Where Do Viruses Come From?
This post was inspired by a paper published in late 2019 on how viruses shift ecosystems to Lamarckian selection - and how this behavior is indicative of their interstellar origins.
We’ve also got a COVID-related story on the mechanics of infection and illness here.
Panspermia is a theory that suggests life came from outer space in the form of bacteria and/or viruses. The theory suggests that they arrived on meteorites or as pieces of minute space dust, propelled through interstellar space by solar radiation. I like the theory, it tickles my poetic preference for some kind of interconnectedness of life in the universe. It also goes against prevailing theories of life originating in deep-sea vents on earth, and so engages my respect for scientific anarchism: a theory isn’t good because it’s old, a theory is good because it’s the best explanation we’ve got for all the phenomena we can observe. But I’ve been trained enough in the dangers of flights of scientific fancy, so I know that just thinking it’s a cool theory doesn’t necessarily make it a reputable or substantial theory. So, this week, I set out to figure out if there’s any good reason to believe that viruses can come from outer space.
The tl;dr is that maybe they do! Research suggests that viruses and bacteria could survive in space given the right conditions. It’s also become apparent in the last few decades that the genetic diversity of viruses is enormous - to the degree that viruses have little similarity to each other, let alone to any other living beings on earth. If we can imagine a mechanism by which viruses arise abiotically, then it’s possible that they do come from outer space, yes. But, is it likely that they come from outer space?
I can’t answer that question with certainty, since likely is a gambler’s game, but I can say that researching a reasonable answer to the question of “can viruses survive in space,” I found all kinds of fascinating details that make me realize that we’re still pretty far from scientific consensus on what viruses are and where they come from. In this post, I’m going to try and explain the following:
Is panspermia a reasonable theory?
What is a virus?
Is it alive?
Does it do anything useful?
Are they in outer space?
Is Panspermia Reasonable?
The idea of panspermia is that life came to earth from somewhere else. It’s been around since the time of the ancient Greeks, and seems like a reasonable theory. Presumably, there was a time in the earth’s history when the surface was sterile but amenable for life. If a meteorite, carrying some kind of dormant life form, crashed on the surface in just the right place, it could have released it’s biological payload on a planet with no competition.
If you’re a life form whose goal is ecological dominance, this hypothetical scenario is basically your dream come true. We’re all learning first hand the power of exponential growth right now - a single dormant organism that doubles, i.e. reproduces asexually every 24 hrs would be 1.23x10^30 organisms in 100 days. If the doubling rate is slower - say once every week - that same number of organisms could be reached in as little as two years.
Chart shows the amount of time it takes for an organism to make it through 100 generations, doubling each generation, as the time between doublings increases. When doubling takes 1 hr, in 100 hrs there are 10^30 organisms. When the doubling takes 1 year, it takes 100 years. Given that the earth is at least 4 billion years old, there’s ample time for a single organism to grown sufficiently dense to weather a sudden change in conditions.
Another aspect of panspermia that lends itself to life having arrived from somewhere else, is the fact that a lot of ancient bacterial lineages can produce spores, hardy little seeds that can withstand long periods of extreme conditions. A common ancestor expressing a given trait would account for many different organisms expressing a similar complex trait.
The theory that life came from somewhere else instead of starting up on Earth has been around for a long time. The term panspermia (greek for “it’s all seeds, baby”) was coined by the philosopher Anaxagoras in the 5th century BCE. In his view, there were seeds of life everywhere throughout the cosmos, and earth was the result of those seeds landing on a fertile planet. The theory was largely forgotten until the beginning of the 20th century, when there was a renewed interest in explaining where, exactly, did humans come from.
Since roughly the time of Anaxagoras, the church had maintained the doctrine of spontaneous generation - a very godly understanding that life could come from nothing. It was not good practice to speak out against fundamental doctrines of the church. Just ask Galileo. But the end of the 1800s was one of those rare times in history that the hold of the church appeared to loosen slightly. It was during one of those periods that Tyndall and Pasteur demonstrated sterility, and finally layed to rest the doctrine of spontaneous generation.
