The paper made a handful of salient points, the first of which put the rest in perspective: Bats come in many, many forms. The order Chiroptera (the “hand-wing” creatures) encompasses 1,116 species, which amounts to 25 percent of all the recognized species of mammals. To say again: One in every four species of mammal is a bat. Such diversity might suggest that bats don’t harbor more than their share of viruses; it could be, instead, that their viral burden is proportional to their share of all mammal diversity, and thus just seems surprisingly large. Maybe their virus-per-bat ratio is no higher than ratios among other mammals.
Then again, maybe it is higher. Calisher and company explored some reasons why that might be so.
Besides being diverse, bats are very abundant and very social. Many kinds roost in huge aggregations that can include millions of individuals at close quarters. They are also a very old lineage, having evolved to roughly their present form about 50 million years ago. Their ancientness provides scope for a long history of associations between viruses and bats, and those intimate associations may have contributed to viral diversity. When a bat lineage split into two new species, their passenger viruses may have split with them, yielding more kinds of virus as well as more kinds of bat. And the abundance of bats, as they gather to roost or to hibernate, may help viruses to persist in such populations, despite acquired immunity in many older individuals. Remember the concept of critical community size? Remember measles, circulating endemically in cities of five hundred thousand people or more? Bats probably meet the critical community size standard more consistently than most other mammals. Their communities are often huge and usually large, offering a steady supply of susceptible newborns to become infected and maintain the viral presence.
That scenario assumes a virus that infects each bat only briefly, leaving recovered individuals with lifelong immunity, as measles does in humans. An alternative scenario involves a virus capable of causing chronic, persistent infection, lasting months or even years within a single bat. If the infection can persist, then the long average lifespan of a bat becomes advantageous for the virus. Some of the smaller, insectivorous bats live twenty or twenty-five years. Such longevity, if the bat is infected and shedding virus, vastly increases the sum of opportunities over time for passing the virus to other bats. In the language of the mathematicians: R0 increases with the lifespan of a persistently infected bat. And a bigger R0, as you know, is always good for the pathogen.
Social intimacy helps too, and many kinds of bat seem to love crowding, at least when they hibernate or roost. Mexican free-tailed bats in Carlsbad Caverns, for instance, snuggle together at about three hundred individuals per square foot. Not even lab mice in an overloaded cage would tolerate that. If a virus can be passed by direct contact, bodily fluids, or tiny droplets sprayed through the air, crowding improves its chances. Under conditions like those in Carlsbad, Calisher’s group noted, even rabies has been known to achieve airborne transmission.
Speaking of airborne: It’s not insignificant that bats fly. An individual fruit bat may travel dozens of miles each night, searching for food, and hundreds of miles in a season as it moves among roosting sites. Some insectivorous bats migrate as much as eight hundred miles between their summer and winter roosts. Rodents don’t make such journeys, and not many larger mammals do. Furthermore, bats move in three dimensions across the landscape, not just two; they fly high, they swoop low, they cruise in between, inhabiting a far greater volume of space than most animals. The breadth and the depth of their sheer presence are large. Does that increase the likelihood that they, or the viruses they carry, will come in contact with humans? Maybe.
Then there’s bat immunology. Calisher’s group could only touch judiciously on this topic, even with Tony Schountz as a coauthor, because little is known by anyone. Mainly they raised questions. Is it possible that the cold temperatures endured by hibernating bats suppress their immune responses, allowing viruses to persist in bat blood? Is it possible that antibodies, which would neutralize a virus, don’t last as long in bats as in other mammals? What about the ancientness of the bat lineage? Did that lineage diverge from other mammals before the mammalian immune system had been well honed by evolution, reaching the level of effectiveness seen in rodents and primates? Do bats have a different “set point” for their immune responses, allowing a virus to replicate freely so long as it doesn’t do the animal any harm?
