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Gonzalez V, Hurtado-Monzón AM, O'Krafka S, Mühlberger E, Letko M, Frank HK, Laing ED, Phelps KL, Becker DJ, Munster VJ, Falzarano D, Schountz T, Seifert SN, Banerjee A. Studying bats using a One Health lens: bridging the gap between bat virology and disease ecology. J Virol 2024; 98:e0145324. [PMID: 39499009 DOI: 10.1128/jvi.01453-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2024] Open
Abstract
Accumulating data suggest that some bat species host emerging viruses that are highly pathogenic in humans and agricultural animals. Laboratory-based studies have highlighted important adaptations in bat immune systems that allow them to better tolerate viral infections compared to humans. Simultaneously, ecological studies have discovered critical extrinsic factors, such as nutritional stress, that correlate with virus shedding in wild-caught bats. Despite some progress in independently understanding the role of bats as reservoirs of emerging viruses, there remains a significant gap in the molecular understanding of factors that drive virus spillover from bats. Driven by a collective goal of bridging the gap between the fields of bat virology, immunology, and disease ecology, we hosted a satellite symposium at the 2024 American Society for Virology meeting. Bringing together virologists, immunologists, and disease ecologists, we discussed the intrinsic and extrinsic factors such as virus receptor engagement, adaptive immunity, and virus ecology that influence spillover from bat hosts. This article summarizes the topics discussed during the symposium and emphasizes the need for interdisciplinary collaborations and resource sharing.
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Affiliation(s)
- Victoria Gonzalez
- Vaccine and Infectious Disease Organization (VIDO), University of Saskatchewan, Saskatoon, Saskatchewan, Canada
- Department of Veterinary Microbiology, University of Saskatchewan, Saskatoon, Saskatchewan, Canada
| | - Arianna M Hurtado-Monzón
- Vaccine and Infectious Disease Organization (VIDO), University of Saskatchewan, Saskatoon, Saskatchewan, Canada
| | - Sabrina O'Krafka
- Vaccine and Infectious Disease Organization (VIDO), University of Saskatchewan, Saskatoon, Saskatchewan, Canada
| | - Elke Mühlberger
- Department of Virology, Immunology, and Microbiology, Boston University, Boston, Massachusetts, USA
- Chobanian and Avedisian School of Medicine, Boston University, Boston, Massachusetts, USA
- National Emerging Infectious Diseases Laboratories, Boston University, Boston, Massachusetts, USA
| | - Michael Letko
- Paul G. Allen School for Global Health, Washington State University, Pullman, Washington, USA
| | - Hannah K Frank
- Department of Ecology and Evolutionary Biology, Tulane University, New Orleans, Louisiana, USA
| | - Eric D Laing
- Department of Microbiology and Immunology, Uniformed Services University, Bethesda, Maryland, USA
| | | | - Daniel J Becker
- School of Biological Sciences, University of Oklahoma, Norman, Oklahoma, USA
| | - Vincent J Munster
- Laboratory of Virology, National Institute of Allergy and Infectious Diseases (NIAID), Hamilton, Montana, USA
| | - Darryl Falzarano
- Vaccine and Infectious Disease Organization (VIDO), University of Saskatchewan, Saskatoon, Saskatchewan, Canada
- Department of Veterinary Microbiology, University of Saskatchewan, Saskatoon, Saskatchewan, Canada
| | - Tony Schountz
- Department of Microbiology, Immunology, and Pathology, Colorado State University, Fort Collins, Colorado, USA
- Center for Vector-Borne Infectious Diseases, Colorado State University, Fort Collins, Colorado, USA
| | - Stephanie N Seifert
- Paul G. Allen School for Global Health, Washington State University, Pullman, Washington, USA
| | - Arinjay Banerjee
- Vaccine and Infectious Disease Organization (VIDO), University of Saskatchewan, Saskatoon, Saskatchewan, Canada
- Department of Veterinary Microbiology, University of Saskatchewan, Saskatoon, Saskatchewan, Canada
- Department of Biology, University of Waterloo, Waterloo, Ontario, Canada
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada
- Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, British Columbia, Canada
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Goldberg TL, Perez AU, Campbell LJ. Isopods infesting Atlantic bonefish ( Albula vulpes) host novel viruses, including reoviruses related to global pathogens, and opportunistically feed on humans. Parasitology 2024; 151:1386-1396. [PMID: 39563628 PMCID: PMC11894014 DOI: 10.1017/s003118202400146x] [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: 05/20/2024] [Revised: 09/06/2024] [Accepted: 10/25/2024] [Indexed: 11/21/2024]
Abstract
Isopods infest fish worldwide, but their role as disease vectors remains poorly understood. Here, we describe infestation of Atlantic bonefish (Albula vulpes) in Belize with isopods in two of three locations studied, with infestation rates of 15 and 44%. Isopods fed aggressively, and infested fish showed missing scales and scars. Gross morphologic and molecular phylogenetic analyses revealed the isopods to cluster within the family Aegidae and to be most closely related to members of the genus Rocinela, which are globally distributed micro-predators of fish. Metagenomic analysis of 10 isopods identified 11 viruses, including two novel reoviruses (Reovirales) in the families Sedoreoviridae and Spinareoviridae. The novel sedoreovirus clustered phylogenetically within an invertebrate-specific clade of viruses related to the genus Orbivirus, which contains arboviruses of global concern for mammal health. The novel spinareovirus clustered within the fish-infecting genus Aquareovirus, which contains viruses of global concern for fish health. Metagenomic analyses revealed no evidence of infection of bonefish with the novel aquareovirus, suggesting that viremia in bonefish is absent, low, or transient, or that isopods may have acquired the virus from other fish. During field collections, isopods aggressively bit humans, and blood meal analysis confirmed that isopods had fed on bonefish, other fish, and humans. Vector-borne transmission may be an underappreciated mechanism for aquareovirus transmission and for virus host switching between fish and other species, which has been inferred across viral families from studies of deep virus evolution.
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Affiliation(s)
- Tony L. Goldberg
- Department of Pathobiological Sciences, School of Veterinary Medicine, University of Wisconsin-Madison, Madison, WI, USA
| | | | - Lewis J. Campbell
- Department of Pathobiological Sciences, School of Veterinary Medicine, University of Wisconsin-Madison, Madison, WI, USA
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Taylor DJ, Barnhart MH. Genomic transfers help to decipher the ancient evolution of filoviruses and interactions with vertebrate hosts. PLoS Pathog 2024; 20:e1011864. [PMID: 39226335 PMCID: PMC11398700 DOI: 10.1371/journal.ppat.1011864] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2023] [Revised: 09/13/2024] [Accepted: 08/21/2024] [Indexed: 09/05/2024] Open
Abstract
Although several filoviruses are dangerous human pathogens, there is conflicting evidence regarding their origins and interactions with animal hosts. Here we attempt to improve this understanding using the paleoviral record over a geological time scale, protein structure predictions, tests for evolutionary maintenance, and phylogenetic methods that alleviate sources of bias and error. We found evidence for long branch attraction bias in the L gene tree for filoviruses, and that using codon-specific models and protein structural comparisons of paleoviruses ameliorated conflict and bias. We found evidence for four ancient filoviral groups, each with extant viruses and paleoviruses with open reading frames. Furthermore, we found evidence of repeated transfers of filovirus-like elements to mouse-like rodents. A filovirus-like nucleoprotein ortholog with an open reading frame was detected in three subfamilies of spalacid rodents (present since the Miocene). We provide evidence that purifying selection is acting to maintain amino acids, protein structure and open reading frames in these elements. Our finding of extant viruses nested within phylogenetic clades of paleoviruses informs virus discovery methods and reveals the existence of Lazarus taxa among RNA viruses. Our results resolve a deep conflict in the evolutionary framework for filoviruses and reveal that genomic transfers to vertebrate hosts with potentially functional co-options have been more widespread than previously appreciated.
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Affiliation(s)
- Derek J Taylor
- Department of Biological Sciences, University at Buffalo, Buffalo, New York, United States of America
| | - Max H Barnhart
- Department of Biological Sciences, University at Buffalo, Buffalo, New York, United States of America
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Groseth A, Hoenen T. Novel filoviruses: indication of a global threat or cause to reassess our risk perception? NPJ VIRUSES 2024; 2:38. [PMID: 40295872 PMCID: PMC11721365 DOI: 10.1038/s44298-024-00050-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/04/2024] [Accepted: 08/06/2024] [Indexed: 04/30/2025]
Abstract
Filoviruses such as Ebola virus are widely known as causative agents of severe human disease, although apathogenic filoviruses also exist. There is now increasing evidence that filoviruses circulate in almost all parts of the world, where they are being discovered in an expanding range of sometimes unexpected host species. Here we summarize the current knowledge regarding these novel filoviruses, and open questions that need answering to assess and prepare for the risk they pose.
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Affiliation(s)
- Allison Groseth
- Institute for Molecular Virology and Cell Biology, Friedrich-Loeffler-Institut, Greifswald - Insel Riems, Greifswald, Germany
| | - Thomas Hoenen
- Institute for Molecular Virology and Cell Biology, Friedrich-Loeffler-Institut, Greifswald - Insel Riems, Greifswald, Germany.
