Alright, so we established that SARS-CoV-2 is big, bad and ugly- now what? Is everything actually going to be okay?
The answer is: probably. So let's start talking about where science moved to next after figuring out the spectrum of damage the virus could do.
After determining that there was, in fact, a virus causing COVID-19, you would think the next reasonable thing to do would be to simply find a treatment for it. But it's not quite that simple. For one thing- a treatment for any disease is a tall order. It's going to take a lot of time for us to find a good therapeutic and preventative treatment for this disease, and because of this large time requirement, scientists got started on that right away. But science takes time, TONS of time. Which is why, though treatments and vaccines have been in-the-works for many months now, there's nothing ready to release to the public.
So while some scientists got to work on the treatments and vaccines, others went about trying to figure out if we could detect infection in individuals- even asymptomatic ones. This was super important, since we watched this disease have such a huge range of effects on different individuals. Some people landed in the hospital, some people felt it like a bad cold, some people got a sniffle, some people felt nothing at all. This range of severity meant it wasn't easy for us to tell immediately if a person had COVID-19 without a molecular test to back up their symptoms.
How do you even start making a molecular test for a virus? Usually, you start with what you know. We knew that SARS-CoV-2 was a ssRNA virus (which means that rather than DNA, this virus had a single strand (ss) of RNA that it uses to infects human body cells).
We know the general structure of the virus as well- but the issue with that is- all viruses are a little different, and they are constantly mutating. You know how you're supposed to go and get a flu shot every year? That's because the virus that causes the flu (influenza) mutates just a little bit every single year. Same thing happens with the virus that causes the common cold (rhinovirus). These mutations often change the proteins that are present on the surfaces of the virus particles- which is what our immune system uses to recognize infectious particles, especially things that it's seen before. Our immune system is completely amazing at remembering invaders it has been before, and if it encounters a virus that looks exactly like another one it's fought before, it can stop the infection before we even feel symptomatic, no problem. But when the invader looks a little different, our immune system has to re-learn to recognize and fight it. This is why creating some sort of test based on the physical appearance of the virus would be difficult- we don't know how it's going to change over time, and we want our tests to be as long-term-effective as possible.
Getting back to this ssRNA concept- now that's something we can take advantage of. There's essentially not a way for this aspect of the virus to change- if RNA is it's way of wreaking havoc, then that's the way it's most likely to stay. RNA is similar to DNA in that it's a code made up of base pairs that tell the machinery in a cell what to do. It contains instructions about how to make the proteins that the virus needs and how to assemble them properly, and how the virus should infect cells. RNA is also where the mutations will happen that will change the way the virus looks over time. Uh-oh... that's tricky. We wanted our test to be able to handle mutations but still be effective, but if the mutations happen in the RNA itself, how do we get around that?
The good news is- mutations can happen in certain parts of the RNA, and the virus can survive, however, there are some parts that are essential to virus structure or it's ability to be infectious. Without those parts, the virus becomes a non-threat, so it's not likely that the virus that we are worried about (one that infects and spreads and makes people sick) will have mutations in the most important parts of it's RNA sequence. So those are the parts that we can target our test to- if a person's mouth or throat swab contains parts of viral RNA that are the most important to the viruses survival, we can confidently say that person is infected.
We also want to make sure our test is specific- so it needs to be a test that will only come back positive when it detects the virus, so it can't be a test that will accidentally detect our own cells. For example, all cells have lipids. The outer membranes of both viruses and human cells are made up of lipids, so if we were to design a test for lipid production, everyone would come back positive because the test would also be testing whether or not the swab was from a human. Scientists identified several potential targets in the viral RNA that would be virus-specific, and unlikely to change too much over the course of the viruses lifetime, such as their RNA-dependent RNA polymerase- which allows the viral RNA to replicate.
The test also needs to be sensitive, even with small viral load- meaning even if a person just got infected and don't have many copies of the viral RNA in their bodies- the test can still detect the presence of the RNA at those low levels. So now we have all the pieces- a test that detects the stable, important parts of viral RNA but not the things that a virus has in common with human cells.
What is available in the ways of designing this test? Obviously it's easier to make a test based on other virus tests that are already in existence and just altering them a bit to our needs (it also tends to be cheaper to do this). The tests that exist already for viral infections also tend to be affordable for the general public as well, which is another important factor if you want to be sure that anyone who wants a COVID-19 test has access to one. One such test that has been used historically for detecting very specific sequences of RNA/DNA in the body is called a PCR test.
PCR stands for polymerase chain reaction. This type of reaction is incredibly cool and very useful in every realm of science, and has been widely used since it was invented. PCR targets sequences of RNA or DNA that scientists specify, and if that sequence is present in the sample PCR is given to work on, it will amplify it. So if there is any viral RNA present in the swab sample that the PCR is being performed on, the reaction will cause a handful of copies of the RNA sequence to turn into hundreds of copies. Scientists have the ability to detect whether or not the PCR reaction is amplifying anything, so if something starts amplifying in the sample, they know that sample is from someone who is infected. PCR is a very specific and reliable reaction, and probably one of the best tests to design for a disease as serious and prevalent as COVID-19.
This has been part 2, because even though things were bad, the fact that we have a concrete test for this disease is certainly a step in the right direction. Stay tuned for part 3- the science is going to get complicated, which means the story is going to get better!
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