Answering those questions, according to Calisher’s group, would require new data derived from new work. And that work couldn’t be done just with the sleek tools and methods of molecular genetics, comparing long sequences of nucleotide bases by way of computer software. They wrote:
Emphasis, sometimes complete emphasis, on nucleotide sequence characterization rather than virus characterization has led us down a primrose path at the expense of having real viruses with which to work.
The paper was a collaborative effort but that sentence sounds like Charlie Calisher. What it means is: Hello, people? We’ve gotta grow these bugs the old-fashioned way, we’ve gotta look at them in the flesh, if we’re gonna understand how they operate. And if we don’t, the paper added, “we are simply waiting for the next disastrous zoonotic virus outbreak to occur.”
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Charlie Calisher and his coauthors, besides touching on broad principles, discussed a handful of bat-related viruses in detail: Nipah, Hendra, rabies and its close relatives (the lyssaviruses), SARS-CoV, and a couple of others. They mentioned Ebola and Marburg, though carefully omitting those two from the list of viruses for which bats had been proven to serve as reservoirs. “The natural reservoir hosts of these viruses have not yet been identified,” they said about Marburg and Ebola—accurately, as of the time of publication. Their paper appeared in 2006. Fragments of Ebola RNA had been detected by then in some bats; antibodies against Ebola virus had been found in other bats. But that wasn’t quite proof enough. Nobody had yet isolated any live filovirus from a bat, and the unsuccessful efforts to do so left Ebola and Marburg well hidden.
Then, in 2007, Marburg virus reappeared, this time among miners in Uganda. It was a small outbreak, affecting only four men, of whom one died, but it served as an opportunity to gain new insight into the virus, thanks in part to a quickly responsive multinational team. The four victims all worked at a site called Kitaka Cave, not far from Queen Elizabeth National Park, in the southwestern corner of Uganda. They dug galena, which is lead ore, plus a little bit of gold. The word “mine” caught the attention of some scientists within the CDC’s Special Pathogens Branch, in Atlanta, because they already had reason to suspect that Marburg’s reservoir, whatever it was, might be associated with cavelike environments. Several of the previous Marburg outbreaks included patients whose case histories involved visits to, or work in, caves or mines. So when the response team arrived at Kitaka Cave, in August 2007, they were ready to go underground.
This group included scientists from the CDC, the National Institute for Communicable Diseases in South Africa, and WHO in Geneva. The CDC sent Pierre Rollin and Jonathan Towner, whom we’ve met before, as well as Brian Amman and Serena Carroll. Bob Swanepoel and Alan Kemp of the NICD flew up from Johannesburg; Pierre Formenty arrived from WHO. All of them possessed extensive experience with Ebola and Marburg, gained variously through outbreak responses, lab research, and field studies. Amman was a mammalogist with a special affinity for bats. During a conversation at the CDC, he described to me what it was like to go to Kitaka Cave.
The cave served as roosting site for about a hundred thousand individuals of the Egyptian fruit bat (Rousettus aegyptiacus), a prime suspect as reservoir for Marburg. The team members, wearing Tyvek suits, rubber boots, goggles, respirators, gloves, and helmets, were shown to the shaft by miners, who as usual were clad only in shorts, T-shirts, and sandals. Guano covered the ground. The miners clapped their hands to scatter low-hanging bats as they went. The bats, panicked, came streaming out. These were sizable animals, each with a two-foot wingspan, no
t quite so large and hefty as the flying foxes of Asia but still daunting, especially with thousands swooshing at you in a narrow tunnel. Before he knew it, Amman had been conked in the face by a bat and suffered a cut over one eyebrow. Towner got hit too, Amman said. Fruit bats have long, sharp thumbnails. Later, because of the cut, Amman would get a postexposure shot against rabies, though Marburg was a more immediate concern. “Yeah,” he thought, “this could be a really good place for transmission.”
The cave had several shafts, Amman explained. The main shaft was about eight feet high. Because of all the mining activity along there, many of the bats had shifted their roosting preference “and went over to what we called the cobra shaft.” That was a smaller shaft, branching off, which—
I interrupted him. “ ‘Cobra’ because there were cobras?”
“Yeah, there was a black forest cobra in there,” he said.
Or maybe a couple. It was good dark habitat for snakes, with water and plenty of bats to eat. Anyway, the miners showed Amman and Towner into the cave, past another narrow shaft that led to a place called the Hole, a pit about ten feet deep accessed by shinnying down a pole, from the bottom of which came much of the ore. The two Americans were looking for the Hole but, following their guides, inadvertently passed that shaft by, continuing about two hundred meters along the main shaft to a chamber containing a body of brown, tepid water. Then the local fellows cleared out, leaving Towner and Amman to do a bit of exploring on their own. They dropped down beside the brown lake and found that the chamber branched into three shafts, each of which seemed blocked by standing water. Peering into those shafts, they could see many more bats. The humidity was high and the temperature maybe ten or fifteen degrees hotter than outside. Their goggles fogged up. Their respirators became soggy and wouldn’t pass much oxygen. They were panting and sweating, zipped into their Tyvek suits, which felt like wearing a trash bag, and by now they were becoming “a little loopy,” Amman recalled. One lakeside shaft seemed to curve back around, possibly connecting with the cobra shaft. They didn’t know how deep the water might be, and the airspace above it was limited. Should they proceed? No, they decided, the increased risk wasn’t worth the potential benefit. Formenty, their WHO colleague, eventually found them down there and said, Hey guys, the Hole is back this way. They crawled out and retraced their path, “but by that time we were spent,” Amman said. “We had to get out and cool off.” It was only their first underground excursion at Kitaka. They would make several.
On a later day, the team investigated a grim, remote chamber they dubbed the Cage. It was where one of the four infected miners had been working just before he got sick. This time Amman, Formenty, and Alan Kemp of the NICD went to the far recesses of the cave. The Cage itself could only be entered by crawling through a low gap at the base of a wall—like sliding under a garage door that hasn’t quite closed. Brian Amman is a large man, six foot three and 220 pounds, and for him the gap was a tight squeeze; his helmet got stuck and he had to pull it through separately. “You come out into this sort of blind room,” he said, “and the first thing you see is just hundreds of these dead bats.”
They were Egyptian fruit bats, the creature of interest, left in various stages of mummification and rot. Piles of dead and liquescent bats seemed a bad sign, potentially invalidating the hypothesis that Egyptian fruit bats might be a reservoir host of Marburg. If these bats had died in masses from the virus, then they couldn’t also be its reservoir. Then again, they might have succumbed to earlier efforts by the locals to exterminate them with fire and smoke. Their cause of death was indeterminable without more evidence, and that’s partly why the team was there. If these bats had died of Marburg, suspicion would shift elsewhere—to another bat, or maybe a rodent, or a tick, or a spider? Those other suspects might have to be investigated. Ticks, for instance: There were plenty of them in crevices near the bat roosts, waiting for a chance to drink some blood. Meanwhile, when Amman and Kemp stood up in the Cage, they realized that not every bat in there was dead. The room was aswirl with live ones, circling around their heads.
The two men went to work, collecting. They stuffed dead bats into bags. They caught a few live bats and bagged them too. Then, back down on their bellies, they squooched out through the low gap. “It was really unnerving,” Amman told me. “I’d probably never do it again.” One little accident, he said, a big rock rolls in the way, and that’s it. You’re trapped.
Wait a minute, lemme get this straight: You’re in a cave in Uganda, surrounded by Marburg and rabies and black forest cobras, wading through a slurry of dead bats, getting hit in the face by live ones like Tippi Hedren in The Birds, and the walls are alive with thirsty ticks, and you can hardly breathe, and you can hardly see, and . . . you’ve got time to be claustrophobic?
“Uganda is not famous for its mine rescue teams,” he said.