Shortly after Tyndall and Pasteur’s demonstration, Swedish chemist Svante Arrhenius publishes an article entitled The Distribution of Life in Space. Given the newfound understanding that it wasn’t possible for life to come from nothing, he made a radical proposal: radiopanspermia. He suggested that life is everywhere in the cosmos, and that planets are always shedding life into the interstellar medium. These shed lifeforms are usually bacteria and viruses that are blown out of the atmosphere by the action of the solar wind, and are carried through interstellar space by the radiation pressure from their resident sun. Sometimes, these pieces of life-dust encounter a rocky surface. Sometimes that rocky surface is a hospitable environment. In those cases, life blooms. In his understanding, life is not the exception - life is the rule, and we were just one of many habitable worlds.
Arrhenius was a busy man, and this was just one of his projects. He set up the Nobel Prize committee, was awarded a Nobel in Chemistry, and The Distribution of Life in Space gathered dust on a library shelf until almost 80 years later.
In 1986, astronomer Fred Hoyle and his graduate student Chandra Wickramasinghe were working on calculating the refractive index of interstellar grains - the dust between stars. They suggest at first the grains are made of carbon, but that’s too refractive for what they observe. They suggest water in the form of ice, but that, too is too refractive. They put the problem aside for some years, and then in a flash of inspiration propose that polysaccharides have the exact right refraction, and are the answer to their difficult riddle. They publish their idea, satisfied with their clever conclusion, and almost no one likes it or agrees. I get the sense, reading Wickramasinghe’s papers since Hoyle’s death, that the argument that life is cosmic is a lonely, difficult road.
One reason that their proposal seemed so absurd in 1986, was that the first exoplanet wasn’t observed until 1988, two years later. Although exitence of expolanets was hypothesized, when they proposed interstellar grains of biological origin, there wasn’t yet another planet in the entire universe the grains could have possibly come from. In the years since, the search for extraterrestrial life has gained more mainstream recognition. 4,000 confirmed exoplanets and thousands more waiting in the wings has softened scientists to the possibility that, perhaps, we aren’t alone.
Number of exoplanets found per year. Something clearly happened in 2014 and 2016! Sourced from here.
Other technical advancements, like DNA sequencing, have gradually pushed back the margin of our ignorance about life, and have shown us just how complicated it gets when you try to trace all the way back to the first organism. Phylogeneticists, the people that uncover evolutionary relationships between species can only do their jobs part of the way with bacteria. At some point, they get to a place where the lines between different microorganisms loosen, blur, and then vanish altogether.
A humorous but also dead serious illustration of the confusing free-for all at the tree of life. Borrowed from Doolittle, 1999
Normally, species and lineages can be traced by similarity on the DNA level. But when you get down to bacteria, the creatures at the very bottom of the tree of life, remnants of the primordial soup that gave rise to current biodiversity…. things get squiggly.
For starters bacteria reproduce asexually. Freed from the stifling confines of chromosome pairing and shuffling, bacteria simply replicate. They get to a certain point in their lives, biological instinct kicks in. They make a second copy of everything, make another bacterium’s worth of cell membrane, and then wall off the space between them. Where there was one, now are two.
This sort of reproduction can only produce an identical copy, since there is no mixing of the genetic material of two different organisms. It’s essentially self-cloning. It’s a perfectly fine reproductive strategy, but comes with a unique challenge. How do you prevent being totally overwhelmed with mutations within a few dozen generations? That’s where horizontal gene transfer comes in.
Horizontal Gene Transfer
Bacteria have a mechanism that prevents the accumulation of mutations, and it’s called horizontal gene transfer. Unlike creatures that reproduce sexually that only exchange genetic material during that one event, bacteria are constantly exchanging genetic material. Most species have one or more plasmids - small structures that contain useful tools encoded in the DNA. These plasmids are mobile, meaning they can be copied and exchanged between completely unrelated individuals, even across species.
They are exchanged either through direct contact between two bacteria - or because a bacterium absorbs an intact plasmid from the environment. Both of these strategies are so widespread that they’re standard tools in any molecular biologist’s toolkit. They’re also so widespread that they’re responsible for the squiggliness at the root of the tree up there.
Except you know what’s weird? Although the absolute diversity of prokaryotes is widely held to be unknown and unknowable at any scale, most new genetic information we find in bacteria is similar to genetic information we’ve seen elsewhere. It’s a comforting reminder that, although large-grain diversity is uncountably large, most genes in diverse bacteria have sequence-based similarity. But when you sequence a sample of mixed viruses, most of that genetic information has never been seen before, anywhere.
