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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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2
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Meyers TR, Hickey N. A perspective: Molecular detections of new agents in finfish-Interpreting biological significance for fish health management: Response to comment. JOURNAL OF AQUATIC ANIMAL HEALTH 2024. [PMID: 39042521 DOI: 10.1002/aah.10222] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/28/2024] [Accepted: 03/28/2024] [Indexed: 07/25/2024]
Abstract
Impact statementThe original paper provides a suggested pathway of investigative criteria to determine viability and pathogenicity of agents detected by molecular methods in fish for the purpose of interpreting biological significance for fish health management. This response defends this position regarding the requirement of certain scientific facts to determine the importance of a particular molecular discovery.
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Affiliation(s)
- Theodore R Meyers
- Alaska Department of Fish and Game, Commercial Fisheries Division, Juneau, Alaska, USA
| | - Nora Hickey
- Washington Animal Disease Diagnostic Laboratory, Olympia, Washington, USA
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Grimwood RM, Waller SJ, Wierenga JR, Lim L, Dubrulle J, Holmes EC, Geoghegan JL. Viromes of Antarctic fish resemble the diversity found at lower latitudes. Virus Evol 2024; 10:veae050. [PMID: 39071139 PMCID: PMC11282168 DOI: 10.1093/ve/veae050] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2024] [Revised: 06/09/2024] [Accepted: 07/10/2024] [Indexed: 07/30/2024] Open
Abstract
Antarctica harbours some of the most isolated and extreme environments on Earth, concealing a largely unexplored and unique component of the global animal virosphere. To understand the diversity and evolutionary histories of viruses in these polar species, we determined the viromes of gill metatranscriptomes from 11 Antarctic fish species with 248 samples collected from the Ross Sea region spanning the Perciformes, Gadiformes, and Scorpaeniformes orders. The continent's shift southward and cooling temperatures >20 million years ago led to a reduction in biodiversity and subsequent radiation of some marine fauna, such as the notothenioid fishes. Despite decreased host species richness in polar regions, we revealed a surprisingly complex virome diversity in Ross Sea fish, with the types and numbers of viruses per host species and individuals sampled comparable to that of fish in warmer marine environments with higher host community diversity. We also observed a higher number of closely related viruses likely representing instances of recent and historic host-switching events among the Perciformes (all notothenioids) than in the Gadiformes, suggesting that rapid speciation events within this order generated closely related host species with few genetic barriers to cross-species transmission. Additionally, we identified novel genomic variation in an arenavirus with a split nucleoprotein sequence containing a stable helical structure, indicating potential adaptation of viral proteins to extreme temperatures. These findings enhance our understanding of virus evolution and virus-host interactions in response to environmental shifts, especially in less diverse ecosystems that are more vulnerable to the impacts of anthropogenic and climate changes.
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Affiliation(s)
- Rebecca M Grimwood
- Department of Microbiology and Immunology, University of Otago, Dunedin 9016, New Zealand
| | - Stephanie J Waller
- Department of Microbiology and Immunology, University of Otago, Dunedin 9016, New Zealand
| | - Janelle R Wierenga
- Department of Microbiology and Immunology, University of Otago, Dunedin 9016, New Zealand
| | - Lauren Lim
- Sydney Institute for Infectious Diseases, School of Medical Sciences, The University of Sydney, Camperdown, NSW 2006, Australia
| | - Jérémy Dubrulle
- Department of Microbiology and Immunology, University of Otago, Dunedin 9016, New Zealand
| | - Edward C Holmes
- Sydney Institute for Infectious Diseases, School of Medical Sciences, The University of Sydney, Camperdown, NSW 2006, Australia
| | - Jemma L Geoghegan
- Department of Microbiology and Immunology, University of Otago, Dunedin 9016, New Zealand
- Institute of Environmental Science and Research, Wellington 5018, New Zealand
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Nuñez IA, Crane A, Crozier I, Worwa G, Kuhn JH. Treatment of highly virulent mammarenavirus infections-status quo and future directions. Expert Opin Drug Discov 2024; 19:537-551. [PMID: 38606475 PMCID: PMC11069405 DOI: 10.1080/17460441.2024.2340494] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2024] [Accepted: 04/04/2024] [Indexed: 04/13/2024]
Abstract
INTRODUCTION Mammarenaviruses are negative-sense bisegmented enveloped RNA viruses that are endemic in Africa, the Americas, and Europe. Several are highly virulent, causing acute human diseases associated with high case fatality rates, and are considered to be significant with respect to public health impact or bioterrorism threat. AREAS COVERED This review summarizes the status quo of treatment development, starting with drugs that are in advanced stages of evaluation in early clinical trials, followed by promising candidate medical countermeasures emerging from bench analyses and investigational animal research. EXPERT OPINION Specific therapeutic treatments for diseases caused by mammarenaviruses remain limited to the off-label use of ribavirin and transfusion of convalescent sera. Progress in identifying novel candidate medical countermeasures against mammarenavirus infection has been slow in part because of the biosafety and biosecurity requirements. However, novel methodologies and tools have enabled increasingly efficient high-throughput molecular screens of regulatory-agency-approved small-molecule drugs and led to the identification of several compounds that could be repurposed for the treatment of infection with several mammarenaviruses. Unfortunately, most of them have not yet been evaluated in vivo. The most promising treatment under development is a monoclonal antibody cocktail that is protective against multiple lineages of the Lassa virus in nonhuman primate disease models.
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Affiliation(s)
- Ivette A. Nuñez
- Integrated Research Facility at Fort Detrick, Division of
Clinical Research, National Institute of Allergy and Infectious Diseases, National
Institutes of Health, Fort Detrick, Frederick, MD21702, USA
| | - Anya Crane
- Integrated Research Facility at Fort Detrick, Division of
Clinical Research, National Institute of Allergy and Infectious Diseases, National
Institutes of Health, Fort Detrick, Frederick, MD21702, USA
| | - Ian Crozier
- Clinical Monitoring Research Program Directorate, Frederick
National Laboratory for Cancer Research, Frederick, MD 21702, USA
| | - Gabriella Worwa
- Integrated Research Facility at Fort Detrick, Division of
Clinical Research, National Institute of Allergy and Infectious Diseases, National
Institutes of Health, Fort Detrick, Frederick, MD21702, USA
| | - Jens H. Kuhn
- Integrated Research Facility at Fort Detrick, Division of
Clinical Research, National Institute of Allergy and Infectious Diseases, National
Institutes of Health, Fort Detrick, Frederick, MD21702, USA
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Lauber C, Zhang X, Vaas J, Klingler F, Mutz P, Dubin A, Pietschmann T, Roth O, Neuman BW, Gorbalenya AE, Bartenschlager R, Seitz S. Deep mining of the Sequence Read Archive reveals major genetic innovations in coronaviruses and other nidoviruses of aquatic vertebrates. PLoS Pathog 2024; 20:e1012163. [PMID: 38648214 PMCID: PMC11065284 DOI: 10.1371/journal.ppat.1012163] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2023] [Revised: 05/02/2024] [Accepted: 03/31/2024] [Indexed: 04/25/2024] Open
Abstract
Virus discovery by genomics and metagenomics empowered studies of viromes, facilitated characterization of pathogen epidemiology, and redefined our understanding of the natural genetic diversity of viruses with profound functional and structural implications. Here we employed a data-driven virus discovery approach that directly queries unprocessed sequencing data in a highly parallelized way and involves a targeted viral genome assembly strategy in a wide range of sequence similarity. By screening more than 269,000 datasets of numerous authors from the Sequence Read Archive and using two metrics that quantitatively assess assembly quality, we discovered 40 nidoviruses from six virus families whose members infect vertebrate hosts. They form 13 and 32 putative viral subfamilies and genera, respectively, and include 11 coronaviruses with bisegmented genomes from fishes and amphibians, a giant 36.1 kilobase coronavirus genome with a duplicated spike glycoprotein (S) gene, 11 tobaniviruses and 17 additional corona-, arteri-, cremega-, nanhypo- and nangoshaviruses. Genome segmentation emerged in a single evolutionary event in the monophyletic lineage encompassing the subfamily Pitovirinae. We recovered the bisegmented genome sequences of two coronaviruses from RNA samples of 69 infected fishes and validated the presence of poly(A) tails at both segments using 3'RACE PCR and subsequent Sanger sequencing. We report a genetic linkage between accessory and structural proteins whose phylogenetic relationships and evolutionary distances are incongruent with the phylogeny of replicase proteins. We rationalize these observations in a model of inter-family S recombination involving at least five ancestral corona- and tobaniviruses of aquatic hosts. In support of this model, we describe an individual fish co-infected with members from the families Coronaviridae and Tobaniviridae. Our results expand the scale of the known extraordinary evolutionary plasticity in nidoviral genome architecture and call for revisiting fundamentals of genome expression, virus particle biology, host range and ecology of vertebrate nidoviruses.
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Affiliation(s)
- Chris Lauber
- Institute for Experimental Virology, TWINCORE Centre for Experimental and Clinical Infection Research, a joint venture between the Hannover Medical School (MHH) and the Helmholtz Centre for Infection Research (HZI), Hannover, Germany
- Cluster of Excellence 2155 RESIST, Hannover, Germany
| | - Xiaoyu Zhang
- Institute for Experimental Virology, TWINCORE Centre for Experimental and Clinical Infection Research, a joint venture between the Hannover Medical School (MHH) and the Helmholtz Centre for Infection Research (HZI), Hannover, Germany
| | - Josef Vaas
- Division of Virus-Associated Carcinogenesis (F170), German Cancer Research Center (DKFZ), Heidelberg, Germany
- Heidelberg University, Medical Faculty Heidelberg, Department of Infectious Diseases, Molecular Virology, Center for Integrative Infectious Disease Research, Heidelberg, Germany
| | - Franziska Klingler
- Division of Virus-Associated Carcinogenesis (F170), German Cancer Research Center (DKFZ), Heidelberg, Germany
- Heidelberg University, Medical Faculty Heidelberg, Department of Infectious Diseases, Molecular Virology, Center for Integrative Infectious Disease Research, Heidelberg, Germany
| | - Pascal Mutz
- Division of Virus-Associated Carcinogenesis (F170), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Arseny Dubin
- Marine Evolutionary Biology, Zoological Institute, Kiel University, Kiel, Germany
| | - Thomas Pietschmann
- Institute for Experimental Virology, TWINCORE Centre for Experimental and Clinical Infection Research, a joint venture between the Hannover Medical School (MHH) and the Helmholtz Centre for Infection Research (HZI), Hannover, Germany
- Cluster of Excellence 2155 RESIST, Hannover, Germany
| | - Olivia Roth
- Marine Evolutionary Biology, Zoological Institute, Kiel University, Kiel, Germany
| | - Benjamin W. Neuman
- Department of Biology and Texas A&M Global Health Research Complex, Texas A&M University, College Station, Texas, United States
| | - Alexander E. Gorbalenya
- Leiden University Center of Infectious Diseases, Leiden University Medical Center, Leiden, The Netherlands
- Faculty of Bioengineering and Bioinformatics and Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russia
| | - Ralf Bartenschlager
- Division of Virus-Associated Carcinogenesis (F170), German Cancer Research Center (DKFZ), Heidelberg, Germany
- Heidelberg University, Medical Faculty Heidelberg, Department of Infectious Diseases, Molecular Virology, Center for Integrative Infectious Disease Research, Heidelberg, Germany
| | - Stefan Seitz
- Division of Virus-Associated Carcinogenesis (F170), German Cancer Research Center (DKFZ), Heidelberg, Germany
- Heidelberg University, Medical Faculty Heidelberg, Department of Infectious Diseases, Molecular Virology, Center for Integrative Infectious Disease Research, Heidelberg, Germany
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Hemnani M, da Silva PG, Thompson G, Poeta P, Rebelo H, Mesquita JR. Presence of Alphacoronavirus in Tree- and Crevice-Dwelling Bats from Portugal. Viruses 2024; 16:434. [PMID: 38543799 PMCID: PMC10976264 DOI: 10.3390/v16030434] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2024] [Revised: 03/04/2024] [Accepted: 03/06/2024] [Indexed: 05/23/2024] Open
Abstract
Coronaviruses (CoVs) are RNA viruses capable of infecting a wide range of hosts, including mammals and birds, and have caused significant epidemics such as the ongoing COVID-19 pandemic. Bats, the second most diverse mammalian order, are hosts for various CoVs due to their unique immune responses and ecological traits. This study investigates CoV prevalence in crevice- and tree-dwelling bats in Portugal, a country with limited prior research on bat CoVs. Using nested RT-PCR and sequencing, we screened 87 stool samples from bats, identifying one sample (1.15%) that was positive for Alphacoronavirus, belonging to Pipistrellus pipistrellus. Phylogenetic analysis revealed close genetic relationships with Alphacoronavirus strains from the same bat species in Europe. The low prevalence suggests habitat-specific differences in viral transmission, with cave-dwelling bats exhibiting higher CoV prevalence due to population density and behaviour. These findings underscore the necessity for sustained surveillance efforts aimed at comprehending CoV dynamics within bat populations, especially concerning the risk of spillover events and viral evolution. Vital to this understanding is the monitoring of bat migration patterns, which serves as a crucial tool for elucidating CoV ecology and epidemiology. Such efforts are essential for ongoing research endeavours aimed at mitigating the potential for future zoonotic disease outbreaks.
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Affiliation(s)
- Mahima Hemnani
- School of Medicine and Biomedical Sciences, Porto University, 4050-313 Porto, Portugal; (M.H.); (P.G.d.S.); (G.T.)
| | - Priscilla Gomes da Silva
- School of Medicine and Biomedical Sciences, Porto University, 4050-313 Porto, Portugal; (M.H.); (P.G.d.S.); (G.T.)
- Epidemiology Research Unit (EPIunit), Institute of Public Health, University of Porto, 4099-002 Porto, Portugal
- Laboratório Para a Investigação Integrativa e Translacional em Saúde Populacional (ITR), 4050-313 Porto, Portugal
- LEPABE—Laboratory for Process Engineering, Environment, Biotechnology and Energy, Faculty of Engineering, University of Porto, 4099-002 Porto, Portugal
- ALiCE—Associate Laboratory in Chemical Engineering, Faculty of Engineering, University of Porto, 4099-002 Porto, Portugal
| | - Gertrude Thompson
- School of Medicine and Biomedical Sciences, Porto University, 4050-313 Porto, Portugal; (M.H.); (P.G.d.S.); (G.T.)
- Biopolis-CIBIO/InBIO Laboratório Associado, Campus de Vairão, 4485-661 Vairão, Portugal;
| | - Patrícia Poeta
- Microbiology and Antibiotic Resistance Team (MicroART), Department of Veterinary Sciences, University of Trás-os Montes e Alto Douro, 5000-801 Vila Real, Portugal;
- Associated Laboratory for Green Chemistry (LAQV), Chemistry Department, Faculty of Science and Technology, University NOVA of Lisbon, 2829-516 Caparica, Portugal
- Associate Laboratory for Animal and Veterinary Science (AL4AnimalS), University of Trás-os-Montes and Alto Douro (UTAD), 5000-801 Vila Real, Portugal
- Veterinary and Animal Research Centre (CECAV), University of Trás-os-Montes and Alto Douro (UTAD), 5000-801 Vila Real, Portugal
| | - Hugo Rebelo
- Biopolis-CIBIO/InBIO Laboratório Associado, Campus de Vairão, 4485-661 Vairão, Portugal;
- cE3c—Centre for Ecology, Evolution and Environmental Changes & CHANGE—Global Change and Sustainability Institute, Faculty of Sciences, University of Lisbon, 1749-016 Lisbon, Portugal
| | - João R. Mesquita
- School of Medicine and Biomedical Sciences, Porto University, 4050-313 Porto, Portugal; (M.H.); (P.G.d.S.); (G.T.)
- Epidemiology Research Unit (EPIunit), Institute of Public Health, University of Porto, 4099-002 Porto, Portugal
- Laboratório Para a Investigação Integrativa e Translacional em Saúde Populacional (ITR), 4050-313 Porto, Portugal
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Ford CE, Dunn CD, Leis EM, Thiel WA, Goldberg TL. Five Species of Wild Freshwater Sport Fish in Wisconsin, USA, Reveal Highly Diverse Viromes. Pathogens 2024; 13:150. [PMID: 38392888 PMCID: PMC10891596 DOI: 10.3390/pathogens13020150] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2023] [Revised: 02/01/2024] [Accepted: 02/05/2024] [Indexed: 02/25/2024] Open
Abstract
Studies of marine fish have revealed distant relatives of viruses important to global fish and animal health, but few such studies exist for freshwater fish. To investigate whether freshwater fish also host such viruses, we characterized the viromes of five wild species of freshwater fish in Wisconsin, USA: bluegill (Lepomis macrochirus), brown trout (Salmo trutta), lake sturgeon (Acipenser fulvescens), northern pike (Esox lucius), and walleye (Sander vitreus). We analyzed 103 blood serum samples collected during a state-wide survey from 2016 to 2020 and used a metagenomic approach for virus detection to identify known and previously uncharacterized virus sequences. We then characterized viruses phylogenetically and quantified prevalence, richness, and relative abundance for each virus. Within these viromes, we identified 19 viruses from 11 viral families: Amnoonviridae, Circoviridae, Coronaviridae, Hepadnaviridae, Peribunyaviridae, Picobirnaviridae, Picornaviridae, Matonaviridae, Narnaviridae, Nudnaviridae, and Spinareoviridae, 17 of which were previously undescribed. Among these viruses was the first fish-associated coronavirus from the Gammacoronavirus genus, which was present in 11/15 (73%) of S. vitreus. These results demonstrate that, similar to marine fish, freshwater fish also harbor diverse relatives of viruses important to the health of fish and other animals, although it currently remains unknown what effect, if any, the viruses we identified may have on fish health.
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Affiliation(s)
- Charlotte E. Ford
- Department of Pathobiological Sciences, University of Wisconsin-Madison, Madison, WI 53706, USA; (C.E.F.); (C.D.D.)
| | - Christopher D. Dunn
- Department of Pathobiological Sciences, University of Wisconsin-Madison, Madison, WI 53706, USA; (C.E.F.); (C.D.D.)
| | - Eric M. Leis
- U.S. Fish and Wildlife Service, La Crosse Fish Health Center—Midwest Fisheries Center, Onalaska, WI 54650, USA;
| | - Whitney A. Thiel
- Robert P. Hanson Laboratories, University of Wisconsin-Madison, Madison, WI 53706, USA;
| | - Tony L. Goldberg
- Department of Pathobiological Sciences, University of Wisconsin-Madison, Madison, WI 53706, USA; (C.E.F.); (C.D.D.)
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Chen G, Jiang J, Sun Y. RNAVirHost: a machine learning-based method for predicting hosts of RNA viruses through viral genomes. Gigascience 2024; 13:giae059. [PMID: 39172545 PMCID: PMC11340644 DOI: 10.1093/gigascience/giae059] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2024] [Revised: 05/29/2024] [Accepted: 07/23/2024] [Indexed: 08/24/2024] Open
Abstract
BACKGROUND The high-throughput sequencing technologies have revolutionized the identification of novel RNA viruses. Given that viruses are infectious agents, identifying hosts of these new viruses carries significant implications for public health and provides valuable insights into the dynamics of the microbiome. However, determining the hosts of these newly discovered viruses is not always straightforward, especially in the case of viruses detected in environmental samples. Even for host-associated samples, it is not always correct to assign the sample origin as the host of the identified viruses. The process of assigning hosts to RNA viruses remains challenging due to their high mutation rates and vast diversity. RESULTS In this study, we introduce RNAVirHost, a machine learning-based tool that predicts the hosts of RNA viruses solely based on viral genomes. RNAVirHost is a hierarchical classification framework that predicts hosts at different taxonomic levels. We demonstrate the superior accuracy of RNAVirHost in predicting hosts of RNA viruses through comprehensive comparisons with various state-of-the-art techniques. When applying to viruses from novel genera, RNAVirHost achieved the highest accuracy of 84.3%, outperforming the alignment-based strategy by 12.1%. CONCLUSIONS The application of machine learning models has proven beneficial in predicting hosts of RNA viruses. By integrating genomic traits and sequence homologies, RNAVirHost provides a cost-effective and efficient strategy for host prediction. We believe that RNAVirHost can greatly assist in RNA virus analyses and contribute to pandemic surveillance.
