TWiV 1351: Ebola Virus Brains and Contagious Catfish Cancers

Old Dude Episode banter

0:00This Week in Virology, the podcast about viruses, the kind that make you sick.

0:10From Microbe TV, this is TWIV. This Week in Virology, episode 1351, recorded on August 21st, 2026. I'm Vincent Bracaniello, and you're listening to the podcast all about viruses. Joining me today from Austin, Texas, Rich Condit. Hey there. My little desktop thing here says it's 101 outside, and I believe it.

0:42It's a clear blue sky. We are in the depths of this stuff now, you know, where you look 10 days out, and it's over 100 degrees every day. It's the end of August. Is that normal? Yeah, that's not all that unusual. Because here it's 26 and cloudy. It's chilling up here. Yeah. No, it's not going to start cooling down until, well, sometime into September.

1:06And cooling is in air quotes there. Cooling. Also joining us from Western Massachusetts, Alan Dove. Good to be here. 74 Fahrenheit, 23 C, and kind of overcast, but not bad. But this is the old dude episode. That's right. I don't like doing old dude episodes, because we do have women on this program, but they all just coincidentally decided not to come today. We do have one, two, three, four women, and actually three guys, right?

1:40Yeah. I think that's right, yeah. Well, I mean, Dixon is vaguely here in the background. Yeah, I see him in the background there. Yeah, he's there. We have a paper that Dixon would like today, actually. Yes, yes. He would have been interesting. Dixon liked all the papers, some more than others. Yeah.

1:59Dixon, I miss Dixon. He was fun. Yeah, absolutely. I wonder what he's doing. Fly fishing. He's probably, yeah, in podcasting a little bit. Do you think that you get, your consciousness comes back in another body? No, not at all. No, I don't. Doesn't happen. How do you know if we didn't ever have any, when you ever studied it, right? No, you can't. Right. It's not a testable hypothesis. And you could come back, and you have no inkling of your former life. Right. It's just a new life.

2:30And you're living it, you could come back at anything, and you wouldn't know. That's the thing. A lot of people hold out for that. Every now and then, I freak out, thinking that, in fact, there's only one consciousness that's just compartmentalized in nine billion bits, okay? So that, and then you can fold in the cats and dogs and other creatures, too, if you want. Yeah. Certainly, scientifically, there's no way that would work, right? I think it's all just, you know, atomic. But a lot of people think that there's stuff that happens that science can't explain.

3:04Of course there's stuff that happens that science can't explain. That's why we have science. Well, but. I mean, every paper ends with more research is needed. Yeah, yeah. So in other words, we know what we don't know. Yeah. We also don't know what we don't know. Yeah. Right? But eventually, you get to it. If it's important, you get to it, right? And if it's testable. I've got no trouble with this. I think most of this stuff about, you know, reincarnation and et cetera, and life after death and that kind of, we're really getting into it here.

3:35But I think it's, you know, mostly fear of death. People, you don't want to die, okay? So you make up stories to keep you around. But in fact, I got, well, I can say this from now because I'm relatively healthy. But, you know, in theory, at least, I have no issue with this. And I kind of like the idea of getting recycled. Amy and I have, my wife and I have conversations now and then about, you know, whether we have atoms from her mom floating around in us, okay? What's the probability?

4:06Or where our atoms are going to wind up? Well, half of your nitrogens are from Haber-Bosch, you know. Yeah. Did you know that? No. Yes. They are synthetic. It goes to fertilizer. You eat plants. Okay. Half of your nitrogen molecules. Because half of the world's population can only be supported by Haber-Bosch. Yep. Biological nitrogen fixation can only support 4 billion people. It's just amazing.

4:34And, of course, we're also full of plastic. But this whole idea of an afterlife is very interesting. I'm not, I'm not, it's not because I'm afraid of death. I just would be interested to come back as someone different, right? And have a different life experience. But you only get to go through once in life. It's like, could you play New Game Plus, you know, make different decisions on the next trip through. And, yeah. Well, just think of the things you'd like to do in life. Like, I would like to have a different career, right? And you can't do it.

5:04It's too late. I want to fly. Man. You could fly. You could go into space. You could be a rock star. You could be a singer. You could be an artist. I mean fly like, I mean fly as a bird. Like an eagle. You want to be a bird. I want to be a bird. I think that or a giraffe. Nah, your lifespan is too short. But you don't know that. Okay? It's all relative. Some birds get snapped up immediately, you know? I wouldn't mind being my cat either, except my human doesn't let me outside enough. Anyway.

5:35Coming back as an orca would be pretty cool. An orca. Something that lives a long time. You get all the cool things about being a dolphin, plus you get to eat polar bears. Yeah, but you have to swim all the time. Yeah, but it would be awesome. You'd be flying. You'd be under the water. I don't really like being in water. Oh, I love it. I can't imagine being a dolphin and what they have to go through. Oh, man. You're having such a great time. They have to all come up and breathe at some point. Of course they do, but they can stay underwater forever, you know, an hour. And yeah.

6:06Actually, sperm whale would be pretty cool. You get to eat. Why are you laughing? And I think these perspectives are important, right? They are. Oh, absolutely. To think about other forms of life or other – just doing something else with your life. That's all I'm talking about. The only reason I'm laughing is that we're broadcasting this to 50,000 people or something. Who can't listen to viruses?

6:29Well, this is our psyches, right? Yeah. And I'm just interested in that. I'm totally with you. I love this stuff. The good question is what – if you did come back, what would you do? Have some ideas. I wouldn't be a scientist again. I would do something – I would be some kind of an artist. Oh, musician. Absolutely. You could be a musician. Yeah. Depends on how far in the future I'm coming back. I don't know.

6:57Well. Anyway. And let's – if you enjoy these conversations, by the way, usually we get right into the science right now and then. You know, because I have thoughts all the time. And here I get to share them with these dudes. I'm just talking to them. I don't get to see anybody most of the time. So unless I go to a meeting. If you enjoy these conversations, we'd love your support to pay the bills. You can go to microbe.tv slash contribute. And there are a couple of ways that you can pay.

7:27We're also adding – you can give us stock. We're adding that option. I'm figuring out how to do that. A few people have said they want to give us stock – give microbe.tv stock, which would be cool if you've got extra stock lying around, right? Or you just want to help us. That's the thing.

NIH grant scoring overhaul

7:43Okay.

NIH grant scoring overhaul

7:44So these two news items, I think, Alan, you put both of them in, right? I think I did.

7:49Or somebody else might have put the first one in, but I was also thinking of it. So first item, this links to a Nature News article. It's also been covered a few other places. The NIH has put out a proposal overhauling the way they evaluate grant proposals. And you can imagine how this has been received coming from the current administration. This is a change that would, instead of giving numerical scores – so the current system is you submit your grant, a study section gives it a numerical score, you get your score

8:24back, and they decide they're going to pick a pay line. We're going to fund the grants above this score. But getting the score back tells you, oh, wow, I got a 90, or I got a 70, or you can say where you are in the hierarchy. And not only do you have a pretty good idea of your odds of getting funded at that point, you also have a good idea of how good your grant writing is. So this has been part of the system for a long time.

8:56The change would be to do away with reporting the numerical score and just bin the grants into good, fair, and poor, I guess, would be the baskets. It's a three-level thing. And you'd be told, okay, you're in the fair category or you're in the good category. And then they would pick funding from there. Of course, the big concern is if you've got a large number of grants of the good category, they're not all going to get funded.

9:27And then the political appointee could come in and say, hey, we like this one because it agrees with our ideology and not that one, even though the numerical scores might have been the other way around. So this is viewed by a lot of people as cover for further politicizing science. The problem with this is that the people running NIH or the guy at the top doesn't know anything about NIH. And so I don't buy anything that comes out of his mouth. Yeah. Including this. Go ahead.

9:57Now I'm finished. So I've actually had some online discussion about this with McFadden who sent me, you know, his opinion was solicited on this by somebody because both of us have been in the system. Um, and, uh, so yes, there is this, in the back of my mind, there is this distrust, which is unfortunate all by itself, uh, because, uh, I don't know, uh, you know, who, uh, was

10:29involved in coming up with this or what their motivations were. And I don't trust everybody at the NIH anymore, though there are still trustworthy people there. Okay. So if for a moment I just assume that this was done by trustworthy people, okay, I don't think it's necessarily a bad idea, uh, because, uh, the, what it does is it gets rid of, rid of pay lines. Uh, first of all, grants are already binned into two bins.

11:01Okay. The lower 50% don't get discussed and they don't even, they don't even really get scored. Um, and I remember, uh, very vividly, uh, the, you know, chasing the pay line on the grant panel. Okay. You're supposed to score these grants based on their merit, but you have an idea in your mind what the pay line it might be. And so, and you've got a grant that you would really like funded.

11:34Okay. So you score it where you think it's going to be above the pay line and it results in this score compression with a huge number of grants with not much differential between them. And you look at that, you may as well bin them, okay, because you, you can't tell from the pay line the difference between one grant and another. Uh, now the, in this system, the grant, uh, the, the grantee, the grantee, the person submitting a grant will still get all of the, uh, written feedback from the panel.

