Table 1 Prevalence of infectious agents in Pacific salmon mixed-tissue marine samples (2008–2018) tested by HT-qRT-PCR (DFO Pacific Biological Station, Nanaimo, BC).

From: The spatial distribution of infectious agents in wild Pacific salmon along the British Columbia coast

Scientific name

Taxonomic class or family (viruses)

Transmission environment

Spring–Summer

Fall–Winter

Chinook

Coho

Sockeye

Chinook

Coho

Sockeye

Aeromonas hydrophila

Gammaproteobacteria

SW

0.0 (37)

0.0 (\(<0.1\))

0.0 (56)

0.0(46)

NA (0)

0.0 (14)

Aeromonas salmonicida

Gammaproteobacteria

FW

0.0 (93)

0.0 (100)

0.0 (99)

0.0 (100)

0.0 (100)

0.0 (100)

Ca. Branchiomonas cysticola

Betaproteobacteria

FW

74.5 (100)

96.7 (100)

89.7 (100)

84.4 (100)

95.4 (100)

74.9 (100)

Flavobacterium psychrophilum

Flavobacteriia

FW

7.9 (100)

3.0 (100)

1.2 (100)

7.3 (100)

1.8 (100)

3.7 (100)

Moritella viscosa

Gammaproteobacteria

SW

0.0 (2)

NA (0)

0.3 (55)

0.0 (10)

NA (0)

0.0 (14)

Ca. Piscichlamydia salmonis

Chlamydiae

SW

0.7 (100)

1.5 (97)

0.2 (100)

0.2 (100)

0.4 (95)

0.0 (100)

Piscirickettsia salmonis

Gammaproteobacteria

SW

2.0 (100)

0.2 (100)

\(<0.1\) (100)

1.8 (100)

0.6 (100)

0.0 (100)

Renibacterium salmoninarum

Actinobacteria

FW

2.1 (100)

1.3 (100)

\(<0.1\) (100)

0.4 (100)

0.7 (100)

0.2 (100)

Rickettsia-like organism

Alphaproteobacteria

FW

4.1 (100)

2.1 (100)

2.1 (100)

5.9 (100)

0.2 (100)

8.6 (100)

Ca. Syngnamydia salmonis

Chlamydiae

SW

25.8 (100)

17.7 (100)

18.0 (100)

16.7 (100)

13.6 (100)

11.9 (100)

Tenacibaculum maritimum

Flavobacteriia

SW

2.5 (66)

4.7 (100)

2.7 (100)

11.3 (64)

10.9 (100)

5.4 (100)

Vibrio anguillarum

Gammaproteobacteria

SW

0.0 (100)

0.0 (100)

0.0 (100)

0.0 (100)

0.0 (100)

0.0 (100)

Aliivibrio salmonicida

Gammaproteobacteria

SW

0.0 (100)

0.0 (100)

0.0 (100)

0.0 (100)

1.8 (100)

0.0 (100)

Yersinia ruckeri

Gammaproteobacteria

SW

0.0 (59)

0.0 (100)

0.0 (99)

0.0 (64)

0.0 (100)

0.0 (100)

Dermocystidium salmonis

Mesomycetozoea

FW

0.1 (100)

0.6 (100)

2.1 (100)

0.0 (100)

0.0 (100)

0.9 (100)

Ichthyophonus hoferi

Mesomycetozoea

SW

11.6 (100)

10.5 (100)

9.3 (100)

23.1 (100)

8.7 (100)

17.3 (100)

Sphaerothecum destruens

Mesomycetozoea

SW

1.1 (98)

2.4 (100)

2.2 (99)

3.6 (100)

4.4 (100)

3.6 (100)

Facilispora margolisi

Microsporea

SW

4.6 (100)

5.0 (100)

2.4 (100)

11.6 (100)

7.0 (100)

4.1 (100)

Loma salmonae

Microsporea

SW

18.2 (100)

37.9 (100)

