Hi. I'm Paul Turner. And today I'd like to talk about the fundamentals of virus ecology and evolution. This is not designed to be a comprehensive overview, but rather an introduction to the very many ways that viruses interact with other organisms, and how they evolve on the planet. I'm currently the Chair and full professor of Ecology and Evolutionary Biology at Yale University, and I also have an appointment in the Microbiology program at Yale School of Medicine. So, we can begin with a very fundamental question of, exactly what is a virus? There are many ways of depicting the relationships between organisms on the planet as a way to catalog biodiversity and evolutionary trees are generally the way that we use, within evolutionary biology, a depiction of relatedness among biological species and groups. So, for example, this is a depiction of the Tree of Life, but it's actually a pretty misleading one. Although many of the organisms are recognizable, here, they're really mostly drawn from only one domain of life, the eukaryotes. These are the most recognizable animals, plants, etc that most people are familiar with. Instead, a more accurate depiction might be something like this wraparound tree, where depicted in purple are the very many bacterial species, in this particular tree, that have a name. And another domain, shown in green, are the archaea which are, like the bacteria, single-celled species, and they are more often found in extreme environments. But you'll note in this tree that the archaea are close relatives to the groups with which we belong, the eukaryotes. So, for your reference, here are you on the tree. And this Tree of Life also is a bit misleading in the sense that it cannot catalog the amazing biodiversity of another very important group of biological entities on this planet, and those are the viruses. So, these three domains of life comprise only cellular life, and viruses are different because they are not cellular. At the top of this diagram, we see very familiar body plans of eukaryotes, including something like a blue whale, a sequoia tree, and even single-celled eukaryotes are very common on Earth. The bacteria and the archaea, as stated earlier, these are single-celled organisms, so even though many of them are close relatives -- closer than the bacteria than within the archaea -- the body plans of bacteria and archaea are very simple in that they have only a single-celled body plan. Now, if we take a closer look at what the body plan is of a typical virus, it has a protein shell as well as nucleic acid, either RNA or DNA, that's protected from environmental degradation by this protein shell that has a very special name, called a capsid. So, at the top we see, here, the influenza virus, which is a very typical virus that's recognizable to most people by name, and it's shown that it's relatively a circular virus, with the RNA as the nucleic acid and that's protected from the environment by a capsid, whereas something like a phage, phage T4, this is a short form of the name bacteriophage, which translates to eater-of-bacteria. These are viruses that are specific to prokaryotes, and this phage, you notice, has a much more elaborate body plan than an influenza virus. But what they both have in common is nucleic acid that is protected from the environment by a protein shell called a capsid. A typical virus life cycle looks like this, in its most simple form. As long as a virus attaches to some cell, that it has the proper protein binding recognition, there's a possibility that it will get in, or that at least its nucleic acid will enter the cell. And, at this point, the primary mission of a virus is to hijack the metabolism of that cell and divert those energy sources towards reproduction of viruses rather than normal cellular function. At this point, the particles can get to maturity within the cell and they can be released, and go on and infect other cells. So, this is very much a generalization, but it's a good way to think about the fundamentals of how viruses replicate and reproduce. So, now, you can really think of biological entities, perhaps life if you want to define viruses as living, as being split into two basic body forms: the capsid-encoding organisms... you can think of these as all viruses because they share the properties of nucleic acid surrounded by a capsid, and the viruses themselves would be specific to either the archaea, the bacteria or the eukaryotes; and ribosome-encoding organisms, the cellular ones, are quite different. They are related to each other and they are the three major domains of bacteria, archaea, and eukaryota. So, the major mystery in all this is whether they all trace back to the same route. This is really an open question in virology. It deals with the evolution of virus origins and it's really unclear how viruses first occurred on this planet, when did they first evolve, and, especially, whether they evolved on the planet preceding cellular life. One major idea that is popular, but is by no means the only idea of how viruses first arose on the planet, is that they might have actually predated the evolution of all cellular life. And there's a key bit of data that supports this idea, in that, if you look at virus genes and compare them in their genetic sequence to cellular life, that is available in genetic databases, you often find a mismatch. So, that suggests that viruses are not simply some more fundamentally simple version of cellular life; instead, they might be something really fundamentally different that might have predated cellular life altogether. So, LUCA, here in this diagram, stands for last unique common ancestor, which is the shorthand version of everything that cellular life perhaps traced back to. And this diagram is indicating that there might have been an ancient virosphere, for which all the viruses that are infecting the archaea, the bacteria, and the eukaryotes existed alongside in this time period or even predating LUCA, and that, today, we see this amazing biodiversity of virus types, but they might have