The Viral Storm

by Nathan Wolfe

  When Don recruited me to join his growing program at Johns Hopkins, he had already established a close collaboration with a Cameroonian scientist examining retroviruses, like HIV, in the region of central Africa where they originally emerged. I would spend many years working with Don and the Cameroonian colleague, Colonel Mpoudi Ngole. During those years, we would put the foundation in place for the first real system attempting to catch novel pandemics before they emerge.

  One of the first people I met when I arrived in central Africa was the aforementioned Colonel Mpoudi (pronounced m-POODY), a large, imposing, mustachioed man who so consistently wore a uniform that I wondered at times if he slept in it. The Colonel, as I refer to him to this day, is a quiet but incredibly productive physician and scientist. He is known by many of the people in Cameroon as Colonel SIDA (SIDA is the French acronym for AIDS) for his years of relentless work to stem the tide of the AIDS pandemic in central Africa. The Colonel has a subtle yet commanding presence, and he’s used to getting his way. During my first years in Cameroon, we did battle from time to time, fighting over the best way to use scarce resources. Yet I always respected him as an effective and caring leader who knew how to negotiate better than anyone I’ve ever met, and even more importantly knew how to get things done. Over time, he came to be an important mentor and dear friend.

  Colonel Mpoudi Ngole. (Nathan Wolfe)

  Among the subjects that Don and the Colonel had thought carefully about was bushmeat, and it would be a central subject for the work we’d do in central Africa. Bushmeat is another word for wild game, although historically the term tends to refer to wild game in tropical locations. In reality, when my friends hunt and eat venison in their yearly New England ritual, they’re eating bushmeat. And when I visit my favorite seafood place in San Francisco—Swan Oyster Bar—the living sea urchin they carve open and serve me in the shell is also bushmeat. Yet as we learned in chapter 2, from the perspective of microbes not all bushmeat is created equal.

  * * *

  When we started our work in Cameroon, the overriding objective was to understand why HIV in central Africa was so diverse compared to the fatal but genetically bland and homogenous cosmopolitan versions of the virus that hit most of the world. The idea was to sample HIV from people throughout rural regions and hopefully explain why so many different genetic variants of the virus existed in this part of the world. All of the evidence pointed toward this region as the place where HIV began, but why did it remain so diverse twenty years after the pandemic had exploded?

  To answer the question, we teamed up with some of Don’s former colleagues at WRAIR (Walter Reed Army Institute of Research), where he had spent most of his career. I remember first meeting the dynamic duo—Jean Carr and Francine McCutchan—at their unremarkable office space in unremarkable Rockville, Maryland. But there was nothing at all bland about the work they’d done.

  Over the five years before I met them, the pair had revolutionized the study of HIV by creating methods to sequence entire HIV genomes and systematically study where their various genetic bits and pieces had come from. Prior to their work, people had largely stitched together smaller pieces of genetic information to get a picture of the sequence of the entire virus. Carr and McCutchan had come up with a way to pull the entire ten thousand bits up in one fell swoop. This permitted them to dive into the history of the different genes that made up the viruses.

  Since HIV recombines, or has the capacity to mix and match genes among different strains, they needed to form a new set of analytical tools to understand which bits fit together and from where each bit had descended. They were practicing virus genealogy. But instead of piecing together the ancestry of a Scandinavian monarch, they were determining the parental strains of particular HIV viruses and mapping them globally to try and reconstruct the course of the pandemic—plotting out a map of how HIV had spread and mixed.

  Along with a dedicated team of local scientists, the Colonel and I would work over the next few years to try to sort out the causes for the intense genetic diversity of HIV in central Africa. Basically, we wanted a snapshot of what HIV looked like before it went global. We started by setting up shop in rural villages throughout Cameroon. The work in the villages was coordinated by Ubald Tamoufe, a soft-spoken and highly meticulous engineer turned biomedical scientist, who still coordinates our joint work in central Africa. We didn’t pick just any rural villages. In order to avoid capturing the relatively boring garden-variety strains of HIV that now spread throughout the globe and even in regions like Cameroon where the pandemic began, we picked isolated villages found where the roads end.

