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Ye RZ, Li YY, Xu DL, Wang BH, Wang XY, Zhang MZ, Wang N, Gao WY, Li C, Han XY, Du LF, Xia LY, Song K, Xu Q, Liu J, Cheng N, Li ZH, Du YD, Yu HJ, Shi XY, Jiang JF, Sun Y, Cui XM, Ding SJ, Zhao L, Cao WC. Virome diversity shaped by genetic evolution and ecological landscape of Haemaphysalis longicornis. MICROBIOME 2024; 12:35. [PMID: 38378577 PMCID: PMC10880243 DOI: 10.1186/s40168-024-01753-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/22/2023] [Accepted: 01/04/2024] [Indexed: 02/22/2024]
Abstract
BACKGROUND Haemaphysalis longicornis is drawing attentions for its geographic invasion, extending population, and emerging disease threat. However, there are still substantial gaps in our knowledge of viral composition in relation to genetic diversity of H. longicornis and ecological factors, which are important for us to understand interactions between virus and vector, as well as between vector and ecological elements. RESULTS We conducted the meta-transcriptomic sequencing of 136 pools of H. longicornis and identified 508 RNA viruses of 48 viral species, 22 of which have never been reported. Phylogenetic analysis of mitochondrion sequences divided the ticks into two genetic clades, each of which was geographically clustered and significantly associated with ecological factors, including altitude, precipitation, and normalized difference vegetation index. The two clades showed significant difference in virome diversity and shared about one fifth number of viral species that might have evolved to "generalists." Notably, Bandavirus dabieense, the pathogen of severe fever with thrombocytopenia syndrome was only detected in ticks of clade 1, and half number of clade 2-specific viruses were aquatic-animal-associated. CONCLUSIONS These findings highlight that the virome diversity is shaped by internal genetic evolution and external ecological landscape of H. longicornis and provide the new foundation for promoting the studies on virus-vector-ecology interaction and eventually for evaluating the risk of H. longicornis for transmitting the viruses to humans and animals. Video Abstract.
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Affiliation(s)
- Run-Ze Ye
- Institute of EcoHealth, School of Public Health, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, People's Republic of China
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, People's Republic of China
| | - Yu-Yu Li
- Institute of EcoHealth, School of Public Health, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, People's Republic of China
- Department of Epidemiology, School of Public Health, Cheeloo College of Medicine, Shandong University, Jinan, People's Republic of China
| | - Da-Li Xu
- Institute of EcoHealth, School of Public Health, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, People's Republic of China
- Shandong Provincial Key Laboratory of Communicable Disease Control and Prevention, Department of Communicable Disease Control and Prevention, Shandong Center for Disease Control and Prevention, Jinan, Shandong, People's Republic of China
| | - Bai-Hui Wang
- Institute of EcoHealth, School of Public Health, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, People's Republic of China
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, People's Republic of China
| | - Xiao-Yang Wang
- Institute of EcoHealth, School of Public Health, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, People's Republic of China
| | - Ming-Zhu Zhang
- Institute of EcoHealth, School of Public Health, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, People's Republic of China
| | - Ning Wang
- Institute of EcoHealth, School of Public Health, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, People's Republic of China
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, People's Republic of China
| | - Wan-Ying Gao
- Institute of EcoHealth, School of Public Health, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, People's Republic of China
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, People's Republic of China
| | - Cheng Li
- Institute of EcoHealth, School of Public Health, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, People's Republic of China
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, People's Republic of China
| | - Xiao-Yu Han
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, People's Republic of China
| | - Li-Feng Du
- Institute of EcoHealth, School of Public Health, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, People's Republic of China
| | - Luo-Yuan Xia
- Institute of EcoHealth, School of Public Health, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, People's Republic of China
| | - Ke Song
- Institute of EcoHealth, School of Public Health, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, People's Republic of China
- Department of Epidemiology, School of Public Health, Cheeloo College of Medicine, Shandong University, Jinan, People's Republic of China
| | - Qing Xu
- Institute of EcoHealth, School of Public Health, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, People's Republic of China
- Department of Epidemiology, School of Public Health, Cheeloo College of Medicine, Shandong University, Jinan, People's Republic of China
| | - Jing Liu
- Institute of EcoHealth, School of Public Health, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, People's Republic of China
- Department of Epidemiology, School of Public Health, Cheeloo College of Medicine, Shandong University, Jinan, People's Republic of China
| | - Nuo Cheng
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, People's Republic of China
| | - Ze-Hui Li
- Institute of EcoHealth, School of Public Health, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, People's Republic of China
| | - Yi-Di Du
- Institute of EcoHealth, School of Public Health, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, People's Republic of China
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, People's Republic of China
| | - Hui-Jun Yu
- Institute of EcoHealth, School of Public Health, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, People's Republic of China
| | - Xiao-Yu Shi
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, People's Republic of China
| | - Jia-Fu Jiang
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, People's Republic of China
| | - Yi Sun
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, People's Republic of China
| | - Xiao-Ming Cui
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, People's Republic of China.
- Research Unit of Discovery and Tracing of Natural Focus Diseases, Chinese Academy of Medical Sciences, Beijing, People's Republic of China.
| | - Shu-Jun Ding
- Shandong Provincial Key Laboratory of Communicable Disease Control and Prevention, Department of Communicable Disease Control and Prevention, Shandong Center for Disease Control and Prevention, Jinan, Shandong, People's Republic of China.
| | - Lin Zhao
- Institute of EcoHealth, School of Public Health, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, People's Republic of China.
- Department of Epidemiology, School of Public Health, Cheeloo College of Medicine, Shandong University, Jinan, People's Republic of China.
| | - Wu-Chun Cao
- Institute of EcoHealth, School of Public Health, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, People's Republic of China.
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, People's Republic of China.
- Research Unit of Discovery and Tracing of Natural Focus Diseases, Chinese Academy of Medical Sciences, Beijing, People's Republic of China.
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Chang T, Hunt BPV, Hirai J, Suttle CA. Divergent RNA viruses infecting sea lice, major ectoparasites of fish. PLoS Pathog 2023; 19:e1011386. [PMID: 37347729 DOI: 10.1371/journal.ppat.1011386] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2022] [Accepted: 04/25/2023] [Indexed: 06/24/2023] Open
Abstract
Sea lice, the major ectoparasites of fish, have significant economic impacts on wild and farmed finfish, and have been implicated in the decline of wild salmon populations. As blood-feeding arthropods, sea lice may also be reservoirs for viruses infecting fish. However, except for two groups of negative-strand RNA viruses within the order Mononegavirales, nothing is known about viruses of sea lice. Here, we used transcriptomic data from three key species of sea lice (Lepeophtheirus salmonis, Caligus clemensi, and Caligus rogercresseyi) to identify 32 previously unknown RNA viruses. The viruses encompassed all the existing phyla of RNA viruses, with many placed in deeply branching lineages that likely represent new families and genera. Importantly, the presence of canonical virus-derived small interfering RNAs (viRNAs) indicates that most of these viruses infect sea lice, even though in some cases their closest classified relatives are only known to infect plants or fungi. We also identified both viRNAs and PIWI-interacting RNAs (piRNAs) from sequences of a bunya-like and two qin-like viruses in C. rogercresseyi. Our analyses showed that most of the viruses found in C. rogercresseyi occurred in multiple life stages, spanning from planktonic to parasitic stages. Phylogenetic analysis revealed that many of the viruses infecting sea lice were closely related to those that infect a wide array of eukaryotes with which arthropods associate, including fungi and parasitic tapeworms, implying that over evolutionary time there has been cross-phylum and cross-kingdom switching of viruses between arthropods and other eukaryotes. Overall, this study greatly expands our view of virus diversity in crustaceans, identifies viruses that infect and replicate in sea lice, and provides evidence that over evolutionary time, viruses have switched between arthropods and eukaryotic hosts in other phyla and kingdoms.
