De novo assembly of Sockeye salmon kidney transcriptomes reveal a limited early response to piscine reovirus with or without infectious hematopoietic necrosis virus superinfection

Abstract Background Piscine reovirus (PRV) has been associated with the serious disease known as Heart and Skeletal Muscle Inflammation (HSMI) in cultured Atlantic salmon Salmo salar in Norway. PRV is also prevalent in wild and farmed salmon without overt disease manifestations, suggesting multifact...

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Main Authors: Polinski, Mark, Bradshaw, Julia, Inkpen, Sabrina, Richard, Jon, Fritsvold, Camilla, Poppe, Trygve, Rise, Matthew, Garver, Kyle, Johnson, Stewart
Format: Article in Journal/Newspaper
Language:unknown
Published: Figshare 2016
Subjects:
Online Access:https://dx.doi.org/10.6084/m9.figshare.c.3639188.v1
https://figshare.com/collections/De_novo_assembly_of_Sockeye_salmon_kidney_transcriptomes_reveal_a_limited_early_response_to_piscine_reovirus_with_or_without_infectious_hematopoietic_necrosis_virus_superinfection/3639188/1
id ftdatacite:10.6084/m9.figshare.c.3639188.v1
record_format openpolar
spelling ftdatacite:10.6084/m9.figshare.c.3639188.v1 2023-05-15T15:33:06+02:00 De novo assembly of Sockeye salmon kidney transcriptomes reveal a limited early response to piscine reovirus with or without infectious hematopoietic necrosis virus superinfection Polinski, Mark Bradshaw, Julia Inkpen, Sabrina Richard, Jon Fritsvold, Camilla Poppe, Trygve Rise, Matthew Garver, Kyle Johnson, Stewart 2016 https://dx.doi.org/10.6084/m9.figshare.c.3639188.v1 https://figshare.com/collections/De_novo_assembly_of_Sockeye_salmon_kidney_transcriptomes_reveal_a_limited_early_response_to_piscine_reovirus_with_or_without_infectious_hematopoietic_necrosis_virus_superinfection/3639188/1 unknown Figshare https://dx.doi.org/10.1186/s12864-016-3196-y https://dx.doi.org/10.6084/m9.figshare.c.3639188 CC BY 4.0 https://creativecommons.org/licenses/by/4.0 CC-BY Biochemistry Microbiology FOS Biological sciences Physiology 59999 Environmental Sciences not elsewhere classified FOS Earth and related environmental sciences Ecology Immunology FOS Clinical medicine 69999 Biological Sciences not elsewhere classified 110309 Infectious Diseases FOS Health sciences 60506 Virology Collection article 2016 ftdatacite https://doi.org/10.6084/m9.figshare.c.3639188.v1 https://doi.org/10.1186/s12864-016-3196-y https://doi.org/10.6084/m9.figshare.c.3639188 2021-11-05T12:55:41Z Abstract Background Piscine reovirus (PRV) has been associated with the serious disease known as Heart and Skeletal Muscle Inflammation (HSMI) in cultured Atlantic salmon Salmo salar in Norway. PRV is also prevalent in wild and farmed salmon without overt disease manifestations, suggesting multifactorial triggers or PRV variant-specific factors are required to initiate disease. In this study, we explore the head kidney transcriptome of Sockeye salmon Oncorhynchus nerka during early PRV infection to identify host responses in the absence of disease in hopes of elucidating mechanisms by which PRV may directly alter host functions and contribute to the development of a disease state. We further investigate the role of PRV as a coinfecting agent following superinfection with infectious hematopoietic necrosis virus (IHNV) – a highly pathogenic rhabdovirus endemic to the west coast of North America. Results Challenge of Sockeye salmon with PRV resulted in high quantities of viral transcripts to become present in the blood and kidney of infected fish without manifestations of disease. De novo transcriptome assembly of over 2.3 billion paired RNA-seq reads from the head kidneys of 36 fish identified more than 320,000 putative unigenes, of which less than 20 were suggested to be differentially expressed in response to PRV at either 2 or 3 weeks post challenge by DESeq2 and edgeR analysis. Of these, only one, Ependymin, was confirmed to be differentially expressed by qPCR in an expanded sample set. In contrast, IHNV induced substantial transcriptional changes (differential expression of > 20,000 unigenes) which included transcripts involved in antiviral and inflammatory response pathways. Prior infection with PRV had no significant effect on host responses to superinfecting IHNV, nor did host responses initiated by IHNV exposure influence increasing PRV loads. Conclusions PRV does not substantially alter the head kidney transcriptome of Sockeye salmon during early (2 to 3 week) infection and dissemination in a period of significant increasing viral load, nor does the presence of PRV change the host transcriptional response to an IHNV superinfection. Further, concurrent infections of PRV and IHNV do not appear to significantly influence the infectivity or severity of IHNV associated disease, or conversely, PRV load. Article in Journal/Newspaper Atlantic salmon Salmo salar DataCite Metadata Store (German National Library of Science and Technology) Norway Sockeye ENVELOPE(-130.143,-130.143,54.160,54.160)
institution Open Polar
collection DataCite Metadata Store (German National Library of Science and Technology)
op_collection_id ftdatacite
language unknown
topic Biochemistry
Microbiology
FOS Biological sciences
Physiology
59999 Environmental Sciences not elsewhere classified
FOS Earth and related environmental sciences
Ecology
Immunology
FOS Clinical medicine
69999 Biological Sciences not elsewhere classified
110309 Infectious Diseases
FOS Health sciences
60506 Virology
spellingShingle Biochemistry
Microbiology
FOS Biological sciences
Physiology
59999 Environmental Sciences not elsewhere classified
