What is really happening with these new Omicron COVID virus variants?

Every week or so there seems to be an impassioned announcement of a new Omicron variant of the COVID virus (SARS-CoV-2) that “threatens our population.” The latest, called XBB.1.5, has arrived with great fanfare. It even has been nicknamed “Kraken” because it is supposedly monstrous!

XBB.1.5 was first identified in the Eastern United States where it has quickly become the dominant COVID virus in that region. But an interesting thing has occurred with the last three Omicron variants (BQ.1.1, XBB.1.1 and XBB.1.5) including Kraken.

Compared to earlier COVID viruses (purple lines) recent variants (black lines) infect more people initially then fall off rapidly in all regions of the world.

All of these viruses arrive and quickly overwhelm other SARS-CoV-2 viruses as the major cause of COVID infections in large regions of the United States. Despite this, the overall number of infections and hospitalizations remains relatively constant, and the viruses seem to fade as quickly as they arrive. There is already data suggesting that XBB.1.5, like the two prior variants, is starting to lose steam despite its dominance.

So, what is happening here? If these viruses are more infectious and menacing than the ones that preceded them, why do they come and go so quickly?

Contrary to what you hear on the news, it now appears that these viruses are not inherently stronger and more dangerous than earlier Omicron variants. Instead, each new variant is mutating to exploit antibody immunity “holes” within our human population. This relates to the last blog post I wrote where I explained how the human population’s combined immunity is now in a battle with the SARS-CoV-2 virus to contain COVID-19.

As I mentioned last week, everyone has a slightly different immune system. We each make antibodies that recognize different parts of virus proteins. When a virus mutates to escape immunity, it alters specific areas of its proteins where neutralizing antibodies bind. People whose antibodies bind to these specific sites lose their antibody immunity and are prone to infection with the new strain. However, not all people recognize this site. Those whose antibodies recognize other parts of the viral protein will still be able to defend against the new variant. In this way each new Omicron variant escapes immunity for only small segments of the population.

Some individuals (subject X) lose antibody protection with COVID virus mutations while others retain immunity (subject Y). This is due to the fact their antibodies recognize different parts of the virus protein. The mutant will infect subject X but not subject Y.

Support for this concept come from the fact that immune escaping mutations are different in each variant, and there is now data showing antibodies from various individuals recognize different sites in variant virus. We can actually look antibodies from each individual and map where they bind to COVID virus proteins. The mutations in new variants correspond to antibody binding sites, but none completely removes antibody protection from the entire population.

Different antibody binding sites in the COVID-19 spike protein (portrayed as red areas). When the virus mutates one area, people whose antibodies bind to that area loose neutralizing immunity and become infected. Cellular immunity recognizes many areas of the protein so it is not easily overcome.

What this means is that each new COVID variant rapidly moves in and infects the subset of the people that lack antibody immunity to the new virus. Once it quickly infects these susceptible individuals it dies out because everyone else has antibodies that neutralize the virus.

Importantly, the reason that recently infected individuals without neutralizing antibodies don’t get deathly ill or die from a new variant is that they have cellular immunity that fights and resolves the infection.

Will the virus eventually mutate all antibody binding sites? The good news is that many mutations make the virus dysfunctional, so although it might be better at escaping immunity to mutate all antibody binding sites doing this results in a virus that can no longer grow or efficiently infect people. When this happens, the virus loses and humans win the battle for survival.

Therefore, while COVID viruses continue to mutate and infect subsets of the human population the disease has essentially reached an equilibrium in the U.S.

This indicates that we have now achieved “herd immune” where the entire human population is reaching a protected state. We will need to maintain this protection by boosting our cellular immunity. This could be accomplished with a yearly or less often booster shot in a similar way that we manage influenza.

In the mean time, unless something radical happens we can tune out the people “crying wolf” whenever a new Omicron variant is identified.

Kudos to Moritz Gerstung for initially highlighting this concept.

Published by jbakerjrblog

Immunologist, former Army MD, former head of allergy and clinical immunology at University of Michigan, vaccine developer and opinionated guy.

One thought on “What is really happening with these new Omicron COVID virus variants?

  1. Thank you – again! – Dr. Baker for injecting sanity that is actually based on science into the Covid vaccination debate. Maybe CDC will get the message and stop trying to shame people into repetitive boosters, and reframe the focus on annual vaccination for the elderly, and specific at risk populations. The other inference I draw from you explanation is that vaccination of children seems particularly pointless since most have likely been exposed to covid and have cellular immunity, and are not at risk of disease/death. Thank you!

    Liked by 1 person

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