The virus itself is really nothing special—until it gets inside a human. Let’s get something out of the way first: it’s Eh-bowl-a, with an emphasis on the middle syllable. If only other facts about the virus were that easy to clear up. Unfortunately, concerns and fears have rapidly outstripped knowledge. Despite the public fears, we do know a fair amount about Ebola and its activities, and what we know tells us a lot about the prospects for treatments and vaccines. To get a clearer picture of what we know about the virus and the illness it causes, we’ve spent some time diving into the papers that describe the virus’ biology. We also called up Vincent Racaniello, a researcher at Columbia University’s Medical School and host of the This Week in Virology podcast, who helpfully provided us with a professional’s perspective on Ebola. A simple virus In some ways, Ebola is remarkably average. Appearance-wise, it forms an unusually long and flexible filament—although other viruses are filamentous, Racaniello was hard pressed to think of any that are quite as bendy as Ebola. On the genetic level, however, things look fairly mundane. Its genome consists of a single linear strand of RNA that’s about 19,000 bases long. It contains only seven genes, most of which encode proteins that give the virus its structure. (For comparison, a typical herpes virus is over 10 times larger and carries over 35 genes.) “It’s a pretty basic complement of proteins—all RNA viruses need the same ones,” Racaniello said. One gene, called NP, encodes a protein that coats the RNA and keeps it packaged inside the virus particle. Two other proteins, VP24 and VP40, coat the inside of the membrane that forms the outer layer of the virus—membrane that was originally produced by an infected cell. Beyond those proteins, things get more interesting. The only genetic material that can be duplicated by the enzymes carried by cells is DNA. But, as we noted, Ebola’s genome is encoded by RNA. Viruses handle this discrepancy in two ways. Some of them, like HIV, encode an enzyme that copies RNA into DNA, and additional copies of the virus are then made from this DNA. Ebola virus takes the alternative route: its genome encodes a protein that can copy RNA into RNA. This gene (creatively called the polymerase, or L) is the largest one carried by the virus. The viral polymerase performs a double role in that it also copies the viral genome into messenger RNAs that are then translated into proteins by the infected cells. So, without a working polymerase, you can’t make any proteins inside an infected cell. For this reason, every copy of the virus has a working polymerase protein packed inside. There’s a second protein that’s involved in making messenger RNAs and copies of the virus—it tells the polymerase where to start copying. It’s called VP 35, and it’s also packed inside the virus when it’s sent off to infect new cells. This all may sound rather exotic, but it’s actually quite common. The group of negative-strand RNA viruses, including Ebola, is quite large. Among human pathogens alone, it includes influenza, measles, mumps, rabies, and hantaviruses. So while this aspect of Ebola is interesting, it’s anything but exotic, and it certainly doesn’t explain the disease’s behavior. Immune shutdown Another gene that’s somewhat more intriguing is called VP35. This protein functions to help the virus evade an immune response. The body’s immune system consists of two parts that work cooperatively. The one we mostly learn about, acquired immunity, involves antibodies and other specialized receptors that recognize specific infectious agents. Acquired immunity is the whole reason vaccines work. But this takes a while to get up to speed when a pathogen has never been encountered before. To help protect the body at that point in the infection, cells rely on what’s called the innate immune system. This isn’t specific to any particular pathogen, but instead this recognizes features that are common to many pathogens, like sugars or lipids made by bacteria. Many viruses carry a protein that helps shut the innate immune system down, and Ebola is no exception. That task is handled by VP35. “Ebola happens to have a protein that antagonizes innate immunity, and most viruses must have one of those, so it’s not really unusual,” Racaniello told Ars. “The innate response is so powerful that, if a virus doesn’t have something to counter it, it’s going to be wiped out pretty quickly.” In Ebola’s case, VP35 does several things to tone down innate immunity. It binds to and inactivates some proteins involved in this response. It also blocks a branch of the innate immune system that recognizes double-stranded RNA. While these are a necessary part of the replication of single-stranded RNA viruses, they’re not normally produced in the cell in any great quantities, so it’s a useful way of identifying when a viral infection may be in progress. Research suggests that VP35 handles its task via a very simple route: it binds to double-stranded RNA and hides it from the innate immune system. Partly as a consequence