Sequencing hundreds of viral genomes, they reconstructed the virus’s voyage into and around the Americas. They’ve shown how often it entered the U.S. and why Miami was a perfect and singular gateway for it. And perhaps most importantly, they’ve confirmed what many had believed: In almost every affected country, Zika was already there for months—or even years—before the first cases were reported.
“It’s a big reminder that surveillance is a major issue, and we need to double down on it,” says Pardis Sabeti from the Broad Institute and Harvard University, one of the leaders of the study. “We’re letting these things go undetected for a long period of time.”
Sabeti and her colleagues used a similar approach to trace the spread and evolution of Ebola during the recent West African outbreak. But Zika is a far more challenging virus. If you draw a milliliter of blood from someone with Ebola, you’ll pick up around 10 billion virus particles. If you do the same for a Zika patient, you’ll be lucky to pick up 10,000. These unusually low levels make Zika very hard to sequence.
To do so, Nicholas Loman from the University of Birmingham had to develop a new method for amplifying the virus in a blood or urine sample. He designed the technique to work on a USB-powered, pocket-sized DNA sequencer called the MinION, so his team could zip around Brazil in a mobile laboratory, screening more than 1,300 people for Zika and deciphering the viruses’ genomes on the fly.
Meanwhile, Sabeti and others were amassing similar sequences from at least 10 other countries and territories. And rather than sitting on their data while they waited to publish their papers, they immediately uploaded everything they had so that the entire scientific community could react.
Loman and Sabeti, together with Oliver Pybus from the University of Oxford, showed that all of their Zika strains descended from an ancestral virus that arrived in the Americas around January 2014—some 16 months before health authorities confirmed the first cases. It arrived in northeast Brazil, possibly using Haiti as a stepping stone. And having landed among people whose naïve immune systems had never encountered Zika before, the virus spread rapidly and established a staging ground.
From there, in the second half of 2014, it spread to populous southeastern cities like Rio de Janeiro and Sao Paulo, and made incursions into Honduras, Colombia, Puerto Rico, and various Caribbean islands. In every case, it landed between four and 12 months before it was detected.
“It’s relatively mild in most people, so it didn’t get picked up,” says Kristian Andersen from the Scripps Research Institute. “We weren’t looking for it at all because we didn’t know it was there.” Even when symptoms show, they often overlap with those of other mosquito-borne diseases like dengue. And even when doctors detect cases, says Sabeti, “it takes a while for every party to communicate enough to really notice what’s happening. … It speaks to the very disjointed way in which we do surveillance.”