12:11So they'll be able to know, even without a score, they'll know what, uh, subjectively at least what the feeling on the grant was. And there's a summary of the discussion and everything else. The other thing is that what it does is, uh, for the, the people above who actually give out the money or don't give out the money, it puts a lot of more power in their hands. Um, which as we've already said, could be a bad thing. But if we, for a moment, assume that there are good people involved, that's, I think

12:43a good thing, because that means that they aren't tied to a pay line either. In particular, in this situation where there's, where it's so hard to discriminate between one grant and another, and some newbie comes in and he's got actually a great idea, but you know, there's too many other established people with good grants that get higher scores and that kind of stuff. It gives the program people a lot more discretion. And it reminds me, and it's mentioned in some of these publications, that's much more like NSF. Yes. Where you get the review and the program officer looks at this and takes a whole range of things

13:16into consideration. How novel is this? How, uh, how experienced is this person? We want to encourage new people. Uh, what areas are being funded and that kind of stuff. And, and can fold all that into the decision rather than being tied to a pay line. Now they do some of that now, but this, uh, would, uh, would allow for more of that. Now I'll have to say that NSF saved my bacon on day one because my first grant, everybody, including NSF said they weren't going to fund me.

13:46Okay. And later on, I got a call from the program officer at, uh, NSF. I can't remember his name. I could remember it for a long time who said, you know, I found a little extra money. We can fund you for half the time at half the amount. Okay. Just to get you going. And I said, yeah, I'll take it. And it got me going. Right. Yeah. And NSF was good about that. Yeah. And I, um, I mean my take on this, so I gave the factual take on it and what people are

14:18saying in the, in the quotes in this article, um, was very similar to riches. Um, the real problem here is not the specific policy. It's that I don't trust the people promulgating it as far as I could throw them. Um, and that's, that's really the essence of it because, uh, as Rich said, NSF and some other grant giving organizations already do something along these lines. They don't do numerical scores for exactly the reasons Rich outlined. Um, and in fact, this is really just one step shy of a proposal that I think we've talked

14:53about on TWIV before that people have suggested, why don't you just, there's, there's lots of research on people's ability to determine quality of things in general and grants and written documents in particular. And it turns out people are really, really good and experts will, will generally converge very well on what the top third is. And within that, nobody can agree. So when you're, when you're saying, oh, this grant is a 92 and this grant's a 91, just

15:24that's nonsensical. So a better, an inherently better way to do it, if everybody was acting, you know, rationally here would be to do that, to say, here's the top third. Now, obviously we don't have the money to fund the entire top third. So we will put them into a lottery and we will fund the number of grants we can, and we'll give out that many tickets. It would accomplish several really good things. First of all, um, it would do away with these numerical scores.

15:55Secondly, it would let everybody involved know, okay, there's a lot of good stuff we're not funding. And it would do away with this, this perception, you know, oh, so-and-so has a lot of grants. Therefore, they're a better scientist than this other person who doesn't have, you know, who only has one grant or has just lost their grant. Um, but if they're both always ending up in the top third, then you'd say, oh, hey, they're just as good. Um, so, um, that's a, that's a proposal, but that's going nowhere, I'm sure.

16:27I think the worst part, the, the, the tragic part about all this is that three of us are sitting here saying we don't trust the people at NIH. Yes. That's a tragedy. And the, the vast majority of people at NIH, I would trust. Absolutely. The problem is that the people at the very top, I do not. Yeah. That's the crux of it. Yeah. And I've, I cannot remember another time in all the years I've been a scientist where I didn't trust people. You may disagree with them.

16:58Yeah. I didn't always agree, but I trusted them to do the right thing. And now, now this, these people at the top have no idea what they're doing. So I don't know if this originates at the top or not. You know, I don't know either, but I think, I think this sort of discussion had been going on for a long time. Oh yeah. Because I think this, I think everybody recognizes the problems with pay lines. Yeah. I, you know, the, the mantra on the study section, Vincent used to be, oh, we don't make funding decisions. And I would say, nonsense.

17:30If we give, if we all give a grant a one, they've got to fund it. Okay. And everybody knows that. So they give all their grants ones. All right. Yeah. So the only thing that they could do, so the program officers have certain areas that they're responsible for, they could take a grant that doesn't do so well and pay it because they think it fits the program. Yeah. You know, as long as it's close enough to the pay line, not too far away. But, but so that's called select pay and that's fine. But this all is a problem when you have politicians mixed in here as well, and they should not

18:05be anywhere near NIH, only, only with the funding, giving it its, its appropriation, but not making any decisions. That's not right. Because politicians, as we have seen, don't know anything about science, especially Rand Paul. He knows nothing about science. And they wind up, because of that, making huge mistakes and terrible policy. Yeah. Yeah. But although historically in, in the Senate, the Republicans have been highly supportive of science. Yeah. Yes. But they just funded it. They didn't say what to do. Yeah. Right. Because they don't know science.

18:36And even, we even have some MDs there who don't seem to know science. Or maybe it's confused with politics. Anyway. Okay. That's a good one.

Bio and agro defense facility

18:46How about the next one, Alan? Uh, yeah. Next one, uh, is also one that I put in. Um, so the, um, I think we've talked a little bit about the, the BSL for the National Bio and Agro Defense Facility in, uh, Kansas, um, out in Manhattan, Kansas, that has been under construction for, um, quite some time now. And this is going to be a BSL for, for working with, um, high-level pathogens, specifically those that are of agricultural importance. Mm-hmm. Um, now we had a facility for this sort of thing at Plum Island, New York, just off, you

19:21know, the end of Long Island. And, um, that was an old facility. I think, Vincent, you actually went there. I've been there, too. Yeah. Okay. Rich, too. I'm glad they closed it. Yeah. I mean, it was, it was a facility from another era and it was, you know, doing things that it, it was adapting to things that it wasn't really built for. And it's on an island, it's logistically complicated. So anyway, this is supposed to be the replacement for it. It was supposed to open in, um, I think 2023.

19:52And in fact, they had a ribbon cutting ceremony. We're opening the facility, except they're really only opening the easy part of the facility, the regular labs and the, up to the BSL-3, which lots of people have BSL-3s. Um, the BSL-4 is, uh, not up to snuff. And according to the Office of Inspector General at USDA, it's not going to be up to snuff for quite a while. They've got a lot of problems. Department of Homeland Security was running this project and apparently didn't do a very good job designing or supervising the contractors or what have you.

20:26Uh, and so the whole thing is sitting there, you know, not fulfilling its mission and we closed Plum Island last year. So now we have no facility for working with these pathogens, which means if we have, I don't know, foot and mouth disease, outbreak in U.S. cattle, um, then we're gonna not be able to study it. But, yep, I, uh, this, it doesn't surprise me. It doesn't concern me too much.

20:56I mean, it's frustrating, I suppose. But how long did it take the needle to get online? Long time. Yeah. Long time. In fact, they had an opening ceremony and it still wasn't open. Yeah. I mean, this stuff, and they're gonna, I guess they're looking at opening a BSL-3 hopefully next year, but BSL-4, they won't even put it in this article. They didn't even put a date on that. Yeah, no, USDA and DHS are not putting dates on anything at this point for this. Um, uh, but, you know, to me, a BSL-4 facility for cows is a big project.

21:31Yes. Okay, so it doesn't surprise me that there are issues. Sounds like they should have done better, but. Yes. Eh. I think it's for cattle. Cattle, not cows, not just cows. Cattle, sorry. Cattle. It's okay. Okay, now on to some literature.

Ebola virus persistence model

21:52Uh, we have an interesting mix today. The first paper is, In Nature, Microbiology, Host Virus Determinants of Ebola Virus Persistence in a Human Cerebral Organoid Model. Alan, you have authors for us? So, uh, first author is Lina Widerspick. Um, the co-senior authors are Gustavo Palacios and Cesar Munoz Fontella. Uh, and the group is from Affiliations at the End, um, which is, I even told myself to remember

22:30what page they were on, um, and I didn't, uh, oh, here we go. You mean they're not on the front page? No, they're not on the front page. Oh, I'll be darned. This is a nature thing. Uh, so the group is from the Bernhard Noct Institute of Tropical Medicine in Hamburg, German Center for Infection Research, also in Hamburg, um, Icahn School of Medicine in Mount Sinai, New York, uh, University Medical Center in Hamburg. Hamburg-Eppendorf. And by the way, I Googled that to figure out, wait a second, there's a, there is in fact

23:01a, a neighborhood or a village within the city of Hamburg that is called Eppendorf. And that's significant to those of us who've spent time in the lab because the little tubes that we use are by a company called Eppendorf. Everybody just calls them Eppendorfs. Anyway, um, they're also from the Liebnitz Institute of Virology in Hamburg, Friedrich Loeffler Institute, Griefswald, Insel, Rheims, Germany, um, NIH in Bethesda, Friedrich, um, National Laboratory for Cancer Research in Friedrich, Maryland, um, and the, um, NIAID facility

23:35at Fort Dietrich, Maryland. Uh, so it's mostly, uh, a group of mostly hamburgers, um, but, uh, then an international collaborative effort as well. So a couple of, uh, TWIV alumni here. Uh. Um, Jens Kuhn is on here and Gustavo Palacios. Uh, Ian Grosler, isn't he the guy who had the, uh, persistent infection in his eye? His eye turned color and, um, he, he, it turned out he had gone to Africa to take care of patients

24:08in the, in the 2015 Ebola outbreak and he got infected, he recovered and then, um, was back in the U.S. and one morning he looked at himself in the mirror and his eye had changed color and it turned, he went and got checked and it turned out he had Ebola virus in his vitreous, is it vitreous humor? Vitreous humor that's in the eye. Vitreous humor. As I recall, it was a load of Ebola virus. It's a lot of virus there. And I, I was talking to my class about it last semester and I said, what happened, what would

24:41you do if you woke up and your eye changed color? And all the women said, oh, I'd go to the doctor right away. And I said, that's it. Guys don't just wait and see. Okay. I got a blue eye on the right now. Whatever. Okay. Whatever. Anyway. So it's interesting in the context of this paper, because this is all about Ebola virus persistence. Um, and in fact, Ebola viruses and, uh, can persist in survivors. And that's, um, you know, now we're getting used to it for RNA viruses, right? We never used to think that happened, but it clearly is more broadly documented.