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Affiliation(s)
- Tianyi Chang
- Department of Earth, Ocean and Atmospheric Sciences, University of British Columbia, Vancouver, Canada
| | - Brian P V Hunt
- Department of Earth, Ocean and Atmospheric Sciences, University of British Columbia, Vancouver, Canada
- Institute for the Oceans and Fisheries, University of British Columbia, Vancouver, Canada
- Hakai Institute, Campbell River, Canada
| | - Junya Hirai
- Atmosphere and Ocean Research Institute, The University of Tokyo, Kashiwa, Japan
| | - Curtis A Suttle
- Department of Earth, Ocean and Atmospheric Sciences, University of British Columbia, Vancouver, Canada
- Institute for the Oceans and Fisheries, University of British Columbia, Vancouver, Canada
- Hakai Institute, Campbell River, Canada
- Department of Microbiology and Immunology, University of British Columbia, Vancouver, Canada
- Department of Botany, University of British Columbia, Vancouver, Canada
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Øvergård AC, Eichner C, Nuñez-Ortiz N, Kongshaug H, Borchel A, Dalvin S. Transcriptomic and targeted immune transcript analyses confirm localized skin immune responses in Atlantic salmon towards the salmon louse. FISH & SHELLFISH IMMUNOLOGY 2023:108835. [PMID: 37236552 DOI: 10.1016/j.fsi.2023.108835] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/20/2023] [Revised: 05/12/2023] [Accepted: 05/16/2023] [Indexed: 05/28/2023]
Abstract
Atlantic salmon (Salmo salar) are highly susceptible to infestations with the ectoparasite Lepeophtheirus salmonis, the salmon louse. Infestations elicit an immune response in the fish, but the response does not lead to parasite clearance, nor does it protect against subsequent infestations. It is, however, not known why the immune response is not adequate, possibly because the local response directly underneath the louse has been poorly evaluated. The present study describes the transcriptomic response by RNA sequencing of skin at the site of copepodid attachment. Analysing differentially expressed genes, 2864 were higher and 1357 were lower expressed at the louse attachment site compared to uninfested sites in the louse infested fish, while gene expression at uninfested sites were similar to uninfested control fish. The transcriptional patterns of selected immune genes were further detailed in three skin compartments/types: Whole skin, scales only and fin tissue. The elevation of pro-inflammatory cytokines and immune cell marker transcripts observed in whole skin and scale samples were not induced in fin, and a higher cytokine transcript level in scale samples suggest it can be used as a nonlethal sampling method to enhance selective breeding trials. Furthermore, the immune response was followed in both skin and anterior kidney as the infestation developed. Here, newly moulted preadult 1 stage lice induced a higher immune response than chalimi and adult lice. Overall, infestation with salmon louse induce a modest but early immune response with an elevation of mainly innate immune transcripts, with the response primarily localized to the site of attachment.
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Affiliation(s)
- Aina-Cathrine Øvergård
- SLCR-Sea Lice Research Centre, Department of Biological Sciences, University of Bergen, Pb. 7803, Bergen, NO-5020, Norway.
| | - Christiane Eichner
- SLCR-Sea Lice Research Centre, Department of Biological Sciences, University of Bergen, Pb. 7803, Bergen, NO-5020, Norway
| | - Noelia Nuñez-Ortiz
- SLCR-Sea Lice Research Centre, Disease and Pathogen Transmission, Institute of Marine Research, Pb. 1870 Nordnes, Bergen, NO-5817, Norway
| | - Heidi Kongshaug
- SLCR-Sea Lice Research Centre, Department of Biological Sciences, University of Bergen, Pb. 7803, Bergen, NO-5020, Norway
| | - Andreas Borchel
- SLCR-Sea Lice Research Centre, Department of Biological Sciences, University of Bergen, Pb. 7803, Bergen, NO-5020, Norway
| | - Sussie Dalvin
- SLCR-Sea Lice Research Centre, Disease and Pathogen Transmission, Institute of Marine Research, Pb. 1870 Nordnes, Bergen, NO-5817, Norway
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4
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Bass D, Rueckert S, Stern R, Cleary AC, Taylor JD, Ward GM, Huys R. Parasites, pathogens, and other symbionts of copepods. Trends Parasitol 2021; 37:875-889. [PMID: 34158247 DOI: 10.1016/j.pt.2021.05.006] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2021] [Revised: 05/03/2021] [Accepted: 05/17/2021] [Indexed: 12/20/2022]
Abstract
There is a large diversity of eukaryotic symbionts of copepods, dominated by epizootic protists such as ciliates, and metazoan parasites. Eukaryotic endoparasites, copepod-associated bacteria, and viruses are less well known, partly due to technical limitations. However, new molecular techniques, combined with a range of other approaches, provide a complementary toolkit for understanding the complete symbiome of copepods and how the symbiome relates to their ecological roles, relationships with other biota, and responses to environmental change. In this review we provide the most complete overview of the copepod symbiome to date, including microeukaryotes, metazoan parasites, bacteria, and viruses, and provide extensive literature databases to inform future studies.
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Affiliation(s)
- David Bass
- International Centre of Excellence in Aquatic Animal Health, Centre for Environment, Fisheries and Aquaculture Science (Cefas), Barrack Road, The Nothe, Weymouth, Dorset DT4 8UB, UK; Department of Life Sciences, The Natural History Museum, Cromwell Road, London SW7 5BD, UK; Sustainable Aquaculture Futures, Biosciences, College of Life and Environmental Sciences, University of Exeter, Stocker Road, Exeter EX4 4QD, UK.
| | - Sonja Rueckert
- School of Applied Sciences, Edinburgh Napier University, Sighthill Court, Edinburgh EH11 4BN, UK
| | - Rowena Stern
- Marine Biological Association, Citadel Hill, Plymouth, PL1 2PB, UK
| | - Alison C Cleary
- Department of Natural Sciences, University of Agder, Universitetsveien 25, Kristiansand, 4630, Norway
| | - Joe D Taylor
- School of Chemistry and Bioscience, University of Bradford, Richmond Rd, Bradford BD7 1DP, UK
| | - Georgia M Ward
- International Centre of Excellence in Aquatic Animal Health, Centre for Environment, Fisheries and Aquaculture Science (Cefas), Barrack Road, The Nothe, Weymouth, Dorset DT4 8UB, UK; Department of Life Sciences, The Natural History Museum, Cromwell Road, London SW7 5BD, UK
| | - Rony Huys
- Department of Life Sciences, The Natural History Museum, Cromwell Road, London SW7 5BD, UK
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Dalvin S, Are Hamre L, Skern-Mauritzen R, Vågseth T, Stien L, Oppedal F, Bui S. The effect of temperature on ability of Lepeophtheirus salmonis to infect and persist on Atlantic salmon. JOURNAL OF FISH DISEASES 2020; 43:1519-1529. [PMID: 32882750 DOI: 10.1111/jfd.13253] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/09/2020] [Revised: 08/05/2020] [Accepted: 08/06/2020] [Indexed: 06/11/2023]
Abstract
The salmon louse (Lepeophtheirus salmonis) is an ecologically and economically important parasite of salmonid fish. Temperature is a strong influencer of biological processes in salmon lice, with development rate increased at higher temperatures. The successful attachment of lice onto a host is also predicted to be influenced by temperature; however, the correlation of temperature with parasite survival is unknown. This study describes the effects of temperature on infection success, and survival on the host during development to the adult stage. To accurately describe infection dynamics with varying temperatures, infection success was recorded on Atlantic salmon (Salmo salar) between 2 and 10°C. Infection success ranged from 20% to 50% and was strongly correlated with temperature, with the highest success at 10°C. Parasite loss was monitored during development at eight temperatures with high loss of lice at 3 and 24°C, whilst no loss was recorded in the temperature range from 6 to 21°C. Sea temperatures thus have large effects on the outcome of salmon louse infections and should be taken into account in the management and risk assessment of this parasite. Improving understanding of the infection dynamics of salmon lice will facilitate epidemiological modelling efforts and efficiency of pest management strategies.