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Pawęska JT, Storm N, Jansen van Vuren P, Markotter W, Kemp A. Attempted Transmission of Marburg Virus by Bat-Associated Fleas Thaumapsylla breviceps breviceps (Ischnopsyllidae: Thaumapsyllinae) to the Egyptian Rousette Bat ( Rousettus aegyptiacus). Viruses 2024; 16:1197. [PMID: 39205171 PMCID: PMC11360628 DOI: 10.3390/v16081197] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2024] [Revised: 07/22/2024] [Accepted: 07/23/2024] [Indexed: 09/04/2024] Open
Abstract
Egyptian rousette bats (ERBs) are implicated as reservoir hosts for Marburg virus (MARV), but natural mechanisms involved in maintenance of MARV in ERB populations remain undefined. A number of hematophagous ectoparasites, including fleas, parasitize bats. Subcutaneous (SC) inoculation of ERBs with MARV consistently results in viremia, suggesting that infectious MARV could be ingested by blood-sucking ectoparasites during feeding. In our study, MARV RNA was detected in fleas that took a blood meal during feeding on viremic bats on days 3, 7, and 11 after SC inoculation. Virus concentration in individual ectoparasites was consistent with detectable levels of viremia in the blood of infected host bats. There was neither seroconversion nor viremia in control bats kept in close contact with MARV-infected bats infested with fleas for up to 40 days post-exposure. In fleas inoculated intracoelomically, MARV was detected up to 14 days after intracoelomic (IC) inoculation, but the virus concentration was lower than that delivered in the inoculum. All bats that had been infested with inoculated, viremic fleas remained virologically and serologically negative up to 38 days after infestation. Of 493 fleas collected from a wild ERB colony in Matlapitsi Cave, South Africa, where the enzootic transmission of MARV occurs, all tested negative for MARV RNA. While our findings seem to demonstrate that bat fleas lack vectorial capacity to transmit MARV biologically, their role in mechanical transmission should not be discounted. Regular blood-feeds, intra- and interhost mobility, direct feeding on blood vessels resulting in venous damage, and roosting behaviour of ERBs provide a potential physical bridge for MARV dissemination in densely populated cave-dwelling bats by fleas. The virus transfer might take place through inoculation of skin, mucosal membranes, and wounds when contaminated fleas are squashed during auto- and allogrooming, eating, biting, or fighting.
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Affiliation(s)
- Janusz T. Pawęska
- Centre for Emerging Zoonotic and Parasitic Diseases, National Institute for Communicable Diseases of the National Health Laboratory Service, Sandringham 2131, South Africa; (N.S.); (P.J.v.V.); (A.K.)
- Centre for Viral Zoonoses, Department of Medical Virology, Faculty of Health Sciences, University of Pretoria, Pretoria 0001, South Africa;
- Faculty of Health Sciences, University of Witwatersrand, Johannesburg 2050, South Africa
| | - Nadia Storm
- Centre for Emerging Zoonotic and Parasitic Diseases, National Institute for Communicable Diseases of the National Health Laboratory Service, Sandringham 2131, South Africa; (N.S.); (P.J.v.V.); (A.K.)
- Department of Microbiology, School of Medicine, Boston University, Boston, MA 02118, USA
| | - Petrus Jansen van Vuren
- Centre for Emerging Zoonotic and Parasitic Diseases, National Institute for Communicable Diseases of the National Health Laboratory Service, Sandringham 2131, South Africa; (N.S.); (P.J.v.V.); (A.K.)
- CSIRO Health & Biosecurity, Australian Centre for Disease Preparedness, Geelong, VIC 3220, Australia
| | - Wanda Markotter
- Centre for Viral Zoonoses, Department of Medical Virology, Faculty of Health Sciences, University of Pretoria, Pretoria 0001, South Africa;
| | - Alan Kemp
- Centre for Emerging Zoonotic and Parasitic Diseases, National Institute for Communicable Diseases of the National Health Laboratory Service, Sandringham 2131, South Africa; (N.S.); (P.J.v.V.); (A.K.)
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Emmenegger EJ, Bueren EK, Conway CM, Sanders GE, Hendrix AN, Schroeder T, Di Cicco E, Pham PH, Lumsden JS, Clouthier SC. Host Jump of an Exotic Fish Rhabdovirus into a New Class of Animals Poses a Disease Threat to Amphibians. Viruses 2024; 16:1193. [PMID: 39205167 PMCID: PMC11360232 DOI: 10.3390/v16081193] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2024] [Revised: 07/17/2024] [Accepted: 07/18/2024] [Indexed: 09/04/2024] Open
Abstract
Spring viremia of carp virus (SVCV) is a rhabdovirus that primarily infects cyprinid finfishes and causes a disease notifiable to the World Organization for Animal Health. Amphibians, which are sympatric with cyprinids in freshwater ecosystems, are considered non-permissive hosts of rhabdoviruses. The potential host range expansion of SVCV in an atypical host species was evaluated by testing the susceptibility of amphibians native to the Pacific Northwest. Larval long-toed salamanders Ambystoma macrodactylum and Pacific tree frog Pseudacris regilla tadpoles were exposed to SVCV strains from genotypes Ia, Ib, Ic, or Id by either intraperitoneal injection, immersion, or cohabitation with virus-infected koi Cyprinus rubrofuscus. Cumulative mortality was 100% for salamanders injected with SVCV, 98-100% for tadpoles exposed to virus via immersion, and 0-100% for tadpoles cohabited with SVCV-infected koi. Many of the animals that died exhibited clinical signs of disease and SVCV RNA was found by in situ hybridization in tissue sections of immersion-exposed tadpoles, particularly in the cells of the gastrointestinal tract and liver. SVCV was also detected by plaque assay and RT-qPCR testing in both amphibian species regardless of the virus exposure method, and viable virus was detected up to 28 days after initial exposure. Recovery of infectious virus from naïve tadpoles cohabited with SVCV-infected koi further demonstrated that SVCV transmission can occur between classes of ectothermic vertebrates. Collectively, these results indicated that SVCV, a fish rhabdovirus, can be transmitted to and cause lethal disease in two amphibian species. Therefore, members of all five of the major vertebrate groups (mammals, birds, reptiles, fish, and amphibians) appear to be vulnerable to rhabdovirus infections. Future research studying potential spillover and spillback infections of aquatic rhabdoviruses between foreign and domestic amphibian and fish species will provide insights into the stressors driving novel interclass virus transmission events.
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Affiliation(s)
- Eveline J Emmenegger
- U.S. Geological Survey, Western Fisheries Research Center (WFRC), 6505 NE 65th Street, Seattle, WA 98115, USA
| | - Emma K Bueren
- U.S. Geological Survey, Western Fisheries Research Center (WFRC), 6505 NE 65th Street, Seattle, WA 98115, USA
- Department of Biology, Indiana University, 1001 E 3rd St, Bloomington, IN 47405, USA
| | - Carla M Conway
- U.S. Geological Survey, Western Fisheries Research Center (WFRC), 6505 NE 65th Street, Seattle, WA 98115, USA
| | - George E Sanders
- Department of Comparative Medicine, University of Washington, Seattle, WA 98195, USA
| | - A Noble Hendrix
- QEDA Consulting, 4007 Densmore Avenue N, Seattle, WA 98103, USA
- School of Aquatic and Fishery Sciences, University of Washington, Seattle, WA 98195, USA
| | - Tamara Schroeder
- Freshwater Institute, Fisheries and Oceans Canada (DFO), 501 University Crescent, Winnipeg, MB R3T 2N6, Canada
| | - Emiliano Di Cicco
- Pacific Salmon Foundation (PSF), 1682 W 7th Ave., Vancouver, BC V6J 4S6, Canada
| | - Phuc H Pham
- Department of Pathobiology, Ontario Veterinary College, University of Guelph, Guelph, ON N1G 2W1, Canada
| | - John S Lumsden
- Department of Pathobiology, Ontario Veterinary College, University of Guelph, Guelph, ON N1G 2W1, Canada
| | - Sharon C Clouthier
- Freshwater Institute, Fisheries and Oceans Canada (DFO), 501 University Crescent, Winnipeg, MB R3T 2N6, Canada
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Costa VA, Holmes EC. Diversity, evolution, and emergence of fish viruses. J Virol 2024; 98:e0011824. [PMID: 38785422 PMCID: PMC11237817 DOI: 10.1128/jvi.00118-24] [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: 05/25/2024] Open
Abstract
The production of aquatic animals has more than doubled over the last 50 years and is anticipated to continually increase. While fish are recognized as a valuable and sustainable source of nutrition, particularly in the context of human population growth and climate change, the rapid expansion of aquaculture coincides with the emergence of highly pathogenic viruses that often spread globally through aquacultural practices. Here, we provide an overview of the fish virome and its relevance for disease emergence, with a focus on the insights gained through metagenomic sequencing, noting potential areas for future study. In particular, we describe the diversity and evolution of fish viruses, for which the majority have no known disease associations, and demonstrate how viruses emerge in fish populations, most notably at an expanding domestic-wild interface. We also show how wild fish are a powerful and tractable model system to study virus ecology and evolution more broadly and can be used to identify the major factors that shape vertebrate viromes. Central to this is a process of virus-host co-divergence that proceeds over many millions of years, combined with ongoing cross-species virus transmission.
