title: Use of molecular epidemiology to trace transmission pathways for infectious salmon anaemia virus (ISAV) in Norwegian salmon farming.
abstract: BACKGROUND
  Infectious Salmon Anaemia (ISA) is a disease affecting farmed Atlantic salmon, and most salmon producing countries have experienced ISA outbreaks. The aim of the present study was to use epidemiological and viral sequence information to trace transmission pathways for ISA virus (ISAV) in Norwegian salmon farming.
  
  
  METHODS
  The study covers a period from January 2007 to July 2009 with a relatively high rate of ISA outbreaks, including a large cluster of outbreaks that emerged in Northern Norway (the North-cluster). Farms with ISA outbreaks and neighbouring salmon farms (At-risk-sites) were tested for the presence of ISAV, and epidemiological information was collected. ISAV hemagglutinin-esterase (HE) and fusion (F) protein genes were sequenced and phylogenetic analyses were performed. Associations between sequence similarities and salmon population data were analysed to substantiate possible transmission pathways.
  
  
  RESULTS
  There was a high degree of genetic similarity between ISAV isolates within the North-cluster. ISAV was detected in 12 of 28 At-risk-sites, and a high proportion of the viruses were identified as putative low virulent genotypes harbouring the full length highly polymorphic region (HPR); HPR0 of the HE protein and the amino acid glutamine (Q) in the F protein at position 266. The sequences from HPR0/F (Q(266)) genotypes revealed larger genetic variation, lower viral loads and lower prevalence of infection than HPR-deleted genotypes. Seaway distance between salmon farms was the only robust explanatory variable to explain genetic similarity between ISAV isolates.
  
  
  CONCLUSIONS
  We suggest that a single HPR-deleted genotype of ISAV has spread between salmon farms in the North-cluster. Furthermore, we find that HPR0/F (Q(266)) genotypes are frequently present in farmed populations of Atlantic salmon. From this, we anticipate a population dynamics of ISAV portrayed by low virulent genotypes occasionally transitioning into virulent genotypes, causing solitary outbreaks or local epidemics through local transmission.
authors.affiliation: National Veterinary Institute, Oslo, Norway. trude.lyngstad@vetinst.no
authors.forename: T M
authors.initials: TM
authors.lastname: Lyngstad
authors.forename: M J
authors.initials: MJ
authors.lastname: Hjortaas
authors.forename: A B
authors.initials: AB
authors.lastname: Kristoffersen
authors.forename: T
authors.initials: T
authors.lastname: Markussen
authors.forename: E T
authors.initials: ET
authors.lastname: Karlsen
authors.forename: C M
authors.initials: CM
authors.lastname: Jonassen
authors.forename: P A
authors.initials: PA
authors.lastname: Jansen
mesh_terms: D000818:Animals; D004196:Disease Outbreaks / Q000662:veterinary; D005393:Fish Diseases / Q000453:epidemiology / Q000235:genetics / Q000635:transmission / Q000821:virology; D005398:Fisheries; D046829:Isavirus / Q000235:genetics* / Q000302:isolation & purification; D017720:Molecular Epidemiology / Q000379:methods*; D009664:Norway / Q000453:epidemiology; D009976:Orthomyxoviridae Infections / Q000453:epidemiology / Q000235:genetics / Q000635:transmission*; D020317:Salmo salar / Q000821:virology*