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Affiliation(s)
- Sussie Dalvin
- SLRC - Sea Lice Research Centre, Institute of Marine Research, Bergen, Norway
- Department of Biological Sciences, SLRC - Sea Lice Research Centre, University of Bergen, Bergen, Norway
| | - Lars Are Hamre
- Department of Biological Sciences, SLRC - Sea Lice Research Centre, University of Bergen, Bergen, Norway
| | | | | | - Lars Stien
- Institute of Marine Research, Matredal, Norway
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Käfer S, Paraskevopoulou S, Zirkel F, Wieseke N, Donath A, Petersen M, Jones TC, Liu S, Zhou X, Middendorf M, Junglen S, Misof B, Drosten C. Re-assessing the diversity of negative strand RNA viruses in insects. PLoS Pathog 2019; 15:e1008224. [PMID: 31830128 PMCID: PMC6932829 DOI: 10.1371/journal.ppat.1008224] [Citation(s) in RCA: 75] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2019] [Revised: 12/26/2019] [Accepted: 11/19/2019] [Indexed: 12/21/2022] Open
Abstract
The spectrum of viruses in insects is important for subjects as diverse as public health, veterinary medicine, food production, and biodiversity conservation. The traditional interest in vector-borne diseases of humans and livestock has drawn the attention of virus studies to hematophagous insect species. However, these represent only a tiny fraction of the broad diversity of Hexapoda, the most speciose group of animals. Here, we systematically probed the diversity of negative strand RNA viruses in the largest and most representative collection of insect transcriptomes from samples representing all 34 extant orders of Hexapoda and 3 orders of Entognatha, as well as outgroups, altogether representing 1243 species. Based on profile hidden Markov models we detected 488 viral RNA-directed RNA polymerase (RdRp) sequences with similarity to negative strand RNA viruses. These were identified in members of 324 arthropod species. Selection for length, quality, and uniqueness left 234 sequences for analyses, showing similarity to genomes of viruses classified in Bunyavirales (n = 86), Articulavirales (n = 54), and several orders within Haploviricotina (n = 94). Coding-complete genomes or nearly-complete subgenomic assemblies were obtained in 61 cases. Based on phylogenetic topology and the availability of coding-complete genomes we estimate that at least 20 novel viral genera in seven families need to be defined, only two of them monospecific. Seven additional viral clades emerge when adding sequences from the present study to formerly monospecific lineages, potentially requiring up to seven additional genera. One long sequence may indicate a novel family. For segmented viruses, cophylogenies between genome segments were generally improved by the inclusion of viruses from the present study, suggesting that in silico misassembly of segmented genomes is rare or absent. Contrary to previous assessments, significant virus-host codivergence was identified in major phylogenetic lineages based on two different approaches of codivergence analysis in a hypotheses testing framework. In spite of these additions to the known spectrum of viruses in insects, we caution that basing taxonomic decisions on genome information alone is challenging due to technical uncertainties, such as the inability to prove integrity of complete genome assemblies of segmented viruses.
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Affiliation(s)
- Simon Käfer
- Institute of Virology, Charité-Universitätsmedizin Berlin, Corporate Member of Free University, Humboldt-University and Berlin Institute of Health, Berlin, Germany
- Center for Molecular Biodiversity Research, Zoological Research Museum Alexander Koenig, Bonn, Germany
| | - Sofia Paraskevopoulou
- Institute of Virology, Charité-Universitätsmedizin Berlin, Corporate Member of Free University, Humboldt-University and Berlin Institute of Health, Berlin, Germany
| | - Florian Zirkel
- Institute of Virology, University of Bonn Medical Centre, Bonn, Germany
| | - Nicolas Wieseke
- Swarm Intelligence and Complex Systems Group, Department of Computer Science, Leipzig University, Leipzig, Germany
| | - Alexander Donath
- Center for Molecular Biodiversity Research, Zoological Research Museum Alexander Koenig, Bonn, Germany
| | - Malte Petersen
- Senckenberg Biodiversity and Climate Research Centre, Senckenberg Gesellschaft für Naturforschung, Frankfurt am Main, Germany
| | - Terry C. Jones
- Institute of Virology, Charité-Universitätsmedizin Berlin, Corporate Member of Free University, Humboldt-University and Berlin Institute of Health, Berlin, Germany
- Center for Pathogen Evolution, Department of Zoology, University of Cambridge, Cambridge, United Kingdom
| | - Shanlin Liu
- BGI-Shenzhen, China Beishan Industrial Zone, Shenzhen, Guangdong Province, China
| | - Xin Zhou
- College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, China
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, China Agricultural University, Beijing, China
| | - Martin Middendorf
- Swarm Intelligence and Complex Systems Group, Department of Computer Science, Leipzig University, Leipzig, Germany
| | - Sandra Junglen
- Institute of Virology, Charité-Universitätsmedizin Berlin, Corporate Member of Free University, Humboldt-University and Berlin Institute of Health, Berlin, Germany
- German Center for Infection Research (DZIF), associated partner site Charité, Berlin, Germany
| | - Bernhard Misof
- Center for Molecular Biodiversity Research, Zoological Research Museum Alexander Koenig, Bonn, Germany
| | - Christian Drosten
- Institute of Virology, Charité-Universitätsmedizin Berlin, Corporate Member of Free University, Humboldt-University and Berlin Institute of Health, Berlin, Germany
- German Center for Infection Research (DZIF), associated partner site Charité, Berlin, Germany
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Smit NJ, Bruce NL, Hadfield KA. Life Cycle and Life History Strategies of Parasitic Crustacea. PARASITIC CRUSTACEA 2019; 3. [PMCID: PMC7124122 DOI: 10.1007/978-3-030-17385-2_5] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/13/2023]
Abstract
Different parasitic life strategies are described including four new life cycles: complex rebrooding, micro-male, mesoparasite and prey-predator transfer. Four new life cycle behaviours are named: nursery hiding, mid-moult stage, positive precursor (intraspecific antagonism) and negative precursor (ambush strategy). Further strategies discussed are opossum attack, double parasitism (doubling of the normal reproductive set), duplex arrangement (separated male-female pairs), simple rebrooding, and describing how displaced parasites and superinfections may partly elucidate life cycles. Proportional stunting masks life history effects of parasitism; cuckoo copepods are true parasites and not just associates; burrowing barnacles (acrothoracicans) are not parasites. Further findings based on life cycle information: branchiurans and pentastomes are possibly not related; firefly seed shrimp are not parasites; copepod pre-adult life cycle stages are common in the western pacific but rare in Caribbean; harpacticoids on vertebrates are not parasites; cuckoo copepods are true parasites; explained the importance of pennellid intermediate hosts. Crustacean parasite life cycles are largely unknown (1% of species). Most crustacean life cycles represent minor modifications from the ancestral free-living mode. Crustacean parasites have less complex and less modified life cycles than other major parasite groups. This limits their exploitation of, and effectiveness, in parasitism. However, these life cycles will be an advantage in Global Change. Most metazoan parasites will be eliminated while crustaceans (and nematodes) will inherit the new world of parasites.
