PESHAWAR, Pakistan—When Navy SEALs raided a high-walled compound in Pakistan in May 2011 and killed the world's most wanted terrorist, another long-standing source of terror also was facing elimination: polio.
After nearly half a century of vaccinating children and adults around the globe, international health workers finally had cornered the polio virus in a few remaining pockets in northern Nigeria, Afghanistan, and Pakistan. Although polio may lack the panic-inducing effect of Ebola—usually crippling its victims rather than killing them—Americans and Europeans over the age of 60 remember a period when the disease loomed as a terrorizing childhood scourge.
But the killing of al Qaeda leader Osama bin Laden that spring and the subsequent fallout in Pakistan and the surrounding region—which included targeted assassinations of polio vaccination teams—allowed the virus to fight back. Almost four years later, polio remains a significant threat in Pakistan, which reported 327 new cases in 2014, 60 percent of the world total. This month, gunmen attacked a polio vaccination team in northwestern Pakistan and another four-member team was kidnapped and murdered in the Balochistan region, near the Afghan border.
Meanwhile, polio has surfaced amid the war and chaos in Iraq and Syria, places where the crippling disease, which is spread via person-to-person contact, had been eradicated as recently as 2000.
Scientists from the World Health Organization (WHO) who study the spread of diseases say that the strain of polio virus now cropping up in jihadist-controlled territories in Iraq and Syria originated in Pakistan and followed the same route taken by the Islamist fighters who left their camps in Pakistan to fight in Syria.
In the nearly four years since bin Laden was killed, pieces of this story have come to light. But many of the unintended consequences of the raid have not been reported. This four-part series offers the first comprehensive narrative of the strange twists the war on polio has taken since bin Laden was killed.
Over the past several months, National Geographic, with support from the Pulitzer Center on Crisis Reporting, sent reporters to Pakistan and the Middle East to interview scientists, members of the intelligence community, government and military officials, foreign policy analysts, and health workers who are risking their lives in conflict zones. Their accounts offer a detailed picture of the political and biological forces that fueled polio's resurgence, and the heroic—and largely unheralded—efforts to vanquish a contagion that has plagued mankind for more than 3,000 years.
Mystery House in Abbottabad
In the spring of 2010, the U.S. Central Intelligence Agency's (CIA) search for bin Laden began to focus on a certain villa in Abbottabad, a garrison town in the Himalayan foothills of Pakistan. A mystery man was shuttered away on the villa's top floor. CIA agents suspected it might be bin Laden, but they needed to be sure before launching a raid. So they devised an imaginative plan to identify him.
Operatives would hire a Pakistani doctor and nurses to conduct a door-to-door hepatitis B vaccination campaign in the neighborhood. After the children who lived at the villa were immunized, DNA from the used syringes would be analyzed to determine whether they were related to bin Laden.
The Pakistani health official approached by CIA operatives was Dr. Shakil Afridi. Tall and stout, with a cropped mustache that gave him a military bearing, Afridi had the right credentials from the CIA's perspective. He was a Pashtun and spoke the local language, Pashto. He had conducted a successful vaccination campaign near the Khyber Pass, in northwestern Pakistan. He had lived in California for several months and had family in the United States.
The doctor says that he never knew he was working for the CIA and that he was approached by a local representative of Save the Children, who asked him to run the vaccination campaign. (Save the Children denies having any connection with the CIA or any intelligence agency, or having any role in the subterfuge.)
Either way, the offer of the equivalent of $12,500 (U.S.) to organize and administer the vaccinations came at a moment when the doctor was short on cash.
Earlier, Afridi had been kidnapped and held for ransom by Lashkar-e-Islam, an extremist militia outlawed in Pakistan. The group's commander claimed that he'd heard rumors the doctor was overcharging patients in his private clinic. Afridi's family denied the allegations but paid a $10,000 ransom. According to Afridi's attorney, the Lashkar-e-Islam commander pocketed half and distributed the rest to the patients that Afridi allegedly had overcharged.
The CIA's vaccination ploy didn't work exactly as planned.
