Spillover: Animal Infections and the Next Human Pandemic (58 page)

And so the Voyager arrived. He rounded a last bend, came to a great pool where the river seemed as wide as it was long, put a large island to his left as advised, and saw white buildings on the right bank, some of them twice as tall as a house, taller even than the circular market hall at Ouesso. He paddled toward the white buildings. Coming near, he held himself some distance out, drifting, observing, until he was well past the docks and the big boats and the bustle of workingmen, and then beached his canoe in a quieter place. Several children gaped, as children do, but no one else noticed him. People were busy and no adults diverted their attention to the sight of a strong young Bakwele coming ashore in tattered clothes with a crocodile skull, a single fine tusk, and half a boatload of rotten fish.

He stepped out of the water and stood alone. No one greeted him.

No one knew what he had done. No one compared him to Lewis and Clark. No one hailed him as the Marco Polo of the upper Congo basin. No one knew that he was Huck Finn and Jim, John Wesley Powell on the Colorado, Teddy Roosevelt on the River of Doubt, Frank Borman circling the moon in
Apollo 8
, and Dr. Richard Kimble at large. No one knew.

The Voyager walked into town and sold his tusk the first afternoon, receiving 120 brass rods, which was a good price, he thought, but also somehow anticlimactic and unsatisfactory. For his crocodile skull, at the benign whim of the ivory buyer, he received another ten brass rods. He bought some palm wine, got drunk, found that experience not to his liking, and never did it again. The rest of his money he saved, or rather set aside, spending it slowly and variously until it was gone. He had arrived.

He found lodging in Poto-Poto, a neighborhood east of the city center, full of others from the upper river, and he found work on the waterfront. He made friends. He settled in. Urban life suited him. He became something of a colorful figure, confident, charming in his river-man way, with stories to tell. No one viewed him as the pariah son of a sorceress. No one guessed that he had ever been a surly young loner. No one knew his real name because he had invented another. And the other thing no one knew, not even he, was that he had brought a new element, a new circumstance, to Brazzaville. A virus, in his blood. More specifically: He had brought HIV-1 group M.

Seven and eight and nine years later, near the end of his life, the Voyager would tell some of his stories to friends, acquaintances, and a few of the women with whom he had relationships, transient or longer: about the Dead Elephant, the Half-Portuguese Merchant, the Tall Boy, the Crocodile, and the Blue-Eyed Bobangi. In his telling, the Tall Boy became an adult and the Crocodile was very large, a leviathan. No one doubted his word. They knew he had come down the river and it must have been perilous. The crocodile skull wasn’t there to belie him. During those years he slept with thirteen women, all of whom were
femmes libres
to one degree or another. One of those, a young Tio girl who had recently arrived in Brazzaville from upriver, and who found that she fancied him more than she did her freedom, became his wife. Eventually he infected her with the virus. He also infected one other, a rather more professional woman who lived in a small house in the Bacongo neighborhood, west of town, where he visited her on an intermittent basis when his wife was pregnant. The other eleven women had only fleeting sexual contacts with him and were luckier. They remained HIV-negative. The Voyager’s personal lifetime
R
0
was therefore precisely 2.0. People liked him and were sorry when he fell ill.

The Bacongo girlfriend was vivacious and pretty and ambitious for wider horizons, so she crossed the pool to Léopoldville, where she had a successful career, though not a long one.

102

I
f the virus reached Léopoldville in 1920 or so, that still leaves a gap of four decades to the time of ZR59 and DRC60, those earliest archival HIV sequences. What happened during the interim? We don’t know, but available evidence allows a rough sketch of the outlines of possibility.

The virus lurked in the city. It replicated within individuals. It passed from one person to another by sexual contact, and possibly also by the reuse of needles and syringes for treatment of well-known diseases such as trypanosomiasis. (More on that possibility, below.) Whatever its means of transmission, presumably HIV caused immune deficiency, eventually death, among most or all people infected—except those who died early from other causes. But it didn’t yet assert itself conspicuously enough to be recognized as a distinct new phenomenon.

It may also have proliferated slowly in Brazzaville, across the pool, helped along there too by changing sexual mores and programs of therapeutic injection. It may have lingered in villages of southeastern Cameroon or elsewhere in the upper Sangha basin.

