Table 1.
Forty-six infectious agents (including two strains for ‘isav’) tested on 2,006 out-migrating Fraser River Sockeye salmon in 2012 and 2013, along with their overall prevalences.
| Agent | Typea | Abbreviation | n | Positive | Prevalence (%)b |
|---|---|---|---|---|---|
| (1) Candidatus Brachiomonas cysticola | B | c_b_cys | 1,996 | 1,800 | 90.18 |
| (2) Myxobolus arcticus | P | my_arc | 1,970 | 1,180 | 59.90 |
| (3) Pacific salmon parvovirus | V | pspv | 1,975 | 1,119 | 56.66 |
| (4) Paraneuclospora theridion | P | pa_ther | 1,982 | 622 | 31.38 |
| (5) Parvicapsula minibicornis | P | pa_min | 1,960 | 503 | 25.66 |
| (6) Parvicapsula kabatai | P | pa_kab | 1,992 | 320 | 16.06 |
| (7) Erythrocytic necrosis virus | V | env | 1,991 | 210 | 10.55 |
| (8) Ichthyophthirius multifiliis | P | ic_mul | 1,888 | 156 | 8.26 |
| (9) Gill chlamydia | B | sch | 1,989 | 135 | 6.79 |
| (10) Parvicapsula pseudobranchiocola | P | pa_pse | 1,978 | 58 | 2.93 |
| (11) Ichthyophonus hoferi | P | ic_hof | 1,985 | 53 | 2.67 |
| (12) Flavobacterium psychrophilum | B | fl_psy | 1,973 | 35 | 1.77 |
| (13) Ceratomyxa shasta | P | ce_sha | 1,998 | 32 | 1.60 |
| (14) Rickettsia-like organism | B | rlo | 1,993 | 27 | 1.35 |
| (15) Dermocystidium salmonis | P | de_sal | 2,004 | 27 | 1.35 |
| (16) Sphaerothecum destructuens | P | sp_des | 2,005 | 21 | 1.05 |
| (17) Tetracapsuloides bryosalmonae | P | te_bry | 2,006 | 19 | 0.95 |
| (18) Loma salmonae | P | lo_sal | 1,996 | 16 | 0.80 |
| (19) Kudoa thyrsites | P | ku_thy | 2,006 | 6∗ | 0.30 |
| (20) Tenacibaculum maritimum | B | te_mar | 2,006 | 5∗ | 0.25 |
| (21) Facilispora margolisi | P | fa_mar | 1,996 | 2∗ | 0.10 |
| (22) Moritella viscosa | B | mo_vis | 2,006 | 2∗ | 0.10 |
| (23) Crybtobia salmonistica | P | cr_sal | 2,006 | 2 | 0.10 |
| (24) Piscine OrthoReovirus | V | prv | 1,929 | 1∗ | 0.05 |
| (25) Piscirickettsia salmonis | B | pisck_sal | 2,005 | 1∗ | 0.05 |
| (26) Nanophyetus salmincola | P | na_sal | 2,006 | 1∗ | 0.05 |
| (27) Aeromonas hydrophila | B | ae_hyd | 2,006 | 0 | 0.00 |
| (28) Aeromonas salmonicida | B | ae_sal | 2,006 | 0 | 0.00 |
| (29) Gyrodactylus salaris | P | gy_sal | 2,006 | 0 | 0.00 |
| (30) Infectious hematopoietic necrosis virus | V | ihnv | 2,006 | 0 | 0.00 |
| (31) Infectious pancreatic necrosis virus | V | ipnv | 2,005 | 0 | 0.00 |
| (32) Infectious salmon anemia virus (S7) | V | isav7 | 1,999 | 0 | 0.00 |
| (33) Infectious salmon anemia virus (S8) | V | isav8 | 2,006 | 0 | 0.00 |
| (34) Myxobolus insidiosus | P | my_ins | 2,005 | 0 | 0.00 |
| (35) Neoparamoeba perurans | P | ne_per | 1,929 | 0 | 0.00 |
| (36) Nucleaospora salmonis | P | nu_sal | 2,000 | 0 | 0.00 |
| (37) Salmonid herpesvirus | V | omv | 2,006 | 0 | 0.00 |
| (38) Piscichlamydia salmonis | B | pch_sal | 2,006 | 0 | 0.00 |
| (39) Piscine myocarditis virus | V | pmcv | 2,004 | 0 | 0.00 |
| (40) Renibacterium salmoninarum | B | re_sal | 2,006 | 0 | 0.00 |
| (41) Salmon alpha virus 1/2/3 | V | sav | 2,003 | 0 | 0.00 |
| (42) Spironucleus salmonicida | P | sp_sal | 2,006 | 0 | 0.00 |
| (43) Viral encephalopathy and retinopathy virus | V | ver | 2,006 | 0 | 0.00 |
| (44) Viral hemorrhagic septicemia virus | V | vhsv | 2,005 | 0 | 0.00 |
| (45) Vibrio anguillarum | B | vi_ang | 2,006 | 0 | 0.00 |
| (46) Vibrio salmonicida | B | vi_sal | 2,006 | 0 | 0.00 |
| (47) Yersinia ruckeri | B | ye_ruc_gln | 2,005 | 0 | 0.00 |
aType of agent: B, bacterium; V, virus; P, parasite.
bOverall ‘prevalence’ was defined as the number of test-positive samples divided by the total number of samples tested for each given infectious agent with conclusive results (i.e., positive/n). The 26 detected agents are presented in decreasing order of their prevalence. Agents first detected around and after salmon farming regions are shown with ‘∗’ under the ‘Positive’ column.