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Mordecai G, Di Cicco E, Deeg C, Bateman A, Teffer A, Miller K. Comment on a perspective: Molecular detections of new agents in finfish-Interpreting biological significance for fish health management. JOURNAL OF AQUATIC ANIMAL HEALTH 2024. [PMID: 39042565 DOI: 10.1002/aah.10221] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/14/2022] [Revised: 08/31/2023] [Accepted: 02/20/2024] [Indexed: 07/25/2024]
Abstract
Impact statementThe rapid development of genomic technologies has begun a new paradigm in the study and management of emerging infectious diseases. To inform the conservation of fish, here we examine different perspectives on how to determine thresholds for management action in the context of molecular tools and fisheries policy.
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Affiliation(s)
- Gideon Mordecai
- Institute for the Oceans and Fisheries, University of British Columbia, Vancouver, British Columbia, Canada
| | | | - Christoph Deeg
- Pacific Salmon Foundation, Vancouver, British Columbia, Canada
- Fisheries and Oceans Canada, Pacific Biological Station, Nanaimo, British Columbia, Canada
| | - Andrew Bateman
- Pacific Salmon Foundation, Vancouver, British Columbia, Canada
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, Ontario, Canada
| | - Amy Teffer
- Department of Environmental Conservation, University of Massachusetts Amherst, Amherst, Massachusetts, USA
| | - Kristi Miller
- Fisheries and Oceans Canada, Pacific Biological Station, Nanaimo, British Columbia, Canada
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Bass AL, Bateman AW, Kaukinen KH, Li S, Ming T, Patterson DA, Hinch SG, Miller KM. The spatial distribution of infectious agents in wild Pacific salmon along the British Columbia coast. Sci Rep 2023; 13:5473. [PMID: 37016008 PMCID: PMC10071257 DOI: 10.1038/s41598-023-32583-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Accepted: 03/29/2023] [Indexed: 04/06/2023] Open
Abstract
Although infectious agents can act as strong population regulators, knowledge of their spatial distributions in wild Pacific salmon is limited, especially in the marine environment. Characterizing pathogen distributions during early marine residence, a period considered a survival bottleneck for Pacific salmon, may reveal where salmon populations are exposed to potentially detrimental pathogens. Using high-throughput qPCR, we determined the prevalence of 56 infectious agents in 5719 Chinook, 2032 Coho and 4062 Sockeye salmon, sampled between 2008 and 2018, in their first year of marine residence along coastal Western Canada. We identified high prevalence clusters, which often shifted geographically with season, for most of the 41 detected agents. A high density of infection clusters was found in the Salish Sea along the east coast of Vancouver Island, an important migration route and residence area for many salmon populations, some experiencing chronically poor marine survival. Maps for each infectious agent taxa showing clusters across all host species are provided. Our novel documentation of salmon pathogen distributions in the marine environment contributes to the ecological knowledge regarding some lesser known pathogens, identifies salmon populations potentially impacted by specific pathogens, and pinpoints priority locations for future research and remediation.
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Affiliation(s)
- Arthur L Bass
- Forest and Conservation Sciences, University of British Columbia, Vancouver, V6T 1Z4, Canada.
