A genetic analysis of seven distinct samples of Zika virus circulating in Brazil has filled in some mysterious gaps regarding the virus’ identity, its port of entry in the Americas and its link to the birth defect microcephaly.

Published today in Science, the study reveals that the Zika virus probably made landfall in the Americas by hitching a ride on an airplane between May and December 2013. That period coincides with outbreaks of Zika in a number of Pacific islands, and it overlaps with the convergence on Brazil of an unusual number of flights from countries in which the Zika virus was already circulating widely.

The chief suspicion of the study’s authors — a consortium of Brazilian, Canadian, American and British researchers — is that the virus arrived in 2013 during the June 15-30 Confederations Cup soccer tournament hosted by Brazil. A team from French Polynesia competed in that tournament, which was a prelude to the 2014 World Cup.

For about 12 months before the viral stowaway was discovered and identified by Brazilian health authorities, it incubated in the salivary glands of “Aedes aegypti” mosquitoes and was passed on to people throughout Bahia state, where most of the earliest cases were reported. During that period, they surmised, Zika virus infection was often misidentified as dengue fever or chikengunya, which can cause similar symptoms of rash and fever.

The researchers found little evidence to suggest that the Zika virus’ genetic signature changed very much as it traveled from the Pacific Islands, spread through 22 of Brazil’s 27 administrative states, and then throughout the Americas.

The virus has sickened more than 30,000 Brazilians and is suspected of harming as many as 6,480 Brazilian babies. Those born with microcephaly have small, misshapen heads and often suffer neurological problems and cognitive deficits.

This week, as experts from the U.S. Centers for Disease Control and Prevention struggled to contain the spread of Zika infection in Puerto Rico, the agency put Cuba on the list of countries where the virus is rampant.

To conduct their investigation, researchers conducted next-generation genetic sequencing on seven samples of the Zika virus collected during Brazil’s outbreak. By taking snippets from the viral samples’ RNA, the study authors generated seven complete coding region sequences — the stretches of RNA that are key to an organism’s ability to sustain itself, replicate and spread. The researchers identified one Zika virus sample as coming from a deceased baby with microcephaly, another from a person with several other health problems who died of his Zika infections, and another from a Brazilian blood donor.

With very small variations, the resulting sequences showed that the virus that has spread throughout Brazil is closely related to the strain of Zika that has crossed Asia and the Pacific, and that they share a common ancestor with the strain that caused a massive outbreak of Zika in French Polynesia in November 2013.

Much of the team’s findings have been discovered by a far-flung community of researchers working on Zika, said Michael Osterholm of the University of Minnesota’s Center for Infectious Disease Research and Policy. And not all of its findings will substantively aid in fighting Zika virus, he added.

“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 was not involved in the current study. “We should have been primed for the fact that an outbreak of Zika was going to happen.”

One of the team’s most intriguing but incomplete findings emerged only from epidemiological data on microcephalic births. An assessment of that data suggests that suspected microcephaly cases are “best predicted by Zika virus incidence during week 17 of pregnancy, on average, or week 14 for suspected severe microcephaly cases,” the researchers wrote.

That timing is consistent with individual reports of Zika symptoms from women who later gave birth to microcephalic babies, whose heads are abnormally small. But the researchers emphasized that their calculation “does not demonstrate a causal link,” and that efforts aimed at pinpointing the Zika virus as the cause of the birth defects must continue.

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©2016 Los Angeles Times