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Affiliation(s)
- Vincenzo A. Costa
- Sydney Institute for Infectious Diseases, School of Medical Sciences, The University of Sydney, Sydney, New South Wales, Australia
| | - Edward C. Holmes
- Sydney Institute for Infectious Diseases, School of Medical Sciences, The University of Sydney, Sydney, New South Wales, Australia
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Lu X, Dai Z, Xue J, Li W, Ni P, Xu J, Zhou C, Zhang W. Discovery of novel RNA viruses through analysis of fungi-associated next-generation sequencing data. BMC Genomics 2024; 25:517. [PMID: 38797853 PMCID: PMC11129472 DOI: 10.1186/s12864-024-10432-w] [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: 03/19/2024] [Accepted: 05/20/2024] [Indexed: 05/29/2024] Open
Abstract
BACKGROUND Like all other species, fungi are susceptible to infection by viruses. The diversity of fungal viruses has been rapidly expanding in recent years due to the availability of advanced sequencing technologies. However, compared to other virome studies, the research on fungi-associated viruses remains limited. RESULTS In this study, we downloaded and analyzed over 200 public datasets from approximately 40 different Bioprojects to explore potential fungal-associated viral dark matter. A total of 12 novel viral sequences were identified, all of which are RNA viruses, with lengths ranging from 1,769 to 9,516 nucleotides. The amino acid sequence identity of all these viruses with any known virus is below 70%. Through phylogenetic analysis, these RNA viruses were classified into different orders or families, such as Mitoviridae, Benyviridae, Botourmiaviridae, Deltaflexiviridae, Mymonaviridae, Bunyavirales, and Partitiviridae. It is possible that these sequences represent new taxa at the level of family, genus, or species. Furthermore, a co-evolution analysis indicated that the evolutionary history of these viruses within their groups is largely driven by cross-species transmission events. CONCLUSIONS These findings are of significant importance for understanding the diversity, evolution, and relationships between genome structure and function of fungal viruses. However, further investigation is needed to study their interactions.
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Affiliation(s)
- Xiang Lu
- Institute of Critical Care Medicine, The Affiliated People's Hospital, Jiangsu University, Zhenjiang, 212002, China
- Department of Microbiology, School of Medicine, Jiangsu University, Zhenjiang, 212013, China
| | - Ziyuan Dai
- Department of Clinical Laboratory, Affiliated Hospital 6 of Nantong University, Yancheng Third People's Hospital, Yancheng, Jiangsu, China
| | - Jiaxin Xue
- Department of Microbiology, School of Medicine, Jiangsu University, Zhenjiang, 212013, China
| | - Wang Li
- Clinical Laboratory Center, The Affiliated Taizhou People's Hospital of Nanjing Medical University, Taizhou, 225300, China
| | - Ping Ni
- Clinical Laboratory Center, The Affiliated Taizhou People's Hospital of Nanjing Medical University, Taizhou, 225300, China
| | - Juan Xu
- Clinical Laboratory Center, The Affiliated Taizhou People's Hospital of Nanjing Medical University, Taizhou, 225300, China.
| | - Chenglin Zhou
- Clinical Laboratory Center, The Affiliated Taizhou People's Hospital of Nanjing Medical University, Taizhou, 225300, China.
| | - Wen Zhang
- Institute of Critical Care Medicine, The Affiliated People's Hospital, Jiangsu University, Zhenjiang, 212002, China.
- Department of Microbiology, School of Medicine, Jiangsu University, Zhenjiang, 212013, China.
- Clinical Laboratory Center, The Affiliated Taizhou People's Hospital of Nanjing Medical University, Taizhou, 225300, China.
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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] [MESH Headings] [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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Taube K, Noreikiene K, Kahar S, Gross R, Ozerov M, Vasemägi A. Subtle transcriptomic response of Eurasian perch ( Perca fluviatilis) associated with Triaenophorus nodulosus plerocercoid infection. Int J Parasitol Parasites Wildl 2023; 22:146-154. [PMID: 37869060 PMCID: PMC10585624 DOI: 10.1016/j.ijppaw.2023.09.009] [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: 07/10/2023] [Revised: 09/20/2023] [Accepted: 09/21/2023] [Indexed: 10/24/2023]
Abstract
Determining the physiological effects of parasites and characterizing genes involved in host responses to infections are essential to improving our understanding of host-parasite interactions and their ecological and evolutionary consequences. This task, however, is complicated by high diversity and complex life histories of many parasite species. The use of transcriptomics in the context of wild-caught specimens can help ameliorate this by providing both qualitative and quantitative information on gene expression patterns in response to parasites in specific host organs and tissues. Here, we evaluated the physiological impact of the widespread parasite, the pike tapeworm (Triaenophorus nodulosus), on its second intermediate host, the Eurasian perch (Perca fluviatilis). We used an RNAseq approach to analyse gene expression in the liver, the target organ of T. nodulosus plerocercoids, and spleen which is one of the main immune organs in teleost fishes. We compared perch collected from multiple lakes consisting of individuals with (n = 8) and without (n = 6) T. nodulosus plerocercoids in the liver. Results revealed a small number of differentially expressed genes (DEGs, adjusted p-value ≤0.05) in both spleen (n = 22) and liver (n = 10). DEGs in spleen consisted of mostly upregulated immune related genes (e.g., JUN, SIK1, THSB1), while those in the liver were often linked to metabolic functions (e.g., FABP1, CADM4, CDAB). However, Gene Ontology (GO) analysis showed lack of functional enrichment among DEGs. This study demonstrates that Eurasian perch displays a subtle response at a gene expression level to T. nodulosus plerocercoid infection. Given that plerocercoids are low-metabolic activity transmission stages, our results suggest that moderate T. nodulosus plerocercoid infection most likely does not provoke an extensive host immune response and have relatively low physiological costs for the host. Our findings illustrate that not all conspicuous infections have severe effects on host gene regulation.
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Affiliation(s)
- Konrad Taube
- Chair of Aquaculture, Estonian University of Life Sciences, Kreutzwaldi 46a, 51014 Tartu, Estonia
| | - Kristina Noreikiene
- Chair of Aquaculture, Estonian University of Life Sciences, Kreutzwaldi 46a, 51014 Tartu, Estonia
- Institute of Biosciences, Life Sciences Center, Vilnius University Vilnius, Lithuania
| | - Siim Kahar
- Chair of Aquaculture, Estonian University of Life Sciences, Kreutzwaldi 46a, 51014 Tartu, Estonia
| | - Riho Gross
- Chair of Aquaculture, Estonian University of Life Sciences, Kreutzwaldi 46a, 51014 Tartu, Estonia
| | - Mikhail Ozerov
- Biodiversity Unit, University of Turku, Vesilinnantie 5, 20500 Turku, Finland
| | - Anti Vasemägi
- Chair of Aquaculture, Estonian University of Life Sciences, Kreutzwaldi 46a, 51014 Tartu, Estonia
- Swedish University of Agricultural Sciences, Sötvattenslaboratoriet, Stångholmsvägen 2, 17893 Drottningholm, Sweden
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11
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Tóth GE, Hume AJ, Suder EL, Zeghbib S, Ábrahám Á, Lanszki Z, Varga Z, Tauber Z, Földes F, Zana B, Scaravelli D, Scicluna MT, Pereswiet-Soltan A, Görföl T, Terregino C, De Benedictis P, Garcia-Dorival I, Alonso C, Jakab F, Mühlberger E, Leopardi S, Kemenesi G. Isolation and genome characterization of Lloviu virus from Italian Schreibers's bats. Sci Rep 2023; 13:11310. [PMID: 37443182 PMCID: PMC10344946 DOI: 10.1038/s41598-023-38364-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2023] [Accepted: 07/06/2023] [Indexed: 07/15/2023] Open
Abstract
Lloviu cuevavirus (LLOV) was the first identified member of Filoviridae family outside the Ebola and Marburgvirus genera. A massive die-off of Schreibers's bats (Miniopterus schreibersii) in the Iberian Peninsula in 2002 led to its initial discovery. Recent studies with recombinant and wild-type LLOV isolates confirmed the zoonotic nature of the virus in vitro. We examined bat samples from Italy for the presence of LLOV in an area outside of the currently known distribution range of the virus. We detected one positive sample from 2020, sequenced the complete coding region of the viral genome and established an infectious isolate of the virus. In addition, we performed the first comprehensive evolutionary analysis of the virus, using the Spanish, Hungarian and the Italian sequences. The most important achievement of this study is the establishment of an additional infectious LLOV isolate from a bat sample using the SuBK12-08 cells, demonstrating that this cell line is highly susceptible to LLOV infection and confirming the previous observation that these bats are effective hosts of the virus in nature. This result further strengthens the role of bats as the natural hosts for zoonotic filoviruses.
