TWiV 1341: Phage breaks and COVID origins

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 1341, recorded on July 17th, 2026. I'm Vincent Racaniello and you're listening to the podcast all about viruses. Joining me today from Ann Arbor, Michigan, Kathy Spindler. Hi, everybody. Here, it's 87 Fahrenheit, and I didn't get it converted to Celsius because when I went to my app to do that, it was linked to a Tour de France site where a friend of mine is going to be riding a practice ride. So I can't tell you what it is in centigrade Celsius, but we were talking about this just a moment ago, and the air quality index here is 259, very unhealthy.

1:02Gosh. Yeah. At one point yesterday, supposedly it was 500, although I didn't see that, so I cannot confirm it. Gosh. Well, that's because you're so close to the source, right? Yeah, closer, I guess. Here it is 31C and sunny. The air quality index is 95. Yesterday it was 195. But it's still very hazy here. I took a picture yesterday. The buildings are all in haze. It's really interesting. But most people are not wearing masks outside, even though you can smell it and the particles are not good for you. Also joining us from College Station, Texas, Jolene Ramsey. Hello there. Here, we don't have smoke.

1:47We have rain, although today it's not raining. It's 89 degrees Fahrenheit, which is 32 in Celsius, which is just a little bit warmer than you have, Kathy. And we have been getting rain this week. We have, unfortunately, some flooding in South Texas, and I think that's keeping the air clear. And from Montreal, Canada, Angela Mingarelli. Hello. Yes, here it is 26C, which I think is 70, what did I say, 77 Fahrenheit. Our air quality index is very low. Like it says two on my phone, which I don't know if it's a different scale, but anyway, it's in the blue, like towards zero. A few days ago, we did have from the, of course, from the Canadian forest fires, we also had some haziness, but now it's actually passed and it also rained.

2:36So it's pretty nice outside. It was cool this morning. It was like 18 degrees this morning. It was so nice. If you enjoy these programs, we'd love your support to to continue them, micro.tv slash contribute, number of ways you can contribute. For some reason today, I was thinking about dreaming, not in the sense when you sleep, but just dreaming, you know, like I have this idea. So I have two dream quotes that I just looked up quotes on dreaming. I have one by Eleanor Roosevelt who said, the future belongs to those who believe in the beauty of their dreams. That's very nice, the beauty of your dreams, right?

3:21I like that a lot. And then Walt Disney said, all our dreams can come true if we have the courage to pursue them. I think that's a very nice sentiment, but not very realistic. I think you need money. If you're Walt Disney, maybe. Yes, and abilities. I mean, that's their slogan. oh is that their slogan I think isn't it like Walt Disneyland where dreams come true something like that well let me tell you when I graduated college I wanted to be a photographer but I did not have the courage to do it because I thought I sucked okay so there's a case where it would have been nice to have some courage I mean could have done it but then we wouldn't be here it's a good question the butterfly effect, right?

4:13I wouldn't be here. Well, I don't know. If I had failed, I might still be here. I just don't know. It's a good question. I might have piddled around for a few years and maybe been half successful and been poor. I think it's good to... I don't know. Well, maybe I'm influenced by some things I have read in the past couple of years. We tell kids that they can be anything that they want to be, but in reality, they can't, But they can be good at something and their dreams might change over time, right? Because maybe you still want to be a photographer, but maybe I had a dream when I was a kid and I don't actually want that dream anymore.

4:52So if you can adjust your view, then you could be living the dream now and not even realizing it. I think you have to dream, though, no matter what the quote is. You have to want something that you don't have and pursue it. I still want to be a photographer, but... You should do it. What's holding you back? I don't want to use this thing. I don't want to use this. It's limited. I want to use a regular phone. A camera. Subliminal stuff. I would love to. I love taking pictures even on this phone, which is not bad, but I want to get a real camera. I have cameras. The camera makes a big difference.

5:35I'll bring it up later in one of the papers, but a real, quote-unquote, real camera compared to phone cameras, the pictures are different? Totally. I mean, I found some old pictures that I took of myself in college, and they were taken on a Nikon on film, and the image quality is just amazing. Of course, every film is different. It gives you a different quality. But these cameras take very harsh pictures with no nuance unless you know what you're doing, and then you can control it to some extent. But I would love to do film again. And film has such a nice dynamic range. And there are a lot of people who still do film, actually, who still shoot film.

6:13And it's not easy because it's hard to get it processed. I used to process my own film. And it was a lot of fun, too. Anyway, dream on, folks. Dream on. The Rosenfeld Lab is looking for a postdoc and a technician to work on viral pathogenesis and immunity. They work on enteroviruses. They're interested in mouse models for pathogenesis, antibody responses, and developing vaccine platforms. You can email Amy Rosenfelda at MLHS.org. Now Kathy is here. She can give us the ASV update. So American Society for Virology annual meeting will be held at University of Minnesota. Coming right up in Minneapolis, July 27th to 30th.

7:02You can visit the website. go to ASV.org and click on ASV 2026 to get more information. And the big news is that the mobile app is out for attendees. And once you're in the mobile app, you can find the program PDF. If you are the ilk that likes to look at PDFs, it can kind of give you a nice overview of the meeting. And you can search it for various things like for names of people or names of viruses in a PDF search format and quickly find things, pages that you want to go to. You can also use the mobile app in the way that it's designed and figure out your schedule because it's important to get an idea of what you want to do before you get to Minneapolis because once you get there, it's like drinking from a fire hose and you will invariably miss some things that you wanted to.

7:57that might happen even with planning but with planning at least you have some idea of what you want to go to so check out the mobile app and the local hosts are launching the viral art initiative and so you can submit original artwork to be showcased throughout ASV 2026. I don't know if there's a deadline for that I didn't look to find that out but you can check on the site for information about that So ASV starts on the Monday. On Saturday and Sunday in Rochester, Minnesota, which is about an hour away, there's a measles mini symposium. And I'm going to that to do a TWIV and to check out the meetings because there are a lot of cool talks on measles.

8:44So anybody go into that. It's Saturday and Sunday. That's cool. All right. Our first paper is from Jolene. Okay. So today's paper is coming from M-Bio. Just came out this week, actually. It is called Concentration-Dependent Dual Activity of a Phage-Encoded Lysin Modulates Infection Dynamics in Mycobacteriophage D29. This is coming to us from the lab of Vikas Jain. The authors are Shinto James, Gokul Nair, and Priyambada Nath. And they are, or were, had a couple of institutes in India. So there is the Indian Institute of Science, Education, and Research in Bhopal, and then Korea University. And I say they were because some of them have moved.

9:45And I think Kathy has a summary for us. I do. And because this is an mBio, it means it's open access. And so I'm going to start at kind of first principles. Phage are viruses that infect bacteria. And phage can encode proteins that allow the newly produced viruses to break out of the infected cell. And these proteins are called lysins because they lyse the cell, L-Y-S-I-N. And this paper identifies a particular lysine called LysB from a particular phage. And this LysB has been shown now to have a second function. Besides lysing the cell, at late times, it accumulates to high levels outside the cell, where it then acts on uninfected cells, and it makes them resistant to infection.

10:38This means that some cells could survive the virus infection, preventing host extinction. In other words, it prevents the virus from wiping out all the host. So understanding the mechanism of this has possible consequences for improving phage therapy. Phage therapy is generally where you have identified phage that are directed against particular bacteria, and oftentimes now we're doing it against bacteria that seem to be resistant to all the other antibiotics available, and so phage is another way of dealing with the bacteria. And so phage therapy can provide a way to thwart the bacteria, but it's known that in some cases, not all of the bacteria are wiped out by the phage, and then the surviving bacteria then may wipe out the patient.

11:33So that's bad. And so if the phage have this type of lysin, this could be one explanation for how and why they don't lyse all the bacteria. And figuring it out could improve phage therapy. So the bacterial host here for this phage is mycobacteria. And these bacteria have a more complex envelope than other bacteria. And we'll get more into the details of that. But there are three functions, at least for this particular phage that we're going to learn about, that help get the phage into the cell, dealing with these different parts. So holins can interact with getting the phage through the cytoplasmic membrane.

12:21Another lysine called lice A is involved with the peptidoglycan. And then Lice B disconnects the third layer, this arabinogalactan, from the mycomembrane. And it's this third layer that makes these mycobacteria more complex than the other bacteria that we usually hear about. And so just in brief, they study Lice B in a particular phage called D29. And they do this several different ways. is they delete lice B from the phage, and they observe what happens. And they treat host cells with purified lice B and observe what happens. And they come up with a model that lice B outside the cell is somehow likely removing the cell surface determinants that the phage needs to absorb to the cells.