| | - Andrew W Bateman
- Pacific Salmon Foundation, Vancouver, V6J 4S6, Canada
- Ecology and Evolutionary Biology, University of Toronto, Toronto, M5S 1A1, Canada
| | - Karia H Kaukinen
- Fisheries and Oceans Canada, Pacific Biological Station, Nanaimo, V9T 6N7, Canada
| | - Shaorong Li
- Fisheries and Oceans Canada, Pacific Biological Station, Nanaimo, V9T 6N7, Canada
| | - Tobi Ming
- Fisheries and Oceans Canada, Pacific Biological Station, Nanaimo, V9T 6N7, Canada
| | - David A Patterson
- Fisheries and Oceans Canada, Science Branch, Pacific Region, School of Resource and Environmental Management, Simon Fraser University, Burnaby, V5A 1S6, Canada
| | - Scott G Hinch
- Forest and Conservation Sciences, University of British Columbia, Vancouver, V6T 1Z4, Canada
| | - Kristina M Miller
- Forest and Conservation Sciences, University of British Columbia, Vancouver, V6T 1Z4, Canada
- Fisheries and Oceans Canada, Pacific Biological Station, Nanaimo, V9T 6N7, Canada
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Hai D, Li J, Lan S, Wu T, Li Y, Cheng J, Fu Y, Lin Y, Jiang D, Wang M, Xie J. Discovery and Evolution of Six Positive-Sense RNA Viruses Co-infecting the Hypovirulent Strain SCH733 of Sclerotinia sclerotiorum. PHYTOPATHOLOGY 2022; 112:2449-2461. [PMID: 35793152 DOI: 10.1094/phyto-05-22-0148-r] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Sclerotinia sclerotiorum is a well-known phytopathogenic fungus with a wide host range. Identifying novel mycoviruses in phytopathogenic fungi is necessary to develop novel strategies for plant health protection and contribute to understanding the origin of viruses. Six new mycoviruses with positive single-stranded RNA genomes co-infecting the hypovirulent strain SCH733 of S. sclerotiorum were identified using a metatranscriptomic approach, and their complete genome sequences were molecularly determined. These mycoviruses belong to the following five families: Narnaviridae, Mitoviridae, Deltaflexviridae, Botourmiaviridae, and Ambiguiviridae. Three of these mycoviruses belong to existing International Committee on Taxonomy of Viruses (ICTV)-recognized species. Two of these newly identified mycoviruses have unique genomic features that are significantly different from those of all known mycoviruses. Phylogenetic analysis revealed that these six mycoviruses included close as well as distant relatives of known mycoviruses, thereby providing new insight into virus evolution and classification. Mycovirus horizontal transmission and elimination experiments revealed that Sclerotinia sclerotiorum narnavirus 5 is associated with hypovirulence of S. sclerotiorum, although we have not shown that it is independently responsible for the hypovirulence phenotype. This study broadens the diversity of known mycoviruses infecting S. sclerotiorum and provides a clue toward limiting hypovirulence in S. sclerotiorum.
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Affiliation(s)
- Du Hai
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China
- Hubei Key Laboratory of Plant Pathology, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
- Hubei Hongshan Laboratory, Wuhan, China
| | - Jincang Li
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China
- Hubei Key Laboratory of Plant Pathology, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
- Hubei Hongshan Laboratory, Wuhan, China
| | - Shangsong Lan
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China
- Hubei Key Laboratory of Plant Pathology, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
- Hubei Hongshan Laboratory, Wuhan, China
| | - Tun Wu
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China
- Hubei Key Laboratory of Plant Pathology, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
- Hubei Hongshan Laboratory, Wuhan, China
| | - Ying Li
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China
- Hubei Key Laboratory of Plant Pathology, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
- Hubei Hongshan Laboratory, Wuhan, China
| | - Jiasen Cheng
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China
- Hubei Key Laboratory of Plant Pathology, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Yanping Fu
- Hubei Key Laboratory of Plant Pathology, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Yang Lin
- Hubei Key Laboratory of Plant Pathology, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Daohong Jiang
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China
- Hubei Key Laboratory of Plant Pathology, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
- Hubei Hongshan Laboratory, Wuhan, China
| | - Minghong Wang
- Hubei Key Laboratory of Biological Resources Protection and Utilization, College of Forestry and Horticulture, Hubei Minzu University, Enshi, China
| | - Jiatao Xie
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China
- Hubei Key Laboratory of Plant Pathology, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
- Hubei Hongshan Laboratory, Wuhan, China
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Abstract
Flaviviruses are positive-sense single-stranded RNA viruses, including some well-known human pathogens such as Zika, dengue, and yellow fever viruses, which are primarily associated with mosquito and tick vectors. The vast majority of flavivirus research has focused on terrestrial environments; however, recent findings indicate that a range of flaviviruses are also present in aquatic environments, both marine and freshwater. These flaviviruses are found in various hosts, including fish, crustaceans, molluscs, and echinoderms. Although the effects of aquatic flaviviruses on the hosts they infect are not all known, some have been detected in farmed species and may have detrimental effects on the aquaculture industry. Exploration of the evolutionary history through the discovery of the Wenzhou shark flavivirus in both a shark and crab host is of particular interest since the potential dual-host nature of this virus may indicate that the invertebrate-vertebrate relationship seen in other flaviviruses may have a more profound evolutionary root than previously expected. Potential endogenous viral elements and the range of novel aquatic flaviviruses discovered thus shed light on virus origins and evolutionary history and may indicate that, like terrestrial life, the origins of flaviviruses may lie in aquatic environments.