25:16Um, but they first start out by saying, let's define persistence. I like this. Yes. Right. Uh, they say, so they said the term persistence is insufficiently defined. So we're going to describe it to highlight continuous release, release of infectious particles, which is in contrast to nonproductive persistence, which so many RNA viruses, you can find RNA for a long time after the host is recovered, but it's not infectious. It's just RNA. Right. Yeah. So they, they draw this distinction here between two kinds of persistence, productive

25:49persistence, which is, yeah, there's infectious particles and nonproductive persistence, which is RNA only. And, you know, you can apply that in other contexts of persistence as well. Yeah. If you persist in doing something that's not useful. And so Ebola viruses, they typically persist in what we call immune privileged tissues of these Ebola disease survivors long after recovery. And it has public health implications, right? There has been persistence in testes. And so the virus will be present in semen and it has actually been sexually transmitted and you can

26:26start new outbreaks as a consequence. It's also persisted in intraocular fluid, as we mentioned, uveitis and cerebrospinal fluid associated with meningoencephalitis and, and relapse. And so they're, they have important consequences. And so, you know, and now the big outbreak in DRC of Bundibugio, a lot, you know, many thousands of cases, a lot of people will end up having virus persisting in them. So it's, it's even when the outbreak is over, you have to be very careful.

27:00So it has very important consequences, but we actually don't know how the virus persists. And we're not going to learn in this paper, but we will make a model for studying it, at least a reasonable model. It's not the greatest model. Plus the technology is interesting. Yes. And, and we have, there have been experiments done before in non-human primates. They have shown that the, the viral genome and viral antigens can be found in microglia macrophages in the CNS, which may be a reservoir, but, you know, it's kind of, they say it's,

27:35these, these have experimental and ethical challenges working in non-human primates. Yeah. And we'll be, we'll be talking a little bit about the limitations of this system that they're going to develop. But the, the fundamental question that they're trying to answer is just really, really hard to get at. It's not like persistence in blood or in any other easily accessible thing. It's like, uh, Hey, you're a, you're a survivor of this virus. Do you mind if we take a brain biopsy? Well, yeah, I would mind, you know, can we take your eye? No, you may not. So they use brain organoids here.

28:07These are three-dimensional structures. They're called mini brains, but they're not really mini brains. They're just three-dimensional structures. They're made from stem cells, induced pluripotent stem cells. And they mimic the structures of a brain. They have even electrical activity and they have a lot of the cells that are present in the brain. And so you can use them to study certain aspects of, uh, of brain function. I think that all by itself is astonishing.

28:38Yes. That you can take, you can manipulate a cell to do all that. And as I understand it, looking at these things, they're even differentiated to the point where they got layers, different cells in different layers. So it, uh, it's really pretty remarkable. And I want to take a moment here. Maybe you planned on doing this, but every time I do a paper like this, I got to go back and look up the cell types because I can never remember them. They're going to talk in this paper about astrocytes and microglia, and they mentioned oligodendrocytes

29:14and they mentioned neurons. Okay. So, uh, any cell in a, in the nervous system that is not a neuron is a glial cell. Okay. That just, that just says I come from the central nervous system and I'm not a neuron. This is, correct me if I'm wrong on this. That's my understanding too. Uh, and microglia are essentially the nervous system's, uh, sort of macrophage-like or whatever immune cells. Astrocytes are sort of workhorses.

29:45They clean up and do all sorts of other stuff. Okay. They also wrap around blood vessels. Uh, yeah. And oligodendrocytes make myelin for the sheet, for the sheath. So they aren't going to talk much about them here. So that's our vocabulary. Yeah. The oligodendrocytes are electricians and the other two are more general perks. Yeah. One I'm sanitation worker and the other one is the immune system. Right. And so they're, um, the, the, um, it's speaking about the cell types that they're going to derive.

30:15These induced pluripotent stem cells, they start out as, you know, they could be anything. Um, and then you treat them with various growth factors and, and you can turn them into specific types of cells. And they're referring to these organoids as cerebral organoids. So this is, um, this is duplicating or not duplicating. This is mimicking the cerebrum, the, the, you know, the bulk of the, of the brain. I do, I find their abbreviation for this, serorgs, um, a little awkward. I mean, they could have called them corgis or they could just, just refer to organoids

30:47and I'll know what you're talking about in this paper. I don't know. Yeah. Serorg doesn't really flow. No. All right. So we know that, uh, we've, we've been able to see persistent antigen in, or RNA before in these non-human primates, microglia. So they take, uh, immortalized microglia. They expose it to Ebola virus at, at multiplicities of one or 10. So just to remind everyone, multiplicity of infection is how many virus particles you add per cell. It's not how many, in fact, it's how many you add to the culture.

31:19So if you have 10 cells and you do a MOI of one, that would be 10, whatever your infectious unit is. Okay. An MOI of 10 would be a hundred. That's what you add.

31:31Okay. So these, then they passage these cells. These microglia are infected with Ebola virus and they're passaged. And by passage 13, they, then the cultures remain infected for 91 days. So these are not from the organoids. These are microglia. No, these are just microglia. These are cell lines that are. Yeah. This is a microglia just to see if you can get persistent infection. Now, remember this is Ebola virus. So this is done in a BSL-4 facility. So.

32:02I'm guessing this is the Fort Detrick contribution here. Yes, exactly right. Gens. Gens. So they also see persistence for 25 days in microglia, astrocytes, Vero cells, which are kidney cells, and HUH7, which are human liver cells, exposed at low MOIs without passageing. So in some cases, you don't have to passage it. And then they also use Lassa virus as a kind of control. It's not a filovirus, right?

32:32And if they infect astrocytes and HUH7s, they see wave-like replication.

32:41But if they infect microglia, you don't get persistent infection. So Lassa doesn't establish persistent infection. And it hasn't been reported to do so, as far as I know. They just mentioned this wave-like infection and kind of sort of blow it off. But I immediately think Von Magnus effect, and I wouldn't want to go back and have a closer look at that. That's a discussion for another day.

33:07Yeah. What Rich is referring to is that the viruses are throwing off defective particles, which then interfere with the infection, and then it recovers. So the titers go up and down and up and down. But it's a cool name, Von Magnus, right? Anything with a Von in front of it, it's just very cool. It sounds like something they would use on Star Trek, the Von Magnus effect, to get out of that situation. I don't want to come back as a Von, though. I would rather not. I don't want to do that. So then they want to see what the cells are doing, right?

33:37So they extract RNA and they sequence it. So they're looking at the bulk transcriptome. So the transcriptome is RNA made from DNA, basically. And then they see changes in both the microglia and the astrocytes. And it is dominated. So when you do this kind of sequencing, you could ask, what are these RNAs encoding that I'm sequencing? And then you can get an idea of what's going on, right? It's a very typical study path right now. And they can see that these cells are mounting a pro-inflammatory response in the microglia,

34:12you know, which makes sense, but not the astrocytes. They're not doing that. And they don't really talk about that. So I don't know what that means. They do see transcriptomic changes associated with Ebola persistence and serially passage to microglia that they infect and then they passage the cells. So passing cells means you let the cells grow, they fill up the dish, they touch each other, and then you disperse them and dilute them and put them into dishes so that they can have room to grow, basically. Okay. So that's what a passage is.

34:44And they see transcriptomic changes in these passage microglia and also in microglia and astrocytes at 20 days post-exposure. And then they compared that to the Lassa virus-exposed cells, which are not continuously infected. So what you can see is that 20 days after infection, the gene transcription in microglia, persistently infected with Ebola, is distinct from that of Lassa-exposed and unexposed microglia, which

35:14is interesting because the Ebola is persistent and the Lassa is not. So we don't know what it means, but it's different, and that's something that you could study in the future and maybe relate it to persistence, right?

