How to diagnose viral infections | 2 methods, which one is best?

How to diagnose viral infections | 2 methods, which one is best?

April 2, 2020 2 By Santiago
Reading Time: 10 minutes

I was about to write another type of post for today, but people keep requesting the answer to one question above all this week. “How do we test for viral infections, and which method is the best?” To satiate your hunger for answers, in particular during these times when the world tries to battle the SARS-CoV-2 coronavirus and COVID-19, I dug into the process of virus diagnosis.

Two of the most common methods to diagnose viral infections rely on detecting viral genetic material (DNA or RNA) or antibodies that your body creates after an infection. We show you why testing for viruses during outbreaks or pandemics is important, the two available methods, how they work, and if one is preferred over the other.  

Viruses are like half organisms that depend entirely on a host (actually host cell) for its survival. Why? Because it cannot process its own genetic material like normal organisms usually can. That is, it cannot make more (replicate) or express (transcribe and translate) its own genetic material, namely DNA or RNA, depending on the virus type. That’s why it needs us to “reproduce” (it’s not a reproduction, though); actually, it’s called the viral life-cycle, which sounds better, in my opinion.

The viral life cycle

This parasitic procedure can vary between different types of viruses but is pretty straightforward. So, let’s not get into too much detail. Instead, this is what you need to know (let’s simplify):

  • The virus enters the cell
  • The virus replicates
  • The virus exits the cell

The virus enters the cell

The virus surface is often covered with proteins that can help to enter cells. Once it has come into contact with a host cell, it connects with it with the help of some of these proteins called fusion proteins. Of course, the host cells in your body usually have several ways to protect themselves against these kinds of attacks. Still, sometimes the virus is one step ahead and manages to circumvent all our defense alternatives. It ultimately succeeds in entering our cells and starting its trajectory to the host cell’s DNA.

The virus replicates

Once inside the cell, the virus seeks out the cell machinery that normally copies the host cell’s DNA (replication) for cell division or creates new proteins (transcription and translation) for survival. By taking advantage of the host cells, the virus can start making more of itself, more genetic material, and more structural proteins; it creates progenies.

The (new) virus exits the cell

And, finally, the virus progeny have to get out of the host cell to continue its dedicated task of infecting other cells in you and your surroundings. This last step may destroy the host cell or not depending on the virus type. In either case, the circle is closed, and the virus has been through one life cycle (and can continue bothering your immune system).

If it makes you feel any better, viruses don’t infect only multicellular organisms like humans and other animals. It’s the enemy number one of bacteria. Actually, we introduced you to the procedures of viruses and how they attack bacteria as an introduction to CRISPR-Cas9. You can find that post here, but keep in mind that it’s written ages ago, so don’t hold me accountable.

Anyway, that went pretty fast, so let’s turn to the topic of today: Virus testing (and that new one that just got approved)!

Why test for viruses?

One of the issues we face in today’s coronavirus situation is that we lack knowledge about the virus, the disease, and its effects on different people. As you could appreciate from our previous post, we know little about these, because we’ve had a hard time estimating the numbers.

If we can estimate the disease prevalence, including the asymptomatic cases, we can start determining how a disease spreads. Who should be getting extra care and who’s ready to re-enter the society?

Related topics in the Embassy: How we can estimate the virus spread through R0 (the basic reproduction number of pathogen infections).

More testing gives us a better representation of reality and improved means to start predicting and protecting. As we’ve also seen, more tests correlate with more detected cases. Although that might seem self-evident, more diagnoses may help to predict the spread and outcome of a disease. This ultimately informs us on how to best battle the pathogen spread.   

Below, I’ve added a so-called dot plot showing the relationship between the number of tests performed for the coronavirus SARS-CoV-2 (the vertical axis, also called the y-axis) and confirmed cases (the horizontal axis, also called the x-axis) for some countries. If you have the chance, go to Our World in Data’s website and scroll through all their statistics. It’s pretty neat.

Not now, though. Stay here a bit longer, or at least come back soon and finish this thing. Because we’re going to talk about two of the most used tests for viral infections, how they work, their benefits and limitations.

