Mink, Ivory, & a Disease Discovered Backwards
It's a regular Noah’s Ark: from the coronavirus strains that have been spreading through minks, to a new DNA test that can track poached elephant ivory, to the genetics of a very useful - and very inbred - cat. Plus: scientists have discovered a brand new genetic disease, via an unlikely approach and an even unlikelier coincidence...
In this episode
00:32 - Mink with coronavirus: what's the danger?
Mink with coronavirus: what's the danger?
Alina Chan, Broad Institute of MIT and Harvard
Since July, over 200 people in Denmark have been infected with copies of the coronavirus that have been spreading through mink farms. And crucially, the mink have given 12 of those people a unique version of the virus. Reportedly this version has been transmitted human-to-human as well, although it’s not clear whether this is still going on. To address the problem scientists are now trying to understand how the virus behaves in minks, and whether the unique version that comes from minks presents a unique problem for treatments. Alina Chan is a scientist from the Broad Institute of MIT and Harvard who wasn’t involved with the Danish research, but has been looking into COVID in minks, and explained the situation to Phil Sansom…
Alina - In Denmark they have more than 1100 mink farms. More than 200 have been found to have COVID-19 outbreaks. And now that virus that has been circulating among the minks has passed back into the human population in Denmark.
Phil - Wow. You know, I wouldn't have put minks as top on my list of COVID threats.
Alina - Yeah, this is not too surprising, although it's really devastating to hear this news. That's because we have known for a while - scientists have known for a while - that SARS-type viruses can infect ferrets, which are in the same family as minks. And so it's not surprising that minks are susceptible to SARS-2.
Phil - So is this the first time that minks have got SARS-CoV-2?
Alina - No, this is not the first time that this whole scenario of transmission from humans, to minks, to humans has been observed. As of today, there are at least six countries that have reported these mink outbreaks. So we've got Denmark; but the first was actually the Netherlands, and they were the first to report a mink outbreak back in April of this year.
Phil - Do we know what happens to the virus when it's in the minks?
Alina - This part is kind of a mystery, pr I'd say at least an ongoing study. There were two publications that just came out. One of them is by the Dutch group; there are a few caveats in their approach, but they said that they see some hints of faster evolution of the virus in the minks. More analysis needs to be done, and by independent groups of scientists. The other publication is by the Danish group, but this is a working paper, and so they have not shared their mink genomes yet; although they have committed to the WHO that they will.
Phil - So we don't have the full picture then of what the virus looks like in the minks. But am I right that we do know what the virus looks like once it's left minks and is back in humans again?
Alina - Yes, we can see what could be the mink associated variants coming out back into the human population in these two countries as well. In Denmark there's one cluster that is particularly concerning; it's called Cluster 5. A cluster is a group of SARS-2 sequences, in this case, that look really similar to each other. This cluster has a combination of different mutations in the spike gene; this is what helps it to infect different host species, and it's also the target of some of the most potent therapeutic antibodies.
Phil - What are the mutations?
Alina - They see about three to four different mutations. And actually each one of them has been around since at least March, across many countries and continents. So the individual mutations, they are not novel, but as a combo, they're novel. But they found that the most recent mutation, I692V... no other country in the world has detected it, and it only appeared in August.
Phil - I mean… what's the implication?
Alina - According to the Danish paper that came out, they got convalescent plasma from patients, and they found that in some of the cases, the plasma was not able to neutralise the new mink associated variants. And so now they are a bit worried that this could have an impact on antibody therapeutics, or vaccines in development. But again, just to emphasise the effect that they saw, it's not that drastic, but it does suggest that people who don't have long lasting immunity could be susceptible to this new variant.
Phil - So what's your take? Is the virus now more dangerous that has gone through minks?
Alina - I don't know. I think that's the answer that most scientists would tell you, is that we just don't know. I don't think people should panic. When I say mutations, it doesn't mean that every single mutation makes these viruses more transmissible, or more dangerous for humans. Not at all. In fact, many of them could actually be taking a step backwards, considering that they are adapting to a different animal species. What the worry here is besides from these mink farms being a pool, they are generating more diverse viruses. So if these different variants, even if some of them are weaker in humans, if they enter the human population again, and we start implementing a widespread vaccination, for example, this will select for those rare variants that vaccines don't work as well against.
05:31 - Ivory: a new DNA test to fight poaching
Ivory: a new DNA test to fight poaching
Adrian Linacre, Purdue University
Forensic scientists have developed a new method to track illegal elephant ivory by looking at the DNA within. Processed ivory contains only tiny and mangled genetic fragments from the original animal, and so previously it’s been difficult to tell anything at all. But Adrian Linacre from Purdue University, and his colleagues, told Phil Sansom that their test can tell Asian elephant from African - and based on their experiments, with 100% accuracy....
