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| Welcome to the Virosphere | Welcome to the Virosphere |
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| In January, Chinese virologists isolated the virus that causes Covid-19. Earlier this month, a team of virologists gave this new virus a new name: SARS-CoV-2. | In January, Chinese virologists isolated the virus that causes Covid-19. Earlier this month, a team of virologists gave this new virus a new name: SARS-CoV-2. |
| To do so, they had to move the virus to the head of a very, very long line. | To do so, they had to move the virus to the head of a very, very long line. |
| In recent years, scientists have discovered that the world of virus diversity — what they sometimes call the virosphere — is unimaginably vast. They have uncovered hundreds of thousands of new species that have yet to be named. And they suspect that there are millions, perhaps even trillions, of species waiting to be found. | In recent years, scientists have discovered that the world of virus diversity — what they sometimes call the virosphere — is unimaginably vast. They have uncovered hundreds of thousands of new species that have yet to be named. And they suspect that there are millions, perhaps even trillions, of species waiting to be found. |
| “Suffice to say that we have only sampled a minuscule fraction of the virosphere,” said Edward Holmes of the University of Sydney in Australia. | “Suffice to say that we have only sampled a minuscule fraction of the virosphere,” said Edward Holmes of the University of Sydney in Australia. |
| With the discovery of viruses in the late 1800s, scientists soon recognized that different species caused different diseases — rabies and influenza, for example. Later, virologists learned how to recognize new kinds of viruses by growing them in labs, where subtler biological features emerged. | With the discovery of viruses in the late 1800s, scientists soon recognized that different species caused different diseases — rabies and influenza, for example. Later, virologists learned how to recognize new kinds of viruses by growing them in labs, where subtler biological features emerged. |
| After decades of this painstaking work, virologists have officially named 6,828 species of viruses; the figure includes 1,000 or so that will be formally accepted in the next few weeks by the International Committee on the Taxonomy of Viruses. That’s a paltry count when you consider that entomologists have named 380,000 species of beetles alone. | After decades of this painstaking work, virologists have officially named 6,828 species of viruses; the figure includes 1,000 or so that will be formally accepted in the next few weeks by the International Committee on the Taxonomy of Viruses. That’s a paltry count when you consider that entomologists have named 380,000 species of beetles alone. |
| But in recent years, virologists have changed the way they hunt. Now they look for bits of genetic material in samples — water, mud, blood — and use sophisticated computer programs to recognize viral genes. | But in recent years, virologists have changed the way they hunt. Now they look for bits of genetic material in samples — water, mud, blood — and use sophisticated computer programs to recognize viral genes. |
| Matthew Sullivan, a virologist at Ohio State University, has used this method to search for viruses that infect life in the ocean. He and his colleagues analyzed genetic material in seawater collected on a scientific voyage around the world. Some genes belonged to species already known to science. But many were new. In 2016, Dr. Sullivan and his colleagues reported over 15,000 viruses, each representing a new species. | Matthew Sullivan, a virologist at Ohio State University, has used this method to search for viruses that infect life in the ocean. He and his colleagues analyzed genetic material in seawater collected on a scientific voyage around the world. Some genes belonged to species already known to science. But many were new. In 2016, Dr. Sullivan and his colleagues reported over 15,000 viruses, each representing a new species. |
| That was more than twice as many species as all the previously identified viruses. And with that, Dr. Sullivan thought he and his colleagues had pretty much finished off the diversity of viruses in the sea. But they went on collecting more water, and invented new ways to search it for the genetic material of viruses. In 2019, they reported finding a total of 200,000 species. | That was more than twice as many species as all the previously identified viruses. And with that, Dr. Sullivan thought he and his colleagues had pretty much finished off the diversity of viruses in the sea. But they went on collecting more water, and invented new ways to search it for the genetic material of viruses. In 2019, they reported finding a total of 200,000 species. |
| “I’ve stopped saying, ‘We’re done,’” Dr. Sullivan said. | “I’ve stopped saying, ‘We’re done,’” Dr. Sullivan said. |
| Other researchers are discovering thousands of new viruses as well. “Right now, we are in the exponential phase,” said Dr. Jens H. Kuhn, the lead virologist at the Integrated Research Facility at Fort Detrick in Maryland. “If someone gives me a million dollars and I go out and sample sea cucumbers, I will present you with 10,000 new viruses.” | Other researchers are discovering thousands of new viruses as well. “Right now, we are in the exponential phase,” said Dr. Jens H. Kuhn, the lead virologist at the Integrated Research Facility at Fort Detrick in Maryland. “If someone gives me a million dollars and I go out and sample sea cucumbers, I will present you with 10,000 new viruses.” |
