“This finding tells us that by focusing on antibodies that target these highly conserved sites on the spike protein, there is a way to overcome the virus’ continual evolution,” said David Veesler, an associate professor at the University of Washington School of Medicine in the US.
The Omicron variant has an unusually high number of 37 mutations in the spike protein, which the virus uses to enter and infect the human cells.
It is thought that these changes explain in part why the variant has been able to spread so rapidly, to infect people who have been vaccinated and to reinfect those who have previously been infected.
“The main questions we were trying to answer were: how has this constellation of mutations in the spike protein of the Omicron variant affected its ability to bind to cells and to evade the immune system’s antibody responses,” Veesler said.
To assess the effect of these mutations, the researchers engineered a disabled, nonreplicating virus, called a pseudovirus, to produce spike proteins on its surface, as coronaviruses do.
They then created pseudoviruses that had spike proteins with the Omicron mutations and those found on the earliest variants identified in the pandemic.
The researchers first looked to see how well the different versions of the spike protein were able to bind to protein on the surface of cells, that the virus uses to latch onto and enter the cell. This protein is called the angiotensin converting enzyme-2 (ACE2) receptor.
They found the Omicron variant spike protein was able to bind 2.4 times better than spike protein found in the virus isolated at the very beginning of the pandemic.
“That is not a huge increase but in the SARS outbreak in 2002-2003, mutations in the spike protein that increased affinity were associated with higher transmissibility and infectivity,” Veesler noted.
They also found that the Omicron version was able to bind to mouse ACE2 receptors efficiently, suggesting Omicron might be able to “ping-pong” between humans and other mammals.
The researchers then looked at how well antibodies against earlier isolates of the virus protected against the Omicron variant.
They did this by using antibodies from patients who had previously been infected with earlier versions of the virus, vaccinated against earlier strains of the virus, or had been infected and then vaccinated.
The team found that antibodies from people who had been infected by earlier strains and from those who had received one of the six most-used vaccines currently available all had reduced ability to block infection.
Antibodies from people who had been infected, recovered, and then had two doses of vaccine also had reduced activity, but the reduction was less, about fivefold, clearly demonstrating that vaccination after infection is useful.
Antibodies from people, in this case a group of renal dialysis patients, who had received a booster with a third dose of the mRNA vaccines produced by Moderna and Pfizer showed only a 4-fold reduction in neutralising activity.
“This shows that a third dose is really, really helpful against Omicron,” Veesler said.
All but one antibody treatments currently authorised or approved to be used with patients exposed to the virus, had no or had markedly reduced activity against Omicron in the laboratory.
The exception was an antibody called sotrovimab, which had a two- to three-fold reduction of neutralising activity, the researchers said.
However, when they tested a larger panel of antibodies that have been generated against earlier versions of the virus, the researchers identified four classes of antibodies that retained their ability to neutralise Omicron.
Members of each of these classes target one of four specific areas of the spike protein present in not only SARS-CoV-2 variants but also a group of related coronaviruses, called sarbecoviruses.
These sites on the protein may persist because they play an essential function that the protein would lose if they mutated. Such areas are called “conserved.”
The finding that antibodies are able to neutralise via recognition of conserved areas in so many different variants of the virus suggests that designing vaccines and antibody treatments that target these regions could be effective against a broad spectrum of variants, Veesler added.