The Subvariants Are Coming


Science-Based Medicine

Steven Novella  on October 26, 2022

A wave of Omicron subvariants are coming. So get vaccinated.

It sort-of feels as if the pandemic is at least partially over, or at least sliding into the next phase where COVID is more endemic, like the flu. It’s something we have to deal with every year in the background, but life goes on as normal. The problem is – the pandemic is not over.

After the initial phase of the pandemic, prior to the vaccine, we started to tamp down new cases and reduce the severity of infections through better treatment and later through vaccine protection. Then the variants started hitting giving us additional waves of infection, often evading earlier immunity. The WHO warns that we seem to be getting into the next phase of the pandemic, marked by swarms of multiple subvariants.

This is how evolution works. The virus has hit upon a successful configuration of proteins in the Omicron variant, and now is developing variations of the Omicron variant that further evade existing immunity. The new subvariants are all Omicron, but labeled with additional letters and numbers, such as BA.2.75. In this nomenclature, all subvariants are contained within the category prior to each period. So the BA.2 subvariant contain all those that start with BA.2, regardless of any further numbers. Essentially these are variations on variations. The virus is further fine-tuning its ability to infect and avoid immunity.

All these Omicron subvariants have tweaks to the binding region of the spike protein, the place where an antibody will bind to the virus in order to destroy it. By altering the binding location, antibodies are less able to identify and bind the virus. Those viruses better able to evade immunity are more likely to spread, so these variants increasingly dominate and generate even more tweaked subvariants. The WHO tracks variants that impact transmissibility, severity, or immunity, and the list of such variants is growing.

All of this likely means that we are in for another wave of COVID this winter, fueled by these subvariants. It won’t be anything like the initial waves of COVID, because at that time the virus was spreading into a “naïve” population without any pre-existing immunity. Now most people have at least partial resistance, and again, we have effective treatments such as Paxlovid.

How can we shore up our immunity to prevent getting hit by this likely winter wave? The answer by now should be obvious – be up to date with your vaccines. The new COVID booster available is a bivalent vaccine, which means it covers the original variant of SARS-CoV-2 (the virus that causes COVID-19), but also the BA.4 and BA.5 variants of the virus. This booster, therefore, is a lot closer to the subvariants likely to be spreading this winter.

It’s important to remember that immunity is not black or white, either with complete immunity or none. Antibodies have a certain amount of affinity for specific binding sites, which can vary anywhere from zero to 100% (perfect match) affinity. Immune effectiveness is partially determined by the number and affinity of circulating antibodies. The booster accomplished two goals – increasing the affinity and numbers of circulating antibodies.

So the answer is simple – get the new booster (when you are eligible). Don’t wait, get it now. Even if you have been previously boosted, or previously infected. These new subvariants can evade your waning immunity. You want the highest number of antibodies that are as close to these new subvariants as possible.

While you’re at it, get the flu vaccine. Experts predict a worse than average flu season, because the last two flu seasons were very mild (because masks and social distancing work, and these prevented most flu infections). But this also means that there is less native immunity out there. Again – the best way to maintain your immunity without having to suffer through the flu is to get vaccinated every year.

It is safe to get both vaccines together (coadministration). This is recommended because it increases the total number of people who get up to date on all their vaccines. There is only a slight (11% vs 8%) increase in side effects from coadministration – not worth the risk of missing out on one of these important vaccines.

What does the existence of these new subvariants mean for the pandemic? First, basically – we blew it. Our COVID response was not a complete failure, but the initial response was, and later compliance was simply not enough to really knock down the virus. Lackluster vaccination rates are what has allowed these subvariants to multiply. India, for example, is about to destroy 100 million doses of unused and expired COVID vaccines because of lack of demand. Only 79% of Americans have received at least one dose of COVID vaccine, and only 68% are considered fully vaccinated. We need these numbers to be in the 90+% range. As a result the US has had 97 million cases of COVID and 1.06 million deaths.

The result is that we likely have more waves of COVID coming. This pandemic is not over yet. It will eventually burn itself out, as more people gain partial immunity through getting infected if not vaccinated. That doesn’t mean it will go away. Expect to get your annual COVID booster along with your flu vaccine for the foreseeable future.

Experts also believe that pandemics in general are likely to become more frequent, due to increasing populations, long-distance travel, and exposure to wild animal populations. We need to improve our global pandemic readiness. The problem is, we seem to have short memories. Our failures with COVID did not prepare us for the later monkeypox. Although this is now getting under control, we did not jump on it as fast as we should have.

Experts are also warning about a new Ebola outbreak, with a variant that evades the Ebola vaccine. This new outbreak has already spread to Kampala, a city of 1.5 million people. This is very concerning. It’s also disappointing. After the 2014 outbreak, for which we were completely unprepared, world governments vowed to be more prepared next time. While readiness has improved, it has not improved to the point that we are really prepared for a major outbreak. We keep taking our eye off the ball.

Many fear the same is happening with COVID. People have COVID fatigue, and are tired of the precautions. But the pandemic is not over, and new pandemics are looming. We need sustainable preventive measures, and we need to have the endurance to maintain them. The world has changed, and we need a cultural change to match it. We need a more robust infrastructure to monitor and respond to outbreaks. And we need to strike a sustainable balance between living our lives, and taking reasonable infection precautions.

This means, above all else, get vaccinated. Further, the anti-vaccine movement is now a threat to global health, and it needs to be treated that way. This is not some fringe we can ignore.

Founder and currently Executive Editor of Science-Based Medicine. Steven Novella, MD is an academic clinical neurologist at the Yale University School of Medicine. He is also the host and producer of the popular weekly science podcast, The Skeptics’ Guide to the Universe, and the author of the NeuroLogicaBlog, a daily blog that covers news and issues in neuroscience, but also general science, scientific skepticism, philosophy of science, critical thinking, and the intersection of science with the media and society. Dr. Novella also has produced two courses with The Great Courses, and published a book on critical thinking – also called The Skeptics Guide to the Universe.