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von Ammon U, Averink T, Kumanan K, Brosnahan CL, Pochon X, Hutson KS, Symonds JE. An Efficient Tetraplex Surveillance Tool for Salmonid Pathogens. Front Microbiol 2022; 13:885585. [PMID: 35531301 PMCID: PMC9069008 DOI: 10.3389/fmicb.2022.885585] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Accepted: 04/01/2022] [Indexed: 12/22/2022] Open
Abstract
Fish disease surveillance methods can be complicated and time consuming, which limits their value for timely intervention strategies on aquaculture farms. Novel molecular-based assays using droplet digital Polymerase Chain Reaction (ddPCR) can produce immediate results and enable high sample throughput with the ability to multiplex several targets using different fluorescent dyes. A ddPCR tetraplex assay was developed for priority salmon diseases for farmers in New Zealand including New Zealand Rickettsia-like organism 1 (NZ-RLO1), NZ-RLO2, Tenacibaculum maritimum, and Yersinia ruckeri. The limit of detection in singleplex and tetraplex assays was reached for most targets at 10−9 ng/μl with, respectively, NZ-RLO1 = 0.931 and 0.14 copies/μl, NZ-RLO2 = 0.162 and 0.21 copies/μl, T. maritimum = 0.345 and 0.93 copies/μl, while the limit of detection for Y. ruckeri was 10−8 with 1.0 copies/μl and 0.7 copies/μl. While specificity of primers was demonstrated in previous studies, we detected cross-reactivity of T. maritimum with some strains of Tenacibaculum dicentrarchi and Y. ruckeri with Serratia liquefaciens, respectively. The tetraplex assay was applied as part of a commercial fish disease surveillance program in New Zealand for 1 year to demonstrate the applicability of tetraplex tools for the salmonid aquaculture industry.
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Affiliation(s)
- Ulla von Ammon
- Aquaculture & Marine Biosecurity, Cawthron Institute, Nelson, New Zealand
- *Correspondence: Ulla von Ammon,
| | - Tessa Averink
- Aquaculture & Marine Biosecurity, Cawthron Institute, Nelson, New Zealand
| | - Karthiga Kumanan
- Aquaculture & Marine Biosecurity, Cawthron Institute, Nelson, New Zealand
- College of Science and Engineering, James Cook University, Townsville, QLD, Australia
| | - Cara L. Brosnahan
- Institute of Marine Science, University of Auckland, Warkworth, New Zealand
| | - Xavier Pochon
- Aquaculture & Marine Biosecurity, Cawthron Institute, Nelson, New Zealand
- Animal Health Laboratory, Ministry for Primary Industries, Upper Hutt, New Zealand
| | - Kate S. Hutson
- Aquaculture & Marine Biosecurity, Cawthron Institute, Nelson, New Zealand
- College of Science and Engineering, James Cook University, Townsville, QLD, Australia
| | - Jane E. Symonds
- Aquaculture & Marine Biosecurity, Cawthron Institute, Nelson, New Zealand
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Mauduit F, Segarra A, Mandic M, Todgham AE, Baerwald MR, Schreier AD, Fangue NA, Connon RE. Understanding risks and consequences of pathogen infections on the physiological performance of outmigrating Chinook salmon. CONSERVATION PHYSIOLOGY 2022; 10:coab102. [PMID: 35492407 PMCID: PMC9040276 DOI: 10.1093/conphys/coab102] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/26/2021] [Revised: 10/20/2021] [Accepted: 12/21/2021] [Indexed: 06/14/2023]
Abstract
The greatest concentration of at-risk anadromous salmonids is found in California (USA)-the populations that have been negatively impacted by the degradation of freshwater ecosystems. While climate-driven environmental changes threaten salmonids directly, they also change the life cycle dynamics and geographic distribution of pathogens, their resulting host-pathogen interactions and potential for disease progression. Recent studies have established the correlation between pathogen detection and salmonid smolt mortality during their migration to the ocean. The objective of the present study was to screen for up to 47 pathogens in juvenile Chinook salmon (Oncorhynchus tshawytscha) that were held in cages at two key sites of the Sacramento River (CA, USA) and