Questions and Answers: A Molecular Toolkit for Building SARS-CoV-2 Research Capabilities

W.When the COVID-19 pandemic hit in early 2020, Sam Wilson and his colleagues quickly found they lacked the basic tools to study the disease-causing virus, SARS-CoV-2. “That’s when we started making these research tools,” says Wilson, a molecular virologist at the MRC University of Glasgow Center for Virus Research. At the same time, Wilson noted that many non-coronavirus laboratories focused their research on COVID-19. “We made reagents for ourselves, so it made sense to make them for the wider research community as well,” he says.

In an article published on February 25 in PLOS biologyWilson and coworkers describe a molecular toolkit for SARS-CoV-2 research, including viral isolates, a reverse genetics system to genetically manipulate the virus, and a set of antibodies that target almost all of its proteins. “The paper just came out, but in fact the tools described will be available to the scientific community as soon as they’re produced,” says Wilson. The resources described in this document can be purchased from their non-profit website.

The scientist speaks with Wilson to learn more about how these tools can help advance research into the origins of SARS-CoV-2, immunity to viral “scariants,” and COVID-19 treatments.

The scientist: Tell me about the tools in this kit.

Sam Wilson: There are many tools, but there are really two main tools that are the most useful functions of the toolkit. The first of these is the newly comprehensive panel of antibodies against proteins in SARS-CoV-2, the virus that causes COVID-19. The second most important tool is the very easy to use Reverse Genetics System, which allows us to genetically modify the SARS-CoV-2 virus in a simple manner in order to carry out experiments.

TS: What Kind of Research Would You Like to Do Using the Reverse Genetics System?

When you make tools, you send them out into the world one way and they will take on a life of their own.

SW: It is important to point out that when you make tools, in some way, you send them out into the world and they will take on a life of their own. In some ways, this is limited by the imagination of investigators and the legal restrictions placed on virus genetic modification. There are a number of simple and predictable things these systems can be used for. For example, one of the things we’ve done is take fluorescent proteins and put them in viruses so that they can be followed in real time in infection experiments. The day-to-day work of a molecular virologist requires an experiment that can take hours. This means that you can do it in real time with no extra work.

The world is obsessed with the emerging coronavirus varieties of concern, or “scariants,” as I’ve heard on social media. You can take a variant of the concern from a person, cultivate it in the laboratory, and study it. It is very difficult to know what individual change is causing the various phenotypes or behaviors that you monitor in the laboratory. So if we take the Kent variant [B.1.1.7]As one of the first known variants, there are around 17 important coding changes in the virus – more than half of them are not in the spike gene. It is very easy to study the spike gene in isolation because you can decorate another virus with the spike and study its properties. But if you think of this as the outer shell when you lift the hood, there are many other proteins that contribute to the behavior of the virus, and you need to be able to modify those to really figure out what contribution they have to make how the virus behaves.

See “A Guide to Emerging SARS-CoV-2 Variants”.

TS: What about the antibody panel you describe in this article? How do you see the used ones?

There are a number of reverse genetics systems available for coronavirus. However, we have tried to create a system that can be used by laboratories that are not coronavirus laboratories.

SW: People are going to come up with really good ideas about what these antibodies can be used for. This will be part of much larger studies to validate how they conduct experiments. I think they will play a really big part in a lot of things in the scientific community. However, when we think of certain things that antibodies are used for in the laboratory, I can think of two main uses. We could take a step back and remember what antibodies are: this is how animals need to be very specific about a component of an invading pathogen. . . . And we can use that by making antibodies in animals against all virus components, and then we can use those antibodies to pull a viral protein out of an infected cell and see what that viral protein is attached to. This can tell us a lot about how this viral protein works, and it can also identify interfaces between host and pathogen. And these are very often drugable. As you become familiar with these interfaces, you will get new ideas for therapeutic interventions.

