Read Online The Chimp and the River: How AIDS Emerged from an African Forest by David Quammen - Free Book Online Page B
Authors: David Quammen
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underside of my rental car for a bomb before letting me pass. Keele, waiting to flag me down outside the door of his building, wore a blue dress shirt, jeans, his black hair moussed back, and a two-day stubble. He is a tall young man, extremely polite, raisedand educated in Utah. We sat in his small office and looked at a map of Cameroon.
The first surprise to emerge from the fecal samples was high prevalence of SIV cpz in some communities of Cameroonian chimps. Two that scored highest, Keele said, were at sites labeled Mambele (near a crossroads by that name) and Lobeke (within a national park). Whereas all other sampling of chimps had suggested that SIV infection was rare, the sampling in southeastern Cameroon showed prevalence rates up to 35 percent. But even there, the prevalence was “spotty,” Keele said. “We can sample hundreds of chimps at a site and find nothing.” But go just a little farther east, cross a certain river, sample again, and the prevalence spikes upward. That was unexpected. The rates were especially high in the farthest southeastern corner of the country, where two rivers converge, forming a wedge-shaped national boundary. This wedge of Cameroon appears to jab down into the Republic of the Congo (not to be confused with the DRC), its neighbor to the southeast. The wedge was a hotspot for SIV cpz .
The second surprise came once he extracted viral fragments from the samples, amplified those fragments, sequenced them, and fed the genetic sequences into a program that would compare these new strains with many other known strains of SIV and HIV. The program expressed its comparisons in the form of a most-probable phylogeny—a family tree. Keele recalled watching the results for a certain chimp, an individual labeled LB7, whose feces had been collected at Lobeke. “We were just shocked,” he said. “I mean, I had ten people around my computer, all waiting to see what that sequence looked like.” What it looked like was the AIDS virus.
When his computer delivered its latest tree, LB7’s isolate of SIV cpz showed up as a twig amid the same little branch that held all known human strains of HIV-1 group M. (In scientific lingo, it fell within the same clade. ) It was at that point “the closest thing” to a match, Keele told me, that had ever been found in a wild chimp. “And then we find more, right? The more we dig, the more we find.” The other close matches came from that same little area: southeastern Cameroon. A chilling, historic epiphany, at which Keele and his colleagues were thrilled. “You can’t make this stuff up, as Beatrice would say. It’s too good.” Their joy lasted about ten seconds, after which everyone became hungry for more samples and more results. Your celebration is always provisional, Keele told me, until you’ve written the paper and gotten that congratulatory note of acceptance from the editors of Science.
Keele and the group now sequenced entire genomes (not just fragments) from four samples, all collected in the same area, and on those sequences ran their genetic analyses again. Again they found the new SIV cpz shockingly similar to HIV-1 group M. The similarity was so close as to leave almost no chance that any other variant, yet undiscovered, could be much closer. Hahn’s lab had located the geographical origin of the pandemic: southeastern Cameroon.
12
S o much for where as well as when. AIDS began with a spillover from one chimp to one human, in or near that small southeastern wedge of Cameroon, around 1908 (give or take a margin of error). From there it grew, slowly but inexorably, from a spillover to an outbreak to a pandemic. That leaves our third question: how?
The Keele paper appeared in Science , on July 28, 2006, under the title “Chimpanzee Reservoirs of Pandemic and Nonpandemic HIV-1.” In addition to Brandon Keele as first author, there was the usual list of coauthors, including Mario Santiago, Martine Peeters, several partners from
The first surprise to emerge from the fecal samples was high prevalence of SIV cpz in some communities of Cameroonian chimps. Two that scored highest, Keele said, were at sites labeled Mambele (near a crossroads by that name) and Lobeke (within a national park). Whereas all other sampling of chimps had suggested that SIV infection was rare, the sampling in southeastern Cameroon showed prevalence rates up to 35 percent. But even there, the prevalence was “spotty,” Keele said. “We can sample hundreds of chimps at a site and find nothing.” But go just a little farther east, cross a certain river, sample again, and the prevalence spikes upward. That was unexpected. The rates were especially high in the farthest southeastern corner of the country, where two rivers converge, forming a wedge-shaped national boundary. This wedge of Cameroon appears to jab down into the Republic of the Congo (not to be confused with the DRC), its neighbor to the southeast. The wedge was a hotspot for SIV cpz .
The second surprise came once he extracted viral fragments from the samples, amplified those fragments, sequenced them, and fed the genetic sequences into a program that would compare these new strains with many other known strains of SIV and HIV. The program expressed its comparisons in the form of a most-probable phylogeny—a family tree. Keele recalled watching the results for a certain chimp, an individual labeled LB7, whose feces had been collected at Lobeke. “We were just shocked,” he said. “I mean, I had ten people around my computer, all waiting to see what that sequence looked like.” What it looked like was the AIDS virus.
When his computer delivered its latest tree, LB7’s isolate of SIV cpz showed up as a twig amid the same little branch that held all known human strains of HIV-1 group M. (In scientific lingo, it fell within the same clade. ) It was at that point “the closest thing” to a match, Keele told me, that had ever been found in a wild chimp. “And then we find more, right? The more we dig, the more we find.” The other close matches came from that same little area: southeastern Cameroon. A chilling, historic epiphany, at which Keele and his colleagues were thrilled. “You can’t make this stuff up, as Beatrice would say. It’s too good.” Their joy lasted about ten seconds, after which everyone became hungry for more samples and more results. Your celebration is always provisional, Keele told me, until you’ve written the paper and gotten that congratulatory note of acceptance from the editors of Science.
Keele and the group now sequenced entire genomes (not just fragments) from four samples, all collected in the same area, and on those sequences ran their genetic analyses again. Again they found the new SIV cpz shockingly similar to HIV-1 group M. The similarity was so close as to leave almost no chance that any other variant, yet undiscovered, could be much closer. Hahn’s lab had located the geographical origin of the pandemic: southeastern Cameroon.
12
S o much for where as well as when. AIDS began with a spillover from one chimp to one human, in or near that small southeastern wedge of Cameroon, around 1908 (give or take a margin of error). From there it grew, slowly but inexorably, from a spillover to an outbreak to a pandemic. That leaves our third question: how?
The Keele paper appeared in Science , on July 28, 2006, under the title “Chimpanzee Reservoirs of Pandemic and Nonpandemic HIV-1.” In addition to Brandon Keele as first author, there was the usual list of coauthors, including Mario Santiago, Martine Peeters, several partners from
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