measure potential consequences on fish health. To do so, we used a combination of transcriptomic analysis, enzymatic assays for energy metabolism and hypoxia and thermal tolerance measures. Results revealed that fish were infected by two myxozoan parasites: Ceratonova shasta and Parvicapsula minibicornis within a 2-week deployment. Compared to the control fish maintained in our rearing facility, infected fish displayed reduced body mass, depleted hepatic glycogen stores and differential regulation of genes involved in the immune and general stress responses. This suggests that infected fish would have lower chances of migration success. In contrast, hypoxia and upper thermal tolerances were not affected by infection, suggesting that infection did not impair their capacity to cope with acute abiotic stressors tested in this study. An evaluation of long-term consequences of the observed reduced body mass and hepatic glycogen depletion is needed to establish a causal relationship between salmon parasitic infection and their migration success. This study highlights that to assess the potential sublethal effects of a stressor, or to determine a suitable management action for fish, studies need to consider a combination of endpoints from the molecular to the organismal level.
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Affiliation(s)
- F Mauduit
- Corresponding author: Department of Anatomy, Physiology & Cell Biology, University of California Davis, 95616 Davis, CA, USA.
| | - A Segarra
- Department of Anatomy, Physiology & Cell Biology, University of California Davis, 95616 Davis, CA, USA
| | - M Mandic
- Department of Animal Science, University of California Davis, 95616 Davis, CA, USA
| | - A E Todgham
- Department of Animal Science, University of California Davis, 95616 Davis, CA, USA
| | - M R Baerwald
- California Department of Water Resources, Division of Environmental Services, 95814 Sacramento, CA, USA
| | - A D Schreier
- Department of Animal Science, University of California Davis, 95616 Davis, CA, USA
| | - N A Fangue
- Department of Wildlife, Fish, and Conservation Biology, University of California Davis, 95616 Davis, CA, USA
| | - R E Connon
- Department of Anatomy, Physiology & Cell Biology, University of California Davis, 95616 Davis, CA, USA
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Bass AL, Bateman AW, Connors BM, Staton BA, Rondeau EB, Mordecai GJ, Teffer AK, Kaukinen KH, Li S, Tabata AM, Patterson DA, Hinch SG, Miller KM. Identification of infectious agents in early marine Chinook and Coho salmon associated with cohort survival. Facets (Ott) 2022. [DOI: 10.1139/facets-2021-0102] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Recent decades have seen an increased appreciation for the role infectious diseases can play in mass mortality events across a diversity of marine taxa. At the same time many Pacific salmon populations have declined in abundance as a result of reduced marine survival. However, few studies have explicitly considered the potential role pathogens could play in these declines. Using a multi-year dataset spanning 59 pathogen taxa in Chinook and Coho salmon sampled along the British Columbia coast, we carried out an exploratory analysis to quantify evidence for associations between pathogen prevalence and cohort survival and between pathogen load and body condition. While a variety of pathogens had moderate to strong negative correlations with body condition or survival for one host species in one season, we found that Tenacibaculum maritimum and Piscine orthoreovirus had consistently negative associations with body condition in both host species and seasons and were negatively associated with survival for Chinook salmon collected in the fall and winter. Our analyses, which offer the most comprehensive examination of associations between pathogen prevalence and Pacific salmon survival to date, suggest that pathogens in Pacific salmon warrant further attention, especially those whose distribution and abundance may be influenced by anthropogenic stressors.