When Afridi banged on the Abbottabad villa's huge metal gate, a woman answered and refused to allow the children inside to be vaccinated. Stubbornly, Afridi demanded the cell phone number of the man of the house so that he could possibly arrange for the children to be vaccinated at a later date. This cell phone number proved to be a vital piece of information to his handlers. It belonged to Ibrahim Saeed Ahmed, who turned out to be bin Laden's guardian and messenger. The CIA knew of his existence but had never located him. Ahmed was the al Qaeda leader's sole link to the world outside the villa's 20-foot-high (6-meter) walls.
Chasing down the lead from that phone number would lead to a major coup in the U.S.-led war on terrorism, but it also would set back the war on polio.
Pakistan's Beleaguered Polio Campaign
For decades, polio ran rife in the densely populated cities of Karachi and Peshawar and among remote settlements along the Afghanistan border—a region of maze-like canyons and mountain ranges that for centuries has been a sanctuary for bandits and smugglers and, more recently, the remnants of al Qaeda and the Taliban.
Pakistan's polio campaign had been dragging on fitfully since the mid-1990s, and even before the CIA's tactics came to light, resentment against the campaign had been building.
Among unschooled Pakistanis, many rumors abounded, including one that said the vaccine drops were part of a Western conspiracy to sterilize Muslims. (It hadn't helped that early on, polio workers wore jackets left over from a family planning campaign.) Some clerics claimed falsely that the vaccine was made of pig products, which are taboo for Muslims. Even more bizarre was a story, widely circulated after the U.S. invasion of Afghanistan, that the vaccine contained urine from then President George W. Bush.
The raid by U.S. forces on bin Laden's compound fueled the anger that many Pakistanis already felt about American involvement in the region, and the revelations about the CIA's covert vaccination plot fed into such rumors and gave them credence, say health experts.
"After Abbottabad, these rumors became fact in the minds of many Pakistanis," says an international health worker who asked not to be identified because the attack on Abbottabad remains a sensitive issue for the Pakistani government.
Afridi was arrested by Pakistan's intelligence services less than a month after the raid on bin Laden's compound, and he was vilified in the Pakistani press.
The doctor made for a convenient scapegoat, and Pakistan's government and military leadership needed one. The killing of bin Laden blindsided Pakistan's military leaders. They were exposed as being ignorant of the fact that bin Laden was hiding out in a town swarming with soldiers and secret police. Or, there was a more sinister possibility: that senior military officers were complicit in keeping the world's most wanted man hidden for years.
Health Workers Under Attack
After rumors spread that Afridi was connected to the CIA, every vaccination worker in Pakistan fell under suspicion. This was especially true in the mountains along the Afghan border, which were both high-contagion areas and Taliban and al Qaeda strongholds.
The Taliban also suspected that polio workers were secretly collecting intelligence for U.S. drone strikes. To the Pashtun tribes that inhabited these mountains, it wasn't so far-fetched. They lived in terror of the drones.
According to the United Kingdom–based Bureau of Investigative Journalism, U.S. aircraft have blasted the mountainous terrain with 400 air strikes from 2010 through 2014, killing dozens of intended targets but also hundreds of Pakistani civilians. (The Obama administration has said that it disagrees with the figures quoted in the news.)
The Bureau of Investigative Journalism reported that as many as 200 of the victims were believed to be children, a fact not lost on the Taliban's propagandists. One Taliban pamphlet circulated in North Waziristan, a tribal area along the Afghan border, inaccurately reads: "Polio infects one child in a million, but hundreds of Waziri women, children, and elders have been killed in these strikes."
Most ominously, this Taliban pamphlet also called for a ban on polio vaccinations. Their June 2012 edict was enforced with a vengeance. Soon after, the Taliban began to systematically kill polio workers, most of whom were local women getting paid $5 a day. The Taliban's method was always the same: Two riders on a motorcycle would race up to a polio worker in the street and shoot the worker twice in the head.
When the polio teams started using police escorts, the Taliban set off hidden roadside bombs that would wipe out an entire convoy. Clinics were bombed or set afire. The attacks occurred in Karachi, Peshawar, and throughout the tribal borderlands until the Pakistani health authorities, the WHO, Rotary International, and UNICEF halted all vaccinations.
