Coronaviruses spread via enclosed air, from bat caves to indoor buildings, not via encounters: a window into respiratory diseases of civilization

To recap the project I've stumbled onto, most diseases thought to be transmitted through personal encounters are in fact spread through a contaminated shared medium, into which a sick individual emits pathogens, and from which a healthy person takes them in -- without needing to be in the same place at the same time, perhaps never coming close to encountering each other during their entire lives. See here for the overview based on the case of 19th-C. cholera in Europe, and here for the contemporary example of SARS-CoV-2 (causing COVID-19).

This post will briefly look at the non-human origin of coronaviruses that now infect humans, and how their transmission dynamics can shed light on how they circulate within a human population.

Recall the most important fact about the transmission of SARS-CoV-2 -- it never occurs outdoors, but only indoors, especially where ventilation is poor. This means the particles are suspended in a stagnant air volume, much like a pond of stagnant water. A sick individual exhales particles into the enclosed air volume, and at some other time, perhaps after the original sick person has left the building, someone else enters the building, immerses themselves in the now-contaminated air volume, and breathes the particles in, becoming sick in turn.

All of these coronaviruses that infect humans ultimately come from pathogens infecting bats. (A separate family of coronaviruses originated in rodents, and infect pigs and other livestock, but via a fecal-to-oral route).

What do bats do? They roost -- hang upside-down while not active, and seek shelter when they are so vulnerable. The large bats that could take on predators may roost in forests, but the microbats that are too small to defend themselves mano-a-mano, roost in more defensible environments like caves. Human-infecting coronaviruses come specifically from these microbat species.

What is a cave? A great big "indoor" enclosure of air, with minimal ventilation inside, and whose opening to the outdoors is small relative to the size of the interior. Ventilation is basically zero where the bats roost -- not right inside the entrance, which would make them easy pickings for predators, but deeper back into the recesses of the cave.

Crucially, these caves are communally shared -- it's not like each bat or its family has its own detached bat-cave like Batman does. There are a whole bunch of them in there, coming and going without any bouncers to regulate the entrance. So the cave air is not only stagnant, but acts as a public medium that connects all of the individual bats that exhale into it and inhale from it, much as a stagnant pond of water connects all of the fish that swim within it -- or all of the ducks that feed from it (but that's for a later post on the non-encounter-based spread of influenza!).

So, one infected bat exhales while roosting in the cave, and the virus particles become aerosolized -- they are part of that air volume, just as inseparable from it as the oxygen. Healthy bats inhale air from this now-contaminated medium, not necessarily right next to the original sick bat. The virus particles travel by diffusion, which is slow, but they also start off with an initial impulse coming from the pressure that the lungs exert to expel the air from within the bat into the surrounding air (even more oomph in that initial burst if the sick individual has a cough or sneeze, as in humans).

The end result is that virus particles spread to regions of the cave far away from the source bat. It doesn't matter if it takes awhile for this spread to happen -- the sick bat is holed up in there roosting for hours on end, day in and day out, and the same is true for the healthy bats. A healthy bat may have a preferred roosting spot that is "far" from the roosting spot of the sick bat -- outside of the distance that a typical breath, cough, or sneeze immediately reaches -- but given some time, those particles can travel to reach him, too. Proximity is not needed.

However, couldn't you explain this indoor transmission by appealing to population density, which is required by the direct contact / encounter model? I.e., if transmission happened through encounters, such encounters are more likely when individuals are packed more tightly into the same space. So a bunch of bats roosting in clusters could be spreading it to each other through close encounters, not through a medium like the stagnant air.

But there are two facts that rule against this alternative explanation. First, it only says that transmission would be greater inside the cave than outside of it -- not that outdoor transmission would be near zero. And bats do in fact encounter other bats, and other species, outside of caves, for enough time to breathe near them and pass along pathogens. And yet spillover from bats to other species only takes place where the two species share an indoor air volume (typically poorly ventilated), such as an indoor market or restaurant. Not out in the wild.

And second, these coronaviruses should also be endemic to the macrobat species that roost in trees rather than caves. They also hang around for hours on end, and in clusters where they are in close proximity to one another. The difference is that these environments have superior ventilation, being outdoors. A really dense forest with leaves enshrouding the branches, or that form a canopy and "walls", could be somewhat of an enclosure, blocking the totally free flow of air. But even that is much more open to air currents than caves.

And forget about it if it's anything other than a tropical rainforest. Bats that roost in trees like you see in a typical park are not immersed in an enclosed volume of stagnant air at all. No structure is enclosing the trees, and the branches and leaves of the tree itself leave lots of open space in multiple directions to the "outside" world.

So much else is shared between the microbat and macrobat species' physiologies, that it should be trivial for coronaviruses to plague the tree-roosting macrobats -- and yet it's only the poor cave-roosting microbats who are beset by coronaviruses. Only the model of a shared medium can account for that, not the encounter / density model.

If some disease were spread among macrobats in trees, it would be the tree that was the public medium connecting all of the individuals. Perhaps if a pathogen they picked up on their feet penetrated the tree bark and spread from one branch to another, where it infected another bat who was roosting far from the original sick bat. But not a pathogen that travels through the respiratory route -- there's no enclosed medium of air in a tree.

That wraps up the proof that coronaviruses among bats are transmitted not through encounters, close contact, and higher density, but through a contaminated shared medium.

We can draw a further lesson, though, by noting that a pathogen is far more likely to cross a species barrier if the new ecology is similar to the old ecology. Fewer selective sweeps of random mutations would be needed to adapt the pathogen to its new host species.

So, is there any similarity between the environments that cave-roosting bats inhabit, and human beings? Well, if those humans have sedentarized and spend enough of their time within enclosed structures, especially ones that are shared with multiple other people. Not hunter-gatherers, and probably not nomadic pastoralists. But agrarian and industrial societies? Absolutely. I think that's what the respiratory class of the "diseases of civilization" are -- pathogens adapted to stagnant indoor air of shared buildings, scarcely different from those infecting untreated public water supplies that arose with sedentary agrarian societies.

And sadly for the animal species we have domesticated, these conditions apply to their structures as well. Unless they belong to purely nomadic pastoralists, they spend a fair amount of time within an enclosed building of some kind -- a barn, a stable, a doghouse, something. Both to corral them into an easily manageable place, rather than chase after them individually, but also to protect them from predators, and provide shelter from the elements.

And in an even sicker twist of fate, their human owners spend a decent amount of time in those animal buildings as well -- they aren't like a detached guest house, where the livestock do their own thing and take care of themselves. Human beings enter those animal buildings to tend to their needs, spending a fair amount of time immersed in the same stagnant volume of air as their animals. Crucially, humans enter the animal building even when the animals are not there -- to clean the place up, to restock the animals' feed, and other barn chores.

That sharing of stagnant air is the route through which a respiratory pathogen crosses the species barrier between humans and their domesticated livestock -- not direct contact or close encounters, since the sick animal could be outside the barn at the time their human owner is inside it doing chores. But the stagnant volume of air containing aerosolized virus particles is still there, even when the animals are out and about, due to limited ventilation.

In the next post in this series, we'll look specifically at two more coronaviruses that have crossed from bats to humans, and perhaps some intermediate species along the way. Namely SARS-1 and MERS. Both cases confirm the model of transmission through a contaminated shared medium rather than encounters between the sick and the healthy.