13:15So if those are removed, then that keeps the virus from infecting those uninfected cells. And so the take-home message then is that this LICE-B is regulating infection dynamics at the population level in addition to being involved in lysing the cell. So that's my summary. So Jolene, you're at the Lysens, right? That's what you work on? I work on the process of Lysis, yeah. Yeah. Yes. So that, I mean, that's what made this paper catch my eye in the first place. But this is a bacterium that I do not study. So Kathy mentioned phage therapy and mycobacteria. So the most famous mycobacteria is mycobacterium tuberculosis, the causative agent of tuberculosis.

14:03And so that makes it a really important bug to be studying. and this bacterium can be killed by D29, as well as the model that they're using here, which is Mycobacterium smicmodus. And they do have this very complex envelope that makes it tricky for the phage to get into the cell, as well as for the phage to get out of the cell.

14:26The interesting thing here that also caught my eye is that they had this observation about blacks. And so just to kind of go a little bit more into what they did at the beginning. So the phage, they knew already that they could delete this third protein that was important for getting out of the cell, the Lyce B protein. But they didn't know exactly what the impact was. Deleting it and you still got phage. There was another group or a couple of other groups that had shown that they seemed to have phage trapped inside of cells after the LiceB gene had been deleted. And so that's kind of what they're following up on in terms of observations here.

15:10And I'll bring in the details of the cell wall as it's important as we go through the data. So to begin with, they just, they deleted the gene and then they showed that they no longer got the production of that protein. And the infection dynamics themselves were not really that different. The cells still ended up being killed from phage and they died at the same rate. They made plaques on plates. They made these clear zones in an even lawn of host bacteria on the plate, and the clear zones looked to be about the same size and number, and so there were no changes there. But the place where they saw a difference between the wild-type parent phage D29 and the delta lice B was when they looked at how many phage actually escape from the cell at the end of the infection.

16:08And they saw that without Lice B, there was a reduction in the number of total phage that got released from infected cells. But even cooler, this was where I had to kind of go and look up some of the work that had been done by this group before. When they add purified Lice B to infected cells, then they could release more phage from basically the husks of cells that were dead and were trapping the phage inside. And so this group has been studying this LiceB protein as something that could be used as a therapeutic on its own. Interestingly, we'll look at some of the other data they have, but basically if you add LiceB from the outside, somehow it seems to be affecting the cells on its own.

16:56And if you think about the layers of the cell from the inside to the outside, there's one membrane, and then there's the cell wall, which is a sugar peptide layer. And then there's another complicated sugar layer called the ravenogalactan. And that is attached to a very complex set of lipids. Some of them are called mycolic acids. And then there are many other free lipids that are present in this layer that becomes a membrane that we call basically wax. So the bacteria have basically covered themselves in wax to protect themselves from the outside. And it works really well. Lice B works between the arabinogalactan layer and the mycomembrane, the waxy layer.

17:41Somehow when you add it to the outside of the waxy layer, it's still having this effect. Not entirely clear how that's happening. But here they clearly show that you can release more phage from the infected cells if you add Lyce B from the outside to supplement when it's not being made on the inside. And so they follow up on this observation, doing something that, well, thinking a couple of things like, okay, so clearly Lyce B is not required for phage to get out of the cell, but it seems to be helping. And so how might it be helping? One possibility is that as the bacteria grow, they dynamically modify the composition of that waxy layer.

18:25And so they thought, well, maybe Lice B works on one composition of the layer versus another, so maybe it works better on growing cells. Actually, maybe it doesn't work as well on growing cells, and it works better on older cells where the mycomembrane is different, or something related to that. So they tested this by essentially watching the plaques on a plate because what happens is you mix together growing cells or you mix together cells that are going to grow on a plate. And you put them on the plate and you can't see anything because there's so few cells. And you also put phage. And then the cells start to grow and they make the thing that we call the lawn.

19:06And as they're growing, the phage are infecting and making the clear zones. And they're all kind of prevented from moving around by this semi-solid auger layer that we've embedded them into. But as they grow, eventually, they start to either run out of nutrients or space. Various different things cause them to stop growing. And as they stop growing, they're older, their membranes are changed, other physiological changes occur inside the cell, and they become less susceptible to phage. And so plaques usually stop growing because phage replication is not continuing. So if they watch plaques over a longer period of time, then they said, okay, well, maybe the plaques will be different after a longer time because the cells are older and maybe Lyce B does something different.

19:50So they just looked at plaques on lawns. Instead of looking after the normal overnight incubation, which we usually call something like 16 hours, they looked at plaques after 60 hours, so like two and a half-ish days. and they saw a dramatic difference, dramatic to a person who looks at plaques all the time, of course, and that is that the wild type has a very clear center and then it has this ring around it that we call a halo. And the Delta Lice B does not have this ring. It's just totally clear. The difference between the plaque and the lawn is very striking. I call that a sharp or a hard plaque.

20:31and they watched them over time. They actually imaged the plaques over time and you can see how the wild type plaques develop this halo and the Delta Lice B plaques do not develop a halo. They use this nifty trick to quantify the gray values in the images and plot it. And they even actually took samples from inside the plaque, inside the ring and in the healthy lawn area and they quantified bacteria and they could see that in delta lice B, there was basically no cells, no living cells in the plaque. But in wild type, that ring, the halo, has cells that can grow back up, cells that are alive. And that suggested, if you look at the image series, which is really cool in the paper, they suggested that the cells actually grew back over time after being exposed to phage.

21:27so then to follow up on try to figure out what was going on with how does wild type form these halos and what's going on in the halos they did a few things one thing they did was is it is it the old cells thing so they made a lawn but they didn't add phage and they let the lawn grow up for 14 hours so almost overnight and then they added phage and they said okay so do we now get halos differently or maybe no halos, but actually the wild type was even more haloed. It was almost all turbid, and then the delta lice B was completely clear. And then they showed that if they put lice B back into cells where it wasn't in the infection, so delta lice B plus lice B, then they got the halos.

22:15So it was just the addition of lice B that made the halos in the plaques. So then they said, okay, maybe it's not the age of the cells, but it's the presence of Lice B and something that Lice B is doing to the cells. So they took advantage again of the fact that purified Lice B has this effect on the cells itself. So they spotted dilutions of Lice B, different concentrations from less concentrated to more concentrated, and they just put that on the plate. And then in the spot where lice B was now on the plate where the lawn was going to grow, they also added phage. And they looked to see what was the effect.

22:56And they saw that when lice B was there, they were not able to form plaques as well as when lice B was not there. And the presence of lice B didn't have a significant effect on the viability of the cells. The cells are still alive. They just didn't grow as well. So then they checked in liquid. So that was on solid media. They checked in liquid, and they saw that when Lice B was there by itself, cells were normal, they grew, and their membrane properties weren't that different because they added this dye that can bind to DNA if it can cross membranes. Most healthy cells exclude these kinds of molecules by their membranes.

23:47And so when they added Lice B and the dye, dye didn't get into the cells. But if the cells were infected by phage and Lice B was there, then the dye could get inside, suggesting that the presence of Lice B changed the permeability of the membrane so that the dye could get into the cells. Okay, so this was really interesting because it suggested that the protein itself was having an effect on the cells independent of its activity for getting the phage out of the cell. And the last kind of thing that I think really tied together, so that they're thinking, okay, so what is happening here? You've got cells that are lysed, a lot of phage are released, Um, now the phage are going to go look for another host and they're going to get into those cells and kill those cells.

24:48And, and it keeps going on like this. And this is how we usually characterize a phage and their role in the environment is they're killers. They go, they attack the bacteria, they wipe them out. But in reality, the environment is full of bacteria. The most viruses do not, cannot wipe out their host because then they will not be able to propagate. So one idea they had here is that, well, maybe when lice B gets to high enough concentration outside, because lots of cells have lysed and released lice B, then that amount of lice B is going to have this effect on bystander cells that haven't been infected yet.