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Affiliation(s)
- Arthur L. Bass
- Pacific Salmon Ecology and Conservation Laboratory, Department of Forest and Conservation Sciences, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
| | - Andrew W. Bateman
- Pacific Salmon Foundation, Vancouver, BC V6J 4S6, Canada
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, ON M5S 3B2, Canada
| | - Brendan M. Connors
- Institute of Ocean Sciences, Fisheries and Oceans Canada, Sidney, BC V8L 5T5, Canada
| | - Benjamin A. Staton
- Fisheries Science Department, Columbia River Inter-Tribal Fish Commission, Portland, OR 97232, USA
| | - Eric B. Rondeau
- Pacific Biological Station, Fisheries and Oceans Canada, Nanaimo, BC, Canada
| | - Gideon J. Mordecai
- Institute for the Oceans and Fisheries, University of British Columbia, Vancouver, BC V9T 6N7, Canada
| | - Amy K. Teffer
- Pacific Salmon Ecology and Conservation Laboratory, Department of Forest and Conservation Sciences, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
| | - Karia H. Kaukinen
- Pacific Biological Station, Fisheries and Oceans Canada, Nanaimo, BC, Canada
| | - Shaorong Li
- Pacific Biological Station, Fisheries and Oceans Canada, Nanaimo, BC, Canada
| | - Amy M. Tabata
- Pacific Biological Station, Fisheries and Oceans Canada, Nanaimo, BC, Canada
| | - David A. Patterson
- Fisheries and Oceans Canada, School of Resource and Environmental Management, Simon Fraser University, Science Branch, Burnaby, BC V5A 1S6, Canada
| | - Scott G. Hinch
- Pacific Salmon Ecology and Conservation Laboratory, Department of Forest and Conservation Sciences, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
| | - Kristina M. Miller
- Pacific Salmon Ecology and Conservation Laboratory, Department of Forest and Conservation Sciences, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
- Pacific Biological Station, Fisheries and Oceans Canada, Nanaimo, BC, Canada
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Krasnov A, Johansen LH, Karlsen C, Sveen L, Ytteborg E, Timmerhaus G, Lazado CC, Afanasyev S. Transcriptome Responses of Atlantic Salmon ( Salmo salar L.) to Viral and Bacterial Pathogens, Inflammation, and Stress. Front Immunol 2021; 12:705601. [PMID: 34621264 PMCID: PMC8490804 DOI: 10.3389/fimmu.2021.705601] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2021] [Accepted: 09/03/2021] [Indexed: 11/15/2022] Open
Abstract
Transcriptomics provides valuable data for functional annotations of genes, the discovery of biomarkers, and quantitative assessment of responses to challenges. Meta-analysis of Nofima’s Atlantic salmon microarray database was performed for the selection of genes that have shown strong and reproducible expression changes. Using data from 127 experiments including 6440 microarrays, four transcription modules (TM) were identified with a total of 902 annotated genes: 161 virus responsive genes – VRG (activated with five viruses and poly I:C), genes that responded to three pathogenic bacteria (523 up and 33 down-regulated genes), inflammation not caused by infections – wounds, melanized foci in skeletal muscle and exposure to PAMP (180 up and 72 down-regulated genes), and stress by exercise, crowding and cortisol implants (33 genes). To assist the selection of gene markers, genes in each TM were ranked according to the scale of expression changes. In terms of functional annotations, association with diseases and stress was unknown or not reflected in public databases for a large part of genes, including several genes with the highest ranks. A set of multifunctional genes was discovered. Cholesterol 25-hydroxylase was present in all TM and 22 genes, including most differentially expressed matrix metalloproteinases 9 and 13 were assigned to three TMs. The meta-analysis has improved understanding of the defense strategies in Atlantic salmon. VRG have demonstrated equal or similar responses to RNA (SAV, IPNV, PRV, and ISAV), and DNA (gill pox) viruses, injection of bacterial DNA (plasmid) and exposure of cells to PAMP (CpG and gardiquimod) and relatively low sensitivity to inflammation and bacteria. Genes of the highest rank show preferential expression in erythrocytes. This group includes multigene families (gig and several trim families) and many paralogs. Of pathogen recognition receptors, only RNA helicases have shown strong expression changes. Most VRG (82%) are effectors with a preponderance of ubiquitin-related genes, GTPases, and genes of nucleotide metabolism. Many VRG have unknown roles. The identification of TMs makes possible quantification of responses and assessment of their interactions. Based on this, we are able to separate pathogen-specific responses from general inflammation and stress.