| Formally describing a new virus remains a time-consuming task. When Chinese researchers isolated the Covid-19-causing virus earlier this year, they found that it had a distinctive crown of proteins. This hallmark told them that the virus belonged to the coronavirus family, which contains 39 known species. The World Health Organization used this finding to give the disease its name — Coronavirus Disease 2019, or Covid-19 for short. | Formally describing a new virus remains a time-consuming task. When Chinese researchers isolated the Covid-19-causing virus earlier this year, they found that it had a distinctive crown of proteins. This hallmark told them that the virus belonged to the coronavirus family, which contains 39 known species. The World Health Organization used this finding to give the disease its name — Coronavirus Disease 2019, or Covid-19 for short. |
| To determine just what kind of coronavirus they were dealing with, virologists sequenced its genes. The virus was genetically similar to the one that caused the SARS outbreak in 2002. In March, the International Committee on Taxonomy of Viruses declared that the two viruses belonged to the same species. The virus that caused SARS is known as SARS-CoV. So they called the Covid-19-causing virus SARS-CoV-2. | To determine just what kind of coronavirus they were dealing with, virologists sequenced its genes. The virus was genetically similar to the one that caused the SARS outbreak in 2002. In March, the International Committee on Taxonomy of Viruses declared that the two viruses belonged to the same species. The virus that caused SARS is known as SARS-CoV. So they called the Covid-19-causing virus SARS-CoV-2. |
| The viruses that infect humans are the best understood of all. But only about 250 species of viruses choose us as their host — “an insignificant fraction of the virosphere infect humans,” Dr. Holmes said. | The viruses that infect humans are the best understood of all. But only about 250 species of viruses choose us as their host — “an insignificant fraction of the virosphere infect humans,” Dr. Holmes said. |
| While hundreds of thousands of new species still await their own names, virologists believe that far more await discovery. Dr. Holmes estimates that the viruses infecting animals, plants, fungi and protozoans (a group called eukaryotes) number 100 million species. | While hundreds of thousands of new species still await their own names, virologists believe that far more await discovery. Dr. Holmes estimates that the viruses infecting animals, plants, fungi and protozoans (a group called eukaryotes) number 100 million species. |
| Bacteria and other single-celled microbes belong to a group called prokaryotes. In a paper published on March 4 in Microbiology and Molecular Biology Reviews, Dr. Kuhn and his colleagues argued that there are, at minimum, 100 million species of viruses that infect prokaryotes. | Bacteria and other single-celled microbes belong to a group called prokaryotes. In a paper published on March 4 in Microbiology and Molecular Biology Reviews, Dr. Kuhn and his colleagues argued that there are, at minimum, 100 million species of viruses that infect prokaryotes. |
| But some researchers suspect there are many more species of prokaryotes in the world — which would mean many more species of viruses. The true figure might be as high as 10 trillion. | But some researchers suspect there are many more species of prokaryotes in the world — which would mean many more species of viruses. The true figure might be as high as 10 trillion. |
| For each of those species, scientists will have to figure out how it is related to other viruses. That is far harder to determine for viruses than for familiar life-forms like animals and plants. | For each of those species, scientists will have to figure out how it is related to other viruses. That is far harder to determine for viruses than for familiar life-forms like animals and plants. |
| Scientists who study animals and plants can rely on the tried and true classification system first established by Carl Linnaeus in the 1700s. Our species belongs to the class Mammalia, for instance, and, above that, the animal kingdom. Virologists have struggled to figure out the classes and kingdoms of the virosphere. Part of the problem is that viruses have a penchant for trading genes with other species, making it hard to draw bright lines between groups of them. | Scientists who study animals and plants can rely on the tried and true classification system first established by Carl Linnaeus in the 1700s. Our species belongs to the class Mammalia, for instance, and, above that, the animal kingdom. Virologists have struggled to figure out the classes and kingdoms of the virosphere. Part of the problem is that viruses have a penchant for trading genes with other species, making it hard to draw bright lines between groups of them. |
| Updated June 5, 2020 | Updated June 5, 2020 |