FOS Earth and related environmental sciences
Ecology
Immunology
FOS Clinical medicine
69999 Biological Sciences not elsewhere classified
110309 Infectious Diseases
FOS Health sciences
60506 Virology
Polinski, Mark
Bradshaw, Julia
Inkpen, Sabrina
Richard, Jon
Fritsvold, Camilla
Poppe, Trygve
Rise, Matthew
Garver, Kyle
Johnson, Stewart
De novo assembly of Sockeye salmon kidney transcriptomes reveal a limited early response to piscine reovirus with or without infectious hematopoietic necrosis virus superinfection
topic_facet Biochemistry
Microbiology
FOS Biological sciences
Physiology
59999 Environmental Sciences not elsewhere classified
FOS Earth and related environmental sciences
Ecology
Immunology
FOS Clinical medicine
69999 Biological Sciences not elsewhere classified
110309 Infectious Diseases
FOS Health sciences
60506 Virology
description Abstract Background Piscine reovirus (PRV) has been associated with the serious disease known as Heart and Skeletal Muscle Inflammation (HSMI) in cultured Atlantic salmon Salmo salar in Norway. PRV is also prevalent in wild and farmed salmon without overt disease manifestations, suggesting multifactorial triggers or PRV variant-specific factors are required to initiate disease. In this study, we explore the head kidney transcriptome of Sockeye salmon Oncorhynchus nerka during early PRV infection to identify host responses in the absence of disease in hopes of elucidating mechanisms by which PRV may directly alter host functions and contribute to the development of a disease state. We further investigate the role of PRV as a coinfecting agent following superinfection with infectious hematopoietic necrosis virus (IHNV) – a highly pathogenic rhabdovirus endemic to the west coast of North America. Results Challenge of Sockeye salmon with PRV resulted in high quantities of viral transcripts to become present in the blood and kidney of infected fish without manifestations of disease. De novo transcriptome assembly of over 2.3 billion paired RNA-seq reads from the head kidneys of 36 fish identified more than 320,000 putative unigenes, of which less than 20 were suggested to be differentially expressed in response to PRV at either 2 or 3 weeks post challenge by DESeq2 and edgeR analysis. Of these, only one, Ependymin, was confirmed to be differentially expressed by qPCR in an expanded sample set. In contrast, IHNV induced substantial transcriptional changes (differential expression of > 20,000 unigenes) which included transcripts involved in antiviral and inflammatory response pathways. Prior infection with PRV had no significant effect on host responses to superinfecting IHNV, nor did host responses initiated by IHNV exposure influence increasing PRV loads. Conclusions PRV does not substantially alter the head kidney transcriptome of Sockeye salmon during early (2 to 3 week) infection and dissemination in a period of significant increasing viral load, nor does the presence of PRV change the host transcriptional response to an IHNV superinfection. Further, concurrent infections of PRV and IHNV do not appear to significantly influence the infectivity or severity of IHNV associated disease, or conversely, PRV load.
format Article in Journal/Newspaper
author Polinski, Mark
Bradshaw, Julia
Inkpen, Sabrina
Richard, Jon
Fritsvold, Camilla
Poppe, Trygve
Rise, Matthew
Garver, Kyle
Johnson, Stewart
author_facet Polinski, Mark
Bradshaw, Julia
Inkpen, Sabrina
Richard, Jon
Fritsvold, Camilla
Poppe, Trygve
Rise, Matthew
Garver, Kyle
Johnson, Stewart
author_sort Polinski, Mark
title De novo assembly of Sockeye salmon kidney transcriptomes reveal a limited early response to piscine reovirus with or without infectious hematopoietic necrosis virus superinfection
title_short De novo assembly of Sockeye salmon kidney transcriptomes reveal a limited early response to piscine reovirus with or without infectious hematopoietic necrosis virus superinfection
title_full De novo assembly of Sockeye salmon kidney transcriptomes reveal a limited early response to piscine reovirus with or without infectious hematopoietic necrosis virus superinfection
title_fullStr De novo assembly of Sockeye salmon kidney transcriptomes reveal a limited early response to piscine reovirus with or without infectious hematopoietic necrosis virus superinfection
title_full_unstemmed De novo assembly of Sockeye salmon kidney transcriptomes reveal a limited early response to piscine reovirus with or without infectious hematopoietic necrosis virus superinfection
title_sort de novo assembly of sockeye salmon kidney transcriptomes reveal a limited early response to piscine reovirus with or without infectious hematopoietic necrosis virus superinfection
publisher Figshare
publishDate 2016
url https://dx.doi.org/10.6084/m9.figshare.c.3639188.v1
https://figshare.com/collections/De_novo_assembly_of_Sockeye_salmon_kidney_transcriptomes_reveal_a_limited_early_response_to_piscine_reovirus_with_or_without_infectious_hematopoietic_necrosis_virus_superinfection/3639188/1
long_lat ENVELOPE(-130.143,-130.143,54.160,54.160)
geographic Norway
Sockeye
geographic_facet Norway
Sockeye
genre Atlantic salmon
Salmo salar
genre_facet Atlantic salmon
Salmo salar
op_relation https://dx.doi.org/10.1186/s12864-016-3196-y
https://dx.doi.org/10.6084/m9.figshare.c.3639188
op_rights CC BY 4.0
https://creativecommons.org/licenses/by/4.0
op_rightsnorm CC-BY
op_doi https://doi.org/10.6084/m9.figshare.c.3639188.v1
https://doi.org/10.1186/s12864-016-3196-y
https://doi.org/10.6084/m9.figshare.c.3639188
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