MAKING THE LEAP
Scientists worry the next devastating disease could be born where animals and humans mix in a Third World slum — then cross the globe. Zika may have been a preview.
NAIROBI, Kenya - Kenyan researcher James Miser Akoko stood at the edge of Nairobi’s vast Dandora dump in the late afternoon heat, staring down into a recipe for the next pandemic.
Below him, dozens of men and women scoured a 30-acre garbage pit in a grim version of recycling, gathering deflated soccer balls, soiled plastic toys, filthy clothing and blankets, even abandoned airline food. They worked with bare hands and no face masks, shrouded by smoke from small fires and shadowed by the large marabou storks with which they compete.
Free-ranging pigs, goats and other livestock grazed on refuse, marking time until the day they become food themselves — human food.
A quarter of a mile away, in the neighboring Korogocho slum that shelters 150,000 of Nairobi’s poorest people, Akoko encountered a middle-aged woman laboring over a large, uncovered pot of simmering chicken intestines. These she would sell to passers-by in the slum. Then, as the sun set, she would turn her attention to another source of food and income: an open bag of raw chicken legs and feet, fought over for now by buzzing flies.
As she tended her pot, dozens of marabou storks appeared, circling overhead.
“One task that is still undone for us,” Akoko said, “is to go into the dump sites and catch the marabou storks to see what they are carrying.
“Studies have shown that they’re quite good for the ecosystem because they basically clear the dead stuff — pieces of meat, dead animals. But we don’t know what they are spreading in Nairobi in terms of disease.”
When scientists worry about the next big outbreak, it is places like this they mention: sprawling Third World cities, with large populations of humans and animals living together amid the squalor of dirty water and poor sanitation. Of Nairobi’s 3.4 million people (more than the combined populations of Chicago and Milwaukee), about 60% live in densely packed slums, sharing muddy roads with goats, pigs, chickens, cows, dogs and rodents.
Imagine a melting pot into which the livestock, the birds, the flies and the people all contribute bacteria and other microbes — a Petri dish for the creation of new threats to human health. Pigs, for example, act as mixing vessels for influenza. They can be infected by both bird and human flu, allowing genetic material from each to combine and form new strains.
A few years ago, researchers at King’s College London imagined how this biology might play out in a slum, devising a hypothetical scenario in which “poor sanitation and high population densities lead to a new outbreak of virulent influenza.”
Their scenario begins with impoverished residents watching their pigs and poultry fall ill, suffering high fevers and bleeding from the mucous membranes in their mouths and noses. Within a day, animals begin to die. Within a few weeks, the new influenza spreads from the animals to the humans who handle them. And because the residents have lives outside the slum, working in hotels and factories, riding on buses, shaking hands with everyone from aid workers to merchants, the influenza advances beyond the slum.
By the time the World Health Organization sounds an alert, the disease has already crossed continents.
Within a month and a half, the authors wrote, “the virus has spread to nearly 80 million people worldwide. Carried abroad by international long distance commercial flights, the illness leapfrogged out of Asia and appeared in Hong Kong, London, Paris, Marseilles, North Africa, New York, Beijing, Calcutta and Dubai almost simultaneously.”
All told, the influenza kills 140 million people.
It is only hypothetical, of course, though “a plausible situation,” said Kristen Bernard, professor of virology at the University of Wisconsin-Madison’s School of Veterinary Medicine. “Absolutely, it’s plausible.”
The authors set their scenario in the povertystricken favelas of São Paulo, Brazil. They chose the favelas because these areas have a high density of humans and animals living in close quarters, sharing poor water and sanitation.
Much like Nairobi. Or Mumbai. Or Mexico City. Or dozens of similar cities around the globe, all expanding, as the world’s population shifts from rural to urban areas.
In Nairobi, where the population has more than doubled in 27 years, Akoko’s employer, the International Livestock Research Institute, is not waiting for the next pandemic. The institute is part of a project studying the interactions between people and animals in the city and how those contacts contribute to disease. The goal: to change the conditions and behaviors that put Nairobi at high risk for outbreaks.