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Affiliation(s)
- Nico J. Smit
- North-West University, and Unit for Environmental Sciences and Management , Potchefstroom, Northwest South Africa
| | - Niel L. Bruce
- Biodiversity & Geosciences Program, Queensland Museum, South Brisbane BC, Queensland 4101, Australia, and Water Research Group, Unit for Environmental Sciences and Management, North-West University, Potchefstroom, South Africa
| | - Kerry A. Hadfield
- Water Research Group, Unit for Environmental Sciences and Management, North-West University, Potchefstroom, South Africa
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8
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Amarasinghe GK, Ayllón MA, Bào Y, Basler CF, Bavari S, Blasdell KR, Briese T, Brown PA, Bukreyev A, Balkema-Buschmann A, Buchholz UJ, Chabi-Jesus C, Chandran K, Chiapponi C, Crozier I, de Swart RL, Dietzgen RG, Dolnik O, Drexler JF, Dürrwald R, Dundon WG, Duprex WP, Dye JM, Easton AJ, Fooks AR, Formenty PBH, Fouchier RAM, Freitas-Astúa J, Griffiths A, Hewson R, Horie M, Hyndman TH, Jiāng D, Kitajima EW, Kobinger GP, Kondō H, Kurath G, Kuzmin IV, Lamb RA, Lavazza A, Lee B, Lelli D, Leroy EM, Lǐ J, Maes P, Marzano SYL, Moreno A, Mühlberger E, Netesov SV, Nowotny N, Nylund A, Økland AL, Palacios G, Pályi B, Pawęska JT, Payne SL, Prosperi A, Ramos-González PL, Rima BK, Rota P, Rubbenstroth D, Shī M, Simmonds P, Smither SJ, Sozzi E, Spann K, Stenglein MD, Stone DM, Takada A, Tesh RB, Tomonaga K, Tordo N, Towner JS, van den Hoogen B, Vasilakis N, Wahl V, Walker PJ, Wang LF, Whitfield AE, Williams JV, Zerbini FM, Zhāng T, Zhang YZ, Kuhn JH. Taxonomy of the order Mononegavirales: update 2019. Arch Virol 2019; 164:1967-1980. [PMID: 31089958 PMCID: PMC6641539 DOI: 10.1007/s00705-019-04247-4] [Citation(s) in RCA: 197] [Impact Index Per Article: 39.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
In February 2019, following the annual taxon ratification vote, the order Mononegavirales was amended by the addition of four new subfamilies and 12 new genera and the creation of 28 novel species. This article presents the updated taxonomy of the order Mononegavirales as now accepted by the International Committee on Taxonomy of Viruses (ICTV).
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Affiliation(s)
- Gaya K Amarasinghe
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO, USA
| | - María A Ayllón
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid-Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria, Campus de Montegancedo, Pozuelo de Alarcón, Madrid, Spain
- Departamento de Biotecnología-Biología Vegetal, Escuela Técnica Superior de Ingeniería Agronómica, Alimentaria y de Biosistemas, UPM, Madrid, Spain
| | - Yīmíng Bào
- Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China
| | - Christopher F Basler
- Center for Microbial Pathogenesis, Institute for Biomedical Sciences, Georgia State University, Atlanta, GA, USA
| | - Sina Bavari
- United States Army Medical Research Institute of Infectious Diseases, Fort Detrick, Frederick, MD, USA
| | - Kim R Blasdell
- Australian Animal Health Laboratory, CSIRO Health and Biosecurity, Geelong, VIC, Australia
| | - Thomas Briese
- Center for Infection and Immunity, and Department of Epidemiology, Mailman School of Public Health, Columbia University, New York, NY, USA
| | - Paul A Brown
- VIPAC Unit, Agence Nationale de Sécurité Sanitaire, Laboratoire de Ploufragan-Plouzané-Niort, Université Bretagne Loire, Ploufragan, France
| | | | - Anne Balkema-Buschmann
- Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Institute of Novel and Emerging Infectious Diseases, Greifswald-Insel Riems, Germany
| | - Ursula J Buchholz
- RNA Viruses Section, Laboratory of Infectious Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | | | - Kartik Chandran
- Department of Microbiology and Immunology, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Chiara Chiapponi
- Istituto Zooprofilattico Sperimentale della Lombardia e dell'Emilia Romagna, Brescia, Italy
| | - Ian Crozier
- Integrated Research Facility at Fort Detrick (IRF-Frederick), Clinical Monitoring Research Program Directorate, Frederick, National Laboratory for Cancer Research sponsored by the National Cancer Institute, Frederick, MD, USA
| | - Rik L de Swart
- Department of Viroscience, Erasmus MC, University Medical Centre Rotterdam, Rotterdam, The Netherlands
| | - Ralf G Dietzgen
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St. Lucia, QLD, Australia
| | - Olga Dolnik
- Institute of Virology, Philipps University Marburg, Marburg, Germany
| | - Jan F Drexler
- Institute of Virology, Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany
| | | | - William G Dundon
- Animal Production and Health Laboratory, Department of Nuclear Sciences and Applications, Joint FAO/IAEA Division of Nuclear Techniques in Food and Agriculture, International Atomic Energy Agency, Vienna, Austria
| | - W Paul Duprex
- School of Medicine, University of Pittsburgh, Pittsburgh, PA, USA
| | - John M Dye
- United States Army Medical Research Institute of Infectious Diseases, Fort Detrick, Frederick, MD, USA
| | - Andrew J Easton
- School of Life Sciences, University of Warwick, Coventry, UK
| | | | | | - Ron A M Fouchier
- Department of Viroscience, Erasmus MC, University Medical Centre Rotterdam, Rotterdam, The Netherlands
| | | | - Anthony Griffiths
- Department of Microbiology and National Emerging Infectious Diseases Laboratories, Boston University School of Medicine, Boston, MA, USA
| | - Roger Hewson
- Public Health England, Porton Down, Wiltshire, Salisbury, UK
| | - Masayuki Horie
- Hakubi Center for Advanced Research, Kyoto University, Kyoto, Japan
| | - Timothy H Hyndman
- School of Veterinary Medicine, Murdoch University, Murdoch, WA, Australia
| | - Dàohóng Jiāng
- State Key Laboratory of Agricultural Microbiology, The Provincial Key Lab of Plant Pathology of Húběi Province, College of Plant Science and Technology, Huázhōng Agricultural University, Wuhan, China
| | - Elliott W Kitajima
- Departamento de Fitopatologia e Nematologia, Escola Superior de Agricultura "Luiz de Queiroz, Universidade de São Paulo, Piracicaba, São Paulo, Brazil
| | - Gary P Kobinger
- Department of Microbiology, Immunology and Infectious Diseases, Université Laval, Quebec City, Canada
| | - Hideki Kondō
- Institute of Plant Science and Resources, Okayama University, Kurashiki, Japan
| | - Gael Kurath
- US Geological Survey Western Fisheries Research Center, Seattle, WA, USA
| | - Ivan V Kuzmin
- US Department of Agriculture, Animal and Plant Health Inspection, National Veterinary Services Laboratories, Diagnostic Virology Laboratory, New York, USA
| | - Robert A Lamb
- Department of Molecular Biosciences, Northwestern University, Evanston, IL, USA
- Howard Hughes Medical Institute, Northwestern University, Evanston, IL, USA
| | - Antonio Lavazza
- Istituto Zooprofilattico Sperimentale della Lombardia e dell'Emilia Romagna, Brescia, Italy