Viruses all the way down
There was a lot of press a few weeks ago about a new virus discovered and sequenced in Brazil, yaravirus. It’s genetic sequence showed very little similarity to any other known viruses - about 90% of the yaravirus sequence had never been seen before. The news flitted across my attention span, triggered huh, that’s weird, and then flitted out of view. Then COVID-19 occupied almost all of my free thoughts, and then there was the panic buying and now almost two months later I’m sitting in the garden at the cat farm, getting a little bit of sun for the first time in three months and Yaravirus is on my mind again.
How is it possible that the majority of the genetic information of an organism is not shared with any other organisms on the planet? I figured it was a misleading popsci headline - but when I read further, what I found out was even more surprising - it turns out that MOST viruses carry genetic information that doesn’t match anything else we’ve ever sequenced. Every time a scientist goes out in search of new viruses, they come back with a pile of information that implies the end of variety is still out of sight. That sort of diversity contradicts everything I know about living beings, and left me with more questions than answers.
A review on the astounding richness of viral genomes was published in 2005. Edwards and Roher confirm the diversity of viral genetic information, and make an interesting comparison:
most of the viral sequences are still unique, despite the fact that the GenBank database has since more than doubled in size. Likewise, 68% of the sequences in the newly published equine faecal metagenome have no similarity to any sequence in GenBank. Genomic analyses of cultured PHAGES also show that most of the OPEN READING FRAMES (ORFs) are novel. By contrast, only about 10% of the sequences from environmental microbial metagenomes and cultured microbial genomes are novel when analysed in similar ways
But 2005 is a long time ago. Perhaps things have changed? Here’s an update from 2013, taken from a lecture by Chris Suttle:
we used high-throughput sequencing and metagenomic analyses to examine 56 viral communities from the Arctic Ocean, 85 from the Pacific, 45 from the Gulf of Mexico, and 1 from the Atlantic near Bermuda. Remarkably, about 95% of the DNA sequences had no obvious homologs in any database, meaning that the functions of the proteins that these sequences code for cannot be inferred. Even now, with longer sequences and much larger databases for comparison, about 70% to 80% of the coding sequences from natural marine viral communities do not have obvious homologs. …Clearly, the genetic diversity in viruses is enormous and largely unknown.
I’ve always heard that there’s a debate about wether or not viruses are alive, but this sort of information makes that question seem like it’s avoiding a far more fundamental question - how is it that are two completely separate bins of genetic information on earth?
What is a virus?
The answer to this question has to be operational - since there isn’t a single genetic element shared by all viruses. Related groups of viruses share genetic elements - but once you wander outside of that tightly clustered group, there’s insufficient overlap that allows for the kind of relational map we see in the tree of life. From a 2018 paper Astrovirology: Viruses at Large in the Universe
The original virus definition was practical: a disease-causing particle that passed through a filter that retains all known bacteria ‘‘contagium vivum fluidum’’ (contagious living fluid) (Beijerinck, 1898). The standard definition of viruses for many decades thereafter was ‘‘a very small disease-causing agent.’’ Later, there were debates whether they were infectious liquid or particles, but the development of the electron microscope in the 1930s revealed that all viruses were found to have an inert extracellular particle state, the virion. Virions consist of a protein shell (also known as a capsid) that packages the viral genomic nucleic acid, which can be composed of DNA or RNA. In addition, some viruses can have a lipid-containing outer layer, called an envelope. Sir Peter Medawar, Nobel laureate and pioneering immunologist, is said to have called viruses ‘‘a piece of bad news wrapped up in a protein.’’ All viruses must transfer their genome inside a host cell and reprogram that cell to produce more virus. This discovery led to the expansion of the standard virus definition to ‘‘a very small obligate intracellular parasite’’ (Acheson, 2011). However, as discussed below, other than ‘‘obligate intracellular’’ this definition is incomplete. A more inclusive definition of viruses, that we prefer, was proposed by Salvador Luria and coauthors: ‘‘Viruses are entities whose genomes are elements of nucleic acid that replicate inside living cells using the cellular synthetic machinery and causing the synthesis of specialized elements that can transfer the viral genome to other cells’’
From left to right, HIV, Influenza, and Zika. Each virus is surrounded by a structure made of repetitive subunits. This is the capsid, a structure that is unique to viruses. Images by D. Goodsell
Another functional definition is that viruses can be defined as capsid-encoding organisms that transform [ribosome-encoding organisms] into a viral factory. Capsids are geometric shells made from repetitive protein arrangements that protect the viral genome. Sometimes they’re surrounded by a lipid membrane derived from the host cell that made them, other times they’re bare, only studded with the proteins necessary for docking onto the next cell.
