The future of COVID mutations depends on this gamble

No wonder the novel coronavirus is mutating. That’s what viruses do. The surprising thing about SARS-CoV-2, the virus that causes COVID, is that it mutates quickly. And two years into the pandemic, it abruptly mutated Yes, really fast – and produced the Omicron variant, whose progeny still dominate around the world today.

The big question now is if and when it will happen again. If and when a new surge of mutations will spawn a new variant even worse than Omicron. There is cause for concern that the conditions for another burst of accelerated evolution are already in place.

The novel coronavirus mutates faster than other pathogens. “The current rate of antigenic evolution of SARS-CoV-2 exceeds that of other viruses,” Richard Neher, a geneticist at the University of Basel in Switzerland and a member of the NextStrain data consortium, told The Daily Beast. “I don’t think we understand the underlying reasons very well.”

Nextstrain’s data visualization depicts the genetic tree of COVID – “phylogeny” is the scientific term – and clearly illustrates the evolutionary trends of the novel coronavirus. During the first two years of the pandemic, the virus mutated steadily, from the original form of SARS-CoV-2 to the alpha variant, then delta.

And then, starting in late 2021, the mutation rate temporarily increased by around a third. The result was Omicron, a variant with so many genetic changes – many of them centered on the spike protein, the part of the virus that helps it to capture and infect our cells – that it was not only more easily transmissible, but for many also increasingly unrecognizable is our COVID antibody.

Scientists call this “immune escape” or “immune escape.” The more immune escape SARS-CoV-2 shows, the less effective our vaccines and therapies are. The latest Omicron subvariants have so much immune evasion built into their genetic makeup that whole classes of monoclonal therapies don’t work at all.

It is of course possible to formulate new vaccines and therapies. But the pharmaceutical industry and the government regulators that approve new drugs are moving at a limited pace. Recently, COVID has been moving faster. The silver lining, if there is one, is that our natural antibodies from previous infections have held up much better than our artificially induced antibodies.

The mutational spurt that created Omicron may have been a genetic fluke. NextStrain data seems to indicate that Omicron has settled down in mid to late 2021 after a heated few months of intense development.

“My personal opinion based on the NextStrain tree is that there were really rapid mutations in the parts of the tree that gave rise to Omicron,” Niema Moshiri, a geneticist at the University of California, San Diego, told The Daily Beast , “but aside from this outlier of the tree, the rest of the tree appears to be mutating at fairly similar rates.”

Since splitting from the alpha variant, Omicron “isn’t mutating 30 percent faster,” Neher said. That might feel like cold consolation considering the fallout when Omicron and its subvariants became dominant. More infections and reinfections. More immune escape.

What if in a month, a year, or two years there’s another sudden surge in mutations that produces a variant worse than Omicron? We have already met the main requirements for another mutation outbreak.

We are now in an arms race between mutations and immunity.

Ironically, all of our antibodies from vaccinations and previous infections helped fuel Omicron’s initial breakneck mutation rate. The more antibodies we throw at the novel coronavirus, the harder the virus works to find a way around those antibodies. “These elevated mutations are in response to the increased immune pressure,” Edwin Michael, an epidemiologist at the Center for Global Health Infectious Disease Research at the University of South Florida, told The Daily Beast.

Now consider how much more contagious Omicron is compared to older variants – and how many more infections there have been, despite the fact that widespread immunity has seen rates of serious illness, hospitalizations and deaths drop somewhat. Antibody resistance fueled Omicron. Now that resistance is even greater.

It’s a paradox. Widespread immunity protects us from one form of COVID only to encourage the development of new and more dangerous forms of the disease. “We are now in an arms race between mutations and immunity,” Michael said.

If it feels like humanity is handling the disease fairly well at the moment, with deaths steadily declining in most parts of the world, it is because we are winning the immunity arms race at the moment. If that changes and the number of deaths increases, it could be because the mutation rate has skyrocketed again. Suddenly the virus wins the arms race.

The devil is in the details. Will the spike accumulate mutations that make the virus more transmissible but not more severe? Will mutations be concentrated in other parts of the pathogen, with unpredictable implications for the effectiveness of vaccines and therapies?

One thing is clear. The virus is everywhere – “hyperendemic” to use an epidemiological term. And “every transmission is an opportunity for mutation,” explained Neher. So new sub-variants and variants will almost certainly come. All we can do is keep tabs on the evolution of the virus, do our best to prepare with updated vaccine boosters, and be ready with new vaccines, therapies, and public health measures as soon as an important one emerges new variant shows.

Expect good seasons and bad. The immunity arms race “will lead to fluctuations in immunity levels and therefore a resurgence of infection in the future,” Michael said. How bad each spike gets in terms of cases and deaths “will be determined by the transmissibility rate and the immune avoidance of emerging variants,” he added.

The best scenario is a virus that doesn’t change too quickly. In that case, “the pandemic will not go away, but will persist with periodic outbreaks,” Michael said. “As long as the mutants don’t get more virulent — which they don’t usually do — and the replay waves aren’t too large, maybe we can live with the virus.”

The worst-case scenario could begin with an increase in mutation rate, as observed by scientists a year ago, before Omicron became dominant. This is a sign that the virus will gain a major advantage over our immunity.

Omicron already evades antibodies from vaccines and therapies. A new variant, repeating Omicron’s 2021 mutation frenzy, could also elude natural antibodies. This could leave us with almost no protection from a rapidly changing virus.

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