| | - Benhur Lee
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Davide Lelli
- Istituto Zooprofilattico Sperimentale della Lombardia e dell'Emilia Romagna, Brescia, Italy
| | - Eric M Leroy
- Centre International de Recherches Médicales de Franceville, Institut de Recherche pour le Développement, Franceville, Gabon
| | - Jiànróng Lǐ
- Department of Veterinary Biosciences, College of Veterinary Medicine, The Ohio State University, Columbus, OH, USA
| | - Piet Maes
- Zoonotic Infectious Diseases Unit, KU Leuven, Rega Institute, Leuven, Belgium
| | - Shin-Yi L Marzano
- Department of Biology and Microbiology, Department of Plant Sciences, South Dakota State University, Brookings, SD, USA
| | - Ana Moreno
- Istituto Zooprofilattico Sperimentale della Lombardia e dell'Emilia Romagna, Brescia, Italy
| | - Elke Mühlberger
- Department of Microbiology and National Emerging Infectious Diseases Laboratories, Boston University School of Medicine, Boston, MA, USA
| | - Sergey V Netesov
- Novosibirsk State University, Novosibirsk, Novosibirsk Oblast, Russia
| | - Norbert Nowotny
- Institute of Virology, University of Veterinary Medicine, Vienna, Austria
- Department of Basic Medical Sciences, College of Medicine, Mohammed Bin Rashid University of Medicine and Health Sciences, Dubai, United Arab Emirates
| | - Are Nylund
- Fish Disease Research Group, Department of Biological Sciences, University of Bergen, Bergen, Norway
| | - Arnfinn L Økland
- Fish Disease Research Group, Department of Biological Sciences, University of Bergen, Bergen, Norway
| | - Gustavo Palacios
- United States Army Medical Research Institute of Infectious Diseases, Fort Detrick, Frederick, MD, USA
| | - Bernadett Pályi
- National Biosafety Laboratory, National Public Health Center, Budapest, Hungary
| | - Janusz T Pawęska
- Center for Emerging Zoonotic and Parasitic Diseases, National Institute for Communicable Diseases of the National Health Laboratory Service, Sandringham-Johannesburg, Gauteng, South Africa
| | - Susan L Payne
- Department of Veterinary Pathobiology, College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, TX, USA
| | - Alice Prosperi
- Istituto Zooprofilattico Sperimentale della Lombardia e dell'Emilia Romagna, Brescia, Italy
| | | | - Bertus K Rima
- Centre for Experimental Medicine, School of Medicine, Dentistry and Biomedical Sciences, The Queen's University of Belfast, Belfast, Northern Ireland, UK
| | - Paul Rota
- National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Dennis Rubbenstroth
- Institute of Diagnostic Virology, Friedrich-Loeffler-Institut, Greifswald-Insel Riems, Germany
| | - Mǎng Shī
- The University of Sydney, Sydney, Australia
| | - Peter Simmonds
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | | | - Enrica Sozzi
- Istituto Zooprofilattico Sperimentale della Lombardia e dell'Emilia Romagna, Brescia, Italy
| | - Kirsten Spann
- School of Biomedical Science, Queensland University of Technology, Brisbane, QLD, Australia
| | - Mark D Stenglein
- Department of Microbiology, Immunology, and Pathology, College of Veterinary Medicine and Biomedical Sciences, Colorado State University, Fort Collins, CO, USA
| | - David M Stone
- Centre for Environment, Fisheries and Aquaculture Science, Weymouth, Dorset, UK
| | - Ayato Takada
- Division of Global Epidemiology, Hokkaido University Research Center for Zoonosis Control, Sapporo, Japan
| | - Robert B Tesh
- The University of Texas Medical Branch, Galveston, TX, USA
| | - Keizō Tomonaga
- Institute for Frontier Life and Medical Sciences (inFront), Kyoto University, Kyoto, Japan
| | - Noël Tordo
- Institut Pasteur, Unité des Stratégies Antivirales, WHO Collaborative Centre for Viral Haemorrhagic Fevers and Arboviruses, OIE Reference Laboratory for RVFV and CCHF, Paris, France
- Institut Pasteur de Guinée, Conakry, Guinea
| | - Jonathan S Towner
- Viral Special Pathogens Branch, Division of High-Consequence Pathogens Pathology, National Center for Emerging and Zoonotic Infectious Diseases, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Bernadette van den Hoogen
- Department of Viroscience, Erasmus MC, University Medical Centre Rotterdam, Rotterdam, The Netherlands
| | | | - Victoria Wahl
- National Biodefense Analysis and Countermeasures Center, Fort Detrick, Frederick, MD, USA
| | - Peter J Walker
- School of Biological Sciences, University of Queensland, St. Lucia, QLD, Australia
| | - Lin-Fa Wang
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore, Singapore
| | - Anna E Whitfield
- Department of Entomology and Plant Pathology, North Carolina State University, Raleigh, NC, USA
| | - John V Williams
- School of Medicine, University of Pittsburgh, Pittsburgh, PA, USA
| | - F Murilo Zerbini
- Departamento de Fitopatologia, Instituto de Biotecnologia Aplicada à Agropecuária, Universidade Federal de Viçosa, Viçosa, Minas Gerais, Brazil
| | - Tāo Zhāng
- Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China
| | - Yong-Zhen Zhang
- Chinese Center for Disease Control and Prevention, National Institute for Communicable Disease Control and Prevention, Changping, Beijing, China
- Shanghai Public Health Clinical Center and Institutes of Biomedical Sciences, Fudan University, Shanghai, China
| | - Jens H Kuhn
- Integrated Research Facility at Fort Detrick (IRF-Frederick), Division of Clinical Research (DCR), National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health (NIH), B-8200 Research Plaza, Fort Detrick, Frederick, MD, 2170, USA.
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9
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Asano T, Seto Y, Hashimoto K, Kurushima H. Mini-review an insect-specific system for terrestrialization: Laccase-mediated cuticle formation. INSECT BIOCHEMISTRY AND MOLECULAR BIOLOGY 2019; 108:61-70. [PMID: 30904465 DOI: 10.1016/j.ibmb.2019.03.007] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/08/2018] [Revised: 03/14/2019] [Accepted: 03/14/2019] [Indexed: 06/09/2023]
Abstract
Insects are often regarded as the most successful group of animals in the terrestrial environment. Their success can be represented by their huge biomass and large impact on ecosystems. Among the factors suggested to be responsible for their success, we focus on the possibility that the cuticle might have affected the process of insects' evolution. The cuticle of insects, like that of other arthropods, is composed mainly of chitin and structural cuticle proteins. However, insects seem to have evolved a specific system for cuticle formation. Oxidation reaction of catecholamines catalyzed by a copper enzyme, laccase, is the key step in the metabolic pathway for hardening of the insect cuticle. Molecular phylogenetic analysis indicates that laccase functioning in cuticle sclerotization has evolved only in insects. In this review, we discuss a theory on how the insect-specific "laccase" function has been advantageous for establishing their current ecological position as terrestrial animals.