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Affiliation(s)
- Gábor E Tóth
- National Laboratory of Virology, Szentágothai Research Centre, University of Pécs, Pécs, Hungary
- Faculty of Sciences, Institute of Biology, University of Pécs, Pécs, Hungary
| | - Adam J Hume
- Department of Virology, Immunology and Microbiology, Boston University Chobanian & Avedisian School of Medicine, Boston, MA, USA
- National Emerging Infectious Diseases Laboratories, Boston University, Boston, MA, USA
- Center for Emerging Infectious Diseases Policy and Research, Boston University, Boston, MA, USA
| | - Ellen L Suder
- Department of Virology, Immunology and Microbiology, Boston University Chobanian & Avedisian School of Medicine, Boston, MA, USA
- National Emerging Infectious Diseases Laboratories, Boston University, Boston, MA, USA
| | - Safia Zeghbib
- National Laboratory of Virology, Szentágothai Research Centre, University of Pécs, Pécs, Hungary
| | - Ágota Ábrahám
- National Laboratory of Virology, Szentágothai Research Centre, University of Pécs, Pécs, Hungary
- Faculty of Sciences, Institute of Biology, University of Pécs, Pécs, Hungary
| | - Zsófia Lanszki
- National Laboratory of Virology, Szentágothai Research Centre, University of Pécs, Pécs, Hungary
- Faculty of Sciences, Institute of Biology, University of Pécs, Pécs, Hungary
| | - Zsaklin Varga
- National Laboratory of Virology, Szentágothai Research Centre, University of Pécs, Pécs, Hungary
- Faculty of Sciences, Institute of Biology, University of Pécs, Pécs, Hungary
| | - Zsófia Tauber
- National Laboratory of Virology, Szentágothai Research Centre, University of Pécs, Pécs, Hungary
| | - Fanni Földes
- National Laboratory of Virology, Szentágothai Research Centre, University of Pécs, Pécs, Hungary
| | - Brigitta Zana
- National Laboratory of Virology, Szentágothai Research Centre, University of Pécs, Pécs, Hungary
| | - Dino Scaravelli
- ST.E.R.N.A., Forlì, Department of Biological, Geological and Environmental Sciences, University of Bologna, Bologna, Italy
| | - Maria Teresa Scicluna
- UOC Virologia, Istituto Zooprofilattico Sperimentale del Lazio e della Toscana "M. Aleandri", Roma, Italy
| | - Andrea Pereswiet-Soltan
- Institute of Systematics and Evolution of Animals, Polish Academy of Sciences, Kraków, Poland
| | - Tamás Görföl
- National Laboratory of Virology, Szentágothai Research Centre, University of Pécs, Pécs, Hungary
| | - Calogero Terregino
- OIE Collaborating Centre and National Reference Centre for Infectious Diseases at the Animal-Human Interface, Istituto Zooprofilattico Sperimentale delle Venezie, Legnaro, Italy
| | - Paola De Benedictis
- OIE Collaborating Centre and National Reference Centre for Infectious Diseases at the Animal-Human Interface, Istituto Zooprofilattico Sperimentale delle Venezie, Legnaro, Italy
| | - Isabel Garcia-Dorival
- INIA-CSIC, Centro Nacional Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria, Madrid, Spain
| | - Covadonga Alonso
- INIA-CSIC, Centro Nacional Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria, Madrid, Spain
| | - Ferenc Jakab
- National Laboratory of Virology, Szentágothai Research Centre, University of Pécs, Pécs, Hungary
- Faculty of Sciences, Institute of Biology, University of Pécs, Pécs, Hungary
| | - Elke Mühlberger
- Department of Virology, Immunology and Microbiology, Boston University Chobanian & Avedisian School of Medicine, Boston, MA, USA
- National Emerging Infectious Diseases Laboratories, Boston University, Boston, MA, USA
| | - Stefania Leopardi
- OIE Collaborating Centre and National Reference Centre for Infectious Diseases at the Animal-Human Interface, Istituto Zooprofilattico Sperimentale delle Venezie, Legnaro, Italy
| | - Gábor Kemenesi
- National Laboratory of Virology, Szentágothai Research Centre, University of Pécs, Pécs, Hungary.
- Faculty of Sciences, Institute of Biology, University of Pécs, Pécs, Hungary.
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12
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Seuberlich T, Kuhn JH, Schmidt-Posthaus H. Near-Complete Genome Sequence of Lötschberg Virus ( Mononegavirales: Filoviridae) Identified in European Perch (Perca fluviatilis Linnaeus, 1758). Microbiol Resour Announc 2023; 12:e0002823. [PMID: 36926992 PMCID: PMC10112208 DOI: 10.1128/mra.00028-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2023] [Accepted: 02/20/2023] [Indexed: 03/18/2023] Open
Abstract
We obtained the near-complete genome sequence of a novel virus, Lötschberg virus (LTBV), from a European perch metatranscriptome. Genome organization and pairwise sequence comparison indicated that LTBV represents a tentative new species and genus of the mononegaviral family Filoviridae.
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Affiliation(s)
- Torsten Seuberlich
- Division of Neurological Sciences, Vetsuisse Faculty, University of Bern, Bern, Switzerland
| | - Jens H. Kuhn
- Integrated Research Facility at Fort Detrick, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Fort Detrick, Frederick, Maryland, USA
| | - Heike Schmidt-Posthaus
- Institute for Fish and Wildlife Health, Vetsuisse Faculty, University of Bern, Bern, Switzerland
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13
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Hu S, Fujita-Fujiharu Y, Sugita Y, Wendt L, Muramoto Y, Nakano M, Hoenen T, Noda T. Cryoelectron microscopic structure of the nucleoprotein-RNA complex of the European filovirus, Lloviu virus. PNAS NEXUS 2023; 2:pgad120. [PMID: 37124400 PMCID: PMC10139700 DOI: 10.1093/pnasnexus/pgad120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/12/2022] [Revised: 03/17/2023] [Accepted: 03/27/2023] [Indexed: 05/02/2023]
Abstract
Lloviu virus (LLOV) is a novel filovirus detected in Schreiber's bats in Europe. The isolation of the infectious LLOV from bats has raised public health concerns. However, the virological and molecular characteristics of LLOV remain largely unknown. The nucleoprotein (NP) of LLOV encapsidates the viral genomic RNA to form a helical NP-RNA complex, which acts as a scaffold for nucleocapsid formation and de novo viral RNA synthesis. In this study, using single-particle cryoelectron microscopy, we determined two structures of the LLOV NP-RNA helical complex, comprising a full-length and a C-terminally truncated NP. The two helical structures were identical, demonstrating that the N-terminal region determines the helical arrangement of the NP. The LLOV NP-RNA protomers displayed a structure similar to that in the Ebola and Marburg virus, but the spatial arrangements in the helix differed. Structure-based mutational analysis identified amino acids involved in the helical assembly and viral RNA synthesis. These structures advance our understanding of the filovirus nucleocapsid formation and provide a structural basis for the development of antifiloviral therapeutics.
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Affiliation(s)
- Shangfan Hu
- Laboratory of Ultrastructural Virology, Institute for Life and Medical Sciences, Kyoto University, 53 Shogoin Kawahara-cho, Sakyo-ku, Kyoto 606-8507, Japan
- Laboratory of Ultrastructural Virology, Graduate School of Biostudies, Kyoto University, 53 Shogoin Kawahara-cho, Sakyo-ku, Kyoto 606-8507, Japan
- CREST, Japan Science and Technology Agency, 4-1-8 Honcho, Kawaguchi, Saitama 332-0012, Japan
| | - Yoko Fujita-Fujiharu
- Laboratory of Ultrastructural Virology, Institute for Life and Medical Sciences, Kyoto University, 53 Shogoin Kawahara-cho, Sakyo-ku, Kyoto 606-8507, Japan
- Laboratory of Ultrastructural Virology, Graduate School of Biostudies, Kyoto University, 53 Shogoin Kawahara-cho, Sakyo-ku, Kyoto 606-8507, Japan
- CREST, Japan Science and Technology Agency, 4-1-8 Honcho, Kawaguchi, Saitama 332-0012, Japan
| | - Yukihiko Sugita
- Laboratory of Ultrastructural Virology, Institute for Life and Medical Sciences, Kyoto University, 53 Shogoin Kawahara-cho, Sakyo-ku, Kyoto 606-8507, Japan
- Laboratory of Ultrastructural Virology, Graduate School of Biostudies, Kyoto University, 53 Shogoin Kawahara-cho, Sakyo-ku, Kyoto 606-8507, Japan
- Hakubi Center for Advanced Research, Kyoto University, 53 Kawahara-cho, Shogoin, Sakyo-ku, Kyoto 606-8507, Japan
| | - Lisa Wendt
- Laboratory for Integrative Cell and Infection Biology, Institute of Molecular Virology and Cell Biology, Friedrich-Loeffler-Institut, Insel Riems, Greifswald 17493, Germany
| | - Yukiko Muramoto
- Laboratory of Ultrastructural Virology, Institute for Life and Medical Sciences, Kyoto University, 53 Shogoin Kawahara-cho, Sakyo-ku, Kyoto 606-8507, Japan
- Laboratory of Ultrastructural Virology, Graduate School of Biostudies, Kyoto University, 53 Shogoin Kawahara-cho, Sakyo-ku, Kyoto 606-8507, Japan
- CREST, Japan Science and Technology Agency, 4-1-8 Honcho, Kawaguchi, Saitama 332-0012, Japan
| | - Masahiro Nakano
- Laboratory of Ultrastructural Virology, Institute for Life and Medical Sciences, Kyoto University, 53 Shogoin Kawahara-cho, Sakyo-ku, Kyoto 606-8507, Japan
- Laboratory of Ultrastructural Virology, Graduate School of Biostudies, Kyoto University, 53 Shogoin Kawahara-cho, Sakyo-ku, Kyoto 606-8507, Japan
- CREST, Japan Science and Technology Agency, 4-1-8 Honcho, Kawaguchi, Saitama 332-0012, Japan
| | - Thomas Hoenen
- Laboratory for Integrative Cell and Infection Biology, Institute of Molecular Virology and Cell Biology, Friedrich-Loeffler-Institut, Insel Riems, Greifswald 17493, Germany
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14
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Kuhn JH, Schmaljohn CS. A Brief History of Bunyaviral Family Hantaviridae. Diseases 2023; 11:38. [PMID: 36975587 PMCID: PMC10047430 DOI: 10.3390/diseases11010038] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2022] [Revised: 02/16/2023] [Accepted: 02/20/2023] [Indexed: 03/05/2023] Open
Abstract
The discovery of Hantaan virus as an etiologic agent of hemorrhagic fever with renal syndrome in South Korea in 1978 led to identification of related pathogenic and nonpathogenic rodent-borne viruses in Asia and Europe. Their global distribution was recognized in 1993 after connecting newly discovered relatives of these viruses to hantavirus pulmonary syndrome in the Americas. The 1971 description of the shrew-infecting Hantaan-virus-like Thottapalayam virus was long considered an anomaly. Today, this virus and many others that infect eulipotyphlans, bats, fish, rodents, and reptiles are classified among several genera in the continuously expanding family Hantaviridae.
