Zika Virus Had Quitely Spread in 40 Countries Before 2015-16 Epidemic, Says Research

Zika virus had quietly made its way to more than 40 countries before it caught world attention as a lethal mosquito-borne disease in 2015-2016, according to a study. Researchers also found that an undetected outbreak was peaking in Cuba in 2017, just as fears regarding Zika had globally begun to subside. A team of scientists at Scripps Research, working in tandem with other organizations, made the discovery by overlaying air-travel patterns with genomic sequencing of virus samples from infected travelers, according to the August 22 issue of journal Cell.

"Infectious diseases such as Zika are global problems, not local problems, and greater international collaboration and coordination is critical if we are to stay ahead of looming threats," said Kristian Andersen, associate professor at Scripps Research and director of Infectious Disease Genomics at the Scripps Research Translational Institute when speaking about the mosquito-borne disease.

"Through this study, we developed a framework for a more global, more proactive way of understanding how viruses are spreading. The traditional reliance on local testing may not always be sufficient on its own."

Scripps Research partnered on this project with Yale University, Florida Gulf Coast University, the Florida Department of Health, and many other organizations.

Although mosquito-borne diseases like malaria, dengue and chikungunya affect millions of people worldwide every year, the 2015–16 Zika epidemic led to fears of a more severe impact on the world population due to the fact that Zika is capable of causing a severe condition known as microcephaly in babies born to women affected by the virus during pregnancy.

But while global health bodies like the World Health Organization ended the designation of Zika as a "Public Health Emergency of International Concern," Andersen's team found that an undetected outbreak was reaching its peak in Cuba.

While investigating travel-associated Zika cases in 2017 to be sure that the epidemic was indeed winding down, the team found that a steady number of travelers from the Caribbean were still contracting the virus.

To estimate local prevalence, the researchers obtained blood samples from infected travelers who had visited Cuba, and used genomic sequencing to reconstruct virus ancestry and outbreak dynamics as part of an approach known as "genomic epidemiology."

Karthik Gangavarapu, a Scripps Research graduate student in Andersen's lab and one of three co-first authors of the study, said all of the Zika viruses from the epidemic in the Americas were traced to a single ancestor.

This allowed the team to create a "family tree" and trace the roots of the virus.

By examining tiny genomic changes in each virus sample, Gangavarapu was able to determine a "clock rate" to reveal the age of the virus. The timeline determined that the outbreak in Cuba was established a year later than other outbreaks in the Caribbean. "We realized there was a whole outbreak that had gone undetected," Gangavarapu said.

Sharada Saraf, an undergraduate intern in the Andersen Lab and co-first author of the study, analyzed airline travel schedules, flight patterns and cruise ship destinations to determine how many people had visited Cuba and other Zika-endemic countries during this time period.

"Given that undetected viral outbreaks have the potential to spread globally, I hope that this study will encourage utilizing both travel surveillance and genomic data—in addition to local reporting—for future surveillance efforts," Saraf said.