25:28And if that were the case, then maybe that would prevent phage from infecting those cells. How would it prevent phage from infecting those cells? Well, Lysb acts on the membrane, and the membrane is going to be the site of the receptor that the phage has to bind to get into the cell. Now, the receptor for D29, as far as I can tell, is not known, but it's going to be something on the surface. It might be a sugar on the surface. It might be a protein that's sticking out. Lysb specifically is an esterase. It cleaves a bond in the arabinogalactan that's linking it with the lipid. but maybe that has a secondary activity and or maybe it's loosening up the mycolic layer and that then no longer makes the receptor likely to be on the surface the cell has some sort of stress response and down regulates it so all of these possibilities the key would be that the phage wouldn't bind as well so that's what they tested they looked at the adsorption of phage to cells that have been treated with Lyce B, as well as cells that have been treated with Lyce B that had a catalytic residue change.

26:42They were no longer active for their activity of cleaving between the arabinogalactan and the lipid. And so when they did that, they saw that the wild type still binds and the cells that are treated with the inactive Lyce B still bind, but the cells that were treated with lice B did not bind as well to the phage. So that suggested that the presence of lice B, active lice B in the media decreased phage adsorption to the cell surface. And if that happened in the natural environment when lice B is high is when lots of phage have been released. That ecologically would make sense for the phage to kind of preserve those host cells so that they could grow and make more host cells and be available for the phage to then attack later.

27:32So it's kind of like cultivating your food. It's like, this is my control mechanism so I don't overeat or something like that. So those are the data that they have. They showed that this Lice B protein is important for phage getting completely out of the cell. And because of that, it may be that as it accumulates in the environment, it makes some change. We don't know what change on the other cells that are there that decreases their susceptibility to binding by the phage itself. So I guess there has to be a balance between infecting enough hosts to get enough virus to move on, you know, keep the population, and not killing too many.

28:17So how do you get that balance? Well, this concept of the release of a protein or something that you release into the environment when you escape, as that builds up, and if it's proportional to enough viruses, then that's a good kind of mechanism, like an independent way to protect the bystanders. So are there related genes to Lice B and other phages that infect other bacterial species? Yes. Well, other bacterial species, other mycobacteria, yes. But in terms of other bacteria that are not mycobacteria, not so clear. Yeah, not so clear that they're... We do know that bacteria respond, kind of like our cells do, respond to molecules that are normally intracellular and should not be extracellular when they are present on the outside, then cells can detect that and turn on stress responses that can be protective.

29:24But it's in terms of like a specific phage protein that helps with that, we don't know. Because obviously you have deleted these related, these lysine genes and other pages. You don't see this phenotype, right? I would say that we probably haven't looked. We are, in my lab, we study a protein that's kind of like this, actually, that gets released and can affect the infection dynamics in later infections. But it's not clear how widespread it is. This is a cool mechanism. You would think it's more widespread, right? But maybe we just haven't looked for it. Exactly. Yeah. Haven't looked for it. Don't usually watch our plaques over the course of four days.

30:06Three days. Jolene, what do you think about, I mean, this was really cool for me because I never think about phages. I think I've only ever thought about phages when talking to you or being on TWIV. I mean, I know that sounds bad, but it's true. I just don't. I'm not exposed to it. I mean, there's actually a lab on our floor, Corinne Morris. They do phages. They do phage therapy and stuff like that. So adjacently sometimes. But for me, this was like so cool. I was learning so much and Googling the entire paper because I didn't know what was going on. But I guess one of the questions that I'm left with is, what do you think this could mean for treatment of mycobacterial infections?

30:41Or if this could be somehow harnessed against tuberculosis? Because we, like, trying to think more broadly, because tuberculosis is obviously very resistant for many other reasons, but this maybe is one of them. Do you know if, like, what type of treatment options this could open up? Or have you thought about it? Yeah. So this is definitely not my area specifically, but the idea of using phage that can self-limit is not ideal for therapy. So if we were going to use this information to improve phage therapy, we would want to use phage that don't have Lysb. We'd want to remove the Lysb, use a recombinant phage.

31:25although we then might be able to take advantage of this because you could potentially use this protein so in this same group the jane group has another paper where they took lice b and they treated cells in culture that have mycobacteria inside because they're an intracellular bacterium and they were able to reduce intracellular viable bacteria by treating with lice b so maybe on its own, it could be useful if you study it more and determine the mechanisms of how that might be working. I think you should tell us the method used to delete the gene. Oh, crispy bread? So cute. So cute when I read that.

32:09Yeah, crispy bread. It's a clever little name to indicate that they use bacteriophage recombineering by electroporation of DNA. That's the bread part. and then they get recombination and then they counter select against the wild type. So they make a mix of wild type and the mutant and then they've got to get rid of the wild type. So they use CRISPR to select against the wild type. They cut up the wild type. Wild type doesn't replicate and they get the mutant out. Okay. Great name. I love it. Like when people go the extra route to try and make it. Yeah. So this paper, I was kind of jealous of the plaque pictures.

32:50They're so beautiful. And so I emailed the authors and asked them how they take their images. And they told me that they use a colony counter. It's a device for putting a plate on that's backlit. And they use a real camera, a DSLR. Because they are really clear. A real camera. Even to the untrained eye. Like, I mean, I've looked at plaques, but I've never looked at, I haven't looked at that many. and the halos here are very, very clear as of like hour 22. Like anyone can see it. It's very clear. But maybe with another camera, maybe with your iPhone, Vincent, we couldn't see it. Exactly. Halos are actually difficult to capture.

33:28I think if you know how to use iPhone cameras, you can be better at it. There are actually apps. So I use it now to record at remote podcasts. I use it as a second camera. and there's actually a movie a video app it's called Filmic which is much better than the native app you can do all kinds of cool things and people use it for shooting theatrical releases and so forth so obviously it's good but if you just take a picture it's just going to make everything exposed the same there's not going to be any nuance but you have to overcome that and there are ways to do it but most people don't do that that's why every picture looks bright and perfectly focused and, you know, it doesn't have to be that way.

34:15Okay, thank you, Jolene. We have, now we move into the eukaryotes. And this is a paper about SARS-CoV-2, and we're continuing the origin hypothesis. This is a paper in the Proceedings of the National Academy of Sciences, evaluation of a proposed link between the SARS-CoV-2 furin cleavage site and mouse-adapted MERS coronavirus MA30. The authors are Metzger, Jones, Meyer, Richter, Klassen, Olmer, Diegmüller, Heimsch, and Christian Drosten. And this is from, um, all the way at the end. I know Drosten is at the Charité Hospital in Berlin. I don't know where everyone else is. Cambridge, Hanover Medical School, and Humboldt University in Berlin.

35:16Okay, thank you. Okay, the furin cleavage site. Everyone remembers the spike protein of SARS-CoV-2, right? this protein on the surface of the particle. It's important for attachment to cell receptors. And this protein needs to be cleaved by proteases so that it can catalyze fusion of the viral and the cell membranes. And there are two cleavage sites in the spike protein that are both needed for efficient fusion. One is by a protease restricted to the respiratory tract called TMPRSS2, TMPRSS2. And the other is furins. Furins are ubiquitous proteases, so they're found in many different tissues. And they have a cleavage site, which in SARS-CoV-2 is RRAR.

36:15Now, the thing about this, so that's the famous furin cleavage site, which some people have said is, including my former postdoc advisor, have said it is a smoking gun for lab origin. It is not a smoking gun for lab origin. And I don't want to speak badly of him because he's deceased, but when I emailed him about it, he said, yeah, I probably shouldn't have said that. People say things that they don't. All right, so in SARS-CoV-2, the furium cleavage site, has RRAR, four amino acids, right? And it's unique among SARS-related beta coronaviruses. So related bat coronaviruses like RATG13 and others, they don't have this site at all.

37:09There are other beta coronaviruses like MERS and the common cold virus HKU1. They have some furin-like sites, but they don't have RRAR. Okay. So the absence of this RRAR led people to say, aha, it must have been put there. So to reiterate this, because I think this was not something I really appreciated early on, but this RRAR is a furin cleavage site and it's found in the SARS-CoV-2 virus, But it's not been found in other SARS-like viruses as RRAR. There are other furin cleavage sites with other amino acid sequences, but not RRAR. And the fact that it doesn't exist in any other viruses and doesn't exist in bat virus sequences made this seem suspicious.

38:16Where did it come from? It's R-R-A-R and it's not anywhere else, right? That's the gist of trying to come up with a hypothesis for it. And the thing is, in science, if you don't see something, it doesn't mean there is a nefarious origin. It just means it's not there for some reason that we don't know. And that's how all of us are raised to think, okay? Trained in science. Not to be suspicious. Oh, there's a splice site here. It must have been put there by someone. Because it's not anywhere else. This is absurd. This is thinking by non-scientists. Unfortunately, many scientists also thought that way.