of this, the innate immune system doesn’t trigger the production of immune signaling molecules called interferons. These interferons normally help marshal specialized immune cells and can boost the adaptive immune response. On the surface The last gene in Ebola is also common to viruses, and it’s one that helps them latch on to and enter cells. It’s called Glycoprotein, with the “glyco” referring to the fact that it’s typically linked up to sugars on its way to the surface of the membrane. The Ebola glycoprotein is hugely important. To begin with, as the only part of the virus that normally sticks out from the membrane, it’s the primary thing that the immune system sees. If someone survives an infection and has antibodies to the virus, the chances are that these antibodies target the glycoprotein. As a result, efforts to develop a vaccine against Ebola—several of which are now fairly advanced—have focused on exposing the immune system to this glycoprotein, either by injecting the protein or by injecting a harmless virus that has been engineered to carry the gene that encodes it. Understanding the Ebola virus The virus itself is really nothing special—until it gets inside a human. by John Timmer – Nov 5 2014, 12:50am CET ShareTweet 66 The ebola virus, magnified 108,000 times. Thinkstock Let’s get something out of the way first: it’s Eh-bowl-a, with an emphasis on the middle syllable. If only other facts about the virus were that easy to clear up. Unfortunately, concerns and fears have rapidly outstripped knowledge. Despite the public fears, we do know a fair amount about Ebola and its activities, and what we know tells us a lot about the prospects for treatments and vaccines. To get a clearer picture of what we know about the virus and the illness it causes, we’ve spent some time diving into the papers that describe the virus’ biology. We also called up Vincent Racaniello, a researcher at Columbia University’s Medical School and host of the This Week in Virology podcast, who helpfully provided us with a professional’s perspective on Ebola. A simple virus In some ways, Ebola is remarkably average. Appearance-wise, it forms an unusually long and flexible filament—although other viruses are filamentous, Racaniello was hard pressed to think of any that are quite as bendy as Ebola. On the genetic level, however, things look fairly mundane. Its genome consists of a single linear strand of RNA that’s about 19,000 bases long. It contains only seven genes, most of which encode proteins that give the virus its structure. (For comparison, a typical herpes virus is over 10 times larger and carries over 35 genes.) “It’s a pretty basic complement of proteins—all RNA viruses need the same ones,” Racaniello said. TOMORROW ON ARS—PART II Beyond its medical impact, the Ebola virus is testing the strength of our civil liberties in the US. On Wednesday, Senior Editor David Kravets presents the second half of our feature series on Ebola, focusing on how the power to quarantine is as “American as apple pie.”One gene, called NP, encodes a protein that coats the RNA and keeps it packaged inside the virus particle. Two other proteins, VP24 and VP40, coat the inside of the membrane that forms the outer layer of the virus—membrane that was originally produced by an infected cell. Beyond those proteins, things get more interesting. The only genetic material that can be duplicated by the enzymes carried by cells is DNA. But, as we noted, Ebola’s genome is encoded by RNA. Viruses handle this discrepancy in two ways. Some of them, like HIV, encode an enzyme that copies RNA into DNA, and additional copies of the virus are then made from this DNA. Ebola virus takes the alternative route: its genome encodes a protein that can copy RNA into RNA. This gene (creatively called the polymerase, or L) is the largest one carried by the virus. The viral polymerase performs a double role in that it also copies the viral genome into messenger RNAs that are then translated into proteins by the infected cells. So, without a working polymerase, you can’t make any proteins inside an infected cell. For this reason, every copy of the virus has a working polymerase protein packed inside. There’s a second protein that’s involved in making messenger RNAs and copies of the virus—it tells the polymerase where to start copying. It’s called VP 35, and it’s also packed inside the virus when it’s sent off to infect new cells. This all may sound rather exotic, but it’s actually quite common. The group of negative-strand RNA viruses, including Ebola, is quite large. Among human pathogens alone, it includes influenza, measles, mumps, rabies, and hantaviruses. So while this aspect of Ebola is interesting, it’s anything but exotic, and it certainly doesn’t explain the disease’s behavior. Immune shutdown Another gene that’s somewhat more intriguing is called VP35. This protein functions to help the virus evade an immune response. The body’s immune system consists of two parts that work cooperatively. The one we mostly learn about, acquired immunity, involves antibodies and other specialized