“Korogocho is a slum and the ground underneath Korogocho is a (former) dump,” explained Eric Fèvre, a researcher at the University of Liverpool who also works for the institute and leads the project Akoko works on. “These guys (in the dump) they’re exposed to birds and rodents and feces . ... Hundreds of people depend on that dump.”
Alongside the dump flows a tributary of the Nairobi River, a waterway so polluted with litter and human and industrial waste that Fèvre called it “basically a sewer full of plastic bags.”
*** Americans seldom see the disease-brewing conditions in Nairobi and similar large cities across Africa and Asia, but scientists say they can no longer afford to dismiss them as problems of the developing world. Our higher standard of living and advanced medical system do not insulate us from diseases emerging halfway around the globe.
The notion that we are safe from distant outbreaks is a “historical misconception” that dates back a century to the days before international air travel, said Amesh Adalja, a senior associate at Johns Hopkins Center for Health Security.
Back then, the U.S. had cholera and yellow fever outbreaks of its own, but it faced much less of a threat from infected travelers. Many died of the diseases they picked up overseas before they could return home to spread them.
Today, “a microbe originating in Africa or Southeast Asia can arrive on North American shores within 24 hours,” according to a 2014 report by the U.S. Centers for Disease Control and Prevention.
We’ve already seen the results. Studies say that a majority of U.S. cases of difficult-to-treat, drug-resistant typhoid fever can be traced to six developing countries.
Last year, a record 213 million international travelers flew in and out of the United States. In 2015, the most recent year for which data is available, more than 29,000 Kenyan citizens visited the U.S.
While air travel now links Kenya and the U.S., offering a path for disease, the countries start out with very different risk profiles. Americans still benefit from basic necessities most Kenyans lack: clean water, good sanitation and mosquitoproof homes equipped with screen windows and air conditioning. The difference in disease toll is staggering.
Each year the U.S. records an estimated 1,500 to 2,000 cases of mosquitoborne malaria, almost all involving travelers from abroad. Kenya records more than nine times as many cases on an average day — some 6.7 million cases a year, including 4,000 deaths.
“It’s a very debilitating disease,” said Bernard Bett, a senior scientist at the Nairobi institute who survived several bouts of malaria during his childhood in the Kenyan highlands. “You get headaches. You don’t eat. You don’t have the strength to do anything.”
Most American children never know the misery of malaria, another reason it is sometimes easy to believe ourselves immune to the pathogens flourishing in the developing world. Still, the U.S. has experienced the havoc that even a single case of a tropical disease can cause.
In 2014, Thomas Eric Duncan showed no symptoms of illness when he boarded a plane in Monrovia, Liberia, bound for the U.S. He arrived in Dallas on Sept. 20 and became ill a few days later — America’s first case of Ebola and its sole fatality.
“The first case of Ebola diagnosed in the U.S. had major cascading effects that rippled through several industries,” said Adalja, the Johns Hopkins researcher. “Every hospital
had to augment their preparedness, public health agencies were tasked with monitoring large numbers of those returning from West Africa, airport screening tools had to be developed, and general panic from the public and politicians ensued.”
While our Ebola scare passed, a longer-term problem arrived last July.
A little more than a year after the Zika virus began storming through Brazil and most of Central and South America, the virus arrived in South Florida. It’s not known for certain whether Zika came to Miami on a plane, but once there, it found a home.
“It was not ‘if,’ but ‘when,’ ” said José Szapocznik, a Zika expert at the University of Miami, explaining that the mosquitoes that carry the virus were already in Florida, “up the East Coast, out to Texas and the Gulf areas.”
All the mosquitoes needed were infected people to bite, and they would find them soon enough.
“There is a huge viral reservoir in the Americas,” Szapocznik said, “and we have people coming from that viral reservoir to Miami on an ongoing basis.”
