Crisis in the Red Zone

by Richard Preston

  At this point Khan realized that he and his own staff in the Lassa program were getting cut off by the virus. The virus was driving away the hospital’s main staff, leaving Khan and his people increasingly exposed. The virus was out there and growing, and it was hitting the hospital harder and harder, and starting to erode the medical system in Kenema the way a rising tide washes away a sand castle. Khan and his people were still at their posts, but it wasn’t clear for how much longer they could hold against the virus. Meanwhile the rest of the world hardly knew that Ebola had broken out in West Africa, and the world hadn’t noticed Kenema hospital at all. It was a small, forgotten hospital hidden in the diamond fields of Sierra Leone, where something very bad was happening. Khan decided he had to act, and he called a meeting of the entire Lassa program staff, with mandatory attendance.

  SPEECH

  CRISIS OP CENTER

  8 a.m., June 12

  Khan’s meeting was held at the crisis operations center—in the Library, next to the Hot Lab. Virtually everybody in the Lassa program showed up—epidemiologists, nurses who weren’t on duty just then, lab technicians, drivers, janitors. An air conditioner was running but the room was boiling hot. People stood pressed against one another, silent and apprehensive.

  Khan spoke in a subdued voice, in the English of Sierra Leone. “Gentlemen, this is a tough encounter with Ebola,” he said. “This is a very tough battle. Extraordinary things are happening, and we have extraordinary things to do.” The nursing staff was abandoning the hospital, yet the general wards were still full of patients. Family members of the patients were taking over the care of their loved ones in the absence of nurses. The virus had gotten into the general wards. People were very, very scared.

  “Since most of the health workers have run away from the hospital, we should be ready to work,” he went on. “If you are working eight hours a day, be prepared to work many more hours. The ministers of government are very definitely looking over us now—the government is watching us closely.” What the Lassa staff had to do was to stay in the fight against Ebola, and not desert their posts the way the general staff was doing. The rest of the hospital might collapse, but Khan’s team had to hold its ground.

  Somebody in the room began crying softly. Other voices joined in the crying.

  Khan spoke over the crying. “This is our work to do. This fight is our fight now. We are working for our nation.”

  More people began weeping.

  Khan raised his voice. “If you say you will not do the work, who will do it? We must do what we can as a national sacrifice.”

  When Khan used the term national sacrifice, the crying went all through the room. The staff of the Lassa program knew exactly what he meant. He was predicting that some of the people in the room were going to die. They were government employees. They worked for the Ministry of Health of Sierra Leone. If any of them died, it would be a sacrifice for the nation. Yet as the staff members of the Lassa program looked around the room, they could see how small their team was. They filled just one room, and they were the only people in their nation who were trained to deal with a hemorrhagic fever virus. They were the front line. As they looked at one another, they had no way to know who would make the sacrifice, who would die. Casualties were coming, and Khan was warning them so.

  “No, don’t cry,” Khan said. “All we can do in this fight is take the precautions. Just be cautious.” The room cleared out and the staff went back to work.

  One member of the Lassa staff wasn’t at the meeting. It was the Kissi ambulance driver Sahr Nyokor. He was at home spitting up blood.

  TEARDROP

  CAMBRIDGE, MASSACHUSETTS

  Next day, Friday, June 13

  Working inside the glass-walled clean rooms, the scientists at the Broad Institute had combined all fourteen droplets of Ebola RNA from fourteen individuals who lived in the Makona Triangle. The result was a single, crystal-clear droplet of water solution. It was the size of a raindrop, and it contained about six trillion snippets of DNA. Each was a mirror image of a piece of RNA from the blood samples collected from the fourteen people. Most of the snippets of DNA in the droplet were human genetic code—bits of DNA from the fourteen people—but among the bits were about two hundred billion pieces of code from Ebola. There were also many billions of fragments of code from bacteria and other viruses—from anything that happened to be living in the blood. This droplet was referred to as a “library.”