Adrian - Something like 25,000 elephants are killed every year for ivory. It's taken from Africa, particularly; traded over into Southeast Asia; processed into trinkets of various descriptions; and then sold on the black market. Now somewhere like Thailand does have strict regulations about what it can and cannot import. But when you've got a bit of ivory in front of you, the question is, firstly: is it ivory? Is it from an elephant? Ivory could come from things like hippopotamus. It could come from other animals, particularly like narwhals. Second question: is it from Asia, or is it from Africa? Because you can't just look at ivory and say, “it's from Africa”, “it's from Asia”, or “it's ivory”, even, right? Now you can do some bits of microscopy and get quite good at that, but it doesn't really answer those detailed questions about African or Asian elephants. Now what we've done in the paper is looked at the smallest bits of DNA we can find: really old samples, really trace materials. And now you're going to get very, very, very small amounts of DNA left, down to what we call picograms: ten to the minus 12 of a gram. It is very, very small. What we've done in our test is developed a methodology whereby very quickly, within a process of only a few hours... a method that will tell whether you've got African or Asian elephant present.
Phil - Who is going to use this test then?
Adrian - Where we hope this could be used is by border guards out in the field. We've got some other tests which can do that, but they do require very sophisticated equipment and it can take a couple of days. Our technology is very portable. It requires very simple equipment. It requires very little training. And so what would like to do is deploy it into the field, into where rangers can work rather than laboratory staff.
Phil - You can tell African from Asian elephant then. Can you tell any more? Can you tell where in Africa the elephant is from - something like that?
Adrian - No, we can't. That's the next part of our test, to try and get that more and more sensitive. Now being able to tell whether it's African or Asian helps an awful lot in legislation; a lot of countries legislate whether it's African or Asian, and that really does help in some sorts of trafficking to work out the routes at which that bit of ivory has been traded.
Phil - Why ivory? What's the priority?
Adrian - Wildlife crime is, by any metric, massive and highly organised: somewhere in the order of between 20 and 30 billion pounds per year. That's only second to narcotics. It's the second-most highly lucrative trade, all of which is illegal. This will be groups of people, often using helicopters; come down, kill elephants very quickly, remove the ivory, back into a vehicle, and shoot off. So you can see that it's a very sophisticated type of crime. One thing I'd like to add is that forensic science has to make sure that there aren't errors in what we do. If you're from a research background, no one goes to jail if you make one error out of a thousand tests, but in forensic science, that might happen. So we need to go to a bit more level of scrutiny to make sure that our tests are robust and reliable.
09:43 - Cat genome sequence reveals cause of dwarfism
Cat genome sequence reveals cause of dwarfism
Leslie Lyons, University of Missouri
Our furry friends have had their most thorough genome sequencing to date. A cat called Cinnamon now serves as the reference genome, the cat against which to compare all other cats. And the team have already discovered new genetic variants that relate to humans as well. Leslie Lyons was part of a team of researchers, and told Phil Sansom the story...
Leslie - We have been able to complete the most contiguous genome assembly for the domestic cat, which rivals that of most any other species. So what that means is that we have most all the puzzle pieces of the genome lined up properly. And that gives us a great genetic resource to do all kinds of health studies and evolutionary studies in cats.
Phil - You'll have to explain this a bit to me, because didn't we have a cat genome before? And isn't a genome a genome?
Leslie - Right? Well, yeah, that's what everyone thinks: once you've sequenced the genome you're done. But no, genomes are quite complex, and so we do them at different levels of resolution, and it all depends on the technology that's available. And so now we have something called ‘long read technology’ which allows us to put the genome into larger pieces. So picture a puzzle: certainly the puzzles with the smaller numbers of pieces are easier to put together, and you get them more correct. Sometimes when you're putting puzzles together, you somewhat try to force a piece and you think that's the right piece. And then later as you do more of the assembly, you realise, "oh, I kind of forced that piece. That's the wrong piece. Let me put the right one in." That's what we're constantly doing with genome assemblies. We're constantly correcting things and making them more finished from beginning to end, so there's no gaps in the sequence.
Phil - What do you have here then that you didn't have before?
Leslie - We have a whole gene, as well as we probably have more of the fragments that are upstream of the gene. And that's like the regulatory sequences of the gene; that's what turns a gene on and off. And that is actually what makes species different. Most species all have about the same number of genes, and the same type of genes. However their regulation, when they get turned on and off during development, and how much they get turned on or off; that makes the difference between a cat being a cat, and a human being a human. For example, we have the gene to make whiskers, but we have a different regulatory element.
