How do Coronavirus tests work?

COVID-19, caused by the novel coronavirus, has captured the attention of scientists, healthcare professionals, and concerned citizens. One way to improve public health efforts to slow COVID-19 spread is to know who is infected. If you have been glued to all the updates, you may have heard that the test uses “RT-PCR.” If you are not a biologist (or not a biologist with a molecular biology background), you may have heard that acronym and relegated it to the parts of your brain where you shoved the memorized list of all the counties in your home state (sorry Mrs. Lorenzen and all the residents of Boyd County, Nebraska). But today, that is ALL ABOUT TO CHANGE! You are going to understand the test for this novel coronavirus (that just so happens to be a widely used technique in biological research).

***[In order to teach you this method efficiently, we are going to use some analogies. These analogies are mostly analogous, but in real life your enzymes do not have eyes. In my lesson, all of your enzymes have eyes…you are just going to have to live with it.]***

Cast of characters:

Mr. Ribosome: Reads RNA, writes proteins

Ms. DNA Polymerase: Reads DNA, writes DNA copy

RNA-Dependent RNA Polymerase: Reads RNA, writes RNA copy

Mr. Reverse Transcriptase: Reads RNA, writes DNA 



Let’s say your DNA is a list of things your cells need to make (it kind of is) and Mr. Ribosome is the thing in charge of making all those things. Unfortunately, the list (the DNA), is written in Spanish and Mr. Ribosome can only speak English. What will we do???

DNA_RNA RT-PCR1


Let me introduce you to Ms. RNA Polymerase (in blue). Ms. RNA polymerase is quite talented, because she can read Spanish (your DNA) and write it as English (RNA). So Ms. RNA Polymerase reads “Manzana, Naranja, Fresa” and writes “Apple, Orange, Strawberry.”

Now that the list is in English (RNA), Mr. Ribosome can read it. When he reads the list, he generates the fruit (proteins) on the list. Simply put, this is how our DNA dictates the functions of our cells.

DNA_RNA RT-PCR2


You may be asking yourself how this is relevant to COVID-19 detection tests. Don’t worry, we are getting there. But first, we have to explain a technique called Polymerase Chain Reaction (PCR).

In PCR, we have a new character: Ms. DNA Polymerase. Ms. DNA Polymerase can read DNA and write a copy of that DNA. So, if we have a list of “Manzana, Naranja, Fresa”, Ms. DNA Polymerase will create many many many copies of that exact list in a [you guessed it] chain reaction. Why is PCR useful? If there is too little DNA to detect with our instruments, we can amplify it into millions of exact copies. This means we can see if the DNA we are interested in is present in a sample (all you crime scene show watchers probably recognize this as a technique to identify the source of a blood stain or hair follicle).

DNA_RNA RT-PCR3


Ah, but we have now arrived at a problem. Coronaviruses don’t encode their information in the same way humans do. See the life cycle of coronavirus below:

Coronavirus Replication

The virus attaches to its receptor and enters the cell. Then, the virus releases its genetic information. But instead of using DNA (Spanish) as the genetic language, coronaviruses use RNA (English). Because their “list” is in English, Mr. Ribosome can immediately read it and turn it into virus proteins (represented by the fruit). One of the virus proteins (the tomato) is an RNA-Dependent RNA Polymerase–this means it reads RNA (English) and copies it into more RNA. Finally, the virus gathers its RNA and proteins into a package and leaves to go infect more cells.

At no point in the virus life cycle does it ever use DNA (Spanish) as its language.


There are some benefits to using RNA as your language, but discussing them is not the point of this lesson. Instead, let’s focus on the problem this poses for diagnosis.

If we want to see if someone is infected with COVID-19, we might want to swab their nose and throat and do PCR to see if we can amplify virus genes. But remember: in our analogy, DNA is Spanish and RNA is English. Ms. DNA Polymerase, the crucial enzyme in PCR, can only read DNA (Spanish) and make DNA copies (Spanish). This means we can’t amplify viral RNA with PCR! Oh no!

VirusRNA-PCR


This is where we introduce the “RT” part of RT-PCR, and the final character in our story. Our last enzyme is Mr. Reverse Transcriptase, who has a unique skill: he can read RNA (English) and copy it over as DNA (Spanish). This creates a DNA version of the viral RNA. When we have that DNA version of the viral RNA, Ms. DNA Polymerase can make many many copies (enough copies to detect with our equipment).

RT-PCR


And this is how RT-PCR works to determine if someone is infected with COVID-19. Feel free to share this with your friends, family, or students for something new to think about during these times of social distancing.

Follow up questions (for open-ended interactions between teachers/students or family/friends):

  1. There are many diverse strategies of virus replication: some replicate in the nucleus, some outside of the nucleus. Some are made of DNA, others are made of RNA. How might the different location of replication or the different composition of the genes impact virus strategies?
  2. What might be some other uses for RT-PCR besides diagnosis of RNA viruses? If you had the ability to do RT-PCR in your home, what experiments would you want to do? What things would you want to test?
  3. Reverse Transcriptase is an enzyme that scientists discovered in a virus. If a virus had the reverse transcriptase enzyme, what might that tell you about how that particular virus replicates? (HINT: HIV is an example of a virus with reverse transcriptase)
  4. RT-PCR has been used to detect COVID-19 in blood and feces, yet the CDC states that this is not a likely route of transmission. Why do you think this is the case?

 

Please contact me if you want to discuss this further or if you would like additional materials to help out your classes during this distancing period.

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