And wherever it was, but definitely in Léopoldville, it continued to mutate. The wide divergence between ZR59 and DRC60 tells us that. It continued to evolve.

Studying the evolutionary history of HIV-1 is more than an idle exercise. The point is to understand how one strain of the virus (group M) made itself so deadly and widespread among humans. Such understanding, in turn, may lead toward better measures to control the devastation of AIDS, possibly by way of a vaccine, more likely by way of improved treatments. That’s why scientists such as Beatrice Hahn, Michael Worobey, and their colleagues explore the molecular phylogenetics of HIV-1, HIV-2, and the various SIVs. One issue they address is whether the virus became virulent before, or only after, its spillover from chimpanzees. To state the question more plainly: Does SIV
cpz
kill chimps, or is it only an innocuous passenger? Answering that one could reveal something important about how human bodies respond to HIV-1.

For a while after the discovery of SIV
cpz
, the prevailing impression was that it’s harmless in chimpanzees, an ancient infection that may once have caused symptoms but no longer does. This impression was bolstered by the fact that, in the earlier years of AIDS research, more than a hundred captive chimpanzees were experimentally infected with HIV-1 and none showed immune system failure. When a single lab chimpanzee
did
progress to AIDS (ten years after experimental infection with three different strains of HIV-1), its case was remarkable enough to merit a six-page paper in the
Journal of Virology
. The researchers implied that this was good news, finally offering hope that chimpanzees do represent a relevant experimental model (that is, a sufficiently analogous test subject) for studying human AIDS. There was even a report, based on genetic analysis of captive animals in the Netherlands, suggesting that chimpanzees had “
survived their own AIDS-like pandemic
” more than 2 million years ago. They emerged from the experience, according to this line of thought, with genetic adaptations that render them resistant to the effects of the virus. They still carry it but apparently don’t get sick. That notion, to repeat, was founded on captive chimpanzees. As for SIV-positive chimps in the wild, no one knew whether they suffer immunodeficiency. It was a difficult question to research.

These suppositions and guesses jibed with available information about other variants of the virus in other primates. SIV is highly diverse and broadly distributed, found as a naturally occurring infection in members of more than forty different species of African monkey and ape. (But it seems to be unique to that continent. Although some Asian primates have acquired the virus in captivity, it hasn’t shown up among wild monkeys in either Asia or South America.) Most of those SIV-carrying African simians are monkeys. Each kind of monkey harbors its own distinct type of SIV, such as SIV
gsn
in the greater spot-nosed monkey, SIV
ver
in the vervet, SIV
rcm
in the red-capped mangabey, and so forth. Based on evidence presently available, none of those SIVs seems to cause immunodeficiency in its natural host. A close evolutionary kinship between two kinds of simian, such as L’Hoest’s monkey and the sun-tailed monkey, both classified in the genus
Cercopithecus
, is sometimes paralleled by a close similarity between their respective SIVs. Those deep taxonomic alignments, plus the absence of noticeable disease, led researchers to suspect that African monkeys have carried their SIV infections for a very long time—probably millions of years. That length of time would allow divergence among the viruses and mutual accommodation between each type of virus and its host.

The same two-part hypothesis applied also to chimps: that their virus, SIV
cpz
, is (1) an ancient infection that now (2) causes no harm. But for chimps those were just tenuous assumptions. Then new evidence and analyses addressed them, and both parts turned out to be wrong.

The first premise, that SIV
cpz
has lurked within chimpanzees for a very long time, began to look doubtful in 2003. That’s when another team of researchers (led by Paul Sharp and Elizabeth Bailes of the University of Nottingham, and including again both Beatrice Hahn and Martine Peeters) noticed that SIV
cpz
seems to be a hybrid virus. The Nottingham group reached that conclusion by comparing the genome of SIV
cpz
with the genomes of several monkey SIVs. They found that one major section of the chimp virus’s genome matches closely to a section of SIV
rcm
. Another major section closely resembles a section in SIV
gsn
. In plain words: The chimp virus contains genetic material from the virus of red-capped mangabeys and also genetic material from the virus of greater spot-nosed monkeys. How did it happen? By recombination—that is, genetic mixing. A chimpanzee infected with both monkey viruses must have served as the mixing bowl in which two viruses traded genes. And
when
did it happen? Possibly just hundreds of years ago, rather than thousands or tens of thousands.