35:29These microglia that were persistently infected with Ebola and serially passage. So for me, that's really interesting. So you can infect these cells and then you can passage them, which implies they're still growing and they're making virus. So that's quite interesting, right? Anyway, these have transcriptional signatures of pro-inflammatory cytokines, right? So that's normal. You're responding to a virus infection. You're making cytokines like IL-1 and IL-6. So were they able to maintain passage of these after infection with a high multiplicity?

36:07Yeah, I think 10 worked. Okay. And do they, I don't recall whether they have any experiments that, say, looks at a late passage culture and asks what fraction of the cells. I didn't see any single cell stuff done in here. What fraction of the cells have genomes in them? They didn't do that, no. Because to me, there's, elaborating on the persistence thing, you could have persistence, which is cells that are actually infected are still growing, or you could have a heterogeneous

36:39population where some fraction are infected and some are not. All right. So back to your question, they didn't do it with MOI of 10. I don't think, I think 10 will kill the cells. I think, yeah, that was my impression. So the point of the lower MOI is you're going to have some uninfected cells and they can serve as hosts for the virus that's released, right? And so that's how it can be persistent. But obviously, cell killing has to be reduced in some way to get a persistent infection, right? That's one of my definitions of persistent infection.

37:10You have to reduce cell killing because if the virus kills all the cells, then that's it. Right. It's not persistent. Yeah. You're not persistent.

37:18Anyway, so these infected microglia make all kinds of pro-inflammatory cytokines. They make pattern recognition transcripts, encoding transcripts like RIG-I, et cetera, TLR3, and interferon as well. And astrocytes don't make an interferon response after Ebola exposure, even though they are productively infected at all time points. Okay. So that's all interesting information, which just sort of makes sense, but how it fits into

37:50persistence, we don't know yet. Okay, so that's all in microglia, basically, in astrocytes. And now let's go into the serorgs, cerebral organoids. And they actually have them with a microglia population. And they have both male and female cell lines. And they can maintain these for 100 days. And then they infect them with Ebola virus or Lassa virus. So mature organoids. And the way they measure infectivity is by focus-forming units.

38:25So think if you're doing a plaque assay, you infect a monolayer. And you would put an agar overlay and eventually stain it to see holes in them. But they can't do that here. But what they do is they stain the monolayer with an antibody. And whenever there is basically what would be a plaque, you're going to see fluorescence. So that's why they're called fluorescent focus units, because you can just count those. It's kind of almost like a plaque assay, right? And these organoids get infected. Over 90% of the organoids get infected.

38:56And they remain productively infected for 120 days. And remember, productively means making infectious virus, as by their definition. But when you do this with Lassa, you make virus for a while, and then it declines. And within 48 days, it's no longer making virus. And they have a nice graph of that. And in fact, the Ebola virus infection, it continues.

39:26And you can see the last. I think that's figure 2A. The Lassa goes down. All right, so the cerebral organoids do support infection. The Ebola virus peaks around 2 weeks, and then it reaches a plateau that lasted for 120 days, which I think is the longest they looked. They can also find RNA in that as well. Okay, so what about other phylos? They expose them to other phyloviruses, including Restin Ebola virus.

40:01And they both establish persistent infections. It's interesting because Restin is not thought to be pathogenic for people. Not that we've had so many infections of people, but yet it still does a productive infection. Okay. So now we get to von Magnus, but they don't call it von Magnus. So they wanted to know if defective interfering particles are being made in these cultures. They're called copyback defective viral genomes because the mechanism of making them is by a copyback. But they can look for these.

40:32And in fact, they find these defective interferes, these defective genomes. Let's say they're defective because we don't know if they're interfering. And so they say maybe they're interfering. There are certainly particles. They can see small particles by transmission EM. And so maybe they're playing a role. So you can imagine that defective particles could be playing a role in keeping the infection limited, but keeping it going. So my... That's something... Go ahead. My sort of overview on defective interfering particles is that they usually comprise...

41:11They can't replicate on their own. They're missing. They may be only a small fraction of the total genome. But they usually have the genomic elements that are essential for replication. Like in a DNA virus, it would be an origin of replication. And I think these copyback things are a similar thing. Stuff that's essential for replication. And the way I think of it is that they replicate really efficiently as long as the factors that are required for their replication are around, supplied by the fully competent virus.

41:44But in the process, they suck up all those factors and use all those resources so the fully competent virus doesn't replicate as well, which in terms of maintaining persistence is probably good. Yeah, because then the interfering genomes would drive down the population of the productive virus until the point where the interfering genomes can't get replicated. And then the productive virus can come back up and then back down and so forth. So, you know, when the spam piles up too deep, the email becomes unusable.

42:15And then, you know, you find a filter and gradually the cycle repeats.

42:21The email was supposed to make things easier, wasn't it? Oh, yeah. Yeah, all this stuff just means you can do more work.

42:29So then they're looking at what's being infected here. They have these organoids infected with the Ebola virus. They look at different times after infection. They're looking for the nuclear protein of the virus by immunofluorescence. And then they're looking at markers to identify neurons, astrocytes, and microglia because all these cells are present in these organoids. And so the first thing they see, which is cool, is that the infection starts at the periphery. These are three-dimensional little balls, right? And it starts at the periphery and then goes towards the center.

43:02The virus moves in because that's where the uninfected cells are, right? Move towards the center. They can find the nuclear protein in neurons at six days. They can find the nuclear protein throughout the 120-day experiment. They can also find nuclear protein in astrocytes and in microglia.

43:20And whenever they see an infected cell, they see that microglia are accumulating around it. And, you know, that's one of the things that microglia do. They respond to infections. That's cool. And so they're showing Ebola virus infection of neurons in these organoids, which had not been previously reported. So that's novel. So not just astrocytes and microglia and oligodendrocytes, but neurons also seem to be able to be infected with the Ebola virus.

43:53So that's important. I mean, I don't know if this is applying to people, right? This is not a person. It's not a person, but it's a very experimentally tractable system that mimics a lot of the biology of the brain. And then they, in the discussion, they go into, you know, things that they can't duplicate here. But, yeah, it's kind of as close as we can currently get. The commentary that I presume you'll stick in the show notes had a really nice paragraph about,

44:24without crashing it, outlining the limitations of the system. That's right. Right.

44:32All right. So then, as we said, sometimes Ebola can persist in the brain. You get inflammation. So they want to see if there were pro-inflammatory cytokines being made by these cerebral organoids after you add virus to them, right? And so they look for that, and they can find them for sure. They have a bunch of pro-inflammatory cytokines and chemokines. And they also can see anti-inflammatory mediators. So when cells get infected and the immune cells are releasing pro-inflammatory mediators,

45:04you also make anti because you have to stop it at some point. You can't let inflammation go on forever. And they can detect those as well, which is kind of suggesting that it's a balanced system, right? Okay. So now they're going to look at how the virus moves through the organoid. You know, and the Ebola viruses and filoviruses in general are released from the cell surface, and then the virus particles can go to another cell. But they can also spread from cell to cell, cell to cell transmission.

45:35And they do see budding from these organoids. And they also see what they call interstitial virions, right? Between the cells, you can see a virus particle. And they can see transmission along long-range actin-mediated cellular connectors. So cells can connect to each other via actin, and they can see the nuclear protein moving along these. This is something that pox virus does too, right, Rich? Yeah. They move via actin microfilaments, yeah.

46:09So they're suggesting that you get both release of virus particles and cell to cell transmission. And so that's what they're thinking is part of persistence, two ways of transmission. Right. So if you're wondering, are mutations occurring? Well, the answer is always yes, right? Viruses are always mutating. But here it would be interesting to know if mutations arise that lend to persistence, right? Or is not.

46:39So they sequence these viruses that are being produced from the organoids, and they find a number of single nucleotide variants in the Ebola virus genomes. And if some of them dominate through the passages, right? So they do take virus with these changes, and they reinfect organoids, and they say they still can infect. Sometimes the virus yield is decreased, which is interesting.

47:10So you take some of the variants that are arising and start over again, and they have a lower yield, which could be part of persistence. Suggests attenuation in that environment. Yeah, attenuate it. And so all these subvariants that they look at, the subvariant is having a change relative to what you put in. And they do make virus particles. They do persistently infect the cells. And so the virus particles have variable replication capacity. And so obviously in a future study, they will want to look at the contribution of these individual changes.

47:43I didn't tell you where they were, but they were in the Ebola genes, including the nuclear protein, the glycoprotein, some transcriptional activator, the polymerase. So a lot of different proteins have amino acid changes. No, but none in one of the polymerase cofactors or the matrix protein, interestingly. So that's it. This is the cerebral organoids. The virus persists in them, which is interesting. And now we can move forward and ask,

48:14what are the mechanisms of persistence? Yeah. And a couple of interesting things they talk about. So we've called the CNS and other places immune privileged, but they point out there are immune cells there, and they do have an immune response, although it may be limited. So that's what we actually call persistence. And the microglia are immune cells. Yep. And one of the, you know, discussions about the,

48:45and they're totally up front with this, about the limits, put it that way, of the organoid culture thing, is that they're separated from an environment that does all sorts of things to contribute to this immune privilege status. Right. You know, the blood-brain barrier, right, which is complex. So. One of the things they point out is that the single nucleotide variations that they find in these human organoids, human brain organoids,

49:15have never been reported in Ebola virus disease survivors. So there's something fundamentally different, which it is, of course, fundamentally different. There's an organoid versus a human, right? Right. So it may be not surprising that you're going to get different changes there. But basically, here's an interesting point. Many of the mutations are proposed to reduce or prevent replication. And reduced replication is a reasonable potential contributor to persistence, right? It limits detection of the virus, and it limits death of the cell population, right?

