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Why do viruses often come from bats? A discussion with your friendly neighborhood virologist

Hello /Science! I’m _Shibboleth_ and I’m a Virologist/Immunologist.
The 4.5 years I spent getting a PhD were dedicated to studying antibody responses against emerging viruses like Ebola and Marburg. So you can imagine how much time I’ve spent thinking about bats.
Here’s some answers about why they always seem to be the culprit when it comes to outbreaks.

Q: Why is it always bats? (that harbor dangerous viruses that spill over into humans)

A: It's complicated.

TL;DR - Bats are a perfect storm of: genetic proximity to humans (as fellow mammals), keystone species interacting with many others in the environment (including via respiratory secretions and blood-transmission), great immune systems for spreading dangerous viruses, flight, social structure, hibernation, etc.
You may not be fully aware, but unless your head has been stuffed in the sand, you've probably heard, at some point, that X virus "lives in bats." It's been said about: Rabies, Hendra/Nipah, Ebola, Chikungunya, Rift Valley Fever, St. Louis Encephalitis, and yes, SARS, MERS, and, now probably SARS-CoV-2 (with the addition of another intermediate species?)
Bats really do harbor more viruses than other species groups!
But why? Why is it always bats? The answer lies in the unique niche bats fill in our ecosystem.
I made dis

Bats are not that far off from humans genetically speaking

They're placental mammals that give birth to live young, that are about as related to us (distance-wise) as dogs. Which means ~84% of our genomes are identical to bat genomes. Just slightly less related to us than, say, mice or rats (~85%).
(this estimate is based upon associations in phylogeny. Yes I know bats are a huge group, but it's useful to estimate at this level right now.)
Why does this matter? Well, genetic relatedness isn't just a fun fancy % number. It also means that all the proteins on the surface of our cells are similar as well.
For example, SARS-CoV-2 is thought to enter our cells using the ACE2 receptor (which is a lil protein that plays a role in regulating blood pressure on the outside of cells in our lungs, arteries, heart, kidney, and intestines). The ACE2 between humans and bats is about 80.5% similar (this link is to a paper using bat ACE2 to figure out viral entry. I just plugged the bat ACE2 and human ACE2 into protein blast to get that 80.5% number).
To give you an idea of what that means for a virus that's crossing species barriers, CD4 (the protein HIV uses to get into T cells) is about 98% similar between chimpanzees and humans. HIV likely had a much easier time than SARS-CoV-2 of jumping onto our ship, but SARS-CoV-2 also has a trick up its sleeve: an extremely promiscuous viral entry protein.
These viruses use their entry protein and bind to the target receptor to enter cells. The more similar the target protein is between species, the easier it will be for viruses to jump ship from their former hosts and join us on a not-so-fun adventure.
Another aspect of this is that there are just so many dang bats. There are roughly 1,300 bat species making up 20-25% of all mammals. So the chances of getting a virus from a bat? Pretty good from the get go. If you had to pick a mammalian species at random, there's a pretty good chance it's gonna be a rodent or a bat.
From: http://palaeos.com/vertebrates/eutheria/eutheria2.html (https://i.imgur.com/kRoRSMU.png)

Bats are in a perfect place to serve as a nexus connecting a bunch of different species together and transmitting viruses

Various bat species do all or some of:
All of this means two things:
  1. bats are getting and giving viruses from all of these different activities. Every time they drink the blood of another animal or eat a mosquito that has done the same, they get some of that species' viruses. And when they urinate on fruit that we eat, or if we directly eat bats, we get those viruses as well.
  2. Bats are, like it or not, an extremely crucial part of the ecosystem that cannot be eliminated. So their viruses are also here to stay. The best thing we can do is pass laws that make it illegal to eat, farm, and sell bats and other wild zoonotic animals, so that we can reduce our risk of contracting their viruses. We can also pass laws protecting their ecological niche, so that they stay in the forest, and we stay in the city!
From: https://journals.sagepub.com/doi/10.1177/1010539512471965 (https://i.imgur.com/YeO2R5F.jpg)

The bat immune system is well tuned to fight and harbor viruses

Their immune systems are actually hyper-reactive, getting rid of viruses from their own cells extremely well. This is probably an adaptation that results from the second point: if you encounter a ton of different viruses, then you also have to avoid getting sick yourself.
This sounds counter-intuitive, right? Why would an animal with an extremely good immune system be a good vector to give us (and other animals) its viruses?
Well, the theory goes that bats act as a sort of "training school" where viruses are educated against robust mammalian immune responses, and learn to adapt and control the usual mechanisms that mammalian cells use to fight back.
The second aspect of this is that bat immune systems* allow for background replication of viruses at a low level, all the time, as a strategy to prevent symptomatic disease. It's a trade-off, and one that bats have executed perfectly.
It just happens to mean that when we get a virus from bats, oh man can it cause some damage.
I do have to say this one is mostly theory and inference, and there isn't amazingly good evidence to support it. But it's very likely that bat immune systems are different from our own, given the overall divergence of their immune system genes in relation to our own and those of other mammals.
My opinion (which echoes most ecologists) is that it's more about the position that bats hold in the environment, their behaviors, their longevity, and their sheer numbers. In general zoonotic transmission is a roulette, and bats have the most positions (and the most advantageous positions) on that wheel.
I think this idea has picked up so much steam because molecular biologists often find ways to use what they know about the micro world to explain phenomena in the macro world. It’s honestly probably counterproductive, since most things are quite a bit more complex than we realize while looking at their analogues in Petri dishes.
That being said, I also think ecologists often underestimate what is possible to figure out in a Petri dish, and undervalue the impact of a robustly well-controlled interventional experiment. But that's a conversation for another day.

