Huge Viruses Are Shaking Up The Tree of Life
Pandoraviruses are challenging some long-held biological beliefs. These newly-discovered beasts are larger, in size and in genetic complexity, than any other virus that we know of (details on the graphic are below). They are not as doom-worthy as their name implies, but they may have opened a box full of new biological forms that will challenge what we think of when we say “alive” or “virus”. For the scientific low-down on pandoraviruses, check out this great article by Carl Zimmer.
Giant viruses of all kinds seem to be more common than we’ve ever imagined. It makes sense, in a way. Just like there is not a clear transition point between any two species, the complexity of life should also exist on a continuum from the small (bacterial viruses) to the complex (us). So maybe these little guys aren’t so surprising after all?
I drew up a little graphic (above) to show just how large and complex pandoraviruses are compared to other life forms.
- Pandoraviruses are huge. A human egg cell is about 100 millionths of a meter across. An E. coli is about 50 times smaller. But pandoraviruses (which dwarf flu viruses) are nearly as big as the bacterium!
- The area of the circles show how many genes each type of cell contains. The human genome has about 20,000 genes, while E. coli has about 4,500. Compared to a measly 13 genes in the flu virus, pandoraviruses have about 2,500!, almost none of which seem to be related to known genes.
- The size of the genome, in bases, is where it gets weird. The human egg’s genome, at 3 billion bases, dwarfs them all. E. coli and pandoraviruses have around 4 and 2 million, respectively. And there’s a tiny little single pixel in there representing the 13,588 letters of the influenza genome.
I can’t wait to see what other kinds of life/not life we find inside this Pandora’s box.
Is This the Future of Flu Vaccines?
See that picture up above? You’re looking at one of the most advanced weapons (to fight a microscopic enemy) the human race has ever created. It’s a nanoparticle (in gray) coated with synthetically produced coat proteins (HA, to be precise) from the influenza virus. Normally, flu mashes its coat proteins together like so:
The nanoparticles may be a major step toward a universal vaccine, which, of course, would be an awesome thing to have, save millions of lives, help us prevent a mass pandemic, etc.
Because flu viruses mutate, shuffle and swap their genes so frequently, the precise shape of the proteins that make up their spiky suit of armor is constantly being tweaked. It’s like how, from afar, a Sarahan sand dune might appear the same shape and height from day to day, but when you look closely, the precise contours of its windswept dimpled have been changed ever so slightly by erosion. On and on it changes, never the same twice.
Our immune system relies on sentry proteins called antibodies in order to recognize foreign invaders like flu based on their binding to those precise contours and shapes, like tiny chinks in the armor. The exact set of antibodies that killed last year’s flu are stored in your immune system’s memory, ready to keep you safe from that infection in the future. Because the flu virus shuffles and tweaks its shape from year to year, we are constantly playing catch-up, reacting to new armor every year. It’s like going home to find the lock changed, every day having to cut a new key.
If we could just make antibodies that bind to an unchanging part of the viral protein, like the trunks of those blue protein trees up there, we might be able to defend ourselves from future mutants with a single vaccination. But the virus keeps those parts hidden just enough to keep otherwise universal antibodies from attacking it.
That’s where this new research from Gary Nabel and his group might come in handy. By attaching the HA coat protein (again, the blue thing) from influenza to nanoparticles, their Achilles Heel is exposed and strong, universal antibodies are amplified and stored in your body’s defense bank. They built this nanoparticle vaccine from a 1999 strain’s HA protein, and it protected animals from a half-century’s worth of H1N1 viruses! It’s as close to universal as I’ve ever heard.
Point: humans. But, these are tricky bugs, and we shouldn’t get cocky, especially without human trials (yet). But we have brains, and they don’t. That’s really our best weapon, no?
The vermin only teaze and pinch
Their foes superior by an inch.
So, naturalists observe, a flea
Has smaller fleas that on him prey;
And these have smaller still to bite ‘em,
And so proceed ad infinitum.
What’s the most common living thing on Earth? A smart guess would be to start with bacteria, which make up over half of all biomass on Earth (you did watch that episode of my YouTube show, right?). And since the oceans cover considerably more than half the planet, a marine bacterium would also make sense.
