In November 2018, the Iraqi fish-farming industry was in crisis. Millions of carp were dead or dying in their enclosures along the length of the Euphrates and Shatt al-Arab Rivers, clogging the rivers with their remains and forcing farmers to use excavation equipment to remove them. The mass deaths doubled the price of carp and put the national dish, masgouf, in jeopardy. Speculation regarding the cause of the outbreak ranged from reasonable to conspiratorial, but the scale of the event demanded an explanation. Because the Tigris-Euphrates watershed passes through several countries, the mass deaths could have become an international incident, adding tension to an already volatile part of the world. Fortunately, researchers from the nearby Faculty of Veterinary Medicine at Jordan University of Science and Technology were able to get to the bottom of the mystery.
The SeqStudio system reveals the mystery behind mass fish deaths in Iraq
Many factors contributed to the difficulty of pinning the mass deaths to a specific cause. Large-scale agriculture surrounds the Euphrates River and its endpoint, the Shatt al-Arab. Iraq’s major urban centers are all relatively close to the Euphrates and the adjoining Tigris River, and this proximity has made agricultural runoff and pollution into ongoing and growing problems. Additionally, the upper reaches of the rivers, outside of Iraq, have dams that restrict their flow, which concentrates downstream pollution. The effects of pollution are exacerbated by rising water temperatures and reduced rainfall in the area due to climate change. Iraqi authorities regularly post toxicity warnings when the water conditions deteriorate and parts of the rivers become unsafe to drink. What all of these factors have in common is that they increase the risk of disease outbreaks among aquatic organisms in the river, particularly in aquaculture facilities where fish are kept in close proximity to one another and farmers count on the river to wash out the fishes’ waste.
Any of these factors, especially the heat, could explain a mass death simply due to the stress imposed on farmed fish, but some of the physiological symptoms of the fish pointed to something more. Affected fish often had skin and gill lesions and sunken eyes — signs of health problems outside of simple physiological stress. Some suspected intentional poisoning, perhaps even an unusually clever terrorist attack. This indeed was a mystery. But the scientists at Jordan University had other ideas.
Many fish diseases cause lesions that become much more prominent when the fish are stressed. Through Sanger sequencing with the Applied Biosystems™ SeqStudio™ Genetic Analyzer, Dr. Mustafa Ababneh and Dr. Mohammad Alzghoul were able to sequence and identify the pathogen. The SeqStudio Genetic Analyzer is well equipped to sequence rare and unusual samples and compare the results to established genomes, including those of bacteria, fungi, viruses and other microbes that attack fish. Drs. Ababneh and Alzghoul determined that the mass deaths were the work of Cyprinid herpesvirus 3, also known as koi herpesvirus (KHV).
KHV is common around the world but had never been reported in Iraq before this outbreak. It presumably entered the country via imported fish from elsewhere, perhaps ornamental koi (a variety of carp raised for their coloration instead of for food). Once in the river, it could easily contaminate the numerous fish farms along the river’s length and the millions of stressed, confined fish they contained. Since this disease specifically affects carp and their close relatives, the outbreak explains what was not observed — a mass dying of other fish species — as well as what was observed. Learning the cause of the mass dying via Sanger sequencing will enable Iraqi farmers and authorities to take appropriate actions to contain the outbreak and prevent future events like it.
Dr. Ababneh reports that the SeqStudio Genetic Analyzer was a key part of unraveling this mystery. “We were amazed by the quality and the ease of sequencing. The presence of such an instrument in our laboratory enables us to serve our customers more efficiently,” he wrote to us. Dr. Ababneh is particularly pleased with the assistance he received from the staff at Thermo Fisher Scientific. He adds, “I would love to recommend the SeqStudio Genetic Analyzer to anyone in the future.”
If you need to solve a country-wide disease outbreak, or have any other gene-sequencing questions you need to answer, have a look at the possibilities the SeqStudio Genetic Analyzer offers.