38:51But anyway, there's now ample evidence that no human ever introduced this. But yet this paper addresses one possibility. And it's good that they addressed it because they put the nails in the coffin quite nicely. And it's not going to happen. So what's the hypothesis? So I just wanted to repeat. So the title of the paper is Evaluation of a Proposed Link Between This Furin Cleavage Site and Mouse Adapted MERS Coronavirus MA30. And if they could have a colon and the answer after that, there is no link, which is the rest of the title. That's right. So this is good. We have a proposal that maybe this was introduced, and they're going to evaluate it.

39:40Now, the thing is, the elephant in the room here that is not even mentioned in this paper, but they don't have to because they disprove it anyway. The idea is, so there's a mouse-adapted MERS coronavirus, right? MERS is a different set of coronavirus. It's not a sarbeco virus. It's a merbeco virus, MERS-like coronaviruses. and a mouse adapted version was made by passaging the virus in mice. And it has a furin cleavage site, which is RRVR. And the only way I remember it is because it's got my initials in it, like VR. Otherwise, I couldn't remember what RRAR or RVR. And so someone proposed that, aha, they took this RRVR VR and stuck it into a ancestor of SARS-CoV-2, and that became the pandemic.

40:35What is wrong with that statement? What ancestor of SARS-CoV-2? Nobody has an ancestor of SARS-CoV-2. And the closest one, like RATG-13, is 1 ,200 bases away. It's too far to be an ancestor. And anyway, they couldn't make virus from, they had a sequence and they never were able to make infectious virus and culture from that. So the whole idea is bogus to begin with. Yet, but Drosten addressed it and his colleagues said, okay, let's look at this, right? So the idea is that this RRVR of MERS, this mouse-adapted MERS coronavirus, somehow got introduced into a SARS-CoV-2 precursor, and that led to the pandemic.

41:25And then at some point, it becomes RRAR, which is the predominant furin cleavage site in SARS-CoV-2. If you look at all the ones, we're going to see that in this paper. That's the predominant circulating cleavage. So it started out as RRVR and became RRAR. So that, I mean, there's so many things wrong with that. I wouldn't have bothered, but Christian wanted to address it. And he could. He could address it, right? He wrote a whole paper on it, which is— I know. I was like, wow. I was like, he went full send. He was like, I am going to shut this down. Well, also, there is another paper by Florence DeBar, who—it's a review article, which I will try and drop in the show notes, where she goes through the furin hypothesis, the If you're in cleavage site, point by point, it just breaks every point.

42:18I mean, this is one part of it, but she goes through it, does the whole thing, and it's really good. But anyway, the conclusion here, our findings do not support any evolutionary links between MERS, this mouse adapted, which is called MERS MA30, and SARS-CoV-2. So if you want to stop listening now, you shouldn't, because good things happen later. That's the conclusion. By the way, last week we had Tom Kysak on, and he actually listened to our stuff after he left. And he said, I really enjoyed your boomer discussion of rock and roll music. Because we're Rich and I, right? We're boomers. You totally riffed on it.

42:55Yes. Oh, I got so into it because he had a pick, and then I had a pick. And lately I've been into this reliving my ute. And that's a reference to my cousin Vinny, by the way. You remember? Anyone see My Cousin Vinny? No. I think maybe when I was young, peripherally, when my parents were watching it. So the judge is played by the guy who played Herman Munster. Remember that TV show, the guy who was supposed to be Frankenstein? I forgot his name. And so Joe Pesci is in front of the judge, and he said, these two are Utes. And the judge said, what? Ute? What is that? And he didn't know what he was talking about.

43:38So anyway, let's go through the data. So what they do, they look at all the available SARS-CoV-2 sequences in a database called GISAID on September 2025. They end up with 16 ,532 ,722 human sequences. So the GISAID database, this is a collection of sequences from all over the world, from patients, many different. This is something I didn't look up, but I was wondering, do you know if the sequences are like all nasal samples, a lot of wastewater samples, anywhere where virus has been found? I think it's a mix. I also have this question. But because they don't specify, I'm guessing that it's multiple samples, like nasopharyngeal wastewater.

44:27Because they're just genomes, right? They're just complete genomes from... Oh, wait, didn't they say people? One second. I think it's mostly human isolates because the wastewater is going to be little pieces. They don't typically get full genomes. That's true. No, they get little PCR amplicons. So I don't think it's wastewater. I mean, you know what's interesting about this, and they actually talk about this in the discussion, that they say that, so the number of, the acknowledged number of people infected, the conservative estimate of the actual number of infection. So worldwide, approximately 778 million cases have been laboratory confirmed.

45:11And so that's a portion of that is in just say. But a several prevalence study has estimated that a quarter of the population worldwide had antibodies to SARS-CoV-2, which would mean the actual numbers of infections were actually 4 billion. And so this collection of 17 million GISAID sequences is less than half a percent of all the genomes that existed. Plus, remember, it is mostly during the epidemic period. We have nothing pre-epidemic. And so that's one of the major points in this paper as well, that we don't know what things look like in the early days. Yeah, this is 2020 to 2025. And looking in the methods, they don't specify.

45:54They just say human sample. So it is human. Yeah, they say they filtered out, but they looked at some of the animal samples. But GIST-8 itself has all the sequences, but then they filtered it down to look at the human samples. So then they look for this valine, part of the RRVR. So that's 684, amino acid 684. And they look at this at the nucleotide level. And they compare. So they know the MERS sequence and they know the SARS-CoV-2 sequence. And they differ in five nucleotide positions. And basically, out of the 18 ,000 translatable genomes, which they have, only all but 28 are identical in this area, in this furin cleavage site, to the Wuhan sequence.

46:46So there are 28 that are not. And of those four were four nucleotides different from the MERS sequence, and the others were five or six. Two of them had a valine at this position, so the RRVR. So two out of 18 ,000. Which is a very small number. It's a very small number, yes. But remember, the idea is, though, that it was originally valine and it changed to alanine. So you can imagine that some valines are still circulating. So we haven't proven anything yet. But basically, they conclude from this, virtually no SARS-CoV-2 sequences in our data set with ambiguous buring cleavage site, third amino acid, right, RR, A, or VR.

47:34Nucleotides are consistent with a predominantly valine-alanine mixture. It's all alanine pretty much.

47:44Then they look at the relative frequencies throughout the pandemic of this 6-amino acid region containing the furin cleavage site. They have some very nice histograms of the prevalence of this. There is a, they call it an extreme preponderance of alanine at this position. they have other surrounding sequences but alanine is present in and valine is present in 0.06 percent of the unambiguous sequences so again very small amount of valine in this position it's pretty telling when you look at the histograms and you look at the first one with the millions and it's all blue and that represents the ones with alanine and then you can't even see the valine and so they They make a separate graph way, way, way, way, way zoomed in to see the ones with the valine.

48:44Which looks like it's a lot on the histogram. But then if you look at the axis, it's 0.05%, just to be clear, because the one on the top is millions. And this is percent, and it's less than 1%. Much far less than 1%. So then they look at phylogenetic trees because if the valine there is important, you should see lineages arising. So you should see some early valine, which are precursors to other isolates, right? So they build phylogenetic trees of their sequences, and they look at—so these are phylogenetic trees, so there are tips, right, the ends of each branch. They look at each of these corresponding to valines, and then they go back and try and trace them, and basically they'll peter out.

49:47The mean time span, because these samples are all dated, so we know the time when they were isolated. The mean time span has a median period of one day that these valines existed. They were found in 94 different geographic regions, and typically one country at a time. So, again, no indication that there were branches on the tree that begin with avaline and continue for a long time. You know, it's not circulating extensively. That's the point. So, they circulate for at most two weeks, and then they disappear. All right. So then they ask, has selection pressure acted on the furin cleavage site? The way they do this is they look at the ratio of non-synonymous to synonymous codons in this region in their database.

50:53So a non-synonymous codon would be a codon coding for a different amino acid. And as you know, there are multiple codons for many of the amino acids. And so a synonymous one would code for the same amino acid. So if you have a ratio of non-synonymous to synonymous greater than one, you consider that there's selection for that residue at that position. So this particular 684 codon where we're debating V versus A has a dNDS value of 9.35. That means it has a huge positive selection at that position. Now, remember, A has already been established, right? It's already been selected for very early on, and most everything has A.