  Each piece of DNA in the droplet had been tagged with a unique bar code—a short combination of eight letters of DNA code—identifying that particular fragment as having come from one of the fourteen patients. “You could consider each bar-coded fragment of DNA as a kind of book,” Stephen Gire said. “The book is bound in covers and has an ISBN [International Standard Book Number] on it. It’s a short book, so a reader can easily digest it. You can find the book by its ISBN number, and that’s why the droplet is called a library. The books in the DNA library are bound so that the library can be put in a machine”—a genetic sequencer—“and the machine reads all the books.” The “books” of DNA letters were all sitting in one immense, jumbled pile, and what was between their covers was unknown. Although the droplet was just a spot of water with DNA in it, it held as much information as the books in fifty thousand Libraries of Congress. This shows the ability of life to store huge amounts of information in a very small space. The library droplet contained fourteen images of Ebola virus, fourteen frames of a movie taken of the virus as it began to chain its way into the human species. The images were jumbled into tiny fragments and mixed together with vast amounts of other fragments inside the library droplet. The fourteen images still had to be found and pulled out of the droplet.

  * * *

  —

  On Friday, June 13, Gire carried a single microtube containing the liquid droplet library to a logging station in the Genomics Platform of the Broad Institute. He left the tube sitting in a box, and logged in a request to have the droplet sequenced as soon as possible. The task was to read the genetic information in the fifty thousand Libraries of Congress in the droplet, and thereby start developing an image of the shifting code of the Ebola swarm as it flowed through human bodies in West Africa.

  In Cambridge, at the logging station at the Broad Institute, a technician picked up the box that contained the small tube with the crystalline droplet inside it—the library of genetic code taken from the Ebola swarm in the Makona Triangle. The technician carried the droplet out of the building, down the street and around a corner, and arrived at a low, mud-colored building that had once been a storage facility for the peanuts and beer that are sold at Fenway Park. The building is now owned by the Broad Institute, and it contains the most powerful array of DNA sequencing machines in the world. Sixty of the machines sit in the center of the former peanut-and-beer warehouse, lined up in rows. The machines, tended by crews of operators, run twenty-four hours a day, seven days a week, reading letters of DNA extracted from biological samples.

  At the time the Ebola blood samples were decoded, each DNA sequencing machine was the size of a chest freezer and cost a million dollars. At the time of this writing, the Broad’s DNA sequencing machines are the size of a desktop printer. They still cost a million dollars apiece, and they are still housed in the ex–Fenway Park peanut-and-beer storage warehouse. Somehow, the Broad scientists haven’t gotten around to moving their most important equipment into the expensive crystalline buildings around the corner.

  Recently, the machines have been reading the DNA of human genes involved in schizophrenia, autism, obsessive-compulsive disorder, major depression, and childhood allergies. The Broad’s machines are also involved in a project to understand how each and every protein in every cell in the human body operates. The machines have been reading the DNA of cancer cells—part of a long-term effort to learn how to kill any cancer cell in any patient. The machines have been reading
the code of the entire human microbiome—of every kind of bacteria that lives on or inside the human body. The human microbiome lives in the intestines, in the sinuses, in fingernail grime, dandruff, tongue fuzz, tooth plaque, earwax, elbow sweat, foreskin smegma, belly button lint, and toe cheese.

  The Broad’s machines have sequenced the genome of tuberculosis bacteria, of the malaria parasite, and of the mosquito that carries malaria. They’ve read the DNA of the coelacanth, of the rabbit, and of 4,400 skeletons of people who lived in various places around Europe during a fairly interesting period of the Bronze Age that occurred shortly after Stonehenge was completed.

  Back to the raindrop of Ebola. In the room of the machines inside the peanut-and-beer building, a technician, using a pipette, sucked up about a tenth of the tiny library droplet—an amount like a fleck of moisture on a wet day—and placed it on a glass slide known as a flow cell. The fleck of liquid contained the full library of code from the blood of the fourteen Ebola patients from the Makona Triangle. The bit of water spread into channels on the flow cell, which sat in the mouth of a sequencing machine.