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Affiliation(s)
- Guowei Chen
- Department of Electrical Engineering, City University of Hong Kong, Kowloon, Hong Kong (SAR), China
| | - Jingzhe Jiang
- Key Laboratory of South China Sea Fishery Resources Exploitation & Utilization, Ministry of Agriculture and Rural Affairs, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou 510300, China
| | - Yanni Sun
- Department of Electrical Engineering, City University of Hong Kong, Kowloon, Hong Kong (SAR), China
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Kononova Y, Adamenko L, Kazachkova E, Solomatina M, Romanenko S, Proskuryakova A, Utkin Y, Gulyaeva M, Spirina A, Kazachinskaia E, Palyanova N, Mishchenko O, Chepurnov A, Shestopalov A. Features of SARS-CoV-2 Replication in Various Types of Reptilian and Fish Cell Cultures. Viruses 2023; 15:2350. [PMID: 38140591 PMCID: PMC10748073 DOI: 10.3390/v15122350] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2023] [Revised: 11/24/2023] [Accepted: 11/28/2023] [Indexed: 12/24/2023] Open
Abstract
BACKGROUND SARS-CoV-2 can enter the environment from the feces of COVID-19 patients and virus carriers through untreated sewage. The virus has shown the ability to adapt to a wide range of hosts, so the question of the possible involvement of aquafauna and animals of coastal ecosystems in maintaining its circulation remains open. METHODS the aim of this work was to study the tropism of SARS-CoV-2 for cells of freshwater fish and reptiles, including those associated with aquatic and coastal ecosystems, and the effect of ambient temperature on this process. In a continuous cell culture FHM (fathead minnow) and diploid fibroblasts CGIB (silver carp), SARS-CoV-2 replication was not maintained at either 25 °C or 29 °C. At 29 °C, the continuous cell culture TH-1 (eastern box turtle) showed high susceptibility to SARS-CoV-2, comparable to Vero E6 (development of virus-induced cytopathic effect (CPE) and an infectious titer of 7.5 ± 0.17 log10 TCID50/mL on day 3 after infection), and primary fibroblasts CNI (Nile crocodile embryo) showed moderate susceptibility (no CPE, infectious titer 4.52 ± 0.14 log10 TCID50/mL on day 5 after infection). At 25 °C, SARS-CoV-2 infection did not develop in TH-1 and CNI. CONCLUSIONS our results show the ability of SARS-CoV-2 to effectively replicate without adaptation in the cells of certain reptile species when the ambient temperature rises.
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Affiliation(s)
- Yulia Kononova
- Federal Research Center of Fundamental and Translational Medicine, The Federal State Budget Scientific Institution, Siberian Branch of the Russian Academy of Sciences, 2, Timakova St., Novosibirsk 630117, Russia; (Y.K.); (L.A.); (E.K.); (M.S.); (A.S.); (E.K.); (N.P.); (A.C.); (A.S.)
| | - Lyubov Adamenko
- Federal Research Center of Fundamental and Translational Medicine, The Federal State Budget Scientific Institution, Siberian Branch of the Russian Academy of Sciences, 2, Timakova St., Novosibirsk 630117, Russia; (Y.K.); (L.A.); (E.K.); (M.S.); (A.S.); (E.K.); (N.P.); (A.C.); (A.S.)
| | - Evgeniya Kazachkova
- Federal Research Center of Fundamental and Translational Medicine, The Federal State Budget Scientific Institution, Siberian Branch of the Russian Academy of Sciences, 2, Timakova St., Novosibirsk 630117, Russia; (Y.K.); (L.A.); (E.K.); (M.S.); (A.S.); (E.K.); (N.P.); (A.C.); (A.S.)
| | - Mariya Solomatina
- Federal Research Center of Fundamental and Translational Medicine, The Federal State Budget Scientific Institution, Siberian Branch of the Russian Academy of Sciences, 2, Timakova St., Novosibirsk 630117, Russia; (Y.K.); (L.A.); (E.K.); (M.S.); (A.S.); (E.K.); (N.P.); (A.C.); (A.S.)
| | - Svetlana Romanenko
- Institute of Molecular and Cellular Biology, Russian Academy of Sciences, Siberian Branch, Novosibirsk 630090, Russia; (S.R.); (A.P.); (Y.U.)
| | - Anastasia Proskuryakova
- Institute of Molecular and Cellular Biology, Russian Academy of Sciences, Siberian Branch, Novosibirsk 630090, Russia; (S.R.); (A.P.); (Y.U.)
| | - Yaroslav Utkin
- Institute of Molecular and Cellular Biology, Russian Academy of Sciences, Siberian Branch, Novosibirsk 630090, Russia; (S.R.); (A.P.); (Y.U.)
| | - Marina Gulyaeva
- Federal Research Center of Fundamental and Translational Medicine, The Federal State Budget Scientific Institution, Siberian Branch of the Russian Academy of Sciences, 2, Timakova St., Novosibirsk 630117, Russia; (Y.K.); (L.A.); (E.K.); (M.S.); (A.S.); (E.K.); (N.P.); (A.C.); (A.S.)
- The Department of Natural Science, Novosibirsk State University, 2, Pirogova St., Novosibirsk 630090, Russia
| | - Anastasia Spirina
- Federal Research Center of Fundamental and Translational Medicine, The Federal State Budget Scientific Institution, Siberian Branch of the Russian Academy of Sciences, 2, Timakova St., Novosibirsk 630117, Russia; (Y.K.); (L.A.); (E.K.); (M.S.); (A.S.); (E.K.); (N.P.); (A.C.); (A.S.)
| | - Elena Kazachinskaia
- Federal Research Center of Fundamental and Translational Medicine, The Federal State Budget Scientific Institution, Siberian Branch of the Russian Academy of Sciences, 2, Timakova St., Novosibirsk 630117, Russia; (Y.K.); (L.A.); (E.K.); (M.S.); (A.S.); (E.K.); (N.P.); (A.C.); (A.S.)
| | - Natalia Palyanova
- Federal Research Center of Fundamental and Translational Medicine, The Federal State Budget Scientific Institution, Siberian Branch of the Russian Academy of Sciences, 2, Timakova St., Novosibirsk 630117, Russia; (Y.K.); (L.A.); (E.K.); (M.S.); (A.S.); (E.K.); (N.P.); (A.C.); (A.S.)
| | - Oksana Mishchenko
- 48 Central Research Institute of the Ministry of Defense of the Russian Federation, Moscow 141306, Russia;
| | - Alexander Chepurnov
- Federal Research Center of Fundamental and Translational Medicine, The Federal State Budget Scientific Institution, Siberian Branch of the Russian Academy of Sciences, 2, Timakova St., Novosibirsk 630117, Russia; (Y.K.); (L.A.); (E.K.); (M.S.); (A.S.); (E.K.); (N.P.); (A.C.); (A.S.)
| | - Alexander Shestopalov
- Federal Research Center of Fundamental and Translational Medicine, The Federal State Budget Scientific Institution, Siberian Branch of the Russian Academy of Sciences, 2, Timakova St., Novosibirsk 630117, Russia; (Y.K.); (L.A.); (E.K.); (M.S.); (A.S.); (E.K.); (N.P.); (A.C.); (A.S.)
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10
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Hastie KM, Melnik LI, Cross RW, Klitting RM, Andersen KG, Saphire EO, Garry RF. The Arenaviridae Family: Knowledge Gaps, Animal Models, Countermeasures, and Prototype Pathogens. J Infect Dis 2023; 228:S359-S375. [PMID: 37849403 PMCID: PMC10582522 DOI: 10.1093/infdis/jiac266] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2023] Open
Abstract
Lassa virus (LASV), Junin virus (JUNV), and several other members of the Arenaviridae family are capable of zoonotic transfer to humans and induction of severe viral hemorrhagic fevers. Despite the importance of arenaviruses as potential pandemic pathogens, numerous gaps exist in scientific knowledge pertaining to this diverse family, including gaps in understanding replication, immunosuppression, receptor usage, and elicitation of neutralizing antibody responses, that in turn complicates development of medical countermeasures. A further challenge to the development of medical countermeasures for arenaviruses is the requirement for use of animal models at high levels of biocontainment, where each model has distinct advantages and limitations depending on, availability of space, animals species-specific reagents, and most importantly the ability of the model to faithfully recapitulate human disease. Designation of LASV and JUNV as prototype pathogens can facilitate progress in addressing the public health challenges posed by members of this important virus family.
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Affiliation(s)
- Kathryn M Hastie
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, La Jolla, California, USA
| | - Lilia I Melnik
- Department of Microbiology and Immunology, Tulane University School of Medicine, New Orleans, Louisiana, USA
| | - Robert W Cross
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston National Laboratory, Galveston, Texas, USA
| | - Raphaëlle M Klitting
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, California, USA
- Scripps Research Translational Institute, La Jolla, California, USA
| | - Kristian G Andersen
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, California, USA
- Scripps Research Translational Institute, La Jolla, California, USA
| | - Erica Ollmann Saphire
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, La Jolla, California, USA
- Department of Medicine, University of California San Diego, La Jolla, California, USA
| | - Robert F Garry
- Department of Microbiology and Immunology, Tulane University School of Medicine, New Orleans, Louisiana, USA
- Zalgen Labs LLC, Frederick, Maryland, USA
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11
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Grimwood RM, Fortune-Kelly G, Holmes EC, Ingram T, Geoghegan JL. Host specificity shapes fish viromes across lakes on an isolated remote island. Virology 2023; 587:109884. [PMID: 37757732 DOI: 10.1016/j.virol.2023.109884] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2023] [Revised: 09/03/2023] [Accepted: 09/11/2023] [Indexed: 09/29/2023]
Abstract
Fish viromes often provide insights into the origin and evolution of viruses affecting tetrapods, including those associated with imporant human diseases. However, despite fish being the most diverse vertebrate group, their viruses are still understudied. We investigated the viromes of fish on Chatham Island (Rēkohu), a geographically isolated island housing 9% of New Zealand's threatened endemic fish species. Using metatranscriptomics, we analyzed samples from seven host species across 16 waterbodies. We identified 19 fish viruses, including 16 potentially novel species, expanding families such as the Coronaviridae, Hantaviridae, Poxviridae, and the recently proposed Tosoviridae. Surprisingly, virome composition was not influenced by the ecological factors measured and smelt (Retropinna retropinna) viromes were consistent across lakes despite differences in host life history, seawater influence, and community richness. Overall, fish viromes across Rēkohu were highly diverse and revealed a long history of co-divergence between host and virus despite their unique and geographically isolated ecosystem.
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Affiliation(s)
- Rebecca M Grimwood
- Department of Microbiology and Immunology, University of Otago, Dunedin, 9016, New Zealand
| | | | - Edward C Holmes
- Sydney Institute for Infectious Diseases, School of Medical Sciences, University of Sydney, Sydney, NSW, 2006, Australia
| | - Travis Ingram
- Department of Zoology, University of Otago, Dunedin, 9016, New Zealand
| | - Jemma L Geoghegan
- Department of Microbiology and Immunology, University of Otago, Dunedin, 9016, New Zealand; Institute of Environmental Science and Research, Wellington, 5018, New Zealand.
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12
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Slanina H, Madhugiri R, Wenk K, Reinke T, Schultheiß K, Schultheis J, Karl N, Linne U, Ziebuhr J. Conserved Characteristics of NMPylation Activities of Alpha- and Betacoronavirus NiRAN Domains. J Virol 2023; 97:e0046523. [PMID: 37199624 PMCID: PMC10308930 DOI: 10.1128/jvi.00465-23] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2023] [Accepted: 04/28/2023] [Indexed: 05/19/2023] Open
Abstract
Coronavirus genome replication and expression are mediated by the viral replication-transcription complex (RTC) which is assembled from multiple nonstructural proteins (nsp). Among these, nsp12 represents the central functional subunit. It harbors the RNA-directed RNA polymerase (RdRp) domain and contains, at its N terminus, an additional domain called NiRAN which is widely conserved in coronaviruses and other nidoviruses. In this study, we produced bacterially expressed coronavirus nsp12s to investigate and compare NiRAN-mediated NMPylation activities from representative alpha- and betacoronaviruses. We found that the four coronavirus NiRAN domains characterized to date have a number of conserved properties, including (i) robust nsp9-specific NMPylation activities that appear to operate largely independently of the C-terminal RdRp domain, (ii) nucleotide substrate preference for UTP followed by ATP and other nucleotides, (iii) dependence on divalent metal ions, with Mn2+ being preferred over Mg2+, and (iv) a key role of N-terminal residues (particularly Asn2) of nsp9 for efficient formation of a covalent phosphoramidate bond between NMP and the N-terminal amino group of nsp9. In this context, a mutational analysis confirmed the conservation and critical role of Asn2 across different subfamilies of the family Coronaviridae, as shown by studies using chimeric coronavirus nsp9 variants in which six N-terminal residues were replaced with those from other corona-, pito- and letovirus nsp9 homologs. The combined data of this and previous studies reveal a remarkable degree of conservation among coronavirus NiRAN-mediated NMPylation activities, supporting a key role of this enzymatic activity in viral RNA synthesis and processing. IMPORTANCE There is strong evidence that coronaviruses and other large nidoviruses evolved a number of unique enzymatic activities, including an additional RdRp-associated NiRAN domain, that are conserved in nidoviruses but not in most other RNA viruses. Previous studies of the NiRAN domain mainly focused on severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and suggested different functions for this domain, such as NMPylation/RNAylation of nsp9, RNA guanylyltransferase activities involved in canonical and/or unconventional RNA capping pathways, and other functions. To help resolve partly conflicting information on substrate specificities and metal ion requirements reported previously for the SARS-CoV-2 NiRAN NMPylation activity, we extended these earlier studies by characterizing representative alpha- and betacoronavirus NiRAN domains. The study revealed that key features of NiRAN-mediated NMPylation activities, such as protein and nucleotide specificity and metal ion requirements, are very well conserved among genetically divergent coronaviruses, suggesting potential avenues for future antiviral drug development targeting this essential viral enzyme.
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Affiliation(s)
- Heiko Slanina
- Institute of Medical Virology, Justus Liebig University, Giessen, Germany
| | | | - Kai Wenk
- Institute of Medical Virology, Justus Liebig University, Giessen, Germany
| | - Tess Reinke
- Institute of Medical Virology, Justus Liebig University, Giessen, Germany
| | - Karin Schultheiß
- Institute of Medical Virology, Justus Liebig University, Giessen, Germany
| | - Julia Schultheis
- Institute of Medical Virology, Justus Liebig University, Giessen, Germany
| | - Nadja Karl
- Institute of Medical Virology, Justus Liebig University, Giessen, Germany
| | - Uwe Linne
- Mass Spectrometry Facility, Department of Chemistry, Philipps University, Marburg, Germany
| | - John Ziebuhr
- Institute of Medical Virology, Justus Liebig University, Giessen, Germany
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13
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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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14
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Luo XL, Lu S, Qin C, Shi M, Lu XB, Wang L, Ga S, Jin D, Ma XL, Yang J, Dai Y, Bao LL, Cheng YP, Ge YJ, Bai YB, Zhu WT, Pu J, Sun H, Huang YY, Xu MC, Lei WJ, Dong K, Yang CX, Jiao YF, Lv Q, Li FD, Xu J. Emergence of an ancient and pathogenic mammarenavirus. Emerg Microbes Infect 2023; 12:e2192816. [PMID: 36939609 DOI: 10.1080/22221751.2023.2192816] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/21/2023]
Abstract
ABSTRACTEmerging zoonoses of wildlife origin caused by previously unknown agents are one of the most important challenges for human health. The Qinghai-Tibet Plateau represents a unique ecological niche with diverse wildlife that harbors several human pathogens and numerous previously uncharacterized pathogens. In this study, we identified and characterized a novel arenavirus (namely, plateau pika virus, PPV) from plateau pikas (Ochotona curzoniae) on the Qinghai-Tibet Plateau by virome analysis. Isolated PPV strains could replicate in several mammalian cells. We further investigated PPV pathogenesis using animal models. PPV administered via an intraventricular route caused trembling and sudden death in IFNαβR-/- mice, and pathological inflammatory lesions in brain tissue were observed. According to a retrospective serological survey in the geographical region where PPV was isolated, PPV-specific IgG antibodies were detected in 8 (2.4%) of 335 outpatients with available sera. Phylogenetic analyses revealed that this virus was clearly separated from previously reported New and Old World mammarenaviruses. Under the co-speciation framework, the estimated divergence time of PPV was 77-88 million years ago (MYA), earlier than that of OW and NW mammarenaviruses (26-34 MYA).
