Where do new variants come from?

BA.1, BA.2, BA.3, BA.4, BA.5… while we’re all getting lost in an alphanumeric soup, it’s important to understand why we continue to see new variants.

Some have speculated vaccines are to blame, arguing that vaccination itself drives the development of variants. Is this true?

Vaccinations do not produce new variants.

Thankfully, no. Variants are not a sign of something nefarious, nor are they the product of vaccination. They are one of the most basic things we expect from any organism. As long as the virus continues to spread, new variants are expected. Let’s dive into some Genetics 101 to find out why.

What are mutations and why do they happen?

First, some definitions. A genetic mutation is a change in the genome of an organism. Every organism has a genome which contains instructions, encoded in long chains of molecules, to make every little protein that the organism needs to function.

Whenever an organism replicates (including dandilions, shih-poos, and viruses), the genome is duplicated so the offspring can have a copy. There are little molecular machines that copy the genome to (ideally) produce an identical version. But sometimes those molecular machines make mistakes. And those mistakes are called mutations.

Not all mutations are bad. Many are just “meh” and have no functional consequence. Some mutations will mess up a critical function, and will make that dandelion, shih-poo, or virus worse off. And a few rare ones provide an advantage (to the organism) — for example, making a virus better at infecting people. Thankfully, viruses cannot “tell” which mutations are going to help it, and then mutate its genome accordingly. It’s just random chance.

What is a ‘variant?’

A variant is a new version of the virus, defined by the presence of new mutations. However, we’ve just mentioned that mutations are happening all the time, so does that mean new variants are arising all the time? The answer is yes and no. If we define a new ‘variant’ as any new mutation in the genome, then the answer is yes. By that definition, millions of SARS-CoV-2 variants are circulating right now, and practically every infection produces a new variant or two.

But during the pandemic whenever we talk about “variants,” we are usually referring to Variants of Concern. These are specific variants that have mutations that change the behavior of the virus (transmissibility, disease severity, etc.). These are given Greek names, like Alpha, Beta, Delta, and Omicron.

Then what are BA.4, BA.5 and all that? Those are the names of “subvariants” of omicron, which just means variants that descended from the original omicron variant. Behind the scenes, scientists have been tracking thousands of different SARS-CoV-2 variants through genetic sequencing, and they created a naming system to keep track of them. So far none of the omicron subvariants have been deemed worthy of their own Greek name, so we’re calling them by their more confusing scientific names (BA.4, BA.5, etc.).

Variants come from infections

So with all that said, where do new variants come from? Variants come from infections. Variants arise from errors during viral replication, and the only time viral replication happens is during an infection. Viruses cannot replicate on their own, so they hijack human cells and use our molecular machinery to do it. This means that the best way to reduce the risk of new variants emerging is to decrease the number of infections, through vaccination and other methods.

Do mutations in the spike protein render vaccines useless? Is vaccine-resistance like antibiotic-resistance?

To learn the answers to these questions, check out the full post here.