| A study by European scientists is the first to document a strong statistical link between genetic variations and Covid-19, the illness caused by the coronavirus. Having Type A blood was linked to a 50 percent increase in the likelihood that a patient would need to get oxygen or to go on a ventilator, according to the new study. | |
| The unemployment rate fell to 13.3 percent in May, the Labor Department said on June 5, an unexpected improvement in the nation’s job market as hiring rebounded faster than economists expected. Economists had forecast the unemployment rate to increase to as much as 20 percent, after it hit 14.7 percent in April, which was the highest since the government began keeping official statistics after World War II. But the unemployment rate dipped instead, with employers adding 2.5 million jobs, after more than 20 million jobs were lost in April. | The unemployment rate fell to 13.3 percent in May, the Labor Department said on June 5, an unexpected improvement in the nation’s job market as hiring rebounded faster than economists expected. Economists had forecast the unemployment rate to increase to as much as 20 percent, after it hit 14.7 percent in April, which was the highest since the government began keeping official statistics after World War II. But the unemployment rate dipped instead, with employers adding 2.5 million jobs, after more than 20 million jobs were lost in April. |
| Mass protests against police brutality that have brought thousands of people onto the streets in cities across America are raising the specter of new coronavirus outbreaks, prompting political leaders, physicians and public health experts to warn that the crowds could cause a surge in cases. While many political leaders affirmed the right of protesters to express themselves, they urged the demonstrators to wear face masks and maintain social distancing, both to protect themselves and to prevent further community spread of the virus. Some infectious disease experts were reassured by the fact that the protests were held outdoors, saying the open air settings could mitigate the risk of transmission. | Mass protests against police brutality that have brought thousands of people onto the streets in cities across America are raising the specter of new coronavirus outbreaks, prompting political leaders, physicians and public health experts to warn that the crowds could cause a surge in cases. While many political leaders affirmed the right of protesters to express themselves, they urged the demonstrators to wear face masks and maintain social distancing, both to protect themselves and to prevent further community spread of the virus. Some infectious disease experts were reassured by the fact that the protests were held outdoors, saying the open air settings could mitigate the risk of transmission. |
| Exercise researchers and physicians have some blunt advice for those of us aiming to return to regular exercise now: Start slowly and then rev up your workouts, also slowly. American adults tended to be about 12 percent less active after the stay-at-home mandates began in March than they were in January. But there are steps you can take to ease your way back into regular exercise safely. First, “start at no more than 50 percent of the exercise you were doing before Covid,” says Dr. Monica Rho, the chief of musculoskeletal medicine at the Shirley Ryan AbilityLab in Chicago. Thread in some preparatory squats, too, she advises. “When you haven’t been exercising, you lose muscle mass.” Expect some muscle twinges after these preliminary, post-lockdown sessions, especially a day or two later. But sudden or increasing pain during exercise is a clarion call to stop and return home. | Exercise researchers and physicians have some blunt advice for those of us aiming to return to regular exercise now: Start slowly and then rev up your workouts, also slowly. American adults tended to be about 12 percent less active after the stay-at-home mandates began in March than they were in January. But there are steps you can take to ease your way back into regular exercise safely. First, “start at no more than 50 percent of the exercise you were doing before Covid,” says Dr. Monica Rho, the chief of musculoskeletal medicine at the Shirley Ryan AbilityLab in Chicago. Thread in some preparatory squats, too, she advises. “When you haven’t been exercising, you lose muscle mass.” Expect some muscle twinges after these preliminary, post-lockdown sessions, especially a day or two later. But sudden or increasing pain during exercise is a clarion call to stop and return home. |
| States are reopening bit by bit. This means that more public spaces are available for use and more and more businesses are being allowed to open again. The federal government is largely leaving the decision up to states, and some state leaders are leaving the decision up to local authorities. Even if you aren’t being told to stay at home, it’s still a good idea to limit trips outside and your interaction with other people. | States are reopening bit by bit. This means that more public spaces are available for use and more and more businesses are being allowed to open again. The federal government is largely leaving the decision up to states, and some state leaders are leaving the decision up to local authorities. Even if you aren’t being told to stay at home, it’s still a good idea to limit trips outside and your interaction with other people. |