Phil - You're joking. I have a whiskers gene?
Leslie - You have a whiskers gene.
Phil - Is there some way I can activate it and become a cat superhero?
Leslie - Yeah. If we can get that regulatory element popped in, which now we can technically do with CRISPR and genome editing, we could probably give you whiskers.
Phil - Wow. Okay. Let's park that for another episode. In this cat genome, did you find bits like that? Little regulatory elements that control things that you didn't expect?
Leslie - Yes. In the new cat genome, we were able to find better regulatory sequences, and also sequences that are called structural variants. And structural variants are just larger DNA changes that are harder to see with the short read sequence. By being able to see these larger structural variants, we were actually able to find a disease mutation that we've been looking for quite a long time. And that is the dwarfism of munchkin cats.
Phil - What does a munchkin cat look like? Because I don't think I've ever seen one before.
Leslie - Yeah. So munchkin cats have a very small structural variant in the gene called UGDH. And this is what causes them to have short legs. So there's many types of what we call ‘disproportionate dwarfism’; If you've watched any of the TV shows like Game of Thrones, you'll recognise characters with disproportionate dwarfism. Cats have the same thing. Their torso is the right size, but just their legs are shortened. And so we found a brand new gene, which means this gene can now be investigated in humans as well.
Phil - Is it really the same between humans and cats?
Leslie - Yeah, absolutely. Most of the genes that we find in humans are what we find in cats as well.
Phil - Are munchkin cats, would you say, more cute than your average cat?
Leslie - That's a very personal opinion. So I think cats are just quite beautiful, moving artwork. There're many beautiful cats, and it's to each his own, really.
Phil - Do you mind if we look at a picture?
Leslie - Please do, there should have been a picture right in the paper too.
Phil - All right. Here's one, the legs are really short. That is quite cute, actually. This cat, is this the one that you got the really well sequenced genome for?
Leslie - Actually no. Cinnamon is the reference sequence, an Abyssinian cat called Cinnamon. And so that becomes our baseline that we compare every other cat to. That is our gold standard.
Phil - Well, thank you to Cinnamon for the gold standard.
Leslie - Yeah!
16:24 - VEXAS: how a deadly disease was discovered
VEXAS: how a deadly disease was discovered
Dan Kastner, NIH
In the second part of this programme: the story that scientists from the USA’s National Institutes of Health have discovered a new disease. It’s a rare autoimmune condition, where your own immune system gets too aggressive and starts attacking parts of your body, often to devastating effect. It’s called VEXAS, and the story of its discovery is pretty surprising. Phil Sansom heard from the NIH’s Dan Kastner...
Dan - VEXAS is a fascinating disorder that was recently discovered by a brilliant physician scientist fellow working in my research laboratory, David Beck. And just as an overview, VEXAS is a disorder that we see in middle-aged to elderly men, only men, at least so far, that is characterised by a number of interesting clinical features - recurrent unexplained fevers, pustular lesions of the skin, inflammation of the cartilage in their ears or in their nose, or sometimes in the trachea. And if it's in the trachea, the trachea could actually collapse and lead to the person's smothering, so that's a terrible thing that can happen. Inflammation of the blood vessels. Sometimes an inflammation in the lungs that can lead to a severe respiratory problem. It is a disorder that unfortunately, patients who have it oftentimes are treated with many different anti-inflammatory medications without a beneficial effect. And most of the patients that we see with this disease actually are on high doses of steroids. And even then, oftentimes, they can be quite ill. So this is a very serious disease and a disease where, at least amongst the series of 25 patients that we first characterised, 40% of those men have succumbed to their illness.
Phil - There’s a lot of overlap, with these symptoms, between VEXAS and other inflammatory conditions; after all, inflammation is a huge part of the body’s immune defenses. But you can’t treat these properly if you don’t know the cause. Investigators like Dan are often trying to find genetic mutations that cause specific syndromes, or that are part of a complex web of causes… and with many patients they hit a brick wall. The NIH had thousands of such undiagnosed people. Enter researcher David Beck.
Dan - The way in which the good Dr Beck discovered Vexas is really extraordinary. We had a clinic of patients who have undiagnosed inflammatory diseases. And so David asked the question, how can we find other genes that might be causative in the patients for whom we don't have an explanation? And the usual way that one would do it would be to group together subsets of patients, according to their clinical manifestations, you might take a group of patients that have a certain kind of arthritis and group them together. And then for each group, you would try looking at their genome to find something in common that could explain their illness. Instead of taking that approach he said, well, you know, we've done that before, and we've already sort of exhausted that approach. I'm going to turn the paradigm on its head. I'm going to do things backwards. I'm going to start with a list of genes, see whether or not I can find a common thread that could tie together some subset of patients amongst our undiagnosed patients. And after applying this approach, there were three middle aged men who actually had a misspelling in a particular gene called UBA1, and they all have the misspelling at the same place.
