Virus Hunters Draw a Map of Zika's Spread With DNA

In April 2015, researchers in Brazil reported the first case of Zika virus---finally putting a name to the mysterious rash, fever, and joint pain-causing illness that had been swarming the northeast corner of the country. By the time the World Health Organization declared Zika a global health emergency nearly a year later, the outbreak had spread to 26 countries and territories in the Americas, infecting hundreds of thousands of people and leaving many babies with an incurable developmental defect called microcephaly.

Since then, researchers have been racing to develop treatments and vaccines, the first of which entered mid-stage human trials at the end of March. But according to new genetic evidence published today, public health efforts to contain and fight the disease could have---and should have---gotten underway much sooner.

Zika, it turns out, had established itself in Brazil as early as 2013.

The revelation comes from the same group of seasoned virus sleuths who used genetics to help stop Ebola's spread through Sierra Leone in 2014. This time, they sequenced more than 100 new Zika genomes, taken from patients and mosquitoes throughout the Americas. They traced the virus’s spread from Brazil to the nations next door, into the Caribbean and then the US. The reconstructed genetic history, published in three separate Nature papers, could help drug developers look for a cure, and public health officials develop containment strategies. But mostly, they make a strong case for developing a genetics-based global surveillance system so that the next outbreak---whether it’s Zika or something else---doesn’t shake the world quite so hard.

Throughout the summer and fall of 2015, as Zika cases poured into public health databases, photos of babies with under-sized skulls made their way to the front pages of newspapers. The whole time, the world’s most famous virus hunterwasn’t lifting a finger to help. She could barely lift a finger at all.

Pardis Sabeti had lost weeks of sleep and five teammates helping crack Ebola's code in 2014. When Zika hit the following summer, the Harvard computational biologist was recovering from something more devastatingly prosaic. In July, while a passenger on all-terrain vehicle in Montana, the vehicle went over a cliff, catapulting Pardis onto boulders, shattering her knees and pelvis and causing a traumatic brain injury. “I was in a wheelchair, the lab was running without me, it didn’t seem like the right time to step in and do something,” she says. “And it was outside of our domain and our region of the world; we didn’t want to just parachute in.”

Sabeti watched the Zika crisis from her bed, as her body and brain continued to heal. Emails poured in, asking for her help. Many of the same people she had worked with on Ebola were trying to tackle this new outbreak the same way they had in Africa---with portable sequencing machines in mobile laboratories that could spit out full viral genomes just a few minutes after diagnosis. But Zika was sneaky. There just wasn’t very much of it in the blood samples. The sequencers couldn’t reliably capture all of Zika’s 10,000-plus base pairs. So as soon as Sabeti was able, she brought her Broad Institute lab into the fray.

Using a new method they developed with partner labs at Oxford University and the University of Birmingham, they eventually were able to sequence whole Zika genomes directly from clinical samples without having to first isolate the virus and culture it. The new approach involved making lots of copies of the genome fragments by carrying out dozens of reactions in just one tube---to cut down on time and opportunities to mess something up. Now they could collect samples from Brazil, Colombia, Honduras, and all over the Caribbean---even Florida. Sabeti’s lab sequenced them all.

As soon as they validated the genomes, they sent them back to their respective health departments, then released the genomes to the public through databases like GenBank and Virological. They uploaded the first 33 sequences last October, and continued to release more as fast as they could process them. They didn’t want to wait for months for other researchers to be able to start using them. “Genomic data is central to creating better diagnostics, treatments, and vaccines,” she says. “This is frightening for people, and with a very vulnerable population we wanted to make sure we’re capturing it as soon as possible.”

Once all the genomes were sequenced, Sabeti and her collaborators still had to figure out how they all fit together. To do that, they used a technique called a "molecular clock." When cells divide, or viruses replicate, the proteins that make copies of the DNA introduce mutations into the genome at specific, predictable rates. Zika, like all RNA viruses, is a pretty fast mutation machine. (Not Ebola fast, but still fast.) You can think of each mutation like the tick of a clock: The more mutations accumulate, the more time has passed. Using that technique, the researchers were able to estimate when Zika actually began showing up in different countries---often many months before the first official reports.

These massive, genomic-based surveillance efforts could potentially foretell an outbreak within days or weeks, rather than waiting months or years for symptoms to start showing up. “This is a big red alert to all countries,” says Sabeti. “We have the tools to monitor outbreaks in as close to real time as possible, but we have to have these systems in place before they hit.”

In the US, only Miami, Florida and Brownsville, Texas would need year-round surveillance—they are they only place where Aedes aegypti mosquitos survive for all 12 months. Kristian Andersen, an infectious disease geneticist at Scripps Research Institute and author of one of the three *Nature *papers, discovered this by layering epidemiological data on the molecular clock-derived evolutionary histories. His team discovered that it was the mosquito's year-round presence that made Zika establish so firmly in those cities. The major airports helped too.

Andersen’s work also turned up some interesting “bonus” tidbits, as he calls them. The first is that Zika cases are perfectly correlated with the number of mosquitoes in the area. If you knock down mosquito populations by half, the number of Zika diagnoses drops by half. “That tells us that vector control is an effective way of preventing human cases from occurring,” Andersen says.

The second has to do with the seasonality of the outbreaks. “We think there’s something special happening in the early spring, when mosquitoes are bouncing back from the winter,” Andersen says. As Aedes aegypti numbers explode, that’s when they’re spreading Zika into humans. Not later, when the symptoms start showing up. “When mosquito populations are expanding dramatically, before you see the first human cases, that’s when you should focus the majority of your control efforts,” says Andersen.

Last week, two years after its first reported Zika case, and more than three years after it first showed up, Brazil officially declared an end to its Zika national emergency. The virus has hit so much of the population that herd immunity seems to have finally caught up. But that kind of protection is fleeting. People still need reliable tests and reliable vaccines, tailored to whatever strains they’re most likely to encounter. Sequencing projects like this one provide a road map for scientists to develop them. But it will take much wider deployment to catch the next outbreak before it happens. In the US alone, more than a dozen new human diseases have cropped up in the last two decades. It's only a matter of time before the next one arrives.