49:52A tissue is a collection of different cells. And if you just infect a few of them at low levels, then you could persist in those cells, right? So there we go. I like this because it's actually infecting cells with a virus, and that's what I really like. Well, it's also, you know, it's important. Yeah. Because we need to recognize that in these viruses, persistence happens.

50:24And we need to try and understand how it happens so that we can deal with it. Yeah. They're very nice drawings also in the extended data. I don't know if you guys looked at them, but the drawings of cells are very nice. They have neurons and microglia and astrocytes and oligodendrocytes, fibroblast collagen, matrix protein, necrotic cells. It's really nice. Very cool. Yeah. So nice, isn't it? Okay. So there we go there.

50:54Now, this is different.

Transmissible catfish melanoma

50:56Here we're going to invoke Dixon. Oh, something completely different. Yes. So this is an article in Nature, and I found this a couple of weeks ago, and I wanted to do it right away. Brown bullhead catfish melanoma represents a novel transmissible tumor cancer. They had me at brown bullhead. The authors are Emily Kurd, Samuel F.M. Hart, Mark Henderson, Peter Emerson, and Julie Dragon. The team is from University of Vermont, Burlington, University of Washington, Seattle, University of Utah in Salt Lake City,

51:34and the Vermont Fish and Wildlife Department in Montpellier, the capital of Vermont. You're going to find out in a moment why there are so many Vermonters on this paper. This was in the popular press, too. It made its way around. So if you were wondering, here it is. Here it is. So the brown bullhead catfish is Amiurus nebulosus, all right, A nebulosus. And beginning in around 2012, although we're going to see it goes back before that,

52:04fishermen and biologists began to see a large number of bullhead, it's a kind of catfish, right, with raised black lesions. And this was in Lake Memphremagog, I think that's how it's pronounced. It's an Indian word via French-Canadian. So this is a lake, a freshwater lake that goes from Vermont into Quebec. It's quite a large lake. Yeah, large body of water. And these lesions, raised black lesions on the surface, are determined to be malignant melanomas.

52:41It's hanging out in the sun too much. I don't know. They got some pictures of these fish, and I'm not feeling good for these fish. No. This does not look like a happy time. No, if I reeled one of these in while fishing, I would know something was very wrong with that fish. They say they don't know the impact on the catfish populations, if there is any. I mean, we don't know if it's lethal or not. 23 to 37 percent of the catfish sampled between 2014 and 17 had these lesions.

53:14Big number. Yeah. And that's, so melanoma can occur in catfish. Every now and then somebody will haul one up, and it's got a black spot on it like this. But it's rare. And to find a quarter of the fish in a particular lake having this, that's weird. Now, these fish in particular, they're distributed across eastern North America, and they're considered to be an indicator of water quality.

53:44All right. We'll get back to that later. And so they initially, when this was first discovered, they thought maybe there's something in the water that's causing cancer. One idea was there was a lot of flooding in 2011 from Irene, the tropical storm, and that could have contaminated the lake due to runoff. And this is an important question because the lake is a source of drinking water for a lot of people.

54:11So they wanted to know what's causing these. Obviously, you need to know what's causing these melanomas because if there's something in the water, that's something you have to know. And the early results said these are really different from the healthy tissues. Most cancers are different, but you can see that they came from healthy tissues. These are really different. And so they thought maybe this is a transmissible cancer because the data they had, and we're going to reinforce it today, was consistent with a cancer cell spreading through a population by moving from a fish to another fish like a parasite, right?

54:49And this is something that's been observed in a few places. And the most famous example, I think, is the Tasmanian devils, which we've talked about on TWIV. I think we had an episode titled Sympathy for the Devil.

55:04And in Tasmanian devils, there's a facial tumor that is contagious from one animal to the next, and they tussle, they fight, and they spread this tumor from one to the next. And that turns out to be a very interesting thing. But then in recent years, people have also characterized this venereal cancer of dogs, which spreads the way it sounds. And that is apparently not terribly deadly to the dogs.

55:36And then several species of saltwater marine mollusks have these types of transmissible cancers. But nobody's ever seen it in a fish, and nobody's ever seen it in fresh water. It's really trashing the devils. It's reduced their population by 90%. Yeah, and they've actually started testing a cancer vaccine for Tasmanian devils. I found an article from 2023. So it has a substantial impact on Tasmanian devil populations to warrant a vaccine.

56:12And in fact, so just to continue that reference a little bit, for people who haven't listened to that episode yet, it turns out that a major mechanism that's allowing it to spread, normally you can't catch tumors from people. But that's because people are very outbred. Tasmanian devils are a very small and smaller population. They've been through a major reduction in population because of us. And that's created this bottleneck.

56:43They're very homogeneous genetically, and that allows the tumor to spread between them. So the idea is that somewhere a cancer cell, or maybe multiple times a cancer cell arose, and then it spread from fish to fish, clams to clams, dog to dog, TD to TD, right? That's the whole idea. And so these cancers should be, in this case, they should be more closely related to each other than to the genome of the host that they're found in, right? So that's what we mean by clonal, because they're all derived from a single cell, or maybe more than one time originally.

57:20And then you also, if there are a lot of variants in the tumors, they may be shared among the tumors. But a conventional cancer, the genome of the cancer will mostly match the host, you know, with the exception of some cancer-specific changes, obviously. But they're a minority. But these transmitted cancers are going to have a lot in common, and they're going to differ a lot from the host. So that's what they're doing here in this paper, to test the hypothesis that this melanoma represents a clonal cancer lineage.

57:54You can't just look at it and say, yeah, it is. You have to have data. That's how science works. You need to generate data for your hypotheses. You can't make stuff up, okay? No? No. You cannot make stuff up. You cannot say, this vaccine kills people without the data, okay? But people do it, and it's disgusting. Okay. So first of all, so they sequence a bunch of tumors from fish. They have 19, so they have these fish that they've collected, seven from Vermont, two from New Hampshire, and one from Maine.

58:31They have brain tissue from normal fish, and also they have 19 paired tumor skin and normal skin or brain tissues collected from the lake. And then they do RNA sequencing and DNA sequencing. You're going to see mitochondrial DNA sequencing is a big part of this. So first, they identify multiple distinct mitochondrial haplotypes within a tissue in a subset of normal skin and brain samples and in all the tumor samples, right?

59:01So multiple distinct mitochondrial haplotypes just means based on the sequence of the mitochondrial DNA. And in a normal tissue, i.e. non-cancerous, that's normal. It's called somatic mosaicism, right? And that happens all the time, but it's pretty rare. But all the tumor samples that they sequenced, all of them exhibited heteroplasmy, which is this multiple distinct mitochondrial haplotypes. And they had over 10 times more heteroplasmic single nucleotide variants relative to the host, and most of them are shared by all tumor samples.

59:42So these are probably mutations that arose in the tumor cells. They're not present in non-cancerous tissues. So they looked at the relationship between these mitochondrial haplotypes. They make phylogenetic trees of them. And you can see that these tumor mitochondrial genomes or mitogenomes make a monophyletic clade. In other words, they had a single origin. I mean, monophyletic means there was one ancestor.

1:00:13And these samples do not resemble in the same fish. They don't resemble the mitochondrial sequences in the same fish or in any of the fish sampled in the lake. Yeah, this phylogenetic tree is pretty much—I mean, this is a smoking gun. It's very, very clear. The tumors are just this one line, and they're all together. And then the fish or the normal fish tissue is scattered out, as you'd expect it to be.

1:00:48So they say this indicates a clonal tumor lineage for the lake mephremagog, a fish that predates 2015. So that's when they first started studying this. Okay, then they look at the nuclear genome as well, because it's there. You can sequence it. And this also will support a clonal cancer lineage. What they look for is single nucleotide variants in the nuclear genome, right? So if you take you and me and sequence our DNA, we're going to have lots of single nucleotide variants.

1:01:20In fact, within a host, you're going to have lots of single nucleotide variants from tissue to tissue, from cell to cell. So they have—and you can find lots of single nucleotide variants. They have 686,000 nuclear SNIVs across all the samples. So they build a phylogenetic tree. And you can see that the tumor genomes, again, form a monophyletic clade. And the tumor tissue clade is more similar to the unaffected reference fish from New Hampshire and Maine than to other fish samples from the lake, which means it didn't start in the lake.

1:02:01It probably came from somewhere else. That, to me, is the coolest part of this whole thing. Yes. Wow, it just—and the same thing with the clams. You know, you get—these clam tumors are up and down the coast. You know, they can travel these—half cancer will travel. Okay, so again, this support—this SNIV analysis supports the idea that the tumors are a clonal lineage, and it originated outside of Lake Memphremagog. That really rolls off the— Memphremagog, yes.