  Dr. Don Burke (far left) with (L-R): Dr. Inrombé Jermias, Major Wangmene, Dr. Nathan Wolfe, Ubald Tamoufe, in Cameroon. (Ubald Tamoufe)

  * * *

  To say these places were challenging to get to only hints at the complex logistics required to obtain the high-quality specimens Carr and McCutchan needed. These were some of the most remote regions of central Africa. Among their incredible stories comes one from a beloved project driver, Ndongo, who like the Colonel, was largely referred to by his rank, sergent-chef, rather than his proper name. Sergent-Chef once had to abandon his car on one side of a river, then crossed it by small canoe to help our team get specimens from the small village of Adjala in the far southeast of the country.

  Sergeant-Chef (L) with GVFI team in Cameroon. L-R: Sergeant-Chef Ndongo, Ubald Tamoufe, Alexis Boupda, Ngongang. (Jeremy Alberga)

  Obtaining the specimens from these incredibly remote locations held out particular challenges and frustrations but also wonderful experiences. During one particularly memorable visit to a rural village, this one in DRC, I spent the day with hunters in the forest. Upon my return, I learned that a baby boy had just been born to a woman in the village and that they wanted to honor me by giving the child my name. Since one of the villagers had heard me referred to as Docteur Natan (French for “Dr. Nathan,” as I’m sometimes called in that part of the world), that was the name they chose for the boy. Not “Nathan” but “Doctor Nathan.” The expert research logistician, Jeremy Alberga, who has kept our administrative, logistical, and financial operations organized over the years, joked that the name would decrease the need for burdensome higher education. The boy was already a doctor.

  But what exactly were the specimens we were collecting? To start with, we needed blood. From the people who enrolled in our studies, we collected two tubes of blood using high tech tubes that would allow us to easily separate the different parts of blood when we got back to the laboratory in Yaoundé. As for the animals, at least to start with, we worked using a simple but innovative approach, a method developed by Mat LeBreton.

  When I originally met Mat in Yaoundé, he was just completing a monumental survey of snakes in Cameroon. Interestingly, he’d done the majority of his sampling by leaving pots of formalin preservative in villages across Cameroon. Since humans throughout the world kill snakes when they find them, he simply asked them to put the dead snakes in the formalin pots, which he’d collect from time to time to study their distribution and diversity. As we talked, we realized that a similar approach could be used to easily collect thousands of specimens from animals. We could adapt the filter-paper techniques I’d learned from Janet and Bal Singh in Malaysia years ago and simply pass out the baseball-card-sized sampling papers to hunters and let them collect specimens whenever they came into contact with blood. The technique proved incredibly successful, and we now have among the most comprehensive wild animal blood collections in the world.

  Filter papers used to collect blood samples from bushmeat and other animals. (Matthew LeBreton)

  In addition to the challenges of simply getting to tough places to collect specimens, we had the difficulty of communicating our intentions to potential participants in our studies. Gossip and rumors abound in these small villages, and the villager’s range of speculations about nefarious purposes for the blood we needed from them was broad. Fortunately, among the excellent staff w
ere some of the most talented communicators I’ve had the good fortune to work with.

  Particularly notable was Paul Delon Menoutou, who had spent years as the chief health correspondent for Cameroonian radio and television, joining us upon his retirement. In many of the rural villages where we worked, people had never had access to television and didn’t recognize his face, but when he began to speak, they instantly knew his voice. As a trusted and amazingly talented communicator on health issues, he helped us to ease our way into these communities, which could otherwise resist answering the scientific questions we asked. He also helped convey critical health messages that were a fundamental part of our mission.

  * * *

  Over the first few years in Cameroon, we managed to build a functional laboratory in an amazing century-old building that hailed from the German colonial period in the capital of Yaoundé. We also established connections to seventeen rural villages in fascinating, biologically diverse parts of the country. The high-quality frozen specimens we obtained held clues to the problems of explaining HIV diversity and, as we’d find, much more.

