A number of viruses which cause deadly disease in humans-- including the rabies and Ebola virus families, as well as the more recently identified MERS and Nipah viruses-- have been found in wild bats. Bats are thought to serve as a continuing wildlife source-- a reservoir- for outbreaks of these viral diseases. Because of the public health risk of these diseases, it's important to understand the role of bats with respect to these and potential new viruses, so that human or livestock outbreaks can be controlled. A couple of recent reviews covering bat biology have started to describe why the life cycle of these animals is conducive to harboring viruses.
A 2012 review by Wood et al. lists several details about bats that may make them very good reservoirs for viruses which might affect humans. First, as the only flying mammals, bats combine the mobility of birds with a mammalian immune system. This means that viruses can be spread from bat to bat, or "spill over" from bats into other mammals, over a much larger range compared to, say, mice. Moreover, different bat species will occassionally share roosting locations, and individual bats occasionally switch colonies, increasing the possible viral exchange even more. And. depending on the dominant bat species, these colonies can be densely packed with animals. For example, nursing mother Mexican free-tailed bats can reach 4000 pups per square meter. Finally, it is possible that bat hibernation suppresses their immune system enough that contagion could slowly spread during the winter months.
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Photo credit: Morning Bray
With a bit more detective work, they found another correlation which might explain increased juvenile rates of infection. Egyptian fruit bats tend to breed in synchrony, and these seasons of human disease and juvenile bats with infections correspond to the highest frequency of juvenile bats being initially weaned. Weanlings are less socially prominent, and have to cluster together at less desirable territory at the edges of the colony-- sometimes directly underneath the main adult mass. Thus a new, synchronized cohort of previously uninfected young bats is exposed to the virus, and some of them will develop active infections. Amman et al. did not speculate if juvenile bats, as inexperienced hunters, would further be more likely to encounter humans. But certainly all of the other elements are in place.
So the ultimate source of viruses causing outbreaks of several diseases lies within bat colonies, but there is still a lot to be learned. In many cases, sick humans were not directly exposed to bats, suggesting that these viruses may pass from bats through intermediaries before ultimately infecting humans. Secondly, bats (and other mammals) harbor many viruses which are not threatening to humans. What makes a particular virus capable of jumping species, and which of those are a threat to cause disease? Finally, it's not understood why, for many of these viruses, infected bats seem neither to clear the infection nor to succumb to them. The answer to this may lie in the specifics of their immune system.
A few other observations are needed to keep perspective on this topic. The first is that, of the approximately 4500 mammalian species, there are more than 1000 species of bats (and nearly 2000 species of rodents, another frequent recipient of the "vermin" tag). It's almost certainly a mistake to ascribe all of these dangerous diseases to all bat species. Secondly, the upswing in these outbreaks is largely due to humans (e.g. miners) coming into bat habitat rather than an invasion of the bats. And finally, even in disease prone areas, bat colonies give a lot of perks to nearby humans, including controlling insect populations, pollinating plants and dispersing fruit seeds.