Spillover

by David Quammen

  The ecology of Ebola virus encompasses the reservoir question: Where does it hide between outbreaks? Another ecological matter is spillover: By what route, and under what circumstances, does the virus pass from its reservoir into other animals, such as apes and humans? To ask those questions is one thing; to get data that might help answer them is more tricky. How does a scientist study the ecology of such an elusive pathogen? Leroy and his team went into the forest, near locations where Ebola-infected gorilla or chimp carcasses had recently been found, and began trapping animals wholesale. They were groping for a hypothesis. Ebola might abide in one of these creatures—but which one?

  In the course of several expeditions between 2001 and 2003, into Ebola-stricken areas of Gabon and the Republic of the Congo, Leroy’s group caught, killed, dissected, and took samples of blood and internal organs from more than a thousand animals. Their harvest included 222 birds of various species, 129 small terrestrial mammals (shrews and rodents), and 679 bats. Back at the lab in Franceville, they tested the samples for traces of Ebola using two different methods. One method was designed to detect Ebola-specific antibodies, which would be present in animals that had responded to infection. The other method used PCR (as it had been used on Kelly Warfield) to screen for fragments of Ebola’s genetic material. Having looked so concertedly at the bat fauna, which accounted for two-thirds of his total collections, Leroy found something: evidence of Ebola virus infection in bats of three species.

  These were all fruit bats, relatively big and ponderous, like the flying foxes harboring Hendra virus in Australia. One of them, the hammer-headed bat (Hypsignathus monstrosus), is the largest bat in Africa, as big as a crow. People hunt it for food. But in this case the evidence linking bats and virus, though significant, wasn’t definitive. Sixteen bats (including four hammer-headed) had antibodies. Thirteen bats (again including some hammer-headed) had bits of the genome of Ebola virus, detectable by PCR. That amounted to twenty-nine individuals, representing a small fraction of the entire sample. And the results among even those twenty-nine seemed ambiguous, in that no individual bat tested positive by both methods. The sixteen bats with antibodies contained no Ebola RNA, and vice versa. Furthermore, Leroy and his team did not find live Ebola virus in a single bat—nor in any of the other animals they opened.

  Ambiguous or not, these results seemed dramatic when they appeared in a paper by Leroy and his colleagues in late 2005. It was a brief communication, barely more than a page, but published by Nature, one of the world’s most august scientific journals. The headline ran: FRUIT BATS AS RESERVOIRS OF EBOLA VIRUS. The text itself, more carefully tentative, said that bats of three species “may be acting as a reservoir” of the virus. Some experts reacted as though the question were now virtually settled, others reserved judgment. “The only thing missing to be sure that bats are the reservoir,” Leroy told me, during our conversation ten months later, “is virus isolation. Live virus from bats.” That was 2006. It still hasn’t happened, so far as the world knows, though not for lack of effort on his part. “We continue to catch bats—to try to isolate the virus from their organs,” he said.

  But the reservoir question, Leroy emphasized, was only one aspect of Ebola that engaged him. Using the methods of molecular genetics, he was also studying its phylogeny—the ancestry and evolutionary history of the whole filovirus lineage, including Marburg virus and the various ebolaviruses. He wanted to learn too about the natural cycle of the virus, how it replicates within its reservoir (or reservoirs) and maintains itself in those populations. Finally, knowing something about the natural cycle would help in discovering how the virus is transmitted to humans: the spillover moment. Does that transmission somehow occur directly (for instance, by people eating bats), or through an intermediate host? “We don’t know if there’s direct transmission from bats to humans,” he said. “We only know there is direct transmission from dead great apes to humans.” Understanding the dynamics of transmission—including seasonal factors, the geographical pattern of outbreaks, and the circumstances that bring reservoir animals or their droppings into contact with apes or humans—might give public health authorities a chance to predict and even prevent some outbreaks. But there exists a grim circularity: Gathering more data requires more outbreaks.

