How does a SARS-CoV-2 (COVID-19) test work?

 

Hundreds of thousands of people are being tested for SARS-CoV-2 (COVID-19) around the world and the tests themselves are a crucial starting point in efforts to flatten the spread of the virus.

In a recent episode of Thermo Fisher Scientific’s Science with a Twist podcast, we talk with Senior Director of Genetic Sciences, Joshua Tratta. Tratta explains how tests are created, how they’re performed and how they’re analyzed.

QUESTION: Prior to the CDC announcement that they have developed a test, there was this kind of race to develop a test. Talk about what it is that encompasses the time that it takes to develop a test. Why does it take so long? What is the process you have to go through to develop a test?

ANSWER: Most outbreaks, and this one is no different, you start with asking the question, ‘Why are people getting sick? We don’t understand.’ So something happens. In this case, someone was getting sick and people didn’t understand why. The first thing that most outbreaks do is use Next Generation Sequencing technology to globally look at the sample and say, ‘What is it? Is it bacterial? Is it viral? Is it fungal? Is it something we have no idea what it is?’ And it allows you to start narrowing down what it is.

Once we’ve done that, as is the case of the Chinese government, they actually published their NextGen sequencing results, which allowed people to actually see that it was in the coronavirus family.

Not only was it a coronavirus, compared to like SARS, which is also a coronavirus – it’s a novel coronavirus. So they kind of knew what it was. They’ve narrowed it down, but there’s something new about this particular virus.

So what you have to do once you identify that, instead of running that big broad screen over and over again, which can be cost prohibitive for trying to ramp up to millions or hundreds of thousands of  people. People move into designing specific qPCR assays to detect just that area which is now identified.

So to do that we use something called bioinformatics tools. It’s designing specific genetic sequences and assays that cover that region. Then, unlike some of the other technologies, qPCR can give you the results in a two-to-2.5 hour timeframe at a reduced cost. And because it’s been a technology that has been around over 25 years, a lot of people are using it for other things. For other viruses. For other bacteria. For research applications. So the prevalence of instrumentation is out there. It’s something you can now push more broadly to people that already have these instruments and can use them to specifically look at something like the coronavirus.

QUESTION: What exactly is an assay?

ANSWER: An assay is a genetic tool that actually helps you identify a virus or a bacteria. Being able to match up that genetic material in one piece versus another that says you actually have this genetic information. ‘I have compared you against this test.’ Or you don’t.

QUESTION: You provided me with an example using Lucky Charms cereal. Can you, using the Lucky Charms analogy talk about how the coronavirus may or may not be present in my Lucky Charms.

Hopefully you don’t have coronavirus in your Lucky Charms. But using it as the analogy… within Lucky Charms you have multiple types of marshmallows. So imagine that the coronavirus is the rainbow marshmallow. Your cereal bowl is your genetic makeup. An assay would try to detect the rainbow. So when you apply that, you would take rainbow – which is the qPCR assay – and you would look over your bowl and say, ‘Are there any rainbows? Are there any rainbows in my cereal?’. And if there was a match, you’d have coronavirus. If not, you’d say ‘I don’t have the coronavirus.’ Doesn’t mean there’s not something else that makes you sick but you can say you don’t have the coronavirus.

QUESTION: I know that qPCR has been around for a long time. What is qPCR? How would I describe qPCR or explain it to someone who doesn’t know what it was?

qPCR has been around for 25 years. It’s a detection methodology that is akin to identifying using genetic information to identify bacteria, viruses, fungal targets. Historically people have used culture for many years. Which is still a robustly and routinely used technology. But in this particular case it allows you to do something faster. It’s being able to use genetic information to identify a pathogen in a very short amount of time.

QUESTION: How does the virus’s genetic code factor into the development of the test?

The genetic code plays into the test. You want to be very specific about identifying just that virus.

So when you develop the test you need to really understand the genetic makeup of the virus. So that you can create the most specific test. Just like for you or for me, I don’t want you to tell me a test that says,  ‘Oh I’m only 30% sure you’ve got the coronavirus.’ I want you to give me an answer so I can feel confident behind it.

That’s what we call specificity.

So you want something to be specifically targeting something you’re concerned I may have. And if you’re not sure, and you have a lower specificity, it means that you could be entering a quarantine with somebody when you shouldn’t have been in quarantine.

I want to make sure we are understating the virus, knowing the details will help you design very specific assays for detection.

QUESTION: Everyone that has a respiratory infection doesn’t necessarily have the coronavirus. Talk about how technology enables you to differentiate between the different sources of infection using, for example, a multi-panel test.  