1:02:33Memphremagog. It is a native name, you said? Yeah. First Nation? So it's Algonquian or something. Yeah, First Nation is how Canada would refer to it. Native American is how we would refer to it. But the tribes that inhabited that area from their language.

1:02:52Okay, so then they have all these variants that they've identified. Do you think it means something like the big water or something along those lines because it's a large lake?

1:03:01So now they take all these variants, these SNIVs, and they want to know which are unique to the tumor and which are unique to—they look at brain tissue, paired brain tissue. So they have 245,000 tumor-specific SNIVs and 61,000 brain-specific SNIVs across the 16 tumor-normal pairs. So they have a tumor and a normal tissue. So they have 3.9 more tumor-only sites relative to normal tissue sites. The distributions across tissues is very different.

1:03:32The distribution of the SNIVs across tumor samples shows that most—59% of them is shared by at least 14 fish. And in contrast, 83% of brain-only SNIVs is found in only one fish. And none are shared by more than 14 normal samples. So these mutations that they're using as kind of markers, right? So again, the tumor is a clonal thing. All the tumors that they've sampled are very, very similar in terms of these SNIVs.

1:04:04So then another way that they can look at it—so conventional cancer that arises in you, right? It can share some tumor-specific variants by chance, right? And there are mutational biases that we see in certain tumors. And so they want to know how many shared tumor-specific variants they would expect between conventional cancers.

1:04:34So there's what's called the Cancer Genome Atlas, TCGA. It's sequences of a lot of tumors, and there's melanomas in there. So they look at 463 human melanomas that are in this database. 94% of SNIVs are unique to a single cancer. 94% of the SNIVs are unique to a single cancer in the human melanoma database. And only 40 out of 500,000, 0.008%, are shared by 10 or more cancers.

1:05:08So these are just random mutations that are arising, and they happen to be shared at a very low frequency. And some number of those are going to be shared because they are part of the mechanism of those cells having become melanoma. That's right. Which is a big point of the normal use. Well, not the normal use. You can use the database for whatever. But the Cancer Genome Atlas, one of the purposes of it is to look for what are the changes that cause this to be a cancer. So, yeah, that's kind of a normal amount of similarity between tumors.

1:05:42So then they want to match this DNA to their 16 bullhead tumors. So what do they do is they calculate the average number of shared mutations across 100 random sampling permutations of 16 TCGA human melanomas. And after that, they find 99.9% of human SNVs are unique to a single cancer. And no SNVs are shared by more than 12 melanoma samples in any of these 100 permutations.

1:06:17In contrast, with the bullhead melanoma, the majority of tumor-specific SNVs are shared by other tumors. And so that is way higher than what you'd see in a normal cancer. Supporting the notion of a clonal origin of this thing. Yes. Yeah. In some fish somewhere other than this lake, sometime. Yeah.

1:06:43Probably once because these seem to be monophyletic, right? Yeah. But that's just this sampling. You may find this elsewhere that it arose from another location. Okay. So then the next thing they can do is look at variation in DNA structure. So this is part of genomic diversity. So single nucleotide. So you can look at mitochondrial DNA. You can look at nuclear DNA, single nucleotide variants. And you can also look at structural variants, deletions, duplications, insertions, inversions.

1:07:13You can look in tumor and normal samples and compare them. And so you have the sequence. So you can do this. And they looked at each kind of structural variation that I just mentioned. They look for tissue-specific ones. They count the number of samples that share each structural variant. They found way more tumor-only structural variants shared by all tumor samples than normal-only structural variants shared by all the paired tissue.

1:07:45For example, they found 2,572 tumor-specific deletions compared with 166 brain-specific. So the brain is the normal tissue control. And of those tissue-specific deletions, 75% were present in at least 14 tumor samples. But no normal-specific deletions were shared by more than 8 normal samples. So again, heavily biased in the tumor.

1:08:20They also can look at copy number variation of genes. That happens, right? There's duplications and deletions across the genome. They find differences between the tumor and the normal samples. The tumor tissue share minimal copy number variation with the paired host tissue. But tumor tissue shared most of their copy number variation with other tumor tissues. And again, all of this suggests that they originated as a clonal lineage.

1:08:52So you got mitochondrial DNA, nuclear DNA, very different analyses. But what about microorganisms? They can cause cancer, right? You know, oncogenic virus or bacterial. We have great evidence for viral oncogenesis, of course. And also for bacterial, some good evidence and growing evidence. So they screened all these tissues for viral and cellular organisms.

1:09:22You know, they're looking at the sequences, right? They found lots of bacteriophages, as you might expect. They said, we're so few viruses of animals or eukaryotes that we're unable to run a formal statistical analysis. I was surprised, actually. I thought they would find more viruses. They found nothing associated with the tumor tissue.

1:09:48And they say, you know, it could be that way back when a virus or a bacteria was involved in starting the cancer. But right here, there's nothing present in the tumor. So, you know, there's no oncogene or anything like that integrated. Even if there was something infectious that was doing this, I wouldn't expect the same sort of clonal profile of the tumor. Yeah, especially, I mean, you've got the nuclear and mitochondrial profiles here. And we have human tumors that are virally caused, papillomavirus tumors.

1:10:23Papillomaviruses are in a bunch of different species. And if you look at those, they're, you know, unique to the individual. The virus triggers things. But couldn't it be that, say, a virus many years ago triggered a cancer, and then that cancer cell just spread in the population? Yes, sure. Yes, absolutely. But then it's the cancer cell that's spreading. It's not the virus that's spreading. So still a transmissible. The virus could have been involved in the generation, but the transmissibility is still the cell. Yeah. Yeah. Okay.

1:10:53So that's the data. There are a bunch of interesting things in the discussion, though. So this shows that this lake mephremagog melanoma in these catfish is a single clonal cancer lineage. These tumors are more closely related to each other than to their hosts through multiple lines of evidence. It's the first transmissible cancer in fish or in fresh water, as we have said. And what do we need to learn? Well, we need to learn how the spread between fish, right?

1:11:23Because you want to be able to interrupt it if it's a problem. And as we said already before, the dogs transmit it sexually, the devils, by biting each other's faces. The bivalves are interesting. They're thought to be in the seawater, which always blew me away that stuff can transmit in seawater. But it can. Sure. Because these clams. And the bullheads hang out when they're spawning, so they're touching each other. They're a schooling fish. Yeah. But cells can transfer to one another, and these cells can move around the aquatic environment.

1:11:59By the way, these fish are scaleless. Yep. So that might be one way that they can acquire the cells. I believe a defining characteristic of catfish. They're scaleless, yeah. Yeah. Dixon would know that, too. Yep. Dixon would know that. If you catch a catfish and you're going to clean it to eat it, you skin it. You don't scale it. Same with eels. Eels, right. They're totally unrelated, but yeah.

1:12:27Because I remember my dad used to like eels, and I would see him peeling the skin off, and I thought that was just weird.

1:12:35Yeah. And this, they reference this in the paper, I think in the introduction. Um, this may not be a new phenomenon. So a couple of important things here. I mean, for the, um, the, the initial spur, one of the initial spurs of the investigation was, you know, a lot of people who drink this water, do we need to worry about pollution? And the answer here is no, probably not, because this is a transmissible tumor of catfish, and that probably is, uh, something that originated elsewhere. Um, it's not from runoff.

1:13:06Um, but the other thing is, they mentioned in the intro that there, there had been observations going back at least to the early 1900s of, um, abnormal numbers of, of brown bullhead catfish, also called pouts, um, with melanoma, with black spots. And they gave the reference, and I thought, wait, what? And so I, sure enough, I was able, I found the reference, uh, it was easy, it was right online. And that reference, it's a paper from 1920-something, I think, or before 1920.

1:13:39And it starts off by saying that it's not the first report of this phenomenon, and, and points to quotes Henry David Thoreau, uh, who many people will know as the, uh, the author of Walden and Civil Disobedience, um, from his journal, July 10th, 1852, on the Concord River, he writes, one of these large pouts had a very large velvet black spot, which included the right pectoral fin, a kind of disease which I have often observed in them.

1:14:11Yeah, interesting. And he didn't take any DNA samples. No, he didn't take any DNA samples. He, unfortunately, his, his phylogenetic tree has been lost to history. Um, but, and that, that early 1900s paper, um, they, the reason it came to their attention was there was a pond in Falmouth, Massachusetts, um, where the majority of fish in it had these, the, of the pouts in it that had these black spots. And the, the guy, the naturalist who was looking at it had pathologists look at it and they,

1:14:43they all said, oh, that's a melanoma. Um, but he couldn't figure out why. So this has probably been drifting around, at least in New England, for quite some time. Well, I'd like to know if it's arisen more than once. Yes. Uh, you know, yeah, we need to sample all these other melanomas. Yeah, for sure. But it's interesting that nobody's found it till now. I mean, they've observed it, but they haven't studied it until now. They didn't have the tools. Well, it was the same, it was the same with the other tumors, you know, they were only

1:15:13identified recently because you have the tools now to be able to show this. Otherwise it's hard to show. But what, what they point out here is very interesting. They say the rapid spread to infect 30% of the fish in the lake. And it was not present at noteworthy levels before indicates a high rate of transmission. So, uh, they, they say really what we need to figure out is how the cancer will affect the fish populations. You know, it's fatal in the, there's the tumor, the Tasmanian devil. The dog tumors are not, the, the clams are okay, but how it's going to affect the bullhead

1:15:49is not known. How do you know if a clam's okay? They're, ask them if they're happy. You ask them. Happy as a clam, right? Good point. Um, and also other populations throughout the North, North America. In fact, um, they, as, as Alan said, the observations go back, but maybe it affects other fish as well. Uh, so this is really an interesting story. Yeah. I really like this. It says in the, one of the last sentences, transmissible cancers are a puzzling biological

1:16:21phenomenon that are not expected to exist, but are now confirmed in over a dozen species with the potential to devastate host populations. So I was thinking, you know, do humans have transmissible cancers? And as Alan said, or Rich said earlier, I forgot who, the, the, the barrier is immune recognition. You know, we have really good MHC systems were outbred. And so any transplanted cells get rejected.