receptors that recognize specific infectious agents. Acquired immunity is the whole reason vaccines work. But this takes a while to get up to speed when a pathogen has never been encountered before. To help protect the body at that point in the infection, cells rely on what’s called the innate immune system. This isn’t specific to any particular pathogen, but instead this recognizes features that are common to many pathogens, like sugars or lipids made by bacteria. Many viruses carry a protein that helps shut the innate immune system down, and Ebola is no exception. That task is handled by VP35. Enlarge / The VP35 domain that blocks the immune system’s interferon response. Rendered by John Timmer using public data “Ebola happens to have a protein that antagonizes innate immunity, and most viruses must have one of those, so it’s not really unusual,” Racaniello told Ars. “The innate response is so powerful that, if a virus doesn’t have something to counter it, it’s going to be wiped out pretty quickly.” In Ebola’s case, VP35 does several things to tone down innate immunity. It binds to and inactivates some proteins involved in this response. It also blocks a branch of the innate immune system that recognizes double-stranded RNA. While these are a necessary part of the replication of single-stranded RNA viruses, they’re not normally produced in the cell in any great quantities, so it’s a useful way of identifying when a viral infection may be in progress. Research suggests that VP35 handles its task via a very simple route: it binds to double-stranded RNA and hides it from the innate immune system. Partly as a consequence of this, the innate immune system doesn’t trigger the production of immune signaling molecules called interferons. These interferons normally help marshal specialized immune cells and can boost the adaptive immune response. On the surface The last gene in Ebola is also common to viruses, and it’s one that helps them latch on to and enter cells. It’s called Glycoprotein, with the “glyco” referring to the fact that it’s typically linked up to sugars on its way to the surface of the membrane. The Ebola glycoprotein is hugely important. To begin with, as the only part of the virus that normally sticks out from the membrane, it’s the primary thing that the immune system sees. If someone survives an infection and has antibodies to the virus, the chances are that these antibodies target the glycoprotein. As a result, efforts to develop a vaccine against Ebola—several of which are now fairly advanced—have focused on exposing the immune system to this glycoprotein, either by injecting the protein or by injecting a harmless virus that has been engineered to carry the gene that encodes it. A cartoon of the virus’ structure, showing the locations of its key proteins. NIH Antibodies that target the glycoprotein would have two effects. The first is that they would create antibody-virus aggregates that the immune system could safely clear. In addition, antibodies that bind to the glycoprotein can physically block it from latching on to cells, thus limiting the chances of further infections. The experimental treatments for Ebola that have been used recently are all based on the same principle, in that they consist of a collection of antibodies that target the glycoprotein. There’s also evidence that the glycoprotein is what actually kills individual cells. Inserting the gene alone into cells that normally line blood vessels is enough to cause their deaths. Glycoprotein appears to kill cells by blocking their ability to put new proteins on their surface. This causes the cells to lose contact with their neighbors and die. (It also has the side effect of limiting cells’ ability to inform the immune system that they are infected.) Further studies suggest that this effect is level-dependent; moderate amounts of glycoprotein don’t cause cells much difficulty. It’s only the high levels that accumulate later in infections that can kill them. This ensures that high levels of virus are made before their host dies. Killing cells, killing organisms If the virus is run-of-the-mill, how does it end up being so lethal? It’s not a matter of anything special about the genes; instead, it’s a matter of the cells that the virus infects. Its initial victims are typically immune cells, like dendritic cells and macrophages. These cells are often the body’s first line of defense against pathogens, and they help alert the immune system. Once infected, these immune cells may start to express immune signaling molecules indiscriminately. This can lead to the fever and malaise that are some of the first symptoms of infection. Another problem caused by the infection of these cells is that they’re mobile. As they move around, they have the potential to spread the infection to new sites, helping the virus transition into the blood stream. That’s a problem because the cells that line the blood vessels (called endothelial cells) are favorite targets of infection. As the virus kills these cells, the blood vessels lose their integrity and begin to leak. The