Until very recently, almost everyone with an opinion on these things would agree. See that bacterium in the electron microscope image above? It’s called Pelagibacter ubique, an ocean-dwelling microbe whose family of relatives make up a stunning one-third of aquatic life forms (by sheer numbers). Why so numerous? One popular theory was that because they are immune to infection by bacterial viruses, they could grow unchecked.
Thanks to some creative science, that theory now appears dead wrong (here’s the paper in Nature). By diluting seawater over and over (that is what grad students are for), Stephen Giovannoni’s team was able to isolate single ocean viruses, most of which had never been identified before. Then they stuck them in with P. ubique and waited. Amazingly, some of the viruses could infect this previously uninfectable bacterium! Those little blobs in the image above are actually viruses ready to burst out of their unfortunate little host.
They sequenced the DNA of those viruses, when back to the ocean, and found that one of them, with the unremarkable name “HTVC010P”, is … well, basically everywhere.
This “smaller flea”, which itself feeds upon something so mind-bogglingly numerous, is now our best candidate for “The World’s Most Abundant Thingy”.
Whether or not it’s a life form? I’ll leave that up to you …
Episode Extra: Life By The Numbers
How do we know how many viruses there are in the ocean?
(This post helps explain some of the science in the latest episode of my show. It’s impossible to get all the details into a few minutes. Watch the episode here if you haven’t already. Seriously. Watch it, already!)
A lot of people seem pretty blown away by one of the numbers I presented in the video, that all the viruses in the ocean, laid end-to-end, would stretch 100 times the diameter of the Milky Way. Here’s where that number comes from:
Curtis Suttle is a biologist at the University of British Columbia who studies marine viruses. In a 2005 Nature paper, he explained how quickly our knowledge of viruses in the seas is growing and how much impact they have on the marine biosphere. First, the math:
After spending years counting (yes, counting) viruses in different parts of the ocean, Suttle determined that any liter of seawater contains about 3 billion viruses (3x109). There’s more near the surface, and fewer deep down (even viruses 100 meters below the seabed!), but that’s an average. These include viruses from many different families, although distant oceans can house viruses with nearly identical genes. This means that the ocean’s viruses are constantly swapping and trading genetic material. Think about what that means for how they drive evolution in marine environments!
Marine biologists have estimated (ESTIMATED) that the oceans hold about 1.3x1021 liters of seawater. Good luck reconciling that number in your head. It’s kind of impossible. Do the math and you get 4x1030 viruses, also a rather ridiculous number. Viruses vary in size quite a bit, but using an average of 100 nanometers, that means they would span 10 million light years. One light year is almost 6 trillion miles, so you can see where this is going … express train to silly-ville. The Milky Way is about 100,000 light years across, so that’s where the number comes from.
Even more interesting is the weight of viruses in the ocean. Ecologists often measure biomass in carbon, because it’s important how much of these building blocks of organic life a particular piece of life (or dead stuff) contains. When something containing a lot of carbon dies, that carbon has to be recycled somewhere. Things that are made of a lot of carbon have to eat a lot of carbon. See what I mean?
The average virus contains about 0.2 femtograms of carbon, which isn’t much by itself. But all of them together contain 200 megatons of carbon, which is the same amount of carbon in 75 million blue whales.
Why is that important? I mean, you can’t picture what 75 million blue whales look like, right? But maybe you can imagine the impact 75 million blue whales could have on the ocean ecosystem. It would be significant to say the least. That’s why it’s important to understand how even the smallest units of the biosphere can really throw their weight around when viewed as a whole.
Does this mean viruses are a successful species? What do you think?
Why Does Flu Always Peak In The Winter?
Is it because we spend more time huddled indoors? Is it because the shorter days cause us to produce less immune system-stimulating vitamin D? Maybe even changes in atmospheric air currents? Or is it because the flu virus just survives better in winter air than in summer air?
Popular Science has put together an illustrated explainer about that last theory. Check it out at the link. It turns out that flu particles do travel better in lower humidity air (perhaps the “sneeze droplets” float longer) and that the particles themselves survive longer in drier air (they don’t degrade and can infect better).
Maybe this is why the “swine flu” epidemic of 2009 wasn’t as bad as feared, because it peaked in warm, humid months in the Northern Hemisphere? Hmm …
Fighting the Viral Wars
How are our body’s hidden viruses like little green army men? Well, they aren’t really. They’re much smaller. But we can use them to learn something about how certain viruses evade our immune system. Meet Dr. Chris Sullivan, virologist at the University of Texas at Austin*.