1:16:51And that's why if you get an organ transplant, you need to be immunosuppressed, but there are some exceptions, right? I found some, so organ transplant recipients have acquired donor derived cancers, sometimes many years later, cause they're immunosuppressed, right? So that's very rare. There has been mother to fetus transmission of cancer. So the fetus has a partially tolerant immune state, which allows that in grafting. And these have been leukemias and melanomas. And then there is a famous case involving two surgery patients who received cancer cells from

1:17:26a single donor through a needle stick accident in the operating room. One developed a tumor and the other did not.

1:17:36Elizabeth Murchison has, has been interested in this and they've pointed out that the rarity of transmissible cancers suggest, you know, evolutionary selection against them. But she said, maybe we're not looking hard enough, you know, bivalve neoplasa went undetected for a long time. And this, the tools in this paper could be applied widely, but really hasn't been all that much. So I think it's, it's a question, an open question, how, how many transmissible cancers

1:18:09there are and what, what's going on in the bullhead particular to allow it, because we don't know anything about its immune system or MHC, I presume, and, and in humans as well. So. I'm guessing it's a lot more common than we might imagine. It always is, isn't it? Yeah.

1:18:27Nope. Kat, you can learn a lot from fish.

1:18:32And they're good eating.

Smallpox mummies in Chile

1:18:35We have a couple of emails. Alan, can you take the first? Oh, let's have that. Rich take the first one. It has to do with smallpox. Okay. Okay. Rich. John writes, Drs. Twiv, Chilean mummies, it is unclear, Google didn't really help, whether the 500-year-old Camerona's mummies in that science paper on smallpox are from the same area as the Chinchorro mummies that I first learned of when a seatmate on a commercial

1:19:07flight long ago was someone whose work involved them. They're also from Chile, and he told me that some of them date to 5,000 years ago. And looking them up, I now see that some are 9,000 years old. As I vaguely recall, he was in Chicago, and I don't recall what his studies involved, but I gathered that he sometimes brought material back, and I asked if he had ever had any problems

1:19:38with that. This was well before 9-11. He said no, except for the time at the x-ray machine when he had his skull, had a skull in his hand baggage. That's pretty good. Yes.

1:19:55The one thing this reminds me of is in that paper, they had some discussion of that population, and if I remember it correctly, the particular population had been kind of subject to some political manipulation in their tribal culture that landed them in this particular area. And I forget the details, but they were moved around politically that, among other things,

1:20:29wound up in this arsenic-rich environment. Death of reading. A long time ago, I heard Richard Dawkins on a phone-in session. Somebody asked him what they thought was a gotcha question and how he would respond to that. His reply, which you could tell was through clenched teeth, was, read a book. There are shelf miles of them.

1:20:57Meanwhile, things are usually getting parched in Greater Braddock by later August this year, but it's oscillating between Alabama humidity and the occasional rain that feels like it's from Virginia mountains. I can't remember an August like this, but then everyone is saying that everywhere for different reasons. Best regards, John.

Wuhan market sampling origins

1:21:25Alan.

Wuhan market sampling origins

1:21:26Okay. Jeff writes, Dear TWIV folks, just a thought to ponder. Lab leak proponents occasionally trot out the factoid that no animal samples showing infection by SARS-CoV-2 were ever recovered from the Wuhan market. The Chinese government clearly instituted a massive response at the presumed epicenter of the pandemic. That included cleansing the market. The Chinese government is also extremely proud of the concept of China as a great power and well aware of the limitation of, for example, its health care system. Given that, an interest in viruses and viral evolution is reasonable from a public health

1:22:01perspective. You have to wonder if there aren't thousands and thousands of biological samples in a warehouse somewhere deeply classified and considered highly sensitive, which would allow their virologists to analyze the full breadth of mutations within individual animals. Granted, modeling viral evolution at the level of infected individuals is an extremely hard problem to solve. But given the virus's ability to reinfect the infected at relatively small timeframes, I've always wondered if the initial spillover event didn't use multiple entry routes for a fairly

1:22:36low R0 per route, and the pandemic spike protein was optimized after that event. Then again, given the Chinese economic system is in some ways a public-private partnership, it could just be that the live animal dealers decided a quick destruction of property was the best way to stay out of trouble. We'll likely never know. Cheers, Jeff. My take on this, Jeff, is that the initial cleanup response was deemed an urgent public health response, and they went in bleaching everything in sight, as one would in that situation, because

1:23:09you have this outbreak and you think it may have come from here, kind of the nuke it from orbit approach. I seriously, seriously doubt that there are warehouses full of samples from that. Um, and I'm pretty sure that if there were, we would have heard about an analysis of them by now, because I'm almost certain that those samples would confirm that it came from the market, which, you know, would be relevant. Uh, yeah. And I would think that the, uh, uh, the Chinese would like to know that.

1:23:44Yes. Um, and you know, as, as, um, embarrassing as it might be to have it come from the market, it's a lot less embarrassing than have it have come from a lab. Yes. So they would want to know that. Of course, the conspiracy theorists will say, oh, they did that and it came from a lab. So they're not telling us. Right. I'm not buying it. No, no, they went in, the, the, the public health folks and the, um, the, whoever was in charge of the market went in and bleached everything and there's nothing left.

1:24:17Oh yeah. So, I mean, I've heard that the animals were all returned to their owners, which is not, it's, that's weird, isn't it? They wouldn't just burn them, but, but people have told me that they were just returned. And so, I don't know, but the fact that they did sample the market after this sterilization meant they were still interested in what was there. Yeah. And we got that information, right? We have the sequences of those samples, which constitute the bulk of evidence for, you know, a market spillover.

1:24:48And we also have samples from before the pandemic, from a completely unrelated study that happened to be going on sampling wildlife. Um, so that's how we get the documentation of what wildlife was there in the market. Yeah. And this quote, no animal samples showing infection of SARS-CoV-2 were ever recovered from the market. Um, there were DNA swabs. Yeah. They're environmental samples. Yes. Contained both animal and SARS-CoV-2. Correct. That doesn't mean the animal was infected, but.

1:25:20No. It's a, it's an inferral, right? Yeah. But you would like to have an animal that you take a sample from and say, yeah, this animal, but we don't have that. We did have it for SARS-1, right? We did sample because they didn't shut down the market then right away. They let it go for months actually. So we could do that. But here, uh, I guess, well, as Alan said, you think it's because of public health. I don't know. It could also have been that they wanted to just shut it down and erase all evidence. I don't know.

1:25:50I don't think it was about erasing evidence. At that point in the pandemic, it was, this was an unknown and it wasn't known how dangerous it was, how contagious it was. Uh, we think it may have come from this market. Sanitize the heck out of the market. I mean, as Rich said, I, and as I agree, I wouldn't have taken samples and I'm a virologist. I, under those circumstances, just clean it, make it go away. Yeah, but I, but we know SARS-1 came from a market, right?

1:26:20So you would want to know if, because they had said we were going to take care of this and make it all safe and they didn't. So I think they want to cover that up. I can see that. Yeah. I mean, there are aspects of this that they would rather not talk about. Like the, the initial, there, there was the initial knee jerk reaction by the Chinese government to suppress all information, um, just because that's the way they react to this type of thing. But there was a fairly quick turnaround from that to, oh, okay, we need to deal with this.

1:26:51And then there was just this overwhelming, again, typical of the Chinese government response, um, where they just pulled out all the stops and, you know, locked everybody in their homes and sanitized everything they could. You could do, you know, you could do a sweep of slobs before you actually did the clean. You could. Yeah. And it would be a good idea in future to anybody who confronts this situation, you know, send in a, a, a gowned up, gloved up crew, you know, and. It could have been done.

1:27:21It could have been done. It could have been done. It could have been done. CSI.

1:27:24What does this mean? The Chinese economic system is in some ways a public private partnership. Yeah. The government is, the government is business and business is the government.

1:27:34They run everything? Uh, yeah. Everything. I, well, not in the micromanaged sense, there are private businesses, but they're very much part of the same kind of system. Okay.

1:27:49All right. We have one more from Steve. Thank you for a marvelous podcast. Remarkably both informative and entertaining.

