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Ultra-deep sequencing of VHSV isolates contributes to understanding the role of viral quasispecies

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 s...

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Autores principales: Schönherz, Anna A., Lorenzen, Niels, Guldbrandtsen, Bernt, Buitenhuis, Bart, Einer-Jensen, Katja
Formato: Online Artículo Texto
Lenguaje:English
Publicado: BioMed Central 2016
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4705744/
https://www.ncbi.nlm.nih.gov/pubmed/26743117
http://dx.doi.org/10.1186/s13567-015-0298-5
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author Schönherz, Anna A.
Lorenzen, Niels
Guldbrandtsen, Bernt
Buitenhuis, Bart
Einer-Jensen, Katja
author_facet Schönherz, Anna A.
Lorenzen, Niels
Guldbrandtsen, Bernt
Buitenhuis, Bart
Einer-Jensen, Katja
author_sort Schönherz, Anna A.
collection PubMed
description 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.
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spelling pubmed-47057442016-01-09 Ultra-deep sequencing of VHSV isolates contributes to understanding the role of viral quasispecies Schönherz, Anna A. Lorenzen, Niels Guldbrandtsen, Bernt Buitenhuis, Bart Einer-Jensen, Katja Vet Res Research Article 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. BioMed Central 2016-01-08 2016 /pmc/articles/PMC4705744/ /pubmed/26743117 http://dx.doi.org/10.1186/s13567-015-0298-5 Text en © Schönherz et al. 2016 Open AccessThis article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.
spellingShingle Research Article
Schönherz, Anna A.
Lorenzen, Niels
Guldbrandtsen, Bernt
Buitenhuis, Bart
Einer-Jensen, Katja
Ultra-deep sequencing of VHSV isolates contributes to understanding the role of viral quasispecies
title Ultra-deep sequencing of VHSV isolates contributes to understanding the role of viral quasispecies
title_full Ultra-deep sequencing of VHSV isolates contributes to understanding the role of viral quasispecies
title_fullStr Ultra-deep sequencing of VHSV isolates contributes to understanding the role of viral quasispecies
title_full_unstemmed Ultra-deep sequencing of VHSV isolates contributes to understanding the role of viral quasispecies
title_short Ultra-deep sequencing of VHSV isolates contributes to understanding the role of viral quasispecies
title_sort ultra-deep sequencing of vhsv isolates contributes to understanding the role of viral quasispecies
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4705744/
https://www.ncbi.nlm.nih.gov/pubmed/26743117
http://dx.doi.org/10.1186/s13567-015-0298-5
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