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Affiliation(s)
- 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, MD 21702, USA
| | - Connie S. Schmaljohn
- Integrated Research Facility at Fort Detrick, Division of Clinical Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Fort Detrick, Frederick, MD 21702, USA
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15
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Characterization of a Panel of Cross-Reactive Hantavirus Nucleocapsid Protein-Specific Monoclonal Antibodies. Viruses 2023; 15:v15020532. [PMID: 36851747 PMCID: PMC9958643 DOI: 10.3390/v15020532] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2022] [Revised: 02/02/2023] [Accepted: 02/07/2023] [Indexed: 02/17/2023] Open
Abstract
Hantaviruses are emerging pathogens with a worldwide distribution that can cause life-threatening diseases in humans. Monoclonal antibodies (MAbs) against hantavirus nucleocapsid (N) proteins are important tools in virus diagnostics, epidemiological studies and basic research studies on virus replication and pathogenesis. Here, we extend the collection of previously generated MAbs raised against a segment of Puumala orthohantavirus (PUUV) N protein harbored on virus-like particles (VLPs) and MAbs against N proteins of Sin Nombre orthohantavirus/Andes orthohantavirus by generating nine novel MAbs against N proteins of Dobrava-Belgrade orthohantavirus (DOBV), Tula orthohantavirus (TULV), Thottapalayam thottimvirus (TPMV) and PUUV. In order to have a wide collection of well-described hantavirus-specific MAbs, the cross-reactivity of novel and previously generated MAbs was determined against N proteins of 15 rodent- and shrew-borne hantaviruses by different immunological methods. We found that all MAbs, excluding TPMV-specific MAbs, demonstrated different cross-reactivity patterns with N proteins of hantaviruses and recognized native viral antigens in infected mammalian cells. This well-characterized collection of cross-reactive hantavirus-specific MAbs has a potential application in various fields of hantavirus research, diagnostics and therapy.
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16
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Pallandre L, Schmidt-Posthaus H, Pozet F, Rupp M, Cristina E, Bigarré L. Further spread of perch rhabdovirus on European percid farms. JOURNAL OF FISH DISEASES 2022; 45:1831-1837. [PMID: 35962585 DOI: 10.1111/jfd.13705] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/13/2022] [Revised: 07/29/2022] [Accepted: 08/01/2022] [Indexed: 06/15/2023]
Abstract
Variants of perch rhabdovirus (PRV) circulate across European percid farms via the fish trade. To trace their circulation, they are usually isolated by cell culture and subsequently identified genetically by sequencing partial or complete genes. Here, a newly developed nested PCR-based method was used to amplify and sequence the complete N and P genes directly from clinical samples obtained during an outbreak on a farm as well as from four batches of fish sampled from two other farms in another country. In an attempt to trace the origin of the five detected viruses, their N and P sequences were concatenated and compared with related viruses. One virus found in pike-perch was highly related to a virus isolated in 2016 in Belgium. Two other viruses detected on a single farm were distinct from one another, with one being almost identical to another virus isolated in 2016 in Belgium and the other being more closely related to a subgroup with different origins, France and Belgium. Two other viruses found in perch from a third farm were identical and were more related to a subgroup of viruses isolated in France. Identifying variants by a direct PCR approach will help to prevent further dissemination in farms.
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Affiliation(s)
- Laurane Pallandre
- Laboratory of Ploufragan-Plouzané-Niort, ANSES, Technopole Brest Iroise, Plouzané, France
| | - Heike Schmidt-Posthaus
- Institute for Fish and Wildlife Health, Vetsuisse Faculty, University of Bern, Bern, Switzerland
| | | | | | - Elodie Cristina
- Institute for Fish and Wildlife Health, Vetsuisse Faculty, University of Bern, Bern, Switzerland
| | - Laurent Bigarré
- Laboratory of Ploufragan-Plouzané-Niort, ANSES, Technopole Brest Iroise, Plouzané, France
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17
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Kuhn JH, Adkins S, Alkhovsky SV, Avšič-Županc T, Ayllón MA, Bahl J, Balkema-Buschmann A, Ballinger MJ, Bandte M, Beer M, Bejerman N, Bergeron É, Biedenkopf N, Bigarré L, Blair CD, Blasdell KR, Bradfute SB, Briese T, Brown PA, Bruggmann R, Buchholz UJ, Buchmeier MJ, Bukreyev A, Burt F, Büttner C, Calisher CH, Candresse T, Carson J, Casas I, Chandran K, Charrel RN, Chiaki Y, Crane A, Crane M, Dacheux L, Bó ED, de la Torre JC, de Lamballerie X, de Souza WM, de Swart RL, Dheilly NM, Di Paola N, Di Serio F, Dietzgen RG, Digiaro M, Drexler JF, Duprex WP, Dürrwald R, Easton AJ, Elbeaino T, Ergünay K, Feng G, Feuvrier C, Firth AE, Fooks AR, Formenty PBH, Freitas-Astúa J, Gago-Zachert S, García ML, García-Sastre A, Garrison AR, Godwin SE, Gonzalez JPJ, de Bellocq JG, Griffiths A, Groschup MH, Günther S, Hammond J, Hepojoki J, Hierweger MM, Hongō S, Horie M, Horikawa H, Hughes HR, Hume AJ, Hyndman TH, Jiāng D, Jonson GB, Junglen S, Kadono F, Karlin DG, Klempa B, Klingström J, Koch MC, Kondō H, Koonin EV, Krásová J, Krupovic M, Kubota K, Kuzmin IV, Laenen L, Lambert AJ, Lǐ J, Li JM, Lieffrig F, Lukashevich IS, Luo D, Maes P, Marklewitz M, Marshall SH, et alKuhn JH, Adkins S, Alkhovsky SV, Avšič-Županc T, Ayllón MA, Bahl J, Balkema-Buschmann A, Ballinger MJ, Bandte M, Beer M, Bejerman N, Bergeron É, Biedenkopf N, Bigarré L, Blair CD, Blasdell KR, Bradfute SB, Briese T, Brown PA, Bruggmann R, Buchholz UJ, Buchmeier MJ, Bukreyev A, Burt F, Büttner C, Calisher CH, Candresse T, Carson J, Casas I, Chandran K, Charrel RN, Chiaki Y, Crane A, Crane M, Dacheux L, Bó ED, de la Torre JC, de Lamballerie X, de Souza WM, de Swart RL, Dheilly NM, Di Paola N, Di Serio F, Dietzgen RG, Digiaro M, Drexler JF, Duprex WP, Dürrwald R, Easton AJ, Elbeaino T, Ergünay K, Feng G, Feuvrier C, Firth AE, Fooks AR, Formenty PBH, Freitas-Astúa J, Gago-Zachert S, García ML, García-Sastre A, Garrison AR, Godwin SE, Gonzalez JPJ, de Bellocq JG, Griffiths A, Groschup MH, Günther S, Hammond J, Hepojoki J, Hierweger MM, Hongō S, Horie M, Horikawa H, Hughes HR, Hume AJ, Hyndman TH, Jiāng D, Jonson GB, Junglen S, Kadono F, Karlin DG, Klempa B, Klingström J, Koch MC, Kondō H, Koonin EV, Krásová J, Krupovic M, Kubota K, Kuzmin IV, Laenen L, Lambert AJ, Lǐ J, Li JM, Lieffrig F, Lukashevich IS, Luo D, Maes P, Marklewitz M, Marshall SH, Marzano SYL, McCauley JW, Mirazimi A, Mohr PG, Moody NJG, Morita Y, Morrison RN, Mühlberger E, Naidu R, Natsuaki T, Navarro JA, Neriya Y, Netesov SV, Neumann G, Nowotny N, Ochoa-Corona FM, Palacios G, Pallandre L, Pallás V, Papa A, Paraskevopoulou S, Parrish CR, Pauvolid-Corrêa A, Pawęska JT, Pérez DR, Pfaff F, Plemper RK, Postler TS, Pozet F, Radoshitzky SR, Ramos-González PL, Rehanek M, Resende RO, Reyes CA, Romanowski V, Rubbenstroth D, Rubino L, Rumbou A, Runstadler JA, Rupp M, Sabanadzovic S, Sasaya T, Schmidt-Posthaus H, Schwemmle M, Seuberlich T, Sharpe SR, Shi M, Sironi M, Smither S, Song JW, Spann KM, Spengler JR, Stenglein MD, Takada A, Tesh RB, Těšíková J, Thornburg NJ, Tischler ND, Tomitaka Y, Tomonaga K, Tordo N, Tsunekawa K, Turina M, Tzanetakis IE, Vaira AM, van den Hoogen B, Vanmechelen B, Vasilakis N, Verbeek M, von Bargen S, Wada J, Wahl V, Walker PJ, Whitfield AE, Williams JV, Wolf YI, Yamasaki J, Yanagisawa H, Ye G, Zhang YZ, Økland AL. 2022 taxonomic update of phylum Negarnaviricota (Riboviria: Orthornavirae), including the large orders Bunyavirales and Mononegavirales. Arch Virol 2022; 167:2857-2906. [PMID: 36437428 PMCID: PMC9847503 DOI: 10.1007/s00705-022-05546-z] [Show More Authors] [Citation(s) in RCA: 43] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
In March 2022, 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 two new families (bunyaviral Discoviridae and Tulasviridae), 41 new genera, and 98 new species. Three hundred forty-nine species were renamed and/or moved. The accidentally misspelled names of seven species were corrected. 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 (IRF-Frederick), National Institute of Allergy and Infectious Diseases, National Institutes of Health (NIH), Fort Detrick, Frederick, MD, USA.