While not a pandemic, Zika offers a case study. From its discovery seven decades ago in a forest in Uganda, Kenya’s neighbor to the west, the virus traveled thousands of miles to the neighborhoods of Miami.
A new disease to test us.
*** Zika arrived last July at the peak of a hot, humid Miami summer.
Tourists and locals were crowding the sandy beaches and bustling, narrow streets of Miami Beach, strolling between stores and sipping drinks
under the beaming sun.
For two local women, Yessica Flores and Sloane Borr, it was a joyous time. They were pregnant.
Flores, 38, was nearly three months into her pregnancy; the child would be her second. An immigrant from Honduras, she lives in a colorful two-story home in Miami’s Wynwood neighborhood with her husband, her mother and her 14-yearold daughter, Andrea. The family had just returned from a trip to Honduras a few weeks earlier, and Flores was alternating between responsibilities at home and her job in the cafeteria of a local school.
“I heard about Zika from the time it started in Miami,” Flores said, speaking through an interpreter. “But I didn’t bother with it.”
Borr, 30, lives a few miles northeast in a gated community near Wynwood. A writer, she works from an office in the home she shares with her husband, Paul, and their dog and cat.
Borr was aware of Zika’s spread through the Americas, but the threat seemed distant. As a soonto-be mother, she sympathized with the mothers of the infected babies in Brazil. But mosquitoes, though a nuisance, were simply nothing new.
“That’s just like a way of life in Miami, to be covered in mosquito bites,” Borr said. “You don’t think anything about it. You don’t realize that, in other countries, a mosquito bites you and you could be dead.”
Watching Zika more closely than the two women was a man named Chalmers Vasquez, operations manager of Miami-Dade County’s mosquito control team. He believed the region was ready to combat the mosquito that carried the virus. In the past, the department had handled such tasks with ease.
The county had recorded cases of dengue fever in 2010 and 2014 and chikungunya, also in 2014. Both viral diseases are transmitted by the same mosquito responsible for Zika: Aedes aegypti.
On July 15, 2016, Vasquez and some co-workers stopped for lunch in Fort Myers on their way back from a visit to another mosquito control district when his phone rang.
Zika had arrived in South Florida. It was the county’s first Zika case caused by local mosquitoes.
That night, he and his team set their first round of mosquito traps and began monitoring the population.
*** For more than half a century, Zika had kept a low profile.
Discovered in 1947 in a monkey from Uganda’s Zika Forest, the virus spread through mosquitoes in Africa and Asia. Humans rarely got the virus, and the symptoms were so mild that those who did rarely sought treatment.
In fact, Zika seemed the least troubling of the various diseases carried by
Aedes aegypti. The others — chikungunya, dengue fever and yellow fever — all continue to ravage countries that lack proper mosquito control.
By comparison, Zika had done little damage.
Before 2007, only 14 cases of Zika had been documented in people, according to the World Health Organization. Because only 20% of patients show symptoms, it can be difficult to track the movement of the virus.
Despite the scarcity of symptoms, blood tests showed the virus was actually very common in Africa and had spread to Southeast Asia: from 2% infected in North Vietnam to 75% in Malaysia.
Still, Zika wasn’t a high international concern until a small island in Micronesia, called Yap, began to notice a new illness causing rashes, pinkeye and joint pain. It looked like dengue, but something was different: the fever was milder and accompanied in some cases by pinkeye. In June 2007, lab samples sent to the CDC confirmed the disease was Zika. The stealth virus had caused its first outbreak.
In the end, an estimated 73% of Yap’s more than 7,000 residents were infected.
Soon, the virus began popping up in other places that had never seen it before — places where people had not developed immunity.
In May 2015, eight years after the outbreak on Yap, researchers in Brazil’s National Reference Laboratory confirmed Zika was circulating in their country. Reports of birth defects that would later be linked to Zika infection began to pour in: babies born with small heads and poor eyesight. The babies wailed in almost constant pain.
Zika’s sudden rise to international prominence continues to baffle experts. It is unclear how the virus went from anonymity to, as the World Health Organization called it, a “public health emergency of international concern.”
