Discovery points the way to protecting a fish that feeds multitudes

An international scientific team led by researchers at Columbia University’s Mailman School of Public Health and Tel Aviv University has identified and characterized a novel virus behind massive die-offs of farmed tilapia in Israel and Ecuador, which threatens the $7.5 billion global tilapia industry. A paper in the journal mBio describes tilapia lake virus (TiLV) and provides information needed to fight the outbreak.

Known in its native Middle East as St. Peter’s fish and thought to be the biblical fish that fed multitudes, tilapia provides inexpensive dietary protein. The world’s second most farmed fish, tilapia is also the basis of aquaculture employment in developing countries in Asia, Latin America, and the Middle East. (The United States is the leading tilapia importer globally.) Since 2009, Israel has seen precipitous declines in tilapia, with annual yields plummeting as much as 85 percent—highly unusual considering the fish is known to be relatively resistant to viral infections. Similar die-offs have been seen in Ecuador and Colombia.

The scientists used high-throughput sequencing to determine the genetic code of the virus from tissue taken from diseased fish in Israel and Ecuador. This process would normally be sufficient to identify the culprit, but in this case, the resulting DNA sequences didn’t match any known virus, with the exception of a small genetic segment that only remotely resembled a virus associated with the reproduction of influenza C.

Undeterred, the researchers employed other tools from their scientific tackle box, providing ample evidence that the genetic material was the same as the implicated virus dubbed TiLV. They used mass spectroscopy to characterize the proteins in cells growing the virus, which matched those they expected to see based on the genetic sequence. By analyzing the structure of viral DNA, they went on to observe 10 gene clusters with complementary endpoints, suggesting a circular form associated with a common type of viral reproduction involving a protein called a polymerase.

Finally and conclusively, healthy fish were exposed to TiLV cultured in a laboratory, resulting in disease that matched with what was seen in those countries: in Israel, the fish had swollen brains; in Ecuador, liver disease. In the coming weeks, the researchers will publish on the link between the TiLV and an outbreak of disease among tilapia in Colombia.

“The TiLV sequence has only minimal similarity in a small region of its genome to other viruses; thus, the methods we typically use to identify and characterize viruses through sequencing alone were insufficient,” says first author Eran Bacharach, a molecular virologist at Tel Aviv University.

“It appears to be most closely related to a family of influenza viruses called orthomyxoviruses; however, we still don’t understand much about its biology,” adds Nischay Mishra, associate research scientist at the Center for Infection and Immunity at Columbia’s Mailman School.

Importantly, the findings provide the genomic and protein sequences necessary for TiLV detection, containment, and vaccine development. “We are shifting our focus now to implementing diagnostic tests for containment of infection and to developing vaccines to prevent disease,” says Avi Eldar of the Kimron Veterinary Institute in Bet Dagan, Israel.

The team of 18 researchers represent five institutions in four countries: the Center for Infection and Immunity and the New York Genome Center in the U.S., Tel Aviv University and Kimron Veterinary Institute in Israel; the University of Edinburgh, Scotland; and St. George’s University, Grenada, West Indies.

“The New York Genome Center was excited to join in characterizing this novel virus and contribute to this important environmental and globally impactful research,” says Toby Bloom, the Center’s deputy scientific director.

“Gumshoe epidemiology, molecular gymnastics, and classical microbiological methods were required to link this new virus to disease,” says Ian Lipkin, senior author, director of the Center for Infection and Immunity and John Snow Professor of Epidemiology at the Mailman School. “Resolution of this mystery was only possible through the concerted efforts of this talented group of international collaborators.”

While best known for identifying viruses behind human disease, the Center for Infection and Immunity, pinpointed the virus behind a disease that decimated salmon farms in Europe in 2010. They have done similar work with seals, sea lions, and Great Apes.

The current research was supported by grants from the United States-Israel Bi-National Agricultural Research & Development Fund (BARD IS-4583-13), the Israel Ministry of Agriculture & Rural Development Chief Scientist Office (847-0389-14), U.S. National Institutes for Health (AI109761), USAID PREDICT, and a fellowship to J.E.K.T. from the Manna Center Program in Food Safety and Security at Tel Aviv University. The authors declare no conflicts.