been here billions of years ago and even before cellular life. So, the rest of the talk will feature several lines of evidence that suggest that viruses just might be the most successful of Earth's inhabitants. So, I'll go through five lines of evidence that really support what I would assert as the extreme biological success of viruses relative to other entities on the planet. The first will be growth potential; next, we'll talk about abundance, biodiversity; adaptability; and, perhaps most important, it's very evident that viruses have huge impact on other organisms on this planet. First of all, growth potential... because there are so many different ways of cataloging and determining what biological... biological success even means, let's begin with just the sheer ability to grow, to reproduce, and produce copies of oneself. So, growth potential can be pretty amazingly impressive for a lot of organisms. Some eukaryotes, our close relatives, are able to reproduce very quickly, such as the fruit fly has a very short developmental cycle, such that progeny are produced in a very short period of time. But, really, the abundance of the number of organisms that are... that can be produced through reproduction... amphibians, they are also pretty impressive. They can sometimes lay hundreds or thousands of eggs that will successfully develop eventually into adults. Now, the bacteria and the archaea, I would say, are even more impressive. They undergo a form of reproduction called binary fission where each cell separates into two daughter cells. So, in this way they can grow very, very quickly, as long as there are abundant resources available. So, I would say the bacteria and the archaea, on average, grow much faster than most eukaryotes that we would consider. All eukaryotes, bacteria, and archaea have genetic inheritance across generations that's through DNA as the nucleic acid. So, they sometimes do have this amazing growth potential, but let's keep in mind that the only way that traits pass across generations is through double-stranded DNA inheritance. Considering the viruses, they grow much, much faster than most bacteria, archaea, and eukaryotes. So, the ability for viruses to enter a cell, hijack the metabolism, and make progeny can sometimes lead to hundreds or thousands of particles exiting that cell. So, this would be the case for bacteriophages that are infecting the bacteria and the archaea, as well as viruses of eukaryotes. If they infect a tissue, for example, in the human body, there can be an amazing capacity for each one of those infected cells to produce upwards of 10,000 or more virus particles per cell. Also, in relation to inheritance across generations, I would say that the viruses have obviously more options for how this occurs in the natural world, whereas the bacteria, archaea, and eukaryotes are confined to largely DNA inheritance through double-stranded nucleic acid, both double-stranded DNA and double-stranded RNA are possibilities for the nucleic acid inheritance in viruses, as well as single-stranded forms of those nucleic acids. So, essentially, viruses are covering the entire gamut of what is possible on this planet for modes of inheritance through genetic... through genetic means. So, now let's move on to talking about virus abundance. And this is very amazing and, when you look at the numbers, you'll see that viruses easily outnumber all other biological forms on this planet. We'll begin with saying that viruses are very abundant and we know this because if you look in natural habitats on Earth, sometimes these support cellular life and there's actually an amazing capacity for cellular life to thrive in deep-sea vents and complete darkness, where there are other forms of resources than the sun to produce progeny, ultimately, when you look at very dry and hot regions, cold regions, atmosphere, soil... everywhere you find on this planet the possibility of cellular life existing, you see alongside it viruses. And the key thing here is that viruses generally outnumber cellular entities ten to one in each of these environments. Therefore, you can make some rough calculations and estimate, across this world, at any one period of time, an estimate of some 10^31 particles of viruses in any instant is a very reasonable one for the viruses on this planet. And we all realize, hopefully you can remember, that nucleic acid exists in a compacted form within cells and also within capsids of viruses, but if you just take these virus genes and genomes, and you unravel them so that they're at their full length, and you lay them end to end, off of the Earth's surface, this would extend to 250 million light years away, which is an incredible distance. That would allow you to reach the Perseus cluster, which is pretty far from Earth. So, now we've talked about the amazing growth potential and the sheer abundance of viruses on this planet, already these are two impressive ways of indicating that biological success of viruses is just amazingly impressive, but now let's look at something that's largely hidden to view. Biodiversity is something that's fascinated humans for a long period of time, probably ever since humans have observed other organisms around them. But there's an invisible kind of biodiversity on this planet, especially in the virus world, that has only been seen relatively recently with the kind of tools and machinery such as electron microscopes that let us glimpse these larger number of entities that surround us on the planet. The first thing to state is that viruses by no means are identical to one another in their morphologies. Some of them are amazingly complex, with beautiful body plans that almost look like a lunar lander -- something incredibly beautiful, I would say, in nature, but often escapes our attention because they are so small. Other forms of viruses are more like tubes and beautiful icosahedrons, so there's an amazing variety, but you'll notice that the line here at the bottom... 0.5 micron, which is 1/2000 of a millimeter... all of these body plans that I'm showing you thus far suggest that viruses are submicroscopic. And I would say that's an amazing amount of beautiful morphology, complexity, and biodiversity that is also amazingly small in size, so I think that that's pretty impressive. But there's a little quirk to viruses and the way that they had been isolated from natural sources through time, that researchers actually missed the fact that some viruses are not submicroscopic. In fact, some of them are actually larger than the smallest-size cells. So, newly discovered viruses, I would say, are macroscopic -- certainly when you consider a virus like mimivirus relative to the size of an E. coli cell. Here's something more typical of what someone would continue... would... would think of as a typical particle size, and that would be HIV. So, the point here is that by no means are all viruses submicroscopic. Instead, some of them rival or exceed the size of cellular life. Now, these mimiviruses did escape our attention through a little quirk of how people isolated viruses from nature, putting them through filtration and assuming that anything that passed through a very small pore size must be a virus, whereas everything that was held back must be cellular or cellular debris. But all one has to do is increase the pore size in these filtration experiments and you'll find that some amazingly large-sized viruses are evident and still thriving on this planet. So, you can go off the coast of Chile, for example, and within sea water you could find these large-sized viruses. It's also available to see them in ice cores in places like Siberia, where researchers very carefully can take old material and bring it up to the Earth's surface, some 30,000-year-old ice cores have been brought up to the Earth's surface. And, within these, we see these large-sized viruses. That alone indicates that large-sized viruses are certainly not anything new; they've been around on this planet for some period of time and they merely escaped our attention through quirks of methodology. And the natural history study of viruses is something that I would say is certainly thriving. There are entire research programs that can go into places like Yellowstone Park in the USA, where there are certain extreme environments, especially hot springs, and one can look for viruses that are infecting some of these extremophiles. And it's very easy to find that these viruses are completely new to virus family classification. We see body forms and, ultimately, when one characterizes these viruses through genetics, they are not at all closely related to other virus families that have been described in the past. So, I would say that natural history is alive and well in virology, and it is possible to go out and very easily, in nature, isolate material that shows you very new viruses that are entirely new to the biological classification. Adaptability... so, this is the ability for organisms to interact with their environment, to undergo selection to become better adapted through time, so that they create a better match to their environment. Darwin was the one who best articulated this through the process of natural selection, so we know... we will now talk about how viruses have an amazing capacity, on average, to adapt, and this certainly contributes to their biological success on the planet. So, Darwin had a way of explaining natural selection that was beautifully elegant. Essentially, if you have these four components, you could think of natural selection occurring in any biological system with inheritance, no matter whether it's on Earth or when we ultimately, probably, will discover life elsewhere. So, if the individuals in a population vary from one another, and if that variation is heritable -- if it could be moved across generations -- one can expect that some of those variants are going to be better advantaged than others in surviving or reproducing, according to whatever the details are of the environment or the ecology that they... that they experience. So, ultimately the population should change genetically, or evolve, to reflect the ones that are the most successful variants. And if all of this is in place, then evolution by natural selection can occur. Darwin best articulated this idea in his most famous book, On the Origin of Species. A great example of this comes from the virus world, where HIV is of course a very important biomedical problem that humans face, HIV that can ultimately progress to AIDS through infection. But not too long after the AIDS epidemic occurred there was a wonder drug called AZT that people thought would be the thing that would just eliminate this problem. Without going into the details, the ability of AZT is to disrupt HIV's capacity as an RNA virus to enter a cell, replicate to turn into a DNA form that inserts into the genetic material, and then exits the cell again as RNA. And this lifestyle in viruses we call a retrovirus. So, here's the problem with treating HIV as an RNA virus that has an amazing mutational capacity with only a single drug. Ultimately, we would expect that drug to fail and unfortunately we only observed this when AZT became popular and used as a drug, and it was seen to widely fail through time. So, through mutation, virus populations can change, especially RNA viruses, which have no ability to correct the errors that just simply occur in the replication process. In this diagram, you see how an infection could begin with a HIV population that is identical to one another, and would be entirely susceptible to AZT. And through time, because of this error ability in the virus population, you are going to have partially resistant or fully resistant forms of the virus simply show up, and these would be resistant to AZT, either partially or completely, as shown in the diagram. And importantly, keep note of this: all of that variation occurs before any AZT is brought into the human patient. So, ultimately, what happens is very similar to what we see with evolution by natural selection -- in fact, it's identical and it's a great description of it. The individuals vary, the variation is heritable, some of those variants are advantaged when AZT eventually is the ecological challenge that the population experiences, and then ultimately those variants take over the population, or it evolves, so that the entire population has escaped AZT as the drug that would ordinarily, we would hope, control it. So, unfortunately, this was observed in every single patient who was administered AZT. It either happened very early on if those mutations occurred early, or later on, if they just happened to occur later. But ultimately, the unfortunate outcome is that AZT always failed. HIV and other disease scourges of humans that are caused by virus... virus infections are not new. Many of them we can find evidence of having occurred in human populations long ago. When one looks at hieroglyphics, mummified remains, artwork from older populations of human from ancient times, this reveals the antiquity of virus diseases. For example, this man, shown in a heiro... in a hieroglyphic from ancient Egypt around 3700 BC, has a very characteristic clubfoot that's associated with poliovirus infection that entered in the gut, like all polio viruses ultimately do, but then sometimes poliovirus moves to your neural system, and it can disrupt your normal development and lead to limb deformities. So, this man is definitely showing a characteristic deformed limb of a poliovirus infection. Smallpox is another old disease of the human population, and this artwork is showing an unfortunate person suffering from a smallpox infection, which would be ultimately lethal. And, fortunately, we don't worry about smallpox anymore because there was a global vaccine campaign that eliminated it as a natural thing that would infect humans, but the point is that we can find, through this ancient material that humans and older populations have left behind, that humans have been suffering virus diseases for a very long time. I would assert that, probably, this has happened as soon as humans evolved as a species on the planet, there would be viruses that would challenge their health. So, I'd like to end with talking about the impact, in general, that viruses have on other organisms on this planet, and this is really quite profound. Similar to the examples I just covered for smallpox and HIV, etc, there are many diseases that humans face that are a challenge to our health and our mortality, and a lot of these are endemic problems, for example, the parasite that is transmitted by a mosquito and causes malaria in sub-Saharan Africa and other tropical regions. This has been around for a very long time -- that happens to be a eukaryote -- and you could see the response, even in our genetics, of ways that we would be naturally better able of fighting off malaria, and it has contributed to ways that the human population has changed genetically through time. But that's different than an epidemic that is highly deadly and rises in frequency very quickly, and impacts a lot of, in this case humans, through mortality, something that happens very quickly. So, here are four examples, and I'm highlighting, in red, that three of them were due to viruses, virus illnesses. So, the Spanish influenza of 1918, amazingly, before humans were traveling around the world through flight, through commercial flight, still 50 to 100 million people around the world contracted influenza and died from this highly virulent form of the virus. More recently, the HIV/AIDS epidemic that started around 1981 is something that has unfortunately left roughly 35 million people dead and many, many more than that are infected. Fortunately, we have new ways, things other than AZT, that keep people alive for a long period of time when they're HIV-infected, but certainly during the early part of that pandemic we saw a high degree of human mortality and we still see it today. Now, it's hard to put exact numbers on the New World smallpox epidemic, around 1520, when this started. This is when Europeans came to the New World, interacted with Native American populations, in some places displacing them, and they introduced into those populations smallpox, something that Native Americans had not seen. So, this was experienced as a highly virulent illness in Native American populations. It's unclear how many people died because we just don't have accurate records of how many people were in these populations at the time. Certainly, this could have been on the order of the two pandemics that I listed above. And last, I will remind you that some bacterial illnesses also have the capacity to have huge impact on human populations. The "Great Plague" in Europe in the middle of the 1300s was something that left in its wake some 28 million people, or roughly 40% of the European population succumbed during the Great Plague. It's a little controversial how this bacterial illness could account for that amount of mortality. Some people believe that the sheer poor living conditions that people experienced at that time left them highly vulnerable to something like virus illnesses, as well, that might have contributed to those millions of people who died. So, again, we're a little uncertain there, but for the most part these examples are grim ones of how impactful viruses can be in terms of mortality. So, I don't want to leave you with all bad news about viruses, because, certainly, there are a lot of viruses that positively impact other organisms, including humans. So, let's begin long, long ago, some billions of years ago when the cyanobacteria appeared on this planet and they started to thrive through evolving photosynthesis, that, 3 billion years ago or more, this changed the Earth's atmosphere so that 50%, today even, of the Earth's oxygen is due to photosynthesis that comes from cyanobacteria living in the ocean. And if they hadn't evolved long ago and changed the average amount of oxygen in the atmosphere, it would have been impossible for large-bodied organisms like us to even evolve in their wake. So, we can thank the cyanobacteria for that. But