IMAGINE an alien creature floating in space. It doesn鈥檛 grow, communicate or move at all under its own steam. Without a home it is inert. We know very little about it, except that it will start reproducing when it enters the atmosphere of a planet that suits it. Is it living? Is it dangerous?
This may not sound like a plausible being, but it pretty much describes viruses, which are little more than bits of genetic material able to replicate only when inside a host. Viruses may seem alien, but they are the most abundant and, arguably, the most important organisms on Earth. They are found just about everywhere, from oceans and forests to the people around you and, of course, in and on you as well. This world of strange, quasi-living things has been dubbed the virosphere, and it is a mysterious one 鈥� we know less about viruses than any other life form. But that is changing rapidly.
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People generally view viruses as synonymous with infection, and there is no doubt they cause some of the most dangerous diseases, including smallpox, AIDS, Ebola and flu. Yet viruses are so much more than indiscriminate killing machines. Our ability to inspect the genetic material they are made of has improved exponentially and, in the past five years, the number of species identified has increased 20 fold. What鈥檚 more, it is becoming increasingly clear that these bizarre and diverse organisms play a key role in evolution and may well have been crucial for the origins of life.
For sheer abundance, no other group of organisms matches viruses. One study estimates the population of viruses in the oceans alone is . Another puts the an order of magnitude higher than that, at 1031, or over a million times more than the estimated number of stars in the universe. According to research published last year, each day some attached to dust particles fall onto every square metre of Earth鈥檚 surface 鈥� and we know almost nothing about most of them.
Even the perennial question of whether viruses are alive or not is still up for grabs. 鈥淓xplain to me what living means and I鈥檒l tell you whether a virus is alive,鈥� says Marilyn Roossinck at Pennsylvania State University. 鈥淎 virus is nothing unless it鈥檚 in a host. It鈥檚 not an important question as to whether these entities are living.鈥�
We do know, however, that the length of time viruses can remain viable outside their host varies hugely. Some survive only seconds while others can persist for decades. Temperature is a big factor. In very hot environments, viruses tend to die quickly, which is why . This may even explain why people evolved the ability to develop fevers in response to infections. In colder temperatures, viruses can survive for months or even years before successfully infecting a host. Variola virus, also known as , can persist for decades at temperatures between 4掳C and 5掳C. Other factors that undermine the survival of viruses include sunlight and the presence of , especially bacteria. They are particularly susceptible to .
Once inside a host, viruses spring into action. Hosts can be any kind of living thing, or even another virus, as became clear a decade ago with the discovery of a virus called Sputnik living within a giant, complex virus known as mamavirus. Within a cell, the virus hijacks the biological machinery it lacks and uses it to copy its genetic material. In the case of Sputnik, the virus competes with mamavirus for its metabolites. . The process can begin within a few hours of infection. Within days, they may be in all of a host鈥檚 cells.
Despite our preconceptions, the interactions between virus and host aren鈥檛 all one-sided: viruses can be beneficial as well as harmful. Take the fungus Pseudogymnoascus destructans, which causes a disease called white nose syndrome that has severely depleted bat populations in North America. , the fungus is more successful, producing spores in greater numbers. Humans benefit from some viruses too. A group called bacteriophages help keep us well by Researchers are starting to use these phages to treat bacterial infections. Viruses can even become an essential part of a host鈥檚 genetic code, providing genes required for survival.
A new field of study known as viral ecology is providing insights into the interactions between viruses and their hosts. It is a gargantuan task. Consider, for instance, the human microbiome: the vast array of microorganisms that live in and on every one of us. Our bodies contain hundreds of different cell types 鈥� including those that make up our complex immune systems and that constantly try to fight off alien organisms 鈥� all of which interact with the thousands or even millions of types of viruses and bacteria in our microbiome. Add the fact that these microbes can both help and compete with one another (see 鈥�The social life of viruses鈥�), and the number of possible interactions might as well be infinite.
Nevertheless, we are starting to see the bigger picture of viral ecology. A 2017 study offered the first map of virus-host networks covering all viral species known then. The authors looked at the and their movements between them (see 鈥�Viruses, viruses, everywhere鈥�). The study also revealed that most viruses have a surprisingly narrow range of habitats, infecting only one or two types of host. Another study from 2017 shed light on an enigmatic part of the virosphere, that infect a domain of single-celled organisms called archaea.
Myriad kinds
This is just the tip of the iceberg, however. We have long suspected that viruses are the most diverse group of organisms on Earth, but we still have only the vaguest idea of how many types there are. In the past two decades, more have been identified than ever before. Until 2003, we didn鈥檛 even know of the existence of , which have more than 1000 genes, compared with as few as 10 in tiny viruses. As of April last year, researchers had identified . That is nearly 20 times more than were known in 2015. Given that viruses tend to be specialised to just a few hosts, their diversity is likely to be .