51:42The question is, in this period that we're sequenced, do we see anything else selected for? And yes, there are other amino acids, all of them. It's almost as if they're changing and none of them confer any deleteriousness or fitness advantage, so they never spread the way they summarize it is here. It suggests that 684 has been under transient positive selection. However, all the observed alternate amino acids were apparently either deleterious or— Sorry, I misspoke. I said not deleterious. They were either deleterious or provided a fitness increment that failed to spread due to stochastic reasons.

52:24So there's a fitness, there's a strong positive selection at this position, but nobody wins except alanine is always there. Okay, so that's very interesting. So V is not positively selected at that position. So then they ask, is the non-fixation of V at this position, is it due to fitness differences? So they now do some experiments in the laboratory. They introduce this amino acid change into an infectious clone of SARS-CoV-2. And they look at replication kinetics of the original virus and the virus with a V in the furin cleavage site. So RRAR versus RRVR. in a bunch of different cells at a very low multiplicity of infection, 0.001.

53:16So very few infectious viruses per cell. So that you can have multiple cycles of reproduction instead of having just one, which could mask any small effects of the change. And so they do plaque assays to measure infectivity. The two viruses have similar replication kinetics. So they don't see any differences in just the replication curves. So then they do a competition between the two viruses. They infect cells with both the ancestor in the RRAV and RRVR, an MOI of 0.01 with ratios of 1 to 1, 1 to 10, and 10 to 1. And they allow them to compete over five different passages. And there, it's very clear that the RRAR outcompetes the RRVR.

54:15So, the RRAR clearly has a fitness advantage over RRVR. Okay? So, another, I mean, all the viruses are RRAR. It's not surprising that this results, right? because every now and then a V pops up just randomly because we've seen that, right? Very few, they don't go anywhere because they're not fit. It turns out that, so remember the furion cleavage site is important for fusion, has to be cleaved for efficient fusion of virus and cell membranes. And so they said maybe this fitness determinant is at the level of entry. So they do entry cell, entry experiments where they add their virus, the two viruses, to cells at four degrees, which allows them to bind.

55:10And then they shift the temperature to 37 and the viruses will all move in. And then they can shortly thereafter break open the cells and measure how much RNA got in. And basically, this RRVR mutant entry is reduced in all the cell lines they look at, including VeroE6s, which are kidney cells. They do not produce Tempris2, and yet still there's a negative effect on entry. So that's quite interesting. So Tempris and furin are both independent mechanisms of entry. All right, then they say, all right, we have this virus with a V, RR, V, R. If we passage it in cells, what will happen to it? And they say, even though we haven't seen it in any phylogenetically basal position, in other words, in the tree that they built, there's never a V in an upstream position that leads to downstream viruses with a V.

56:14They've never seen that, but let's just test it anyway. Anyway, it could be that a virus with a V early on was there, but then it changed to an A because A is better. You know, that can happen very easily. And they say this could have happened before the onset of SARS-CoV-2 surveillance. So this is the one weakness of the paper, right? The arguers who say this RAV was introduced because it was introduced early on, and that started the pandemic, but we weren't sequencing, and then it went to an A, and that's all we see now. But it really was the cause, right? So they can't really address that, right, because we have no sequences for them.

57:05But they can do an experiment to say— Show that it's less fit in general. Less fit. And it's unlikely that that would have happened, right? Highly unlikely. The passaging is informative. And that's the goal here is to show like, yes, you can go from one to the other, but it doesn't stick. It doesn't stick to go from V to V or from A to V and stay at V because A is better in that position for this virus under these passaging conditions, which are not the same as humans. but they already just told us about all the human data where it's pretty much all A. That's true. This is the one thing the data can't rule out, right?

57:45And so there is an experiment that suggests it's implausible, but it is something you cannot prove, right? And in the human data, every time it arose, which was very, very infrequently, what did you say, 28 in like 16 million or something like that? It didn't ever persist in time. It was gone within two weeks maximum, I think. A day. Yeah, so maybe it wouldn't have circulated long enough to establish. I just don't know. Anyway, they passage the S684V virus in Kalu cells, lung cancer cells, and they sequence it to see the change. And it's basically, in five passages, they find that the A is unstable.

58:34They say non-alanine minorities arise spontaneously in all five passages in these cells. And so the non-alanine percentage is 20 % by passage five. So it's not favorable for the virus to have an alanine at this position. It's not really consistent with a virus that has gone on to cause a global pandemic, right? Okay. So if you remember, not many people may remember, we've talked about this a lot, early in the pandemic, an amino acid change in another position happened in the spike in early 2020, and that's aspartic acid 614th of glycine. And all viruses nowadays have D614G in them. and this conferred some more effective cleavage by proteases and receptor binding and so forth.

59:36So they addressed the hypothesis. Maybe this 684 change happened before the D614G. Maybe that would make a difference. So they constructed a D614G or D in the presence of both fur and cleavage sites. And still in this background, whether or not you have D614G, the V at the third position or RVR, it still has an adverse effect on viral fitness. So it doesn't matter what 614 is. So which amino acids? So all of this is in non-human cells. So they look at primary human bronchial epithelial cells, which are cultured in an air-liquid interface to approximate as close as possible, right, human epithelial cells.

1:00:36And so they infect them with these viruses. and they infect it with viruses with a V and collect this and keep passaging it. And they do three independent experiments over five passages. In one lineage, the V is gone after passage four. It just can't handle it. There's no fitness. It doesn't replicate. And then in the other, they see changes to other amino acids. and they never see an alanine coming up. It always changes to something else. So these viruses with AV don't do well in these human bronchial epithelial cells either. So that's the data. So this MM, RRVR is unlikely to be the origin of the furin cleavage site in SARS-CoV-2.

1:01:39So it's not present, as we've said in the data. It confers a fitness disadvantage. And whenever it appeared, it disappeared rapidly and didn't transmit between regions. So unlikely to have been the origin. Now, they do admit, as I said earlier, that this is a fraction of the 4 billion infections. and so we can't, due to a lack of sequence data from the pre-epidemic period, we can't formally exclude the existence of any hypothetical sequences before emergence of the extant virus. So that's how science works. You can only address what you can do, right? And that's why lab leakers and anti-vaxxers exist because they can say things that are not scientific.

1:02:31And they're never going to come and read this paper and actually understand what it means anyway. So I wish this paper were to reach those people or to understand that from 17 million. Yeah. But they don't want to listen to us. Also, from that many cases sampled like whole genomes that they only found less than 20 or 20 something and that they did not ever persist. Like if they could just common sense. I mean, obviously the data suggests that it's not from the MA30 like MERS coronavirus. But, of course, that's another thing that people don't like to hear, that in science you can't really prove anything.

1:03:09You can't say definitively, like, no, it's not, which people don't like. But that's just how it goes. No, you get data to support one side or the other of the hypothesis. It's the best you can do. But that's what they always hold on to. Like, oh, but you didn't say exactly. It begs the question of, like, why bother doing this at all? if the scientists already were convinced by the data and the people who weren't convinced by the data aren't going to be convinced. So I was wondering who funded the study, and it says that they received funding from the German Federal Ministry of Education and Research and the EU HERA Project Durable.

1:03:51So I looked that up, and this is a project where they are funding infectious disease research. to help with pandemic preparedness and things like that. So I think the question was, you know, did something like this happen? Whether it came from a MERS-like mouse-adapted virus or something else, is this a pattern we should be looking for in the future when we see a new emergence of the next SARS-like virus that could happen or whatever other virus might have this kind of fear and cleavage site. So I was like, why would they fund something like this? But I guess if this informs us about what kinds of patterns we could expect in the future, then it's useful.

1:04:37But they did some like very intense digging deeply into the data that we usually don't look at because it's so low frequency that it's not that helpful. And here this, this like really, if I, if this were my lab, we were deciding what to do next. I'd be like, we're not going to pursue this because it does not represent anything meaningful for the human population. I think it was testable also. So, you know, they suggested this, and it's testable, right? It's not easy to do it, but it can be tested. And it's just another nail in the coffin to say this didn't happen. And I think the problem is that the people who believe in the lab origin are never going to change their mind.