| | - Scott Adkins
- United States Department of Agriculture, Agricultural Research Service, US Horticultural Research Laboratory, Fort Pierce, FL, USA
| | - 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
| | - Tatjana Avšič-Županc
- Institute of Microbiology and Immunology, Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia
| | - 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
- Friedrich-Loeffler-Institut, Institute of Novel and Emerging Infectious Diseases, Greifswald-Insel Riems, Greifswald, Germany
| | - Matthew J Ballinger
- Department of Biological Sciences, Mississippi State University, Mississippi State, Starkville, MS, USA
| | - Martina Bandte
- Division Phytomedicine, Faculty of Life Sciences, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Martin Beer
- Institute of Diagnostic Virology, Friedrich-Loeffler-Institut, Greifswald-Insel Riems, Germany
| | | | - Éric Bergeron
- Division of High-Consequence Pathogens and Pathology, Viral Special Pathogens Branch, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Nadine Biedenkopf
- Institute of Virology, Philipps-University Marburg, Marburg, Germany
| | - Laurent Bigarré
- French Agency for Food, Environmental and Occupational Heath Safety ANSES, Laboratory of Ploufragan-Plouzané-Niort, Ploufragan, France
| | - 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
| | - Steven B Bradfute
- University of New Mexico Health Sciences Center, Albuquerque, NM, USA
| | - Thomas Briese
- Center for Infection and Immunity, and Department of Epidemiology, Mailman School of Public Health, Columbia University, New York, New York, USA
| | - Paul A Brown
- French Agency for Food, Environmental and Occupational Heath Safety ANSES, Laboratory of Ploufragan-Plouzané-Niort, Ploufragan, France
| | - Rémy Bruggmann
- Interfaculty Bioinformatics Unit, University of Bern, Bern, Switzerland
| | - 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, CA, USA
| | - Alexander Bukreyev
- Galveston National Laboratory, The University of Texas Medical Branch at Galveston, Galveston, TX, USA
- 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
| | | | | | - Jeremy Carson
- Centre for Aquatic Animal Health and Vaccines, Department of Natural Resources and Environment Tasmania, Launceston, TAS, Australia
| | - 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
| | - Yuya Chiaki
- Division of Fruit Tree and Tea Pest Control Research, Institute for Plant Protection, NARO, Tsukuba, Ibaraki, Japan
| | - Anya Crane
- Integrated Research Facility at Fort Detrick, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Frederick, MD, USA
| | - Mark Crane
- CSIRO Australian Centre for Disease Preparedness, East Geelong, VIC, Australia
| | - Laurent Dacheux
- Institut Pasteur, Université Paris Cité, Unit Lyssavirus Epidemiology and Neuropathology, National Reference Center for Rabies, WHO Collaborating Center for Reference and Research on Rabies, Paris, France
| | - 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
| | - William M de Souza
- World Reference Center for Emerging Viruses and Arboviruses and Department of Microbiology and Immunology, The University of Texas Medical Branch at Galveston, Galveston, TX, USA
| | - Rik L de Swart
- Department of Virology, Wageningen Bioveterinary Research, Lelystad, The Netherlands
| | - Nolwenn M Dheilly
- UMR 1161 Virology ANSES/INRAE/ENVA, ANSES Animal Health Laboratory, 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
| | - J Felix Drexler
- Institute of Virology, Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, Berlin, Germany
| | - W Paul Duprex
- School of Medicine, University of Pittsburgh, Pittsburgh, PA, USA
| | | | - Andrew J Easton
- School of Life Sciences, University of Warwick, Coventry, UK
| | - Toufic Elbeaino
- CIHEAM, Istituto Agronomico Mediterraneo di Bari, Valenzano, Italy
| | - Koray Ergünay
- Department of Medical Microbiology, Virology Unit, Hacettepe University Faculty of Medicine, Ankara, Turkey
- Walter Reed Biosystematics Unit (WRBU), Smithsonian Institution, Museum Support Center, Suitland, MD, USA
- One Health Branch, Walter Reed Army Institute of Research (WRAIR), Silver Spring, MD, USA
- Department of Entomology, Smithsonian Institution-National Museum of Natural History (NMNH), Washington, DC, USA
| | - Guozhong Feng
- China National Rice Research Institute, Hangzhou, China
| | | | - Andrew E Firth
- Department of Pathology, University of Cambridge, Cambridge, UK
| | | | | | | | - Selma Gago-Zachert
- Institute of Biochemistry and Biotechnology, Martin Luther University Halle-Wittenberg, Halle/Saale, Germany
| | - María Laura García
- Instituto de Biotecnología y Biología Molecular, Facultad de Ciencias Exactas, CONICET UNLP, La Plata, Argentina
| | | | - Aura R Garrison
- United States Army Medical Research Institute of Infectious Diseases, Fort Detrick, Frederick, MD, USA
| | - Scott E Godwin
- Centre for Aquatic Animal Health and Vaccines, Department of Natural Resources and Environment Tasmania, Launceston, TAS, Australia
| | - Jean-Paul J Gonzalez
- Department of Microbiology and Immunology, Division of Biomedical Graduate Research Organization, School of Medicine, Georgetown University, Washington, DC, USA
| | | | - Anthony Griffiths
- Department of Microbiology and National Emerging Infectious Diseases Laboratories, Boston University School of Medicine, Boston, MA, USA
| | - Martin H Groschup
- Institute of Novel and Emerging Infectious Diseases, Friedrich-Loeffler-Institut, Greifswald-Insel Riems, Germany
| | - Stephan Günther
- Department of Virology, WHO Collaborating Centre for Arboviruses and Hemorrhagic Fever Reference and Research, Bernhard-Nocht Institute for Tropical Medicine, Hamburg, Germany
| | - John Hammond
- United States Department of Agriculture, Agricultural Research Service, USNA, Floral and Nursery Plants Research Unit, Beltsville, MD, USA
| | - Jussi Hepojoki
- Department of Virology, University of Helsinki, Medicum, Helsinki, Finland
- Institute of Veterinary Pathology, Vetsuisse Faculty, University of Zurich, Zurich, Switzerland
| | - Melanie M Hierweger
- Division of Neurological Sciences, Vetsuisse Faculty, University of Bern, Bern, Switzerland
| | - Seiji Hongō
- Department of Infectious Diseases, Yamagata University Faculty of Medicine, Yamagata, Japan
| | - Masayuki Horie
- Graduate School of Veterinary Science, Osaka Metropolitan University, Izumisano, Osaka, Japan
- Osaka International Research Center for Infectious Diseases, Osaka Metropolitan University, Izumisano, Osaka, Japan
| | | | - Holly R Hughes
- Centers for Disease Control and Prevention, Fort Collins, CO, USA
| | - Adam J Hume
- Department of Microbiology and National Emerging Infectious Diseases Laboratories, Boston University School of Medicine, Boston, MA, USA
- Center for Emerging Infectious Diseases Policy and Research, Boston University School of Medicine, Boston, Massachusetts, USA
| | - Timothy H Hyndman
- School of Veterinary Medicine, Murdoch University, Murdoch, WA, Australia
| | - Dàohóng Jiāng
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, Hubei Province, China
| | - Gilda B Jonson
- International Rice Research Institute, College, Los Baños, 4032, Laguna, Philippines
| | - Sandra Junglen
- Institute of Virology, Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Fujio Kadono
- Clinical Plant Science Center, Hosei University, Tokyo, Japan
| | - David G Karlin
- Division Phytomedicine, Faculty of Life Sciences, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Boris Klempa
- Institute of Virology, Biomedical Research Center, Slovak Academy of Sciences, Bratislava, Slovakia
| | - Jonas Klingström
- Department of Medicine Huddinge, Center for Infectious Medicine, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
| | - Michel C Koch
- Division of Neurological Sciences, Vetsuisse Faculty, University of Bern, Bern, Switzerland
| | - 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
| | - Jarmila Krásová
- Institute of Vertebrate Biology of the Czech Academy of Sciences, Brno, Czech Republic
| | - Mart Krupovic
- Institut Pasteur, Université Paris Cité, CNRS UMR6047, Archaeal Virology Unit, Paris, France
| | - Kenji Kubota
- Institute for Plant Protection, NARO, Tsukuba, Ibaraki, Japan
| | - Ivan V Kuzmin
- The University of Texas Medical Branch at Galveston, Galveston, TX, 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
| | - Jiànróng Lǐ
- Department of Veterinary Biosciences, College of Veterinary Medicine, The Ohio State University, Columbus, OH, USA
| | - Jun-Min Li
- Institute of Plant Virology, Ningbo University, Ningbo, 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
| | - Dongsheng Luo
- Institut Pasteur, Université Paris Cité, Unit Lyssavirus Epidemiology and Neuropathology, Paris, France
- CAS Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, Hubei, China
| | - Piet Maes
- KU Leuven, Rega Institute, Zoonotic Infectious Diseases unit, Leuven, Belgium
| | | | - Sergio H Marshall
- Instituto de Biología-Laboratorio de Genética Molecular-Campus Curauma, Valparaíso, Chile
| | - Shin-Yi L Marzano
- United States Department of Agriculture, Agricultural Research Service, Toledo, OH, USA
| | - John W McCauley
- Worldwide Influenza Centre, Francis Crick Institute, London, UK
| | | | - Peter G Mohr
- CSIRO Australian Centre for Disease Preparedness, East Geelong, VIC, Australia
| | - Nick J G Moody
- CSIRO Australian Centre for Disease Preparedness, East Geelong, VIC, Australia
| | | | - Richard N Morrison
