Just a year ago, poliovirus seemed on its last legs in Pakistan, one of its final strongholds. Polio cases were steadily falling, from 306 in 2014 to 54 in 2015, 20 in 2016, and, by last count, eight in 2017. Blood tests showed that, overall, immunity to the virus had never been higher, even among children aged 6 to 11 months, thanks to years of tireless vaccination campaigns. Surely, there were not enough susceptible kids to sustain transmission, and the virus would burn itself out within a year.
Unsettling new findings, however, show it is far from gone. In the most extensive effort in any country to scour the environment for traces of the virus, polio workers are finding it widely across Pakistan, in places they thought it had disappeared. They are wondering “just what the hell is going on” and how worried they should be, says epidemiologist Chris Maher of the World Health Organization (WHO) in Geneva, Switzerland, who runs polio operations in the eastern Mediterranean region. Does this mean the virus is more entrenched than anyone realized and is poised to resurge? Or is this how a virus behaves in its final days—persisting in the environment but not causing disease until it fades out?
“We have never had this level of environmental sampling anywhere else. We have nothing to compare it to,” Maher says. “We don’t understand the dynamic,” agrees Michel Zaffran, who leads the Global Polio Eradication Initiative at WHO. “But we take it very seriously.” In response to the sampling data, he and his colleagues are already changing their tactics—and their definition of success.
Along with Afghanistan and Nigeria, Pakistan is one of just three endemic countries—places where indigenous wild poliovirus has never been vanquished. With its dysfunctional government, unceasing violence, poverty, and huge numbers of people on the move, it may well be the toughest challenge for eradication. The border with Afghanistan is so porous that the two countries are considered one epidemiologic block in which the virus circulates freely. Conventional wisdom is that if Pakistan defeats polio, Afghanistan will soon follow. That could be the key to global eradication, as no virus has been detected in Nigeria for the past 15 months.
Since the eradication effort began in 1988, the gold standard for detecting poliovirus has been surveillance for acute flaccid paralysis (AFP)—finding and testing every child with a sudden weakness or floppiness in the arms or legs. The yearly case count has been the benchmark for success: After 12 months without a polio case, WHO has historically removed a country from the endemic list.
But as case numbers fell to today’s low levels, AFP surveillance is no longer the only meaningful indicator. Only about one in 200 or 300 people infected with the virus becomes paralyzed; the rest show no symptoms but can still shed the virus in their stool and infect others. Environmental surveillance can detect that hidden virus.
Polio workers collect sewage samples, usually from open drainage ditches, and test them for virus. If the test is positive, that means someone in the catchment area is infected and actively excreting it. Pakistan now has 53 sampling sites, more than any other country. And at a time when cases are the lowest on record, 16% of samples from across the country are testing positive.
“It is extraordinary to have so much virus in sewage and so few cases,” Zaffran says.
What makes the environmental samples so hard to interpret is that a catchment area may contain the combined feces of 50,000 or 100,000 people. “If you isolate a virus from a child, you know who is infected. When you find it in an environmental sample, you don’t know if three people are infected or 3000,” Maher explains.
One possible explanation for the disconnect is that AFP surveillance is missing cases. Maher doubts that the number is significant, but others suspect that too many children among the mobile populations, including the marginalized Pashtun minority, still aren’t being vaccinated despite ramped up efforts to reach them. “I don’t think polio is entrenched across Pakistan, but this last reservoir of ‘people on the move’ is sustaining the virus,” says Steve Cochi, a polio expert at the U.S. Centers for Disease Control and Prevention in Atlanta.
Maher has another view. “My own suspicion is this is part of what we see at the end,” he says. “The lack of cases means immunity is high, but because of the very difficult circumstance in Pakistan,” the virus still has a tenuous hold. Ultimately, he says, “The virus will die out because it is not getting enough purchase.”
The program is not taking any chances. The response to each positive environmental test is now as aggressive as to a case of paralysis. And the program is hammering the virus with repeated vaccination campaigns throughout the “low season,” between December and May, when cold weather makes it tougher for the virus to survive. Whether the strategy works will become clear later this year when the weather turns warm. But one thing is certain: The absence of cases is no longer enough to declare victory over polio. Going forward, a country will not be considered polio-free until 12 months have passed without a case—or a positive environmental sample.