1:05:24They're already convinced and nothing they hear. But they're not being scientifically rigorous. They're just... But at least the scientists that had some doubts, now there's another piece of data to support that it is not the case. Because there were scientists, like you said. I mean, your deceased postdoctoral advisor. Maybe if he saw this, he would change his mind. But I think the more important thing is that science works a certain way. and you need evidence to make conclusions. And science does not work by throwing out accusations in the absence of data and saying this is how it happened, this is where it came from.

1:06:03It doesn't work that way. And unfortunately, a lot of people have believed things that are not supported by any evidence, right? So the evidence that SARS-CoV-2 arose in a lab, There is very little plausible evidence, whereas there is a great deal of plausible evidence that it rose elsewhere. But they choose to ignore that. So put another way, you know, you could put forward this hypothesis that the virus arose from this MA30 mouse adapted Merbeco virus. But then you can test certain aspects of that, which is what, in a way, they've done in this paper. and in this paper then they show well it couldn't have done this thing that you say it would have had to do or it couldn't have done this and it couldn't have done this and it couldn't have done this and so it seems to me that's the best you can do with people throwing up a hypothesis is to try to disprove it and I think that's what they've tried to do here to disprove it so their conclusion is Our results do not support early circulation of RRVR or MERS-MA30-derived nucleotide sequences in the furin cleavage site coding region of SARS-CoV-2.

1:07:28They also refute direct evolution of RRAR from RRVR and SARS-CoV-2. So, yes, I think that you take care of each of these things one by one, and this is just another aspect of it. But as I said, Florence DeBauer has a wonderful article on all aspects of the furin cleavage site, right, which go beyond this. This is a specific part of it. But people have made other arguments as to why it's important. Yeah. That's all wrong, pretty much. The other take-home interesting fact for me is that they have done this calculation that a conservative estimate of the actual number of infections through the end of 2025 might thus be 4 billion.

1:08:16Yes. Okay. And the population of the Earth is 8.3 billion. So not saying that only half the population was infected because some people were infected. You know, this number of infections includes people being infected more than one time. But 4 billion is the conservative estimate. It's amazing. It is. Actually, this is a random question, Vincent. Maybe you have, or Kathy or Jolene. Just saying that about SARS-CoV-2 within the last, what, five years, six years, I guess, 4 billion. What do you think it would be for influenza? do you think it would be 100 %? I guess like 90 plus percent of people, adults, infected at some point with, let's say, I guess influenza A, I guess maybe not that high.

1:09:05Or an influenza virus, do you think there's another virus where the prevalence would be that high? Or like maybe a circulating endemic coronavirus? Do we know if there's other viruses that high? There are chronic viruses that infect everybody, right? So an LO virus is a little circular, single-stranded DNA virus. A lot of the herpes viruses are almost 100 % of the population. I mean respiratory. I should say respiratory viruses. Yeah, they don't approach that much. Those numbers, no? So according to a paper here, I'm looking at about a billion people are infected with flu every year. Yeah. One billion.

1:09:44A billion. A billion every year. Kathy's point about that reinfections is important, though, right? Prevalence is different than total ever cases. It's true. Yeah, of course. And with flu, it could be yearly infections around the same people as well, which is very possible. Yes, my poor friends who always get the flu versus those of us who don't. Yeah. Thanks. But then, of course, yeah, then we say we have the flu, but if we don't sequence, do we really know that we have the flu? So it's like, which strain is it? Yeah. Yeah. I have this wonderful figure in one of my lectures. It's on persistent infections.

1:10:23Yeah. Let me show you. It's a figure on the percent of the world's population infected with different viruses. So this is from a cell paper a number of years ago. So everybody has anelloviruses, herpesviruses, and let's see, polyoma, BK, JC, adeno-associated virus. And then where do we got some respiratory? The first one that comes up is adenovirus, which is affecting about half of the world's population. Oh, wow. And that's the only way. Of course, it has multiple transmission modes. But then there's HIV and hepatitis delta and HTLV-1 going down on that curve. So, yeah. It's very interesting.

1:11:11Very interesting. I wanted to – all right, go ahead. No, no, it's fine. I was just going to continue to ramble about viruses. So this paper by Florence Debar and Zach Hensel, this is published in CR Biology in 2025. Theories of the origin of SARS-CoV-2 in the light of its continuing evolution. I'm going to read a little bit of this, the abstract. The exact details of the emergence of SARS-CoV-2, the virus causing COVID, remain unknown. That's a perfect statement of what we have, right? Scientific publications using data available to date point to a natural origin linked to the wildlife trade at a market in Wuhan.

1:11:50Yet theories postulating a research-related origin currently dominate the public discussion. And so here we attempt to characterize the diversity of research-related origin scenarios, discuss their characteristics and evidence base or lack thereof, and highlight mutual incompatibilities. we focus on the fur and cleavage site. And she goes through every proposal that has been made about it. And she starts by saying, oh, this is possible. And then at the end, it's destroyed. It's really very good. You have to read it. It's totally accessible. How do you spell the name? D-E-B-A-R-R-E. It's very unfortunate, though, because people that I meet on the street, let's say even at a coffee shop where I go in the morning, where I went with you, Vincent, this place I go to every day.

1:12:44I'll meet people and they ask me what I do and I'll say I'm a scientist and that I work in immunology and whatever, doing my PhD. And everybody always talks about SARS-CoV-2. Now less, but like two years ago, it was extremely prevalent. And they would all directly say, oh yeah, so it came from a lab, right? And make a joke that like it came from my lab. And I would just look at them and be like, we don't know. What are you talking about. But it's like now it is established in the general population that they kind of accept, a lot of people accept that it's come from a lab and they don't even know why they think that.

1:13:15But because three years ago at some point, there were scientists talking about it, doctors, and unfortunately, it never made it. These papers like we're discussing today never made it, or ideally they would make it back to the general population, but most people actually don't think it came from an animal source or it's highly probable from an animal source and that it's actually from some mad scientist that just let it go in a lab and wanted to kill half the world. I've heard so many stories. I just, it's wild to me. I know. It's very discouraging. Yeah. It is. I just tell them the preponderance of credible evidence indicates the natural origin.

1:13:53That's the best you can say. You can't say it definitely did this or that. And then, of course, a lot of people will leap on that. I say, you don't actually know, do you? That's not what I said. That's not what I just said. Yeah, it's unfortunate. It's hard. I also find people talk about vaccines a lot these days, right? And, well, I don't get these vaccines or I'm afraid of them or something like that. So there's a much, origin's not as much anymore, but now it's all about vaccines because this is the focal point now in this country, right? Well, and it all also came from the mandates during SARS-CoV-2 because before that, nobody really cared that much about vaccines or having to get their vaccines to go to school.

1:14:32It wasn't, there was always vaccine hesitancy, but it wasn't to the level that it is now. Like this is all, unfortunately, stemmed from. This is also a fabricated thing. Of course, of course. I mean, people say, oh, we don't like, we didn't like the lockdowns. What are you talking about? I mean, in China, they had lockdowns. You couldn't leave your house. We could leave our houses. We didn't get locked down. I think there are also people who, so there was, there is more in the public eye. But the hostility is quite high from a larger number of people. But there are also people who appreciate and use and advocate their vaccines.

1:15:10I mean, I remember you interviewed, I can't remember her name, someone here in Texas who was helping with the vaccines for children. And because there were organizations that were trying to combat vaccine hesitancy. So it's not going to go away. and accusing people of things isn't going to change the minds of one side or the other. We're not convinced that vaccines don't work because someone says they don't work. And people who are convinced that they don't work aren't convinced by us. But the people who are searching and listening, they can be reached. And our minds change. So minds can be changed, but not by combative tactics.

1:15:52I think the majority of people appreciate the value of vaccination. There is a minority who is into this medical freedom business that you should. And look how well that worked in the army in Texas, right? Giving people freedom. And then you have an outbreak of influenza in a population that should not have it. But, you know, you have safe vaccines that have measles, mumps, rubella vaccine, totally safe. Human papillomavirus vaccines, totally safe. And yet people attack them. And I just read an article in the Times that a few people convinced RFK Jr. not to withdraw the recommendation for MMR.

1:16:29He wanted to withdraw it completely, completely. A vaccine that doesn't do anything bad, but he thinks it does. And so for that, it's just crazy where we are now. It's not science. So the person you were trying to think of, Jolene, is Ginny Su, the founder and leader of Immunize Texas. We had her on TWIV 500 in Austin. Right. That's right. I'd also like to highlight that, I know this is unfortunate because you're all in the United States, but the whole world is not on board, which is good. It's good. Most of the world is still more coherent regarding vaccines as opposed to some things going on in the United States.

