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

I was about to write another post for today, but people keep requesting the answer to one question above all this week. You want to know how to diagnose virus infections; the best method. To satiate your hunger for answers, particularly during these times when the world is trying 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 are detecting viral genetic material (DNA or RNA) or antibodies your body creates after an infection. We show you why testing for viruses during outbreaks or pandemics is essential, 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 (host cell) for survival. Why? Because it cannot process its genetic material like normal organisms. That is, it cannot make more (replicate) or express (transcribe and translate) its genetic material (DNA or RNA, depending on the virus type.) That’s why it needs us to “reproduce” (it’s not a reproduction); 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 help it to enter cells. Once the virus encounters the host cell, it connects with it with the help of these so-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 circumvents 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 usually 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 has 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 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 number-one enemy of bacteria. We introduced you to the procedures of viruses and how they attack bacteria as an introduction to CRISPR-Cas9. You can find that old fart of a post here.

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 can 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 get extra care, and who’s ready to re-enter 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 predict a disease’s spread and outcome. This ultimately informs us on how to battle the pathogen spread best.   

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, and their benefits and limitations.

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. Diagnosing 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, a long stick with a cotton top, up your nose or throat to collect the virus. I did the swab-thing test long ago, and it was the devil (but then again, I was a wuss).

Alternatively, the healthcare worker can take a bit of a blood sample 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:

• 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 tests products from the host.

The conventional way to detect the genetic material of viruses

The nasopharyngeal swab catches whatever you have deep 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 fish for the virus material alone, not the human one, we’d be gold. We are in this golden situation, and the method’s name is polymerase chain reaction (PCR).

Labs can isolate the virus and its genetic material from that sample, 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. The machine can copy the surrounding sequence by adding short DNA sequences that recognize particular parts of the viral sequence to a prepared PCR mix (with buffers, enzymes, and other goodies). It does it repeatedly 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 virus’ or the DNA’s presence. 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.

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” 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, several labs and companies are 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 tests take only 5 minutes for results.]

The most common “speedy” alternative for measuring viral material is a toaster-like (according to news releases and news sites) machine, 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 starting 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 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 develop faster devices (I’m guessing they’ll maintain the toaster-looking design).

Companies are now getting so-called emergency-use authorizations (EUSs) from 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 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 creates these antibodies that can keep you forever safe from particular (already encountered) pathogens.

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

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 and attach these (like 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 the virus has infected you at some point, and a dark sample means that you’re not – or you’ve not yet had time to develop antibodies.  

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. These can detect the antibodies 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 the presence of antibodies: which one is best?

The simple answer is that none of them is best. They both fill their specific purposes.

Testing the genetic material gives you information about whether you have the virus or (maybe) not. These tests provide information about your current state: do you carry the specific pathogen? 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. However, these tests usually cannot confirm whether you have been exposed to the virus at some earlier point in your life. (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. Several people are locked inside their homes in many parts of the world during 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, caring for the patients without worrying about getting infected or spreading the infection.

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

Related: 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 transportation, 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 must remember that these speedy alternatives are speedy at an individual level but not necessarily at a population level. While the conventional diagnoses for viral infections may be slow, they can test several samples simultaneously (in the case of PCR, close to 100). By contrast, the point-of-care alternatives handle one at a time.

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

Imagine that you want to diagnose 96 patients individually with 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. An 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, or 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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