So if you look at the symptoms associated with the coronavirus, how do you differentiate between someone who has the flu – that’s pretty prevalent and spreading across the globe right now – or if you have the coronavirus? Or if you have some bacteria? The beauty of technologies like qPCR, we have something that’s called a syndromic approach. Which is having multiple targets that you can design for and test for them all at once. So in a case like for what Thermo Fisher has designed, we have a test that can test for 42 different targets. And they will look at the most common bacterial, viral and fungal targets that cause respiratory illness. Imagine you walk in and somebody suspects that you have the coronavirus, on that test is something that will say ‘yes or no – you have the coronavirus.’ If the answer is no, wouldn’t it be great to say that you actually have a bacteria, and there’s a specific antibiotic that will be used to treat you. Or that you have flu, and it’s just flu A. They’re going to tell you to go home, get some rest and drink some fluids.

QUESTION: Talk about the importance of detection and the importance of testing.

I’d say detection is the beginning of ensuring that we don’t spread the thing. Detection is the starting point. Knowing how to make good decisions from that point.

QUESTION: We talked about a little bit about the sample – it’s a nasal swab/throat swab. If you could just help us understand how you get from swab to test result, that would be really helpful.

Imagine a swab – for any of our listeners who don’t know what that is – imagine a big Q-Tip that is long. For any of you who have had the unpleasant experience of going to your doctor because you thought you had strep throat. Same approach. They’re going to take a sample from your throat or nose and pull out what seems like nothing. But it will have material on that which that material is what we want to extract to get your DNA. So being able to get that DNA extracted, Thermo Fisher Scientific also makes kits to be able to do that. We have one that is focused on viral pathogens and extracts the DNA. That’s kind of the starting point. We got to get the DNA so we can go back to our Lucky Charms example and do some comparisons of understanding if the rainbow is there. DNA extraction works in that way. And then you will actually move over into using multiplex assay. So you combine those pieces together with a single tube sample that they’ve taken and some other reagents and you put it on to an instrument. Let it run for a few hours and a result will come back that will say the lucky charm rainbow is there or it is not.

 

 

 

 

FULL PODCAST TRANSCRIPTION:

In this episode of Science with a Twist, we talk with Joshua Tratta, a Senior Director of Genetic Sciences at Thermo Fisher Scientific who is helping oversee the company’s collaboration with government and industry groups to accelerate diagnostic testing and vaccine development.

Joshua, thank you for joining us.

We’ve been talking recently and reading a lot the spread of the virus, which was detected in China and has spread to as many countries around the world as there are.

What is Thermo Fisher doing in response to the coronavirus?

So, Thermo Fisher has played multiple roles in kind of looking at how to address the coronavirus. So kind of two-fold; enabling our customers with tools that can help create new diagnostics and as well have instrumentation that can detect the virus. 2. Actually developing and using our innovation engine of deep roots of science and technology innovation to actually develop our own tools. If someone is looking for a specific type of test that maybe the CDC doesn’t make or maybe the WHO doesn’t make, we have tools that can help them there as well.

For the benefit of our listeners, what exactly is the coronavirus?

So the coronavirus is a novel virus that actually comes from the corona family. It’s unique, which unlike SARS – which was a coronavirus – this particular strain of coronavirus is a novel virus. And it’s an infectious agent that is creating symptoms not too dissimilar to the flu. There’s lot of viruses that can do this. This is a new one.

One of the questions that we have heard often is how is the virus transmitted from one individual to another? Can you give us a sense of how that happens.

It’s not too dissimilar… a lot of times people think that this is unique and totally different than anything we’ve ever seen. And while genetically, that is true…. The transmission is very much like getting the flu. So, things like being able to pass things from your hands to your mouth. Maybe you touch something. Maybe you’re going into large crowded spaces and somebody coughs on you. It’s being able to be transmitted through saliva, aerosolization… if I can use that term of people getting fluid out of their mouth. That virus can stay alive. So if you touch something, just like kids bringing back the flu from daycare, the same way that happens with the coronavirus.

Are there steps that a person can take to avoid the likelihood of acquiring the infection?

The key things you can use are just basic hygiene. It’s not of a super exciting nature, but wash your hands regularly. Be aware that if you’re out in public spaces and you’re touching lots of surfaces, the same would be true for the coronavirus as it is for the flu – you don’t want to touch all of these things and then go to a restaurant where you’re using your hands, for instance, without having a wash.

In other areas you see utilization of masks. It’s only as good as you apply it. So if you kind of only pseudo put your mask on, or you aren’t abiding by the right type of mask that can filter out a virus… You gotta do your homework a little bit as far as utilizing it correctly and buying the right type of mask.

We read recently that the CDC has received Emergency Use Authorization for the test to detect the coronavirus. What was thermo fisher’s role in helping the CDC obtainin that Emergency Use Authorization and specifically the development of the test?

