Minnesota's Swine & U

Sarah Schieck Boelke:
Alright hello and welcome to Minnesota Swine and U Podcast series. A university of Minnesota, extension Swine program. Today's Podcast is another research Update. And today the guests that I have joining me. We are going to be talking about Pers virus classification.

My name is Sarah Schieck Boelke, your host and I'm a swine extension educator with the University of Minnesota. Joining me today is Kim Vanderwall and Igor Pablowski. Both are in the University of Minnesota's Veterinary population Medicine Department as faculty members so welcome to the 2 of you. And would you please introduce yourselves a little bit more than what I just gave.

Igor Paploski UMN:
Yeah. So Sarah, first, thank you for having us. I really appreciate the opportunity to talk to. You know, the listeners of the podcast. I think it's a nice opportunity for us to discuss this very important topic of per specification. So, as you mentioned, my name is Igor Paplowski, I am an assistant professor here at the University of Minnesota, on the Veterinary Population Medicine Department. I am an epidemiologist by training, which means that I like to understand how diseases circulate in populations. In this case, in animal populations. I've been working with Pers, Pd and other swine diseases for the past 7 years. Maybe.

Kimberly VanderWaal:
Yes, and thanks to you for hosting us on this. Podcast we're very excited to have the opportunity to share some of our research with your listeners. So I'm Kim Vanderwaal. I'm an associate professor in the department of veterinary population medicine. I have been working on swine viruses for 10 plus years now and focus primarily on virus evolution, molecular epidemiology and also, like Igor trying to understand what drives circulation of viruses in livestock's populations.

Sarah Schieck Boelke:
Well, thank you to both of you and your willingness to do this podcast and have a discussion on what you've been working on lately. So I mentioned in the intro that you 2 will be talking about persvirus classification. But are you able to explain a little bit more about what you'll be sharing today regarding that.

Kimberly VanderWaal:
Yes, of course, I'd like to maybe start by stepping back and talk a little bit about sequence data. And this is what we're talking about is the genetic sequence of the viruses. Swine veterinarians in the swine. Industry as a whole is very unusual in the types of diagnostics we're doing in our animals. So typically when a farm and usually a sow farm breaks with Pers, which is the virus we're talking about today. Of course, in reproductive and respiratory syndrome virus.

The veterinarian will do a series of diagnostics, and one of the diagnostic tests that they often request will be to get a genetic sequence of the virus that's affecting that farm. And this is really unique, because, you know, if I get the flu and I go to the doctor.

I may not even get a diagnosis of what I have, and I'm certainly not going to get the sequence of the virus that I have right. There's no way that that's going to happen. But this is what we do in swine medicine. And the reason that veterinarians are requesting sequences is they're trying to answer really specific questions they want to know is the virus I have now on my farm, the same as the one I had, you know, 6 months ago, one year ago? Or is it something completely new?

Is it the same as what my neighbors have? Or maybe it's different. Can I figure out how it may have been introduced, if I know who I may have spread it to, and in general, you know, we want to be able to track the spread of these different genetic variants of the virus. So that we can, we can better understand these sort of epidemic waves that we experience in the Us swine industry.

So because of that, Pers is one of the most sequenced viruses in the world, and for veterinarians to use this information, it's often useful for them to have some sort of label or name that they can put to their genetic sequence, so they can talk about it with other veterinarians, with the diagnostic lab with researchers like us. And so that's what we're really going to get to today is, how do we label the viruses? And so we call this the genetic classification of the virus.

So that's that's what we're going to talk about today about the the current advances that we are doing in terms of virus classification, and how these improve on what we used to do and and why the the previous tools didn't work.So the research that we're sharing today is the work that we've done to establish a new genetic classification system for this virus. Which will give us better ways to name and label different circulating variants of the viruses, and then be able to have better and improved communication amongst those of us that have to interact with pers virus on a daily or weekly basis.

Sarah Schieck Boelke: Great. I'm excited to learn more about this before we get too far, though. I'm assuming that you've had a funding source for, and it's probably also been several research projects that have led you to where you are today and with what you're going to talk about. So are you able to share and give recognition to those funding sources that have funded your research to date on this.

Kimberly VanderWaal:
Absolutely. We have had several grants that have incorporated some aspect of this. The most important one is that we did receive a grant from the American Association of Swine Veterinarians, and that's been really key support from the industry. And actually, the work that we have done has been done underneath the umbrella of the Aasv Pers Committee.So we're we're pretty much, or we work very close with Aasv on this, the other Funder, for this is the the USDA NIFA program which have supported a lot of our work, including this project.
Sarah Schieck Boelke:
Those of us that do research. We are always grateful for those funding sources, because this research is not possible, often possible without those funding sources. So thank you for giving recognition to those.