And cases of polio were beginning to soar. By that point, says Dr. Elias Durry, the WHO's emergency coordinator for polio eradication in Pakistan, "we'd pretty much given up all hope of eradicating polio from Pakistan." Meanwhile, the number of polio cases in Pakistan rocketed from 93 in 2013 to 327 cases last year, according to the Global Polio Eradication Initiative, which monitors the disease.
Durry, who is from Ethiopia, isn't the type to give up easily. Dressed in battered leather hat, jeans, and cowboy boots, he looks more like a Western gunslinger than a renowned polio expert who has successfully battled the virus in some of the world's most dangerous places, including Yemen, Somalia, and Sudan.
"[The Taliban] see that the world would do anything to eradicate polio, and this was a way to hold the Pakistani government and the world hostage," he says.
In other words, the Taliban were willing to use a contagious disease, one that could cripple their own children, as political blackmail to end the drone strikes.
However, this strategy didn't stop several top Taliban commanders from secretly buying polio vaccine drops and giving them to their own children, according to a health worker in Peshawar, who told National Geographic that he personally provided doses of the vaccine to one militant chief and his family.
Virus Follows Jihadists
Meanwhile, the upheavals of the Arab Spring were starting to reverberate inside the al Qaeda and Taliban encampments in Pakistan. The overthrow of despots in Tunisia, Egypt, and Libya, starting in December 2010, inspired the departure of a first wave of Arab militants, who had been fighting in Afghanistan for more than three decades, first against the Soviets, then against NATO forces. Numbering several hundred, they and their families left hideouts along the Afghan-Pakistani border and set off to join in the foment roiling the Middle East.
According to Muhammad Amir Rana, director of an Islamabad-based think tank called the Pak Institute of Peace Studies, high-profile terrorists traveled by road across Balochistan Province in southwestern Pakistan into Iran, aided by Sunni tribes opposed to the ayatollahs in Tehran, and from there made their way into Iraq, Syria, and Egypt. Another preferred route was to hop aboard one of the many smugglers' boats plying the waters between the Pakistani coastline and the Persian Gulf ports of Dubai and Bahrain. From there, the jihadists headed back home to stir up revolt.
Most of these Islamic militants were coming from areas near the Afghan border or from the polio-infected slums of Karachi and Peshawar. Adults can be carriers of the polio virus but otherwise remain healthy. Children are more susceptible to the crippling paralysis of the disease.
A second, larger wave of Islamic militants began to leave Pakistan once fighting erupted in Syria in the spring of 2011, and this migration of fighters continues today.
They departed for a variety of reasons: Drone strikes had taken their toll; fighting was winding down in Afghanistan with the rollback of NATO forces; and al Qaeda and its extremist Sunni offshoots had called for a jihad against Bashar al Assad's regime in Syria.
But according to Rana and other defense analysts in Islamabad, another incentive compelled Pakistanis to join the jihad in Syria: money. "The financing came from rich individuals from the Middle East," says Rana. They recruited from the Taliban training camps and among Pakistan's own homegrown extremist Sunni groups, such as Lashkar-e-Jhangvi and Sipah-e-Sahaba.
In March 2014, Matthew Olsen, who was then director of the National Counterterrorism Center, warned a Senate panel, "What we've seen is a coalescence in Syria of al Qaeda veterans from Afghanistan and Pakistan."
This second wave of fighters had also been hiding in the same tribal regions where polio was prevalent. And after the killing of polio workers brought a halt to vaccinations, the virus began spreading rapidly, and many analysts believe some of these jihadists, almost certainly, would have become infected carriers.
This stream of jihadists from Pakistan to Syria increased in early 2012. By December, two children with the telltale paralysis of polio were identified in Syria's eastern province of Dayr az Zawr, which was under the control of Islamist rebel factions.
The number of cases soon multiplied. WHO officials say 36 new cases have so far been detected in Syria. As Islamist rebels swept into Iraq, several other polio cases appeared in their wake. Genetic sequencing by the U.S. Centers for Disease Control and Prevention (CDC) revealed that this strain of the virus originated in Pakistan.
