title: Ultra-deep sequencing of VHSV isolates contributes to understanding the role of viral quasispecies.
abstract: The high mutation rate of RNA viruses enables the generation of a genetically diverse viral population, termed a quasispecies, within a single infected host. This high in-host genetic diversity enables an RNA virus to adapt to a diverse array of selective pressures such as host immune response and switching between host species. The negative-sense, single-stranded RNA virus, viral haemorrhagic septicaemia virus (VHSV), was originally considered an epidemic virus of cultured rainbow trout in Europe, but was later proved to be endemic among a range of marine fish species in the Northern hemisphere. To better understand the nature of a virus quasispecies related to the evolutionary potential of VHSV, a deep-sequencing protocol specific to VHSV was established and applied to 4 VHSV isolates, 2 originating from rainbow trout and 2 from Atlantic herring. Each isolate was subjected to Illumina paired end shotgun sequencing after PCR amplification and the 11.1 kb genome was successfully sequenced with an average coverage of 0.5-1.9 × 10(6) sequenced copies. Differences in single nucleotide polymorphism (SNP) frequency were detected both within and between isolates, possibly related to their stage of adaptation to host species and host immune reactions. The N, M, P and Nv genes appeared nearly fixed, while genetic variation in the G and L genes demonstrated presence of diverse genetic populations particularly in two isolates. The results demonstrate that deep sequencing and analysis methodologies can be useful for future in vivo host adaption studies of VHSV.
authors.affiliation: Department of Molecular Biology and Genetics, Center for Quantitative Genetics and Genomics, Aarhus University, Blichers Allé 20, P.O. Box 50, 8830, Tjele, Denmark. anna.schonherz@mbg.au.dk.
authors.forename: Anna A
authors.initials: AA
authors.lastname: Schönherz
authors.affiliation: Department of Animal Science, Aarhus University, Blichers Allé 20, P.O. Box 50, 8830, Tjele, Denmark. niels.lorenzen@anis.au.dk.
authors.forename: Niels
authors.initials: N
authors.lastname: Lorenzen
authors.affiliation: Department of Molecular Biology and Genetics, Center for Quantitative Genetics and Genomics, Aarhus University, Blichers Allé 20, P.O. Box 50, 8830, Tjele, Denmark. bernt.guldbrandtsen@mbg.au.dk.
authors.forename: Bernt
authors.initials: B
authors.lastname: Guldbrandtsen
authors.affiliation: Department of Molecular Biology and Genetics, Center for Quantitative Genetics and Genomics, Aarhus University, Blichers Allé 20, P.O. Box 50, 8830, Tjele, Denmark. bart.buitenhuis@mbg.au.dk.
authors.forename: Bart
authors.initials: B
authors.lastname: Buitenhuis
authors.affiliation: QIAGEN AAR, 8000, Århus, Denmark. katja.einer@qiagen.com.
authors.forename: Katja
authors.initials: K
authors.lastname: Einer-Jensen
mesh_terms: D000818:Animals; D019295:Computational Biology; D005393:Fish Diseases / Q000821:virology; D005399:Fishes; D015967:Gene Expression Regulation, Viral; D014644:Genetic Variation; D059014:High-Throughput Nucleotide Sequencing / Q000662:veterinary*; D029141:Novirhabdovirus / Q000235:genetics / Q000378:metabolism*; D012367:RNA, Viral / Q000235:genetics
chemical_list: D012367:RNA, Viral