1:27:58Wait till you hear this one. This small correction. In Twiv, August 16th, Brianne referred to a NASA page showing a wide field photo with zoomed in details, detail photos around the edge. The main wide field image is actually the one from the new Rubin telescope, which is designed to produce large scale images surveying the entire sky. However, it doesn't have nearly the resolution of the Hubble or Webb space-based scopes, which can only look at a small area, but in much greater detail.

1:28:31Thank you for all your fine work. Okay. Thank you, Steve.

1:28:37You get that? Do you guys understand that? You space guys? Rich, you're a space guy.

1:28:43Yeah. I think I understand it. I didn't realize that a specialty of the Rubin telescope was taking large area pictures. Okay. And it's got lower resolution, but... Lower resolution. So, it makes me wonder if the surrounding pictures were actually blowups of the Rubin telescope. Or taken by a different telescope. Taken by a different telescope. That's not clear to me. All right. Let's do some picks of the week.

Picks of the week

1:29:12What do you have, Rich? So, about a month ago, I picked the first book and first novella of the new series by the pen-named James S.A. Corey, who were actually Daniel Abraham and Ty Frank, who wrote the Expanse series, a space opera-type science fiction stuff. And so, I will now add the second book called The Faith of Beasts, which I have finished.

1:29:44And it's weirder than sunshine, I'll tell you. And I'm not going to say anything more. Because if I say even anything, I guess I should say, and I probably said this in the first book, think alien abduction on a large scale. And intergalactic war. Okay? That's what we're talking about. With a myriad of strange alien creatures. So, this goes on. And I don't know how they're going to wrap this up in the third novel, which we expect, I suppose,

1:30:15within a year or so. So, there you go. I recommend it. It's good fun. The first one is The Expanse. Did you like that? The whole series? Yeah. Oh, I love the Expanse series. I read them all. And I like this thing that they do, where they write a bunch of novels, and they have these novellas that sort of fit in the cracks, that will do stuff like take one character or one phenomenon and elaborate on it in a really quick read. Right? So.

1:30:46Cool. Got it. Really good stuff. The novella in this case, I picked in the last one, it's called Live Suit. It's quite good.

1:30:58Alan, what do you have for us? I have a book. It's nonfiction. This is Ingrained, The Making of a Craftsman by Callum Robinson.

1:31:08It's a book about a woodworker. So, this guy, he's the son of a woodworker and grew up around trees and turning them into things and went on to become a successful custom cabinet maker, high-end stuff, and ran a business with several employees and was doing okay. And then he had a major, major contract coming up, and they pulled the budget. It was like some major architectural client was going to buy a bunch of stuff.

1:31:42And then they said, yeah, we've had a change of direction. We're not going to do this. And so, his whole business was sitting there, you know, he's got employees to pay, and he's got a family to support, and he's got no job, basically, you know, just sitting there in his workshop. And so, he decided to try opening his own independent shop and doing the kind of woodworking he wanted to do, which is this, it's really a great, I'm not, I'm selling it short just in trying

1:32:13to summarize it, but it is a great philosophical memoir of the meaning of craft and of work. And he is, I have not seen any of his woodworking, any of his furniture, but if it's anything like the way he builds prose, it must be absolutely gorgeous. He's an excellent writer. And this is just a beautifully crafted book, and it'll make you think. Great. I appreciate craft very much.

1:32:43Yeah. I love seeing people who are good at what they do, no matter what it is, right? It's really great to see humans do these kinds of things. The things they're capable of is just incredible. Do you get your books at a library, Alan? Mostly. Well, my, so I buy some and I check others out of the library. I now read so many books that if I bought all of them, it would be a significant expenditure and my house would be full. So, I do check out a lot, especially fiction.

1:33:14I tend to check out from the library because I like to read that in a hard volume. You know, I don't want to accumulate a bunch of books. But nonfiction, I mostly read at the gym on my phone, and I buy those. I've actually been buying them from a site. Did I pick bookshop.org? Yeah, I think so. Okay. That's now where I buy my nonfiction books because I'm cutting back on Amazon. And it's great. I get, you know, the book on my phone and I read it there in the gym. So, this one I bought.

1:33:44So, when you get from bookshop.org, what do you read it on? I read it on their app. They have an app. Okay. They have an app, which is on my phone. Well, look, two out of three of us picked books. So, here at TWIV, reading is not dead. However, I picked something that is the opposite of reading, which we complained about. Well, actually, the article in The Atlantic that I kind of summarized last time, we complained

1:34:16about people getting information from YouTube videos because that's what I'm picking this week. I do spend time on YouTube because I'm there to work on microbe TV. And then, you know, on the right, there's always a list of things that they want you to look at. And this one came up. It's called New York City's Five Broken Skyscrapers. Which one dies first? So, if you've been to New York lately, you know that there are these very narrow buildings that go really high.

1:34:47It's insane. One of them, the tallest one at the south end of Central Park is on a footprint of 60 square feet. It's ridiculous. And this thing is almost one of the tallest buildings in Manhattan. That's actually the only one that's engineered properly. All the other ones are failures and they're breaking. And it's a matter of time before bad things happen. And so, this video goes through. I mean, one of them is leaning.

1:35:17One of them is cracking. The one that's actually engineered property is empty because these apartments are $15 million each. Yep. Who the hell can afford that? I mean, they're gorgeous. They're totally, the whole floor is your apartment. It's surrounded in glass. You have views of the park. Of course, it's gorgeous, but it's totally crazy. And anyway, the others are structurally screwed up. And there's one down by NYU on the East River, which is leaning.

1:35:47And they don't, nobody knows how to fix it. And nobody knows who's going to pay for it because it has to be taken down. And that's going to cost $150 million. And this is a crazy situation here. I don't know why you needed to make these pencil things. I guess because you could, right? Well, it's because they had these tiny, tiny properties available. That's true. And the only direction to go in Manhattan is up. And they're aiming for the richest clients because they're the ones who can actually afford

1:36:18to live in Manhattan anymore because everybody else has been priced out of the market. And so they're building these absurd buildings. I watched this video, and at the end of it, my prevailing thought was become a real estate lawyer because that's who's making money off all this. I mean, every one of these buildings, they're with the structural problems, and there's everybody suing everybody. And then even the one that's engineered properly, the companies went bankrupt because nobody was

1:36:49buying. I mean, the market, there are maybe 100 people in the world. You can afford these damned apartments, and they already have places to live, so they didn't buy that. It's just absurd.

1:37:01I think it messes up the skyline. Of course. To have these pencils sticking up. You can see in this picture in the video. It's just ridiculous. I was walking downtown once a couple of months ago, and they were building one of these. It was completely obstructing the view of the Empire State Building, which you would normally have walking around in this area where I was. And now it's gone. You can't see the—which is—the Empire State Building is a very nice-looking building, right? And now that view is gone, and this thing is right next to it.

1:37:32It was one of these pencil buildings, you know, many millions of dollars. And, well, this is a capitalist society. You know, money goes—money runs everything. It's not just capitalist. It's too capitalist. We've taken things a little too far these days. Yeah, well, money runs everything, right? That's the problem. That is the problem. And I just don't think it's right that a few people have it all. Yeah, that's the fundamental problem. Well, I'm sort of gratified to hear complaining about these buildings, because they've always

1:38:12mystified me. And it is perplexing to think—I mean, somehow you would think you could hold the contractor liable and say, okay, we've got to take this sucker down. Um, you're paying for it. I guess that's where the lawyers come in. Well, right. I mean, in many cases, the contractors who build it, they're not the problem. It's the design. And then you've got to sue the architect, but they've got, you know, a company, the shell

1:38:43company that can just go bankrupt. And, yeah. And it looks like there are a bunch of these issues that are probably subcontractor issues as well. Yes. Yeah, it too. So there's a bunch of them. I would—I mean, even if I could afford it, I wouldn't live in one of these. No, it's creepy. I'd be scared. I'd be scared. And also, they move. They do move, because they have to have flexibility. I couldn't handle that. Be seriously creepy.

1:39:10It's TWIV 1351. This is incredible. We've done 1,351 episodes. You guys have been on most of them, too. A lot of them. I look back the other day. I first showed up on TWIV 26 as a guest. It took me a while to become full-time. That was around TWIV 68, which we referenced today, that was Ode to a Plaque. Ah, yes. One of my favorites. That's the— I enjoy doing it a lot.

1:39:41That's why it's at 1351. Great stuff. Anyway, you can find the show notes at microbe.tv slash TWIV. You can send us questions, comments, picks of the week to TWIV at microbe.tv. And if you enjoy these programs, we'd love your support, microbe.tv slash contribute. Rich Condit is an emeritus professor, University of Florida, Gainesville. He's currently in Austin, Texas. Thank you, Rich. Sure enough. Thank you. Always a good time. Alan Dove is at alandove.com, turbidplack.com.

1:40:14Thank you, Alan. Thanks. It's always a pleasure. I'm Vincent Racaniello. You can find me at microbe.tv. I'd like to thank the American Society for Virology and the American Society for Microbiology for their support of TWIV, Ronald Jenkes for the music, and Jolene Ramsey for the timestamps. You've been listening to This Week in Virology. Thanks for joining us. We'll be back next week. Another TWIV is viral.