A couple of summers ago, the threat of mosquito-borne Zika virus disease in tropical areas of the Americas caused major concern, and altered the travel plans of many. The concern was driven by reports of Zika-infected women giving birth to babies with small heads and incompletely developed brains (microcephaly), as well as other serious birth defects. So, with another summer vacation season now upon us, you might wonder what’s become of Zika.
While pregnant women and couples planning on having kids should still take extra precautions  when travelling outside the country, the near-term risk of disease outbreaks has largely subsided because so many folks living in affected areas have already been exposed to the virus and developed protective immunity. But the Zika virus—first identified in the Ziika Forest in Uganda in 1947—has by no means been eliminated, making it crucial to learn more about how it spreads to avert future outbreaks. It’s very likely we have not heard the last of Zika in the Western hemisphere.
Recently, an international research team, partly funded by NIH, used genomic tools to trace the spread of the Zika virus. Genomic analysis can be used to build a “family tree” of viral isolates, and such analysis suggests that the first Zika cases in Central America were reported about a year after the virus had actually arrived and begun to spread.
The Zika virus, having circulated for decades in Africa and Asia before sparking a major outbreak in French Polynesia in 2013, slipped undetected across the Pacific Ocean into Brazil early in 2014, as established in previous studies. The new work reveals that by that summer, the bug had already hopped unnoticed to Honduras, spreading rapidly to other Central American nations and Mexico—likely by late 2014 and into 2015 .
Researchers have become quite adept over the past few decades at parsing genetic information not only to tell people more about their ancestry, but also to track the spread of infectious disease in cities or, in the case of Zika, across continents. While previous studies have offered some clues as to the timing of Zika’s spread, the new study—led by Charles Chiu, University of California, San Francisco, and Oliver Pybus, University of Oxford, United Kingdom—set out in 2016 to fill in additional details. The strategy was to isolate Zika’s RNA-based genetic material from the blood and urine of people who lived or visited Central America or Mexico and later showed symptoms consistent with Zika infection.
Because Zika is detectable in people only for a few days and usually at low levels, collecting enough of the virus’ genetic material to track its spread from country to country has been a real challenge. The team used a newly developed strategy designed to sequence all DNA and RNA present in a sample, while specifically enriching for genetic material from the Zika virus. Such an approach helps to ensure Zika virus was detected without missing other potential viral pathogens, which often produce similar symptoms.
Of 95 specimens collected from January to August 2016, they generated full and partial sequences for 61 Zika virus genomes. To understand the relationships among those 61 Zika virus strains, the researchers combined their new genomic information with existing data for another 298 Zika strains from around the world. They then analyzed that evidence to construct the viruses’ family tree.