The global outbreak left scientists wondering how the severe effects of Zika, including the birth defects, went unnoticed for decades.
Some have suggested that in the new areas, there were simply more pregnant women vulnerable to infection. In Asia and Africa, where many had already caught the virus, the only people left to infect were children, and they would have immunity by the time they reached childbearing age, said Sharon Isern, a researcher at Florida Gulf Coast University.
Matt Aliota, a researcher at UW, suggested another possibility: The virus had never infected a population large enough to allow scientists to track the effects.
One other factor could be at play, according to a 2016 article in the journal Clinical and Translational Immunology by Isern and her colleagues: Dengue.
Lab work by Isern suggests a prior dengue infection could allow Zika to proliferate more in the body, causing the severe infection characterized by birth defects in babies. However, the theory remains controversial, and early research in primates at UW has shown there may be no such effect.
Brazil’s outbreak was curbed, thanks to a wideranging strategy of mosquito control — from fumigating 20 million homes, to releasing millions of genetically modified mosquitoes that produce infertile offspring. Even so, the outbreak crossed borders. As of March 2017, 84 countries have reported evidence of Zika in native mosquitoes.
The breeding habits and distribution of Aedes
aegypti make it a beast to control, said Vasquez in Miami. Still, the mosquitoes themselves can’t travel very far — only a quarter mile in their lifetimes.
But people can. And so, Zika crossed the ocean and made its way to Miami.
*** In Kenya, the second week of January this year brought a fairly typical burden of disease: 61,000 new cases of malaria (30 years’ worth for the U.S.), and 3,200 cases of typhoid fever (six months’ worth for the U.S.).
On this particular week, though, the challenges facing Nairobi’s health care system were more of the slowly ticking, time bomb sort: the kind illustrated by the gap between city laws and the lives of city residents such as Paul Mugai Ngage.
Ngage lives in a place that is absent from most maps, a blank space where more than 133,000 people live. Officially, the Kawangware slum does not exist. Neither does Korogocho, where the scavenged goods from the dump are sold. All of Nairobi’s slums are considered illegal settlements.
Yet there stood Ngage, smiling as he gestured across his yard.
“Welcome to my home,” he said, laughing and describing his age as “over 75.”
The little property where he lives belonged to his father, who now lies buried behind the house. Today, Ngage shares the modest concrete home — essentially one large open room — with his wife, six children and “many grandchildren.”
In Nairobi, keeping livestock in the city is illegal, as it is in many large cities around the world. The practice began falling into disfavor in the 19th century, considered unsanitary and a disease risk.
Yet there in Ngage’s yard roamed an assortment of goats, sheep, geese, chickens and the family dog. The jawbone of a dead cow lay in the dirt, just outside the pen where the family’s lone surviving cow was resting. Rabbits and pigeons stared out from a stack of hutches.
“What you should appreciate is that the goats, sheep, the geese, the chickens, all of them are in one area, where they interact,” explained Patrick Muinde, a veterinary research assistant at the Nairobi institute. “A disease which can be transmitted by geese can be passed to chickens with severe consequences.”
Ngage’s yard and the air around it amounted to a microbial stew, a single place in which different species deposited their wastes, bodily fluids, even the tiny droplets that spread influenza.
Many animals have their own strains of influenza.
When they are kept in close quarters, a single animal may be infected with two different strains. As a result, segments of genetic material from one strain can mix with those from the other to form something new, a process scientists call reassortment.
This is how new pathogens are born.
None of the conditions in the yard is unique to Ngage’s home, but they are common in the slums, where poverty and tradition dictate behavior. For poor families, soap is a commodity that must be weighed against necessities such as water, food, shelter and school fees for the children.
“They’ll tell you, ‘I’ve not been washing my hands. I’m OK. What does it matter?’ ” Muinde said of the residents.
Here open-pit latrines — slits in the ground that must be crouched over — are a luxury. Those who do not have one must pay 5 shillings (roughly 5 cents) each time they need to go. Some lack the money, and at night, women feel unsafe venturing out in the slums.
