Ultra-deep pyrosequencing of partial surface protein genes from infectious Salmon Anaemia virus (ISAV) suggest novel mechanisms involved in transition to virulence

PLoS One. 2013 Nov 26;8(11):e81571. doi: 10.1371/journal.pone.0081571. eCollection 2013.


Uncultivable HPR0 strains of infectious salmon anaemia viruses (ISAVs) infecting gills are non-virulent putative precursors of virulent ISAVs (vISAVs) causing systemic disease in farmed Atlantic salmon (Salmo salar). The transition to virulence involves two molecular events, a deletion in the highly polymorphic region (HPR) of the hemagglutinin-esterase (HE) gene and a Q266→L266 substitution or insertion next to the putative cleavage site (R267) in the fusion protein (F). We have performed ultra-deep pyrosequencing (UDPS) of these gene regions from healthy fish positive for HPR0 virus carrying full-length HPR sampled in a screening program, and a vISAV strain from an ISA outbreak at the same farming site three weeks later, and compared the mutant spectra. As the UDPS data shows the presence of both HE genotypes at both sampling times, and the outbreak strain was unlikely to be directly related to the HPR0 strain, this is the first report of a double infection with HPR0s and vISAVs. For F amplicon reads, mutation frequencies generating L266 codons in screening samples and Q266 codons in outbreak samples were not higher than at any random site. We suggest quasispecies heterogeneity as well as RNA structural properties are linked to transition to virulence. More specifically, a mechanism where selected single point mutations in the full-length HPR alter the RNA structure facilitating single- or sequential deletions in this region is proposed. The data provides stronger support for the deletion hypothesis, as opposed to recombination, as the responsible mechanism for generating the sequence deletions in HE.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Animals
  • Fish Diseases / virology
  • Hemagglutinins, Viral / chemistry
  • Hemagglutinins, Viral / genetics
  • High-Throughput Nucleotide Sequencing
  • Isavirus / genetics*
  • Isavirus / pathogenicity*
  • Molecular Sequence Data
  • Mutation
  • Nucleic Acid Conformation
  • Polymorphism, Single Nucleotide
  • Salmo salar / virology
  • Viral Envelope Proteins / chemistry
  • Viral Envelope Proteins / genetics*
  • Viral Fusion Proteins / chemistry
  • Viral Fusion Proteins / genetics
  • Virulence / genetics


  • Hemagglutinins, Viral
  • Viral Envelope Proteins
  • Viral Fusion Proteins
  • hemagglutinin esterase

Associated data

  • GENBANK/KC907278
  • GENBANK/KC907279
  • GENBANK/KC907280
  • GENBANK/KC907281
  • GENBANK/KC907282
  • GENBANK/KC907283
  • GENBANK/KC907284
  • GENBANK/KC907285
  • GENBANK/KC907286
  • GENBANK/KC907287
  • GENBANK/KC907288
  • GENBANK/KC907289
  • GENBANK/KC907290
  • GENBANK/KC907291
  • GENBANK/KC907292
  • GENBANK/KC907293

Grant support

This work was supported by The Norwegian Research Council (project no. 207024/E40). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.