  Ebola is difficult to study, Leroy explained, because of the character of the virus. It strikes rarely, it progresses quickly through the course of infection, it kills or it doesn’t kill within just a few days, it affects only dozens or hundreds of people in each outbreak, and those people generally live in remote areas, far from research hospitals and medical institutes—far even from his institute, CIRMF. (It takes about two days to travel, by road and river, from Franceville to Mayibout 2.) Then the outbreak exhausts itself locally, coming to a dead end, or is successfully stanched by intervention. The virus disappears like a band of jungle guerrillas. “There is nothing to do,” Leroy said, expressing the momentary perplexity of an otherwise patient man. He meant, nothing to do except keep trying, keep working, keep sampling from the forest, keep responding to outbreaks as they occur. No one can predict when and where Ebola virus will next spill. “The virus seems to decide for itself.”

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  The geographical pattern of Ebola outbreaks among humans is, as I’ve mentioned, controversial. Everyone knows what that pattern looks like but experts dispute what it means. The dispute involves Ebola virus in particular, the one among those five ebolaviruses that has emerged most frequently, in multiple locations across Africa, and therefore cries most loudly for explanation. From its first known appearance to the present, from Yambuku (1976) to Tandala (1977) to the upper Ivindo River gold camps (1994) to Kikwit (1995) to Mayibout 2 (1996) to Booué (later 1996) to the northern border region between Gabon and the Republic of the Congo (2001–2002) to the Mbomo area (2002–2003) to its recurrence at Mbomo (2005) and then to its two more recent appearances near the Kasai River in what’s now the Democratic Republic of the Congo (2007–2009), Ebola virus has seemingly hopscotched its way around Central Africa. What’s going on? Is that pattern random or does it have causes? If it has causes, what are they?

  Two schools of thought have arisen. I think of them as the wave school and the particle school—my little parody of the classic wave-or-particle conundrum about the nature of light. Back in the seventeenth century, as your keen memory for high-school physics will tell you, Christiaan Huygens proposed that light consists of waves, whereas Isaac Newton argued that light is particulate. They each had some experimental grounds for believing as they did. It took quantum mechanics, more than two centuries later, to explain that wave-versus-particle is not a resolvable dichotomy but an ineffable duality, or at least an artifact of the limitations of different modes of observing.

  The particle view of Ebola sees it as a relatively old and ubiquitous virus in Central African forests, and each human outbreak as an independent event, primarily explicable by an immediate cause. For instance: Somebody scavenges an infected chimpanzee carcass; the carcass is infected because the chimp itself scavenged a piece of fruit previously gnawed by a reservoir host. The subsequent outbreak among humans results from a local, accidental event, each outbreak therefore representing a particle, discrete from others. Eric Leroy is the leading proponent of this view. “I think the virus is present all the time, within reservoir species,” he told me. “And sometimes there is transmission from reservoir species to other species.”

  The wave view suggests that Ebola has not been present throughout Central Africa for a long time—that, on the contrary, it’s a rather new virus, descended from some viral ancestor, perhaps in the Yambuku area, and come lately to other sites where it has emerged. The local outbreaks are not independent events, but connected as part of a wave phenomenon. The virus has been expanding its range within recent decades, infecting new populations of reservoir in new places. Each outbreak, by this view, represents a local event primarily explicable by a larger cause—the arrival of the wave. The main pro
ponent of the wave idea is Peter D. Walsh, an American ecologist who has worked often in Central Africa and specializes in mathematical theory about ecological facts.

  “I think it’s spreading from host to host in a reservoir host,” Walsh said, when I asked him to explain where the virus was traveling and how. This was another conversation in Libreville, a teeming Gabonese city with pockets of quietude, through which all Ebola researchers eventually pass. “Probably a reservoir host that’s got large population sizes and doesn’t move very much. At least, it doesn’t transmit the virus very far.” Walsh didn’t claim to know the identity of that reservoir, but it had to be some animal that’s abundant and relatively sedentary. A rodent? A small bird? A nonmigrating bat?