1:17:10How do you explain the increases in measles in other countries besides U.S.? Canada, you guys have a big outbreak. This is true. This is true. But I think a lot of it is, unfortunately, the United States has a huge influence on the entire world. And the influence of the United States is very, very great. Not that other countries don't have their own, you know, systems in place, obviously, but the United States is a superpower and it does have a lot of influence. So hopefully you guys will have some changes to your government fairly soon. Maybe that'll change something. It has to. It has to. It can't continue the way it is.

1:17:44Yeah. Okay. Well, um... Also, there are many countries that can't do measles immunization. They have lots of cases as a consequence, right? I'm sure they would love to be able to vaccinate against it, but they don't. Okay, anyway, we don't have any emails, folks. Send some emails to us. We'd like to hear from you. It's either feast or famine here at the TWIV email place. Either we have too many or not enough. Send us emails. You can send it to twiv at microbe.tv. So let's go on to our picks of the week. Angela, what do you have for us? So this is kind of a funny pick, but I wanted to have a funny pick anyway.

1:18:28So my pick is pigeons. So pigeons, actually, this is my pick because my boyfriend and I, the other day, we actually found a wounded pigeon, and then I took her to a rescue. And she was doing much better the next day. And I was just reminded by how cool pigeons are. And she was very sweet. She was like non-combative, even though she had an injured wing. But anyway, pigeons are so cool because, if you didn't know, they have 320-degree vision. They can see almost like owls. They have this huge range in vision. They can also see in the UV spectrum. So they are tetrachromatic as opposed to humans and other mammals.

1:19:09Most mammals are, well, I mean, mammals are divergent, but humans are trichromatic. So they have red, green, and blue cones in their eyes. But pigeons also have a UV violet. So they can see everything in the UV violet spectrum, which is interesting because pigeons kind of look gray. And they have like these refrigerancies on them like with colors. But to another pigeon, they actually look a lot more vibrant than they do to us because they have these cones, this other part of their head now. I always call them iridescent pigeons. It's true. Yeah. And we can't see most of the beauty in their feathers.

1:19:43Oh, cool. So pigeon moms really can see what's happening behind them? I mean, almost. Yeah, literally like here. And so there's a lot of things about pigeons that are cool. There's that. There's also that they are positive for the mark test. So a lot of animals like dolphins, apes, elephants, when you put them in front of a mirror and you put like some sort of mark on their forehead, so you put them first in front of the mirror without a mark, let them observe themselves to see if they can recognize themselves. then you put them back in front of the mirror with some sort of thing on their face.

1:20:15And then if they try to remove it or there's different ways of testing this, you can then show that the animal recognizes that it is itself that it's seeing in the mirror. And pigeons are positive for this test and crows are not. So people think crows are really smart, which they are. They're intelligent in their own ways, but they're actually negative for this mark test, but pigeons are positive. Uh, they also, this paper that came out in, in science like two weeks ago, such a cool paper. Please go read it. Uh, Vincent attached to the show notes. It is called, okay, wait, the, the name of the paper.

1:20:50Let me just open it again. Uh, homing pigeon navigation relies on super paramedic magnetic macrophages under overcast conditions. So wait, I'm doing a journal club on this paper because it's so cool. So basically they show that pigeons in their liver have these macrophages that are necessary for them guiding themselves home, flying home when it's overcast outside. So, you know, there's been a lot of talks about like magnetite and all of these different things that maybe birds have to sense like migratory patterns and how to get home and etc. But anyway, this paper specifically, they did a clodronate depletion.

1:21:27So they killed other macrophages. and they saw that on cloudy days, if the pigeons didn't have these macrophages in their liver, they couldn't, like their navigation was completely random and they couldn't go home. On sunny days though, without these macrophages, they could go home. It's so cool. And they basically realized that these macrophages have a soup, like a very paramagnetic from what I understand just means like light magnetic property. So they have this like some sort of magnetism, which they didn't define how this mechanism is working specifically, but something is sending the pigeon, a macrophage is somehow connecting to the pigeon's brain and telling it where to go, which is just, animals are wild.

1:22:06Animals are so cool. So, oh, you're not done yet. Okay, go ahead. I'll ask you later. There's one more thing that they're cool with, which is pattern recognition. So they can actually detect, I'm sure everybody or many people have heard about this, but if you haven't, they can also detect in histological and radiological images, the difference between cancer. So if there's like cancer in a histological section versus in a radiological section, normal versus cancerous, they can actually do this with 85 % accuracy if they've been trained for over 10 days, which is very cool. You put them in like a little box and you show them pictures of like normal tissues and then you give them pictures of abnormal tissues.

1:22:46And of course, they're slightly hungry, like they're not fed before this. So when they get it right, they get food. So they can recognize the patterns between the different images and that when they're given enough of the regular image, like a homeostatic image, when they're given a cancerous one, they can actually, like with 85 % accuracy show that it is different, which I thought was really cool. How does that compare to, you know, trained radiology? Actually, they said it was like similar numbers to trained radiologists, which is crazy. Of course, the pigeon is just looking for patterns, and radiologists are too, right?

1:23:19But maybe they have more information, obviously they have more information about cell types and density and things like that, but it's very cool. pigeons. All of this is for like the, I don't know how many kinds of pigeons that are there are, but I know there's more than one. This is for like, you're talking about the common pigeon that lives in the city. Yes, that the cancer detection one is the common pigeon. So the, the paper, the science paper is a different species of homing pigeon, but that's for the macrophage thing. But the cancer detection and the mark test and UV vision, all of that is for your regular little pigeon that's like outside your door right now, just hanging out.

1:23:56They're so cool. That's awesome. So we did a Tweevo on pigeons many years ago. Oh, really? There's a guy at, I think it was Utah, who studies. They're these amazing pigeons feathers. They have different feathers, especially on their feet. They have incredible feathers on their feet. And so this episode was called Pigeon Fashion Week, Feathery Boots Edition. So Mike Shapiro works on the genetics of these feathers on pigeon feet. You wouldn't even recognize them as pigeons. If you just think about New York City pigeons, nothing like it whatsoever. It's amazing. I'm going to have to go listen to this.

1:24:33Angela, why do they, some of them don't have feet? What's going on there? Oh, well, that's just because they're injured. You mean like in New York when they have like studs and stuff like that? They walk around with one, they hop around. I feel so bad for them. But they can still exist with just one foot. But they had an injury or something, right? Normally they're from injuries, yeah. They'll lose toes or lose their whole limb. but they're very resilient. They're extremely resilient little pigeons. This pigeon that I found, she was like, she had looked like she had been hit by a car or something because it was like her full left wing and left leg.

1:25:08Like she couldn't use it. And she was like pushing herself along the sidewalk. And then I took her, put her in a box overnight because the rescue wasn't open until the next morning. And she gave her some water and some seeds. And the next morning she was like fully trying to fly in the box, even though her wing was like broken. And I was like, okay, calm down. But they're very, very resilient. She wanted to just leave. And I was like, no, we need to get you checked out. That's great. But she was doing so well. So if you find a bird outside and you want to save it, put it in a box. Don't stress it.

1:25:35Close the box, darkness, give it some water, and then take it to a rescue. That's the best course of action. So you bonded with this pigeon, eh? She was very cute. And then I remembered about all the cool things that pigeons do. But you didn't name the pigeon, right? No, I just called her pigeon. It was like a 16-hour relationship. You have a lot of pigeons in Montreal? We do. We do. I think they're a big city thing. They're all over the place. Sometimes they fly inside and they fly around inside buildings. It's very cool. That's neat. That's a neat one. Kathy, what do you have for us? Well, I have two.

1:26:13The first is what I'm calling a snippet pick of the week, which is just Wednesday's astronomy picture of the day, which shows sprites. And if you read through the caption, so this is this really cool formation having to do with lightning and red streamers. And anyway, if you read through it, you can answer the question that I posed, what gaseous element glows red when heated? And that's what's showing in this astronomy picture of the day from July 15, 2026. So that's the snippet. And then the second one is this paper that when you first see it, I mean, it has all the looks of, I mean, of a legitimate paper, and it's in a journal that is the publication of the American Chemical Society.

