COVID variants and our future

Awhile back I wrote a post on everything you needed to know about the COVID vaccine (here), I talked about the science, my experience with it (as someone who got vaccinated very early on), and more importantly why you should feel safe getting your shots too. Very ominously I mentioned that the target for the vaccine was the spike protein because it would (ideally, but not for sure) be conserved across mutations, well it’s time for an update and the news isn’t great.

First my credentials. I’m not an epidemiologist or someone who’s develops vaccines. I am a neuroengineer (PhD candidate) and a mechanical engineer (BS and MS), but I’m also a science communicator and someone who knows a lot of biology because of the work I’ve done and am currently doing. I could get things wrong (and if I’m being honest usually do!), but I always try to provide sources for any claims I make and highlight when I’m giving an opinion. That said, it’s my opinion that a small, but vocal group of science denying assholes are screwing everything up for the rest of us. Because of that, COVID may be here longer than we would like and it could very well change the world for the worse.

In just a minute roughly 96 million cells divided in your body (source). Don’t worry, you probably didn’t notice. Cell division is an important part of life and the accuracy rate of that duplication is amazingly high. That’s good news for you and me who rely on exact copies of our cells to be made. While mutations in comics lead to super powers and incredible abilities, in real life it leads to things like cancers and that’s not a good thing!

That’s evolution at work though, small changes sometimes do convey a tiny super power, nothing extravagant mind you, but sometimes you are born with a unique trait that makes you more suited for your environment and that trait is preserved and passed on because of it. There’s something called evolutionary pressure that is placed on all of us and in particular we place it on the things we live with, the bacteria and viruses we deal with on a daily basis are placed under evolutionary pressure by things like antibiotics and our immune system.

If just one bacteria divides incorrectly, but that error prevents an antibiotic from killing it, then that trait gets passed on every time it replicates. Good news for the bacteria is bad news for us, who rely on things like antibiotics to keep us from dying of an infection. And we see this happen, several times in our own lifetimes in fact.(more). It’s a evolutionary arms race, we develop new antibiotics, they develop resistance, and the cycle continues until inevitably we either lose or find better and different ways to treat bacterial infections.

This evolutionary pressure doesn’t just affect bacteria. We need a yearly flu shot to stay ahead of expected flu mutations (more). Which is why we’re trying to develop universal vaccines in the hopes of wiping it off the map before it can adapt and we’ve successfully done this in the past! We completely eliminated smallpox (more). We (mostly) eliminated polio and only in certain countries is this still a problem. The point being simply that the quick deployment of a vaccine along with preventative measures to stop the spread of a disease is needed in order to eradicate it. Surprisingly, measles is making a comeback for example thanks to antivaxxers (more).

Which brings us to COVID. Due in part to our inept government (here in the US) and other inept governments (looking at you Britain), COVID cases exploded at the exponential rate we were warning would happen, because anyone who understood the science saw that it was going to happen without proper precautions. We shut down briefly, sporadically, and not completely, and it wasn’t enough. It was a half assed attempt to claim we did something and now it’s out of our hands. Masks, our best weapon for any resemblance of normality are not required in a lot of states where cases are sky high, and wearing them has been actively discouraged by a whole political party.

Let me be clear about the science. Every single fucking time the virus enters a person it replicates millions of times (more)(still more)(even more). Each and every one of those replications is a chance for mutation. Some of those mutations are benign, do nothing, or can even be harmful to the virus itself. Others are beneficial, look at the Britain variant B.1.1.7, which is not only more transmissible (virulent), but is also more deadly (more). All because some unlucky person got infected and the virus changed because of the selective pressure that is placed on it by our immune system. It has been suggested (not known to be fact) that the amount of mutations in the B.1.1.7 variant were likely caused by months of infection in a single person who was most likely immunocompromised (more).

The COVID vaccine was released targeting the spike proteins (the weird spiky looking things on the outside of the cell seen above). Those proteins are important to the COVID virus because those are how it gets into the cell to replicate. If your cell is a house, the cell wall has a bunch of doors, the spike protein would be a key that opens one of those doors. The hope was that by creating a vaccine that targeted the spike protein (the key) we would be able to stay ahead of the virus because the key was so important to how it worked.

Now, imagine a house full covered in doors, that’s your cell. There are many doors and many ways to get in. That one door isn’t the only way COVID could get in, but scientists hoped that it would be the only way COVID would attempt to use. The vaccine was a huge success and now it’s being rolled out across the world in blinding speed (but unfortunately also very unequally, specifically here in the US). That speed is key, we need everyone to be vaccinated ASAP to prevent COVID from finding new keys to get into the cell.

Unfortunately we weren’t as fast as COVID was and now there are variants that target different doors, variants covered in different “keys” or spike proteins (more). Variants that are different enough from the original that the vaccine is suddenly not so useful against them (more) (also more). That of course means we are back to our arms race and are literally producing vaccines for the variants now (more). The speed at which we are developing these vaccines is uprecetentend, which isn’t to say that they are unsafe or untested, they are both safe and very tested (more). It means that the science we’re using to develop the vaccines is mature enough for us to keep up. A good reminder that the US in particular has been cutting science funding for ages now…

The problem is that we’re playing viral whack-a-mole. As new variants that circumvent the vaccine come about, we have to develop a booster shot for that new strain. The logistical challenges of getting people vaccinated aside, the more mutations, the harder this will be to stop. Which is why we need to be wearing masks, staying 6 feet (~2 meters) apart, and why we can’t go back to normal. Restrictions are being lifted all across the US because cases are dropping, but cases are dropping because people are following the restrictions (better late than never I guess).

In the end, if we are going to beat this, we need to work together. Wear the damn mask, wash your hands, and don’t start celebrating until it’s been declared eradicated. Things are going to get better eventually, but they could also get a lot worse if we don’t take this seriously. And let’s be real, there are enough people out there not taking it seriously enough that are ruining it for the people who are. It takes just a single unlucky person to get the infection to cause a whole new strain that could keep this cycle going for a long time. I would prefer to not drag this out and have even more completely preventable and unnecessary death occur. I don’t understand how that is a controversial take in some circles.