there's an interesting thing that most people don't know and that is cyanobacteria undergo a lot of mortality from cyanophages. These are viruses that live alongside them in the ocean and they outnumber the cyanobacteria and they thrive on the cyanobacteria, essentially as resources. But there was an interesting finding not long ago that these cyanophages have genes that allow for photosynthesis to occur. And that was a very strange discovery, because we know that viruses don't undergo metabolism. What would they be doing with photosynthesis genes? It starts to make more sense when we think about the virus life cycle and the necessity of keeping the cell going and churning through its metabolism, so that viruses can undergo proper replication. Therefore, it's not surprising that they bring these genes into the cell with them, so that those processes can occur. But a factoid I'll leave you with is that perhaps 5% of the breaths that you'll take today ultimately come from those genes that are on cyanophages, rather than any other source of oxygen. We are more and more familiar with microbiomes -- you hear more and more about this in the news. So, these are the fungi, the bacteria, and the viruses that live on and in macroorganisms such as humans. And it's really interesting how these communities vary, even through locations in our body. Inside and outside, you have different communities of these microbes thriving on and in your body. Well, the same thing goes, but different composition of those communities exists, for animals, plants, and other macroorganisms on the planet. Some of these we keep in our homes or we rely on for food, so it's important to think about how these interactions are occurring with organisms that are essential to us, or that simply give us pleasure, like as pets in our home, they have their own characteristic microbiomes that we're learning more and more about. And I should also emphasize that, certainly, all wild animals and also wild animals that we rely on for food, they have their own characteristic microbiomes too. So, viruses in your microbiome... you hear in the news about how the microbiome is probably the thing that is causing certain traits in humans, making... making us more disease-prone or disease-averse, so you'll hear a lot more about this in the coming decades, but you actually don't hear that much about your virome, the component of your microbiome that is the viruses. There was a neat discovery recently that, perhaps, these viruses that exist on and in your body are interacting with your body to make you healthier. This diagram is showing how phages, which cannot infect our cells, can interact with the mucus layers that we naturally produce that help protect us as a barrier from bacterial infection. Interestingly, these phages will interact with the mucus layer and be oriented in a way such that their tail fibers are able to interact with any bacteria getting to the mucus layer and trying to transit through to get to your cells. This provides an extra barrier that protects you against those bacteria, because the phage will attach, replicate, kill the bacteria, exit the cell, and more of those infection events can occur. This is certainly to our benefit, but we have a lot more to learn about whether this is something that has been an... an adaptation that evolved for these phages to interact with macroorganisms to do this, or whether they're simply taking advantage of the fact that phages are everywhere, sometimes they are in the correct place for this to happen. So, a final thing that I'll leave you with is that the human genome project gave many surprising results, but there was a very surprising one in terms of, if you look at our DNA com... our... our... our DNA chromosomes, you'll find a nice match between roughly 8% of your human DNA seems to be viral-derived. And one might ask, well, how is that possible? You can think of this as the ghost of infections past. In our long ago species ancestors that led to humans, ultimately, there were some virus infections that those organisms suffered and interestingly there can be viruses that avoid detection by their hosts because they have special genes that make them hide, so, essentially, what has occurred in the evolution of placental mammals is that we could not have existed on this planet unless, long ago, our ancient ancestors had undergone these virus infections, and those genes, instead of becoming deleterious and helping viruses avoid detection by our long ago ancestors, instead they were genes that were co-opted and taken into our genome, and ultimately helped placental mammal mothers not reject the baby in the body. And this is an amazing thing due to what are called syncytian proteins and genes that come from viruses. This is clearly a way that virus genes can be highly useful to other organisms and, in fact, there's no way that you would be sitting here listening to me give this talk unless these ancient infection events had occurred, and had led, ultimately, to the evolution of placental mammals. So, I've covered a lot of evidence for what we would say indicates that viruses are the most biologically successful entities on this planet. If you look at their growth potential, their abundance, and their biodiversity, they simply outnumber, and can grow faster, and produce a larger number of forms than any other organisms that we know of. In addition to that, they can interact with other organisms in their environment, and have an amazing capacity to adapt to environmental change, which I find completely fascinating because, essentially, viruses cannot control where they go in the environment, and yet they can encounter environments that are challenging to them and improve through time through adaptation by natural selection. Ultimately, their impact on the rest of the biological world is profound and immense, and literally we thank viruses for some genes that they have devoted and given to us in our genome, and this is something that's clearly impacted -- positively -- the human species through time.