Ribosomes on the other hand, are large structures inside of living cells that produce proteins from RNA. It’s this distinction, capsid production vs ribosome production, that highlights why many consider viruses not to be alive. A virus without a host cell to replicate in is nothing but a piece of dead information. It’s like a 3 1/2” floppy in 2020 - basically useless, totally harmless. In the presence of a host cell, however, viruses become much more menacing.
From the Scripps Institute: A cross-section of a small portion of an Escherichia coli cell. The cell wall, with two concentric membranes studded with transmembrane proteins, is shown in green. A large flagellar motor crosses the entire wall, turning the flagellum that extends upwards from the surface. The cytoplasmic area is colored blue and purple. The large purple molecules are ribosomes and the small, L-shaped maroon molecules are tRNA, and the white strands are mRNA. Enzymes are shown in blue. The nucleoid region is shown in yellow and orange, with the long DNA circle shown in yellow, wrapped around HU protein (bacterial nucleosomes). In the center of the nucleoid region shown here, you might find a replication fork, with DNA polymerase (in red-orange) replicating new DNA.
After gaining entry into the cell (understanding the mechanics of which requires a PhD unto itself..), viral proteins translate the viral genome into a language that can be read by the ribosome. Expression of host genes is suspended, and the entire cell becomes a factory for producing more viruses. Once the program is fulfilled, the cell lyses, and the newly minted viruses go on to repeat the process.
This behavior is what leads to the debate about whether or not viruses are alive. They fulfill some basic functions of life, but they always need a host cell that allows them to do so. There are other parasitic organisms that require a host to complete their life cycle, but none that have as few essential functions as viruses. There’s even a strange cnidarian parasite of salmon which is the only animal discovered to date that doesn’t need oxygen to breathe - but without a breathing apparatus, it still codes for far more functions than a virus does.
What are all these viruses doing?
The world we live in is covered in viruses. They’re so numerous in seawater that one paper referred to the ocean as “virus soup,” which in addition to being disgusting, raises the question - what are they doing?
The most obvious answer is that they’re providing a vast quantity of nutrients for the bottom of the food chain in every ecosystem on earth. When they attack and destroy their host cells, the contents of the targeted cells spill out into the environment. The kind of nutrient content their activity provides is, by definition, formative for the biological abundance.
In addition to nutrient content, all that unique genetic information we talked about earlier also comes in handy. The sheer amount of viruses present in the environment, and the sheer amount of genetic diversity in them, means that viruses contain the greatest reservoir of genetic information in the world. People frequently wonder where new genes come from - and the answer is they most likely come from viruses.
This sort of genetic exchange has already been recorded. Some strains of E. coli contain enormous sections in their genomes that came directly from viruses. These so-called “prophages” account for 16% of some E. Coli DNA sequences. The integrated viral DNA has various functions. Some excerpts from Start-up entities in the origin of new genes
… in Pseudomonas aeruginosa, genes encoding the tail of two different bacteriophages have been converted into bacteriocins used by the bacteria to kill its competitors
In eukaryotes, it also seems that transposable elements have served as substrates for new genes: in Drosophila, the extension of chromosome ends involves proteins similar to those encoded by two long interdispersed element (LINE)-like retrotransposons, TART (telomere-associated retrotransposon) and HeT-A, suggesting that, in the fly lineage, genes from transposable elements have assumed the function usually achieved by telomerases
Recently, Mallet et al. have reported that a gene from a human endogenous retrovirus, which is restricted to the hominoid lineage has taken on an active role in formation of the human placenta, possibly by favoring cell fusion
Where did they come from?