- Centre for Aquatic Animal Health and Vaccines, Department of Natural Resources and Environment Tasmania, Launceston, TAS, Australia
| | - 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
| | | | - José A Navarro
- Instituto de Biología Molecular y Celular de Plantas, Universitat Politècnica de València-Consejo Superior de Investigaciones Científicas, Valencia, Spain
| | - Yutaro Neriya
- School of Agriculture, Utsunomiya University, Utsunomiya, Japan
| | - Sergey V Netesov
- Novosibirsk State University, Novosibirsk, Novosibirsk Oblast, Russia
| | - Gabriele Neumann
- Department of Pathobiological Sciences, Influenza Research Institute, University of Wisconsin-Madison, Madison, 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
| | - Francisco M Ochoa-Corona
- Institute for Biosecurity and Microbial Forensics. Stillwater, Oklahoma State University, Oklahoma, USA
| | - Gustavo Palacios
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Laurane Pallandre
- French Agency for Food, Environmental and Occupational Heath Safety ANSES, Laboratory of Ploufragan-Plouzané-Niort, Ploufragan, France
| | - Vicente Pallás
- Instituto de Biología Molecular y Celular de Plantas (IBMCP), Consejo Superior de Investigaciones Cientificas-Universidat Politècnica de Valencia, Valencia, Spain
| | - Anna Papa
- National Reference Centre for Arboviruses and Haemorrhagic Fever viruses, Department of Microbiology, Medical School, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Sofia Paraskevopoulou
- Methods Development and Research Infrastructure, Bioinformatics and Systems Biology, Robert Koch Institute, Berlin, Germany
| | - Colin R Parrish
- College of Veterinary Medicine, Baker Institute for Animal Health, Cornell University, Ithaca, NY, USA
| | | | - 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
| | - Daniel R Pérez
- Department of Population Health, College of Veterinary Medicine, University of Georgia, Athens, GA, USA
| | | | - Richard K Plemper
- Institute of Diagnostic Virology, Friedrich-Loeffler-Institut, Greifswald-Insel Riems, Germany
| | - Thomas S Postler
- Department of Microbiology and Immunology, Vagelos College of Physicians and Surgeons, Columbia University Irving Medical Center, New York, NY, USA
| | | | - Sheli R Radoshitzky
- United States Army Medical Research Institute of Infectious Diseases (USAMRIID), Frederick, MD, USA
| | | | - Marius Rehanek
- Division Phytomedicine, Faculty of Life Sciences, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Renato O Resende
- Departamento de Biologia Celular, Universidade de Brasília, Brasília, Brazil
| | - Carina A Reyes
- Instituto de Biotecnología y Biología Molecular, CONICET-UNLP, Facultad de Ciencias Exactas, Unversidad Nacional de La Plata, Buenos Aires, Argentina
| | - Víctor Romanowski
- Instituto de Biotecnología y Biología Molecular, CONICET-UNLP, Facultad de Ciencias Exactas, Unversidad Nacional de La Plata, Buenos Aires, Argentina
| | - Dennis Rubbenstroth
- Institute of Diagnostic Virology, Friedrich-Loeffler-Institut, Greifswald-Insel Riems, Germany
| | - Luisa Rubino
- Istituto per la Protezione Sostenibile delle Piante, Consiglio Nazionale delle Ricerche, Bari, Italy
| | - Artemis Rumbou
- Division Phytomedicine, Faculty of Life Sciences, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Jonathan A Runstadler
- Department of Infectious Disease & Global Health, Tufts University Cummings School of Veterinary Medicine, North Grafton, MA, USA
| | - Melanie Rupp
- Institute for Fish and Wildlife Health, Vetsuisse Faculty, University of Bern, Bern, Switzerland
| | - Sead Sabanadzovic
- Department of Biochemistry, Molecular Biology, Entomology and Plant Pathology, Mississippi State University, Mississippi State, MS, USA
| | - Takahide Sasaya
- Institute for Plant Protection, National Agriculture and Food Research Organization, Tsukuba, Japan
| | - Heike Schmidt-Posthaus
- Institute for Fish and Wildlife Health, Vetsuisse Faculty, University of Bern, Bern, Switzerland
| | - Martin Schwemmle
- Faculty of Medicine, University Medical Center-University Freiburg, Freiburg, Germany
| | - Torsten Seuberlich
- Division of Neurological Sciences, Vetsuisse Faculty, University of Bern, Bern, Switzerland
| | - Stephen R Sharpe
- Hawkesbury Institute for the Environment, Western Sydney University, Sydney, NSW, Australia
| | - Mang Shi
- Sun Yat-sen University, Shenzhen, China
| | - Manuela Sironi
- Bioinformatics Unit, Scientific Institute IRCCS "E. Medea", Bosisio Parini, Italy
| | - 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 M 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, GA, USA
| | - Mark D Stenglein
- Department of Microbiology, Immunology, and Pathology, College of Veterinary Medicine and Biomedical Sciences, Colorado State University, Fort Collins, CO, USA
| | - Ayato Takada
- Division of Global Epidemiology, International Institute for Zoonosis Control, Hokkaido University, Sapporo, Japan
| | - Robert B Tesh
- The University of Texas Medical Branch at Galveston, Galveston, TX, USA
| | - Jana Těšíková
- Institute of Vertebrate Biology of the Czech Academy of Sciences, Brno, Czech Republic
- Department of Botany and Zoology, Faculty of Science, Masaryk University, Brno, Czech Republic
| | | | - Nicole D Tischler
- Laboratorio de Virología Molecular, Centro Ciencia & Vida, Fundación Ciencia & Vida and Facultad de Medicina y Ciencia, Universidad San Sebastián, Santiago, Chile
| | - Yasuhiro Tomitaka
- Institute for Plant Protection, National Agriculture and Food Research Organization, Tsukuba, Japan
| | - Keizō Tomonaga
- Institute for Life and Medical Sciences (LiMe), Kyoto University, Kyoto, Japan
| | - Noël Tordo
- Institut Pasteur de Guinée, BP 4416, Conakry, Guinea
| | | | - Massimo Turina
- Institute for Sustainable Plant Protection, National Research Council of Italy (IPSP-CNR), Torino, Italy
| | - Ioannis E Tzanetakis
- Department of Entomology and Plant Pathology, Division of Agriculture, University of Arkansas System, Fayetteville, AR, USA
| | - Anna Maria Vaira
- Institute for Sustainable Plant Protection, National Research Council of Italy (IPSP-CNR), Torino, Italy
| | - Bernadette van den Hoogen
- Department of Viroscience, Erasmus MC, University Medical Centre Rotterdam, Rotterdam, The Netherlands
| | - Bert Vanmechelen
- Department of Microbiology, Immunology and Transplantation, KU Leuven, Leuven, Belgium
| | - Nikos Vasilakis
- The University of Texas Medical Branch at Galveston, 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
| | - 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
| | - Junki Yamasaki
- Environmental Agriculture Promotion Division, Department of Agricultural Development, Kochi Prefectural Government, Kochi, Kochi, Japan
| | | | - Gongyin Ye
- Institute of Insect Sciences, Zhejiang University, Hangzhou, China
| | - Yong-Zhen Zhang
- National Institute for Communicable Disease Control and Prevention, China Center for Disease Control and Prevention, Beijing, China
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Zhang QY, Ke F, Gui L, Zhao Z. Recent insights into aquatic viruses: Emerging and reemerging pathogens, molecular features, biological effects, and novel investigative approaches. WATER BIOLOGY AND SECURITY 2022; 1:100062. [DOI: 10.1016/j.watbs.2022.100062] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/05/2025]
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Goodfellow SM, Nofchissey RA, Ye C, Dunnum JL, Cook JA, Bradfute SB. Use of a Novel Detection Tool to Survey Orthohantaviruses in Wild-Caught Rodent Populations. Viruses 2022; 14:682. [PMID: 35458412 PMCID: PMC9024935 DOI: 10.3390/v14040682] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2022] [Revised: 03/20/2022] [Accepted: 03/23/2022] [Indexed: 02/07/2023] Open
Abstract
Orthohantaviruses are negative-stranded RNA viruses with trisegmented genomes that can cause severe disease in humans and are carried by several host reservoirs throughout the world. Old World orthohantaviruses are primarily located throughout Europe and Asia, causing hemorrhagic fever with renal syndrome, and New World orthohantaviruses are found in North, Central, and South America, causing hantavirus cardiopulmonary syndrome (HCPS). In the United States, Sin Nombre orthohantavirus (SNV) is the primary cause of HCPS with a fatality rate of ~36%. The primary SNV host reservoir is thought to be the North American deer mouse, Peromyscus maniculatus. However, it has been shown that other species of Peromyscus can carry different orthohantaviruses. Few studies have systemically surveyed which orthohantaviruses may exist in wild-caught rodents or monitored spillover events into additional rodent reservoirs. A method for the rapid detection of orthohantaviruses is needed to screen large collections of rodent samples. Here, we report a pan-orthohantavirus, two-step reverse-transcription quantitative real-time PCR (RT-qPCR) tool designed to detect both Old and New World pathogenic orthohantavirus sequences of the S segment of the genome and validated them using plasmids and authentic viruses. We then performed a screening of wild-caught rodents and identified orthohantaviruses in lung tissue, and we confirmed the findings by Sanger sequencing. Furthermore, we identified new rodent reservoirs that have not been previously reported as orthohantavirus carriers. This novel tool can be used for the efficient and rapid detection of various orthohantaviruses, while uncovering potential new orthohantaviruses and host reservoirs that may otherwise go undetected.