Dot plot showing number of tests performed for SARS-CoV-2 vs. cases. How to diagnose viral infections.
Dot plot showing the relationship between the number of tests performed for the coronavirus SARS-CoV-2 and confirmed cases for some countries. Credits: Esteban Ortiz-Ospina and Joe Hasell, and Our World in Data (CC BY 4.0)

How to diagnose viral infections: Two virus testing approaches

Before we can even start understanding the purposes of each virus diagnosis approach, we need to know what they test. You see, diagnosis of viral infections can be performed differently, and they measure different aspects of the infection.

When diagnosing viral infections, you can isolate cells from different sources. You can, for instance, do a so-called nasopharyngeal swab, meaning that they (hopefully a professional healthcare worker) shove a swab, basically a long stick with a cotton top, up your nose or throat to collect the virus. I did the swab-thing test a long time ago, and it was the devil (but then again, I was a wuss).

Alternatively, the healthcare worker can take a bit of a sample of blood from your finger and test it for different parameters.

Let’s look at the two most common types of tests that laboratories (or labs, if you’re down with the lingo) use to confirm virus presence or susceptibility of a particular virus. These ones:

  • Detect the genetic material of viruses
  • Test for virus-specific antibodies

As you can see, one of the tests detects products from the virus, and the other one tests products from the host.

The conventional way to detect the genetic material of viruses

The nasopharyngeal swab catches whatever you have deep down inside your throat, including saliva, mucus, bacteria, other cells, or viruses.

Since genetic material (DNA or RNA) is unique between different organisms, it’s safe to say that it differs between viruses and humans. So, if we could only find a way to kind of fish for the virus material alone and not the human one, we’d be gold. By now, you guessed it: We are in this golden situation, and the name of the method is polymerase chain reaction (or just remember PCR).

The basics of polymerase chain reaction (PCR). The music is so fitting.

From that sample, labs can isolate the virus and its genetic material, which means that they can select for this. The PCR’s task is to find parts of virus-specific sequences among all the genetic material from the swab sample. By adding short sequences of DNA that recognizes particular parts of the viral sequence to a prepared PCR mix (with buffers, enzymes, and other goodies), the machine can copy the surrounding sequence. It does it over and over again until you have millions of sequence products with the same virus sequence. With special fluorescent markers in the mix, you’ll be able to directly spot or record the presence of the virus or the DNA. If your sample is fluorescent, you know you have the virus (you’re positive), and if it’s not… well, then you might not have it. Yes, “might”.

False negatives are common in these types of diagnoses for many reasons. You might have performed the test too early before you have enough virus in you to be detectable. It can be that the samples have degraded before the test. Or maybe the PCR mix you used was suboptimal. It can be many things. But a positive is usually positive.

The speedy way to detect genetic material

The “speedy way,” as I so delicately call it, refers to the point-of-care testing that can diagnose virus infections at the point of care, for example, the clinic. At the moment of writing this, several labs and companies are kept busy trying to develop the fastest methods to detect the coronavirus SARS-CoV-2. But it’s not a new concept. [it sounds like I’m not impressed, but believe me, I am; some of the tests take only 5 minutes for results.]

For measuring viral material, the most common “speedy” alternative is a toaster-like (according to news releases and news sites) machine that works like a superfast PCR machine. You can test one sample at a time by adding your swab sample [still shivering from it] into premixed reagents and start the PCR-like reaction.

One device, developed by the US-based company Abbott Laboratories called ID NOW, can, for example, give you a positive SARS-CoV-2 result in just 5 minutes and a negative one in about 13 minutes. The longer time required for the negative is to rule out or at list minimize the risk of a false-negative result.

Abbott Laboratories is, however, not the only company developing these tools. Many companies are now racing to come up with faster devices (I’m guessing they’re all toaster-looking still).

Companies are now getting so-called emergency-use authorizations (EUSs) by the US Food and Drug Administration (FDA) to diagnose SARS-CoV-2, and things are moving fast at the moment. [faster, faster, faster]

The conventional way to test for virus-specific antibodies

Also called serological tests, the antibody test doesn’t detect viral genetic materials. Instead, it tests for antibodies that your immune cells produce after an infection to neutralize the guilty pathogen.  

You might remember from our previous post about coronavirus responses in different age groups that you have an immune system that, crudely, can be divided into a goon-like defense and a more sophisticated defense with a memory. Well, a specific branch of the sophisticated (smart) immune cells create these antibodies that can keep you safe from particular (already encountered) pathogens forever.