Bats can FLY!

This allows them to travel long distances, meet and interact with many different animals, hunt and be hunted, and survive to tell the tale. Meaning they also survive to pass on their virus.

Bats are unusually long lived!

Many bat species live longer than 25 years. On the curve of "body size and metabolism" vs "lifespan" bats are a massive over-performer. The closely related foxes, for example, live on average 2-5 years in the wild.
This is probably interrelated with all the other factors listed. Bats can fly, so they live longer; bats live longer, so they can spread slowly growing virus infections better. This combination of long lifespan and persistent viral infection means that bats may, more often, keep viruses around long enough to pass them onto other vertebrates (like us!).
From: https://doi.org/10.1371/journal.pcbi.1004524.g002 (https://i.imgur.com/7j7DJ3i.png)

Their social structure and hibernation behaviors

These characteristics are uniquely positioned to help them harbor a number of different viruses.
Bats roost, meaning they hole up inside the roofs of caves and hibernate together for long periods of time (on the order of months), passing viruses amongst the colony in close isolation. The Mexican free-tailed bat, for example, packs ~300 bats/ft^2 in cave systems like Carlsbad caverns in the southwestern United States.
The complex social hierarchy of bats also likely plays a role. Bats exist in so-called "micropopulations" that have different migratory patterns. They interweave and interact and combine and separate in a dizzying mix of complex social networks among different "micropopulations."
A given virus may have the chance to interact with hundreds of thousands or millions of different individual bats in a short period of time as a result. This also means that viruses with different life cycles (short, long, persistent, with flare-ups, etc) can always find what they need to survive, since different bat groupings have different habits.
And this may partially explain how outbreaks of certain viruses happen according to seasonality. If you're a virus and your bat micropopulation of choice is around and out to play, it's more likely you will get a chance to jump around to different species.
From: https://doi.org/10.1890/ES13-00023.1 (https://i.imgur.com/QLYevsN.png)

Echolocation may also play a role

Bats echolocate, and it involves the intense production of powerful sound waves, which are also perfect for disseminating lots of small virus-containing respiratory droplets across long distances! (1 2)

Finally, a note on viral ecology in general:

If you read this post, and think bats are the only ones out there with viruses, then I have failed.
The reality is that every species out there, from the tiniest stink bug to the massive elephant, likely has millions of different viruses infecting it all the time! If you take a drop (mL) of seawater, it contains ~10 million bacteriophages.
In our genome, there are remnants and scars and evidence of millions of retroviruses that once infected us. Greater than 8% of our genome is made up of these "endogenous retroviruses," most of which don't make any RNA or proteins or anything like that. They just sit there. They've truly won the war for remembrance.
That's what viruses do, they try and stick around for as long as possible. And, in a sense, these endogenous retroviruses have won. They live with us, and get to stick around as long as we survive in one form or another.
The vast vast majority of viruses are inert, asymptomatic, and cause no notable disease. It is only the very tip of the iceberg, the smallest tiny % of viruses, that cause disease and make us bleed out various orifices. Viral disease, in terms of all viruses, is the exception, not the rule. It's an accident. We are an accidental host for most of these "zoonotic" viruses.
Viruses are everywhere, and it is only the unique and interesting aspects of bats noted above that mean we are forced to deal with their viruses more than other species.
(Dengue, like most viruses, follows this idea. The vast majority of people are asymptomatic. Pathogenicity and disease are the exception, not the rule. But that doesn't mean they don't cause damage to society and to lots of people! They do!)
From: https://doi.org/10.1038/s41577-019-0123-x (https://i.imgur.com/KcuutRz.png)
The last thing I want to reiterate at the end of this post is something I said earlier:
Bats are a keystone species!
A keystone species is one that, when you remove it, the system falls apart. Much like the keystone in an arched entryway.
Removing bats from the Earth would likely kill many more millions of humans than CoVID-19 or Ebola ever could.
We rely on the plants they pollinate for the food we eat and for the air we breathe. We rely on them for pest control and for population control. And, in turn, they serve as good for other crucial species.
Bat populations keep mosquitos like Aedes and Anopheles species in check. Aedes Aegypti kills many more millions than CoVID-19 by spreading dengue, chikungunya, yellow fever, Zika, and other viruses. Anopheles females spread malaria, one of the most deadly diseases in human history. Without bats, these mosquitoes could overgrow to unknown and unpredictable levels, and the diseases they transmit could spread even further, like wildfire, decimating the earth's human population.
In terms of pure biomass and impacts...to remove 20% of mammals on the Earth... That could be absolutely devastating! Possibly world-ending on its own.
We need bats.
We also don't know what would replace the niche that bats hold in the Earth's ecosystem. And whether or not that animal or animals would be worse or better for human zoonotic infections.
We need bats. We just don't need them to be close enough to human society that we contract their viruses so easily.
Other people have actually done this calculation. And they agree with me:
(1 2 3 4 5 6 7 8 9)
Bats are, like it or not, an extremely crucial part of the ecosystem that cannot be eliminated. So their viruses are also here to stay.
The best thing we can do is pass laws that make it illegal to eat, farm, and sell bats and other wild zoonotic animals , so that we can reduce our risk of contracting their viruses. We can also pass laws protecting their ecological niche, so that they stay in the forest, and we stay in the city!
Deforestation, climate change, the bushmeat trade, and the trafficking of animals for alternative medicine are what is to blame for this mess. Not bats.

Further reading/sources:

submitted by _Shibboleth_ to science

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