end result is some of the classic symptoms of hemorrhagic fevers: edema, or the build up of fluids leaked from blood vessels; and hemorrhages, as blood vessels fail entirely. For good measure, infected macrophages start expressing proteins that influence coagulation, activating it in an uncontrolled manner and thus enhancing hemorrhages. “Every organ is a target, though,” Racaniello said. “There aren’t too many viruses that can infect so many different tissues, and that’s part of where the pathology comes from.” And although the worst effects come from the circulatory and immune systems, the widespread targeting of cells affects other tissues as well. Ebola doesn’t necessarily create the bloody, explosive messes that its reputation would have people expect, though. This reputation is based in part on Richard Preston’s book, The Hot Zone, that appears to have been wildly exaggerated, if not partly fictional. If you’re killed by Ebola, it’s far more likely to happen because your body can’t cope with the loss of fluid from the blood, which influences things like salt balance, nutrient content, and other life essentials. In fact, Racaniello told Ars that, “dehydration is eventually what kills you if you don’t get intravenous fluids.” If infected individuals could be properly supplied with intravenous fluids, the fatality rate would likely be much lower. “A lot of the virulence depends on where you are taken care of,” Racaniello said. This might explain the apparently rapid recovery of the two nurses who were infected with the virus in Dallas. In any case, it’s clear that Ebola isn’t doing anything unusual to manipulate its human hosts. As one review of the virus put it, “It is thus the host response to infection, rather than any toxic effect of the virus, that is responsible for the fever, malaise, vasodilatation, increased vascular permeability, hypotension, and shock of filoviral disease.” Racaniello, for his part, said “there isn’t anything you can point at and say ‘this is the reason that these viruses are so lethal.” Although the virus isn’t especially picky about which cells it infects, the fact that immune and blood vessel cells are among its victims can explain the majority of the symptoms, as well as the high lethality in areas where high-intensity medical care isn’t an option. Host to host Even if the impacts of the virus are largely a matter of the cells it attacks, its route of attack also explains the unfortunate pattern of infections in the current and past outbreaks. The virus is present in high volumes in the bodily fluids that leak from various tissues in the individuals who are dying from an infection. As a result, the people at highest risk of further infection are those who care for the most severely ill or those who handle the bodies that are left behind. That doesn’t mean it’s impossible to transmit the virus through less intensive contact—but it’s much, much harder. This is why individuals who are displaying no symptoms are considered to pose no risk of spreading the disease. It also explains why, at the earliest stages of fever, someone’s unlikely to pass the virus on even when riding the subway. It’s only after patients start losing fluids in large volumes that passing the virus on gets easier. And by that point, an infected individual is likely to be so ill that they won’t be leaving the house for any place other than the hospital. When the infected individual is most in need of care, however, corresponds to the period when they are most likely to pass on the infection. And so the people who are most likely to get infected are doctors, other health care workers, family members, and so on. While horrifying, it’s not a hyperefficient way to spread infections. Note that this outbreak has been going since last December and only just saw its 10,000th infection. Compare that to what a flu strain will do in the same time span—half a million deaths globally and infection of 10-15 percent of the population of affected areas. Still, it seems Ebola has a moderately effective infection strategy, one that might appear to have evolved to take advantage of human healthcare. Racaniello quickly put that idea to rest. “We’re not the natural host of this virus—it has not evolved in us.” Ebola, he pointed out, hasn’t had the chance to adapt to its human hosts much to speak of at all. Each outbreak we’ve experienced has been an entirely new transfer of a virus to humans. While the virus undoubtedly adapts a bit during its time in human hosts, any mutations that are specifically useful in us are lost each time an outbreak fizzles out. Although there’s still considerable uncertainty about how exactly Ebola makes its way to humans, evidence suggests that the primary natural reservoir for it is in bat populations. And Racaniello suggested that, in its natural host, spreading by lethal hemorrhage and fluid imbalance is unlikely to be a viable way to spread infections. After all, bats don’t care for their ill, and a bat that lacks the strength to cling to surfaces isn’t going to end up close to any other bats. Ebola’s route