| Touching contaminated objects and then infecting ourselves with the germs is not typically how the virus spreads. But it can happen. A number of studies of flu, rhinovirus, coronavirus and other microbes have shown that respiratory illnesses, including the new coronavirus, can spread by touching contaminated surfaces, particularly in places like day care centers, offices and hospitals. But a long chain of events has to happen for the disease to spread that way. The best way to protect yourself from coronavirus — whether it’s surface transmission or close human contact — is still social distancing, washing your hands, not touching your face and wearing masks. | Touching contaminated objects and then infecting ourselves with the germs is not typically how the virus spreads. But it can happen. A number of studies of flu, rhinovirus, coronavirus and other microbes have shown that respiratory illnesses, including the new coronavirus, can spread by touching contaminated surfaces, particularly in places like day care centers, offices and hospitals. But a long chain of events has to happen for the disease to spread that way. The best way to protect yourself from coronavirus — whether it’s surface transmission or close human contact — is still social distancing, washing your hands, not touching your face and wearing masks. |
| Common symptoms include fever, a dry cough, fatigue and difficulty breathing or shortness of breath. Some of these symptoms overlap with those of the flu, making detection difficult, but runny noses and stuffy sinuses are less common. The C.D.C. has also added chills, muscle pain, sore throat, headache and a new loss of the sense of taste or smell as symptoms to look out for. Most people fall ill five to seven days after exposure, but symptoms may appear in as few as two days or as many as 14 days. | Common symptoms include fever, a dry cough, fatigue and difficulty breathing or shortness of breath. Some of these symptoms overlap with those of the flu, making detection difficult, but runny noses and stuffy sinuses are less common. The C.D.C. has also added chills, muscle pain, sore throat, headache and a new loss of the sense of taste or smell as symptoms to look out for. Most people fall ill five to seven days after exposure, but symptoms may appear in as few as two days or as many as 14 days. |
| If air travel is unavoidable, there are some steps you can take to protect yourself. Most important: Wash your hands often, and stop touching your face. If possible, choose a window seat. A study from Emory University found that during flu season, the safest place to sit on a plane is by a window, as people sitting in window seats had less contact with potentially sick people. Disinfect hard surfaces. When you get to your seat and your hands are clean, use disinfecting wipes to clean the hard surfaces at your seat like the head and arm rest, the seatbelt buckle, the remote, screen, seat back pocket and the tray table. If the seat is hard and nonporous or leather or pleather, you can wipe that down, too. (Using wipes on upholstered seats could lead to a wet seat and spreading of germs rather than killing them.) | If air travel is unavoidable, there are some steps you can take to protect yourself. Most important: Wash your hands often, and stop touching your face. If possible, choose a window seat. A study from Emory University found that during flu season, the safest place to sit on a plane is by a window, as people sitting in window seats had less contact with potentially sick people. Disinfect hard surfaces. When you get to your seat and your hands are clean, use disinfecting wipes to clean the hard surfaces at your seat like the head and arm rest, the seatbelt buckle, the remote, screen, seat back pocket and the tray table. If the seat is hard and nonporous or leather or pleather, you can wipe that down, too. (Using wipes on upholstered seats could lead to a wet seat and spreading of germs rather than killing them.) |
| Taking one’s temperature to look for signs of fever is not as easy as it sounds, as “normal” temperature numbers can vary, but generally, keep an eye out for a temperature of 100.5 degrees Fahrenheit or higher. If you don’t have a thermometer (they can be pricey these days), there are other ways to figure out if you have a fever, or are at risk of Covid-19 complications. | Taking one’s temperature to look for signs of fever is not as easy as it sounds, as “normal” temperature numbers can vary, but generally, keep an eye out for a temperature of 100.5 degrees Fahrenheit or higher. If you don’t have a thermometer (they can be pricey these days), there are other ways to figure out if you have a fever, or are at risk of Covid-19 complications. |
| The C.D.C. has recommended that all Americans wear cloth masks if they go out in public. This is a shift in federal guidance reflecting new concerns that the coronavirus is being spread by infected people who have no symptoms. Until now, the C.D.C., like the W.H.O., has advised that ordinary people don’t need to wear masks unless they are sick and coughing. Part of the reason was to preserve medical-grade masks for health care workers who desperately need them at a time when they are in continuously short supply. Masks don’t replace hand washing and social distancing. | The C.D.C. has recommended that all Americans wear cloth masks if they go out in public. This is a shift in federal guidance reflecting new concerns that the coronavirus is being spread by infected people who have no symptoms. Until now, the C.D.C., like the W.H.O., has advised that ordinary people don’t need to wear masks unless they are sick and coughing. Part of the reason was to preserve medical-grade masks for health care workers who desperately need them at a time when they are in continuously short supply. Masks don’t replace hand washing and social distancing. |