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Affiliation(s)
- Tsunaki Asano
- Department of Biological Sciences, Tokyo Metropolitan University, Tokyo, 192-0397, Japan.
| | - Yosuke Seto
- Department of Biological Sciences, Tokyo Metropolitan University, Tokyo, 192-0397, Japan
| | - Kosei Hashimoto
- Department of Biological Sciences, Tokyo Metropolitan University, Tokyo, 192-0397, Japan
| | - Hiroaki Kurushima
- Department of Biological Sciences, Tokyo Metropolitan University, Tokyo, 192-0397, Japan
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10
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Økland AL, Nylund A, Øvergård AC, Skoge RH, Kongshaug H. Genomic characterization, phylogenetic position and in situ localization of a novel putative mononegavirus in Lepeophtheirus salmonis. Arch Virol 2019; 164:675-689. [PMID: 30535526 PMCID: PMC6394706 DOI: 10.1007/s00705-018-04119-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2018] [Accepted: 11/15/2018] [Indexed: 11/28/2022]
Abstract
The complete genome sequence of a novel mononegavirus, Lepeophtheirus salmonis negative-stranded RNA virus 1 (LsNSRV-1), obtained from a salmonid ectoparasite, Lepeophtheirus salmonis was determined. The viral genome contains five open reading frames encoding three unknown proteins (ORF I, II and III), a putative glycoprotein (G), and a large (L) protein. Phylogenetic analysis placed LsNSRV-1 in the recently established mononegaviral family Artoviridae. LsNSRV-1 showed a prevalence of around 97% and was detected in all L. salmonis developmental stages. Viral genomic and antigenomic RNA was localized to nerve tissue, connective tissue, epithelial cells of the gut, subepidermal tissue, exocrine and cement glands, as well as the testis, vas deferens and spermatophore sac of male L. salmonis and the ovaries and oocytes of females. Viral RNA was detected in both the cytoplasm and the nucleoli of infected cells, and putative nuclear export and localization signals were found within the ORF I, III and L proteins, suggesting nuclear replication of LsNSRV-1. RNA interference (RNAi) was induced twice during development by the introduction of a double-stranded RNA fragment of ORF I, resulting in a transient knockdown of viral RNA. A large variation in the knockdown level was seen in adult males and off springs of knockdown animals, whereas the RNA level was more stable in adult females. Together with the localization of viral RNA within the male spermatophore and female oocytes and the amplification of viral RNA in developing embryos, this suggests that LsNSRV-1 is transmitted both maternally and paternally. Small amounts of viral RNA were detected at the site where chalimi were attached to the skin of Atlantic salmon (Salmo salar). However, as the RNAi-mediated treatment did not result in LsNSRV-1-negative offspring and the virus failed to replicate in the tested fish cell cultures, it is difficult to investigate the influence of secreted LsNSRV-1 on the salmon immune response.
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Affiliation(s)
- Arnfinn Lodden Økland
- Fish Disease Research Group, Department of Biological Sciences, University of Bergen, Thormøhlensgt. 55, Pb. 7803, 5020, Bergen, Norway.
| | - Are Nylund
- Fish Disease Research Group, Department of Biological Sciences, University of Bergen, Thormøhlensgt. 55, Pb. 7803, 5020, Bergen, Norway
| | - Aina-Cathrine Øvergård
- Sea Lice Research Centre, Department of Biological Sciences, University of Bergen, Thormøhlensgt. 55, Pb. 7803, 5020, Bergen, Norway
| | - Renate Hvidsten Skoge
- Fish Disease Research Group, Department of Biological Sciences, University of Bergen, Thormøhlensgt. 55, Pb. 7803, 5020, Bergen, Norway
| | - Heidi Kongshaug
- Sea Lice Research Centre, Department of Biological Sciences, University of Bergen, Thormøhlensgt. 55, Pb. 7803, 5020, Bergen, Norway
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11
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Øvergård AC, Hamre LA, Grotmol S, Nilsen F. Salmon louse rhabdoviruses: Impact on louse development and transcription of selected Atlantic salmon immune genes. DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY 2018; 86:86-95. [PMID: 29747070 DOI: 10.1016/j.dci.2018.04.023] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/24/2018] [Revised: 04/27/2018] [Accepted: 04/27/2018] [Indexed: 06/08/2023]
Abstract
Recently, it has been shown that the salmon louse (Lepeophtheirus salmonis) is commonly infected by one or two vertically transmitted Lepeophtheirus salmonis rhabdoviruses (LsRVs). As shown in the present study, the viruses have limited effect on louse survival, developmental rate and fecundity. Since the LsRVs were confirmed to be present in the louse salivary glands, the salmon cutaneous immune response towards LsRV positive and negative lice was analyzed. In general, L. salmonis increased the expression of IL1β, IL8 and IL4/13A at the attachment site, in addition to the non-specific cytotoxic cell receptor protein 1 (NCCRP-1). Interestingly, LsRV free lice induced a higher skin expression of IL1β, IL8, and NCCRP-1 than the LsRV infected lice. The inflammatory response is important for louse clearance, and the present results suggest that the LsRVs can be beneficial for the louse by dampening inflammation. Further research is, however; needed to ascertain whether this is a direct modulatory effect of secreted virions, or if virus replication is altering the level of louse salivary gland proteins.
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Affiliation(s)
- Aina-Cathrine Øvergård
- SLRC - Sea Lice Research Centre, Department of Biological Sciences, University of Bergen, Thormøhlensgt. 55, Pb. 7803, 5020, Bergen, Norway.
| | - Lars Are Hamre
- SLRC - Sea Lice Research Centre, Department of Biological Sciences, University of Bergen, Thormøhlensgt. 55, Pb. 7803, 5020, Bergen, Norway.
| | - Sindre Grotmol
- SLRC - Sea Lice Research Centre, Department of Biological Sciences, University of Bergen, Thormøhlensgt. 55, Pb. 7803, 5020, Bergen, Norway.
| | - Frank Nilsen
- SLRC - Sea Lice Research Centre, Department of Biological Sciences, University of Bergen, Thormøhlensgt. 55, Pb. 7803, 5020, Bergen, Norway.
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12
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Økland AL, Skoge RH, Nylund A. The complete genome sequence of CrRV-Ch01, a new member of the family Rhabdoviridae in the parasitic copepod Caligus rogercresseyi present on farmed Atlantic salmon (Salmo salar) in Chile. Arch Virol 2018; 163:1657-1661. [PMID: 29445987 PMCID: PMC5958147 DOI: 10.1007/s00705-018-3768-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2017] [Accepted: 02/01/2018] [Indexed: 11/25/2022]
Abstract
We have determined the complete genome sequence of a new rhabdovirus, tentatively named Caligus rogercresseyi rhabdovirus Ch01 (CrRV-Ch01), which was found in the parasite Caligus rogercresseyi, present on farmed Atlantic salmon (Salmo salar) in Chile. The genome encodes the five canonical rhabdovirus proteins in addition to an unknown protein, in the order N-P-M-U (unknown)-G-L. Phylogenetic analysis showed that the virus clusters with two rhabdoviruses (Lepeophtheirus salmonis rhabdovirus No9 and Lepeophtheirus salmonis rhabdovirus No127) obtained from another parasitic caligid, Lepeophtheirus salmonis, present on farmed Atlantic salmon on the west coast of Norway.
