How The Hell Do We Deal With The Virus Mutating?

New mutations of SARS-CoV-2 require us to think ahead.

SARS-CoV-2 is mutating. By itself, that shouldn’t cause too much concern - all viruses do that. But the way in which it is mutating in the UK and South Africa is quite troubling. The new strains have changes in the spike protein (not just genetic, actual amino acid changes). Why is that a problem? To answer that we first need to consider how mRNA vaccines (the only kind that has been approved in the US so far) work.

Our DNA contains instructions about how to make all kinds of proteins . To make a particular protein, certain biological machinery reads your DNA, makes a copy of a portion of it, and sends a molecule with that copy to the protein factories (ribosomes). That molecule, which contains protein-making-instructions is known as messenger RNA, or mRNA.

SARS-CoV-2 mRNA vaccines work by sending instructions containing the recipe for the spike protein (the one the virus uses to get into our cells) to our protein factories. The factories then make a lot of that protein, the immune system notices it and learns how to fight it. Then, if you get infected, your immune system will recognize the spike protein immediately as something it should fight, and it’ll get straight to work.

mRNA vaccines are really cool for many reasons (notably that they are quick to design and very effective), but there is a drawback to them - the spike protein is the ONLY part of the virus that your immune system will recognize. Should the virus mutate in a way that significantly changes the spike protein… The vaccine might not protect you against the new strain.

Which brings us back to the new strains found in the UK and South Africa. Those strains already have slightly different spike proteins. Now, so far, the changes appear to be relatively minor. But at some point, if new strains evolve significantly different spike proteins, the current mRNA vaccines will not protect us against those strains.

I have no idea how much change will be enough for the virus to become effective against vaccinated people. One possibility is that every new mutation in the spike protein just lowers the vaccine effectiveness somewhat. Or it may be that at some point there will be a step change, and the vaccine will not protect against the new strain at all. Again, I don’t know exactly how this will play out, and I am not certain if anybody knows for sure (there are some studies looking at somewhat similar situations).

Our predicament is further complicated by the fact that as we vaccinate more and more people, we will be putting evolutionary pressure on the virus to evolve different spike proteins.

Which means that at some point we will likely need a new vaccine.

That’s the bad news. The good news is that mRNA vaccines are designed very quickly. The Moderna vaccine was famously designed in just two days. So, as we notice strains with changes in the spike protein, we can design vaccine candidates for those strains very rapidly. However, if we make those vaccine candidates go through the full gauntlet of clinical trials, there will be a very long gap between designing the vaccine and vaccinating the population. The Moderna vaccine was designed in January; it took almost a year to approve it.

The FDA has approved two vaccines so far. We have population-wide vaccination plans. So now the agency has some breathing room. Using that breathing room to plan an expedited approval process for vaccine candidates designed for new strains of SARS-CoV-2 makes perfect sense. A good place to start is considering allowing vaccination after the safety trials, without waiting for efficacy trials.

The important thing is that, for once, we must get ahead of the virus. We need a plan to vaccinate against new strains of the virus, and we need it now. We can’t afford to wait until new strains arrive at our freshly vaccinated shores and go on a rampage against a population that is finally returning to normal.