Zika Was Soaring Across Cuba. Few Outside the Country Knew.

A previously unknown outbreak of the Zika virus swept across Cuba in 2017, a year after the global health emergency was declared over, scientists reported on Thursday.

Until now, the Pan American Health Organization had no record of any Zika infection in Cuba in 2017, much less an outbreak. Following inquiries by The New York Times about the new study, published in the journal Cell, officials acknowledged that they had failed to tally 1,384 cases reported by Cuban officials that year.

That figure is a sharp increase over the 187 cases confirmed in 2016 and is “in line with the estimates for 2017 from our own study,” said Kristian Andersen, an infectious disease researcher at Scripps Research Translational Institute in La Jolla, Calif., and a co-author of the new study.

Because most cases of Zika go unconfirmed, Dr. Andersen added, the outbreak actually may have comprised tens of thousands of infections.

Cuba saw record tourism in 2017, raising the possibility that many travelers were unknowingly exposed. Some 4.7 million foreign visitors arrived that year, an increase of 16 percent over 2016. More than one million were Canadians.

“If we want to stay ahead of communicable diseases, we need to know where they are and how many cases are occurring,” said Jennifer Gardy of the Bill & Melinda Gates Foundation in Seattle. “For some diseases in some settings, this is pretty straightforward. For others, like Zika, it isn’t.”

Officials at P.A.H.O., an arm of the World Health Organization, blamed the failure to publish timely data on the Cuba outbreak on a “technical glitch.” The information was held in a database, they said, but not visible on the website. By Thursday afternoon, the website had been updated.

Dr. Andersen and his colleagues began tracking Zika’s spread when the mosquito-borne virus first appeared in the Americas in 2015. The epidemic first came to light in Brazil, where babies of some infected mothers were born with severe brain damage. The virus spread swiftly to neighboring countries.

Dr. Andersen and his colleagues collected blood from people infected with the virus. The researchers plucked the virus’s genetic material from the samples and used mutations in the DNA to estimate the timing of Zika’s spread.

Before Zika was identified in Brazil, the scientists discovered, it had been quietly circulating in the country for over a year. “And by that time, it had spread across all the Americas,” Dr. Andersen said.

Even in Florida, where the state government keeps careful tabs on new outbreaks, Zika arrived three months before it was detected, the scientists learned.

In November 2016, the World Health Organization announced that the epidemic was no longer a global public health emergency. “But we sat here with this question,” Dr. Andersen recalled. “Is it really over?”

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The scientists continued tracking the Zika virus across the Americas. They reviewed data on local outbreaks that countries reported to P.A.H.O. They also tallied confirmed cases of Zika in travelers coming home to Florida.

Across the Americas, both sets of statistics told the same story: The number of Zika cases crashed toward the end of 2016 and remained low afterward. But there was one glaring exception in the data.

In 2016, only a few people returning to Florida from Cuba were infected with Zika. In 2017, however, Cuba accounted for 98 percent of the travel-associated Zika cases in Florida.

This was an unexpected finding. Cuba has a sophisticated public health system, and it had seemed to be winning the war against Zika, apparently avoiding the outbreaks seen on other Caribbean islands.

To see if the initial results held up, Dr. Andersen and his colleagues turned to public health data in Europe and discovered a similar pattern among visitors to Cuba. The team developed a statistical model to predict the size of a Zika outbreak in a country, based on the number of travelers who went to Cuba and came back sick.

They concluded that Cuba’s outbreak in 2017 was “the same size as on other Caribbean islands, meaning thousands of reported cases,” Dr. Andersen said. But because reported cases typically comprise about 10 percent of a given outbreak, “we’re actually talking about tens of thousands of cases.”

The researchers also examined blood samples from travelers to Cuba to learn the history of the outbreak and determined that the virus appeared in Cuba in the summer of 2016. There was no Patient Zero; instead, Zika arrived several times from other islands. Then it smoldered, as it had elsewhere, for a year.

Dr. Andersen suspects that Cuba’s aggressive mosquito control and disease surveillance held back the virus while it raged elsewhere in 2016. Other mosquito-borne viruses, such as dengue, were also surging through the Caribbean, but Cuba didn’t see many cases of those, either.

But after the global emergency was called off, Zika gained momentum in Cuba in 2017, the researchers speculated.

“It is easy to miss an outbreak,” said Dr. Ester Sabino, the director of the Institute of Tropical Medicine at the University of São Paulo in Brazil, who was not involved in the new study. Many people infected with Zika don’t feel any symptoms, while some suffer only a mild fever for a few days.

It is rare in many Latin American countries for an infection to be confirmed with a sophisticated genetic test, Dr. Sabino said. The methods used by Dr. Andersen’s team were “a smart way to do world surveillance” for diseases like Zika, she added.

Dr. Andersen said that the new study adds to the evidence that public health workers should look for signs of outbreaks earlier.

“In many of these cases, we wait until we see weird symptoms and diseases in patients, and then we realize we have an outbreak,” he said. “If we look at the mosquitoes, we could detect it much earlier.”