
Originally Posted by
LegoSkier
I feel it’s a good time for a discussion of ways to detect pathogens and our body’s response to them.
There are two basic ways to detect stuff floating around in your body.
1. Look for amino acids and their polymers. That means detecting proteins.
2. Look for nucleic acids and their polymers. That means detecting DNA or RNA.
Each of those has its advantages and disadvantages. For DNA/RNA the main advantage is that we have this technique of Polymerase Chain Reaction (PCR) which effectively can take one single strand of DNA/RNA and quickly make millions of exact copies of that strand. That way it is able to create a very powerful amplifier of that DNA/RNA “signal” that you can then detect much easier.
For Proteins, we have no equivalent way to amplify the signal. The best we can do is attach things to the protein molecules that make them easier to see like dyes or phosphorescent molecules that light up. But still there is only a one-to-one ratio of proteins to detect in the original sample to lighted things to detect in the test, whereas with PCR DNA/RNA test, there is a one-to-millions ratio.
Next, comes where we get the “sample” from. The thing we are trying to detect can either be from:
A. The pathogen itself.
B. Our body’s response to the pathogen (our immune response).
So far with COVID we have the following:
- The RT-PCR test which is a DNA/RNA test detecting the pathogen itself. Combining the two lists above that is option 2A.
- Antibody tests which detect protein antibodies produced by our immune system in response to the virus. That is option 1B.
Now the PCR test is great in that it is super sensitive at detecting the presence of RNA from the viral genome. Sometimes perhaps too sensitive in that it can detect RNA that is not at all from a “viable” virus. i.e. it is just detecting the desiccated remains of a virus that was once there but cannot actually infect you anymore. In addition to being very sensitive, they also tend to be very specific in that cross contamination and the reasons for it are very well understood and managed through proper primer design. The downside to this is of course it is only directly looking for the pathogen so it only tells you “you are actively infected and shedding the virus”. It tells you noting about how your body is responding to the virus or if you already had it.
The antibody test is the opposite of that. It is detecting that your body has seen this virus and has started to respond to it. These protein-based tests are easy to create, easy to manufacture at a large scale, can be very cheap, and can even be packaged to be administered at home (pregnancy test). The main problems with them are that if you have the virus but your immune system hasn’t started to respond yet, it won’t tell you that. It also is of course a protein test so there is no magic way to amplify the signal like DNA/RNA has with PCR, so they are less sensitive. They also tend to be less specific in that it is easier for other similar antibodies to cross-react or interfere with the results. Finally, with them being cheaper, easier to make, and available outside of controlled lab environments, the prevalence of user error is much higher than with PCR based tests.
So the whole thing is definitely a balancing act. Which one to use changes by what question you are are asking. Option 2A? 1B? Both? Then add in time, environment, and a whole host of other factors. It is all about gathering the proper information to give you the best available data to make the decisions you need to make.
You will also notice that 2A and 1B aren’t the only options from the list above. You could also have option 1A, where you are detecting proteins present in the pathogen. Or you could have option 2B, where you are detecting the DNA of our body’s immune response, effectively looking at a genetic picture of how our body is responding to the virus during the course of the disease.
1B
Good write up. Made me dust off some college brain cells.
But yeah. PCR can amplify all kinds of shit.
Give me antibodies or give me death
#patrickhenry
Kill all the telemarkers
But they’ll put us in jail if we kill all the telemarkers
Telemarketers! Kill the telemarketers!
Oh we can do that. We don’t even need a reason
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