It is apparent that viruses play an instrumental role in biology, but it’s less clear where they came from. There are three different opinions, which can be classified as:
Virus first
Reductive virus
Escaped genes
Virus first suggests that viruses were here before any other kind of life, that they arrived on a barren but chemically rich planet. It doesn’t really account for the fact that viruses need someone else’s workbench in order to make more of themselves. Given their tendency to fall apart when outside of cells for too long, there’s too many different things that aren’t likely..
The reductive virus theory suggests that viruses were more complex organisms that were whittled down over time to just be these informational packets.
Escaped genes suggests that the genetic contents of viruses are “self aware” entities that escaped from known organisms in order to make a go of it themselves.
Proponents of this theory consider viruses to be inevitable outcomes of a genetic system - parasites that arise to take advantage of machinery without having to pay the cost of producing it. And the reason that they’re still around is because “the unescapable cost of maintaining sufficiently powerful defense systems.”
Others simply sidestep the question of where they came from and if they’re alive or not, and call them an illustration of the replicator paradigm - a paradigm that contains the whole collection of self-replicating oddities found in cells. Transposons, plasmids, even chromosomes and organelles all copy themselves and move between cells. Sure, we make a distinction that their movement is part of a “normal” process - but, perhaps, so is viral movement.
None of these theories, though, account for the astounding genetic diversity of viruses. If viruses originate from the cells that they interact with, one would expect there to be significant genetic overlap between the host and the parasite. However, that just simply isn’t the case. Viruses show almost the exact opposite - as far as we can tell, there’s no end to their diversity. It’s almost like new ones are being added as quickly as old ones degrade and disappear.
Okay Doc, Be Straight With Me. Are Viruses From Outer Space?
We’re almost there, hang in there. A brief recap of what has been shown about viruses:
There’s a seeming endless supply of them
They outnumber all other life forms on earth
They’re entirely dissimilar from each other
They’re entirely dissimilar from all other forms of life
No genetic sequence appears in all viruses
Bacterial and human DNA contains large sections of inactivated viral DNA
Bacteria re-appropriate viral genes for other necessary functions
All of these facts together suggest that viruses are the raw material from which living creatures build their genetic material. They’re like bricks in a building, and cellular processes the mortar that holds it all together. If that’s the case, you’d expect to end up with enormous viruses, ones that rival the structural complexity of the simplest bacteria…
And, in fact, that’s exactly what you see - viruses like the Pandoravius, and the megaviridae, and tupanvirus have enormous genomes, rivaling the complexity of their bacterial counterparts. The only pieces they’re still missing before they get classified along with the rest of the bacterial oddities on the tree of life? The ability to produce their own proteins. Once they acquire the software necessary for that, or accidentally envelop a compatible ribosomal protein factory, the transition would happen spontaneously.
Three giant viruses - Pandoravirus, Tupanvirus, and Megavirus. Bacterium on the small end (2 um) and a big bacterium (200 um) is shown for comparis. Tupanvirus is about 1.2 um tall.
The sheer number and virus types in the environment suggests a constant influx of new genetic material. What if the novel genetic material isn’t coming from bacteria, archea, and eukaryota - what if it’s the result of an abiotic process? I know we haven’t had much luck reproducing de novo amino acid synthesis in the laboratory, but experimental failures don’t always translate to impossibility.
If genetic information is constantly being synthesized in the form of free-floating nucleic acids, and if one of these free-floating nucleic acids can form a shell made from a small polypeptide that’s freely available in the environment, then you would expect to find viruses absolutely anywhere in the cosmos that has the right conditions for spontaneous assembly of nucleic acids.
However, this is a big, fat, IF.
It totally depends on whether or not it’s possible for nucleic acids and polypeptides to be synthesized without a living cell there to make them.
If that’s the case, it’s possible that the absolute simplest viruses, ones who consist of genetic information encased in a capsid made from a single repeating subunit, could be abiotic products of the cosmos. If that’s the case, we would expect to still find viruses as you got further and further away from the surface of the Earth. What’s the data say?
Ghosts in the Atmosphere
To start with, I stumbled on a small, correlative analysis published by Hoyle and Wickramasinghe as a Letter to Nature magazine. In it, they show a repetitive correlation between influenza outbreaks and increased solar activity.