This video tells the story of herpes simplex virus, a virus that currently infects ~60% of Americans and is the cause of cold sores around the mouth and nose. That’s true for type 1, anyway. HSV type 2 infects … well, somewhere else. Although it “pops up” using a similar principle to the one you’re about to learn about.
When viruses are out in the open, with infected cells sending viral particles on the search for a way to infect new cells or make their way to a new host, they are at their most vulnerable. This is when the immune system can recognize them as foreign and sound the alarm. Viruses like herpes instead spend most of their time in something called “latency”. They lie in hibernation, inside of certain cells way back at the root of a nerve bundle. Only when they sense stress do they wake up and prepare for battle.
This brief flurry of activity results in a scout team of viruses being sent along that nerve bundle (the green army men marching to the Lego tower) until they reach the cells of the mouth and nose. There, the immune system kicks into high gear, forming a sore and causing virus particles to be shed off as the skin is enflamed and exposed. This is precisely why cold sores come in times of stress, and why they spread by physical contact.
Your body eventually fights the viral army men back to their safe, hidden base of “latency”. But the original army is never eliminated, lying in wait like an invisible Trojan horse, waiting for the next trigger of stress to start the cycle again. Hence, no “cure” for herpes infections.
Labs like Dr. Sullivan’s are trying to come up with ways to target that “latent” viral Trojan horse, and instead of just silencing those infections, getting rid of them once and for all. Even the most careful criminal leaves a trace of their crime. Viral detectives like these just need to sniff it out. After they’re done playing with their toys, of course.
*Full disclosure: I am also at UT-Austin and have had beers with Dr. Sullivan several times, which isn’t really important, just to say that it doesn’t surprise me that he’s playing with toys. Awesome video by Dan Oppenheimer and the UT CNS team.
Norovirus: The Human Pathogen That Turns Your Digestive System Into A Two-Way Firehose of Infection
Behold the humble norovirus. The humbly evil norovirus, one of the most perfect human pathogens. To be fair, viruses can’t be evil or not evil, they just want to reproduce. And how that happens to make their hosts feel is none of their concern. Noroviruses are masters of replication and infection, and they wreak havoc on the human digestive system in order to to their bidding.
That’s right. You know where this is going. Carl Zimmer reports, disgustingly:
Noroviruses come roaring out of the infected cells in vast numbers. And then they come roaring out of the body. Within a day of infection, noroviruses have rewired our digestive system so that stuff comes flying out from both ends.
How can a virus with just nine protein-coding genes do so much damage to a creature (us) with 20,000? Over a million people have come down with norovirus vomitorrhea in just the UK this winter.
These wee beasties replicate in the digestive system, waiting for you to “eject” them out of one end of your body. People who come in contact with the remnants of that “ejection”, even after cleaning, on planes or other crowded places, can be infected at alarming rates. Chances are it’s happened to you at some point in your life and you just called it a “stomach bug”.
Such a simple biological entity, refined by centuries upon centuries of molecular evolution, to exploit the digestive system of one class of mammals, reproducing in the safe warm home of our gut, and getting a free bi-directional rocket ride to their next host. Viruses never cease to amaze. And sometimes disgust.
Check out more on this virus from Carl Zimmer at Phenomena: The Loom.
Source: National Geographic
Bamboo and pasta reimagined as viruses and bacteria, by Sinead Foley.
You can go ahead and thank Carl Zimmer in advance for the hours of sleep you’re about to lose.
As part of his role as the internet’s cataloguer for all that is tiny, invisible and mildly terrifying, he stumbled upon a study that counted the number of viruses and bacteria in a cubic meter of air. Ready for this?
- It contains between 860,000 and 11 million bacteria.
- It contains between 1.6 million and 40 million viruses.
- In each minute of breathing, you intake several hundred thousand viruses, and who knows how many bacteria.
Of course, without viruses, and the genes they have donated to us, mammals couldn’t be born. And the number we breathe is nothing compared to how many are in the ocean (light years’ worth!!). I guess there’s a silver lining … most of them can’t infect humans? If you need me, I’ll be in my Contagion bubble.
So, uh … how long can you hold your breath?