So, Kim, I know you kind of explained a little bit about what you're going to be talking about here. But can you give a brief introduction to the Pers virus classification research and explain why it's a valuable area to work on, and why you've chosen to focus in this area.

Kimberly VanderWaal:
Yes, of course. So the the research that we've done on pers classification really began a few years ago with actually work that was led by Igor on Pers lineages. And so we can start there as in terms of how we're classifying the virus.

So a lineage for this virus refers to the ancestral family group of a particular virus. Right? So typically when we sequence the virus, we only sequence one gene we call that the or 5 gene.Which accounts for about 4% of the genome. But it is a variable part of the genome that has been typically the target of most of the sequences that are generated, and it does have some importance in kind of the immune recognition of the virus.

And so what a lineage is is. Basically it takes all of these sequences and builds the family tree or the phylogenetic tree of all the viruses, and it assigns sequences according to these sort of ancestral groups. And there's been 11 lineages described worldwide. And then we divided these lineages into sublineages.

So which is basically just a smaller portion of a lineage. So in the Us. In the past 10 to 15 years, nearly all wild type sequences. So those non-vaccine sequences belong to lineage one. and then lineage. One is composed of a number of different sub lineages that we refer to with a letter, so 1a, 1 b, 1c, ect. But even sub lineages are still really large groups, and maybe too large to really get at that question. That I referred to earlier. A veterinarian wants to know if this virus is the same as what I haven't had in my farm, or different from what I had in my farm before. Sub Lineages are still a little bit too diverse to make that call.

So in the last few years we've taken this one step forward and then divided sublineages into genetic variants. So a genetic variant is a group of sequences that is genetically, closely related. They're on average around 2.5% from one another. If those sequences belong to the same variant. That's an average. So that value can be up to maybe around 5%.

And then sequences belonging to different variants are generally at least around 2.5% or sorry around 5% different from from a related but different variant. So this is starting to give us that granularity that we need to be able to make these sorts of monitoring for resident strains in a farm for outbreak investigations, for tracking emerging variants in the population. And so that's really the goal of our research has been to develop the criteria and the framework for making those classifications and we tested this on over 30,000 sequences over the past decade from the Morrison Swine health monitoring project. And we really want to make sure that the definition that we chose

Was able to answer the questions that veterinarians need answered, and that it is going to be able to evolve and adapt, as the virus continues to grow that we can create new variants as needed. So we did a lot of testing on it. And that's a portion of the research. That part is maybe a little bit nerdy. And then we also created a web tool for veterinarians and diagnosticians to upload their sequences.

And we don't keep the sequences, but they can upload their sequences and get them assigned to the best matched variant, so they can get that label to put on their viruses. So we can link to that in your show notes as well. So that's really the applied portion. So we did the research. And now we're making this tool available for use and the major diagnostic laboratories that work with swine are using this system now as part of their reporting to their clients. They've either already adopted it or are in the process of adopting this new variant nomenclature for the virus.

Sarah Schieck Boelke:
All right. Thank you for that explanation. So how was Pers previously classified? And what were the flaws with that.

Igor Paploski UMN:
That's a great question, Sarah. And and you know, part of the problem is that the industry has relied on a classification system for the last, maybe 30 or so years. That is called RFLPs. It's an acronym, It does have a meaning. Again, it's a very lab oriented meeting, meaning. But essentially what this classification did is it tried to cluster Pers viruses based on enzymes. And that's the very simple way of putting it. And that's where the names that we used to call Pers viruses came from. So you know, listeners may be more familiar with, you know.

People will talk about the purse 1, 7, 4, or the Pers, 2, 5, 2, or the Pers, 1, 4, 4. So those are all RFLP names for groups of Persviruses. The problem with that, or with that classification is that it doesn't really, really take genetic similarity into account. It uses proxies for that. And those proxies were often flawed. What I mean by that is that often you could have viruses that were significantly distinct from one another, that would still receive the same name

that that RFLP would give them, and on the flip side of that you could have viruses that they would be very similar to one another, but because they had one particular mutation. In one particular location of their genome, they would receive a very distinct RFLP name. So the RFLP name. It wasn't really measuring what people wanted it to measure. So

this we believe that this was presenting problems to the industry because people were relying on a classification method to do something that it wasn't really doing. So. That's that was one of the motives that made us pursue this. Okay, if this is a problem, let's try to address this by developing or coming up with a better classification system for a person.