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Affiliation(s)
- Xue-Lian Luo
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Changping, Beijing 102206, China.,Department of Laboratorial Science and Technology & Vaccine Research Center, School of Public Health, Peking University, Beijing, China.,Research Units of Discovery of Unknown Bacteria and Function, Chinese Academy of Medical Sciences, Beijing, China.,Department of Epidemiology, School of Public Health, Shanxi Medical University, Taiyuan, Shanxi province, China
| | - Shan Lu
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Changping, Beijing 102206, China.,Department of Laboratorial Science and Technology & Vaccine Research Center, School of Public Health, Peking University, Beijing, China.,Research Units of Discovery of Unknown Bacteria and Function, Chinese Academy of Medical Sciences, Beijing, China.,Department of Epidemiology, School of Public Health, Shanxi Medical University, Taiyuan, Shanxi province, China
| | - Chuan Qin
- Key Laboratory of Human Disease Comparative Medicine, Chinese Ministry of Health, Beijing Key Laboratory for Animal Models of Emerging and Remerging Infectious Diseases, Institute of Laboratory Animal Science, Chinese Academy of Medical Sciences and Comparative Medicine Center, Peking Union Medical College, Beijing, China
| | - Mang Shi
- The Center for Infection & Immunity Study, School of Medicine, Shenzhen campus of Sun Yat-sen University, Shenzhen, People's Republic of China
| | - Xiao-Bo Lu
- Infectious diseases department, First Affiliated Hospital, Xinjiang Medical University, Urumqi, Xinjiang Autonomous Region, China
| | - Lu Wang
- Kashi Center for Disease Control and Prevention, Kashi, Xinjiang Autonomous Region, China
| | - Sang Ga
- Yushu Prefecture Center for Disease Control and Prevention, Yushu, Qinghai Province, China
| | - Dong Jin
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Changping, Beijing 102206, China
| | - Xin-Li Ma
- Kashi first people's hospital, Kashi, Xinjiang Autonomous Region, China
| | - Jing Yang
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Changping, Beijing 102206, China
| | - Yan Dai
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Changping, Beijing 102206, China
| | - Lin-Lin Bao
- Key Laboratory of Human Disease Comparative Medicine, Chinese Ministry of Health, Beijing Key Laboratory for Animal Models of Emerging and Remerging Infectious Diseases, Institute of Laboratory Animal Science, Chinese Academy of Medical Sciences and Comparative Medicine Center, Peking Union Medical College, Beijing, China
| | - Yan-Peng Cheng
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Changping, Beijing 102206, China.,Department of Epidemiology, School of Public Health, Shanxi Medical University, Taiyuan, Shanxi province, China
| | - Ya-Jun Ge
- Department of Laboratorial Science and Technology & Vaccine Research Center, School of Public Health, Peking University, Beijing, China
| | - Yi-Bo Bai
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Changping, Beijing 102206, China.,Department of Epidemiology, School of Public Health, Shanxi Medical University, Taiyuan, Shanxi province, China
| | - Wen-Tao Zhu
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Changping, Beijing 102206, China
| | - Ji Pu
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Changping, Beijing 102206, China
| | - Hui Sun
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Changping, Beijing 102206, China
| | - Yu-Yuan Huang
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Changping, Beijing 102206, China
| | - Ming-Chao Xu
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Changping, Beijing 102206, China
| | - Wen-Jing Lei
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Changping, Beijing 102206, China.,Department of Epidemiology, School of Public Health, Shanxi Medical University, Taiyuan, Shanxi province, China
| | - Kui Dong
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Changping, Beijing 102206, China.,Department of Epidemiology, School of Public Health, Shanxi Medical University, Taiyuan, Shanxi province, China
| | - Cai-Xin Yang
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Changping, Beijing 102206, China.,Department of Epidemiology, School of Public Health, Shanxi Medical University, Taiyuan, Shanxi province, China
| | - Yi-Fan Jiao
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Changping, Beijing 102206, China.,Department of Epidemiology, School of Public Health, Shanxi Medical University, Taiyuan, Shanxi province, China
| | - Qi Lv
- Key Laboratory of Human Disease Comparative Medicine, Chinese Ministry of Health, Beijing Key Laboratory for Animal Models of Emerging and Remerging Infectious Diseases, Institute of Laboratory Animal Science, Chinese Academy of Medical Sciences and Comparative Medicine Center, Peking Union Medical College, Beijing, China
| | - Feng-Di Li
- Key Laboratory of Human Disease Comparative Medicine, Chinese Ministry of Health, Beijing Key Laboratory for Animal Models of Emerging and Remerging Infectious Diseases, Institute of Laboratory Animal Science, Chinese Academy of Medical Sciences and Comparative Medicine Center, Peking Union Medical College, Beijing, China
| | - Jianguo Xu
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Changping, Beijing 102206, China.,Department of Laboratorial Science and Technology & Vaccine Research Center, School of Public Health, Peking University, Beijing, China.,Research Units of Discovery of Unknown Bacteria and Function, Chinese Academy of Medical Sciences, Beijing, China.,Department of Epidemiology, School of Public Health, Shanxi Medical University, Taiyuan, Shanxi province, China.,Institute of Public Health, Nankai University, Tianjin, China
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15
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Mammarenavirus Genetic Diversity and Its Biological Implications. Curr Top Microbiol Immunol 2023; 439:265-303. [PMID: 36592249 DOI: 10.1007/978-3-031-15640-3_8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Members of the family Arenaviridae are classified into four genera: Antennavirus, Hartmanivirus, Mammarenavirus, and Reptarenavirus. Reptarenaviruses and hartmaniviruses infect (captive) snakes and have been shown to cause boid inclusion body disease (BIBD). Antennaviruses have genomes consisting of 3, rather than 2, segments, and were discovered in actinopterygian fish by next-generation sequencing but no biological isolate has been reported yet. The hosts of mammarenaviruses are mainly rodents and infections are generally asymptomatic. Current knowledge about the biology of reptarenaviruses, hartmaniviruses, and antennaviruses is very limited and their zoonotic potential is unknown. In contrast, some mammarenaviruses are associated with zoonotic events that pose a threat to human health. This review will focus on mammarenavirus genetic diversity and its biological implications. Some mammarenaviruses including lymphocytic choriomeningitis virus (LCMV) are excellent experimental model systems for the investigation of acute and persistent viral infections, whereas others including Lassa (LASV) and Junin (JUNV) viruses, the causative agents of Lassa fever (LF) and Argentine hemorrhagic fever (AHF), respectively, are important human pathogens. Mammarenaviruses were thought to have high degree of intra-and inter-species amino acid sequence identities, but recent evidence has revealed a high degree of mammarenavirus genetic diversity in the field. Moreover, closely related mammarenavirus can display dramatic phenotypic differences in vivo. These findings support a role of genetic variability in mammarenavirus adaptability and pathogenesis. Here, we will review the molecular biology of mammarenaviruses, phylogeny, and evolution, as well as the quasispecies dynamics of mammarenavirus populations and their biological implications.
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16
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Neuromasts and Olfactory Organs of Zebrafish Larvae Represent Possible Sites of SARS-CoV-2 Pseudovirus Host Cell Entry. J Virol 2022; 96:e0141822. [PMID: 36448804 PMCID: PMC9769390 DOI: 10.1128/jvi.01418-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022] Open
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the causative agent of the acute respiratory disease coronavirus disease 2019 (COVID-19), which has resulted in millions of deaths globally. Here, we explored the mechanism of host cell entry of a luciferase-ZsGreen spike (SARS-CoV-2)-pseudotyped lentivirus using zebrafish embryos/larvae as an in vivo model. Successful pseudovirus entry was demonstrated via the expression of the luciferase (luc) gene, which was validated by reverse transcription-PCR (RT-PCR). Treatment of larvae with chloroquine (a broad-spectrum viral inhibitor that blocks membrane fusion) or bafilomycin A1 (a specific inhibitor of vacuolar proton ATPases, which blocks endolysosomal trafficking) significantly reduced luc expression, indicating the possible involvement of the endolysosomal system in the viral entry mechanism. The pharmacological inhibition of two-pore channel (TPC) activity or use of the tpcn2dhkz1a mutant zebrafish line also led to diminished luc expression. The localized expression of ACE2 and TPC2 in the anterior neuromasts and the forming olfactory organs was demonstrated, and the occurrence of endocytosis in both locations was confirmed. Together, our data indicate that zebrafish embryos/larvae are a viable and tractable model to explore the mechanism of SARS-CoV-2 host cell entry, that the peripheral sense organs are a likely site for viral host cell entry, and that TPC2 plays a key role in the translocation of the virus through the endolysosomal system. IMPORTANCE Despite the development of effective vaccines to combat the COVID-19 pandemic, which help prevent the most life-threatening symptoms, full protection cannot be guaranteed, especially with the emergence of new viral variants. Moreover, some resistance to vaccination remains in certain age groups and cultures. As such, there is an urgent need for the development of new strategies and therapies to help combat this deadly disease. Here, we provide compelling evidence that the peripheral sensory organs of zebrafish possess several key components required for SARS-CoV-2 host cell entry. The nearly transparent larvae provide a most amenable complementary platform to investigate the key steps of viral entry into host cells, as well as its spread through the tissues and organs. This will help in the identification of key viral entry steps for therapeutic intervention, provide an inexpensive model for screening novel antiviral compounds, and assist in the development of new and more effective vaccines.
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17
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Focus on Marine Animal Safety and Marine Bioresources in Response to the SARS-CoV-2 Crisis. Int J Mol Sci 2022; 23:ijms232315136. [PMID: 36499463 PMCID: PMC9737530 DOI: 10.3390/ijms232315136] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2022] [Revised: 11/18/2022] [Accepted: 11/29/2022] [Indexed: 12/04/2022] Open
Abstract
SARS-CoV-2 as a zoonotic virus has significantly affected daily life and social behavior since its outbreak in late 2019. The concerns over its transmission through different media directly or indirectly have evoked great attention about the survival of SARS-CoV-2 virions in the environment and its potential infection of other animals. To evaluate the risk of infection by SARS-CoV-2 and to counteract the COVID-19 disease, extensive studies have been performed to understand SARS-CoV-2 biogenesis and its pathogenesis. This review mainly focuses on the molecular architecture of SARS-CoV-2, its potential for infecting marine animals, and the prospect of drug discovery using marine natural products to combat SARS-CoV-2. The main purposes of this review are to piece together progress in SARS-CoV-2 functional genomic studies and antiviral drug development, and to raise our awareness of marine animal safety on exposure to SARS-CoV-2.
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18
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Glidden CK, Field LC, Bachhuber S, Hennessey SM, Cates R, Cohen L, Crockett E, Degnin M, Feezell MK, Fulton‐Bennett HK, Pires D, Poirson BN, Randell ZH, White E, Gravem SA. Strategies for managing marine disease. ECOLOGICAL APPLICATIONS : A PUBLICATION OF THE ECOLOGICAL SOCIETY OF AMERICA 2022; 32:e2643. [PMID: 35470930 PMCID: PMC9786832 DOI: 10.1002/eap.2643] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/25/2021] [Accepted: 02/24/2022] [Indexed: 06/14/2023]
Abstract
The incidence of emerging infectious diseases (EIDs) has increased in wildlife populations in recent years and is expected to continue to increase with global environmental change. Marine diseases are relatively understudied compared with terrestrial diseases but warrant parallel attention as they can disrupt ecosystems, cause economic loss, and threaten human livelihoods. Although there are many existing tools to combat the direct and indirect consequences of EIDs, these management strategies are often insufficient or ineffective in marine habitats compared with their terrestrial counterparts, often due to fundamental differences between marine and terrestrial systems. Here, we first illustrate how the marine environment and marine organism life histories present challenges and opportunities for wildlife disease management. We then assess the application of common disease management strategies to marine versus terrestrial systems to identify those that may be most effective for marine disease outbreak prevention, response, and recovery. Finally, we recommend multiple actions that will enable more successful management of marine wildlife disease emergencies in the future. These include prioritizing marine disease research and understanding its links to climate change, improving marine ecosystem health, forming better monitoring and response networks, developing marine veterinary medicine programs, and enacting policy that addresses marine and other wildlife diseases. Overall, we encourage a more proactive rather than reactive approach to marine wildlife disease management and emphasize that multidisciplinary collaborations are crucial to managing marine wildlife health.
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Affiliation(s)
- Caroline K. Glidden
- Department of Integrative BiologyOregon State UniversityCorvallisOregonUSA
- Present address:
Department of BiologyStanford UniversityStanfordCaliforniaUSA
| | - Laurel C. Field
- Department of Integrative BiologyOregon State UniversityCorvallisOregonUSA
| | - Silke Bachhuber
- Department of Integrative BiologyOregon State UniversityCorvallisOregonUSA
| | | | - Robyn Cates
- College of Veterinary MedicineOregon State UniversityCorvallisOregonUSA
| | - Lesley Cohen
- College of Veterinary MedicineOregon State UniversityCorvallisOregonUSA
| | - Elin Crockett
- College of Veterinary MedicineOregon State UniversityCorvallisOregonUSA
| | - Michelle Degnin
- College of Veterinary MedicineOregon State UniversityCorvallisOregonUSA
| | - Maya K. Feezell
- Department of Integrative BiologyOregon State UniversityCorvallisOregonUSA
| | | | - Devyn Pires
- College of Veterinary MedicineOregon State UniversityCorvallisOregonUSA
| | | | - Zachary H. Randell
- Department of Integrative BiologyOregon State UniversityCorvallisOregonUSA
| | - Erick White
- Department of Integrative BiologyOregon State UniversityCorvallisOregonUSA
| | - Sarah A. Gravem
- Department of Integrative BiologyOregon State UniversityCorvallisOregonUSA
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19
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Abstract
Mammarenaviruses establish a persistent infection in their rodent and bat hosts, and the evidence suggests that reptarenaviruses and hartmaniviruses found in captive snakes act similarly. In snakes, reptarenaviruses cause boid inclusion body disease (BIBD), which is often associated with secondary infections. Snakes with BIBD usually carry more than a single pair of reptarenavirus S and L segments and occasionally demonstrate hartmanivirus coinfection. Here, we reported the generation of cell lines persistently infected with a single or two reptarenavirus(es) and a cell line with persistent reptarenavirus-hartmanivirus coinfection. By RT-PCR we demonstrated that the amount of viral RNA within the persistently infected cells remains at levels similar to those observed following initial infection. Using antibodies against the glycoproteins (GPs) and nucleoprotein (NP) of reptarenaviruses, we studied the levels of viral protein in cells passaged 10 times after the original inoculation and observed that the expression of GPs declines dramatically during persistent infection, unlike the expression of NP. Immunofluorescence (IF) staining served to demonstrate differences in the distribution of NP within the persistently infected compared to freshly infected cells. IF staining of cells inoculated with the viruses secreted from the persistently infected cell lines produced similar NP staining compared to cells infected with a traditionally passaged virus, suggesting that the altered NP expression pattern of persistently infected cells does not relate to changes in the virus. The cell cultures described herein can serve as tools for studying the coinfection and superinfection interplay between reptarenaviruses and studying the BIBD pathogenesis mechanisms. IMPORTANCE Mammarenaviruses cause a persistent infection in their natural rodent and bat hosts. Reptarenaviruses cause boid inclusion body disease (BIBD) in constrictor snakes, but it is unclear whether snakes are the natural host of these viruses. In this study, we showed that reptarenaviruses established a persistent infection in cultured Boa constrictor cells and that the persistently infected cells continued to produce infectious virus. Our results showed that persistent infection results from subsequent passaging of cells inoculated with a single reptarenavirus, two reptarenaviruses, or even when inoculating the cells with reptarenavirus and hartmanivirus (another arenavirus genus). The results further suggested that coinfection would not result in overt competition between the different reptarenaviruses, thus helping to explain the frequent reptarenavirus coinfections in snakes with BIBD. The established cell culture models of persistent infection could help to elucidate the role of coinfection and superinfection and potential immunosuppression as the pathogenic mechanisms behind BIBD.
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20
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Meyers TR, Hickey N. A Perspective: Molecular Detections of New Agents in Finfish-Interpreting Biological Significance for Fish Health Management. JOURNAL OF AQUATIC ANIMAL HEALTH 2022; 34:47-57. [PMID: 35384072 DOI: 10.1002/aah.10155] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/17/2021] [Revised: 12/31/2021] [Accepted: 03/31/2022] [Indexed: 06/14/2023]
Abstract
The increased sensitivity of advanced molecular techniques greatly exceeds the sensitivities of traditional detection methods for infectious agents. This sensitivity causes difficulty in interpreting the biological significance of such detections in fish (and shellfish), especially when the agent(s) cannot be cultured in the laboratory. In the Pacific Northwest, including Canada and Alaska, molecular detections of "new" (unknown or known but discovered in a different geographic location or fish host) potentially infectious agents in fish have received extensive media attention and misinterpretation that call for resource agencies to change current fish health surveillance practices or policies to include these agents. Fish health specialists from several of these agencies and organizations (see Acknowledgments) advise that any policy changes should be made only after further investigations to avoid wasting resources to conduct surveillance for organisms that are not significant to fish health or for noninfectious genetic material that does not represent a viable agent. Molecular detection is not proof of agent viability within or on host tissues and requires further investigation regarding the agent's ability to replicate and evidence that the agent causes substantial risk of disease to exposed fish populations. This document provides examples of molecularly detected agents causing public concern that were accompanied by little or no data to provide context and assessment of biological significance, highlights important questions to be answered regarding these detections, and provides a suggested pathway of investigative criteria to determine viability and pathogenicity of such agents that are necessary for consideration of any changes to aquatic animal health practices and policies.
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Affiliation(s)
- Theodore R Meyers
- Alaska Department of Fish and Game, Commercial Fisheries Division, Post Office Box 115526, Juneau, Alaska, 99811, USA
| | - Nora Hickey
- Northwest Indian Fisheries Commission, 6730 Martin Way East, Olympia, Washington, 98516, USA
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21
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Tang X, Shang J, Sun Y. RdRp-based sensitive taxonomic classification of RNA viruses for metagenomic data. Brief Bioinform 2022; 23:6523411. [PMID: 35136930 PMCID: PMC8921650 DOI: 10.1093/bib/bbac011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2021] [Revised: 12/24/2021] [Accepted: 01/10/2022] [Indexed: 11/30/2022] Open
Abstract
With advances in library construction protocols and next-generation sequencing technologies, viral metagenomic sequencing has become the major source for novel virus discovery. Conducting taxonomic classification for metagenomic data is an important means to characterize the viral composition in the underlying samples. However, RNA viruses are abundant and highly diverse, jeopardizing the sensitivity of comparison-based classification methods. To improve the sensitivity of read-level taxonomic classification, we developed an RNA-dependent RNA polymerase (RdRp) gene-based read classification tool RdRpBin. It combines alignment-based strategy with machine learning models in order to fully exploit the sequence properties of RdRp. We tested our method and compared its performance with the state-of-the-art tools on the simulated and real sequencing data. RdRpBin competes favorably with all. In particular, when the query RNA viruses share low sequence similarity with the known viruses (\documentclass[12pt]{minimal}
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}{}$\sim 0.4$\end{document}), our tool can still maintain a higher F-score than the state-of-the-art tools. The experimental results on real data also showed that RdRpBin can classify more RNA viral reads with a relatively low false-positive rate. Thus, RdRpBin can be utilized to classify novel and diverged RNA viruses.
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Affiliation(s)
- Xubo Tang
- Department of Electrical Engineering, City University of Hong Kong, Tat Chee Avenue, Kowloon, Hong Kong, China SAR
| | - Jiayu Shang
- Department of Electrical Engineering, City University of Hong Kong, Tat Chee Avenue, Kowloon, Hong Kong, China SAR
| | - Yanni Sun
- Department of Electrical Engineering, City University of Hong Kong, Tat Chee Avenue, Kowloon, Hong Kong, China SAR
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22
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Edgar RC, Taylor B, Lin V, Altman T, Barbera P, Meleshko D, Lohr D, Novakovsky G, Buchfink B, Al-Shayeb B, Banfield JF, de la Peña M, Korobeynikov A, Chikhi R, Babaian A. Petabase-scale sequence alignment catalyses viral discovery. Nature 2022; 602:142-147. [PMID: 35082445 DOI: 10.1038/s41586-021-04332-2] [Citation(s) in RCA: 157] [Impact Index Per Article: 78.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2020] [Accepted: 12/10/2021] [Indexed: 01/20/2023]
Abstract
Public databases contain a planetary collection of nucleic acid sequences, but their systematic exploration has been inhibited by a lack of efficient methods for searching this corpus, which (at the time of writing) exceeds 20 petabases and is growing exponentially1. Here we developed a cloud computing infrastructure, Serratus, to enable ultra-high-throughput sequence alignment at the petabase scale. We searched 5.7 million biologically diverse samples (10.2 petabases) for the hallmark gene RNA-dependent RNA polymerase and identified well over 105 novel RNA viruses, thereby expanding the number of known species by roughly an order of magnitude. We characterized novel viruses related to coronaviruses, hepatitis delta virus and huge phages, respectively, and analysed their environmental reservoirs. To catalyse the ongoing revolution of viral discovery, we established a free and comprehensive database of these data and tools. Expanding the known sequence diversity of viruses can reveal the evolutionary origins of emerging pathogens and improve pathogen surveillance for the anticipation and mitigation of future pandemics.
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Affiliation(s)
| | - Brie Taylor
- Independent researcher, Vancouver, British Columbia, Canada
| | - Victor Lin
- Independent researcher, Seattle, WA, USA
| | | | - Pierre Barbera
- Computational Molecular Evolution Group, Heidelberg Institute for Theoretical Studies, Heidelberg, Germany
| | - Dmitry Meleshko
- Center for Algorithmic Biotechnology, St Petersburg State University, St Petersburg, Russia
- Tri-Institutional PhD Program in Computational Biology and Medicine, Weill Cornell Medical College, New York, NY, USA
| | | | - Gherman Novakovsky
- Bioinformatics Graduate Program, University of British Columbia, Vancouver, British Columbia, Canada
| | - Benjamin Buchfink
- Computational Biology Group, Max Planck Institute for Biology, Tübingen, Germany
| | - Basem Al-Shayeb
- Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley, CA, USA
| | - Jillian F Banfield
- Department of Earth and Planetary Science, University of California, Berkeley, Berkeley, CA, USA
| | - Marcos de la Peña
- Instituto de Biología Molecular y Celular de Plantas, Universidad Politécnica de Valencia-CSIC, Valencia, Spain
| | - Anton Korobeynikov
- Center for Algorithmic Biotechnology, St Petersburg State University, St Petersburg, Russia
- Department of Statistical Modelling, St Petersburg State University, St Petersburg, Russia
| | - Rayan Chikhi
- G5 Sequence Bioinformatics, Department of Computational Biology, Institut Pasteur, Paris, France
| | - Artem Babaian
- Independent researcher, Vancouver, British Columbia, Canada.