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Affiliation(s)
| | | | | | - Lene Sveen
- Fish Health Department, Nofima AS, Ås, Norway
| | | | | | | | - Sergey Afanasyev
- Laboratory of Neurophysiology and Behavioral Pathology, I. M. Sechenov Institute of Evolutionary Physiology and Biochemistry, Saint-Petersburg, Russia
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Distribution and Pathogenicity of Two Cutthroat Trout Virus (CTV) Genotypes in Canada. Viruses 2021; 13:v13091730. [PMID: 34578311 PMCID: PMC8472430 DOI: 10.3390/v13091730] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2021] [Revised: 08/25/2021] [Accepted: 08/26/2021] [Indexed: 12/14/2022] Open
Abstract
The sole member of the Piscihepevirus genus (family Hepeviridae) is cutthroat trout virus (CTV) but recent metatranscriptomic studies have identified numerous fish hepevirus sequences including CTV-2. In the current study, viruses with sequences resembling both CTV and CTV-2 were isolated from salmonids in eastern and western Canada. Phylogenetic analysis of eight full genomes delineated the Canadian CTV isolates into two genotypes (CTV-1 and CTV-2) within the Piscihepevirus genus. Hepevirus genomes typically have three open reading frames but an ORF3 counterpart was not predicted in the Canadian CTV isolates. In vitro replication of a CTV-2 isolate produced cytopathic effects in the CHSE-214 cell line with similar amplification efficiency as CTV. Likewise, the morphology of the CTV-2 isolate resembled CTV, yet viral replication caused dilation of the endoplasmic reticulum lumen which was not previously observed. Controlled laboratory studies exposing sockeye (Oncorhynchus nerka), pink (O. gorbuscha), and chinook salmon (O. tshawytscha) to CTV-2 resulted in persistent infections without disease and mortality. Infected Atlantic salmon (Salmo salar) and chinook salmon served as hosts and potential reservoirs of CTV-2. The data presented herein provides the first in vitro and in vivo characterization of CTV-2 and reveals greater diversity of piscihepeviruses extending the known host range and geographic distribution of CTV viruses.