Reading it, I wasn’t sure what was more odd, that influenza appeared to correlate to sunspot activity, or that Nature published the proposal in the first place. In the letter, they posit that the increased radiation pressure from the solar wind during sunspot activity drove viruses down onto earth from the upper atmosphere. This seems like a reasonably simple claim to evaluate. If there’s a flow of viruses from space onto the surface of the earth, you would expect them to be detectable at all levels of the atmosphere, including in near-earth orbit at the ISS.
Heading outwards from the Earth’s surface, we find that while measurements vary wildly (3-25%), scientists are in agreement that some significant fraction of the atmosphere is actually biomass.
There’s viruses in the troposphere, the layer of the atmosphere that’s closest to the surface:
We quantified the wet and dry deposition of (free and attached) viruses and bacteria above the atmospheric boundary layer at the Observatory (OSN) and Veleta Peak (VSN) in Spain, and demonstrated that in each square meter, tens of millions of bacteria and billions of viruses are deposited each day.
As you rise farther away from the surface of the earth, this remains the case: 20km above the Atlantic Ocean, aerobiologists found earthbound microbes and fungi.
As far back as the 1970s, there have been suggestions that there are microbes at 70 km above the surface, well into the region that is called near space:
“By using meterological rockets fitted with specially designed analyzers, samples for microbiological investigation have been taken. The analyzer design prevented extraneous microorganisms from penetrating into the analyzer. Before being used, the analyzers were sterilized with high gamma-ray doses. For the first time microorganisms have been detected in the mesosphere at an altitude of 48 to 77 km. The microorganisms are microscopic fungi having black conidia or spores (Circinella muscae, Aspergillus niger, Papulaspora anomala) and one species forming green conidia (Penicillium notatum). Colonies of Mycobacterium luteum and Micrococcus albus have also grown. Five of the six species have synthesized pigments. The presence of pigmented microbial forms leads us to believe that natural selection is occurring in the mesosphere because cells possessing chromogenous pigments (carotenoids, melanins) are more resistant to ultraviolet-ray action. A greater number of microorganisms have been registered in the mesosphere during dust storms than in the absence of strong winds.
An obvious shortcoming of these studies is that there just aren’t that many of them. Extraordinary claims require extraordinary evidence, and this doesn’t really reach that bar. Tantalizing, sure. Interesting? Definitely. But not extraordinary. There’s just too many things that can go wrong in an experiment, and too much of a desire to be the first one to report on something incredible. As a scientist, until many independent investigators observe the same effect, I have to assume that it’s just a fluke. One worth investigating, but not a definitive answer.
What’s reassuring to those of us who want an answer to the question are viruses from space, is that people are working on it. The Tanpopo mission collected data for three years at the ISS, but hasn’t released much data. But people the 2018 paper, Astrovirology: Viruses at large in the Universe, makes sure the folks looking keep asking the question:
Given the extremely large numbers of viral particles in Earth’s oceans, it would be very interesting to determine if there are virions in recently observed water plumes from Europa (Sparks et al., 2016) and previously observed plumes from Enceladus (Hansen et al., 2008). Unfortunately, to our knowledge, no mission is currently planned that will screen for extraterrestrial viral particles in these plumes.
The Search for Viruses in Outer Space Continues
Every now and then, there’s a piece of data that implies a cosmic source of organic materials. Amino acids, sugars, even proteins have been found in meteorites that make it to earth. There could be viruses out there, but that might not necessarily be a sign of life - more a sign that our understanding of how life came to be needs some updating.
Thoughts I had during research that didn’t make the cut I couldn’t fit in anywhere:
https://en.wikipedia.org/wiki/Crookes_radiometer
learned this wasn’t due to radiation pressure but has a black body radiation explanation
https://en.wikipedia.org/wiki/Svante_Arrhenius#Nobel_Prizes
I kept saying the guy had a nobel prize in Chemistry but apparently he was involved in putting together the committee in the first place and was a total jerk
https://en.wikipedia.org/wiki/Spontaneous_generation#Pasteur_and_Tyndall
still working on how to tell this story better. I know there’s a much longer process than sudden reversal on spontaneous generation but don’t know the details.
https://www.tandfonline.com/doi/full/10.1080/19490976.2019.1701353
mechanism by which food induces remodeling of the gut microbiome - different foods make different viruses come alive
https://pubmed.ncbi.nlm.nih.gov/11540166/
There’s pretty detailed models of conditions necessary for panspermia