  The evidence on each side of this dichotomy is varied and intriguing, though inconclusive. One form of that evidence is the genetic differences among variants of Ebola virus as they have been found, or left traces of themselves, in human victims, gorillas, and other animals sampled at different times and places. Ebola virus in general seems to mutate at a rate comparable to other RNA viruses (which means relatively quickly), and the amount of variation detectable between one strain of Ebola virus and another can be a very important clue about their origins in space and time. Peter Walsh, working with two coauthors on a paper published in 2005, combined such genetic data with geographical analysis to suggest that all known variants of Ebola virus descended from an ancestor closely resembling the Yambuku virus of 1976.

  Walsh’s collaborators were Leslie Real, a highly respected disease ecologist and theoretician at Emory University, and a bright younger colleague named Roman Biek. Together they presented maps, graphs, and family trees illustrating strong correlations among three kinds of distance: distance in miles from Yambuku, distance in time from that 1976 event, and distance in genetic differences from the Yambuku-like common ancestor. “Taken together, our results clearly point to the conclusion that [Ebola virus] has gradually spread across central Africa from an origin near Yambuku in the mid-1970s,” they wrote. Their headline, stating the thesis plainly, was WAVE-LIKE SPREAD OF EBOLA ZAIRE. It may or may not be a new pathogen—at least, new in these places. (Other evidence, published more recently, suggests that filoviruses may be millions of years old.) But maybe something happened, and happened rather recently, to reshape the virus and unleash it upon humans and apes. “Under this scenario, the distinct phylogenetic tree structure, the strong correlation between outbreak date and distance from Yambuku, and the correlation between genetic and geographic distances can be interpreted as the outcome of a consistently moving wave of [Ebola virus] infection.” One consequence of the moving wave, they argued, is massive mortality among the apes. Some regional populations have been virtually exterminated—such as the gorillas of the Minkébé forest, of the Lossi sanctuary, of the area around Moba Bai—because Ebola hit them like a tsunami.

  So much for the wave hypothesis. The particle hypothesis embraces much of the same data, construed differently, to arrive at a vision of independent spillovers, not a traveling wave. Eric Leroy’s group also collected more data, including samples of muscle and bone from gorillas, chimps, and duikers found dead near human outbreak sites. In some of the carcasses (especially the gorillas), they detected evidence of Ebola virus infection, with small but significant genetic differences in the virus among individual animals. Likewise they looked at a number of human samples, from the outbreaks in Gabon and the Congo during 2001–2003, and identified eight different viral variants. (These were lesser degrees of difference than the gaps among the five ebolaviruses.) Such distinct viruses, they proposed, should be understood in the context that their genetic character is relatively stable. The differences among variants suggest long isolation in separate locales, not a rolling wave of newly arrived, rather uniform virus. “Thus, Ebola outbreaks probably do not occur as a single outbreak spreading throughout the Congo basin as others have proposed,” Leroy’s team wrote, alluding pointedly to Walsh’s hypothesis, “but are due to multiple episodic infection of great apes from the reservoir.”

  This apparent contradiction between Leroy’s particle hypothesis and Walsh’s wave hypothesis reflects an argument at cross-purposes, I think. The confusion may have arisen from back-channel communications and a certain sense of competition as much as from ambiguity in their published papers. What Walsh suggested—to recapitulate in simplest form—is a wave of Ebola virus sweeping across Central Africa by newly infecting some reservoir host or hosts. From its recent establishment in the host, according to Walsh, the virus spilled over, here and there, into ape and human populations. The result of that process is manifest as a sequence of human outbreaks coinciding with clusters of dead chimps and gorillas—almost as though the virus were sweeping through ape populations across Central Africa. Walsh insisted during our Libreville chat, though, that he had never proposed a continental wave of dying gorillas, one group infecting another. His wave of Ebola, he explained, has been traveling mainly through the reservoir populations, not through the apes. Ape deaths have been numerous and widespread, yes, and to some degree amplified by ape-to-ape contagion, but the larger pattern reflects progressive viral establishment in some other group of animals, still unidentified, with which apes frequently come into contact. Leroy, on the other hand, has presented his particle hypothesis of “multiple independent introductions” as a diametric alternative not to Walsh’s idea as here stated but to the notion of a continuous wave among the apes.