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Affiliation(s)
- Samuel M. Goodfellow
- Center for Global Health, Department of Internal Medicine, University of New Mexico Health Sciences Center, Albuquerque, NM 87131, USA; (S.M.G.); (R.A.N.); (C.Y.)
| | - Robert A. Nofchissey
- Center for Global Health, Department of Internal Medicine, University of New Mexico Health Sciences Center, Albuquerque, NM 87131, USA; (S.M.G.); (R.A.N.); (C.Y.)
| | - Chunyan Ye
- Center for Global Health, Department of Internal Medicine, University of New Mexico Health Sciences Center, Albuquerque, NM 87131, USA; (S.M.G.); (R.A.N.); (C.Y.)
| | - Jonathan L. Dunnum
- Museum of Southwestern Biology, Biology Department, University of New Mexico, Albuquerque, NM 87131, USA; (J.L.D.); (J.A.C.)
| | - Joseph A. Cook
- Museum of Southwestern Biology, Biology Department, University of New Mexico, Albuquerque, NM 87131, USA; (J.L.D.); (J.A.C.)
| | - Steven B. Bradfute
- Center for Global Health, Department of Internal Medicine, University of New Mexico Health Sciences Center, Albuquerque, NM 87131, USA; (S.M.G.); (R.A.N.); (C.Y.)
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20
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Waltzek TB, Stacy BA, Ossiboff RJ, Stacy NI, Fraser WA, Yan A, Mohan S, Koonin EV, Wolf YI, Rodrigues TCS, Viadanna PHO, Subramaniam K, Popov VL, Guzman-Vargas V, Shender LA. A novel group of negative-sense RNA viruses associated with epizootics in managed and free-ranging freshwater turtles in Florida, USA. PLoS Pathog 2022; 18:e1010258. [PMID: 35275967 PMCID: PMC8916662 DOI: 10.1371/journal.ppat.1010258] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Accepted: 01/07/2022] [Indexed: 11/18/2022] Open
Abstract
Few aquatic animal negative-sense RNA viruses have been characterized, and their role in disease is poorly understood. Here, we describe a virus isolated from diseased freshwater turtles from a Florida farm in 2007 and from an ongoing epizootic among free-ranging populations of Florida softshell turtles (Apalone ferox), Florida red-bellied cooters (Pseudemys nelsoni), and peninsula cooters (Pseudemys peninsularis). Affected turtles presented with similar neurological signs, oral and genital ulceration, and secondary microbial infections. Microscopic lesions were most severe in the softshell turtles and included heterophilic/histiocytic meningoencephalitis, multi-organ vasculitis, and cytologic observation of leukocytic intracytoplasmic inclusions. The virus was isolated using Terrapene heart (TH-1) cells. Ultrastructurally, viral particles were round to pleomorphic and acquired an envelope with prominent surface projections by budding from the cell membrane. Viral genomes were sequenced from cDNA libraries of two nearly identical isolates and determined to be bi-segmented, with an ambisense coding arrangement. The larger segment encodes a predicted RNA-directed RNA polymerase (RdRP) and a putative zinc-binding matrix protein. The smaller segment encodes a putative nucleoprotein and an envelope glycoprotein precursor (GPC). Thus, the genome organization of this turtle virus resembles that of arenaviruses. Phylogenetic analysis shows that the RdRP of the turtle virus is highly diverged from the RdRPs of all known negative-sense RNA viruses and forms a deep branch within the phylum Negarnaviricota, that is not affiliated with any known group of viruses, even at the class level. In contrast, the GPC protein of the turtle virus is confidently affiliated with homologs from a distinct group of fish hantaviruses. Thus, the turtle virus is expected to become the founder of a new taxon of negative-sense RNA viruses, at least with a family rank, but likely, an order or even a class. These viruses probably evolved either by reassortment or by intrasegment recombination between a virus from a distinct branch of negarnaviruses distant from all known groups and a hanta-like aquatic virus. We suggest the provisional name Tosoviridae for the putative new family, with Turtle fraservirus 1 (TFV1) as the type species within the genus Fraservirus. A conventional RT-PCR assay, targeting the TFV1 RdRP, confirmed the presence of viral RNA in multiple tissues and exudates from diseased turtles. The systemic nature of the TFV1 infection was further supported by labeling of cells within lesions using in situ hybridization targeting the RNA of the TFV1 RdRP.
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Affiliation(s)
- Thomas B. Waltzek
- Department of Infectious Diseases and Immunology, College of Veterinary Medicine, University of Florida, Gainesville, Florida, United States of America
- * E-mail:
| | - Brian A. Stacy
- NOAA, National Marine Fisheries Service, Office of Protected Resources, University of Florida (duty station), Gainesville, Florida, United States of America
| | - Robert J. Ossiboff
- Department of Comparative, Diagnostic, and Population Medicine, College of Veterinary Medicine, University of Florida, Gainesville, Florida, United States of America
| | - Nicole I. Stacy
- Department of Comparative, Diagnostic, and Population Medicine, College of Veterinary Medicine, University of Florida, Gainesville, Florida, United States of America
| | - William A. Fraser
- Florida Department of Agriculture and Consumer Services, Bronson Animal Disease Diagnostic Laboratory, Kissimmee, Florida, United States of America
| | - Annie Yan
- Florida Department of Agriculture and Consumer Services, Bronson Animal Disease Diagnostic Laboratory, Kissimmee, Florida, United States of America
| | - Shipra Mohan
- Florida Department of Agriculture and Consumer Services, Bronson Animal Disease Diagnostic Laboratory, Kissimmee, Florida, United States of America
| | - Eugene V. Koonin
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Yuri I. Wolf
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Thais C. S. Rodrigues
- Department of Infectious Diseases and Immunology, College of Veterinary Medicine, University of Florida, Gainesville, Florida, United States of America
| | - Pedro H. O. Viadanna
- Department of Infectious Diseases and Immunology, College of Veterinary Medicine, University of Florida, Gainesville, Florida, United States of America
| | - Kuttichantran Subramaniam
- Department of Infectious Diseases and Immunology, College of Veterinary Medicine, University of Florida, Gainesville, Florida, United States of America
| | - Vsevolod L. Popov
- Center for Biodefense and Emerging Infectious Diseases, Institute for Human Infections and Immunity, the University of Texas Medical Branch, Galveston, Texas, United States of America
| | - Veronica Guzman-Vargas
- Fish and Wildlife Research Institute, Florida Fish and Wildlife Conservation Commission, Gainesville, Florida, United States of America
| | - Lisa A. Shender
- Fish and Wildlife Research Institute, Florida Fish and Wildlife Conservation Commission, Gainesville, Florida, United States of America
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