to new infections in humans simply appears to be a matter of unfortunate chance. Should Ebola manage to continue circulating in human hosts, however, it certainly has the potential to undergo significant adaptation. RNA polymerases like the one it uses to duplicate its genome are prone to generating new mutations because they lack a function called “proofreading” that helps limit the errors that occur each time a genome is copied. Each time the DNA in your cells is copied, the enzyme that does the copying sporadically makes mistakes, adding the wrong base to the growing DNA chain—an A instead of a G, for example. These enzymes have a proofreading ability, however. This allows them to recognize the changed local environment caused by the mismatch, and simply back up, chewing off the mismatched base and trying again. Without proofreading, Ebola’s enzyme can’t do anything other than leave the error in place and move on. As a result, the error rate of this polymerase is roughly one mistake out of every 10,000 bases. Remember that Ebola’s genome is 19,000 bases long. That means, on average, every new virus produced by a cell is likely to contain at least one mutation. Since an infected cell can produce thousands of viruses, Racaniello said that each infected cell could essentially produce a population of viruses where every single base in the genome was, on average, changed. That’s a lot of evolutionary potential. Should it worry us? To an extent, viruses tend to adapt to their hosts in ways that keep more of the hosts alive and therefore provide a larger potential pool of virus factories. (Bat infections probably fit this category, Racaniello suggested.) But they also evolve to spread more efficiently. The worry would be that the latter would happen before the former. Worries about the virus gaining the ability to spread in small, airborne droplets, however, probably shouldn’t be keeping us awake at night, according to Racaniello. He told Ars that we’re simply not aware of any cases where a virus has changed its route of infection. Clearly, this must have taken place in the deep evolutionary past—viruses probably predate the existence of blood, for example—but it’s apparently an extremely rare event. What’s next? Ebola and other hemorrhagic fever viruses have drawn the attention of the scientific and health communities for several decades now. But, unlike HIV, we’ve yet to develop an effective treatment, and no vaccines have undergone significant testing in humans. Part of the reason for the lack of progress is a difference in attention paid to the threats. But another part is the challenge of doing any research on a deadly virus like Ebola. “It’s hard to work with because it’s dangerous—you have to work with it in BSL-4 [biosafety level] labs,” Racaniello told Ars. “So we don’t make as much progress as with other viruses like flu or measles or polio. But we have learned quite a bit.” All of the information above, and quite a bit more, is now available in the published literature, including atomic-level details of the structures of the viral proteins. That progress comes despite the fact that there are less than 20 BSL-4 labs in the US, and not too many more exist in the rest of the world. (For details and a map based on data that’s a bit out of date, you can check here.) Obviously, each of the facilities will have to divide access time between Ebola projects and those involving other dangerous diseases. The current outbreak, however, has added urgency to efforts that were already underway. As mentioned above, there are several antibody-based therapies ready for human testing, and these may help control the disease once an infection has started. But this approach may not be enough to limit the spread of the virus, as treatments will only begin after an infection is obvious, and only for those with good access to healthcare. Obviously, a vaccine would be preferable. Despite the limited BSL-4 space, animal testing of potential vaccines has already taken place. “There are a couple of good vaccine candidates that protect primates, and those are going into people in phase one [trials],” Racaniello told Ars. Phase one is a very basic test of safety, and it gets followed by further trials that determine effectiveness. “There’s no reason you can see that they wouldn’t work,” he said. “But many vaccines do fail when they go into people because animals are not the same, so we’ll see.” If they prove safe, we could start seeing their use in affected areas as soon as early next year. Both vaccines were built using recombinant DNA technology, which spliced the Ebola glycoprotein into a virus that causes a harmless, low-level infection. That means they’ll need to be refrigerated prior to use, which may limit their utility in remote regions where outbreaks may start. But they could certainly be given to the people who are most likely to become infected—not you or me, but the healthcare workers who are on the front lines of this outbreak. ift.tt/13HTp3v
Posted on: Wed, 05 Nov 2014 14:55:47 +0000
Trending Topics
Recently Viewed Topics
© 2015