Sarah Schieck Boelke:
That makes sense as to why you would want to come up with a new system. So how did you come up with the Pers virus classification that you are using now, and recommending that our veterinary diagnostic labs use it?

Kimberly VanderWaal:
So we came up with a system. Or the 1st thing that we did is we actually put together a working group that included members of the industry as well as employees that are involved with purse sequencing at the major diagnostic laboratories as well as members of the major monitoring or disease monitoring programs in the Us. Which would be the Morrison swine health monitoring project and the swine disease reporting system which both do look at this sort of data on a large scale. And so we put together all of these mine.The same room had a series of meetings. So we made sure that we had input from all these players in kind of devising. You know, what's these, how we're going to divide the viruses, how granular or not granular we need to be. And then what is that naming convention that we're going to use that would encapsulate

What we wanted to talk about? You know the position of these different genetic variants within the large diversity of the virus, but also is going to be simple enough that a veterinarian or a producer can remember the name that's assigned, and simple enough. They can maybe text it if they need to text it with someone and not get it overly complicated.

so we really try to both consider both the scientific aspects of this and and more technical aspects of this project, as well as the usability of the system for our target audience, which is, which is swine practitioners and and producers.

A lot of the research to devise this new system was based on the Morrison Swine health Monitoring project, which monitors around 55% of the Us. Population and part of the data that they integrate includes sequences both from sow farms as well as the grow finish side.

And we believe that those sequences or that database is quite representative of what's going on nationwide for swine.

So the system was built off that tested with that database. And that's every 3 months we update our variant classification system based on new data coming from Morrison swine, health monitoring project. So every every month or every 3 months, we'll get the new data, add them into the system. Look for if there's anything new out

There needs to be a new label, or recently, with the one c 5 variant we've made a split in that, because it's become so big that, and that we can now see that there are offshoots of that large variant that deserve their own label. So we can start monitoring these.

these kind of offshoots of that one c. 5 variant. So for these variants, the naming convention that we ended up choosing after a lot of debate is that the variant name includes the sublineage of the virus. That's that broader kind of ancestral family. So typically, we'll see the one A's the one C's then there's a decimal point, and then there's an integer, and we take the integers just in the order that these variants are identified. So for the one C's, we have one c, 1, 2, 3, 4, you know, and onwards we go, the major one that a lot of people have known about is the one c 5 variants. That's the one that's really spread recently.

And then if you ever see a middle number in that variant Id. That middle number is a parent variant. so the one c. 5 s. Are split. Now we have the one c. 5, 32 s. And so now we know that that 32 is that next integer, and we still see the parental relationship to one c. 5. But we're only ever going to show the immediate parents. We're not going to do the grandparents and the great grandparents and the great great grandparents, because we don't want a really long, clunky name that no one can remember. So the Max you'll ever see is the lineage with 2 integers after that. That represents the parent child relationship.

So that's what we settled on and have been using the system in real time now for about one year and fully rolled out. and the University of Minnesota Diagnostic lab kind of led the Transition last August of where they only are reporting variants now, and have discontinued the use of RFLP. Other labs are taking more of a phase transition. And that's okay, too. But our goal is to help people adapt to from the previous RFLP system to hopefully, a more meaningful system than that but one that they're less used to.

Sarah Schieck Boelke:
Thank you for explaining that. Yeah. So it seems like, yeah, you had a lot of background work with that. And I didn't realize that you kind of rolled this out last year. So now you kind of have a year or the diagnostic labs kind of have a year under their belt, or, like you said, are phasing the transition. So of this and newer systems? What are the pros and cons of the new classification?

Igor Paploski UMN:
Yeah, no, this is a great question, Sarah. So there are several pros and several cons. And I think it's important to highlight them. Right. So maybe even the way that we adopt it can be seen as a pro and also as a con right? Because as a pro, because everyone that submits samples to the VDL. University of Minnesota. Vdl. Nowadays we receive it so in a sense, it's something that people are having contact with already on a con that can be also seen as a pro is that it forces us to reach out to people, you know, to participate in this type of podcast which is amazing because we should be reaching out to you.

That is, you know, to your listener, because you are the ones using this classification. And you should be the ones that understand what it means, what it does and what it does not do. So you know, just to try to follow up on your exact question. So Kim just mentioned that these variants end up having a lineage which is a number and a letter a sublineage, follow that. So, for example, lineage one C, and then a variant number, so you could see a variant that is called 1 c 2.