Think about how vaccines work, for example, By injecting parts of a virus into your system, you can trigger the onset of your immune memory for a long time.

The different parts of the immune system. Not virus specific but to give you an idea.

So now the test. You (or better yet, a lab technician) can extract these antibodies from your blood, that is, if you’ve ever been infected. You can now test the antibodies in the blood by adding them to a surface covered with virus parts. The antibody would recognize these and attach them (kind of like they do in your body to neutralize a pathogen). Next, wash away all non-bound junk and link the (possibly) bound antibodies with a fluorescent marker that you can spot, for instance, through a fluorescence detector.  

A fluorescence signal from your sample means that you have been infected by the virus at some point, and a dark sample means that you’ve not – or you’ve not had time to develop antibodies yet.  

The speedy way to test for virus-specific antibodies

Similar to genetic material testing, medical device developers are also developing point-of-care testing for antibody-related diagnoses. Basically, these can detect the antibodies that are present in your blood by giving you a colored mark if it detects the presence of a specific antibody. Kind of like pissing on a stick (not the swab stick).    

Testing genetic material vs. testing presence of antibodies: which one is best?

What? Eh, what kind of question is that? None of them is best, they both fill their specific purposes. Nah, it’s a good question, I’ll admit.

Testing the genetic material gives you information whether you have the virus or (maybe) not. These types of tests provide you with information about your current state: do you carry the specific pathogen or not? You can, for instance, test the presence of viral genetic material to verify whether a person needs extra care or even be isolated from a specific hospital section.

The tests can also inform healthcare professionals about their condition and prevent them from spreading the virus in a hospital environment in case they are infected. What these types of tests usually cannot confirm is whether you, at some earlier point in your life, have been exposed to the virus. (I say “usually” because they can’t unless the viral gene was integrated into your DNA, which I’ll push to another post.)

And, that’s one of the central values of an antibody test, it can test if you, at some earlier timepoint, got infected by a specific virus. But how’s that useful? Easy. You know how people are locked inside their homes in many parts of the world in today’s coronavirus pandemic? If you test positive in a test that detects virus-specific antibodies, you’d be free to go out and help your society. As a doctor or nurse, you’d be safe to work in any virus-specific environment, taking care of the patients without worrying about getting infected or spreading the infection.

Another benefit of these antibody tests is that they can identify people that are eligible to transfuse their blood to patients with severe symptoms. (The other week, the FDA approved the emergency use of these types of transfusions for patients with severe symptoms from the coronavirus SARS-CoV-2.)

Related in the Embassy: Who’s in the high-risk groups, and why?

And how about the point-of-care approaches (or the “speedy” tests)?

Considering all the problems related to normal PCR-based or antibody diagnoses, the point-of-care approaches could fill a significant gap in many cases. As we’ve seen, conventional tests can take a long time, depending on sample transportations, reagent availability, or sample handling, among other things.

Point-of-care diagnoses could help the diagnostic processes, especially considering all the points mentioned in the previous section.

However, we have to keep in mind that these speedy alternatives are speedy at an individual level but not necessarily so at a population level. While the conventional diagnoses for viral infections may be slow, they can test several samples at ones (in the case off PCR, close to 100). By contrast, the point-of-care alternatives handle one at the time.

Let’s finish up with some math to clarify this:

Imagine that you want to diagnose 96 patients individually with the point-of-care testing from Abbott Laboratories. If all those patients, by coincidence, are negative for the coronavirus [let’s assume], the test would take at least 13 minutes per patient.

So, 96 patients x 13 minutes = 1,248 minutes, which is about 21 hours (this is considering no rest time between samples). By contrast, one PCR run can fit all these 96 samples at once and takes between 1.5 and 2.5 hours to finish.

The magic of PCRs. The indispensable tool that all research institutes use. They are as common in research as eating soup with a spoon (well, except for those regions where they eat with chopsticks or their hands).     

I think I’m done writing about coronavirus, SARS-CoV-2, COVID-19, and viruses in general for at least a while. It’s been interesting to dig into these topics, but there’s more to science and critical thinking than viruses. Next time, maybe we look into the effects of isolation, perhaps we write about the mental stress upon confinement. Or about viruses? Anyway, until then, stay inside and wash your hands.  

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