7.6 (100)

29.7 (100)

46.8 (100)

21.9 (100)

Paranucleospora theridion (syn. Desmozoon lepeophtherii)

Microsporea

SW

62.4 (100)

63.1 (100)

75.2 (100)

64.3 (100)

76.9 (100)

49.9 (100)

Ceratonova shasta

Myxosporea

FW

24.8 (100)

10.8 (100)

8.4 (100)

22.5 (100)

5.8 (100)

4.5 (100)

Kudoa thyrsites

Myxosporea

SW

5.9 (100)

3.1 (100)

1.2 (100)

6.1 (100)

2.9 (100)

0.5 (100)

Myxobolus arcticus

Myxosporea

FW

33.6 (100)

14.8 (100)

65.1 (100)

30.2 (100)

13.0 (100)

66.0 (100)

Myxobolus cerebalis

Myxosporea

FW

0.0 (34)

0.0 (0.1)

0.0 (0.2)

0.0 (36)

NA (0)

0.0 (0.2)

Myxobolus insidiosus

Myxosporea

FW

0.6 (100)

3 (100)

0.1 (100)

0.3 (100)

3 (100)

0.0 (100)

Parvicapsula kabatai

Myxosporea

SW

15.5 (100)

10.2 (100)

22.1 (100)

1.1 (100)

4.1 (100)

6.6 (100)

Parvicapsula minibicornis

Myxosporea

FW

36.1 (100)

40.3 (100)

55.8 (100)

35.6 (100)

35.5 (100)

60.4 (100)

Parvicapsula pseudobranchicola

Myxosporea

SW

25.1 (100)

35.3 (100)

14.5 (100)

77.3 (100)

74.6 (100)

50.8 (100)

Tetracapsuloides bryosalmonae

Myxosporea

FW

12.8 (100)

11.7 (100)

2.2 (100)

11.9 (100)

2.1 (100)

1.1 (100)

Gyrodactylus salaris

Monogenea

FW

0.0 (37)

0.0 (0.1)

0.0 (56)

0.0 (46)

NA (0)

0.0 (14)

Nanophyetus salmincola

Trematoda

FW

0.7 (100)

2.7 (100)

\(<0.1\) (100)

2.8 (100)

2.6 (100)

0.0 (100)

Cryptobia salmositica

Kinetoplastida

FW

0.2 (93)

2.0 (100)

\(<0.1\) (99)

0.1 (100)

2.1 (100)

0.0 (100)

Ichthyophthirius multifiliis

Oligohymenophorea

FW

12.5 (98)

4.8 (100)

4.3 (99)

7.3 (100)

4.3 (100)

2.1 (100)

Neoparamoeba perurans

Discosea

SW

\(<0.1\) (98)

0.0 (100)

0.0 (97)

0.6 (100)

0.5 (100)

0.0 (100)

Spironucleus salmonicida

Trepomonadea

SW

0.0 (37)

0.0 (\(<0.1\))

0.0 (56)

0.0 (46)

NA (0)

0.0 (14)

Atlantic Salmon Calicivirus

Caliciviridae

SW

0.1 (65)

0.2 (100)

0.0 (46)

0.5 (62)

0.4 (100)

0.0 (85)

Atlantic Salmon Paramyxovirus

Paramyxoviridae

SW

0.0 (34)

0.0 (\(<0.1\))

0.0 (0.2)

0.0 (36)

NA (0)

0.0 (0.2)

Chinook aquareovirus

Reoviridae

FW

0.0 (65)

0.0 (100)

0.0 (46)

0.0 (62)

0.0 (100)

0.0 (84)

Cutthroat Trout virus 2

Hepeviridae

SW

\(<0.1\) (65)

0.0 (100)

\(<0.1\) (46)

0.0 (62)

0.0 (100)

0.0 (85)

Erythrocytic necrosis virus

Iridoviridae

SW

13.9 (100)

6.8 (100)

17.8 (100)