You could see another variant that is called one c. 5. So one of the cons of this classification is that the proximity of the number does not necessarily mean that the viruses are closer to one another. What I mean by that is, one c. 5 is not necessarily closer to one c. 6 than it is to one c. 2 at the end of the day. Those are just names. They don't carry intrinsic meaning. They're just names.

One thing that we hear often from people on the field is that they would love to have a classification system that would allow them to estimate how severe a bird's infection would be on their herd. So essentially, they're trying to understand. Hey, I've seen this particular virus. Is this going to be bad

on my animals? Am I going to have a lot of abortions, you know. Am I going to have a lot of mummified animals, or what is going to be the production impact on my farm? And this is one of the things that the classification no classification system can do so. This is a cone of

our classification system, but not only of ours right. No classification system for PERS can reliably do that. We are in the process of investigating that. And what we can do is we can try to summarize how often herbs infected with a given variant have more severe production outcomes, and that might allow us to give some sort of estimate of that.

But the classification system was not designed to capture that by design. on a very similar note. Right? A producer might ask, okay, my herd just saw. you know, just had an outbreak of a 1 c. 5. Variant. Here. Will it be protected against a 1 c. 5, 32.

You know a descendant of this one c. 5. Again, the classification system was not designed to capture this sort of cross protection between these different variants. It would be great if it did, but it was not designed to do that. So those are things to keep in mind. And and it's important to highlight those limitations, to make sure that people are knowing, or people know, what this classification system does

to them on their herds, and a more nerdy limitation, I guess, is again at the end of the day. We are only using a small portion of the viral genome to do this classification. As Kim mentioned before, we're still using only our 5, which is 4% of the viral genome. So there is a whole lot of genetic data outside of this 4% that we are not using.

There's a reason why we do that, and it's mostly because at the end of the day people, whenever they submit samples to be sequenced at any Vdl, they will, 95 plus percent of the time.

Request the sequencing of the R. 5 gene. So even though we could have developed a classification system that used more of the viral genome into account. That's not what people use, at least not currently. So, you know, we decided we opted to be closer to the field reality, because we think that's going to be what people will use.

Sarah Schieck Boelke:
Thank you for explaining those pros and cons. So you might have alluded to this a little bit already. But how can producers use the information on the classification generated by the veterinary diagnostic lab to their advantage.

Igor Paploski UMN:
Yeah, so this is great. It goes back to the pro session a little bit. You know things that are. This classification does better than previous alternatives that we had one of the things that it does. Far, far better is it allows us to better understand

routes of transmission, or at least to establish epidemiological links between farms. If you have a given variant on your farm.

You might want to understand, hey? Which other farms have seen this exact variant, and because variant classification clusters or groups viruses based on genetic similarity.

Other 1st viruses that receive the same variant name as yours, they are more genetically closer to you or to your virus than other variants. Right? So this is far better than what we had or what we could do with our FLPs before. So one of the ways in which producers can use this information is to try to do these epidemiological investigations of

Igor Paploski UMN:
Where did this virus come from? So this variant classification provides a very valuable tool to better do this type of investigations. Another thing that the variant classification can do is it allows producers to understand if if their herd has seen this virus before, what I mean by that is, a producer might have had a challenge of purse. I don't know. Last year, for example, and it may have been a 1 c. 5 variant, so the producer might try to understand that, hey? Or might assume that their animals has seen, have seen this virus.

And this may be valuable information. This may better allow him to understand them, to understand how the circulation of other variants around their herd might affect his herd.

Sarah Schieck Boelke:
Which you brought up a lot of good points. Yeah, like you mentioned a lot of times when a farm is hit with. Pers, yeah, those are some of the 1st questions the producer will ask is, Where did this come from? Have I seen it before? Meaning? Have had the pigs here on the farm, seen this before.

Kimberly VanderWaal:
Yeah. And absolutely this, this system will give you a better, clearer answer to that than using RFLP types will.

And we can. We can very clearly demonstrate with examples. And so we're hoping that we're able to better tailor these tools. And one of the things that we did as part of the working group is actually to do a survey where we asked practitioners why they were getting viruses sequenced, and we really tailored our system so that the naming system would help answer those questions which which largely stemmed around this sort of epidemiological monitoring on a farm or within a system.

so that's why we've really tailored the system to answer those sorts of questions as opposed to.You know, trying to answer immunological questions.

