to Covid-19 antibodies. She said that Omicron has many mutations in the same regions of the spike protein pinpointed in their own research. “The overlap is pretty striking,” she said.
That overlap has Dr. Hatziioannou concerned that Omicron will be able to evade some of the antibodies that people have acquired either from vaccines or from Covid-19 infections. Some monoclonal antibody treatments won’t work against Omicron either, she predicted, because the variant’s spike protein is protected from them.
Still, vaccines are expected to provide some protection against Omicron because they stimulate not only antibodies but immune cells that can attack infected cells, Dr. Hatziioannou said. Mutations to the spike protein do not blunt that immune-cell response.
And booster shots could potentially broaden the range of antibodies people make, enabling them to fight against new variants like Omicron. “We will see, because these studies are only now ongoing,” she said. [Continue reading…]
With 8.2 million HIV-infected people, more than anywhere else in the world, South Africa’s fight against Covid-19 has been particularly complicated as these patients struggle to clear the virus, meaning it can linger in their bodies for longer.
But while many virologists were expecting the next major Covid-19 variant to be an extension of Delta, Omicron is completely unrelated. Instead it combines some of the most problematic mutations seen in the Alpha, Beta and Gamma variants, along with some newly acquired ones. For Ravi Gupta, professor of clinical microbiology at the University of Cambridge, who said earlier this month in an interview with the Observer that he was 80% sure a new super variant would emerge, the evidence so far is worrying.
“It’s not a twist on Delta as people were expecting, but a new thing based around mutations we have seen before all mixed into one virus,” he said. “That worries me. It’s had a long time to adapt and clearly has done a good job if we accept the rapid expansion in South Africa. Without concerted international action now, we are in for many more lost lives globally due to this variant.” [Continue reading…]
Are we actually giving the virus an opportunity to spread unrestricted in certain places and drive its evolutionary trend? It’s basically exposing ourselves to the emergence of more variants. So this was predictable. If the virus has the opportunity to spread unchecked in the population, then we’re giving it multiple ways in which to evolve and adapt.
If we had ensured that everyone had equal access to vaccination and really pushed the agenda on getting global vaccination to a high level, then maybe we could have possibly delayed the emergence of new variants, such as the ones that we’re witnessing. [Continue reading…]