The other thing that people do very often is to use antibodies to find out where the virus is – in infected tissue, for example – or you can use the antibodies to find out exactly where that viral protein is in a cell is located. And again, this can help you understand what this viral protein is doing.

TS: In the article, you mention that part of the reason these tools were developed was to facilitate research in laboratories that may not have worked on coronavirus in the past. Can you tell me about it

SW: I think now there are a large number of laboratories around the world working on SARS-CoV-2 and COVID-19. But at the beginning [of the pandemic] There was a real hunger for tailored reagents – there are certain scientific tools that need to be tailored for the virus. If you think about the reverse genetic tools and the antibodies, both of them can help with research in laboratories unaccustomed to working with coronaviruses. There are a number of reverse genetics systems available for coronavirus. However, we have tried to develop a system that can be used by laboratories that are not coronavirus laboratories – molecular virology laboratories but with no prior experience with coronaviruses. It’s a very stable and simple genetic system that you can use to extract viruses from what is called a miniprep, a very simple method of making DNA. So there are no complicated upstream steps in what we call rescue from infectious viruses.

TS: Did you see many laboratories devoted to coronavirus research during the pandemic? How has this helped fuel research on SARS-CoV-2 and COVID-19?

SW: I think it’s both amazing and a huge risk. I think that at no point in human history has there probably been such a universal step across the world in science to focus on any particular global problem. That means the pace of research has been faster than ever before in my life. I’ve never seen so much collaboration, preprints, and research data sharing before publication. I’ve heard the term “covidization” in global research used to describe this. And of course there is a risk here too – all of the research that people have done before was probably very important [has halted]. Just as hospitals suffered when they switched to treating COVID-19 because patients were no longer being treated for other diseases, so too has research – a lot of time and effort has been put into SARS-CoV-2 and COVID -19 research which was amazing but I wonder what we lost instead.

See “Scientists around the globe are converting their research to SARS-CoV-2”

TS: What do you see as the big research questions about COVID-19 that are still open?

Another big question mark, which is probably the most important one for humankind right now, is how long and how robust the immunity of currently used vaccines against SARS-CoV-2 is.

SW: There are many, many big questions. So I’m going to answer that from a very personal point of view. My research interests lie in the transmission between different species and the origin of viruses. I am very interested in the events that led to the development of SARS-CoV-2. There is currently some debate about which bat the SARS-CoV-2 virus came from and whether there were intermediate species that were involved in transmission between different species to humans. I think this is really important if we are to understand how this could happen again.

I think another big question mark, which is probably the most important one for humankind right now, is how long and how robust the immunity of the vaccines currently in use to SARS-CoV-2 is. Do we need to move to a model of repeatedly vaccinating people in order to create lifelong sterilizing immunity with a vaccine against SARS-CoV-2? I think that’s a pretty open question.

See “Vaccines Against the Mutants”

TS: What is the current understanding of the development of SARS-CoV-2?

I think that at no point in human history has there probably been such a universal step across the world in science to focus on any particular global problem.

SW: If we look at bats, especially horseshoe bats, Rhinolophidae, you can find viruses very closely related to SARS-CoV-2. So we assume that there is one or more bat species that contain viruses that are very closely related to SASR-CoV-2. What special circumstances favor transmission between different species to humans, possibly through an intermediate species? Had it happened before but didn’t start for some reason? Or was there a certain event that led to this virus formation? I think these are the questions that a lot of people are dealing with right now and that a lot of sampling will be required.

See “Are Climate-Related Changes in Bat Diversity Responsible for COVID-19?”

TS: How do you hope this study will be received by the research community?

SW: I think this differs from most scientists in that it is not a piece of discovery. . . . I think when you make reagents like these the main hope is that someone will be using them somewhere to do something useful or very interesting. And then I think our job will be done.

SJ Rihn et al.A SARS-CoV-2 reverse genetics system introduced by plasmid DNA and a coronavirus toolkit for COVID-19 research. ” PLOS Biol, 19: e3001901, 2021.

Editor’s Note: This interview has been edited for brevity.

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