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Affiliation(s)
| | | | - Are Nylund
- Department of Biology, University of Bergen, 5020, Bergen, Norway
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13
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Skoge RH, Brattespe J, Økland AL, Plarre H, Nylund A. New virus of the family Flaviviridae detected in lumpfish (Cyclopterus lumpus). Arch Virol 2017; 163:679-685. [PMID: 29147783 PMCID: PMC5814470 DOI: 10.1007/s00705-017-3643-3] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2017] [Accepted: 11/02/2017] [Indexed: 12/15/2022]
Abstract
In this study, we determined the complete coding sequence of a putative new member of the family Flaviviridae, named “Cyclopterus lumpus virus” (CLuV), which is associated with a serious disease in lumpfish (Cyclopterus lumpus). The virus was present in all tissues tested, but pathology was primarily observed in the liver and kidneys. CLuV shows low but distinct similarity to the unassigned Tamana bat virus (TABV). Unlike other known members of the family Flaviviridae, translation of the entire CLuV polyprotein is dependent on a − 1 ribosomal frameshift in the NS2A region.
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Affiliation(s)
- Renate Hvidsten Skoge
- Department of Biology, University of Bergen, Thormøhlensgt. 55, Pb. 7803, 5020, Bergen, Norway.
| | - Jarle Brattespe
- Department of Biology, University of Bergen, Thormøhlensgt. 55, Pb. 7803, 5020, Bergen, Norway
| | - Arnfinn Lodden Økland
- Department of Biology, University of Bergen, Thormøhlensgt. 55, Pb. 7803, 5020, Bergen, Norway
| | - Heidrun Plarre
- Department of Biology, University of Bergen, Thormøhlensgt. 55, Pb. 7803, 5020, Bergen, Norway
| | - Are Nylund
- Department of Biology, University of Bergen, Thormøhlensgt. 55, Pb. 7803, 5020, Bergen, Norway
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14
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Øvergård AC, Hamre LA, Kongshaug H, Nilsen F. RNAi-mediated treatment of two vertically transmitted rhabdovirus infecting the salmon louse (Lepeophtheirus salmonis). Sci Rep 2017; 7:14030. [PMID: 29070796 PMCID: PMC5656668 DOI: 10.1038/s41598-017-14282-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2017] [Accepted: 10/06/2017] [Indexed: 12/21/2022] Open
Abstract
Rhabdoviruses are a family of enveloped negative-sense single-stranded RNA viruses infecting a variety of hosts. Recently, two vertically transmitted salmon louse (Lepeophtheirus salmonis) rhabdoviruses (LsRV) have been identified. The prevalence of these viruses was measured along the Norwegian coast and found to be close to 100%, and with the present lack of suitable cell lines to propagate these viruses, it is challenging to obtain material to study their host impact and infection routes. Thus, virus free lice strains were established from virus infected lice carrying one or both LsRVs by treating them with N protein dsRNA twice during development. The viral replication of the N protein was specifically down-regulated following introduction of virus-specific dsRNA, and virus-free lice strains were maintained for several generations. A preliminary study on infection routes suggested that the LsRV-No9 is maternally transmitted, and that the virus transmits from males to females horizontally. The ability to produce virus free strains allows for further studies on transmission modes and how these viruses influences on the L.salmonis interaction with its salmonid host. Moreover, this study provides a general fundament for future studies on how vertically transmitted rhabdoviruses influence the biology of their arthropod hosts.
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Affiliation(s)
- Aina-Cathrine Øvergård
- SLCR-Sea Lice Research Centre, Department of Biology, University of Bergen, Thormøhlensgt. 55, Pb. 7803, NO-5020, Bergen, Norway.
| | - Lars Are Hamre
- SLCR-Sea Lice Research Centre, Department of Biology, University of Bergen, Thormøhlensgt. 55, Pb. 7803, NO-5020, Bergen, Norway
| | - Heidi Kongshaug
- SLCR-Sea Lice Research Centre, Department of Biology, University of Bergen, Thormøhlensgt. 55, Pb. 7803, NO-5020, Bergen, Norway
| | - Frank Nilsen
- SLCR-Sea Lice Research Centre, Department of Biology, University of Bergen, Thormøhlensgt. 55, Pb. 7803, NO-5020, Bergen, Norway
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15
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Poley JD, Sutherland BJG, Fast MD, Koop BF, Jones SRM. Effects of the vertically transmitted microsporidian Facilispora margolisi and the parasiticide emamectin benzoate on salmon lice (Lepeophtheirus salmonis). BMC Genomics 2017; 18:630. [PMID: 28818044 PMCID: PMC5561633 DOI: 10.1186/s12864-017-4040-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2017] [Accepted: 08/08/2017] [Indexed: 12/15/2022] Open
Abstract
Background Microsporidia are highly specialized, parasitic fungi that infect a wide range of eukaryotic hosts from all major taxa. Infections cause a variety of damaging effects on host physiology from increased stress to death. The microsporidian Facilispora margolisi infects the Pacific salmon louse (Lepeophtheirus salmonis oncorhynchi), an economically and ecologically important ectoparasitic copepod that can impact wild and cultured salmonids. Results Vertical transmission of F. margolisi was demonstrated by using PCR and in situ hybridization to identify and localize microsporidia in female L. salmonis and their offspring. Spores and developmental structures of F. margolisi were identified in 77% of F1 generation copepods derived from infected females while offspring from uninfected females all tested negative for the microsporidia. The transcriptomic response of the salmon louse to F. margolisi was profiled at both the copepodid larval stage and the pre-adult stage using microarray technology. Infected copepodids differentially expressed 577 transcripts related to stress, ATP generation and structural components of muscle and cuticle. The infection also impacted the response of the copepodid to the parasiticide emamectin benzoate (EMB) at a low dose of 1.0 ppb for 24 h. A set of 48 transcripts putatively involved in feeding and host immunomodulation were up to 8-fold underexpressed in the F. margolisi infected copepodids treated with EMB compared with controls or either stressor alone. Additionally, these infected lice treated with EMB also overexpressed 101 transcripts involved in stress resistance and signalling compared to the other groups. In contrast, infected pre-adult lice did not display a stress response, suggesting a decrease in microsporidian virulence associated with lice maturity. Furthermore, copepodid infectivity and moulting was not affected by the microsporidian infection. Conclusions This study demonstrated that F. margolisi is transmitted vertically between salmon louse generations and that biological impacts of infection differ depending on the stage of the copepod host. The infection caused significant perturbations of larval transcriptomes and therefore must be considered in future studies in which impacts to host development and environmental factors are assessed. Fitness impacts are probably minor, although the interaction between pesticide exposure and microsporidian infection merits further study. Electronic supplementary material The online version of this article (doi:10.1186/s12864-017-4040-8) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Jordan D Poley
- Atlantic Veterinary College, University of Prince Edward Island, Department of Pathology & Microbiology, 550 University Ave, Charlottetown, PE, C1A 4P3, Canada
| | - Ben J G Sutherland
- Centre for Biomedical Research, Department of Biology, University of Victoria, 3800 Finnerty Rd, Victoria, BC, V8W 3N5, Canada.,Institut de Biologie Intégrative et des Systèmes (IBIS), Département de biologie, Université Laval, 1030 Avenue de la Medecine, Québec, QC, G1V 0A6, Canada
| | - Mark D Fast
- Atlantic Veterinary College, University of Prince Edward Island, Department of Pathology & Microbiology, 550 University Ave, Charlottetown, PE, C1A 4P3, Canada
| | - Ben F Koop
- Centre for Biomedical Research, Department of Biology, University of Victoria, 3800 Finnerty Rd, Victoria, BC, V8W 3N5, Canada
| | - Simon R M Jones
- Pacific Biological Station, 3190 Hammond Bay Road, Nanaimo, BC, V9T 6N7, Canada.