So Thermo Fisher’s specific actions in supporting the CDC is to be a tools provider. When you look at the Emergency Use Authorization, what you specifically see are guidelines – kind of like a recipe book of what you can and cannot do. So like baking cookies, there are certain things you have to put in that particular recipe to follow. In this particular case, what is included in the recipe book for coronavirus detection from the CDC from Thermo Fisher is our master mixes, our instrumentation – like our qPCR instrument, and then there’s recommendations for various plates and tubes. Things like water and extraction devices. There’s a host of products that Thermo Fisher makes that goes into that recipe book.

Now that the CDC is shipping these kits to labs for purposes of validation. What are you working on now and what is the big development as it relates to the ability to detect the coronavirus?

There are multiple ways, again not just continuing to look at the robustness of continuing to manufacture for the CDC,. One piece is to say as they scale and they need more tests… internally we work with manufacturing across the globe to be able to supply the tools – not just the reagents but the instrumentation. But then as I mentioned earlier, is the innovation side of things. Looking at as more knowledge of the coronavirus becomes available, and when I say knowledge, using things like Next Gen Sequencing to look at the genome coverage of the virus. More information becomes available so people can design better tools, things like assays, which are the tests that the CDC has made. That can be more specific, more sensitive.

Specifically our group is working on developing different iterations of tests that can be used by ministries of health, other global entities around the world, should they need a solution that they’re not buying from the CDC.

What exactly is an assay?

An assay is a genetic tool that actually helps you identify a virus or a bacteria. Being able to match up that genetic material in one piece versus another that says you actually have this genetic information. ‘I have compared you against this test.’ Or you don’t.

You provided me with an example using Lucky Charms cereal. Can you, using the Lucky Charms analogy talk about how the coronavirus may or may not be present in my Lucky Charms.

Hopefully you don’t have coronavirus in your Lucky Charms. But using it as the analogy… within Lucky Charms you have multiple types of marshmallows. So imagine that the coronavirus is the rainbow marshmallow. Your cereal bowl is your genetic makeup. An assay would try to detect the rainbow. So when you apply that, you would take rainbow – which is the qPCR assay – and you would look over your bowl and say, ‘Are there any rainbows? Are there any rainbows in my cereal?’. And if there was a match, you’d have coronavirus. If not, you’d say ‘I don’t have the coronavirus.’ Doesn’t mean there’s not something else that makes you sick but you can say you don’t have the coronavirus.

I know that qPCR has been around for a long time. What is qPCR? How would I describe qPCR or explain it to someone who doesn’t know what it was?

qPCR has been around for 25 years. It’s a detection methodology that is akin to identifying using genetic information to identify bacteria, viruses, fungal targets. Historically people have use culture for many years. Which is still a robustly and routinely used technology. But in this particular case it allows you to do something faster. It’s being able to use genetic information to identify a pathogen in a very short amount of time.

Prior to the CDC announcement that they have developed a test, there was this kind of race to develop a test. Talk about what it is that encompasses the time that it takes to develop a test. Why does it take so long? What is the process you have to go through to develop a test?

Most outbreaks, and this one is no different, you start with asking the question, ‘Why are people getting sick? We don’t understand.’ So something happens. In this case, someone was getting sick and people didn’t understand why. The first thing that most outbreaks do is use Next Generation Sequencing technology to globally look at the sample and say, ‘What is it? Is it bacterial? Is it viral? Is it fungal? Is it something we have no idea what it is?’ And it allows you to start narrowing down what it is. Once we’ve done that, as is the case of the Chinese government, they actually published their NextGen sequencing results. Which allowed people to actually see that it was in the coronavirus family. Not only was it a coronavirus, compared to like SARS, which is also a coronavirus – it’s a novel coronavirus. So it’s something they kind of knew what it was. They’ve narrowed it down, but there’s something new about this particular virus.

So what you have to do once you identify that, instead of running that big broad screen over and over again,  which can be cost prohibitive for trying to ramp up to millions or hundreds of thousands of  people. People move into designing specific qPCR assays to detect just that  area which is now identified.

So to do that we use something called bioinformatics tools. It’s designing specific genetic sequences and assays that cover that region. Then, unlike some of the other technologies, qPCR can give you the results in a 2, 2.5 hour timeframe at a reduced cost. And because it’s been a technology that has been around over 25 years, a lot of people are using it for other things. For other viruses. For other bacteria. For research applications. So the prevalence of instrumentation is out there. It’s something you can now push more broadly to people that already have these instruments and can use them to specifically look at something like the coronavirus.

How does the virus’s genetic code factor into the development of the test?

