‘You Dirty Rat’: Experts Posit That Omicron Hatched in Rodents

The number of mutations to the spike protein in Omicron suggests a very different evolutionary trail than had been seen in other iterations of COVID-19, say some experts.

Kevin Kavanagh, MD, a member of Infection Control Today®’s (ICT®’s) Editorial Advisory Board, has sounded the alarm for months about the dangers posed by the fact that COVID-19 can jump from humans, to animals, and then back again (or vice versa), and pick up more mutations along the way. Kavanagh most recently noted this possibility in a Q&A with ICT® on November 22. In that interview, Kavanagh said that “deer apparently live with COVID-19 quite well, but, yet rapidly spread it amongst the herds. And that’s actually very problematic, because if it finds a host that it doesn’t make sick, but yet it can mutate and change and then reinfect other animals and plus mankind, that is one of the worrisome scenarios that could take place.”

Turns out that this “worrisome” scenario might be what brought Omicron about, except the animal culprit isn’t a deer but a rodent. As STAT reports this morning, other experts have started to echo Kavanagh’s concern when it comes to animal hosts. It’s possible that in mid-2020, rodents were infected with SARS-CoV-2, where the coronavirus evolved. Researchers have said that Omicron contains anywhere from 43 to 50 mutations to its spike protein. Delta has 18 mutations.

Kristian Andersen, an immunologist at the Scripps Research Institute, tells STAT that “I know that most people think that these [come from] immunocompromised individuals, and I do think that that’s plausible, but to be perfectly honest, I actually think this reverse zoonosis followed by new zoonosis seems more likely to me given just the available evidence of the really deep branch, and then the mutations themselves, because some of them are quite unusual…. I don’t think we should dismiss that possibility, because I think it’s definitely on the table.”

SARS-CoV-2 is what experts call a promiscuous virus, able to infect a number of species. Most experts are cautious when it comes to trying track the evolution of Omicron, and many believe that that evolution took place in an immunocompromised person. But more experts are looking into the possibility that Omicron had been hatched in a rodent.

STAT talks to Robert Garry, PhD, a professor of microbiology and immunology at Tulane Medical School, who says that 7 SARS-CoV-2 mutations allow it infect mice and rats, and all 7 can be found in Omicron.

Angela Rasmussen, PhD, a coronavirus virologist at the University of Saskatchewan’s Vaccine and Infectious Disease Organization, tells STAT that “I think it’s pretty obvious to everybody … that this virus has been on an independent evolutionary track for quite some time and it’s very surprising, which to me just kind of goes back to say well, the idea that this could be … plausible,” she said.

Kavanagh has thought that the idea is plausible for some time.

The hope, for a while now, is that COVID-19 become endemic. That we learn to live with it the same way we live with other seasonal—but not lethal—maladies such as influenza and the common cold.

Back in January 2021, Kavanagh noted that the reason we’ll need to learn to deal with endemic COVID-19, and not something that can be completely eradicated with a vaccine—such as smallpox—is that SARS-CoV-2 can jump from humans to animals and back again. “The problem is, if you have animal hosts, if your immunity drops––and it will over a couple of years––they’ll just reinfect you,” Kavanagh said in a Q&A with ICT®. “The idea of going out getting infected and the virus will go away, that’s not going to happen. It’ll get better, infections will drop dramatically, [and] we can return to a more normal life. But I think right now, it’s going to be pretty much endemic either in animals or in ourselves.”

Kavanagh again cited the danger posed by animal hosts in an article that he wrote for ICT® in August, when concern arose over that the more lethal Lambda variant, which displayed earmarks of potentially evading antibodies produced by vaccines or prior infections, and might be able to shove aside the dominant Delta variant. (That didn’t happen.) In that article, among other things, Kavanagh cited a study by the United States Department of Agriculture that showed that 40% of 385 samples taken from white tail deer were positive for SARS-CoV-2. Kavanagh noted that white tail deer are abundant near urban settings and that “this is very problematic; control may involve special handling and precautions when around deer, or even possible culling.”

It may certainly be problematic for the pharmaceutical companies that manufacture the COVID-19 vaccines and booster shots.

Stéphane Bancel, the CEO of Moderna, told the Financial Times that he worries that the vaccine his company manufactures (which some studies show to be more effective than the Pfizer/BioNTech and Johnson & Johnson vaccines) might not be as effective against Omicron as it has been against the Alpha and Beta strains of COVID-19, the original dominant strains until Delta.

“I’ve been told they can design a new vaccine in three days,” Kavanagh told ICT® in a Q&A on July 27. “And that’s great news, but you can’t make 300 million doses and get them in arms that quickly, especially when you have half of the country being anti-vaxxers and not wanting to take the vaccine.”

Garry, of Tulane Medical School tells STAT that he predicts that “we’re going to have to keep tweaking the vaccines.”