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16
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Longdon B, Murray GGR, Palmer WJ, Day JP, Parker DJ, Welch JJ, Obbard DJ, Jiggins FM. The evolution, diversity, and host associations of rhabdoviruses. Virus Evol 2015; 1:vev014. [PMID: 27774286 PMCID: PMC5014481 DOI: 10.1093/ve/vev014] [Citation(s) in RCA: 59] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
Metagenomic studies are leading to the discovery of a hidden diversity of RNA viruses. These new viruses are poorly characterized and new approaches are needed predict the host species these viruses pose a risk to. The rhabdoviruses are a diverse family of RNA viruses that includes important pathogens of humans, animals, and plants. We have discovered thirty-two new rhabdoviruses through a combination of our own RNA sequencing of insects and searching public sequence databases. Combining these with previously known sequences we reconstructed the phylogeny of 195 rhabdovirus sequences, and produced the most in depth analysis of the family to date. In most cases we know nothing about the biology of the viruses beyond the host they were identified from, but our dataset provides a powerful phylogenetic approach to predict which are vector-borne viruses and which are specific to vertebrates or arthropods. By reconstructing ancestral and present host states we found that switches between major groups of hosts have occurred rarely during rhabdovirus evolution. This allowed us to propose seventy-six new likely vector-borne vertebrate viruses among viruses identified from vertebrates or biting insects. Based on currently available data, our analysis suggests it is likely there was a single origin of the known plant viruses and arthropod-borne vertebrate viruses, while vertebrate- and arthropod-specific viruses arose at least twice. There are also few transitions between aquatic and terrestrial ecosystems. Viruses also cluster together at a finer scale, with closely related viruses tending to be found in closely related hosts. Our data therefore suggest that throughout their evolution, rhabdoviruses have occasionally jumped between distantly related host species before spreading through related hosts in the same environment. This approach offers a way to predict the most probable biology and key traits of newly discovered viruses.
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Affiliation(s)
- Ben Longdon
- Department of Genetics, University of Cambridge, Cambridge, CB2 3EH
| | | | | | - Jonathan P. Day
- Department of Genetics, University of Cambridge, Cambridge, CB2 3EH
| | - Darren J Parker
- School of Biology, University of St Andrews, St Andrews, KY19 9ST, UK
- Department of Biological and Environmental Science, University of Jyväskylä, Jyväskylä, Finland and
| | - John J. Welch
- Department of Genetics, University of Cambridge, Cambridge, CB2 3EH
| | - Darren J. Obbard
- Institute of Evolutionary Biology, and Centre for Immunity Infection and Evolution, University of Edinburgh, Edinburgh, EH9 3JT, UK
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Metegnier G, Becking T, Chebbi MA, Giraud I, Moumen B, Schaack S, Cordaux R, Gilbert C. Comparative paleovirological analysis of crustaceans identifies multiple widespread viral groups. Mob DNA 2015; 6:16. [PMID: 26388953 PMCID: PMC4573495 DOI: 10.1186/s13100-015-0047-3] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2015] [Accepted: 09/10/2015] [Indexed: 01/08/2023] Open
Abstract
Background The discovery of many fragments of viral genomes integrated in the genome of their eukaryotic host (endogenous viral elements; EVEs) has recently opened new avenues to further our understanding of viral evolution and of host-virus interactions. Here, we report the results of a comprehensive screen for EVEs in crustaceans. Following up on the recent discovery of EVEs in the terrestrial isopod, Armadillidium vulgare, we scanned the genomes of six crustacean species: a terrestrial isopod (Armadillidium nasatum), two water fleas (Daphnia pulex and D. pulicaria), two copepods (the salmon louse, Lepeophtheirus salmonis and Eurytemora affinis), and a freshwater amphipod (Hyalella azteca). Results In total, we found 210 EVEs representing 14 different lineages belonging to five different viral groups that are present in two to five species: Bunyaviridae (−ssRNA), Circoviridae (ssDNA), Mononegavirales (−ssRNA), Parvoviridae (ssDNA) and Totiviridae (dsRNA). The identification of shared orthologous insertions between A. nasatum and A. vulgare indicates that EVEs have been maintained over several millions of years, although we did not find any evidence supporting exaptation. Overall, the different degrees of EVE degradation (from none to >10 nonsense mutations) suggest that endogenization has been recurrent during the evolution of the various crustacean taxa. Our study is the first to report EVEs in D. pulicaria, E. affinis and H. azteca, many of which are likely to result from recent endogenization of currently circulating viruses. Conclusions In conclusion, we have unearthed a large diversity of EVEs from crustacean genomes, and shown that four of the five viral groups we uncovered (Bunyaviridae, Circoviridae, Mononegavirales, Parvoviridae) were and may still be present in three to four highly divergent crustacean taxa. In addition, the discovery of recent EVEs offers an interesting opportunity to characterize new exogenous viruses currently circulating in economically or ecologically important copepod species. Electronic supplementary material The online version of this article (doi:10.1186/s13100-015-0047-3) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Gabriel Metegnier
- Université de Poitiers, UMR CNRS 7267 Ecologie et Biologie des Interactions, Equipe Ecologie Evolution Symbiose, building B8-B35, 6 rue Michel Brunet, TSA 51106 F-86073 Poitiers, Cedex 9 France
| | - Thomas Becking
- Université de Poitiers, UMR CNRS 7267 Ecologie et Biologie des Interactions, Equipe Ecologie Evolution Symbiose, building B8-B35, 6 rue Michel Brunet, TSA 51106 F-86073 Poitiers, Cedex 9 France
| | - Mohamed Amine Chebbi
- Université de Poitiers, UMR CNRS 7267 Ecologie et Biologie des Interactions, Equipe Ecologie Evolution Symbiose, building B8-B35, 6 rue Michel Brunet, TSA 51106 F-86073 Poitiers, Cedex 9 France
| | - Isabelle Giraud
- Université de Poitiers, UMR CNRS 7267 Ecologie et Biologie des Interactions, Equipe Ecologie Evolution Symbiose, building B8-B35, 6 rue Michel Brunet, TSA 51106 F-86073 Poitiers, Cedex 9 France
| | - Bouziane Moumen
- Université de Poitiers, UMR CNRS 7267 Ecologie et Biologie des Interactions, Equipe Ecologie Evolution Symbiose, building B8-B35, 6 rue Michel Brunet, TSA 51106 F-86073 Poitiers, Cedex 9 France
| | - Sarah Schaack
- Department of Biology, Reed College, Portland, OR USA
| | - Richard Cordaux
- Université de Poitiers, UMR CNRS 7267 Ecologie et Biologie des Interactions, Equipe Ecologie Evolution Symbiose, building B8-B35, 6 rue Michel Brunet, TSA 51106 F-86073 Poitiers, Cedex 9 France
| | - Clément Gilbert
- Université de Poitiers, UMR CNRS 7267 Ecologie et Biologie des Interactions, Equipe Ecologie Evolution Symbiose, building B8-B35, 6 rue Michel Brunet, TSA 51106 F-86073 Poitiers, Cedex 9 France
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