Field of Science

Deadly viruses, bats and Python Cave

 How would you like to adventure inside a tunnel that is 15 metres in length, 12 metres wide and in parts only 3.5 metres tall? Doesn't sound too bad. The catch is that this very popular tourist attraction - known as 'Python Cave' in Queen Elizabeth National Park in Uganda - is crammed full of 40,000 Egyptian fruit bats, African rock pythons (who actually feed on those bats) and a couple of forest cobras. It's also incredibly dark and piled with bat poo but most importantly it's known to harbour one scary virus: Marburg virus.

This cave has already lead to the death of one Dutch tourist and the infection of one from the US sparking major scientific interest in it. This story is nicely written up in the recent book: Spillover by David Quammen. But up until a couple of years ago we didn't know how these people got the virus and that's why the Centers for Disease Control, alongside teams from South Africa and Uganda itself have made it their mission to uncover the secrets of Python Cave and specifically, why did those tourists get infected at that particular place and time? If we know that, maybe we can rationally defend ourselves against getting infected. Well,  a recent paper appears to answer that question.
Publishing in PLoS Pathogens today, the CDC lead team report a detailed ecological investigation into Python Cave and especially the Fruit bats that roost there. In 2009 the same team documented their initial study of a nearby cave associated with an outbreak of marburg virus in miners working there. They found that the Egyptian Fruit bats roosting inside harboured a very diverse mixture of marburg viruses, indicating that they were the natural source of the infections. For an excellent set of pictures of the bats, including a nice shot of a bat and a python, see here:

A schematic of a marburg virus particle - from ViralZone.

So when the next outbreaks happened they repeated the analaysis in that cave to see if the same bats were the source again, involving the capture and analysis of over 1,500 individual bats. But this time they were able to assess how virus infection in the bats differed over their lifetime and from season to season and through this they were able to identify some alarming patterns. They wanted to know precisely whether these bats still contained marburg, how did they transmit the infection to each other and to humans and how did the virus persist among the population?

Using sensitive PCR analysis combined with antibody testing and virus isolation, just less than one fifth of all their bats sampled showed some evidence of current or past infection with marburg virus. And these viruses were pretty similiar to those found in the nearby mine - even one of the bats had been tracked all the way from the mine indicating long range transport of infection. Inside each of the bats they were able to find evidence of the virus in numerous organs, like the lungs, kidney, blood, colon and even their reproductive tract indicating that infection could be transmitted via multiple routes: poo, urine, biting and scratches, through birth and even via ticks and other biting insects.
the peaks and troughs of marbug infection correlate with birthing in the bat colony

But one of the most interesting findings was this: bats of around 6 months of age were the major carriers of the virus. Adults only showed a relatively low and constant level of infection, while very young pups had low levels indicating that virus infection peaks at a particular age level and then the incidence shoots back down. Clearly something is controlling this pattern of infection but what that is is unknown. Yet when they alligned their virus detection data with historical numbers on when humans had been infected with marburg in the past, they showed that the peak in risk of symptomatic infection correlates with the bat birthing season, the time when pups born in the last season reach 6 months of age. They predict that every year a total of 20,000 pups are born. That is a lot of virus infected baby bats. We've even seen this pattern before.

So what the hell is the take home message here? Ok so we know bat populations all around the world contain masses of viruses and in the future we're only going to find a heck of a lot more. And in many cases these viruses have jumped species and killed lots of people and nearby animals and the rate of this may even be increasing. And probably many of our common pathogens nowadays, like mumps and maybe even the common cold originally came from bats. So in the future we would like to stop it happening - lots of lives and money could be saved. 

But it's probably very hard and ethically wrong to a) kill all the bats, b) vaccinate against every bat-borne potential virus and c) do nothing. So what many people have called for is a more general, ecological answer to address the whole swathe of potential emerging pathogens and this paper begins to lay down concrete data that provides one mechanism to prevent virus emergence: don't go anywhere near bat roosts during birthing season if you can help it. Of course these answers will probably also lie in the spheres of cultural and economic changes in behaviour as well. So remember that this study of marburg in Africa is but one peice of a very large and complicated ecological problem.

Amman BR, Carroll SA, Reed ZD, Sealy TK, Balinandi S, et al. (2012) Seasonal Pulses of Marburg Virus Circulation in Juvenile Rousettus aegyptiacus Bats Coincide with Periods of Increased Risk of Human Infection. PLoS Pathog 8(10): e1002877. doi:10.1371/journal.ppat.1002877


  1. Great breakdown and info on the cave, thanks Conor. It's interesting similar observations have yet to be made for Ebola, at least to my knowledge - which may not be up to date, given they've scoured caves like this for it too. Given the huge numbers of bats and the existing ecosystem some sort of ethical, ecological approach is best at the moment, with the hopes that maybe someday there'll be an easy-to-use either prophylactically or post-exposure, effective vaccine. Just out of interest, did you hear of the National Geographic photographer who had a close-encounter with Marburg at this very cave? Here's the link:

  2. yeah you know I haven't really seen much re: ebola, but you could imagine given the same scenarios (a cave) it would follow the same dynamics. With ebola and other ones like Hendra and Nipah you would also have to factor in amplifying host animals. I could see it would get very complicated. But that's why there are these guys:

  3. Ebola virus is hypothesized to be found more in forest fruit bats in Africa (H. monstrosus etc. whereas Marburg virus obviously in cave-dwelling Egyptian Fruit bats. Ebola virus has not been isolated from bats in nature yet (only RNA and antibodies shown) - and studying forest bats which do not congregate to the same numbers as cave bats ensures that this hunt will still be continuing for a few years at least.


Markup Key:
- <b>bold</b> = bold
- <i>italic</i> = italic
- <a href="">FoS</a> = FoS