Phil - All three men seemed to be heterozygous for this mutation - they had one normal copy of UBA1, and one messed-up copy.
Dan - The thing that was curious about all this, these were three middle aged men, and they had mutations in a gene that's encoded on the X chromosome. And it looked like they had two different copies of this gene, one normal copy, and one that was the mutant copy. Now, if you have been paying attention to me you know that there's something wrong with this story because of course, men only have, usually, one X chromosome. What's going on here? How can that be?
Phil - According to Dan there are three possible explanations. Firstly, the machine made three identical mistakes. Unlikely, but possible. Secondly, that the three patients were males with two X chromosomes - again possible. But the unusual insight here was realising that there’s a third option. Maybe this mutation in UBA1 didn’t appear in these men at conception, or even early during development. Maybe it’s what called a somatic mutation, a mutation that happened in these men’s adult bodies. Specifically, in their blood.
Dan - These are mutations that arise just in a particular subset of white blood cells, which of course are the cells that are responsible for inflammation. Rather than just thinking it was a mistake, instead David said, maybe what's going on is that this actually is a somatic mutation where a subset of the cells in the blood have the mutation and a subset of the cells don't have the mutation. And that would give you the same kind of a picture where it looks like one normal copy and one mutant copy of the gene.
Phil - Some of this type of white blood cell had the normal UBA1. And some of them had the mutation. The gene sequencing shows you both versions, and so you assume, all of the cells have them both. Except in this case, the researchers guessed that wasn’t true - and turned out to be right.
Phil - They’re really on the hunt now. Where have these mutated cells come from? Well, white blood cells like these are born out of precursor cells. And when Dan went after the precursor cells, the story took another twist.
Dan - It is fact stranger than fiction. We went to the haematopathologist. We were looking at the precursor cells in these patients' bone marrow. And Dr Calvo, the haematopathologist told us, well, you know, there are these funny looking bubble-like structures in the precursor cells in the bone marrow, they're called vacuoles. And all three of these men have these vacuoles. And she was saying, well, you know, I've seen this somewhere before. A few days later, we came back to the haematopathology lab and Dr Calvo was there waiting for us. And very ceremoniously she presented to us two reports. And she said, here Dan, these are reports of your patients from eight years ago, who had these vacuoles. You guys should go back and check this gene and see if those patients have mutations in this gene too. So we did. And sure enough, she was right. These patients from eight years ago had the same mutation. As we started to expand the spectrum, it turns out that in fact, we could find 25 patients.
Phil - They now have 50 patients and counting with VEXAS, which I can now confidently explain, stands for the five key characteristics of the condition. V for vacuoles; E for E1-ligase, which is related to the gene UBA1; X for X-linked, the gene being on the X chromosome; A for autoinflammatory; and S for somatic, because it’s a somatic mutation. I know, I know - let’s just stick with VEXAS, why don’t we.
Phil - The story of VEXAS holds an important lesson for the investigators looking for rare diseases. Sometimes - not always - it helps to start the hunt in the genes.
Dan - This approach is sometimes called the genotype first approach, and this is really the first vindication of this approach in inflammatory diseases. Now, the other big take home message from this is that in fact, these mutations are mutations that are only seen in a subset of white blood cells and where we infer that these mutations probably arose later on in life. And this sort of expands the concept, if you will, of somatic mutation - of mutation that arises in cells in the body. We have known for a long time that somatic mutations can give rise to cancer. But what this new disease Vexas is teaching us is that somatic mutations can sometimes give rise to adult onset inflammatory disease. So that's really an important take home message and leads us to believe that probably there are other adult onset inflammatory diseases out there that maybe, could be, discovered by this genotype first approach. And then the third take home message is the devilishly clever insight that in fact, when one sees two versions of a gene on the X chromosome in a male, it may be mosaicism rather than a sequencing error. And this is going to revolutionise the way that we look at genes that are encoded on the X chromosome in terms of their mutational profile.
Phil - Which is all very well for the future of research, but a nothing conclusion if I’m one of those living with VEXAS. I might have inflamed blood vessels, lungs, cartilage, throat… can Dan help me out?
Dan - Is there anything that we can do for our patients now that we know what's going on? It just so happens that actually one of the patients eventually underwent a bone marrow transplant and the bone marrow transplant has been very effective in controlling his clinical picture. And so this suggests to us that perhaps bone marrow transplantation, at least under some circumstances, may be helpful.