| If you’ve been exposed to the coronavirus or think you have, and have a fever or symptoms like a cough or difficulty breathing, call a doctor. They should give you advice on whether you should be tested, how to get tested, and how to seek medical treatment without potentially infecting or exposing others. | If you’ve been exposed to the coronavirus or think you have, and have a fever or symptoms like a cough or difficulty breathing, call a doctor. They should give you advice on whether you should be tested, how to get tested, and how to seek medical treatment without potentially infecting or exposing others. |
| If you’re sick and you think you’ve been exposed to the new coronavirus, the C.D.C. recommends that you call your healthcare provider and explain your symptoms and fears. They will decide if you need to be tested. Keep in mind that there’s a chance — because of a lack of testing kits or because you’re asymptomatic, for instance — you won’t be able to get tested. | If you’re sick and you think you’ve been exposed to the new coronavirus, the C.D.C. recommends that you call your healthcare provider and explain your symptoms and fears. They will decide if you need to be tested. Keep in mind that there’s a chance — because of a lack of testing kits or because you’re asymptomatic, for instance — you won’t be able to get tested. |
| And very often, a new virus simply makes no sense. An extreme example came to light in February when scientists searching for viruses in a lake found a new one they named Yaravirus. Of Yaravirus’s 74 genes, 68 are unlike any ever found in any virus. | And very often, a new virus simply makes no sense. An extreme example came to light in February when scientists searching for viruses in a lake found a new one they named Yaravirus. Of Yaravirus’s 74 genes, 68 are unlike any ever found in any virus. |
| In recent years, Dr. Kuhn and his colleagues have sought to tame this chaos. They have developed what they call a “megataxonomy” to classify viruses that seems to work. The team sorted viruses based on whether they carried one or more of a few “hallmark genes.” They also looked for groups of species that trade genes among each other, and less so with other groups. | In recent years, Dr. Kuhn and his colleagues have sought to tame this chaos. They have developed what they call a “megataxonomy” to classify viruses that seems to work. The team sorted viruses based on whether they carried one or more of a few “hallmark genes.” They also looked for groups of species that trade genes among each other, and less so with other groups. |
| “A coherent account of the global organization of the virus world is now within reach,” they wrote in their new paper. Dr. Kuhn, in an interview, said, “We were all a bit surprised this system is so logical in the end.” | “A coherent account of the global organization of the virus world is now within reach,” they wrote in their new paper. Dr. Kuhn, in an interview, said, “We were all a bit surprised this system is so logical in the end.” |
| Dr. Kuhn and his colleagues submitted their system to the taxonomy committee, and he said it would likely be accepted soon. Still, the megataxonomy is far from complete. Yaravirus, for instance, still floats on its own, lonely and unclassifiable. | Dr. Kuhn and his colleagues submitted their system to the taxonomy committee, and he said it would likely be accepted soon. Still, the megataxonomy is far from complete. Yaravirus, for instance, still floats on its own, lonely and unclassifiable. |
| Some researchers are skeptical about the megataxonomy. Dr. Holmes thinks it is too soon to attempt one, given that researchers have found so few viruses. “Why build something so rigid when it may just fall as we sample more?” he asked. Dr. Kuhn argues that it’s worth starting to build a system, even if it needs to be adjusted later. | Some researchers are skeptical about the megataxonomy. Dr. Holmes thinks it is too soon to attempt one, given that researchers have found so few viruses. “Why build something so rigid when it may just fall as we sample more?” he asked. Dr. Kuhn argues that it’s worth starting to build a system, even if it needs to be adjusted later. |
| Making sense of the virosphere is not just an intellectually challenging puzzle, Dr. Kuhn said. At Fort Dietrick, he runs experiments on some of the world’s most dangerous viruses, such as Ebola and SARS-CoV-2. A better understanding of the virosphere could help him and his colleagues come up with ways to combat these threats and others we don’t even know about yet. | Making sense of the virosphere is not just an intellectually challenging puzzle, Dr. Kuhn said. At Fort Dietrick, he runs experiments on some of the world’s most dangerous viruses, such as Ebola and SARS-CoV-2. A better understanding of the virosphere could help him and his colleagues come up with ways to combat these threats and others we don’t even know about yet. |
| “We have to understand what is out there,” he said. | “We have to understand what is out there,” he said. |