The genetic goes plays into the test. You want to be very specific about identifying just that virus. So when you develop the test you need to really understand the genetic makeup of the virus. So that you can create the most specific test. Just like for you or for me, I don’t want you to tell me a test that says, “ ‘Oh I’m only 30% sure you’ve got the coronavirus.” I want you to give me an answer so I can feel confident behind it. That’s what we call specificity. So you want something to be specifically targeting something you’re concerned I may have. And if you’re not sure, and you have a lower specificity, it means that you could be entering a quarantine with somebody when you shouldn’t have been in quarantine.

I want to make sure we are understating the virus, knowing the details will help you design very specific assays for detection.

We’ve read about the difficulty in getting protective equipment to parts of the world where it’s needed most. I know Thermo Fisher is doing what it can to try and keep up with the demand. But when I think about the number of samples that will ultimately be tested, what are we doing to ensure labs are able to keep up with the demand for testing?

I think it goes back to a couple ways to answer that. Because of the instrumentation we manufacture as Thermo Fisher Scientific, it’s utilized globally and there’s an increase in demand. So just scaling our manufacturing capabilities for instrumentation, that’s one.

Second thing is the actual tests. Scaling manufacturing for groups like the CDC and the WHO for that matter, who also use components of our master mixes. Being able to ramp and scale with those partners to meet the demands that they have.

The third piece is working with other entities, ministries of health, that are looking for tests that maybe Thermo Fisher has designed in our innovation. Meet their demands, understand what their needs are to make sure that they have these tools available to them so that they can not only look at their analytical performance but actually clinically test them for themselves.

Everyone that has a respiratory infection doesn’t necessarily have the coronavirus. Talk about how technology enables you to differentiate between the different sources of infection using, for example, a multi-panel test.  

So if you look at the symptoms associated with the coronavirus, how do you differentiate between someone who has the flu – that’s pretty prevalent and spreading across the globe right now – or if you have the coronavirus? Or if you have some bacteria? The beauty of technologies like qPCR, we have something that’s called a syndromic approach. Which is having multiple targets that you can design for and test for them all at once. So in a case like for what Thermo Fisher has designed, we have a test that can test for 42 different targets. And they will look at the most common bacterial, viral and fungal targets that cause respiratory illness. Imagine you walk in and somebody suspects that you have the coronavirus, on that test is something that will say ‘yes or no – you have the coronavirus.’ If the answer is no, wouldn’t it be great to say that you actually have a bacteria, and there’s a specific antibiotic that will be used to treat you. Or that you have flu, and it’s just flu A. They’re going to tell you to go home, get some rest and drink some fluids.

There have been any number of these types of pandemics or infections that seem to infect large numbers of people. What have we learned as a company that enables us to response to this situations more quickly?

Over my 13 years with the company, I’ve been involved with H1N1, MERS, SARS, Ebola….I think Thermo Fisher Scientific has tools that reach across a broad spectrum of needs. In the ways we’ve been able to hone that in over the years is to say, ‘Who are the groups we need to work with immediately. Who are those call points? Developing partnership and relationships with groups like the World Health Organization and the U.S. CDC. There’s a confidence and there’s a trust level not just in the times of outbreak, but as they look at us as trusted partners. Maintaining those relationships and supporting them with their needs prior to and after this outbreak occurs. So continuing to do that. And also looking at ways when an outbreak happens to be responsive. One way the company has worked is just dedicating core teams that say, ‘Hey – this is going to be your job.’ A dedicated team to focus on this important moment in public health. We’re well suited to address unmet needs. Let’s really live by the mantra of making the world a healthier, cleaner and safer place to live. This is our opportunity to shine. I think being able to step up and be able to step into that moment and do what we are good at and live up to our mission.

Talk about the importance of detection and the importance of testing.

I’d say detection is the beginning of ensuring that we don’t spread the thing. Detection is the starting point. Knowing how to make good decisions from that point.

We talked about a little bit about the sample – it’s a nasal swab/throat swab. If you could just help us understand how you get from swab to test result, that would be really helpful.

Imagine a swab – for any of our listeners who don’t know what that is – imagine a big Q-Tip that is long. For any of you who have had the unpleasant experience of going to your doctor because you thought you had strep throat. Same approach. They’re going to take a sample from your throat or nose and pull out what seems like nothing. But it will have material on that which that material is what we want to extract to get your DNA. So being able to get that DNA extracted, Thermo Fisher Scientific also makes kits to be able to do that. We have one that is focused on viral pathogens and extracts the DNA. That’s kind of the starting point. We got to get the DNA so we can go back to our Lucky Charms example and do some comparisons of understanding if the rainbow is there. DNA extraction works in that way. And then you will actually move over into using multiplex assay. So you combine those pieces together with a single tube sample that they’ve taken and some other reagents and you put it on to an instrument. Let it run for a few hours and a result will come back that will say the lucky charm rainbow is there or it is