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23
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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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24
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Deeg CM, Kanzeparova AN, Somov AA, Esenkulova S, Di Cicco E, Kaukinen KH, Tabata A, Ming TJ, Li S, Mordecai G, Schulze A, Miller KM. Way out there: pathogens, health, and condition of overwintering salmon in the Gulf of Alaska. Facets (Ott) 2022. [DOI: 10.1139/facets-2021-0052] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
Salmon are keystone species across the North Pacific, supporting ecosystems, commercial opportunities, and cultural identity. Nevertheless, many wild salmon stocks have experienced significant declines. Salmon restoration efforts focus on fresh and coastal waters, but little is known about the open ocean environment. Here we use high throughput RT-qPCR tools to provide the first report on the health, condition, and infection profile of coho, chum, pink, and sockeye salmon in the Gulf of Alaska during the 2019 winter. We found lower infectious agent number, diversity, and burden compared with coastal British Columbia in all species except coho, which exhibited elevated stock-specific infection profiles. We identified Loma sp. and Ichthyophonus hoferi as key pathogens, suggesting transmission in the open ocean. Reduced prey availability, potentially linked to change in ocean conditions due to an El Niño event, correlated with energetic deficits and immunosuppression in salmon. Immunosuppressed individuals showed higher relative infection burden and higher prevalence of opportunistic pathogens. We highlight the cumulative effects of infection and environmental stressors on overwintering salmon, establishing a baseline to document the impacts of a changing ocean on salmon.
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Affiliation(s)
- Christoph M. Deeg
- Department of Forest & Conservation Science, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
- Pacific Salmon Foundation, Vancouver, BC V6J 4S6, Canada
| | | | - Alexei A. Somov
- Pacific branch of VNIRO (“TINRO”), Vladivostok, Russia 690091
| | | | | | - Karia H. Kaukinen
- Fisheries and Oceans Canada, Pacific Biological Station, Nanaimo, BC V9T 6N7, Canada
| | - Amy Tabata
- Fisheries and Oceans Canada, Pacific Biological Station, Nanaimo, BC V9T 6N7, Canada
| | - Tobi J. Ming
- Fisheries and Oceans Canada, Pacific Biological Station, Nanaimo, BC V9T 6N7, Canada
| | - Shaorong Li
- Fisheries and Oceans Canada, Pacific Biological Station, Nanaimo, BC V9T 6N7, Canada
| | - Gideon Mordecai
- Department of Medicine, University of British Columbia, Vancouver, BC V6T 1Z3, Canada
| | - Angela Schulze
- Fisheries and Oceans Canada, Pacific Biological Station, Nanaimo, BC V9T 6N7, Canada
| | - Kristina M. Miller
- Department of Forest & Conservation Science, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
- Fisheries and Oceans Canada, Pacific Biological Station, Nanaimo, BC V9T 6N7, Canada
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25
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Kuhn JH, Adkins S, Agwanda BR, Al Kubrusli R, Alkhovsky SV, Amarasinghe GK, Avšič-Županc T, Ayllón MA, Bahl J, Balkema-Buschmann A, Ballinger MJ, Basler CF, Bavari S, Beer M, Bejerman N, Bennett AJ, Bente DA, Bergeron É, Bird BH, Blair CD, Blasdell KR, Blystad DR, Bojko J, Borth WB, Bradfute S, Breyta R, Briese T, Brown PA, Brown JK, Buchholz UJ, Buchmeier MJ, Bukreyev A, Burt F, Büttner C, Calisher CH, Cao M, Casas I, Chandran K, Charrel RN, Cheng Q, Chiaki Y, Chiapello M, Choi IR, Ciuffo M, Clegg JCS, Crozier I, Dal Bó E, de la Torre JC, de Lamballerie X, de Swart RL, Debat H, Dheilly NM, Di Cicco E, Di Paola N, Di Serio F, Dietzgen RG, Digiaro M, Dolnik O, Drebot MA, Drexler JF, Dundon WG, Duprex WP, Dürrwald R, Dye JM, Easton AJ, Ebihara H, Elbeaino T, Ergünay K, Ferguson HW, Fooks AR, Forgia M, Formenty PBH, Fránová J, Freitas-Astúa J, Fu J, Fürl S, Gago-Zachert S, Gāo GF, García ML, García-Sastre A, Garrison AR, Gaskin T, Gonzalez JPJ, Griffiths A, Goldberg TL, Groschup MH, Günther S, Hall RA, Hammond J, Han T, Hepojoki J, Hewson R, Hong J, Hong N, Hongo S, Horie M, Hu JS, Hu T, Hughes HR, Hüttner F, Hyndman TH, Ilyas M, Jalkanen R, Jiāng D, Jonson GB, Junglen S, Kadono F, Kaukinen KH, Kawate M, Klempa B, Klingström J, Kobinger G, Koloniuk I, Kondō H, Koonin EV, Krupovic M, Kubota K, Kurath G, Laenen L, Lambert AJ, Langevin SL, Lee B, Lefkowitz EJ, Leroy EM, Li S, Li L, Lǐ J, Liu H, Lukashevich IS, Maes P, de Souza WM, Marklewitz M, Marshall SH, Marzano SYL, Massart S, McCauley JW, Melzer M, Mielke-Ehret N, Miller KM, Ming TJ, Mirazimi A, Mordecai GJ, Mühlbach HP, Mühlberger E, Naidu R, Natsuaki T, Navarro JA, Netesov SV, Neumann G, Nowotny N, Nunes MRT, Olmedo-Velarde A, Palacios G, Pallás V, Pályi B, Papa A, Paraskevopoulou S, Park AC, Parrish CR, Patterson DA, Pauvolid-Corrêa A, Pawęska JT, Payne S, Peracchio C, Pérez DR, Postler TS, Qi L, Radoshitzky SR, Resende RO, Reyes CA, Rima BK, Luna GR, Romanowski V, Rota P, Rubbenstroth D, Rubino L, Runstadler JA, Sabanadzovic S, Sall AA, Salvato MS, Sang R, Sasaya T, Schulze AD, Schwemmle M, Shi M, Shí X, Shí Z, Shimomoto Y, Shirako Y, Siddell SG, Simmonds P, Sironi M, Smagghe G, Smither S, Song JW, Spann K, Spengler JR, Stenglein MD, Stone DM, Sugano J, Suttle CA, Tabata A, Takada A, Takeuchi S, Tchouassi DP, Teffer A, Tesh RB, Thornburg NJ, Tomitaka Y, Tomonaga K, Tordo N, Torto B, Towner JS, Tsuda S, Tu C, Turina M, Tzanetakis IE, Uchida J, Usugi T, Vaira AM, Vallino M, van den Hoogen B, Varsani A, Vasilakis N, Verbeek M, von Bargen S, Wada J, Wahl V, Walker PJ, Wang LF, Wang G, Wang Y, Wang Y, Waqas M, Wèi T, Wen S, Whitfield AE, Williams JV, Wolf YI, Wu J, Xu L, Yanagisawa H, Yang C, Yang Z, Zerbini FM, Zhai L, Zhang YZ, Zhang S, Zhang J, Zhang Z, Zhou X. 2021 Taxonomic update of phylum Negarnaviricota (Riboviria: Orthornavirae), including the large orders Bunyavirales and Mononegavirales. Arch Virol 2021; 166:3513-3566. [PMID: 34463877 PMCID: PMC8627462 DOI: 10.1007/s00705-021-05143-6] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
In March 2021, following the annual International Committee on Taxonomy of Viruses (ICTV) ratification vote on newly proposed taxa, the phylum Negarnaviricota was amended and emended. The phylum was expanded by four families (Aliusviridae, Crepuscuviridae, Myriaviridae, and Natareviridae), three subfamilies (Alpharhabdovirinae, Betarhabdovirinae, and Gammarhabdovirinae), 42 genera, and 200 species. Thirty-nine species were renamed and/or moved and seven species were abolished. This article presents the updated taxonomy of Negarnaviricota as now accepted by the ICTV.
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Affiliation(s)
- Jens H Kuhn
- Integrated Research Facility at Fort Detrick, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Frederick, MD, USA.
| | - Scott Adkins
- United States Department of Agriculture, Agricultural Research Service, US Horticultural Research Laboratory, Fort Pierce, FL, USA
| | - Bernard R Agwanda
- Zoology Department, National Museums of Kenya, Nairobi, Kenya
- Jomo Kenyatta University of Agriculture & Technology, Nairobi, Kenya
| | - Rim Al Kubrusli
- Division Phytomedicine, Faculty of Life Sciences, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Sergey V Alkhovsky
- D.I. Ivanovsky Institute of Virology of N.F. Gamaleya National Center on Epidemiology and Microbiology of Ministry of Health of Russian Federation, Moscow, Russia
| | - 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, Universidad Politécnica de Madrid, Madrid, Spain
| | - Justin Bahl
- Center for Ecology of Infectious Diseases, Department of Infectious Diseases, Department of Epidemiology and Biostatistics, Insitute of Bioinformatics, University of Georgia, Athens, GA, USA
| | - Anne Balkema-Buschmann
- Institute of Novel and Emerging Infectious Diseases, Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Greifswald-Insel Riems, Germany
| | - Matthew J Ballinger
- Department of Biological Sciences, Mississippi State University, Mississippi State, MS, USA
| | - Christopher F Basler
- Center for Microbial Pathogenesis, Institute for Biomedical Sciences, Georgia State University, Atlanta, GA, USA
| | - Sina Bavari
- Edge BioInnovation Consulting and Mgt, Frederick, MD, USA
| | - Martin Beer
- Institute of Diagnostic Virology, Friedrich-Loeffler-Institut, Greifswald-Insel Riems, Germany
| | | | - Andrew J Bennett
- Genomics and Bioinformatics Department, Biological Defense Research Directorate, Naval Medical Research Center-Frederick, Fort Detrick, Frederick, MD, USA
| | | | - Éric Bergeron
- Viral Special Pathogens Branch, Division of High-Consequence Pathogens and Pathology, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Brian H Bird
- School of Veterinary Medicine, One Health Institute, University of California, Davis, Davis, CA, USA
| | - Carol D Blair
- Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, CO, USA
| | - Kim R Blasdell
- Commonwealth Scientific and Industrial Research Organisation (CSIRO), Australian Centre for Disease Preparedness, Geelong, VIC, Australia
| | | | - Jamie Bojko
- School of Health and Life Sciences, Teesside University, Middlesbrough, TS1 3BX, UK
- National Horizons Centre, Teesside University, Darlington, DL1 1HG, UK
| | | | - Steven Bradfute
- University of New Mexico Health Sciences Center, Albuquerque, NM, USA
| | - Rachel Breyta
- University of Washington, Seattle, WA, USA
- US Geological Survey, Western Fisheries Research Center, Seattle, WA, USA
| | - 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
- Laboratory of Ploufragan-Plouzané-Niort, French Agency for Food, Environmental and Occupational Heath Safety ANSES, Ploufragan, France
| | - Judith K Brown
- School of Plant Sciences, University of Arizona, Tucson, AZ, USA
| | - Ursula J Buchholz
- RNA Viruses Section, Laboratory of Infectious Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Michael J Buchmeier
- Department of Molecular Biology and Biochemistry, University of California, Irvine, Irvine, CA, USA
| | - Alexander Bukreyev
- Galveston National Laboratory, The University of Texas Medical Branch at Galveston, Galveston, TX, USA
| | - Felicity Burt
- Division of Virology, National Health Laboratory Service and Division of Virology, University of the Free State, Bloemfontein, Republic of South Africa
| | - Carmen Büttner
- Division Phytomedicine, Faculty of Life Sciences, Humboldt-Universität zu Berlin, Berlin, Germany
| | | | - Mengji Cao
- National Citrus Engineering and Technology Research Center, Citrus Research Institute, Southwest University, Beibei, Chongqing, People's Republic of China
| | - Inmaculada Casas
- Respiratory Virus and Influenza Unit, National Microbiology Center, Instituto de Salud Carlos III, Madrid, Spain
| | - Kartik Chandran
- Department of Microbiology and Immunology, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Rémi N Charrel
- Unité des Virus Emergents (Aix-Marseille Univ, IRD 190, Inserm 1207, IHU Méditerranée Infection), Marseille, France
| | - Qi Cheng
- State Key Laboratory of Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou, People's Republic of China
| | - Yuya Chiaki
- Grape and Persimmon Research Station, Institute of Fruit tree and Tea Science, NARO, Higashihiroshima, Hiroshima, Japan
| | - Marco Chiapello
- Institute for Sustainable Plant Protection, National Research Council of Italy (CNR), Strada delle Cacce 73, 10135, Turin, Italy
| | - Il-Ryong Choi
- Plant Breeding Genetics and Biotechnology Division and International Rice Research Institute, Los Baños, Philippines
| | - Marina Ciuffo
- Institute for Sustainable Plant Protection, National Research Council of Italy (CNR), Strada delle Cacce 73, 10135, Turin, Italy
| | | | - Ian Crozier
- Clinical Monitoring Research Program Directorate, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Elena Dal Bó
- CIDEFI, Facultad de Ciencias Agrarias y Forestales, Universidad de La Plata, La Plata, Argentina
| | - Juan Carlos de la Torre
- Department of Immunology and Microbiology IMM-6, The Scripps Research Institute, La Jolla, CA, USA
| | - Xavier de Lamballerie
- Unité des Virus Emergents (Aix-Marseille Univ, IRD 190, Inserm 1207, IHU Méditerranée Infection), Marseille, France
| | - Rik L de Swart
- Department Viroscience, Erasmus MC, University Medical Centre Rotterdam, Rotterdam, The Netherlands
| | - Humberto Debat
- Centro de Investigaciones Agropecuarias, Instituto Nacional de Tecnología Agropecuaria (IPAVE-CIAP-INTA), Córdoba, Argentina
- Unidad de Fitopatología y Modelización Agrícola, Consejo Nacional de Investigaciones Científicas y Técnicas (UFYMA-CONICET), Córdoba, Argentina
| | - Nolwenn M Dheilly
- UMR 1161 Virology ANSES/INRAE/ENVA, ANSES Animal Health Laboratory, 94704, Maisons-Alfort, France
| | | | - Nicholas Di Paola
- United States Army Medical Research Institute of Infectious Diseases, Fort Detrick, Frederick, MD, USA
| | - Francesco Di Serio
- Istituto per la Protezione Sostenibile delle Piante, Consiglio Nazionale delle Ricerche, Bari, Italy
| | - Ralf G Dietzgen
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St. Lucia, QLD, Australia
| | - Michele Digiaro
- CIHEAM, Istituto Agronomico Mediterraneo di Bari, Valenzano, Italy
| | - Olga Dolnik
- Institute of Virology, Philipps University Marburg, Marburg, Germany
| | - Michael A Drebot
- Zoonotic Diseases and Special Pathogens, National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, MB, Canada
| | - J Felix Drexler
- Institute of Virology, Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt Universität Berlin, Berlin, Germany
| | - William G Dundon
- Animal Production and Health Laboratory, Joint FAO/IAEA Division of Nuclear Techniques in Food and Agriculture, Department of Nuclear Sciences and Applications, 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
| | - Hideki Ebihara
- Department of Molecular Medicine, Mayo Clinic, Rochester, MN, USA
| | | | - Koray Ergünay
- Virology Unit, Department of Medical Microbiology, Hacettepe University Faculty of Medicine, Ankara, Turkey
| | - Hugh W Ferguson
- School of Veterinary Medicine, St. George's University, True Blue, Grenada
| | | | - Marco Forgia
- Institute for sustainable plant protection, CNR, Turin, Italy
| | | | - Jana Fránová
- Plant Virology Department, Institute of Plant Molecular Biology, Biology Centre CAS, Ceske Budejovice, Czech Republic
| | | | - Jingjing Fu
- College of Life Science and Engineering, Shenyang University, Shenyang, Liaoning, People's Republic of China
| | - Stephanie Fürl
- Albrecht Daniel Thaer-Institute for Crop and Animal Sciences, Division Phytomedicine, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Selma Gago-Zachert
- Institute of Biochemistry and Biotechnology, Martin Luther University Halle-Wittenberg, Halle/Saale, Germany
| | - George Fú Gāo
- National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, People's Republic of China
| | - María Laura García
- nstituto de Biotecnología y Biología Molecular, Facultad de Ciencias Exactas, I, CONICET UNLP, La Plata, Argentina
| | | | - Aura R Garrison
- United States Army Medical Research Institute of Infectious Diseases, Fort Detrick, Frederick, MD, USA
| | - Thomas Gaskin
- Division Phytomedicine, Faculty of Life Sciences, Humboldt-Universität zu Berlin, Berlin, Germany
- Landwirtschaft und Flurneuordnung, Landesamt für ländliche Entwicklung, Frankfurt (Oder), Germany
| | - Jean-Paul J Gonzalez
- Department of Microbiology and Immunology, Division of Biomedical Graduate Research Organization, School of Medicine, Georgetown University, Washington, DC, 20057, USA
- Centaurus Biotechnologies, CTP, Manassas, VA, USA
| | - Anthony Griffiths
- Department of Microbiology and National Emerging Infectious Diseases Laboratories, Boston University School of Medicine, Boston, MA, USA
| | - Tony L Goldberg
- Department of Pathobiological Sciences, School of Veterinary Medicine, University of Wisconsin-Madison, Madison, WI, USA
| | - Martin H Groschup
- Institute of Novel and Emerging Infectious Diseases, Friedrich-Loeffler-Institut, Greifswald-Insel Riems, Germany
| | - Stephan Günther
- WHO Collaborating Centre for Arboviruses and Hemorrhagic Fever Reference and Research, Department of Virology, Bernhard-Nocht Institute for Tropical Medicine, Hamburg, Germany
| | - Roy A Hall
- Australian Infectious Diseases Research Centre, School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Australia
| | - John Hammond
- Floral and Nursery Plants Research Unit, United States Department of Agriculture, Agricultural Research Service, USNA, Beltsville, MD, USA
| | - Tong Han
- College of Life Science and Engineering, Shenyang University, Shenyang, Liaoning, People's Republic of China
| | - Jussi Hepojoki
- Department of Virology, University of Helsinki, Medicum, Helsinki, Finland
- Institute of Veterinary Pathology, Vetsuisse Faculty, University of Zurich, Zurich, Switzerland
| | - Roger Hewson
- London School of Hygeine and Tropical Medicine, London, UK
| | - Jiang Hong
- Analysis Center of Agrobiology and Environmental Sciences, Zhejiang University, Hangzhou, People's Republic of China
| | - Ni Hong
- Key Lab of Plant Pathology of Hubei Province, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, People's Republic of China
| | - Seiji Hongo
- Department of Infectious Diseases, Yamagata University Faculty of Medicine, Yamagata, Japan
| | - Masayuki Horie
- Hakubi Center for Advanced Research, Kyoto University, Kyoto, Japan
- Division of Veterinary Sciences, Graduate School of Life and Environmental Sciences, Osaka Prefecture University, Izumisano, Japan
| | - John S Hu
- University of Hawaii, Honolulu, HI, USA
| | - Tao Hu
- State Key Laboratory of Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou, People's Republic of China
| | - Holly R Hughes
- Centers for Disease Control and Prevention, Fort Collins, CO, USA
| | - Florian Hüttner
- Division Phytomedicine, Faculty of Life Sciences, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Timothy H Hyndman
- School of Veterinary Medicine, Murdoch University, Murdoch, WA, Australia
| | - M Ilyas
- Entomology and Plant Pathology, North Carolina State University, Raleigh, NC, USA
| | | | - Dàohóng Jiāng
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, Hubei Province, People's Republic of China
| | - Gilda B Jonson
- Rice Breeding Innovations Platform, International Rice Research Institute, Los Baños, Laguna, Philippines
| | - Sandra Junglen
- Institute of Virology, Charité-Universitätsmedizin Berlin, Corporate Member of Free University Berlin, Humboldt-University Berlin, and Berlin Institute of Health, Berlin, Germany
- German Centre for Infection Research, Berlin, Germany
| | - Fujio Kadono
- Department of Clinical Plant Science, Faculty of Bioscience and Applied Chemistry, Hosei University, Koganei, Tokyo, Japan
| | - Karia H Kaukinen
- Pacific Biological Station, Fisheries and Oceans Canada, Nanaimo, BC, Canada
| | | | - Boris Klempa
- Institute of Virology, Biomedical Research Center, Slovak Academy of Sciences, Bratislava, Slovakia
| | - Jonas Klingström
- Center for Infectious Medicine, Department of Medicine Huddinge, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
| | - Gary Kobinger
- Department of Microbiology, Immunology and Infectious Diseases, Université Laval, Quebec City, Canada
| | - Igor Koloniuk
- Plant Virology Department, Institute of Plant Molecular Biology, Biology Centre CAS, Ceske Budejovice, Czech Republic
| | - Hideki Kondō
- Institute of Plant Science and Resources, Okayama University, Kurashiki, Japan
| | - Eugene V Koonin
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA
| | - Mart Krupovic
- Archaeal Virology Unit, Institut Pasteur, Paris, France
| | - Kenji Kubota
- Central Region Agricultural Research Center, NARO, Tsukuba, Ibaraki, Japan
| | - Gael Kurath
- US Geological Survey Western Fisheries Research Center, Seattle, WA, USA
| | - Lies Laenen
- KU Leuven, Rega Institute, Zoonotic Infectious Diseases unit, Leuven, Belgium