How did a single chimpanzee become infected with two monkey viruses? Presumably that occurred through predation, or through the combined circumstances of predation (bringing aboard one virus) plus sexual transmission (bringing aboard a second), followed by a chance rearrangement of genes between one virus and the other during viral replication. Chimpanzees are omnivores who love an occasional taste of meat. They kill monkeys, rip them apart, fight over the pieces or share out gobbets and joints; then they eat the flesh, red and raw. It doesn’t happen often, just whenever the opportunity and the hankering arise. Such gore fests must sometimes involve blood-to-blood contact. Chimpanzees, even without the use of machetes, suffer wounds on their hands and in their mouths. Bloody meat plus an open sore equals exposure. What the Nottingham group suggested was another chimpanzee version of the cut-hunter hypothesis—except in this case the cut hunter was the chimp.

103

S
o the very existence of SIV
cpz
is relatively recent. It has no ancient association with chimpanzees. And now, based on a study published in 2009, part two of the two-part hypothesis has also been cast into doubt. The virus is not so harmless in its chimpanzee host. Evidence from the chimps of Gombe—Jane Goodall’s study population, known and beloved around the world—suggests that SIV
cpz
causes simian AIDS.

I’ve mentioned already that the first wild chimp to test SIV-positive was at Gombe. What I didn’t say, but will here, is that SIV-positive status among Gombe’s chimpanzees correlates strongly with failing health and early death. Again it was Beatrice Hahn and her group who made the discovery.

Having found SIV
cpz
in captive chimps, Hahn wanted to look for it in the wild. But she and her team of young molecular biologists knew little about sampling chimpanzees in an African forest. What do you do, go out and dart one? Knock the ape out with ketamine, take blood, wake him up, and send him on his way? (That’s what Billy Karesh had been equipped to do, with gorillas, during our eight-day stakeout at Moba Bai in the Republic of the Congo. But the protocols for well-studied and habituated chimpanzee populations are very different.) Egads, no! said field primatologists, horrified at the prospect of any such invasive violation of their sensitive, trusting subjects. It was a new realm for Hahn, with a new set of concerns and methods, to which she quickly became attuned. At a scientific meeting that brought primate researchers together with virologists, she met Richard Wrangham, of Harvard, highly respected for his work on the behavioral ecology and evolution of apes. Wrangham has for many years led a study of chimpanzees at Kibale National Park, in western Uganda; before that, four decades ago, he did his own PhD fieldwork at Gombe. He responded enthusiastically to Hahn’s idea of screening wild chimps, and ultimately it was Wrangham, she recalled, “who convinced Jane that we were okay to work with.” But before any such work began at Gombe, they looked at the chimps of Kibale, Wrangham’s own research site. Crucial help came from a Wrangham grad student named Martin Muller, who in 1998 had collected urine samples for a study of testosterone, aggression, and stress. Mario Santiago, of Hahn’s lab, cooked up the requisite tools for detecting SIV
cpz
antibodies in a few milliliters of piss, and Martin Muller supplied some frozen samples from his collections at Kibale. For this part of the story, I went to Albuquerque and talked with Muller, now an associate professor of anthropology at the University of New Mexico.

The Kibale samples all tested negative for SIV. “We were slightly disappointed,” Muller recalled. “That was because, at the time, the conventional wisdom was that this didn’t have any negative impacts on chimps.” Meanwhile, though, he was getting some interesting results in the hormone study and wanted to broaden his data. He and Wrangham agreed that it might be instructive to sample a few other chimp populations for comparison. That led Muller down to Gombe, in August 2000, with his urine-collecting bottles and all the cumbersome equipment necessary to keep samples frozen. He stayed only a couple weeks, training Tanzanian field assistants to continue the collecting, and brought away just a few samples himself. Back home in the United States, he emailed Hahn to ask whether she would like six tubes of frozen Gombe urine, to which she replied: “YES, YES, YES.” He sent them with coded labels, standard procedure, so Hahn had no way of knowing whose was whose. Two of the six tested positive for SIV antibodies. Breaking the code, Muller informed her that both samples came from a chimp named Gimble, a twenty-three-year-old male.