Last year, the World Health Organization declared the country to be "polio-free." That milestone meant the disease was gone from the entire continent of Africa, a major triumph in the multibillion-dollar global effort to eradicate the disease.
But that declaration of "polio-free" turned out to be premature.
Three new cases of polio have been confirmed in areas liberated from Boko Haram militants, prompting health officials to launch a massive campaign to vaccinate millions of children across four countries in West and Central Africa
Before the cases were found, the world appeared extremely close to making polio the second human disease after smallpox to be eradicated. There had been fewer than two-dozen polio cases in 2016, clustered in Pakistan and Afghanistan.
Then health officials in Nigeria found three paralyzed kids inside parts of Borno state that had been held by the Islamic militant group Boko Haram.
Dr. Chima Ohuabunwo, an epidemiologist who's been working with the U.S. Centers for Disease Control and Prevention in Nigeria for the past five years, says Boko Haram has cut off parts of Borno state, in Nigeria's northeast, from the rest of the world.
"There's been no direct in and out movement of persons, or access to health care, for the past two to three years," Ohuabunwo says.
Earlier this year, he says, half of Borno state was a no-go zone. Government health care workers and international relief groups, including polio vaccination teams, could be attacked or killed if they tried to enter those areas. At the same time, Boko Haram was pillaging farms and destroying health clinics.
"Of about 38 secondary health care facilities in the entire state, 16 were totally burnt down by these insurgents," Ohuabunwo says.
It's only after recent military offensives by the Nigerian army into Boko Haram territory that health officials were able to find the three kids who'd been paralyzed by polio. One was a 4-year-old girl in a family that had escaped and made it to a displaced persons camp.
The immediate concern is to make sure all children in Borno state are vaccinated, but parts of the state remain under the militants' control. So polio immunizers have set up vaccination posts on the roads just outside the Boko Haram-controlled areas.
"We only get access to the children when there's some incursion by the military and they [the children] come out," Ohuabunwo says. "We have prepared health teams called border post teams who sit and wait. As soon as the children come out, we get them, assess them, administer vaccines."
In addition to these roadside vaccinators, Nigeria is conducting three mass polio immunization campaigns across accessible parts of Borno state. The goal is to vaccinate every child they can find under age 5. One mass campaign was held in August. Another starts next week, and a third launches in October.
"One of the problems with polio is that the infections that lead to paralysis are just the tip of the iceberg," says Dr. Walt Orenstein, a professor of medicine at Emory University who has worked for years on polio eradication efforts.
"Generally less than one in 200 infections actually leads to paralysis."
This means there is probably a lot more polio virus floating around in the Boko Haram-controlled parts of northeastern Nigeria than has been detected. The World Health Organization is concerned about the virus spilling over into Cameroon, Chad and Niger, so WHO is planning additional emergency polio vaccination campaigns in those neighboring countries.
The security situation makes it nearly impossible to eradicate polio in militant-controlled parts of West Africa. But Orenstein points out that it has been done elsewhere, in lots of other complicated conflicts, and he's confident that eventually polio will be defeated in northern Nigeria too.
