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A newly discovered case of wild polio in Malawi has raised the possibility that a virus that had been driven out of the African continent could again find a toehold there.

Teams of international disease investigators arrived in the East African nation over the weekend to probe how it came to have its first wild polio case in three decades and the continent’s first in five years.

“The reported case in Malawi comes as a big disappointment, but sadly not as a surprise,” said Kim Thompson, president of Kid Risk, a nonprofit organization that does disease modeling for the Global Polio Eradication Initiative. “It’s definitely showing us that the quality of immunization has not been high enough. But it also raises questions about the quality of surveillance.”


The case is a 3-year-old girl who lives on the outskirts of the capital, Lilongwe. She was paralyzed on Nov. 19; testing showed she’d been infected with a type 1 wild poliovirus. Comparison of the virus’ genetic sequence to other previous viruses revealed that it derived from a family of viruses that was seen circulating in Pakistan’s Sindh Province in October 2019.

The government of Malawi has declared the outbreak a public health emergency.


How the virus traveled more than 3,500 miles is unknown. How many children were exposed to it over that 25-month period is unknowable.

“That’s the $1 million dollar question. How did it get there?” said Derek Ehrhardt, acting branch chief for polio eradication at the Centers for Disease Control and Prevention, one of the partners in the polio eradication program.

Aidan O’Leary, director of the World Health Organization’s polio eradication program, admitted to being taken aback that wild poliovirus popped up in Malawi. “It certainly wasn’t on our radar as one of our highest-risk areas,” O’Leary told STAT.

Investigators will now try to determine how broadly the virus may have spread within Malawi, or perhaps even into neighboring countries. Already the polio eradication partners are considering whether it will be necessary to conduct emergency rounds of vaccinations in Tanzania, Zambia, and Mozambique as well as in Malawi.

“The virus is there. We need to respond to it in a robust way,” Ehrhardt said. “Not only in Malawi but also making sure that we appreciate the risk of the neighboring countries. Because we have mobile populations and we need to make sure that that surrounding area is also protected.”

The disheartening discovery comes at a time when — on the surface of things, anyway — the polio eradication effort seems closer than ever before to halting spread of wild polioviruses. (The state of efforts to stamp out transmission of vaccine-derived viruses is another matter entirely. More on that later.)

Of the three original polio viruses, only type 1 remains. Type 2 viruses were declared eradicated in 2015 and type 3 viruses were declared wiped out in 2019.

For several years, type 1 viruses had been cornered in just two countries, Pakistan and Afghanistan. Thirty-four years into the polio eradication campaign, those are the only two countries in which wild polio viruses remain endemic.


After years of struggling to eliminate transmission there too, health officials saw an unprecedentedly low number of cases in 2021. Afghanistan reported four cases and Pakistan a mere one. In late January, Pakistan marked a full year without having recorded a single case of polio — a first for the country.

But the Covid-19 pandemic has had an impact on public health programs the world over, raising questions about how good surveillance has been over the past couple of years and how well countries have managed to maintain routine vaccination efforts. The WHO and UNICEF, the United Nations Children’s Fund, estimated that in 2020, nearly 23 million children were unvaccinated or under-vaccinated against important childhood diseases.

O’Leary said in Pakistan, wastewater surveillance supports the idea that polio is spreading there at historically low levels. Sampling sewage for polioviruses is a critical part of surveillance in a number of countries, as is the case with Covid-19 as well.

However, Malawi and its at-risk neighbors do not use wastewater surveillance for polio. Their sole tool for detecting cases is what’s known as acute flaccid paralysis surveillance — looking for children who have become paralyzed and testing them to see if polioviruses are the culprit.

O’Leary said the response teams hope to do some wastewater sampling around the country to try to get a handle on “the scale and scope of the risk we actually face.” He acknowledged surveillance declined during the first year of the pandemic but picked up again in 2021.

There was a three-month gap between the time when the child in Malawi was paralyzed and the announcement that her paralysis was caused by a type 1 virus.

Though stool samples from the child were collected within a week of the onset of her paralysis, those specimens were not shipped to South Africa’s National Institute of Communicable Disease for testing for several weeks. O’Leary said that “unusually long delay” in getting the sample from Malawi to South Africa was due to logistical hurdles of transporting specimens that have been aggravated by the pandemic.

The South African lab initially characterized the virus from the stool specimens as a type 2 vaccine-derived virus. But followup testing, both in South Africa and at the CDC determined that the virus was actually a type 1 wild virus.

Among the challenges the response teams face will be which vaccine to use to try to tamp out spread of the type 1 virus.

Live virus polio vaccine — known as OPV — is the vaccine of choice in outbreak responses, because it develops immunity in the gut, where polioviruses attack when they infect. The injectable vaccine used in the United States, known as IPV, prevents paralysis, but does not trigger immunity in the gut, so children can be infected — without harm to themselves — and spread the virus onward through their stools.

But OPV vaccines carry a risk. Vaccinated children shed the weakened vaccine viruses and, in places where immunity is low, they can move from child to child. At times that’s beneficial; some children get vaccinated indirectly. But if the vaccine viruses spread long enough, they can regain the power to paralyze.

For several years now, more children have been paralyzed by vaccine-derived viruses than by wild polioviruses. Last year, 628 children in 23 countries were paralyzed by vaccine-derived viruses; most of those cases were in  Africa and the Middle East.

The type 2 viruses in live polio vaccine were the most likely to regain virulence. As a result, in 2016 the polio eradication partners moved from a trivalent (three-in-one vaccine) to a bivalent version, dropping the type 2 component. But the move did not go as hoped; most of the vaccine-derived cases recorded globally are type 2.

O’Leary said the bivalent form of the vaccine will likely be the formulation used in the Malawi response. But Mozambique is one of the countries that has been struggling with type 2 vaccine-derived polio, so there will need to be discussion about whether to use the trivalent version of the vaccine there.

Thompson, who has been calling for a much more aggressive effort to combat the vaccine-derived polio outbreaks, suggested the case in Malawi could provide an opportunity to get that effort on track.

“This could actually be a good wake-up call to remind people that you do have to keep the immunization intensity for polio high — otherwise you can have not just type 2 as an emergency, but type 1 also coming back as an emergency,” she said.

Correction: An earlier version of this story suggested Malawi has a lab that tests for polio.

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