- Department of Laboratory Medicine, University Hospitals Leuven, Leuven, Belgium
| | - Amy J Lambert
- Centers for Disease Control and Prevention, Fort Collins, CO, USA
| | | | - Benhur Lee
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | | | - Eric M Leroy
- MIVEGEC (IRD-CNRS-Montpellier university) Unit, French National Research Institute for Sustainable Development (IRD), Montpellier, France
| | - Shaorong Li
- Fisheries and Oceans Canada, Pacific Biological Station, 3190 Hammond Bay Road, Nanaimo, BC, V9T 6N7, Canada
| | - Longhui Li
- Key Lab of Plant Pathology of Hubei Province, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, People's Republic of China
| | - Jiànróng Lǐ
- Department of Veterinary Biosciences, College of Veterinary Medicine, The Ohio State University, Columbus, OH, USA
| | - Huazhen Liu
- Key Lab of Plant Pathology of Hubei Province, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, People's Republic of China
| | - Igor S Lukashevich
- Department of Pharmacology and Toxicology, School of Medicine, and the Center for Predictive Medicine for Biodefense and Emerging Infectious Diseases, University of Louisville, Louisville, KY, USA
| | - Piet Maes
- KU Leuven, Rega Institute, Zoonotic Infectious Diseases unit, Leuven, Belgium
| | | | - Marco Marklewitz
- Institute of Virology, Charité-Universitätsmedizin Berlin, Corporate Member of Free University Berlin, Humboldt-University Berlin, and Berlin Institute of Health, Berlin, Germany
- German Center for Infection Research (DZIF), Berlin, Germany
| | - Sergio H Marshall
- Pontificia Universidad Católica de Valparaíso, Campus Curauma, Valparaíso, Chile
| | - Shin-Yi L Marzano
- United States Department of Agriculture, Agricultural Research Service , Washington, USA
| | - Sebastien Massart
- Gembloux Agro-Bio Tech, TERRA, Plant Pathology Laboratory, Liège University, Liege, Belgium
| | - John W McCauley
- Worldwide Influenza Centre, Francis Crick Institute, London, UK
| | - Michael Melzer
- Plant and Environmental Protection Sciences, University of Hawai'i at Mānoa, Honolulu, HI, USA
| | | | - Kristina M Miller
- Pacific Biological Station, Fisheries and Oceans Canada, Nanaimo, BC, Canada
| | - Tobi J Ming
- Molecular Genetics, Pacific Biological Station, Department of Fisheries and Oceans, Nanaimo, Canada
| | | | - Gideon J Mordecai
- Department of Medicine, Univeristy of British Columbia, Vancouver, Canada
| | | | - Elke Mühlberger
- Department of Microbiology and National Emerging Infectious Diseases Laboratories, Boston University School of Medicine, Boston, MA, USA
| | - Rayapati Naidu
- Department of Plant Pathology, Irrigated Agricultural Research and Extension Center, Washington State University, Prosser, WA, USA
| | - Tomohide Natsuaki
- School of Agriculture, Utsunomiya University, Utsunomiya, Tochigi, Japan
| | - José A Navarro
- Instituto de Biología Molecular y Celular de Plantas, Universitat Politècnica de València-Consejo Superior de Investigaciones Científicas, Valencia, Spain
| | - Sergey V Netesov
- Novosibirsk State University, Novosibirsk, Novosibirsk Oblast, Russia
| | - Gabriele Neumann
- Influenza Research Institute, Department of Pathobiological Sciences, University of Wisconsin-Madison, Madison, WI, USA
| | - Norbert Nowotny
- Institute of Virology, University of Veterinary Medicine Vienna, Vienna, Austria
- College of Medicine, Mohammed Bin Rashid University of Medicine and Health Sciences, Dubai, United Arab Emirates
| | | | | | - Gustavo Palacios
- United States Army Medical Research Institute of Infectious Diseases, Fort Detrick, Frederick, MD, USA
| | - Vicente Pallás
- Instituto de Biología Molecular y Celular de Plantas (IBMCP), Consejo Superior de Investigaciones Cientificas-Universidad Politécnica de Valencia, Valencia, Spain
| | - Bernadett Pályi
- National Biosafety Laboratory, National Public Health Center, Budapest, Hungary
| | - Anna Papa
- National Reference Centre for Arboviruses and Haemorrhagic Fever Viruses, Department of Microbiology, Medical School, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Sofia Paraskevopoulou
- Institute of Virology, Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany
| | - Adam C Park
- University of Hawaii, Honolulu, HI, USA
- Hawaii Department of Agriculture, Honolulu, HI, USA
| | - Colin R Parrish
- Baker Institute for Animal Health, College of Veterinary Medicine, Cornell University, Ithaca, NY, USA
| | - David A Patterson
- Fisheries and Oceans Canada, Resource and Environmental Management, Simon Fraser University, Burnaby, BC, Canada
| | - Alex Pauvolid-Corrêa
- Department of Veterinary Integrated Biosciences and Department of Entomology, Texas A&M University, College Station, USA
- Laboratory of Respiratory Viruses and Measles, Fiocruz, Rio de Janeiro, Brazil
| | - 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 Payne
- Department of Veterinary Pathobiology, College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, TX, USA
| | - Carlotta Peracchio
- Institute for Sustainable Plant Protection, National Research Council of Italy (CNR), Strada delle Cacce 73, 10135, Turin, Italy
| | - Daniel R Pérez
- Department of Population Health, College of Veterinary Medicine, University of Georgia, Athens, GA, USA
| | - Thomas S Postler
- Department of Microbiology and Immunology, Vagelos College of Physicians and Surgeons, Columbia University Irving Medical Center, New York, NY, 10032, USA
| | - Liying Qi
- Jiangxi Academy of Agricultural Sciences, Nanchang, Jiangxi, People's Republic of China
| | | | - Renato O Resende
- Departamento de Biologia Celular, Universidade de Brasília, Brasília, Brazil
| | - Carina A Reyes
- Instituto de Biotecnología y Biología Molecular, CCT-La Plata, CONICET-UNLP, La Plata, Buenos Aires, Argentina
| | - Bertus K Rima
- Centre for Experimental Medicine, School of Medicine, Dentistry and Biomedical Sciences, The Queen's University of Belfast, Belfast, Northern Ireland, UK
| | - Gabriel Robles Luna
- Instituto de Biotecnología y Biología Molecular, CCT-La Plata, CONICET-UNLP, La Plata, Buenos Aires, Argentina
| | - Víctor Romanowski
- Instituto de Biotecnología y Biología Molecular, Centro Cientifico Technológico-La Plata, Consejo Nacional de Investigaciones Científico Tecnológico-Universidad Nacional de La Plata, La Plata, Argentina
| | - 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
| | - Luisa Rubino
- Consiglio Nazionale delle Ricerche, Istituto per la Protezione Sostenibile delle Piante, Bari, Italy
| | - Jonathan A Runstadler
- Department of Infectious Disease and Global Health, Tufts University Cummings School of Veterinary Medicine, 200 Westboro Road, North Grafton, MA, 01536, USA
| | - Sead Sabanadzovic
- Department of Biochemistry, Molecular Biology, Entomology and Plant Pathology, Mississippi State University, Mississippi State, MS, USA
| | | | - Maria S Salvato
- Institute of Human Virology, University of Maryland School of Medicine, Baltimore, MA, USA
| | - Rosemary Sang
- International Centre of Insect Physiology and Ecology, Nairobi, Kenya
| | - Takahide Sasaya
- Institute for Plant Protection, National Agriculture and Food Research Organization, Tsukuba, Japan
| | - Angela D Schulze
- Molecular Genetics Lab, Pacific Biological Station, Fisheries and Oceans Canada, Nanaimo, BC, Canada
| | - Martin Schwemmle
- Faculty of Medicine, University Medical Center-University Freiburg, Freiburg, Germany
| | - Mang Shi
- Sun Yat-sen University, Shenzhen, People's Republic of China
| | - Xiǎohóng Shí
- MRC-University of Glasgow Centre for Virus Research, Glasgow, Scotland, UK
| | - Zhènglì Shí
- CAS Key Laboratory of Special Pathogens, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, Hubei, People's Republic of China
| | | | - Yukio Shirako
- Asian Center for Bioresources and Environmental Sciences, University of Tokyo, Tokyo, Japan
| | - Stuart G Siddell
- School of Cellular and Molecular Medicine, University of Bristol, Bristol, UK
| | - Peter Simmonds
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Manuela Sironi
- Bioinformatics Unit, Scientific Institute IRCCS "E. Medea", Bosisio Parini, Italy
| | - Guy Smagghe
- Faculty of Bioscience Engineering, Department of Plants and Crops, Ghent University, Ghent, Belgium
| | - Sophie Smither
- CBR Division, DSTL, Porton Down, Salisbury, Wiltshire, UK
| | - Jin-Won Song
- Department of Microbiology, College of Medicine, Korea University, Seoul, Republic of Korea
| | - Kirsten Spann
- School of Biomedical Sciences, Faculty of Health, Queensland University of Technology, Brisbane, QLD, Australia
| | - Jessica R Spengler
- Viral Special Pathogens Branch, Division of High-Consequence Pathogens and Pathology, Centers for Disease Control and Prevention, Atlanta, USA
| | - 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
| | | | - Curtis A Suttle
- Departments of Earth, Ocean and Atmospheric Sciences, Microbiology and Immunology, and Botany, and the Institute for Oceans and Fisheries, University of British Columbia, Vancouver, Canada
| | - Amy Tabata
- Pacific Biological Station, Fisheries and Oceans Canada, Nanaimo, BC, Canada
| | - Ayato Takada
- Division of Global Epidemiology, Research Center for Zoonosis Control, Hokkaido University, Sapporo, Japan
| | - Shigeharu Takeuchi
- Japan Plant Protection Association Kochi Experiment Station, Konan, Kochi, Japan
| | - David P Tchouassi
- International Centre of Insect Physiology and Ecology, Nairobi, Kenya
| | - Amy Teffer
- Department of Forest Sciences, University of British Columbia, Vancouver, Canada
| | - Robert B Tesh
- Department of Pathology, The University of Texas Medical Branch, Galveston, TX, USA
| | | | - Yasuhiro Tomitaka
- Kyushu Okinawa Agricultural Research Center, NARO, Koshi, Kumamoto, Japan
| | - Keizō Tomonaga
- Institute for Frontier Life and Medical Sciences (inFront), , Kyoto University, Kyoto, Japan
| | - Noël Tordo
- Unité des Stratégies Antivirales, WHO Collaborative Centre for Viral Haemorrhagic Fevers and Arboviruses, OIE Reference Laboratory for RVFV & CCHFV, Institut Pasteur, Paris, France
| | - Baldwyn Torto
- International Centre of Insect Physiology and Ecology, Nairobi, Kenya
| | - 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
- Institut Pasteur de Guinée, Conakry, Guinea
| | - Shinya Tsuda
- Department of Clinical Plant Science, Faculty of Bioscience and Applied Chemistry, Hosei University, Koganei, Tokyo, Japan
| | - Changchun Tu
- Changchun Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Changchun, Jilin Province, People's Republic of China
| | - Massimo Turina
- National Institute of Optics, National Research Council of Italy (INO-CNR), Via Branze 45, 25123Brescia, Italy
| | - Ioannis E Tzanetakis
- Department of Entomology and Plant Pathology, Division of Agriculture, University of Arkansas System,, Fayetteville, AR, 72701, USA
| | | | - Tomio Usugi
- Central Region Agricultural Research Center, NARO, Tsukuba, Ibaraki, Japan
| | - Anna Maria Vaira
- Institute for Sustainable Plant Protection, National Research Council of Italy (CNR), Strada delle Cacce 73, 10135, Turin, Italy
| | - Marta Vallino
- Institute for Sustainable Plant Protection, National Research Council of Italy (CNR), Strada delle Cacce 73, 10135, Turin, Italy
| | - Bernadette van den Hoogen
- Department of Viroscience, Erasmus MC, University Medical Centre Rotterdam, Rotterdam, The Netherlands
| | - Arvind Varsani
- The Biodesign Center for Fundamental and Applied Microbiomics, Center for Evolution and Medicine School of Life Sciences, Arizona State University, Tempe, AZ, USA
- Structural Biology Research Unit, Department of Clinical Laboratory Sciences, University of Cape Town, Observatory, Cape Town, South Africa
| | - Nikos Vasilakis
- Department of Pathology, The University of Texas Medical Branch, Galveston, TX, USA
| | - Martin Verbeek
- Wageningen University and Research, Biointeractions and Plant Health, Wageningen, The Netherlands
| | - Susanne von Bargen
- Division Phytomedicine, Faculty of Life Sciences, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Jiro Wada
- Integrated Research Facility at Fort Detrick, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Frederick, MD, USA
| | - Victoria Wahl
- National Biodefense Analysis and Countermeasures Center, Fort Detrick, Frederick, MD, USA
| | - Peter J Walker
- School of Chemistry and Molecular Biosciences, University of Queensland, St. Lucia, QLD, Australia
| | - Lin-Fa Wang
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore, Singapore
| | - Guoping Wang
- Key Lab of Plant Pathology of Hubei Province, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, People's Republic of China
| | - Yanxiang Wang
- Key Lab of Plant Pathology of Hubei Province, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, People's Republic of China
| | - Yaqin Wang
- State Key Laboratory of Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou, People's Republic of China
| | - Muhammad Waqas
- Key Laboratory of Crop Disease Monitoring and Safety Control in Hubei Province, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, Hubei, People's Republic of China
| | - Tàiyún Wèi
- Fujian Province Key Laboratory of Plant Virology, Institute of Plant Virology, Fujian Agriculture and Forestry University, Fuzhou, Fujian, People's Republic of China
| | - Shaohua Wen
- Key Lab of Plant Pathology of Hubei Province, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, People's Republic of China
| | - 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
| | - Yuri I Wolf
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA
| | - Jiangxiang Wu
- State Key Laboratory of Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou, People's Republic of China
| | - Lei Xu
- Jiangxi Academy of Agricultural Sciences, Nanchang, Jiangxi, People's Republic of China
| | | | - Caixia Yang
- College of Life Science and Engineering, Shenyang University, Shenyang, Liaoning, People's Republic of China
| | - Zuokun Yang
- Key Lab of Plant Pathology of Hubei Province, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, People's Republic of China
| | - F Murilo Zerbini
- Departamento de Fitopatologia, Instituto de Biotecnologia Aplicada à Agropecuária, Universidade Federal de Viçosa, Viçosa, Minas Gerais, Brazil
| | - Lifeng Zhai
- Key Laboratory of Horticultural Plant Biology, Ministry of Education, Wuhan, 430070, Hubei , People's Republic of China
| | - Yong-Zhen Zhang
- National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Changping, Beijing, People's Republic of China
- Shanghai Public Health Clinical Center & Institutes of Biomedical Sciences, Fudan University, Shanghai, People's Republic of China
| | - Song Zhang
- National Citrus Engineering and Technology Research Center, Citrus Research Institute, Southwest University, Beibei, Chongqing, People's Republic of China
| | - Jinguo Zhang
- National Sand Pear Germplasm Repository in Wuchang, Research Institute of Fruit and Tea, Hubei Academy of Agricultural Science, Wuhan, Hubei, People's Republic of China
| | - Zhe Zhang
- Key Lab of Plant Pathology of Hubei Province, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, People's Republic of China
| | - Xueping Zhou
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, People's Republic of China
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Andresen AMS, Gjøen T. Chitosan nanoparticle formulation attenuates poly (I:C) induced innate immune responses against inactivated virus vaccine in Atlantic salmon (Salmo salar). COMPARATIVE BIOCHEMISTRY AND PHYSIOLOGY. PART D, GENOMICS & PROTEOMICS 2021; 40:100915. [PMID: 34634571 DOI: 10.1016/j.cbd.2021.100915] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/16/2021] [Revised: 09/08/2021] [Accepted: 09/08/2021] [Indexed: 06/13/2023]
Abstract
Many vaccine formulations, in particular vaccines based on inactivated virus, needs adjuvants to boost immunogenicity. In aquaculture, mineral and plant oil are used as adjuvant in commercial vaccines, and the advent of oil-adjuvanted vaccines was crucial to aquaculture development. Nevertheless, some of these approved vaccines display suboptimal performance in the field compared to experimental conditions. Therefore, there is a need to improve adjuvants and delivery methods for fish vaccines against viruses. We used RNA sequencing of Atlantic salmon head kidney to analyse the difference in gene expression 24 h after injection of different experimental vaccine formulations. We compared five different formulations in addition to a PBS control: inactivated virus alone (group V), soluble poly (I:C) (group P), nanoparticles containing poly (I:C) (group N), soluble poly (I:C) + inactivated virus (group PV) and finally nanoparticles containing poly (I:C) + inactivated virus (group NV). Our results showed poly (I:C)'s ability as adjuvant and its capacity influence innate immune genes expression in Atlantic salmon. Soluble poly (I:C) upregulated multiple immune related genes and was more effective compared to poly (I:C) formulated into chitosan nanoparticles (more than 10 fold increase in differentially expressed genes, DEGs). However, inclusion of inactivated ISA virus in the nanoparticle vaccine, increased the number of DEGs fivefold suggesting a synergistic effect of adjuvant and antigen. Our results indicate that the way poly (I:C) is formulated and the presence of antigen is important for the magnitude of the innate immune response in Atlantic salmon.
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Affiliation(s)
| | - Tor Gjøen
- Department of Pharmacy, Section for Pharmacology and Pharmaceutical Biosciences, University of Oslo, Oslo, Norway.
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Akbarzadeh A, Selbie DT, Pon LB, Miller KM. Endangered Cultus Lake sockeye salmon exhibit genomic evidence of hypoxic and thermal stresses while rearing in degrading freshwater lacustrine critical habitat. CONSERVATION PHYSIOLOGY 2021; 9:coab089. [PMID: 34858597 PMCID: PMC8633632 DOI: 10.1093/conphys/coab089] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/03/2021] [Revised: 10/25/2021] [Accepted: 11/01/2021] [Indexed: 06/13/2023]
Abstract
Water quality degradation due to lake eutrophication and climate change contributes to the risk of extirpation for the endangered Cultus Lake sockeye salmon. Sockeye salmon juveniles experience both low-oxygen water in profundal lake habitats and elevated temperatures above the thermocline during diel vertical migrations in summer and fall when the lake is thermally stratified. We used a transcriptomic tool (Salmon Fit-Chip) to determine whether salmon were experiencing thermal and/or hypoxic stress during this period. The results showed that over one-third of the fish were responding to either hypoxic (35.5%) or thermal stress (40.9%) during periods when these environmental stressors were pronounced within the lake, but not during periods when profundal dissolved oxygen was elevated and the water column was isothermal and cool. The most consistent signs of hypoxic stress occurred during July (52.2%) and September (44.4%). A total of 25.7% of individual fish sampled during months when both stressors were occurring (July, September, October) showed signatures of both stressors. When a combination of hypoxic and thermal stress biomarkers was applied, 92% of fish showed evidence of one or both stressors; hence, for at least several months of the year, most sockeye salmon juveniles in Cultus Lake are experiencing anthropogenically environmentally induced stress. We also detected the presence of pathogenic ciliate Ichthyoptherius multifiliis in the gill tissue of juveniles, with a higher infection signal in Cultus Lake compared to juveniles from nearby Chilliwack Lake. These data provide powerful new evidence that Cultus Lake sockeye salmon, which experience relatively lower juvenile survival than Chilliwack sockeye salmon, are more compromised by stress and carry a higher level of infection of at least one pathogenic agent. Thus, we hypothesize that the cumulative or synergistic interplay between stressors and diseases, clearly documented to be occurring within Cultus Lake, are contributing to increased mortality of endangered sockeye salmon.