  For the next twenty-four hours, the sequencer worked automatically, pulsing liquids across the flow cell, while lasers shone on it. On the surface of the flow cell, hundreds of millions of fragments of DNA had gathered into hundreds of millions of microscopic colored spots. The colors of the individual spots were changing as the process went on, and a camera took pictures of the changing field of spots and stored the data. Twenty-four hours later, the machine had finished reading Gire’s library of bar-coded fragments of DNA. The data were sent to the Broad Institute’s computer arrays, which assembled all the fragments into finished genetic code—it organized the vast pile of books in the library and placed the letters of all the books in their proper order on shelves.

  Late afternoon, Sunday, June 15

  Gire and Sabeti got word that the computers had finished their work. The result was twelve full genomes of Ebola virus—the Ebolas that had “lived” in the bodies of twelve of the fourteen people. (The computers had not been able to assemble the Ebola genomes of two of the people.) Sabeti and her team started the work of analyzing the code, to see how Ebola was changing. They printed out sequences of letters of Ebola code, and began staring at the letters, looking for patterns. They worked until dark that day.

  As the sun went down on the East Coast of the United States, in West Africa it was night, and Lina Moses was working late in the crisis center. Abruptly she heard the sound of a diesel engine starting—it was one of the ambulances, she thought. The ambulance crews were forbidden to go out after dark because people were hostile to the ambulances and the roads were getting dangerous. But this ambulance was going out at night. Something bad was happening, but Moses had no idea what it might be.

  The ambulance crew had gone out to pick up one of their own. It was Sahr Nyokor, who on two separate occasions had saved Michael Gbakie’s and other team members’ lives. It was Nyokor who had heard the crowd talking by the clinic and warned Michael they were getting ready to attack, and Nyokor who had driven the getaway ambulance at Kolusu amid an ambush. Now Nyokor was heaving blood. Somebody at his house had called for an ambulance.

  His fellow drivers took him to the best ward at the hospital, called the Annexe ward. It was a private ward, where patients paid extra for their care, and was situated next to the Ebola ward. He was admitted to the Annexe late that night. Almost as soon as he got settled into bed, he started feeling better; he had stopped throwing up.

  SWARM

  KENEMA GOVERNMENT HOSPITAL

  June 16

  It was the next day that Dr. Tom Fletcher, the advance operative from the WHO, understood that his mission was going to fail. He was not going to be able to stabilize the Kenema hospital and prepare it for Ebola doctors. Fletcher discovered twenty-eight new Ebola cases in the town of Daru, on the outer edge of the Makona Triangle and an hour’s drive from Kenema. Twenty of the cases were in the Daru community clinic, which had gotten flooded with Ebola, and another eight people were found sick or dead in their houses in Daru. Fletcher had been optimistic, thinking he could help Khan get control of the situation, but now he saw that the virus was coming out of the Makona Triangle in a wave, inside people. People riding motorbikes, taking jitneys and taxis, arriving at the Kenema hospital, going to stay with relatives, going anywhere for help, heading for Freetown. The road to Freetown went from Daru through Kenema. Fletcher foresaw that a wave of Ebola was going to come out of Daru and sweep through Kenema in about a week’s time. The coming Ebola wave was likely to overwhelm Humarr Khan and his people. The virus was no longer under anybody’s control. It had gone beyond human control and had become a force of nature.

  Fletcher had to leave for important work elsewhere; he had been sent to Humarr Khan on a short assignment and he couldn’t stay. He called the WHO and asked for several Ebola doctors to be sent to Kenema immediately to give Khan backup. But there weren’t any doctors available to help Khan. The doctors who knew anything about Ebola were busy fighting the virus elsewhere in West Africa. Fletcher did get a commitment from Dan Bausch, Khan’s friend, to send two Ebola-veteran WHO doctors to Kenema in about two weeks. One of those doctors would be Dan Bausch himself. But there would be a gap of about two weeks during which Khan would be alone at the Kenema hospital. Fletcher feared that chaos could overwhelm Khan and his people during those two weeks. The wave of Ebola was coming.

