A team from Columbia University's Mailman School of Public Health has used high-throughput sequencing techniques from 454 Life Sciences, a Roche company, to identify a virus threatening salmon.
A study published online in the 'PLoS One' journal sheds new light on a disease that has caused widespread damage to farmed salmon populations in Norway and the UK.
Heart and skeletal muscle inflammation (HSMI), an often fatal disease, was first detected in salmon on a farm in Norway in 1999 and has now been reported in 417 fish farms in Norway and the UK.
The disease destroys heart and muscle tissue and kills up to 20 per cent of infected fish.
Although studies have indicated an infectious basis, recent efforts to identify the pathogen causing the disease have been unsuccessful.
Using high-throughput sequencing techniques with 454 Sequencing Systems, an international team led by W Ian Lipkin, managing director of the John Snow Professor of Epidemiology and director of the Center for Infection and Immunity at Columbia University's Mailman School of Public Health, has found evidence that the disease may be caused by a previously unknown virus.
The newly identified virus is related but distinct from previously known reoviruses, which are double-stranded RNA viruses that infect a range of vertebrates.
'Our data provides compelling evidence that HSMI is associated with infection with a new reovirus,' said Gustavo Palacios, first author of the study and assistant professor of epidemiology in the centre.
To identify the virus, the Columbia University investigators used 454 Life Sciences' GS FLX System and software tools, including a new tool called Frequency Analysis of Sequence Data (FASD), pioneered by Raul Rabadan of Columbia's Department of Biomedical Informatics.
Investigators in Norway and the US then looked for viral sequences in heart and kidney samples from 29 salmon representing three different HSMI outbreaks and 10 samples from healthy farmed fish.
A total of 28 out of the 29 (96.5 per cent) known HSMI samples were positive; meanwhile, none of the 10 healthy salmon samples tested positive.
The investigators also tested 66 samples obtained from wild salmon living in nine coastal rivers in Norway.
The virus was detected in 16 of these samples (24.2 per cent), although generally in lower concentrations than found in ailing farmed fish.
Additional research will be needed to confirm that the reovirus is the cause of HSMI.
Meanwhile, work has already begun in Norway to develop a vaccine to protect farmed Atlantic salmon.