  In other words, one has cried: Apples! The other has replied: Not oranges, no! Either might be right, or not, but in any case their arguments don’t quite meet nose to nose.

  So . . . is light a wave or a particle? The coy, modern, quantum-mechanical answer is yes. And is Peter Walsh correct about Ebola virus or is Eric Leroy? The best answer again may be yes. Walsh and Leroy eventually coauthored a paper, along with Roman Biek and Les Real as deft reconcilers, offering a logical amalgam of their respective views on the family tree of Ebola virus variants (all descended from Yambuku) and of the hammer-headed bat and those two other kinds of bats as (relatively new) reservoir hosts. But even that paper left certain questions unanswered, including this one: If the bats have just recently become infected with Ebola virus, why don’t they suffer symptoms?

  The four coauthors did agree on a couple other basic points. First, fruit bats might be reservoirs of Ebola virus but not necessarily the only reservoirs. Maybe another animal is involved—a more ancient reservoir, long since adapted to the virus. (If so, where is that creature hiding?) Second, they agreed that too many people have died of Ebola virus disease, but not nearly so many people as gorillas.

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  After our fruitless stakeout near Moba Bai, in northwestern Congo, Billy Karesh and I and the expert gorilla guide Prosper Balo, along with other members of the team, traveled three hours back down the Mambili River by pirogue. We carried no samples of frozen gorilla blood, but I was nevertheless glad to have had the chance to come looking. From the lower Mambili we turned upstream on one of its branches, motored to a landing, and then drove a dirt road to the town of Mbomo, central to the area where Ebola virus had killed 128 people during the 2002–2003 outbreak.

  Mbomo is where Barry Hewlett, arriving just after the four teachers were hacked to death, had encountered murderous suspicions between one resident and another that the Ebola deaths resulted from sorcery. We stopped at a little hospital, a U-shaped arrangement of low concrete structures surrounding a dirt courtyard, like a barebones motel. Each of the rooms, tiny and cell-like, gave directly onto the courtyard through a louvered door. As we stood in the heat, Alain Ondzie told me that Mbomo’s presiding physician, Dr. Catherine Atsangandako, had famously locked an Ebola patient into one of those cells just a year earlier, supplying him with food and water through the slats. The man was a hunter, presumably infected by handling one form or another of wild meat. He had died behind his louvered door, a lonely end, but the doctor’s draconian quarantine was generally cre
dited with having prevented a wider outbreak.

  Dr. Catherine herself was out of town today. The only evidence of her firm hand was a sign, painted in stark red letters:

  ATTENTION EBOLA

  NE TOUCHONS JAMAIS

  NE MANIPULONS JAMAIS

  LES ANIMAUX TROUVES

  MORTS EN FORET

  Don’t touch dead animals in the forest.

  Mbomo had another small distinction: It was Prosper Balo’s hometown. We visited his house, walking to it along a narrow byway and then a grassy path, and found its dirt courtyard neatly swept, with wooden chairs set out for us under a palm. We met his wife, Estelle, and some of his many children. His mother offered us palm whiskey. The children jostled for their father’s attention; other relatives gathered to meet the strange visitors; we took group photos. Amid this cheery socializing, in response to a few gentle queries, we learned some details about how Ebola had affected Estelle and her family during that grim period in 2003, when Prosper had been away.

  We learned that her sister, two brothers, and a child had all died in the outbreak, and that Estelle herself was shunned by townspeople because of her association with those fatalities. No one would sell food to her. No one would touch her money. Whether it was infection they feared, or dark magic, is uncertain. She had to hide in the forest. She would have died herself, Prosper said, if he hadn’t taught her the precautions he’d learned from Dr. Leroy and the other scientists, around that time, while helping them in their search for infected animals: Sterilize everything with bleach, wash your hands, and don’t touch corpses. But now the bad days were past and, with Prosper’s arm around her, Estelle was a smiling, healthy young woman.