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Polinski MP, Zhang Y, Morrison PR, Marty GD, Brauner CJ, Farrell AP, Garver KA. Innate antiviral defense demonstrates high energetic efficiency in a bony fish. BMC Biol 2021; 19:138. [PMID: 34253202 PMCID: PMC8276435 DOI: 10.1186/s12915-021-01069-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2021] [Accepted: 06/09/2021] [Indexed: 11/18/2022] Open
Abstract
Background Viruses can impose energetic demands on organisms they infect, in part by hosts mounting resistance. Recognizing that oxygen uptake reliably indicates steady-state energy consumption in all vertebrates, we comprehensively evaluated oxygen uptake and select transcriptomic messaging in sockeye salmon challenged with either a virulent rhabdovirus (IHNV) or a low-virulent reovirus (PRV). We tested three hypotheses relating to the energetic costs of viral resistance and tolerance in this vertebrate system: (1) mounting resistance incurs a metabolic cost or limitation, (2) induction of the innate antiviral interferon system compromises homeostasis, and (3) antiviral defenses are weakened by acute stress. Results IHNV infections either produced mortality within 1–4 weeks or the survivors cleared infections within 1–9 weeks. Transcription of three interferon-stimulated genes (ISGs) was strongly correlated with IHNV load but not respiratory performance. Instead, early IHNV resistance was associated with a mean 19% (95% CI = 7–31%; p = 0.003) reduction in standard metabolic rate. The stress of exhaustive exercise did not increase IHNV transcript loads, but elevated host inflammatory transcriptional signaling up to sevenfold. For PRV, sockeye tolerated high-load systemic PRV blood infections. ISG transcription was transiently induced at peak PRV loads without associated morbidity, microscopic lesions, or major changes in aerobic or anaerobic respiratory performance, but some individuals with high-load blood infections experienced a transient, minor reduction in hemoglobin concentration and increased duration of excess post-exercise oxygen consumption. Conclusions Contrary to our first hypothesis, effective resistance against life-threatening rhabdovirus infections or tolerance to high-load reovirus infections incurred minimal metabolic costs to salmon. Even robust systemic activation of the interferon system did not levy an allostatic load sufficient to compromise host homeostasis or respiratory performance, rejecting our second hypothesis that this ancient innate vertebrate antiviral defense is itself energetically expensive. Lastly, an acute stress experienced during testing did not weaken host antiviral defenses sufficiently to promote viral replication; however, a possibility for disease intensification contingent upon underlying inflammation was indicated. These data cumulatively demonstrate that fundamental innate vertebrate defense strategies against potentially life-threatening viral exposure impose limited putative costs on concurrent aerobic or energetic demands of the organism. Supplementary Information The online version contains supplementary material available at 10.1186/s12915-021-01069-2.
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Affiliation(s)
- Mark P Polinski
- Fisheries and Oceans Canada Pacific Biological Station, 3190 Hammond Bay Road, Nanaimo, V9T6N7, Canada.
| | - Yangfan Zhang
- Faculty of Land and Food Systems, University of British Columbia, MCML 344-2357 Main Mall, Vancouver, V6T1Z4, Canada
| | - Phillip R Morrison
- Department of Zoology, University of British Columbia, 6270 University Blvd, Vancouver, V6T1Z4, Canada
| | - Gary D Marty
- Animal Health Centre, Ministry of Agriculture, Food and Fisheries, 1767 Angus Campbell Rd, Abbotsford, V3G2M3, Canada
| | - Colin J Brauner
- Department of Zoology, University of British Columbia, 6270 University Blvd, Vancouver, V6T1Z4, Canada
| | - Anthony P Farrell
- Faculty of Land and Food Systems, University of British Columbia, MCML 344-2357 Main Mall, Vancouver, V6T1Z4, Canada.,Department of Zoology, University of British Columbia, 6270 University Blvd, Vancouver, V6T1Z4, Canada
| | - Kyle A Garver
- Fisheries and Oceans Canada Pacific Biological Station, 3190 Hammond Bay Road, Nanaimo, V9T6N7, Canada.
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11
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Comparative Molecular Characterization of Novel and Known Piscine Toti-Like Viruses. Viruses 2021; 13:v13061063. [PMID: 34205093 PMCID: PMC8229945 DOI: 10.3390/v13061063] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2021] [Revised: 05/28/2021] [Accepted: 05/29/2021] [Indexed: 12/17/2022] Open
Abstract
Totiviridae is a virus family well known to infect uni-cellular organisms like fungi and protozoa. In more recent years, viruses characterized as toti-like viruses, have been found in primarily arthropods, but also a couple in planarians and piscine species. These toti-like viruses share phylogenetic similarities to totiviruses; however, their genomes also includes additional coding sequences in either 5′ or 3′ ends expected to relate to more advanced infection mechanisms in more advanced hosts. Here, we applied next generation sequencing (NGS) technologies and discovered three new toti-like viruses, one in wild common carp and one in bluegill from the USA and one in farmed lumpsucker from Norway. These are named common carp toti-like virus 1 (CCTLV-1), bluegill toti-like virus 1 (BGTLV-1), and Cyclopterus lumpus toti-like virus (CLuTLV), respectively. The genomes of these viruses have been characterized and compared to the three previously known piscine toti-like viruses, piscine myocarditis virus (PMCV) found in Atlantic salmon and the two from golden shiner, now named golden shiner toti-like virus 1 and 2 (GSTLV-1 and -2), and also to totiviruses and other toti-like viruses. We found that four piscine toti-like viruses had additional gene(s) in the 3′ end of the genome, and also clustered phylogenetically based on both capsid and RdRp-genes. This cluster constituted a distant branch in the Totiviridae, and we suggest this should be defined as a separate genus named Pistolvirus, to reflect this major cluster of piscine toti-like viruses. The remaining two piscine toti-like viruses differentiated from these by lacking any additional 3′ end genes and also by phylogenetical relation, but were both clustering with arthropod viruses in two different clusters.