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Affiliation(s)
- Arash Akbarzadeh
- Fisheries and Oceans Canada, Pacific Biological Station, 3190 Hammond Bay Road, Nanaimo, British Columbia, V9T 6N7, Canada
- Department of Fisheries, Faculty of Marine Science and Technology, University of Hormozgan, 9th km of Minab Road, Bandar Abbas, 79161 93145, Iran
| | - Daniel T Selbie
- Fisheries and Oceans Canada, Science Branch, Pacific Region, Cultus Lake Salmon Research Laboratory, 4222 Columbia Valley Hwy, Cultus Lake, British Columbia, V2R 5B6, Canada
| | - Lucas B Pon
- Fisheries and Oceans Canada, Science Branch, Pacific Region, Cultus Lake Salmon Research Laboratory, 4222 Columbia Valley Hwy, Cultus Lake, British Columbia, V2R 5B6, Canada
| | - Kristina M Miller
- Department of Fisheries, Faculty of Marine Science and Technology, University of Hormozgan, 9th km of Minab Road, Bandar Abbas, 79161 93145, Iran
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Facciolà A, Laganà P, Caruso G. The COVID-19 pandemic and its implications on the environment. ENVIRONMENTAL RESEARCH 2021; 201:111648. [PMID: 34242676 PMCID: PMC8261195 DOI: 10.1016/j.envres.2021.111648] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/16/2021] [Revised: 07/01/2021] [Accepted: 07/02/2021] [Indexed: 05/06/2023]
Abstract
The emerging threat posed by COVID-19 pandemic has strongly modified our lifestyle, making urgent to re-consider the humans-environment relationships and stimulating towards more sustainable choices in our daily behavior. Scientific evidences showed that the onset of new viral pathogens with a high epidemic-pandemic potential is often the result of complex interactions between animals, humans and environment. In this context, the interest of the scientific community has also been attracted towards the potential interactions of SARS-CoV-2 with environmental compartments. Many issues, ranging from the epidemiology and persistence of SARS-CoV-2 in water bodies to the potential implications of lockdown measures on environmental quality status are here reviewed, with a special reference to marine ecosystems. Due to current sanitary emergence, the relevance of pilot studies regarding the interactions between SARS-CoV-2 spread and the direct and indirect environmental impacts of the COVID-19 pandemic, that are still a matter of scientific debate, is underlined.
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Affiliation(s)
- Alessio Facciolà
- Department of Biomedical and Dental Sciences and Morphofunctional Imaging, University of Messina, Italy
| | - Pasqualina Laganà
- Department of Biomedical and Dental Sciences and Morphofunctional Imaging, University of Messina, Italy.
| | - Gabriella Caruso
- Institute of Polar Sciences (ISP), National Research Council (CNR), Messina, Italy
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Hayman DTS, Knox MA. Estimating the age of the subfamily Orthocoronavirinae using host divergence times as calibration ages at two internal nodes. Virology 2021; 563:20-27. [PMID: 34411808 PMCID: PMC8365511 DOI: 10.1016/j.virol.2021.08.004] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2021] [Revised: 08/11/2021] [Accepted: 08/11/2021] [Indexed: 12/04/2022]
Abstract
Viruses of the subfamily Orthocoronavirinae can cause mild to severe disease in people, including COVID-19, MERS and SARS. Their most common natural hosts are bat and bird species, which are mostly split across four virus genera. Molecular clock analyses of orthocoronaviruses suggested the most recent common ancestor of these viruses might have emerged either around 10,000 years ago or, using models accounting for selection, many millions of years. Here, we reassess the evolutionary history of these viruses. We present time-aware phylogenetic analyses of a RNA-dependent RNA polymerase locus from 123 orthocoronaviruses isolated from birds and bats, including those in New Zealand, which were geographically isolated from other bats around 35 million years ago. We used this age, as well as the age of the avian-mammals split, to calibrate the molecular clocks, under the assumption that these ages are applicable to the analyzed viruses. We found that the time to the most recent ancestor common for all orthocoronaviruses is likely 150 or more million years, supporting clock analyses that account for selection.
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Affiliation(s)
- David T S Hayman
- Molecular Epidemiology and Public Health Laboratory, School of Veterinary Science, Massey University, New Zealand.
| | - Matthew A Knox
- Molecular Epidemiology and Public Health Laboratory, School of Veterinary Science, Massey University, New Zealand
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30
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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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31
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Finn RJR, Chalifour L, Gergel SE, Hinch SG, Scott DC, Martin TG. Quantifying lost and inaccessible habitat for Pacific salmon in Canada’s Lower Fraser River. Ecosphere 2021. [DOI: 10.1002/ecs2.3646] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Affiliation(s)
- Riley J. R. Finn
- Department of Forest and Conservation Science Faculty of Forestry The Conservation Decisions Lab University of British Columbia 2424 Main Mall Vancouver British ColumbiaV6T 1Z4Canada
- Raincoast Conservation Foundation Sidney British ColumbiaV8L 3Y3Canada
| | - Lia Chalifour
- Department of Forest and Conservation Science Faculty of Forestry The Conservation Decisions Lab University of British Columbia 2424 Main Mall Vancouver British ColumbiaV6T 1Z4Canada
- Department of Biology University of Victoria Victoria British ColumbiaV8W 2Y2Canada
| | - Sarah E. Gergel
- Department of Forest and Conservation Science Faculty of Forestry University of British Columbia 2424 Main Mall Vancouver British ColumbiaV6T 1Z4Canada
| | - Scott G. Hinch
- Department of Forest and Conservation Science Faculty of Forestry Pacific Salmon Ecology and Conservation Laboratory University of British Columbia 2424 Main Mall Vancouver British ColumbiaV6T 1Z4Canada
| | - David C. Scott
- Raincoast Conservation Foundation Sidney British ColumbiaV8L 3Y3Canada
- Department of Forest and Conservation Science Faculty of Forestry Pacific Salmon Ecology and Conservation Laboratory University of British Columbia 2424 Main Mall Vancouver British ColumbiaV6T 1Z4Canada
| | - Tara G. Martin
- Department of Forest and Conservation Science Faculty of Forestry The Conservation Decisions Lab University of British Columbia 2424 Main Mall Vancouver British ColumbiaV6T 1Z4Canada
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32
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Wu Y, Peng Z, Yan Y, Hu J, Wang Y, Wang X, Peng R, Watterson D, Shi Y. Current knowledge of COVID-19: Advances, challenges and future perspectives. BIOSAFETY AND HEALTH 2021; 3:202-209. [PMID: 34104880 PMCID: PMC8176881 DOI: 10.1016/j.bsheal.2021.06.001] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2020] [Revised: 05/31/2021] [Accepted: 06/01/2021] [Indexed: 01/18/2023] Open
Abstract
The pandemic of coronavirus disease 2019 (COVID-19) has already evoked massive influence. The global pandemic has been ravaging the whole world for a year, with the number of confirmed human infection cases over 150 million and a death toll exceeding 3 million. Although the genomic sequence of the cognate pathogen SARS-CoV-2 (severe acute respiratory syndrome coronavirus 2) has been quickly determined, there are still many unknown aspects, including the virus origin and evolution trend, and the effectiveness of current vaccines and drugs against the mutating virus. This review summarizes current knowledge and advances about COVID-19, including virus origin, transmission and infection, with the aim to improve the understanding of COVID-19 and provide a new perspective for future studies.
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Affiliation(s)
- Yuhan Wu
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China.,MGI, BGI-Shenzhen, Shenzhen 518083, China
| | - Zhuobing Peng
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yongxue Yan
- Huitong Experimental Station of Forest Ecology, CAS Key Laboratory of Forest Ecology and Management, Institute of Applied Ecology, Shenyang 110164, China
| | - Jintao Hu
- Melbourne School of Engineering, the University of Melbourne, Parkville, VIC 3010, Australia
| | - Yalong Wang
- The State Key Laboratory of Membrane Biology, Tsinghua-Peking Center for Life Science, School of Life Science, Tsinghua University, Beijing 100084, China
| | - Xiaoyu Wang
- MOE Laboratory of Biosystem Homeostasis and Protection, College of Life Sciences, Zhejiang University, Hangzhou 310058, China
| | - Ruchao Peng
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Daniel Watterson
- Australian Infectious Diseases Research Centre, School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - Yi Shi
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
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33
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Miller AK, Mifsud JCO, Costa VA, Grimwood RM, Kitson J, Baker C, Brosnahan CL, Pande A, Holmes EC, Gemmell NJ, Geoghegan JL. Slippery when wet: cross-species transmission of divergent coronaviruses in bony and jawless fish and the evolutionary history of the Coronaviridae. Virus Evol 2021; 7:veab050. [PMID: 34527280 PMCID: PMC8244743 DOI: 10.1093/ve/veab050] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2021] [Revised: 05/19/2021] [Accepted: 05/28/2021] [Indexed: 01/31/2023] Open
Abstract
The Nidovirales comprise a genetically diverse group of positive-sense single-stranded RNA virus families that infect a range of invertebrate and vertebrate hosts. Recent metagenomic studies have identified nido-like virus sequences, particularly those related to the Coronaviridae, in a range of aquatic hosts including fish, amphibians, and reptiles. We sought to identify additional members of the Coronaviridae in both bony and jawless fish through a combination of total RNA sequencing (meta-transcriptomics) and data mining of published RNA sequencing data and from this reveal more of the long-term patterns and processes of coronavirus evolution. Accordingly, we identified a number of divergent viruses that fell within the Letovirinae subfamily of the Coronaviridae, including those in a jawless fish-the pouched lamprey. By mining fish transcriptome data, we identified additional virus transcripts matching these viruses in bony fish from both marine and freshwater environments. These new viruses retained sequence conservation in the RNA-dependant RNA polymerase across the Coronaviridae but formed a distinct and diverse phylogenetic group. Although there are broad-scale topological similarities between the phylogenies of the major groups of coronaviruses and their vertebrate hosts, the evolutionary relationship of viruses within the Letovirinae does not mirror that of their hosts. For example, the coronavirus found in the pouched lamprey fell within the phylogenetic diversity of bony fish letoviruses, indicative of past host switching events. Hence, despite possessing a phylogenetic history that likely spans the entire history of the vertebrates, coronavirus evolution has been characterised by relatively frequent cross-species transmission, particularly in hosts that reside in aquatic habitats.
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Affiliation(s)
| | | | | | - Rebecca M Grimwood
- Department of Microbiology and Immunology, University of Otago, Dunedin 9016, New Zealand
| | - Jane Kitson
- Kitson Consulting Ltd 9 Black Road, Invercargill 9879, Invercargill/Waihopai, New Zealand
| | - Cindy Baker
- National Institute of Water and Atmospheric Research, Hamilton 3216, New Zealand
| | - Cara L Brosnahan
- Animal Health Laboratory and Diagnostic and Surveillance Directorate, Ministry for Primary Industries, Upper Hutt 5018, New Zealand
| | - Anjali Pande
- National Institute of Water and Atmospheric Research, Hamilton 3216, New Zealand,Animal Health Laboratory and Diagnostic and Surveillance Directorate, Ministry for Primary Industries, Upper Hutt 5018, New Zealand
| | - Edward C Holmes
- Marie Bashir Institute for Infectious Diseases and Biosecurity, School of Life and Environmental Sciences and School of Medical Sciences, Johns Hopkins Drive, The University of Sydney, Sydney, NSW 2006, Australia
| | - Neil J Gemmell
- Department of Anatomy, University of Otago, Dunedin 9016, New Zealand
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34
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Jeffries KM, Teffer A, Michaleski S, Bernier NJ, Heath DD, Miller KM. The use of non-lethal sampling for transcriptomics to assess the physiological status of wild fishes. Comp Biochem Physiol B Biochem Mol Biol 2021; 256:110629. [PMID: 34058376 DOI: 10.1016/j.cbpb.2021.110629] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2020] [Revised: 05/19/2021] [Accepted: 05/25/2021] [Indexed: 12/14/2022]
Abstract
Fishes respond to different abiotic and biotic stressors through changes in gene expression as a part of an integrated physiological response. Transcriptomics approaches have been used to quantify gene expression patterns as a reductionist approach to understand responses to environmental stressors in animal physiology and have become more commonly used to study wild fishes. We argue that non-lethal sampling for transcriptomics should become the norm for assessing the physiological status of wild fishes, especially when there are conservation implications. Processes at the level of the transcriptome provide a "snapshot" of the cellular conditions at a given time; however, by using a non-lethal sampling protocol, researchers can connect the transcriptome profile with fitness-relevant ecological endpoints such as reproduction, movement patterns and survival. Furthermore, telemetry is a widely used approach in fisheries to understand movement patterns in the wild, and when combined with transcriptional profiling, provides arguably the most powerful use of non-lethal sampling for transcriptomics in wild fishes. In this review, we discuss the different tissues that can be successfully incorporated into non-lethal sampling strategies, which is particularly useful in the context of the emerging field of conservation transcriptomics. We briefly describe different methods for transcriptional profiling in fishes from high-throughput qPCR to whole transcriptome approaches. Further, we discuss strategies and the limitations of using transcriptomics for non-lethally studying fishes. Lastly, as 'omics' technology continues to advance, transcriptomics paired with different omics approaches to study wild fishes will provide insight into the factors that regulate phenotypic variation and the physiological responses to changing environmental conditions in the future.
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Affiliation(s)
- Ken M Jeffries
- Department of Biological Sciences, University of Manitoba, 50 Sifton Road, Winnipeg, Manitoba R3T 2N2, Canada.
| | - Amy Teffer
- Department of Environmental Conservation, University of Massachusetts Amherst, Amherst, MA 01003, United States of America
| | - Sonya Michaleski
- Department of Biological Sciences, University of Manitoba, 50 Sifton Road, Winnipeg, Manitoba R3T 2N2, Canada
| | - Nicholas J Bernier
- Department of Integrative Biology, University of Guelph, Guelph, ON N1G 2W1, Canada
| | - Daniel D Heath
- Department of Integrative Biology, Great Lakes Institute for Environmental Research, University of Windsor, Windsor, ON N9B 3P4, Canada
| | - Kristina M Miller
- Pacific Biological Station, Fisheries and Oceans Canada, 3190 Hammond Bay Rd, Nanaimo, BC V9T 6N7, Canada
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35
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Těšíková J, Krásová J, Goüy de Bellocq J. Multiple Mammarenaviruses Circulating in Angolan Rodents. Viruses 2021; 13:982. [PMID: 34070551 PMCID: PMC8227972 DOI: 10.3390/v13060982] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Revised: 05/17/2021] [Accepted: 05/20/2021] [Indexed: 12/14/2022] Open
Abstract
Rodents are a speciose group of mammals with strong zoonotic potential. Some parts of Africa are still underexplored for the occurrence of rodent-borne pathogens, despite this high potential. Angola is at the convergence of three major biogeographical regions of sub-Saharan Africa, each harbouring a specific rodent community. This rodent-rich area is, therefore, strategic for studying the diversity and evolution of rodent-borne viruses. In this study we examined 290 small mammals, almost all rodents, for the presence of mammarenavirus and hantavirus RNA. While no hantavirus was detected, we found three rodent species positive for distinct mammarenaviruses with a particularly high prevalence in Namaqua rock rats (Micaelamys namaquensis). We characterised four complete virus genomes, which showed typical mammarenavirus organisation. Phylogenetic and genetic distance analyses revealed: (i) the presence of a significantly divergent strain of Luna virus in Angolan representatives of the ubiquitous Natal multimammate mouse (Mastomys natalensis), (ii) a novel Okahandja-related virus associated with the Angolan lineage of Micaelamys namaquensis for which we propose the name Bitu virus (BITV) and (iii) the occurrence of a novel Mobala-like mammarenavirus in the grey-bellied pygmy mouse (Mus triton) for which we propose the name Kwanza virus (KWAV). This high virus diversity in a limited host sample size and in a relatively small geographical area supports the idea that Angola is a hotspot for mammarenavirus diversity.
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Affiliation(s)
- Jana Těšíková
- Institute of Vertebrate Biology of the Czech Academy of Sciences, 603 65 Brno, Czech Republic; (J.K.); (J.G.B.)
- Department of Botany and Zoology, Faculty of Science, Masaryk University, 611 37 Brno, Czech Republic
| | - Jarmila Krásová
- Institute of Vertebrate Biology of the Czech Academy of Sciences, 603 65 Brno, Czech Republic; (J.K.); (J.G.B.)
- Department of Zoology, Faculty of Science, University of South Bohemia, 370 05 České Budějovice, Czech Republic
| | - Joëlle Goüy de Bellocq
- Institute of Vertebrate Biology of the Czech Academy of Sciences, 603 65 Brno, Czech Republic; (J.K.); (J.G.B.)
- Department of Zoology and Fisheries, Faculty of Agrobiology, Food and Natural Resources, Czech University of Life Sciences Prague, 165 00 Prague, Czech Republic
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36
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Mordecai GJ, Miller KM, Bass AL, Bateman AW, Teffer AK, Caleta JM, Di Cicco E, Schulze AD, Kaukinen KH, Li S, Tabata A, Jones BR, Ming TJ, Joy JB. Aquaculture mediates global transmission of a viral pathogen to wild salmon. SCIENCE ADVANCES 2021; 7:7/22/eabe2592. [PMID: 34039598 PMCID: PMC8153721 DOI: 10.1126/sciadv.abe2592] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/10/2020] [Accepted: 04/07/2021] [Indexed: 05/07/2023]
Abstract
Global expansion of aquaculture and agriculture facilitates disease emergence and catalyzes transmission to sympatric wildlife populations. The health of wild salmon stocks critically concerns Indigenous peoples, commercial and recreational fishers, and the general public. Despite potential impact of viral pathogens such as Piscine orthoreovirus-1 (PRV-1) on endangered wild salmon populations, their epidemiology in wild fish populations remains obscure, as does the role of aquaculture in global and local spread. Our phylogeographic analyses of PRV-1 suggest that development of Atlantic salmon aquaculture facilitated spread from Europe to the North and South East Pacific. Phylogenetic analysis and reverse transcription polymerase chain reaction surveillance further illuminate the circumstances of emergence of PRV-1 in the North East Pacific and provide strong evidence for Atlantic salmon aquaculture as a source of infection in wild Pacific salmon. PRV-1 is now an important infectious agent in critically endangered wild Pacific salmon populations, fueled by aquacultural transmission.
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Affiliation(s)
- Gideon J Mordecai
- Department of Medicine, University of British Columbia, Vancouver, BC, Canada.
| | - Kristina M Miller
- Pacific Biological Station, Fisheries and Oceans Canada, Nanaimo, BC, Canada.
