Roosting with Bats (Not a Good Idea)
A few months before the pandemic my family stayed at a hotel on Lake Turkana in northern Kenya. The place was run by an expatriate European and had an extremely tolerant attitude toward small animals. Mostly I think this reflected a desire not to be bothered about things.
There were various creepy crawlies on the ground and mosquitos breeding in the hot spring bath, but the most disconcerting animal companions were the bats in the rafters of our room. There were three or four of them, and when they wanted to leave, they flew out through a hole in the bathroom wall. We left after one night due to a general sense of unease.
A few months later, the pandemic made clear just how not-ok that whole thing was. SARS-CoV-2, the virus which causes Covid-19, is ultimately a bat virus. We know this based on comparisons with related viruses, something that can be illustrated with a phylogenetic tree:
The tips on the right correspond to different viral strains. This tree includes SARS-CoV-2 and a number of related coronavirus strains. The host species where a strain is found is also indicated. In this tree, the strains have bat, human and pangolin hosts.
These viruses descended from a common ancestor, represented by the purple dot on the left. That ancestor infected a single host species, and the fact that descendant strains have a variety of hosts implies that there have been transfer events where the virus moved from one host to another.
It is very likely that the common ancestor virus infected a bat host. This follows from parsimony. Host transfer events are unlikely, and so we prefer explanations that require less of them. For this tree, the number of host transfer events required is minimized if the common ancestor existed in bats. The same logic implies that these viruses spent a lot of their evolutionary history in bats. (If you’re interested in more on how we infer viral origins from phylogenetic trees you can take a look at this video).
This tree includes two coronaviruses that have successfully jumped to humans, the strains that cause SARS and Covid-19, shown in orange. A more detailed tree would also include the coronavirus that causes MERS and several that cause the common cold (colds can be due to a variety of viruses). These examples show that coronaviruses are very capable of moving from their original bat hosts into humans.
It turns out they are not alone in this. A number of other viruses have entered humans from bats, including Ebola and rabies. A zoonosis is a pathogen that transfers to human from another species. Bats are an especially large source of viral zoonoses.
There are a number of factors which affect the propensity of a species to harbor viral zoonoses. One is relatedness to humans. Viruses which infect a closely related species (e.g. a non-human primate) probably have an easier time adjusting to human biology. This doesn’t seem to be a huge factor in the case of bats. They are mammals of course, but not as closely related to humans as monkeys and apes (which are the source of HIV, another viral zoonosis).
Another factor affecting zoonoses is range overlap with humans, and opportunity for human contact. Vampire bats may leap into your mind in this context. However, most bats eat insects or fruit, and the majority of zoonoses are due to non-vampire bats. The coronaviruses come from non-vampires, and most bat-connected rabies cases worldwide also come from non-vampires.
Hunting can be a significant source of contact between humans and other species. HIV jumped into the human population multiple times, and many (if not all) of these cases are associated with humans hunting and eating non-human primates. Bats are also hunted, and it’s possible this is a source of contact. At least one outbreak of Ebola is thought to be due to the hunting of fruit bats. It’s not clear however whether the hunting of bats is widespread enough to explain the unusual number of bat zoonoses.
Another factor may be how much host transfer is going on between bat species. There seems to be something about bats that makes it especially common for viruses to jump from one species to another. It may have to do with how they roost. In nature, many bats sleep in caves. They’re also known to occupy human structures such as water pipes and abandoned mines (also the occasional hotel). In these roosts it is not uncommon for there to be multiple species mixed together, providing opportunities for viral transfer between species. Such a situation might well create an evolutionary advantage for generalist viruses that can switch hosts easily.
There is also another potential factor related to roosts. Bats look for places that are safe and tucked away, and such places typically have limited airflow. The group of coronaviruses that causes Covid-19, SARS and MERS is very adept at spreading through the air in such settings. As it happens, humans also spend significant time in enclosed spaces with limited airflow. Our indoor lifestyle seems to represent an analogous ecological setting, and may be one reason coronaviruses are so prone to jumping from bats to humans.
Which is all to say that it’s best if humans and bats do not become roost mates. The bats in our hotel felt the same way — at some point we left the curtain drawn across the bathroom door, unintentionally blocking their exit. At dusk, we ended up with bats fluttering and flapping around our heads.