  * * *

  —

  Fletcher hesitated; he thought he should stay with Khan for an extra two weeks while Khan waited for backup doctors. Fletcher phoned his bosses at the Liverpool School of Tropical Medicine. “I’m having a really hard time walking away from this.”

  He was deeply worried about Humarr Khan. And when he departed, Lina Moses and Nadia Wauquier would be the only two foreigners left working at the hospital. He felt that their lives were in danger.

  Nevertheless, on June 17, Tom Fletcher loaded his backpack into a Land Cruiser and said goodbye to Moses and Wauquier. “It’s going to get a lot worse,” he said to the women in a shaky voice. He embraced them, and they thought his eyes were wet.

  “I was close to tears,” Fletcher said later. “It was very difficult leaving. We couldn’t send in just kids from the WHO to help Khan. He needed doctors who were experienced with Ebola.” Fletcher didn’t know if he would ever see Humarr Khan or the two women alive again.

  The women watched Fletcher’s vehicle go slowly up a hill along a dirt road, heading for the hospital gates. “Lina and I felt completely abandoned,” Nadia Wauquier later recalled. “We didn’t know when any others were coming to help.”

  After Fletcher left, Humarr Khan phoned Pardis Sabeti in Cambridge. “I feel all alone here,” he said to her. “We need more resources. We aren’t getting the help we need. All the aid organizations are entrenched in Guinea. We need more foreign aid and more doctors working at Kenema.”

  Sabeti thought Khan sounded desperate, and it made her feel desperate. The War Room group was growing larger by the day, but she felt impotent, unable to help him. She also felt close to the nurses at the hospital. She had visited the hospital and had been deeply impressed by them. The ties to Kenema were strong. But all the DNA sequencing machines in the world weren’t going to help Humarr Khan and those nurses. Feeling afraid for Khan, she tried to give him a sense that she and the War Room group were doing everything possible to get more doctors to Kenema. “Know that we are working to get you help, Humarr. We’re calling all over the place.” But Sabeti wasn’t getting results with her phone calls. It was easy to get a promise of help from an organization or a government, but it was extremely difficult to get any actual help.

  Sabeti’s colleague Robert Garry, who had collected the blood samples in the Kenema Hot Lab for Sabeti, had flown to Washington to try to get some U.S. government help for the Kenema hospital and for Sierra Leone in general. H
e had just left Kenema. He knew what was happening in the Ebola ward, and he had visited Daru himself and had seen with his own eyes some of the twenty-eight people with Ebola who had just been found there. Like Tom Fletcher, Robert Garry could see the explosion of cases happening in real time, and he knew that an Ebola wave was heading for Kenema, and he tried to warn people in the U.S. government. “I went to a bunch of places in Washington,” Garry said later. “I went to Health and Human Services, I went to USAID, I talked to people in the State Department and at the NIH.” He was going around Washington just as the World Cup soccer matches were taking place. “I was giving a seminar on the Ebola situation, and maybe I’m a bad speaker, but I couldn’t help but notice people checking the soccer scores on their phones. God, they could have taken it a little bit more seriously.” In the end Garry couldn’t get anybody in the U.S. government to arrange actual immediate help for Kenema, or, he thought, to consider the possibility that a crisis in a small hospital in Africa might actually be a crisis for every person in North America. “They finally took it seriously when Ebola got to a Dallas hospital,” Garry said.

  There was a widespread view among public health experts that Ebola “burned itself out” when it entered the human species. The virus was too hot, too lethal; it killed people too quickly to be able to establish itself as a permanent disease of humans. This was the widespread opinion, anyway. The simple fact is that Ebola virus just wasn’t perceived as a serious threat.