- Department of Forest and Conservation Sciences, Forest Sciences Centre, 3041 2424 Main Mall, Vancouver, BC V6T 1Z4, Canada
| | - Arthur L Bass
- Department of Forest and Conservation Sciences, University of British Columbia, Vancouver, BC, Canada
| | - Andrew W Bateman
- Pacific Salmon Foundation, 1682 W 7th Ave., Vancouver, BC V6J 4S6, Canada
- Department of Ecology and Evolutionary Biology, University of Toronto, 25 Willcocks Street, Room 3055, Toronto, ON M5S 3B2, Canada
- Salmon Coast Field Station General Delivery, Simoom Sound, BC V0P 1S0, Canada
| | - Amy K Teffer
- David H. Smith Conservation Research Fellowship, Society for Conservation Biology, Washington, DC, USA
| | - Jessica M Caleta
- Department of Microbiology and Immunology, University of British Columbia, Vancouver, BC, Canada
| | - Emiliano Di Cicco
- Pacific Salmon Foundation, 1682 W 7th Ave., Vancouver, BC V6J 4S6, Canada
| | - Angela D Schulze
- Pacific Biological Station, Fisheries and Oceans Canada, Nanaimo, BC, 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 Tabata
- Pacific Biological Station, Fisheries and Oceans Canada, Nanaimo, BC, Canada
| | - Brad R Jones
- BC Centre for Excellence in HIV/AIDS, Vancouver, BC, Canada
- Bioinformatics Programme, University of British Columbia, Vancouver, BC, Canada
| | - Tobi J Ming
- Pacific Biological Station, Fisheries and Oceans Canada, Nanaimo, BC, Canada
| | - Jeffrey B Joy
- Department of Medicine, University of British Columbia, Vancouver, BC, Canada
- BC Centre for Excellence in HIV/AIDS, Vancouver, BC, Canada
- Bioinformatics Programme, University of British Columbia, Vancouver, BC, Canada
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37
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Godoy MG, Kibenge MJT, Kibenge FSB. SARS-CoV-2 transmission via aquatic food animal species or their products: A review. AQUACULTURE (AMSTERDAM, NETHERLANDS) 2021; 536:736460. [PMID: 33564203 PMCID: PMC7860939 DOI: 10.1016/j.aquaculture.2021.736460] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Revised: 01/28/2021] [Accepted: 01/30/2021] [Indexed: 05/06/2023]
Abstract
Outbreaks of COVID-19 (coronavirus disease 2019) have been reported in workers in fish farms and fish processing plants arising from person-to-person transmission, raising concerns about aquatic animal food products' safety. A better understanding of such incidents is important for the aquaculture industry's sustainability, particularly with the global trade in fresh and frozen aquatic animal food products where contaminating virus could survive for some time. Despite a plethora of COVID-19-related scientific publications, there is a lack of reports on the risk of contact with aquatic food animal species or their products. This review aimed to examine the potential for Severe Acute Respiratory Syndrome-Coronavirus-2 (SARS-CoV-2) contamination and the potential transmission via aquatic food animals or their products and wastewater effluents. The extracellular viability of SARS-CoV-2 and how the virus is spread are reviewed, supporting the understanding that contaminated cold-chain food sources may introduce SAR-CoV-2 via food imports although the virus is unlikely to infect humans through consumption of aquatic food animals or their products or drinking water; i.e., SARS-CoV-2 is not a foodborne virus and should not be managed as such but instead through strong, multifaceted public health interventions including physical distancing, rapid contact tracing, and testing, enhanced hand and respiratory hygiene, frequent disinfection of high-touch surfaces, isolation of infected workers and their contacts, as well as enhanced screening protocols for international seafood trade.
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Affiliation(s)
- Marcos G Godoy
- Centro de Investigaciones Biológicas Aplicadas (CIBA), Lago Panguipulli 1390, Puerto Montt, Chile
- Laboratorio de Biotecnología Aplicada, Facultad de Medicina Veterinaria, Sede De La Patagonia, Lago Panguipulli 1390, Puerto Montt, 5480000, Chile
- Doctorado en Acuicultura. Programa Cooperativo Universidad de Chile, Universidad Católica del Norte, Pontificia Universidad Católica de Valparaíso, Chile
| | - Molly J T Kibenge
- Department of Pathology and Microbiology, Atlantic Veterinary College, University of Prince Edward Island, 550 University Ave., Charlottetown, P.E.I., C1A 4P3, Canada
| | - Frederick S B Kibenge
- Department of Pathology and Microbiology, Atlantic Veterinary College, University of Prince Edward Island, 550 University Ave., Charlottetown, P.E.I., C1A 4P3, Canada
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38
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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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39
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Chen X, Kang Y, Luo J, Pang K, Xu X, Wu J, Li X, Jin S. Next-Generation Sequencing Reveals the Progression of COVID-19. Front Cell Infect Microbiol 2021; 11:632490. [PMID: 33777844 PMCID: PMC7991797 DOI: 10.3389/fcimb.2021.632490] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2020] [Accepted: 02/10/2021] [Indexed: 01/08/2023] Open
Abstract
The novel coronavirus SARS-CoV-2 (causing the disease COVID-19) has caused a highly transmissible and ongoing pandemic worldwide. Due to its rapid development, next-generation sequencing plays vital roles in many aspects. Here, we summarize the current knowledge on the origin and human transmission of SARS-CoV-2 based on NGS analysis. The ACE2 expression levels in various human tissues and relevant cells were compared to provide insights into the mechanism of SAS-CoV-2 infection. Gut microbiota dysbiosis observed by metagenome sequencing and the immunogenetics of COVID-19 patients according to single-cell sequencing analysis were also highlighted. Overall, the application of these sequencing techniques could be meaningful for finding novel intermediate SARS-CoV-2 hosts to block interspecies transmission. This information will further benefit SARS-CoV-2 diagnostic development and new therapeutic target discovery. The extensive application of NGS will provide powerful support for our fight against future public health emergencies.
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Affiliation(s)
- Xiaomin Chen
- Institute of Genomic Medicine, Wenzhou Medical University, Wenzhou, China
| | - Yutong Kang
- Wenzhou Key Laboratory of Sanitary Microbiology, Ministry of Education, Wenzhou, China
- Key Laboratory of Laboratory Medicine, Ministry of Education, Wenzhou, China
- School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, China
| | - Jing Luo
- Rheumatology Department, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
| | - Kun Pang
- Institute of Genomic Medicine, Wenzhou Medical University, Wenzhou, China
| | - Xin Xu
- Institute of Genomic Medicine, Wenzhou Medical University, Wenzhou, China
| | - Jinyu Wu
- Institute of Genomic Medicine, Wenzhou Medical University, Wenzhou, China
| | - Xiaokun Li
- Chemical Biology Research Center, School of Pharmaceutical Sciences, Wenzhou Medical University, Wenzhou, China
| | - Shengwei Jin
- Department of Anesthesia and Critical Care, Second Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
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40
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Bateman AW, Schulze AD, Kaukinen KH, Tabata A, Mordecai G, Flynn K, Bass A, Di Cicco E, Miller KM. Descriptive multi-agent epidemiology via molecular screening on Atlantic salmon farms in the northeast Pacific Ocean. Sci Rep 2021; 11:3466. [PMID: 33568681 PMCID: PMC7876018 DOI: 10.1038/s41598-020-78978-9] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2020] [Accepted: 11/24/2020] [Indexed: 02/07/2023] Open
Abstract
Rapid expansion of salmon aquaculture has resulted in high-density populations that host diverse infectious agents, for which surveillance and monitoring are critical to disease management. Screening can reveal infection diversity from which disease arises, differential patterns of infection in live and dead fish that are difficult to collect in wild populations, and potential risks associated with agent transmission between wild and farmed hosts. We report results from a multi-year infectious-agent screening program of farmed salmon in British Columbia, Canada, using quantitative PCR to assess presence and load of 58 infective agents (viruses, bacteria, and eukaryotes) in 2931 Atlantic salmon (Salmo salar). Our analysis reveals temporal trends, agent correlations within hosts, and agent-associated mortality signatures. Multiple agents, most notably Tenacibaculum maritimum, were elevated in dead and dying salmon. We also report detections of agents only recently shown to infect farmed salmon in BC (Atlantic salmon calicivirus, Cutthroat trout virus-2), detection in freshwater hatcheries of two marine agents (Kudoa thyrsites and Tenacibaculum maritimum), and detection in the ocean of a freshwater agent (Flavobacterium psychrophilum). Our results provide information for farm managers, regulators, and conservationists, and enable further work to explore patterns of multi-agent infection and farm/wild transmission risk.
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Affiliation(s)
- Andrew W Bateman
- Pacific Salmon Foundation, Vancouver, Canada. .,Ecology and Evolutionary Biology, University of Toronto, Toronto, Canada.
| | - Angela D Schulze
- Molecular Genetics, Fisheries and Oceans Canada, Nanaimo, Canada
| | - Karia H Kaukinen
- Molecular Genetics, Fisheries and Oceans Canada, Nanaimo, Canada
| | - Amy Tabata
- Molecular Genetics, Fisheries and Oceans Canada, Nanaimo, Canada
| | - Gideon Mordecai
- Department of Medicine, University of British Columbia, Vancouver, Canada
| | - Kelsey Flynn
- Molecular Genetics, Fisheries and Oceans Canada, Nanaimo, Canada
| | - Arthur Bass
- Pacific Salmon Foundation, Vancouver, Canada.,Forest and Conservation Sciences, University of British Columbia, Vancouver, Canada
| | | | - Kristina M Miller
- Molecular Genetics, Fisheries and Oceans Canada, Nanaimo, Canada.,Forest and Conservation Sciences, University of British Columbia, Vancouver, Canada
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41
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Abstract
The classification of viruses is relevant to a number of scientific and clinical disciplines, including the practice of diagnostic virology. Here, we provide an update to our previous review of taxonomic changes for disease-causing viruses in humans and vertebrate animals, covering changes between 2018 and 2020. Recent advances in virus taxonomy structure by the International Committee on Taxonomy of Viruses inform this update.
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42
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Costa VA, Mifsud JCO, Gilligan D, Williamson JE, Holmes EC, Geoghegan JL. Metagenomic sequencing reveals a lack of virus exchange between native and invasive freshwater fish across the Murray-Darling Basin, Australia. Virus Evol 2021; 7:veab034. [PMID: 34017611 PMCID: PMC8121191 DOI: 10.1093/ve/veab034] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Biological invasions are among the biggest threats to freshwater biodiversity. This is increasingly relevant in the Murray-Darling Basin, Australia, particularly since the introduction of the common carp (Cyprinus carpio). This invasive species now occupies up to ninety per cent of fish biomass, with hugely detrimental impacts on native fauna and flora. To address the ongoing impacts of carp, cyprinid herpesvirus 3 (CyHV-3) has been proposed as a potentially effective biological control agent. Crucially, however, it is unknown whether CyHV-3 and other cyprinid herpesviruses already exist in the Murray-Darling. Further, little is known about those viruses that naturally occur in wild freshwater fauna, and the frequency with which these viruses jump species boundaries. To document the evolution and diversity of freshwater fish viromes and better understand the ecological context to the proposed introduction of CyHV-3, we performed a meta-transcriptomic viral survey of invasive and native fish across the Murray-Darling Basin, covering over 2,200 km of the river system. Across a total of thirty-six RNA libraries representing ten species, we failed to detect CyHV-3 nor any closely related viruses. Rather, meta-transcriptomic analysis identified eighteen vertebrate-associated viruses that could be assigned to the Arenaviridae, Astroviridae, Bornaviridae, Caliciviridae, Coronaviridae, Chuviridae, Flaviviridae, Hantaviridae, Hepeviridae, Paramyxoviridae, Picornaviridae, Poxviridae, Reoviridae and Rhabdoviridae families, and a further twenty-seven that were deemed to be associated with non-vertebrate hosts. Notably, we revealed a marked lack of viruses that are shared among invasive and native fish sampled here, suggesting that there is little virus transmission from common carp to native fish species, despite co-existing for over fifty years. Overall, this study provides the first data on the viruses naturally circulating in a major river system and supports the notion that fish harbour a large diversity of viruses with often deep evolutionary histories.
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Affiliation(s)
- Vincenzo A Costa
- Department of Biological Sciences, Macquarie University, Sydney, NSW 2109, Australia
| | - Jonathon C O Mifsud
- Department of Biological Sciences, Macquarie University, Sydney, NSW 2109, Australia
| | - Dean Gilligan
- NSW Department of Primary Industries, Batemans Bay Fisheries Office, Batemans Bay 2536, Australia
| | - Jane E Williamson
- Department of Biological Sciences, Macquarie University, Sydney, NSW 2109, Australia
| | - Edward C Holmes
- Marie Bashir Institute for Infectious Diseases and Biosecurity, Charles Perkins Centre, School of Life and Environmental Sciences and Sydney Medical School, The University of Sydney, Sydney, NSW 2006, Australia
| | - Jemma L Geoghegan
- Department of Biological Sciences, Macquarie University, Sydney, NSW 2109, Australia
- Department of Microbiology and Immunology, University of Otago, Dunedin 9016, New Zealand
- Institute of Environmental Science and Research, Wellington, Porirua 5022, New Zealand
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43
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Landrigan PJ, Stegeman JJ, Fleming LE, Allemand D, Anderson DM, Backer LC, Brucker-Davis F, Chevalier N, Corra L, Czerucka D, Bottein MYD, Demeneix B, Depledge M, Deheyn DD, Dorman CJ, Fénichel P, Fisher S, Gaill F, Galgani F, Gaze WH, Giuliano L, Grandjean P, Hahn ME, Hamdoun A, Hess P, Judson B, Laborde A, McGlade J, Mu J, Mustapha A, Neira M, Noble RT, Pedrotti ML, Reddy C, Rocklöv J, Scharler UM, Shanmugam H, Taghian G, van de Water JA, Vezzulli L, Weihe P, Zeka A, Raps H, Rampal P. Human Health and Ocean Pollution. Ann Glob Health 2020; 86:151. [PMID: 33354517 PMCID: PMC7731724 DOI: 10.5334/aogh.2831] [Citation(s) in RCA: 141] [Impact Index Per Article: 35.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Background Pollution - unwanted waste released to air, water, and land by human activity - is the largest environmental cause of disease in the world today. It is responsible for an estimated nine million premature deaths per year, enormous economic losses, erosion of human capital, and degradation of ecosystems. Ocean pollution is an important, but insufficiently recognized and inadequately controlled component of global pollution. It poses serious threats to human health and well-being. The nature and magnitude of these impacts are only beginning to be understood. Goals (1) Broadly examine the known and potential impacts of ocean pollution on human health. (2) Inform policy makers, government leaders, international organizations, civil society, and the global public of these threats. (3) Propose priorities for interventions to control and prevent pollution of the seas and safeguard human health. Methods Topic-focused reviews that examine the effects of ocean pollution on human health, identify gaps in knowledge, project future trends, and offer evidence-based guidance for effective intervention. Environmental Findings Pollution of the oceans is widespread, worsening, and in most countries poorly controlled. It is a complex mixture of toxic metals, plastics, manufactured chemicals, petroleum, urban and industrial wastes, pesticides, fertilizers, pharmaceutical chemicals, agricultural runoff, and sewage. More than 80% arises from land-based sources. It reaches the oceans through rivers, runoff, atmospheric deposition and direct discharges. It is often heaviest near the coasts and most highly concentrated along the coasts of low- and middle-income countries. Plastic is a rapidly increasing and highly visible component of ocean pollution, and an estimated 10 million metric tons of plastic waste enter the seas each year. Mercury is the metal pollutant of greatest concern in the oceans; it is released from two main sources - coal combustion and small-scale gold mining. Global spread of industrialized agriculture with increasing use of chemical fertilizer leads to extension of Harmful Algal Blooms (HABs) to previously unaffected regions. Chemical pollutants are ubiquitous and contaminate seas and marine organisms from the high Arctic to the abyssal depths. Ecosystem Findings Ocean pollution has multiple negative impacts on marine ecosystems, and these impacts are exacerbated by global climate change. Petroleum-based pollutants reduce photosynthesis in marine microorganisms that generate oxygen. Increasing absorption of carbon dioxide into the seas causes ocean acidification, which destroys coral reefs, impairs shellfish development, dissolves calcium-containing microorganisms at the base of the marine food web, and increases the toxicity of some pollutants. Plastic pollution threatens marine mammals, fish, and seabirds and accumulates in large mid-ocean gyres. It breaks down into microplastic and nanoplastic particles containing multiple manufactured chemicals that can enter the tissues of marine organisms, including species consumed by humans. Industrial releases, runoff, and sewage increase frequency and severity of HABs, bacterial pollution, and anti-microbial resistance. Pollution and sea surface warming are triggering poleward migration of dangerous pathogens such as the Vibrio species. Industrial discharges, pharmaceutical wastes, pesticides, and sewage contribute to global declines in fish stocks. Human Health Findings Methylmercury and PCBs are the ocean pollutants whose human health effects are best understood. Exposures of infants in utero to these pollutants through maternal consumption of contaminated seafood can damage developing brains, reduce IQ and increase children's risks for autism, ADHD and learning disorders. Adult exposures to methylmercury increase risks for cardiovascular disease and dementia. Manufactured chemicals - phthalates, bisphenol A, flame retardants, and perfluorinated chemicals, many of them released into the seas from plastic waste - can disrupt endocrine signaling, reduce male fertility, damage the nervous system, and increase risk of cancer. HABs produce potent toxins that accumulate in fish and shellfish. When ingested, these toxins can cause severe neurological impairment and rapid death. HAB toxins can also become airborne and cause respiratory disease. Pathogenic marine bacteria cause gastrointestinal diseases and deep wound infections. With climate change and increasing pollution, risk is high that Vibrio infections, including cholera, will increase in frequency and extend to new areas. All of the health impacts of ocean pollution fall disproportionately on vulnerable populations in the Global South - environmental injustice on a planetary scale. Conclusions Ocean pollution is a global problem. It arises from multiple sources and crosses national boundaries. It is the consequence of reckless, shortsighted, and unsustainable exploitation of the earth's resources. It endangers marine ecosystems. It impedes the production of atmospheric oxygen. Its threats to human health are great and growing, but still incompletely understood. Its economic costs are only beginning to be counted.Ocean pollution can be prevented. Like all forms of pollution, ocean pollution can be controlled by deploying data-driven strategies based on law, policy, technology, and enforcement that target priority pollution sources. Many countries have used these tools to control air and water pollution and are now applying them to ocean pollution. Successes achieved to date demonstrate that broader control is feasible. Heavily polluted harbors have been cleaned, estuaries rejuvenated, and coral reefs restored.Prevention of ocean pollution creates many benefits. It boosts economies, increases tourism, helps restore fisheries, and improves human health and well-being. It advances the Sustainable Development Goals (SDG). These benefits will last for centuries. Recommendations World leaders who recognize the gravity of ocean pollution, acknowledge its growing dangers, engage civil society and the global public, and take bold, evidence-based action to stop pollution at source will be critical to preventing ocean pollution and safeguarding human health.Prevention of pollution from land-based sources is key. Eliminating coal combustion and banning all uses of mercury will reduce mercury pollution. Bans on single-use plastic and better management of plastic waste reduce plastic pollution. Bans on persistent organic pollutants (POPs) have reduced pollution by PCBs and DDT. Control of industrial discharges, treatment of sewage, and reduced applications of fertilizers have mitigated coastal pollution and are reducing frequency of HABs. National, regional and international marine pollution control programs that are adequately funded and backed by strong enforcement have been shown to be effective. Robust monitoring is essential to track progress.Further interventions that hold great promise include wide-scale transition to renewable fuels; transition to a circular economy that creates little waste and focuses on equity rather than on endless growth; embracing the principles of green chemistry; and building scientific capacity in all countries.Designation of Marine Protected Areas (MPAs) will safeguard critical ecosystems, protect vulnerable fish stocks, and enhance human health and well-being. Creation of MPAs is an important manifestation of national and international commitment to protecting the health of the seas.
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Affiliation(s)
| | - John J. Stegeman
- Woods Hole Center for Oceans and Human Health, Woods Hole Oceanographic Institution, US
| | - Lora E. Fleming
- European Centre for Environment and Human Health, GB
- University of Exeter Medical School, GB
| | | | - Donald M. Anderson
- Woods Hole Center for Oceans and Human Health, Woods Hole Oceanographic Institution, US
| | | | | | - Nicolas Chevalier
- Université Côte d’Azur, FR
- Centre Hospitalier Universitaire de Nice, Inserm, C3M, FR
| | - Lilian Corra
- International Society of Doctors for the Environment (ISDE), CH
- Health and Environment of the Global Alliance on Health and Pollution (GAHP), AR
| | | | - Marie-Yasmine Dechraoui Bottein
- Intergovernmental Oceanographic Commission of UNESCO, FR
- IOC Science and Communication Centre on Harmful Algae, University of Copenhagen, DK
- Ecotoxicologie et développement durable expertise ECODD, Valbonne, FR
| | - Barbara Demeneix
- Centre National de la Recherche Scientifique, FR
- Muséum National d’Histoire Naturelle, Paris, FR
| | | | - Dimitri D. Deheyn
- Scripps Institution of Oceanography, University of California San Diego, US
| | | | - Patrick Fénichel
- Université Côte d’Azur, FR
- Centre Hospitalier Universitaire de Nice, Inserm, C3M, FR
| | | | | | | | | | | | | | - Mark E. Hahn
- Woods Hole Center for Oceans and Human Health, Woods Hole Oceanographic Institution, US
| | | | - Philipp Hess
- Institut Français de Recherche pour l’Exploitation des Mers, FR
| | | | | | - Jacqueline McGlade
- Institute for Global Prosperity, University College London, GB
- Strathmore University Business School, Nairobi, KE
| | | | - Adetoun Mustapha
- Nigerian Institute for Medical Research, Lagos, NG
- Imperial College London, GB
| | | | | | | | - Christopher Reddy
- Department of Marine Chemistry and Geochemistry, Woods Hole Oceanographic Institution, US
| | - Joacim Rocklöv
- Department of Public Health and Clinical Medicine, Section of Sustainable Health, Umeå University, Umeå, SE
| | | | | | | | | | | | - Pál Weihe
- University of the Faroe Islands and Department of Occupational Medicine and Public Health, FO
| | | | - Hervé Raps
- Centre Scientifique de Monaco, MC
- WHO Collaborating Centre for Health and Sustainable Development, MC
| | - Patrick Rampal
- Centre Scientifique de Monaco, MC
- WHO Collaborating Centre for Health and Sustainable Development, MC
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44
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Shea D, Bateman A, Li S, Tabata A, Schulze A, Mordecai G, Ogston L, Volpe JP, Neil Frazer L, Connors B, Miller KM, Short S, Krkošek M. Environmental DNA from multiple pathogens is elevated near active Atlantic salmon farms. Proc Biol Sci 2020; 287:20202010. [PMID: 33081614 PMCID: PMC7661312 DOI: 10.1098/rspb.2020.2010] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
Abstract
The spread of infection from reservoir host populations is a key mechanism for disease emergence and extinction risk and is a management concern for salmon aquaculture and fisheries. Using a quantitative environmental DNA methodology, we assessed pathogen environmental DNA in relation to salmon farms in coastal British Columbia, Canada, by testing for 39 species of salmon pathogens (viral, bacterial, and eukaryotic) in 134 marine environmental samples at 58 salmon farm sites (both active and inactive) over 3 years. Environmental DNA from 22 pathogen species was detected 496 times and species varied in their occurrence among years and sites, likely reflecting variation in environmental factors, other native host species, and strength of association with domesticated Atlantic salmon. Overall, we found that the probability of detecting pathogen environmental DNA (eDNA) was 2.72 (95% CI: 1.48, 5.02) times higher at active versus inactive salmon farm sites and 1.76 (95% CI: 1.28, 2.42) times higher per standard deviation increase in domesticated Atlantic salmon eDNA concentration at a site. If the distribution of pathogen eDNA accurately reflects the distribution of viable pathogens, our findings suggest that salmon farms serve as a potential reservoir for a number of infectious agents; thereby elevating the risk of exposure for wild salmon and other fish species that share the marine environment.
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Affiliation(s)
- Dylan Shea
- Department of Ecology and Evolutionary Biology, University of Toronto, Ontario, Canada
| | - Andrew Bateman
- Department of Ecology and Evolutionary Biology, University of Toronto, Ontario, Canada.,Salmon Coast Field Station, Simoom Sound, British Columbia, Canada.,Pacific Salmon Foundation, Vancouver, British Columbia, Canada
| | - Shaorong Li
- Pacific Biological Station, Fisheries and Oceans Canada, Nanaimo, British Columbia, Canada
| | - Amy Tabata
- Pacific Biological Station, Fisheries and Oceans Canada, Nanaimo, British Columbia, Canada
| | - Angela Schulze
- Pacific Biological Station, Fisheries and Oceans Canada, Nanaimo, British Columbia, Canada
| | - Gideon Mordecai
- Department of Medicine, University of British Columbia, Vancouver, British Columbia, Canada
| | - Lindsey Ogston
- Department of Ecology and Evolutionary Biology, University of Toronto, Ontario, Canada
| | - John P Volpe
- School of Environmental Studies, University of Victoria, Victoria, British Columbia, Canada
| | - L Neil Frazer
- Department of Earth Sciences, University of Hawaii at Mānoa, Honolulu, Hawaii, Canada
| | - Brendan Connors
- Institute of Ocean Sciences, Fisheries and Oceans Canada, Sidney, British Columbia, Canada
| | - Kristina M Miller
- Pacific Biological Station, Fisheries and Oceans Canada, Nanaimo, British Columbia, Canada
| | - Steven Short
- Department of Ecology and Evolutionary Biology, University of Toronto, Ontario, Canada.,Department of Biology, University of Toronto Mississauga, Mississauga, British Columbia, Canada
| | - Martin Krkošek
- Department of Ecology and Evolutionary Biology, University of Toronto, Ontario, Canada.,Salmon Coast Field Station, Simoom Sound, British Columbia, Canada
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45
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Identification of Hypoxia-Specific Biomarkers in Salmonids Using RNA-Sequencing and Validation Using High-Throughput qPCR. G3-GENES GENOMES GENETICS 2020; 10:3321-3336. [PMID: 32694198 PMCID: PMC7466982 DOI: 10.1534/g3.120.401487] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Identifying early gene expression responses to hypoxia (i.e., low dissolved oxygen) as a tool to assess the degree of exposure to this stressor is crucial for salmonids, because they are increasingly exposed to hypoxic stress due to anthropogenic habitat change, e.g., global warming, excessive nutrient loading, and persistent algal blooms. Our goal was to discover and validate gill gene expression biomarkers specific to the hypoxia response in salmonids across multi-stressor conditions. Gill tissue was collected from 24 freshwater juvenile Chinook salmon (Oncorhynchus tshawytscha), held in normoxia [dissolved oxygen (DO) > 8 mg L-1] and hypoxia (DO = 4‒5 mg L-1) in 10 and 18° temperatures for up to six days. RNA-sequencing (RNA-seq) was then used to discover 240 differentially expressed genes between hypoxic and normoxic conditions, but not affected by temperature. The most significantly differentially expressed genes had functional roles in the cell cycle and suppression of cell proliferation associated with hypoxic conditions. The most significant genes (n = 30) were selected for real-time qPCR assay development. These assays demonstrated a strong correlation (r = 0.88; P < 0.001) between the expression values from RNA-seq and the fold changes from qPCR. Further, qPCR of the 30 candidate hypoxia biomarkers was applied to an additional 322 Chinook salmon exposed to hypoxic and normoxic conditions to reveal the top biomarkers to define hypoxic stress. Multivariate analyses revealed that smolt stage, water salinity, and morbidity status were relevant factors to consider with the expression of these genes in relation to hypoxic stress. These hypoxia candidate genes will be put into application screening Chinook salmon to determine the identity of stressors impacting the fish.
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46
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Mordecai GJ, Di Cicco E, Günther OP, Schulze AD, Kaukinen KH, Li S, Tabata A, Ming TJ, Ferguson HW, Suttle CA, Miller KM. Discovery and surveillance of viruses from salmon in British Columbia using viral immune-response biomarkers, metatranscriptomics, and high-throughput RT-PCR. Virus Evol 2020; 7:veaa069. [PMID: 33623707 PMCID: PMC7887441 DOI: 10.1093/ve/veaa069] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
The emergence of infectious agents poses a continual economic and environmental challenge to aquaculture production, yet the diversity, abundance, and epidemiology of aquatic viruses are poorly characterised. In this study, we applied salmon host transcriptional biomarkers to identify and select fish in a viral disease state, but only those that were negative for known viruses based on RT-PCR screening. These fish were selected for metatranscriptomic sequencing to discover potential viral pathogens of dead and dying farmed Atlantic (Salmo salar) and Chinook (Oncorhynchus tshawytscha) salmon in British Columbia (BC). We found that the application of the biomarker panel increased the probability of discovering viruses in aquaculture populations. We discovered two viruses that have not previously been characterised in Atlantic salmon farms in BC (Atlantic salmon calicivirus and Cutthroat trout virus-2), as well as partially sequenced three putative novel viruses. To determine the epidemiology of the newly discovered or emerging viruses, we conducted high-throughput reverse transcription polymerase chain reaction (RT-PCR) and screened over 9,000 farmed and wild salmon sampled over one decade. Atlantic salmon calicivirus and Cutthroat trout virus-2 were in more than half of the farmed Atlantic salmon we tested. Importantly we detected some of the viruses we first discovered in farmed Atlantic salmon in Chinook salmon, suggesting a broad host range. Finally, we applied in situ hybridisation to determine infection and found differing cell tropism for each virus tested. Our study demonstrates that continual discovery and surveillance of emerging viruses in these ecologically important salmon will be vital for management of both aquaculture and wild resources in the future.
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Affiliation(s)
- Gideon J Mordecai
- Department of Medicine, University of British Columbia, 2775 Laurel Street, 10th Floor Vancouver, BC Canada V5Z 1M9, Canada
- Corresponding author: E-mail:
| | - Emiliano Di Cicco
- Pacific Biological Station, Fisheries and Oceans Canada, 3190 Hammond Bay Rd, Nanaimo, BC V9T 6N7, Canada
- Pacific Salmon Foundation, 1682 W 7th Ave, Vancouver, BC V6J 4S6, Canada
| | - Oliver P Günther
- Günther Analytics, 402-5775 Hampton Place, Vancouver, BC, V6T 2G6, Canada
| | - Angela D Schulze
- Pacific Biological Station, Fisheries and Oceans Canada, 3190 Hammond Bay Rd, Nanaimo, BC V9T 6N7, Canada
| | - Karia H Kaukinen
- Pacific Biological Station, Fisheries and Oceans Canada, 3190 Hammond Bay Rd, Nanaimo, BC V9T 6N7, Canada
| | - Shaorong Li
- Pacific Biological Station, Fisheries and Oceans Canada, 3190 Hammond Bay Rd, Nanaimo, BC V9T 6N7, Canada
| | - Amy Tabata
- Pacific Biological Station, Fisheries and Oceans Canada, 3190 Hammond Bay Rd, Nanaimo, BC V9T 6N7, Canada
| | - Tobi J Ming
- Pacific Biological Station, Fisheries and Oceans Canada, 3190 Hammond Bay Rd, Nanaimo, BC V9T 6N7, Canada
| | - Hugh W Ferguson
- School of Veterinary Medicine, St George’s University, True Blue, GrenadaWest Indies
| | - Curtis A Suttle
- Department of Earth, Ocean and Atmospheric Sciences, University of British Columbia, Vancouver, Canada
- Department of Microbiology and Immunology, University of British Columbia, 1365 - 2350 Health Sciences Mall Vancouver, British Columbia Canada V6T 1Z3
- Department of Botany, University of British Columbia, 3156-6270 University Blvd. Vancouver, BC Canada V6T 1Z4, Canada
- Institute for the Oceans and Fisheries, University of British Columbia, 2202 Main Mall, Vancouver, BC V6T 1Z4, Canada
| | - Kristina M Miller
- Pacific Biological Station, Fisheries and Oceans Canada, 3190 Hammond Bay Rd, Nanaimo, BC V9T 6N7, Canada
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47
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Abstract
Interest in coronaviruses because of the 2019 novel coronavirus (SARS-CoV-2) pandemic has generated concern about their occurrence and persistence in aquatic habitats. Coronaviruses are not quantitatively significant constituents of marine virioplankton. Members of the Nidovirales (to which human coronaviruses belong) infect marine mammals, teleosts and possibly invertebrates, and human coronaviruses may persist in marine plankton receiving wastewater effluent. However, virions likely experience significant particle and infectivity decay rates in surface seawater, similar to other enveloped RNA viruses.
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Affiliation(s)
- Gideon J. Mordecai
- Department of Earth, Ocean and Atmospheric Sciences, The University of British Columbia, Vancouver, BC, Canada
| | - Ian Hewson
- Department of Microbiology, Cornell University, Ithaca, NY, United States
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48
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Riccio G, Ruocco N, Mutalipassi M, Costantini M, Zupo V, Coppola D, de Pascale D, Lauritano C. Ten-Year Research Update Review: Antiviral Activities from Marine Organisms. Biomolecules 2020; 10:biom10071007. [PMID: 32645994 PMCID: PMC7407529 DOI: 10.3390/biom10071007] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2020] [Revised: 06/25/2020] [Accepted: 06/28/2020] [Indexed: 02/08/2023] Open
Abstract
Oceans cover more than 70 percent of the surface of our planet and are characterized by huge taxonomic and chemical diversity of marine organisms. Several studies have shown that marine organisms produce a variety of compounds, derived from primary or secondary metabolism, which may have antiviral activities. In particular, certain marine metabolites are active towards a plethora of viruses. Multiple mechanisms of action have been found, as well as different targets. This review gives an overview of the marine-derived compounds discovered in the last 10 years. Even if marine organisms produce a wide variety of different compounds, there is only one compound available on the market, Ara-A, and only another one is in phase I clinical trials, named Griffithsin. The recent pandemic emergency caused by SARS-CoV-2, also known as COVID-19, highlights the need to further invest in this field, in order to shed light on marine compound potentiality and discover new drugs from the sea.
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Affiliation(s)
- Gennaro Riccio
- Marine Biotechnology Department, Stazione Zoologica Anton Dohrn, CAP, 80121 Naples, Italy; (G.R.); (N.R.); (M.M.); (M.C.); (V.Z.); (D.C.); (D.d.P.)
| | - Nadia Ruocco
- Marine Biotechnology Department, Stazione Zoologica Anton Dohrn, CAP, 80121 Naples, Italy; (G.R.); (N.R.); (M.M.); (M.C.); (V.Z.); (D.C.); (D.d.P.)
| | - Mirko Mutalipassi
- Marine Biotechnology Department, Stazione Zoologica Anton Dohrn, CAP, 80121 Naples, Italy; (G.R.); (N.R.); (M.M.); (M.C.); (V.Z.); (D.C.); (D.d.P.)
| | - Maria Costantini
- Marine Biotechnology Department, Stazione Zoologica Anton Dohrn, CAP, 80121 Naples, Italy; (G.R.); (N.R.); (M.M.); (M.C.); (V.Z.); (D.C.); (D.d.P.)
| | - Valerio Zupo
- Marine Biotechnology Department, Stazione Zoologica Anton Dohrn, CAP, 80121 Naples, Italy; (G.R.); (N.R.); (M.M.); (M.C.); (V.Z.); (D.C.); (D.d.P.)
| | - Daniela Coppola
- Marine Biotechnology Department, Stazione Zoologica Anton Dohrn, CAP, 80121 Naples, Italy; (G.R.); (N.R.); (M.M.); (M.C.); (V.Z.); (D.C.); (D.d.P.)
- Institute of Biosciences and BioResources (IBBR), National Research Council, Via Pietro Castellino 111, 80131 Naples, Italy
| | - Donatella de Pascale
- Marine Biotechnology Department, Stazione Zoologica Anton Dohrn, CAP, 80121 Naples, Italy; (G.R.); (N.R.); (M.M.); (M.C.); (V.Z.); (D.C.); (D.d.P.)
- Institute of Biochemistry and Cell Biology (IBBC), National Research Council, Via Pietro Castellino 111, 80131 Naples, Italy
| | - Chiara Lauritano
- Marine Biotechnology Department, Stazione Zoologica Anton Dohrn, CAP, 80121 Naples, Italy; (G.R.); (N.R.); (M.M.); (M.C.); (V.Z.); (D.C.); (D.d.P.)
- Correspondence: ; Tel.: +39-081-5833-221
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49
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Lennox RJ, Eldøy SH, Vollset KW, Miller KM, Li S, Kaukinen KH, Isaksen TE, Davidsen JG. How pathogens affect the marine habitat use and migration of sea trout (Salmo trutta) in two Norwegian fjord systems. JOURNAL OF FISH DISEASES 2020; 43:729-746. [PMID: 32364277 DOI: 10.1111/jfd.13170] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/06/2020] [Revised: 03/09/2020] [Accepted: 03/11/2020] [Indexed: 06/11/2023]
Abstract
Wild fish are confronting changing pathogen dynamics arising from anthropogenic disturbance and climate change. Pathogens can influence animal behaviour and life histories, yet there are little such data from fish in the high north where pathogen dynamics may differ from comparatively southern regions. We aimed to compare the pathogen communities of 160 wild anadromous brown trout in two fjords in northern Norway and to determine whether pathogens influenced area use or return to spawn. Application of high-throughput qPCR detected 11 of the 46 pathogens screened for; most frequently encountered were Ichthyobodo spp., Flavobacterium psychrophilum and Candidatus Branchiomonas cysticola. The rate of returning to freshwater during the spawning season was significantly lower for the Skjerstadfjord fish. Piscichlamydia salmonis and F. psychrophilum were indicator species for the Skjerstadfjord and pathogen communities in the two fjords differed according to perMANOVA. Individual length, Fulton's condition factor and the time between first and last detection of the fish were not related to the presence of pathogens ordinated using non-metric multidimensional scaling (NMDS). However, there was evidence that pathogen load was correlated with the expression of smoltification genes, which are upregulated by salmonids in freshwater. Correspondingly, percentage of time in freshwater after release was longer for fish with greater pathogen burdens.
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Affiliation(s)
- Robert J Lennox
- Laboratory for Freshwater Ecology and Inland Fisheries, NORCE Norwegian Research Centre, Bergen, Norway
| | - Sindre H Eldøy
- NTNU University Museum, Norwegian University of Science and Technology, Trondheim, Norway
| | - Knut W Vollset
- Laboratory for Freshwater Ecology and Inland Fisheries, NORCE Norwegian Research Centre, Bergen, Norway
| | - Kristi M Miller
- Pacific Biological Station, Fisheries and Oceans, The Canadian Coastguard, Nanaimo, BC, Canada
| | - Shaorong Li
- Pacific Biological Station, Fisheries and Oceans, The Canadian Coastguard, Nanaimo, BC, Canada
| | - Karia H Kaukinen
- Pacific Biological Station, Fisheries and Oceans, The Canadian Coastguard, Nanaimo, BC, Canada
| | - Trond E Isaksen
- Laboratory for Freshwater Ecology and Inland Fisheries, NORCE Norwegian Research Centre, Bergen, Norway
| | - Jan G Davidsen
- NTNU University Museum, Norwegian University of Science and Technology, Trondheim, Norway
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50
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On the Coronaviruses and Their Associations with the Aquatic Environment and Wastewater. WATER 2020. [DOI: 10.3390/w12061598] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
The outbreak of Coronavirus Disease 2019 (COVID-19), a severe respiratory disease caused by betacoronavirus SARS-CoV-2, in 2019 that further developed into a pandemic has received an unprecedented response from the scientific community and sparked a general research interest into the biology and ecology of Coronaviridae, a family of positive-sense single-stranded RNA viruses. Aquatic environments, lakes, rivers and ponds, are important habitats for bats and birds, which are hosts for various coronavirus species and strains and which shed viral particles in their feces. It is therefore of high interest to fully explore the role that aquatic environments may play in coronavirus spread, including cross-species transmissions. Besides the respiratory tract, coronaviruses pathogenic to humans can also infect the digestive system and be subsequently defecated. Considering this, it is pivotal to understand whether wastewater can play a role in their dissemination, particularly in areas with poor sanitation. This review provides an overview of the taxonomy, molecular biology, natural reservoirs and pathogenicity of coronaviruses; outlines their potential to survive in aquatic environments and wastewater; and demonstrates their association with aquatic biota, mainly waterfowl. It also calls for further, interdisciplinary research in the field of aquatic virology to explore the potential hotspots of coronaviruses in the aquatic environment and the routes through which they may enter it.
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