So, residents have devised an alternative, the so-called “flying toilet.” The poor use plastic bags for their excrement, then throw the bags as far as they can.
Although human waste is a source of many diseases, including cholera, typhoid and hepatitis, discouraging residents from resorting to the use of flying toilets is not as simple as it might seem.
“People don’t use flying toilets because they want to, but because they don’t have any choice,” said Fèvre.
Residents in the slums have made the same point while admitting to researchers that they have eaten airline food collected from the dump or chicken feet from the floor of a slaughterhouse.
“They know there may be risks,” Fèvre said, “and they don’t like those risks, but they don’t have a choice . ... So it is a survival strategy, and changing that means changing the root cause, which is poverty.”
Fèvre and his fellow researchers have spent years earning the trust of Nairobi residents in the course of a study called “99 Households.” The project examines a variety of homes, from the slums to the wealthy neighborhoods, focusing on the comparative disease risks of those who keep livestock at home and those who do not.
Researchers visit each home once with a medical and veterinary team, taking stool samples from every individual in the household — humans and livestock — and walking around kitchen and livestock areas in special absorbent shoes that pick up microbes from the floor.
They also set traps to catch the wildlife — everything from birds and bats to rats, mice, squirrels and mongooses.
Whenever they see risky behaviors, the researchers try to correct them. But in the slums the prohibition on keeping livestock takes a backseat to survival.
“There is a difference between the letter of the law and the practice of it,” Fèvre said. “We stumbled across a guy living in a three-story shack built with scavenged wood and keeping 6,000 chickens.”
*** In the days after Zika arrived in Miami, Vasquez’s team worked quickly, walking through neighborhoods spraying insecticides from their backpacks. The day after the virus made its first appearance, they searched for anything that could collect water for the mosquitoes to breed in — no bottle cap was too small.
Borr, one of the mothers-to-be, watched the virus change the city she’d lived in since she was 4.
“It felt like a zombie apocalypse was happening, or something. It felt so weird,” she said. “I’ve never seen anything like it.”
Within a few days, Borr and her husband had decided that she should leave Miami to live with family in Boston. She stayed there for a month and tested negative for the virus.
Still, she missed her husband so much that she returned to Miami in September.
Borr stayed in her home for the rest of the outbreak, armed with hand-held bug zappers and shielded by citronella candles and mosquito netting. She and her husband covered themselves in bug spray and layers of clothing any time they went out. They refused to eat in restaurants where the doors and windows were open.
She wore an impenetrable beekeeper’s suit for her outdoor pregnancy photo, then added a wry, Hollywood-style caption: “Love in the time of Zika.”
Meanwhile, by August, Flores was about five months into her pregnancy. One day, while working at her job in the school cafeteria she received a phone call. It was the lab processing her Zika test. The voice on the other end kept asking questions until Flores posed one of her own.
“Does this mean I have Zika?”
She was told she would need to talk to her doctor.
The answer she finally got was not the one she wanted.
“I started to cry, ‘Oh Lord.’ And then one of the women doctors told me, ‘Take it easy, everything will be OK.’ My reaction was something strong,” she said. “But I asked the doctor, because there was all this talk about Zika, I told her that I had no symptoms, I had felt nothing.”
No fever, no rash, no joint or muscle pain. But the test was positive.
As of mid-June 2017, Flores was one of 351 pregnant women in Florida to show lab evidence of the Zika infection.
It is still early in our understanding of Zika’s link to the birth defect microcephaly: babies born with abnormally small heads due to underdeveloped brains. Doctors could not tell Flores and the other mothers whether their babies would have the birth defects.
They could only monitor the babies’ development every week.
Flores began to pray.
The Pulitzer Center on Crisis Reporting, which funds international reporting on underreported topics, is providing support for this ongoing series of stories.
Coming Monday: How Zika played out in Miami, and what researchers are learning in Nairobi to prepare for the next outbreak.