  By the time they got into the Rockville laboratories, the specimens had moved thousands of miles by road and air yet remained frozen and viable for testing. I spent some time working in the lab myself, anxious to see exactly what was in the specimens. However, much of the heavy lifting of characterizing the viruses in the specimens was left to McCutchan and Carr and their capable lab teams.

  In the end, they found remarkable diversity in these HIV specimens. Twelve of the villages we worked in had completely unique forms of HIV—viruses that were patched together of different sorts of HIV variants, ones that had never been seen together before. In nine of the villages, there were two or more of these unique forms of HIV. Our conclusion was that these locations likely showed what HIV looked like prior to its global spread. Essentially, following the entry of the virus from chimpanzees in the early twentieth century, it likely maintained itself in small villages like the ones we’d studied. Over time, as the virus changed, the newly diverged forms came into contact with each other, shuffling their genetic information and producing an incredible assortment of genetic novelties. Only some of these strains would win the microbial lottery and spread. The rest would remain interesting viruses near the place where their ancestor viruses continued to live in wild chimpanzees, staying put but almost certainly causing disease like their more prolific kin.

  While in these rural villages, we did more than just collect specimens to answer our questions about HIV diversity. We also looked into the ways that people interacted with wildlife, a study coordinated at the time by Adria Tassy Prosser, an anthropologist and epidemiologist now based at the Centers for Disease Control in Atlanta. We learned that people in these rural villages had an incredible and intimate level of contact with wild animals. The process of butchering involved direct contact with virtually all of the blood and body fluids that viruses call home. As we expected, people who were engaging in hunting and butchering were at the front line of viral transmission from animals to humans. As we worked in these villages, I became convinced of the potential for these populations to serve as sentinels to allow us to monitor viral chatter. Bushmeat and human contact with it became an almost obsessive focus for me.

  * * *

  But my first real encounter with bushmeat was not in a village. It was at Colonel Mpoudi’s house. One of the things the Colonel and I did well together was eat. It was something we’d do in countless villages and cities across the central African region. When you eat dinner at the Colonel’s house, you can always expect something special. Along with his gracious wife, Evelyne, herself a successful official of the Ministry of Education, the Colonel has an incredible capacity to make people from any country or class feel comfortable. His dinners in recent times have come to include performances by an excellent local singer—a prominent and vocal member of a group of people living with HIV/AIDS. But whatever the crowd or entertainment, flowing champagne and food are always among the memorable features of the evening. And among the eclectic foods served are always local wild game delicacies. Perhaps my favorite at Chez Mpoudi is porcupine, which tastes a bit like rabbit.

  People, wherever they are, traditionally eat wild animals. And while the conservation implications of the consumption of wild animals are important, it’s also important that we don’t demonize the people that consume these animals to survive. If we could snap our fingers and instantly provide access to high-quality protein sources that didn’t involve contact with wild animals, that would be best. It would aid in the conservation of some of the most important endangered species, and it would decrease the prevalence of pandemics. But the problem runs deep.

  During the past twelve years, I’ve worked with many hunters throughout central Africa and in Asia. While illegal commercial hunting exists and must be eliminated, the majority of animals that are hunted in the regions where we work are hunted to provide basic food to needy families. It is subsistence, not entertainment. Hunting is hard work. It requires tremendous energy for a fairly modest outcome in calories.

  While many of the hunters we work with are excellent at hunting and some even enjoy it, most would likely choose a cheap and nutritious form of protein that didn’t involve hours tracking through incredibly hard-to-negotiate landscapes—fish, for example. I remember my encounter with a man who was headed to his village, carrying a monkey he’d hunted on his back. One of my first thoughts when looking at the bloody and battered animal was how unfortunate it was to lose such a beautiful and important part of our planet’s wild heritage. But I also saw that the man was wearing flip-flops and ragged clothing and was sweaty and dirty from a whole day in the forest. He certainly was doing this for his livelihood and not for sport! Subsistence-level hunters are not the enemies and, as we’ll explore further in chapter 12, the solution is to work with them rather than against them.