Sarah Schieck Boelke:
Makes sense to wrap up our discussion here. Are there any closing remarks, or or maybe there's a question you'd like to answer that I didn't ask you so anything else that you would like to say before we wrap up here.

Igor Paploski UMN:
Yeah, I I like to say a few words. I, you know, I feel like as part of the swine industry, you know. Frustration with Pers is continuous, right? Everyone that is listening to this. If they have a swine farm, they may have had, they likely had a purse outbreak recently in the past few years. So one way that we could look at this problem is.

Are we satisfied with how we are? Are we controlling Pers for the last. I don't know. 30, 35 or so years since purse has been around, and the overwhelming answer to that will most likely be. No, I'm not satisfied.

So I think it's important for us to keep in mind that we should be perhaps changing how we are tackling this disease, how we are getting information from this disease, and I think that classification system, or a better, a more refined classification system, such as the one that we have proposed that we are pushing out. It's a step in the right direction. It doesn't solve all of the problems.

Again, as I mentioned before, there are still several things associated with virulence, with immunogenicity. That would be great if we could have some sort of information from the classification system. But I do believe that it's a step in the right direction. I do believe that we are helping producers

Address questions that are meaningful to them in a more accurate fashion, and that to me is important. So I think we are. We are, you know. We are walking in the right direction. I see a light at the end of the tunnel. I'm not sure how much we're going to be able to prevent PURS from happening by using a classification system. But I know that we're going to be able to do

A more informed, a better informed, more accurate evaluation of what is happening on our herds, and at the end of the day this does matter.

Kimberly VanderWaal:
Yeah, I agree with everything, Igor said. And just to add, having the system in place is going. It won't solve Pers by getting rid of RFLPs types. A lot of people have complained about RFLP types for decades and doing away with RFLP types is helpful. It's not going to solve PURS, but it's going to help us be more agile in our identification of emerging new variants and responding to them. We can already see that in action, when the one c. 5 variant emerged in 2020,

we didn't have this system. So we were using Rflp types in combination with lineage. We were calling them the one C. 144 s. And it was messy, and people didn't know if their farms were part of this or not, because that 1, 44 was so imprecise in identifying

viruses or herds that were being impacted by this virus. And so it was just very messy, and took us a while to really get a handle on what was going on in the field.

And already I can see we're kind of in the middle of another major emergence event right now with the one c. 5, 32 s.

But what I can already tell you is that we are more on top of it.

We have better communication amongst our lab and our university, as well as with other diagnostic labs. Elsewhere. We're able to talk the same language and say, What are you seeing with the one c. 5, 32 s. This is what we're seeing.

If we didn't have a label. We can't even start with that conversation right?

So this is hopefully going to allow us to be more agile in our response, and really is going to lay the groundwork for actually doing additional research on these other things that people are interested in, like the immunology and the virulence in the field, because now we have a way to group the viruses and make those sorts of measurements, and then we can study it better.

So I'm really excited about this whole system. It's been a fantastic and fun project to work on. And I do think that we're moving the needle in terms of trying to be able to have a better way, to be able to at least communicate and track the virus.

Igor Paploski UMN:
May I add one additional word here? So many of your listeners? They may have sequences of their own, that they may be curious now to to see, hey? To which variant does my virus belong right, or does this that I have on my farm belong?

So if you know if this is one of you listeners, there's a website that you can use to classify your purse viruses. I will ask you to either contact Sarah directly, and then, Sarah, can, you know, share our content with you, and then we can help you classify yours. This is something that is very simple. It's very easy to do, and, you know, consider us as resources. If we're able to help you on the field.

Get answers that allow you to better manage your herd. I'm more than happy with that.

Sarah Schieck Boelke
Alright. I will put that in the show notes so yeah, folks can get in contact with me, and then I can get them in contact with you.

Well, thank you to both of you, Kim and Igor, for sharing your research on PURS virus classification.And I want to thank everyone who has been listening to this University of Minnesota swine. And you Podcast

Once again, my name is Sarah Schieck Boelke. I'm a swine extension educator. And I've been speaking today with Kim van der Waal and Igor Papowski, who are both faculty in the Veterinary Population Medicine Department to further connect with the University of Minnesota. Swine extension. Please visit the swine specific web pages on the Universities of Minnesota Extension's website at www.extension.umn.edu\swine, and on those pages you will find connections. My contact information as well as connections to our blog and Facebook page to learn about research being done by our swine faculty in veterinary medicine. Please visit their swine in Minnesota blog at www.umnswinenews.com.