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Furey NB, Bass AL, Miller KM, Li S, Lotto AG, Healy SJ, Drenner SM, Hinch SG. Infected juvenile salmon can experience increased predation during freshwater migration. ROYAL SOCIETY OPEN SCIENCE 2021; 8:201522. [PMID: 33959321 PMCID: PMC8074935 DOI: 10.1098/rsos.201522] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/02/2020] [Accepted: 03/03/2021] [Indexed: 05/07/2023]
Abstract
Predation risk for animal migrants can be impacted by physical condition. Although size- or condition-based selection is often observed, observing infection-based predation is rare due to the difficulties in assessing infectious agents in predated samples. We examined predation of outmigrating sockeye salmon (Oncorhynchus nerka) smolts by bull trout (Salvelinus confluentus) in south-central British Columbia, Canada. We used a high-throughput quantitative polymerase chain reaction (qPCR) platform to screen for the presence of 17 infectious agents found in salmon and assess 14 host genes associated with viral responses. In one (2014) of the two years assessed (2014 and 2015), the presence of infectious haematopoietic necrosis virus (IHNv) resulted in 15-26 times greater chance of predation; in 2015 IHNv was absent among all samples, predated or not. Thus, we provide further evidence that infection can impact predation risk in migrants. Some smolts with high IHNv loads also exhibited gene expression profiles consistent with a virus-induced disease state. Nine other infectious agents were observed between the two years, none of which were associated with increased selection by bull trout. In 2014, richness of infectious agents was also associated with greater predation risk. This is a rare demonstration of predator consumption resulting in selection for prey that carry infectious agents. The mechanism by which this selection occurs is not yet determined. By culling infectious agents from migrant populations, fish predators could provide an ecological benefit to prey.
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Affiliation(s)
- Nathan B. Furey
- Department of Biological Sciences, University of New Hampshire, Durham, NH, USA
| | - Arthur L. Bass
- Pacific Salmon Ecology and Conservation Laboratory, Department of Forest and Conservation Sciences, University of British Columbia, Vancouver, Canada
| | - Kristi M. Miller
- Fisheries and Oceans Canada, Molecular Genetics Section, Pacific Biological Station, Nanaimo, Canada
| | - Shaorong Li
- Fisheries and Oceans Canada, Molecular Genetics Section, Pacific Biological Station, Nanaimo, Canada
| | - Andrew G. Lotto
- Pacific Salmon Ecology and Conservation Laboratory, Department of Forest and Conservation Sciences, University of British Columbia, Vancouver, Canada
| | - Stephen J. Healy
- Fisheries and Oceans Canada, Science Branch, Pacific Region, 4160 Marine Dr., West Vancouver, British Columbia, Canada
| | - S. Matthew Drenner
- Stillwater Sciences, 555 W. Fifth St, 35th floor, Los Angeles, CA, USA
- Marine Science Institute, University of California Santa Barbara, Santa Barbara, CA, USA
| | - Scott G. Hinch
- Pacific Salmon Ecology and Conservation Laboratory, Department of Forest and Conservation Sciences, University of British Columbia, Vancouver, Canada
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