Tracking Polio's Path
With some diseases, scientists can pinpoint not only its geographic source and its fatal trajectory as it spreads from village to town, country to country, but also the identity of the individual who was its first victim. In October 2010, for example, a cholera epidemic in Haiti, which infected more than 600,000 people and killed another 8,000, was traced back to a brigade of UN peacekeepers from Nepal.
But with polio, medical experts say, it is impossible to find "patient zero" and thus track the disease's movements. The virus remains submerged in a community, manifesting its symptoms in only one out of every 200 to 1,000 people. Infants are most vulnerable to the virus, which attacks the brain and the spinal cord, causing paralysis.
Polio has been afflicting humans since ancient times. Highly contagious, the polio virus lodges in an infected person's throat and intestines. It then spreads to others who come in contact with a polio carrier's feces or droplets from a sneeze or a cough.
But over the ages, the virus has reached a kind of accommodation with its human hosts. As Mark Pallansch, director of the Division of Viral Diseases at the CDC, explains: "Polio is well adapted to its host, and causing paralysis is almost an accident. It just wants to infect, replicate, and go infect someone else."
Its stealthy nature makes it hard to detect, Pallansch says. "The virology [laboratory] can't distinguish between the many ways that the virus has spread."
Since polio's symptom of paralysis strikes only a few people within a community, the best way to detect the virus's presence is through periodic tests of sewage water. Once the virus is located, scientists use genetic sequencing to find its geographical origin.
Meanwhile, the Pakistani strain left several clues along its zigzag course to Syria. Scientists found traces of it in the sewage of Cairo, the Sinai, Gaza, and even in Israel's Negev, but the disease never claimed any victims in any of those places, which notably have all maintained effective polio inoculation programs.
"For the virus to gain purchase, it's easier if there's an immunity gap in the population," says Chris Maher, the WHO's manager for polio eradication and emergency support. "After three years of war in Syria, there were hundreds of thousands of kids who missed vaccination."
Even so, Maher doubts that jihadists from Pakistan spread the disease to Syria. More likely, he says, the disease was carried by one of the thousands of Pakistani migrants seeking work in the Middle East.
But by 2012, Syria was engulfed in war, and few if any Pakistanis were venturing into the chaos looking for jobs, especially in the besieged parts of eastern Syria. And given the numbers of fighters leaving their polio-ridden strongholds in the Pakistani border region, it would seem a greater likelihood that one or more of them may have been carriers.
Intelligence officials in Washington, D.C., concur. "It's a plausible scenario, given what is known about the prevalence of polio in Pakistan," says one official who requested anonymity.
Despite the fighting in Syria and the flood of refugees, local health workers and representatives from UNICEF, the WHO, the Global Polio Eradication Initiative, and numerous other health agencies quickly responded to the outbreak. "It's a miracle how rapidly it came under control. We could have been looking at thousands of cases," says Maher.
Help came from an unexpected corner: The Islamic State—the extremist group known for beheading foreigners and massacring hundreds of Syrians and Iraqis—has allowed polio workers to vaccinate in the broad swaths of desert territory now under its medieval rule.
"My experience," says Maher, "is that opposition to vaccinations is rarely religious. It's political. It's a way of influencing the situation."
Unlike the Taliban, Islamic State chiefs were savvy enough to realize that they needed to avoid a full-blown polio epidemic in the areas under their control.
Back in Pakistan, Durry and other health experts were in a quandary over how to keep the steady rise of polio cases from turning into an epidemic.
First, health officials had to figure out a way to restart the polio vaccinations without risking the lives of any more workers. Vaccination drives usually take place over three days, and the WHO had noticed that Taliban assassins usually scoped out their ambush on the first day of vaccinations and attacked on the second day.
"We hit on the idea of getting it all done in a single day, so the Taliban wouldn't have time to react," one international health worker explains.
Peshawar, a city of three million, was at the top of the WHO's list. But the ancient crossroads was a deadly hive of narrow lanes and bazaars hiding thousands of Taliban and their sympathizers. WHO officials first had to win the provincial governor, Imran Khan, to their side.
A charismatic former cricket idol, Khan was stridently anti-American in his views and an outspoken critic of the drone strikes in his northwestern province. Khan also knew how unpopular the polio campaign had become to his fellow Pashtuns, especially after it was erroneously linked to the U.S. raid in Abbottabad.