  Hunter carrying his bushmeat, Cameroon. (Nathan Wolfe)

  As we pushed forward with our work to characterize the diversity of HIV among these rural hunting communities, we also began what would become a main focus of my work over the past ten years—to discover completely novel viruses jumping into these highly exposed peoples. To do so, we approached one of the world’s top laboratory teams for discovering novel retroviruses, the broader family of viruses that includes HIV—the CDC’s Retrovirology Branch.

  The CDC team included Tom Folks and Walid Heneine, two of the world’s leaders in retrovirology, but the person I’d spend most of my time working with was Bill Switzer. Bill has a youthful appearance that belies his actual age and a mellow demeanor that masks his relentless drive to chart the evolution of some of the most interesting viruses of our time. Whether face-to-face or by phone, Bill and I would spend the next ten years working together on an almost daily basis to assess what viruses besides HIV had jumped into those hunting populations.

  My first major discovery with Bill was of an ominously named virus, the simian foamy virus (SFV). SFV received its name because of the way it kills cells. When you look at a culture infected with the virus, the cells die and bubble up, leading to a foamy appearance under a microscope. It’s a virus that infects virtually all nonhuman primates. And since each primate has its own particular version of the virus, it provides a great model for comparison. By sequencing the viruses, if we were then to find one in humans we’d know exactly what animal it had come from.

  Interestingly, humans have no indigenous foamy virus. Bill and his colleagues showed some years ago that foamy virus has the unusual feature among viruses of cospeciation. In other words, the common ancestor of all living primates some seventy million years ago had a foamy virus, and as the various branches of the primate tree speciated over time, the virus passed along. The amazing result is that the evolutionary tree of foamy viruses and the evolutionary tree of primates are virtually identical. SFV may very well have been one of the viruses we lost during the pathogen bottleneck discussed in chapter 3. />
  When Bill and I and our colleagues started the work with primate foamy viruses we already knew that they could theoretically infect humans, as a few lab workers had previously acquired the virus. But we had no idea if this occurred under natural settings. We were surprised and quite excited to find that it did. I remember well the exact day it became clear. We were working together in Bill’s lab, and I went downstairs to get the images of a lab test called the Western blot, which shows whether or not individuals have produced antibodies against, in this case, the simian foamy virus. Bill came down that day to help me interpret the images. As soon as we saw the results, it was obvious that some of our study participants had been infected. I remember Bill and I looking at each other with equal parts shock and excitement. In a tangible way the work over the past years changed dramatically at that moment. To this day I have a framed copy of the Western blot on my wall.

  Western blot showing the first evidence of antibodies against simian foamy virus in hunters. (Nathan Wolfe)

  On the one hand, there was relief—the research had succeeded. But there was also a sense of foreboding for us—retroviruses, viruses from the class that had produced HIV, were crossing into humans. And if we were seeing it within the first few hundred hunters we’d studied, it was by no means rare.

  Over the coming months we saw that in fact a number of the people in our study who had reported hunting and butchering nonhuman primates had been exposed to SFV. More amazingly, some of the exposures had gone on to become long-lasting infections. After finding evidence that these individuals produced antibodies to the virus, we tried to obtain actual SFV genetic sequence, and what we saw surprised us. We found multiple people who were infected with strains of SFV from primates, ranging from the DeBrazza’s guenon, a small leaf-eating monkey, to the massive lowland gorilla. To our great satisfaction, we found that the results of our behavioral surveys matched. The gorilla SFV, for example, came from a man who had reported hunting and butchering gorilla meat. While many of the people in our survey had exposure to primates, few participated in the dangerous and highly specialized hunting of gorillas. The link was a smoking gun—the gorilla hunter had acquired the virus while hunting or butchering his prey.