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Just when international fears of contracting Zika began to fade in 2017, an undetected outbreak was peaking in Cuba—a mere 300 miles off the coast of Miami. A team of scientists at Scripps Research, working in concert with several other organizations, uncovered the hidden outbreak by overlaying air-travel patterns with genomic sequencing of virus samples from infected travelers. The discovery is featured on the cover of the Aug. 22 issue of 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," says Kristian Andersen, Ph.D., associate professor at Scripps Research and director of Infectious Disease Genomics at the Scripps Research Translational Institute. "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.
However, Andersen and his collaborators found that an undetected outbreak was reaching its peak in Cuba at that time, off the radar of international health agencies. Surprisingly, the outbreak lagged other Caribbean countries by a year, likely due to an aggressive mosquito-control campaign that delayed the disease's emergence, according to the study. The researchers noted that other infectious diseases spread by Aedes aegypti mosquitoes, including dengue, also were absent in Cuba at the same time. Andersen's team had no idea it would expose an unknown outbreak when it began investigating travel-associated Zika cases in 2017. The scientists simply wanted to know if the epidemic really was winding down. Instead, they found that a steady number of travelers from the Caribbean were still contracting the virus. With limited access to reliable local case reporting, the team devised a way to estimate local prevalence by obtaining blood samples from infected travelers who had visited Cuba, then using genomic sequencing to reconstruct virus ancestry and outbreak dynamics. The approach is known as "genomic epidemiology." 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 says.
Findings were published in Cell on August 22, 2019:
