1. Ecology
  2. Microbiology and Infectious Disease
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Endangered wild salmon infected by newly discovered viruses

  1. Gideon J Mordecai  Is a corresponding author
  2. Kristina M Miller  Is a corresponding author
  3. Emiliano Di Cicco
  4. Angela D Schulze
  5. Karia H Kaukinen
  6. Tobi J Ming
  7. Shaorong Li
  8. Amy Tabata
  9. Amy Teffer
  10. David A Patterson
  11. Hugh W Ferguson
  12. Curtis A Suttle  Is a corresponding author
  1. University of British Columbia, Canada
  2. Fisheries and Oceans Canada, Canada
  3. Pacific Salmon Foundation, Canada
  4. Simon Fraser University, Canada
  5. St. George’s University, Grenada
Short Report
Cite this article as: eLife 2019;8:e47615 doi: 10.7554/eLife.47615
4 figures, 19 data sets and 3 additional files

Figures

Figure 1 with 1 supplement
Maximum likelihood phylogenetic tree based on MAFFT alignments of the predicted replicase protein of (A) Salmon pescarenavirus and related arenaviruses, (B) Chinook Aquareovirus and related Aqua and orthoreoviruses and (C) Pacific salmon nidovirus and related Nidovirales.

Sequences from this study are marked with an asterisk, scale bar represents the number of amino substitutions per site, node labels show the bootstrap support and host groups are shown by colour. Trees are mid-point rooted, so do not necessarily represent the ancestral relationship of the viruses. Amino acid alignments have been provided in the source data for Figure 1.

https://doi.org/10.7554/eLife.47615.003
Figure 1—source data 1

Arenavirus amino acid alignment.

https://doi.org/10.7554/eLife.47615.006
Figure 1—source data 2

Nidovirus amino acid alignment.

https://doi.org/10.7554/eLife.47615.007
Figure 1—source data 3

Reovirus amino acid alignment.

https://doi.org/10.7554/eLife.47615.008
Figure 1—source data 4

Arenavirus phylogenetic tree.

https://doi.org/10.7554/eLife.47615.009
Figure 1—source data 5

Reovirus phylogenetic tree.

https://doi.org/10.7554/eLife.47615.010
Figure 1—source data 6

Nidovirus phylogenetic tree.

https://doi.org/10.7554/eLife.47615.011
Figure 1—figure supplement 1
Genome organisation and coverage.

(A) Genome organisation, ORF prediction and (B) Genome coverage for Salmon pescarenavirus 1 and 2 (SPAV), Chinook Aquareovirus (CAV) segments 1-and Pacific salmon Nidovirus (PsNV). Black lines represent the genome and boxes show the predicted open reading frames. Nucleotide sequences are provided in fasta format in the source data for Figure 1.

https://doi.org/10.7554/eLife.47615.004
Figure 1—figure supplement 1—source data 1

Viral genomic nucleotide sequences.

https://doi.org/10.7554/eLife.47615.005
Figure 2 with 2 supplements
Epidemiological maps of Salmon pescarenavirus 1 and 2 (SPAV-1 and SPAV-2), Chinook aquareovirus (CAV) and Pacific salmon nidovirus (PsNV) around the coast of Vancouver Island.

Individual samples are shown at the location collected, negative samples are black, and positive samples are coloured and sized according to the virus copy number. A small degree of random noise was added to the longitude and latitude to prevent overplotting.

https://doi.org/10.7554/eLife.47615.012
Figure 2—source data 1

Source data (RT-PCR copy number and sampling locations) for hte epidemiological maps.

https://doi.org/10.7554/eLife.47615.015
Figure 2—figure supplement 1
Summary of RT-PCR for SPAV-1 and −2, PsNV and CAV using the Biomark Fluidigm platform.