By the end of this fieldtrip, the scientists had collected about eight hundred bats for dissection and sampling, half of those belonging to Rousettus aegyptiacus. The CDC team, including Towner and Amman, returned to Kitaka Cave seven months later, in April 2008, catching and sampling two hundred more individuals of R. aegyptiacus to see if Marburg persisted in the population. If so, that would strongly suggest that this species was in fact a reservoir. During the second trip, they also marked and released more than a thousand bats, hoping that from later recaptures they could deduce the overall size of the population. Knowing the population size, as well as the prevalence of infection among their sampled bats, would indicate how many infected bats might be roosting in Kitaka at any one time. Towner and Amman used beaded collars (which seemed less discomfiting to the bats than the usual method of marking, leg bands), each collar coded with a number. The two scientists took some heat for this mark-recapture study; skeptical colleagues argued that it was wasted effort, given the vast size of the bat population and the odds against recapture. But, in Amman’s words, “we kind of stuck to our guns,” and they eventually released 1,329 tagged bats.
Less speculative, less controversial, were the samples of blood and tissue from dissected bats. Those went back to Atlanta, where Towner took part in the laboratory efforts to find traces of Marburg virus. One year later came a paper, authored by Towner, Amman, Rollin, and their WHO and NICD colleagues, announcing some important results. All the cave crawling, bat sampling, and lab work had yielded a dramatic breakthrough in the understanding of filoviruses, meaning both Marburg and Ebola. Not only did the team detect antibodies against Marburg (in thirteen of the roughly six hundred fruit bats sampled) and fragments of Marburg RNA (in thirty-one of the bats), but they also did something more difficult and compelling. Antibodies and RNA fragments, though significant, were just the same sorts of secondary evidence that had provisionally linked the Ebola virus to bats. This team had gone a step farther: They’d found live virus.
Working in one of the CDC’s BSL-4 units, Towner and his co-workers had isolated viable, replicating Marburg virus from five different bats. Furthermore, the five strains of virus were genetically diverse, suggesting an extended history of viral presence and evolution within Egyptian fruit bats. Those data, plus the fragmentary RNA, constituted strong evidence that the Egyptian fruit bat is a reservoir—if not the reservoir—of Marburg virus. Based on the isolation work, it’s definitely there in the bats. Based on the RNA fragments, it seems to infect about 5 percent of the bat population at a given time. Putting those numbers together with the overall population estimate of a hundred thousand bats at Kitaka, the team could say that about five thousand Marburg-infected bats flew out of the cave every night.
An interesting thought: five thousand infected bats passing overhead. Where were they going? How far to the fruiting trees? Whose livestock or little gardens got shat upon as they went? Jon Epstein’s advice would have been apt: “Keep your mouth closed when you look up.” And the Kitaka aggregation, Towner and his coauthors added, “is only one of many such cave populations throughout Africa.”
Where else might Marburg virus be traveling on the wings of these bats? An answer to that arrived in the summer of 2008.
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Astrid Joosten was a forty-one-year-old Dutch woman who, in June 2008, went to Uganda with her husband on an adventure vacation. It wasn’t their first, but it would be more consequential than the others.
At home in Noord-Brabant (the same area, by coincidence, then being hard hit with Q fever), Joosten worked as a business analyst for an electrical company. Both she and her spouse, a financial manager, enjoyed escaping from the Netherlands on annual getaways to experience the landscapes and cultures of other countries, especially in Africa. In 2002 they had flown to Johannesburg and, stepping off the airplane, felt love at first sight. On later trips they visited Mozambique, Zambia, and Mali. The journey in 2008, booked through an adventure-travel outfitter, would allow them to see mountain gorillas in the southwestern highlands of the country as well as some other wildlife and cultures. They worked their way south toward Bwindi Impenetrable Forest, where the Ugandan gorillas reside. On one intervening day, the operators offered a side trip, an option, to a place called the Maramagambo Forest, where the chief attraction was a peculiar site that everyone knew as Python Cave. African rock pythons lived there, languid and content, grown large and fat on a diet of bats.
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