The Zika virus has probably been circulating quietly and undetected in Brazil since 2013, a new genetic study shows.
A large international team of experts used a "genetic clock" to show Zika virus has changed about as much as would be expected if it had been carried into the country in 2013.
They used samples taken Zika cases across Brazil and looked for mutations in the genetic sequence. All DNA mutates over time and the seven genes of a Zika virus can be matched to samples taken from elsewhere.
The Zika now spreading explosively across Brazil, the rest of the Americas and the Caribbean very closely matches a strain that circulated in French Polynesia in 2013, the team reports in the journal Science.
"We estimate that the date of the most common ancestor of all Brazilian genomes is August 2013 to April 2014," they write. The most likely date: December 2013.
Brazilian officials first noticed Zika spreading in May of 2015. Zika is a close relative of dengue virus, which has been spreading for longer. And it's similar — it is spread by the same Aedes aegyptis mosquito. But Zika is usually milder than dengue, not even causing noticeable symptoms in most people and usually causing little more than a rash, fever and body aches.
It would have been easy to think that people showing Zika symptoms had dengue. The most commonly used blood tests even mix up the two viruses.
But by November 2015, Brazilian authorities declared an emergency over a large increase in birth defects, notably one called microcephaly, in which a baby's head and brain are markedly underdeveloped. They have noticed more than 4,000 cases since then.
The World Health Organization now says Zika "is highly likely to be a cause of microcephaly", as well as other birth defects and the paralyzing Guillain-Barre syndrome that can kill or disable patients for years. WHO says 34 countries and territories in the Americas now have Zika spreading locally.
Related: Your Questions About Zika
Zika was first seen in Uganda in 1947 — which is why it's named after a forest there. It's since been spread by travelers: If someone actively infected with Zika is bitten by an Aedes mosquito, that mosquito can spread it to other people. And five countries have reported sexual transmission of the virus.
Brazil had thought athletes or spectators brought the virus with them during the 2014 World Cup Soccer tournament. But Oliver Pybus of the University of Oxford in Britain and colleagues at Brazil's Evandro Chagas Institute said their study shows it must have been circulating earlier.
So they checked airline records, too.
"From late 2012 onwards, there was a 50 percent rise in the number of passengers traveling to Brazil from countries with Zika," they wrote.
"Although the American outbreak virus is most closely related to a strain from French Polynesia, it's also possible that Zika was introduced separately to the Americas and French Polynesia from Southeast Asia. To better understand Zika transmission history, we need more information about the epidemiology and genetic diversity of Zika viruses in Southeast Asia."
Dr. Nuno Faria of the University of Oxford and Brazil's Evandro Chagas Institute, who worked on the study, says his team cannot say for certain that the Zika virus causes microcephaly. Other studies have strongly suggested that it does, and other viruses are known to cause similar birth defects.
The researchers also doubt that Zika mutated somehow into a form more likely to cause birth defects. Birth defects had not been noticed before in Zika outbreaks, but this is by far the biggest one, hitting a huge population that has no immunity at all to the virus, so effects will be more obvious.
"If Zika is the cause of microcephaly (and at the moment this looks increasingly likely), then a more subtle interaction between virus, patient and environment is involved, rather than some new property arising within the virus due to mutation," said Mark Woolhouse, a professor of infectious diseases at the University of Edinburgh in Britain, who was not involved in the study.