The data shown are the prevalence (percentage) of positive amplifications above the calculated limit of detection (95%). Numbers show the sample size and error bars show Wilson’s binomial confidence intervals. Hatchery Chinook are fish with clipped fins, whilst wild represent all other wild caught fish.

https://doi.org/10.7554/eLife.47615.013
Figure 2—figure supplement 2
Epidemiological maps from Washington to Alaska of Salmon pescarenavirus 1 and 2 (SPAV-1 and SPAV-2).

Individual samples are shown at the location collected, samples negative for SPAV are black, and positive samples are coloured and sized according to the virus copy number. A small degree of random noise was added to the latitude and longitude to prevent overplotting.

https://doi.org/10.7554/eLife.47615.014
Figure 3 with 1 supplement
In Situ Hybridization staining of SPAV-1 in Chinook salmon.

The red stain indicates localisation of viral RNA as well as viral transcripts. (A) Spleen: staining mostly localised in the macrophages (arrows) located around the sinusoids, although scattered positive red blood cells (arrowheads) are also present (scale bar 50 µm). (B) Posterior Kidney: the virus appears to be primarily localised in the peritubular capillaries (renal portal vessels) and macrophages (arrows) (scale bar 100 µm). (C) Liver: nodules of inflammation are mainly concentrated in a highly marked area. (scale bar 100 µm), dashed rectangle is enlarged in (D) showing lymphocytes and macrophages in the inflammatory nodule (several of which are positive for the virus). (scale bar 20 µm). (E) Heart: positive macrophages (arrows) are present between the fibres of the spongy myocardium, along with several positive red blood cells (arrowhead) and endothelial cells (open arrowheads). (scale bar 100 µm). (F) Intestine: staining for SPAV-1 is primarily localised to the gut-associated lymphoid tissue (arrows). (scale bar 100 µm).

https://doi.org/10.7554/eLife.47615.016
Figure 3—figure supplement 1
In Situ Hybridization staining of SPAV-2 in sockeye salmon.

The red stain indicates localisation of viral RNA as well as viral transcripts (A) Spleen: staining mostly localised to the macrophages (arrows) scattered throughout the tissue. (scale bar 100 µm). (B) SPAV-2 appears to be primarily localised to the peritubular capillaries (renal portal vessels) and macrophages (arrows) (scale bar 100 µm). (C) Liver: macrophages (arrows) and red blood cells (arrowhead) positive for SPAV-2 are present in the blood circulating in the sinusoids. (scale bar 100 µm). (D) Liver: SPAV-2 is localised to the blood, inside macrophages (arrows) and red blood cells (arrowheads). (scale bar 20 µm). (E) Gills: several red blood cells (arrowhead) were positive for SPAV-2. (scale bar 100 µm). (F) Heart: virus was localised to macrophages (arrows) in the blood circulating in the myocardium. (scale bar 100 µm).

https://doi.org/10.7554/eLife.47615.017
Pacific salmon nidovirus localisation and detections at a single salmon enhancement hatchery.

(A) Average relative quantity of Pacific salmon nidovirus in dissected tissues of eight Chinook. Each sample was run and plotted in duplicate. (B) Prevalence of Pacific salmon nidovirus in fish collected in fresh and saltwater at a single salmon enhancement hatchery over four years. The data shown are the prevalence of positive amplifications above the calculated limit of detection (95%). Numbers show the sample size and error bars show Wilson’s binomial confidence intervals.

https://doi.org/10.7554/eLife.47615.018

Data availability

Assembled viral genomes have been deposited to Genbank under accession numbers MK611979–MK611996 and sequencing reads have been submitted to the Sequence Read Archive under the accession: PRJNA547678.

The following data sets were generated
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Additional files

Supplementary file 1

Table of primers and taqman assays used in this study.

https://doi.org/10.7554/eLife.47615.019
Supplementary file 2

Commands used in the bioinformatic pipeline.

https://doi.org/10.7554/eLife.47615.020
Transparent reporting form
https://doi.org/10.7554/eLife.47615.021

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