Genetic sleuths uncover Zika's viral secrets

The Zika outbreak that has spread to 34 countries in the Western Hemisphere can be traced to a single viral carrier who brought it to Brazil in 2013, scientists reported this week.

The researchers don’t know this carrier’s identity — but it may well have been a soccer fan.

That theory is based on a genetic analysis of seven distinct samples of Zika virus now circulating in Brazil. The results, published this week in the journal Science, help fill in some mysterious gaps regarding the virus' identity, its port of entry in the Americas and its link to the birth defect microcephaly.

A team of Brazilian, Canadian, American and British researchers began their work by sequencing the genomes from the seven Zika samples. One of them came from an adult who died of the virus; another came from a newborn with microcephaly, a condition characterized by a small, misshapen head and an increased risk of neurological problems and cognitive deficits. None of the seven patients who contributed viral samples had ever left Brazil.

The researchers were able to decode the stretches of RNA that allow the virus to sustain itself, replicate and spread. They saw that sequences were closely related to the strain of Zika that had crossed Asia and the Pacific. In addition, they shared a common ancestor with a strain that caused a massive outbreak in French Polynesia in November 2013.

Comparisons of the seven samples also allowed the scientists to calculate how quickly the virus was evolving. That helped them determine that the most recent common ancestor of all the samples probably arose between May and December of 2013.

Not only does that period coincide with Zika outbreaks in a number of Pacific islands, it also overlaps with a big increase in air travel to Brazil from countries where Zika was circulating widely. In early 2013, for instance, about 3,775 people were arriving from these countries each month. One year later, there were 5,754 such travelers per month, the study authors said.

Their chief suspicion is that the virus arrived while Brazil was hosting the Confederations Cup soccer tournament in late June of 2013. A team from French Polynesia competed in that tournament, which was a prelude to the 2014 World Cup.

Other researchers have previously suggested that the virus came to Brazil during the 2014 World Cup, but the new study made the right call by ruling that out, according to Derek Gatherer, a bioinformatics expert at Lancaster University in England who wasn’t involved in the new analysis.

However, he also expressed doubt that the 2013 Confederations Cup was to blame, since the virus would have needed to depart Polynesia for Brazil before the Polynesian outbreak had really gotten started.

“It seems likely that no specific sporting event is to blame,” he said in a statement.

If the study authors are right that Zika got to Brazil in mid- to late 2013, the virus would have had about a year to incubate in the salivary glands of Aedes aegypti mosquitoes before it was discovered and identified by Brazilian authorities.

During that time, it could have spread to people throughout Bahia state — where most of the earliest cases were reported — but been misidentified as dengue fever or chikungunya, which can cause similar symptoms of rash and fever.

Many scientists have wondered whether the virus, after arriving in Brazil, had acquired a mutation that put pregnant women at a heightened risk of having babies with microcephaly. The new data suggest this was not the case, Gatherer said.

If there were a “particularly nasty mutation,” he said, then it should be more common in babies with microcephaly than in other Zika patients. But it’s not.

“If Zika is the cause of microcephaly,” he said, “then a more subtle interaction between virus, patient and environment is involved.”

The idea that a single carrier could cause such a widespread outbreak may be hard to fathom, but it shouldn’t be, according to Martin Hibberd, who studies emerging infectious diseases at the London School of Hygiene and Tropical Medicine but wasn’t involved in the research.

“In the right conditions, with sufficient mosquitoes and closely packed humans, the virus can spread rapidly,” he said in a statement. “Given the amount of human travel between countries, any region with dengue could suffer from Zika. That means 3.6 billion people from the tropical regions are at potential risk.”

Michael Osterholm of the University of Minnesota's Center for Infectious Disease Research and Policy said the new findings won’t do much to help government experts fight Zika on the ground in Brazil and in other affected countries.

“We didn't need to know when the virus arrived in Brazil to know we had a public health problem on our hands,” said Osterholm, who also didn’t work on the study. “We should have been primed for the fact that an outbreak of Zika was going to happen.”

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Copyright © 2016, Los Angeles Times

UPDATE

7:38 p.m. Friday, March 25: This post has been updated with changes throughout.

11:19 a.m.: This post has been updated with comments from an independent expert.

This post was originally published at 11:04 a.m. Thursday, March 24.

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