The recent advances in our knowledge of viral diversity have been . This allows researchers to identify viral genes present in an environmental sample without having to isolate individual organisms. They literally scoop up seawater or soil and analyse it to see how much viral genetic material it contains. But there is a downside. 鈥淭he frustrating thing is that metagenomic data contain lots of unidentified sequences 鈥� what we call the 鈥榙ark matter鈥�,鈥� says Edward Holmes at the University of Sydney, Australia. Currently, it is difficult to work out what this dark matter actually is. Assigning genes to a particular species of virus is made even harder because of the incredible rate at which these organisms evolve. To properly analyse viruses, we need to be able to 鈥渟ee鈥� them, says Holmes. That will require looking at features beyond genetic sequences, such as the structure of virus proteins.
Another problem with mapping the virosphere is that researchers are unsure how to categorise viruses. At the moment, they use a system similar to the one used to classify all organisms, with categories ranging from kingdom (viriae) to genus and species. So far, fewer than 5000 viruses have been classified in this way. What鈥檚 more, there is a growing realisation that the current classification system has . There is a push to do something about this, though. In March, the International Committee on Taxonomy of Viruses called for classification of the entire virosphere. It acknowledges this is a massive undertaking, but argues that the potential benefits are huge. 鈥淲e cannot know what the trove of 鈥榰nimportant鈥� viruses could possibly amount to until we have examined them,鈥� it wrote in Nature. 鈥淰irus classification is a straightforward way to contribute today to solving the global problems of tomorrow.鈥�
That may sound grandiose, but it is justified. Viruses aren鈥檛 simply a threat to people鈥檚 health and livelihoods, they are also essential to life on Earth. What they offer, evolutionary biologists are starting to realise, is access to new genetic material that can help organisms adapt and survive. Viruses 鈥� as much as a million times faster than we do 鈥� giving them a constant supply of new genetic material. They can share these genes with their hosts in a process called horizontal gene transfer. Think of it as a trading game where players can swap cards to improve their deck. Two players will soon have both acquired the best possible combinations. But if they can swap with new players with rapidly changing decks (viruses), they can build a far more competitive hand.
Horizontal gene transfer with viruses doesn鈥檛 help individual people directly, as our genome is pretty much defined from conception. But gene swapping may help to explain the complexity of life on Earth: fast evolution, coupled with the ability to trade genes, allows simple organisms to quickly adapt to almost any environment. This was crucial for the earliest forms of life 鈥� and viruses may have played an important part in their success. So, learning more about the relationships between viruses, hosts and their environments should give us key insights into the evolution of life and even its origins.
In addition, can help us understand 鈥� and one day possibly even predict 鈥� the outcomes of interactions between viruses and their hosts. The benefits are clear when that host is us. One large-scale project, known as the , aims 鈥渢o detect the majority of our planet鈥檚 unknown viral threats鈥�, to predict which viruses are likely to jump hosts and infect and possibly kill us. That won鈥檛 be easy. 鈥淭he sequencing of a virus itself tells you nothing about the odds of its emerging in humans,鈥� say Holmes, who has expressed some doubts about the project. 鈥淟ots more needs to be done, including studies about how the viruses actually behave.鈥�
鈥淭here are over a million times more viruses on Earth than stars in the universe鈥�
Historically, our approach to virus research has been almost completely anthropocentric 鈥� focused primarily on viruses likely to harm our health or economic well-being. Now, virologists are arguing that . We should confront our biased view of viruses as being inherently dangerous, they argue. We need a greater understanding of what viruses actually are, where they come from and how they continue to affect every aspect of life on Earth.
Opening our eyes to this weird world will do everything from helping us to prevent disease to understanding life鈥檚 origins. It could even give us insights into how the natural world is likely to change in the future.
The social life of viruses
Viruses may be inert when outside their host but, once inside, their behaviour is surprisingly sophisticated. Two decades ago, researchers discovered that some send out signals that help them decide whether to compete or cooperate with one another in a of the prisoner鈥檚 dilemma game.
Recent discoveries reveal that this communication relies on tiny proteins called peptides to convey information. Such peptide-based signalling has been found in a variety of viruses, including those that cause flu, measles and polio. However, most of the research has been done in bacteriophages, a group of viruses that infect bacteria. They communicate to coordinate their behaviour, especially when they need to decide whether to attack or stay dormant. It turns out that different virus species have secret signals all of their own. They are also capable of eavesdropping on other viruses and on host species.
We could use these discoveries to our advantage 鈥� to fight diseases, for example. In fact, researchers at Princeton University have engineered viral assassins that can sense signals unique to other microbes, including E. coli and Salmonella, and then home in and destroy them. This suggests that we may one day be able to on demand. As antibiotic resistance increases worldwide, this could become a crucial .