Khan was persuaded that his province's capital would bear the brunt of the epidemic if the disease went unchecked. The key, according to health officials, was to repackage the campaign as "Justice for Health" to rid it of its American connotations. Nor was the word "polio" much mentioned. Khan himself appeared in a Peshawar mosque doling out drops. More important, Khan authorized 6,000 police officers to man checkpoints around Peshawar, enforce a ban on all motorcyclists, and provide armed escorts to the vaccinators.
In March, more than 8,000 volunteers fanned out across Peshawar, venturing into slums and neighborhoods that, only a day before, would have been too dangerous to enter. There were no attacks, and soon after, health workers tested the sewage in Peshawar for signs of the virus.
Durry was ecstatic. "We had consecutive negative samples. The polio reservoirs had been cleared out." Since then, he says, traces of the virus from the nearby tribal areas have been detected, but still not the local "Peshawar strain."
A similar, one-day blitz was carried out in Karachi, a chaotic megalopolis of nine million inhabitants, and not a single health worker was gunned down, nor were any attacks reported.
Military Offensive Leads to Inoculating Refugees
All that remained were the tribal areas controlled by the Taliban, but those seemed off-limits. Then, June 8 of last year a band of heavily armed Taliban fighters, joined by Uzbek terrorists, attacked Karachi's international airport. A five-hour gunfight ensued, leaving 38 dead, including the 10 attackers.
It was the final provocation for the Pakistani military. The generals launched an aerial bombardment and a ground offensive into the tribal areas of North and South Waziristan. The Taliban and al Qaeda fighters knew the assault was coming and scrambled through the juniper and pine forests of the Shawal Valley leading straight into Afghanistan. No longer were there any U.S. troops waiting on the other side to ambush them as they moved across the border.
In the meantime, the Pakistani military's attack was so intense and the bombings so devastating in Waziristan that hundreds of thousands of tribesmen and their families were forced to flee their mountain villages and head for safety in the settled plains along the Indus River. They fled on trucks, on tractors, even on camels and donkeys.
The offensive may have failed to wipe out the Taliban, but this mass exodus gave health authorities the perfect chance to inoculate the Pashtun tribes—people who, for years, had been beyond their reach.
Under the watch of armed guards, health workers set up checkpoints on the few main roads leading out of the tribal areas and began a massive vaccination campaign. They boarded buses and set up mandatory vaccination stalls at the British Raj–era train stations and at the village squares where men in turbans and women in powder-blue burkas pile into "flying coaches," gaudily painted pickup trucks that cram in more passengers than seems humanly possible. In all, the health workers vaccinated more than 650,000 fleeing Pashtuns, according to the WHO.
Thousands of families were driven from their bombed-out villages and forced to endure the sweltering 105°F (40.5°C) heat of the plains. They slept in tent camps or in schools, slinging blankets over the classroom windows to keep the women in purdah, away from the eyes of strangers.
But for the vaccinators, "this was a rare opportunity," says Mazhar Nisar Sheikh, a Pakistani health ministry official. "Before, there was definitely a reign of fear that stopped the tribesmen from having their children vaccinated."
That fear wasn't eliminated. Even after the Taliban fled into Afghanistan, the tribesmen were pleading with health workers not to leave the ink smear on their finger that shows they were inoculated.
Their concerns were well founded. Last December, seven Taliban gunmen sneaked back to take revenge for the military offensive: They stormed an army school in Peshawar and killed at least 150 people, mostly children. Even after the school attack, polio workers kept up their campaign.
However, after the four vaccination workers were abducted and murdered in Balochistan on February 16, officials halted vaccinations in four districts near the Afghan border.
The pitched battle to eradicate polio continues.
Editor's Note: This is the second of four articles on the forces that fueled polio's resurgence in the shadow of war. Read the second story "He Led the CIA to Bin Laden—and Unwittingly Fueled a Vaccine Backlash" here. This series was reported in cooperation with the Investigative Reporting Program at the University of California, Berkeley, Graduate School of Journalism and supported in part with a grant from the Pulitzer Center to Tim McGirk and Jason Motlagh, the lead reporters on the series.