20.4 (100)

10.1 (100)

8.6 (100)

Infectious hematopoietic necrosis virus

Rhabdoviridae

FW

0.1 (100)

0.0 (100)

0.2 (100)

0.1 (100)

0.0 (100)

0.0 (100)

Infectious pancreatic necrosis virus

Birnaviridae

SW

0.0 (37)

0.0 (\(<0.1\))

0.0 (56)

0.0 (46)

NA (0)

0.0 (14)

Infectious salmon anemia virus

Orthomyxoviridae

SW

0.0 (37)

0.0 (\(<0.1\))

0.0 (56)

0.0 (46)

NA (0)

0.0 (14)

Pacific salmon nidovirus

Coronaviridae

FW

8.6 (63)

0.7 (100)

0.0 (46)

0.2 (54)

0.0 (100)

0.0 (85)

Pacific salmon parvovirus

Parvoviridae

FW

0.4 (96)

0.6 (100)

57.2 (100)

0.5 (94)

0.0 (100)

24.3 (100)

Piscine myocarditis virus

Totiviridae

SW

0.0 (37)

0.0 (\(<0.1\))

0.0 (56)

0.0 (46)

NA (0)

0.0 (14)

Piscine orthoreovirus

Reoviridae

SW

4.9 (100)

9.4 (100)

0.9 (100)

4.9 (100)

2.4 (100)

0.7 (100)

Putative RNA virus 1

Unclassified

SW

0.4 (63)

0.8 (100)

1.1 (46)

3.6 (54)

0.7 (100)

2.7 (86)

Putative toti-like virus

Unclassified

SW

0.0 (58)

0.0 (100)

\(<0.1\) (46)

0.0 (62)

0.0 (100)

0.0 (85)

Rainbow trout orthomyxovirus

Orthomyxoviridae

FW

0.0 (58)

0.0 (100)

0.0 (45)

0.0 (62)

0.0 (100)

0.0 (84)

Salmon alphavirus

Togaviridae

SW

0.0 (37)

0.0 (\(<0.1\))

0.0 (56)

0.0 (46)

NA (0)

0.0 (14)

Salmon gill pox virus

Poxviridae

FW

0.0 (59)

0.0 (25)

0.0 (40)

0.0 (63)

0.0 (14)

0.0 (86)

Salmon Pescarenavirus 1

Arenaviridae

SW

5.4 (65)

0.3 (100)

0.3 (46)

6.5 (61)

0.3 (100)

0.0 (85)

Salmon Pescarenavirus 2

Arenaviridae

SW

0.5 (63)

0.4 (100)

19.0 (44)

0.3 (53)

0.2 (100)

2.6 (83)

Viral encephalopathy and retinopathy virus

Nodaviridae

SW

0.0 (93)

0.0 (100)

\(<0.1\) (99)

1.1 (100)

0.1 (100)

0.4 (100)

Viral hemorrhagic septicemia virus

Rhabdoviridae

SW

1.2 (100)

0.9 (100)

\(<0.1\) (100)

0.5 (100)

0.8 (100)

0.0 (100)

Total pathogen taxa (mean ± SD)

NA

NA

4.1 ± 2.1

4.0 ± 1.6

4.4 ± 1.8

4.8 ± 1.8

4.3 ± 1.4

4.2 ± 1.6

  1. Mean total pathogen taxa per individual with standard deviation is included at the bottom. Pathogen taxa with positive detections are in bold. Prevalence of each pathogen taxa is provided for each host species in both seasons (% of each group assayed for the given assay presented in parentheses). NAs indicate that no individuals from the given group were assayed (see “Methods”). Sample sizes were 2883, 1062, 2826 and 2836, 997, 561 for Chinook, Coho, and Sockeye salmon in spring-summer and fall-winter. Primer and probe sequences for each assay are available in Supplementary Material 1, Table S4. Transmission environments in italics are the presumed predominant environment, although transmission in both environments has been documented.
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