The new Omicron variant of the pandemic coronavirus has provided an avalanche of mutations, many never seen before, for scientists to ponder. And as with earlier variants, Omicron researchers are focused on numerous changes to the spike protein, which studs the surface of SARS-CoV-2 and allows it to latch on to and invade human cells.
But about 20 Omicron mutations reside outside the spike gene, affecting some of the nearly 30 other proteins made by the virus. Findings published in Nature on 23 December suggest it’s perilous to ignore them.
In the new report, researchers led by University of California, San Francisco, systems biologist Nevan Krogan scrutinize an earlier variant of concern, Alpha, to show how a mutation outside of spike drives up levels of an immune-suppressing viral protein called ORF9b. This little-studied protein temporarily pummels the body’s innate immune response, its first line defense against pathogens, and likely plays a role in infection with the Alpha, Delta, and Omicron variants.
The work emphasizes the importance of looking beyond spike, says Matthew Frieman, a corona virologist at the University of Maryland School of Medicine. “The mutations outside of spike are as important to how the virus replicates and sickens people, if not more, than just spike alone.”
The finding also fits with previous studies showing that SARS-CoV-2 inhibits the body’s essential early warning system for viruses and suggests possible molecular targets for drug development to restore that system. Although the current Nature report only delivers data on the Alpha variant that emerged a year ago, the Delta variant that until recently dominated the globe shares the mutation that boosts levels of ORF9b. And the still-more-contagious Omicron variant is mutated at almost exactly the same spot. “Nobody cares about Alpha now,” Krogan says. “But you should. Because these mutations … exist in Delta and Omicron.”
Other scientists caution, however, that more study is needed to understand whether the mutation has the same effect when acting in concert with Omicron’s dozens of other mutations. Krogan and colleagues are working overtime to understand how Omicron affects ORF9b.
Since Alpha emerged, Krogan’s team has been unfurling how a particular mutation inhibits the crucial molecular messenger interferon. That molecule plays a starring role in the body’s first line defense against infection, tripping off a cascade of immune activity that kills viruses.
In a 2020 Nature paper, the researchers showed that ORF9b, a small SARS-CoV-2 protein known to inhibit innate immunity, binds to another human protein called Tom70, which sits on the surface of the energy-generating organelles called mitochondria. When a cell recognizes viral RNA, Tom70 is vital for receiving and relaying the alarm to other signaling molecules, launching a cascade that causes interferon production.
Then, in two more papers last year, the team identified a possible strategy that human cells use to fight back against ORF9b: slapping phosphate groups onto a couple of the protein’s amino acids. One paper showed the phosphate groups were in the perfect position to prevent the immune-suppressing protein from binding to Tom70.
In the new Nature paper, Krogan and his colleagues confirm that this defensive strategy is working in human cells—but also demonstrate that the Alpha variant can potentially overwhelm it by dramatically ramping up production of ORF9b. The team zeroed in on a mutation in Alpha’s gene for nucleocapsid, a protein that, among many functions, initiates the translation of RNA instructions for the building of ORF9b. (The Delta and Omicron variants have mutations in this same location.) The researchers hypothesized that the mutation essentially lowered the bar for translation, resulting in much more ORF9b protein being made. Sure enough, after adding the Alpha variant to human airway cells in the lab, ORF9b levels skyrocketed compared with levels in cells infected with earlier viral strains. And adding ORF9b alone to human lung cells caused interferon synthesis to plummet.
Finally, the team did a key experiment: Researchers made a mutant form of ORF9b that mimicked the addition of the phosphate groups. They found that the mutant protein could no longer bind to Tom70—and the interferon response recovered. That shows the body’s own trick of adding phosphate groups works to blunt ORF9b’s action.
The research points to possible drug targets, Krogan says. For instance, a compound might turn up the activity of the as-yet-unidentified enzyme that adds phosphates to ORF9b, or physically block the binding of ORF9b to Tom70. Krogan’s team is already searching for such blocking molecules.
“It’s really an important story, and the ORF9b protein, that’s the center,” says Maudry Laurent-Rolle, a virologist and infectious disease physician at Yale School of Medicine.
There are cautions. Although Cecile King, an immunologist at the University of New South Wales, calls the study’s findings “fascinating,” she stresses that its data come from the Alpha variant. “There is no proof that the mutation … is having an impact in Omicron. That’s real speculation.”
But if follow-up work reveals that high levels of ORF9b are also present in Omicron, that will provide “one [possible] explanation of Omicron’s ability to spread so quickly, because it can suppress innate immunity more effectively,” says William Haseltine, a viral genomicist who is chair and president of the nonprofit ACCESS Health International.
The broader message, Frieman says, is that “we have to understand the basic virology of these viruses to be able to develop better therapeutics.”