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Gene Test Traces a Polio Epidemic in the Making

By Cheryl Simon Silver


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Last week, epidemiologists from the World Health Organization (WHO) confirmed that a girl in Sudan is suffering from polio and noted that the strain of the virus is genetically linked to the poliovirus strain endemic to northern Nigeria.

The rapid analysis of poliovirus genomes has become a valuable tool in efforts to contain polio. The WHO Global Polio Eradication Initiative, based in Geneva, Switzerland, is using the strategy to monitor the pathogen.

“The linkage between specific cases can significantly supplement the understanding of how the virus is circulating in communities as well as how it is imported into specific areas,” says virologist Mark Pallansch, who, along with his colleague Olen Kew, heads the polio laboratory at the Centers for Disease Control and Prevention in Atlanta.

In certain regions of Africa, when a child displays symptoms of polio such as high fever or paralysis, a physician will take stool samples and send them to one of 145 accredited laboratories now part of the Global Polio Laboratory Network coordinated by WHO. The virus is extracted and cultured. If it turns out to be poliovirus, scientists conduct genetic analysis to determine whether it resembles other viruses in the country or from another country.

Far from the labor-intensive manual gene sequencing used by Kew and others to study poliovirus in 1985, scientists can now use automated gene sequencers to screen a key region of the poliovirus genome, called VP1. The poliovirus evolves very rapidly, but the VP1 region is stable, allowing scientists to determine clear genetic lineages that can be used to infer a chain of transmission.

“Everything we do now is by automated sequencing,” says Pallansch. “The same techniques are applied routinely at multiple laboratories around the world.”

Wide differences in the gene sequences indicate the steps by which a virus has mutated. Thus, a case of polio last year in Lebanon was traced back to India, and scientists know that the virus identified in Sudan moved with the population from Nigeria through Chad.

The virus that causes polio, also known as poliomyelitis, lives in the throat and intestinal tract, and is spread through contact with bodily wastes.

There is no treatment for polio, only prevention. Thus, proof that the poliovirus has been introduced into a country that has been polio free activates what WHO calls a “mop up” to eliminate the virus before it becomes established. This means that every child within a given radius of the identified outbreak is immunized within a few weeks.

“It’s a very effective strategy. It’s how we got polio down to a small number of countries,” says David Featherstone, coordinator of the WHO Vaccine Preventable Disease Laboratory Network.

As recently as last year, hopes were high that the world soon could be polio free. While in 1988, there were 125 countries with endemic polio — polio had been present for 12 months or more — polio today is endemic in six African countries: Nigeria, India, Pakistan, Niger, Afghanistan, and Egypt.

Now, however, the virus from Nigeria is moving through Africa, and children are paralyzed by polio in ten African countries that had been polio free, says David Heymann, the WHO representative for polio eradication.

The surge in cases in Nigeria raises alarm about a major epidemic, especially as the rainy season, known for high transmission rates, approaches. While WHO cites the number of cases in Nigeria by the end of April as 257, the true number is much higher because it takes weeks to culture and identify the virus. Kew estimates that there could be as many as a thousand cases by the end of the year.

“To be quite blunt, it’s a disaster,” Kew says. “Stemming the tide will be much more difficult because there are so many chains of transmission.”

Health officials believe the current outbreak stems from a decision last year by the government of the state of Kano, in northern Nigeria, to suspend its child immunization program. Religious and political leaders alleged that the U.S.-made vaccine was laced with chemicals intended to make African girls infertile.

WHO tests have refuted these claims. This week, Ibrahim Shekarau, the governor of Kano, informed WHO that he intends to resume polio immunizations in early July.

“All of the children born in that period in that part of Nigeria are not immunized,” Pallansch says. “At this stage, the virus is so widespread, and there are so many rounds of immunization are needed to control the outbreak, that it will be months before there is a decrease in cases.”


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