1:27:11So the first snippet had this gaseous element, so that's a little bit of chemistry. And then this is chemistry. The title of the paper is, Will Any Crap We Put Into Graphene Increase Its Electrocatalytic Effect? And so until just now, I didn't think to figure out whether it was completely open access. So just in case it's not, I'm going to read you a few key things in case you can't read the paper, but the paper is hilarious if you can get it to read. So the doping of graphene with a plethora of elements has been reported as enhancing its electrocatalytic performance. Okay. So then they say, partway down, it seems that whatever crap, in quotation marks, we put into graphene, electrocatalysis increases.

1:27:59One may exaggerate only a little by saying if we spit on graphene, it becomes a better electrocatalyst. Having 84 reasonably stable elements, apart from the noble gases and carbon, one can produce 84 articles on mono-elemental doping of graphene. With two dopants, we have 3 ,486 possible combinations. So they're talking about ways to generate publications. Okay. And then, okay, so the key point of the paper, To make our point of meaninglessness of efforts to co-dope graphene with various elements experimentally, we evaluate in this work whether guano-doped graphene poses any advantages over non-guano-doped graphene.

1:28:44Okay, hence the title of the paper. And then the conclusion, I'll cut to the chase for you. In summary, we demonstrated that bird-dropping treated graphenes indeed make graphene more electrocatalytic than non-doped graphene. So it does seem that any crap that you put into crafting will make it more electrocatalytic. But it's like it's something you would expect from the Ig Nobel Prizes or the Journal of Irreproducible Results or something like that. So this is real. Yeah, it's real. It looks kind of fake because it said most trusted, most cited, most read. That seems like – Yeah. So maybe it is some AI generated thing, but I don't know.

1:29:29It's cute, but that's hilarious, even if it's not. They say that graphene for fuel cells in a hydrogen economy could be enhanced by bird droppings. Yeah. Yeah. All the nitrogen, maybe, in the bird droppings? Who knows? There's a lot. Because guano is a mix between the urine and the feces from birds. They both fall into the same compartment, and then it all comes out together, which is why it's kind of fluid. Yeah. Fun fact. So according to the astronomy picture, so it's nitrogen that gets heated and turns red. Is that right? So everything's kind of linked. It's such a cool picture. Nitrogen, guano, yeah, pigeons, yeah.

1:30:16Jolene, what do you have for us? I am picking another science communication outreach type of thing. So this is a website for a science exhibit called Microbial Puppet Masters. It was hosted and developed by teams with Dr. Chloe James and Dr. Heather Allison at the University of Salford and the University of Liverpool in the UK. They put together this really cool multimedia learning, active learning exhibit on phage. And they called it Microbial Puppet Masters. They have in this exhibit virtual reality that they put together where people put on the glasses and they can see the bacteria and the phage inside of a human lung with the idea of what would be happening in a cystic fibrosis.

1:31:06They made these, this is what attracted me to it in the first place, these super cool interactive 3D printed models of bacteria. and there are two pieces and they're held together by springs and then there are these holes in the outside of the bacterial model and they made little phages that are like keys that fit into the holes and when you put the correct phage into the the key spot the keyhole then the bacteria will burst open and release some phages that they had on the inside to simulate lysis so the idea of phages are super specific they have to interact with a receptor and they come out and make more of themselves.

1:31:44And so they made them at 1 million times life size, and they're kind of fun. They also have these human phage, or larger than human phage light balls. They're like disco balls. They have crafts where not just kids, everybody can bedazzle. They're little phage models, short animations that people drew, and explanations of the research, of course. So this was part of the Royal Society Summer Science Exhibit this last month and this month, I think. They have lots of popular articles. They have a peer-reviewed article about it and lots of short videos on their website. I was super interested in the models.

1:32:25Apparently, they take, at least with their printers, they took 10 to 11 hours to print each model. And they, just in their pictures, they had over a dozen of them. And they really put a lot into their design. Sounds like lots of people were involved. They put their designs for printing the bacterial models and the phages on Maker World. And they have two kinds, the kind that is a temperate infection. So virus that can integrate and go latent. That kind, when you put the key in, it opens, but it doesn't release phage to indicate the quote-unquote partnership that has been formed between the phage and the bacterium.

1:33:08So yeah, that's my pick, this really cool science communication exhibit. I didn't have time to look at it ahead of time, but if you scroll down and you see these still pictures, there's this thing where it looks like a person has put the phage in as a key into this giant gray thing. And that's, is that the bacterial cell? Yeah. Lysing and that's really cool. So it's like two pieces that are held together by the spring. And when the phage goes in, then they pop apart. And the opening that's created between the pieces is filled with the little phages that come out. Yeah, that's great. Definitely some active learning, but a lot of investment to make the tools to do it.

1:33:46Very neat. Cool. My pick is a book by Roxanne Kamzi, who, well, the book's called Beyond Inheritance. This is all about somatic mutation. Really good, really well done, nicely written, very clear. Most people think our DNA is all the same in us, right? But every cell is different. And that can have consequences, and she talks a lot about that in this book. For example, sometimes mutations arise in blood cells. Remember, these are somatic mutations. They are not passed on, but they can affect you in your lifetime. So you can have problems with the blood. You can have increased risks of heart attacks.

1:34:33You can have also resilience as a consequence of these changes that happen. And a lot of things you probably didn't know. I certainly didn't know. She was on Twevo not too long ago. That was episode 126, where she talked about the book with me and Nell. So I really like it very much, and you should check it out. By the way, she is up in Montreal. Angela, you should go have coffee with her. Yeah. Would be a fun conversation, right? So the idea is that the human genome is a consensus, like if you were to sequence my genome, which nobody really does, that it would be a consensus of all the cells in my body.

1:35:19That's right. But she's talking about the differences between every cell and how... If you did single cell sequencing, you'd find differences. And sometimes populations arise that have deleterious effects. There's also some examples of, I mean, also our germ cells undergo mutation, right? So the whole thing is the more a cell divides, the more mutations it's going to sustain. So some cells that don't divide very often have very few mutations, but others like germ cells divide very quickly and they sustain lots of mutations and they can be passed on as well. But it covers a lot of different scenarios.

1:36:05It's really good. I highly recommend it. It's very well done. And the Twevo is really good too. You should listen to that. Actually, I think she's giving a talk. I just looked at the Twevo and I saw her face and that picture is all over the hallways in my building right now. And I was like, wait, I think she's giving a talk next week. Well, if you can go, you should go up and introduce you. She knows about TWIV. I will. Of course she has. Her face. Hopefully, I think it's next week. It might be the week after. But yeah, she's coming to give it a hug. There you should go. That's cool. Neat. We have a listener pick from Matt.

1:36:38Doctors TWIV, I want to thank especially Dr. Ramsey for presenting papers on phage. As a software engineer, it never crossed my mind that there would be viruses that attack bacteria. I thought that they just both attacked humans. But thanks to your podcast, I felt well prepared to understand this. interview with the CEO of Locus Biosciences and their work on using phage to fight disease. I thought that other listeners might enjoy it as well, so please consider it as a listener pick. So this is Paul Garofalo. What's your problem using viruses to fight disease? Thanks to all the TWIV hosts for presenting science to us all.

1:37:21Thank you, Matt. It's another thing, folks, you could do. You could send us pics of the week. Twiv at microbe.tv. I'll take a listen. I don't think I've met more than maybe one of the people who is involved in the locust biosciences, but I've strongly considered multiple times doing the paper on the phage that they modified to use phage to deliver CRISPR. They call it the sniper, but I haven't ever actually picked it. I will take a listen. Thank you, Matt. Yeah. That's TWIV 1341. You can find the show notes at microbe.tv slash TWIV. Questions or comments, picks of the week, TWIV at microbe.tv.

1:38:03If you enjoy these programs, we would love your support. microbe.tv slash contribute. Kathy Spindler is Professor Emerita at the University of Michigan in Ann Arbor. Thank you, Kathy. Thanks. This is a lot of fun. Nice to see you again. Nice to be here. Jolene Ramsey is at Texas A &M. ramseylab.versecell.app. Thank you, Jolene. Thanks for all the fun. Angela Mingarelli is at McGill University Immune Vet on Blue Sky. Thank you, Angela. Thank you. I had a great time. On the stream the other night, someone asked me if we ever had a physicist guest. And I said, of course, Chiara Mingarelli. Yes, we have.

1:38:48That was a great episode. How is Chiara doing? Is she okay? She's doing very well. She just got married like two, three weeks ago. Yeah. To another physicist, more physicists. Imagine that. She's doing great. Yeah. Very good. 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, 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.