So I do not mean a covid test where it is clear what pathogen to look for. More like:
“Hey lab, here is a sample of a patient that feels bad. Please find out what pathogen is inside of it.”
How does it work? And how does it work so fast that they usually return the results within 1 or 2 days?
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There are various ways. Until recently, they’d take samples and, in the case of bacteria, mix with a little water and spread it on this nutritious gel in a little dish. After a few days at body temperature, any bacteria in the sample would grow a splotches on the plate. You could stain them with colors and look at them under a microscope. You could feed them different foods and see how they do, and do other things to nail it down.
Viruses were harder because you’d try to grow them in cells and see what kinds of cells they’d infect, then maybe look with a powerful microscope. You would also take purified virus and run tests to see if it would stock to certain proteins. Later, you’d purify a bunch of genetic material from it and sequence it.
Today, things are a bit different. We may still do the standard tests for bacteria because they’re cheap, simple, and don’t require very specialized tools. However, the quick and accurate method is genetic sequencing: you take a sample, wash it with chemicals that remove everting except the genetic material, add enzymes that make copies of the genetic material so you have a bunch, then stick it in a machine that will sequence the genetic material.
As you can imagine, the genetic sequencing gets the sequence of everything in the sample, which includes sequence from the person the sample was taken from. Nearly 20 years back, we worked out the human genetic sequence, so a computer can just identify and ignore that sequence and work with the rest. It takes random genetic sequence fragments and can rebuild the original sequence based on the way random pieces overlap, like putting together a jigsaw puzzle.
The result is that the computer spits out the full genetic sequence of everting in the sample that is not human. We now have very extensive databases of gene sequence from hundreds of thousands of things, and we can almost certainly find it or something related to it in the database. We can also get some understanding of its genes and how it functions. With the genetic sequence, we can produce genetic tests to detect it, and ways to quickly purify it from samples.
COVID-19 was identified using this genetic tools: we took fluid from a patient’s lung and used a kit (a lab can order online) to separate out the genetic material. A machine called a “next generation sequencer” used some crazy elegant chemistry and electronics to get the sequence of billions of ti y bots of genetic material. Software tossed out the bits that were fuzzy and uncertain, then it tossed out bits that were definitely from a human, then it lined up all the other bits that overlapped one another to reconstruct the full genetic sequence of the virus. Then, we used a different computer program to figure out if this sequence matched something we’ve seen before, and we found “yes, the individual genes and their arrangement is very typical of betacononaviruses, and this one is particularly similar to one that caused a disease called SARS in 2004”. With that information, genetic tests to detect it were trivial to make, and we had a jump start on making vaccines and drugs to treat it. The most important part, though, is that we didn’t need to have any idea what we were looking for to start; we didn’t have to figure out how to grow or purify it; we simply used molecular biology and computers to figure it out.
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