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Nkamwesiga J, Lumu P, Nalumenya DP, Korennoy F, Roesel K, Wieland B, Perez A, Kiara H, Muhanguzi D. Seroprevalence and risk factors of Peste des petits ruminants in different production systems in Uganda. Prev Vet Med 2023; 221:106051. [PMID: 37918209 DOI: 10.1016/j.prevetmed.2023.106051] [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] [Received: 05/08/2023] [Revised: 09/20/2023] [Accepted: 10/15/2023] [Indexed: 11/04/2023]
Abstract
Peste des petits ruminants (PPR) is a highly contagious and fatal disease of mostly domestic goats and sheep. First reported in Uganda in 2007, the extent of peste des petits ruminants virus (PPRV) exposure, geographical distribution and risk factors of its transmission and spread are not clearly understood. In this study, we used cluster random sampling methodology to select study villages from three districts representing three different production systems along Uganda's "cattle corridor". Between October and December 2022, 2520 goat and sheep serum samples were collected from 252 households with no history of PPR vaccination in the past one year. The household heads were interviewed to assess possible risk factors of PPRV transmission using a structured questionnaire. The serum samples were screened with a commercial competitive enzyme-linked immunosorbent assay (cELISA) for PPRV antibodies. The determined overall true seroprevalence of PPRV was 27.3% [95% CI: 25.4-29.1]. The seroprevalence of PPRV antibodies in different production systems was 44.1% [95% CI: 40.6-47.7], 31.7% [95% CI: 28.4-35.0] and 6.1% [95% CI: 4.4-7.9] for pastoral, agropastoral and mixed crop-livestock production systems respectively. A mixed-effects multivariable logistic regression model revealed strong statistical evidence of association between female animals and PPRV antibody seropositivity compared to males [OR= 2.45, 95% CI: 1.7-3.5, p < 0.001]. The likelihood of being PPRV antibody seropositive significantly increased with increasing small ruminant age. Animals older than 3 years were more than three times as likely to be PPRV seropositive compared to animals aged under 1 year [OR= 3.41, 95% CI: 2.39-4.85, p < 0.001]. There was no statistical evidence of association between small ruminant species and PPRV antibody seropositivity (p = 0.423). Village flocks that interacted with neighboring flocks daily during grazing (IRR = 1.59, 95% CI: 1.19-2.13) and watering around swamps (IRR = 1.59, 95% CI: 1.19-2.13) were highly correlated with increased number of PPRV seropositive animals as compared to flocks that were more restricted in grazing and watered around other water sources other than swamps. Flocks from pastoral and agropastoral production systems were more than 10 times more likely to have seropositive animals than mixed crop-livestock flocks. Targeting PPR control interventions (vaccination and livestock movement control) to pastoral and agro-pastoral small ruminant production systems that are very prone to PPR incursions is recommended to prevent PPRV spread to low-risk smallholder mixed crop-livestock production systems.
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Affiliation(s)
- Joseph Nkamwesiga
- Dahlem Research School of Biomedical Sciences, Department of Veterinary Medicine, Freie Universität Berlin, Berlin, Germany; International Livestock Research Institute, Nairobi, Kenya.
| | - Paul Lumu
- Ministry of Agriculture Animal Industry and Fisheries, Entebbe, Uganda
| | - David Paul Nalumenya
- College of Veterinary Medicine, Animal Resources, and Biosecurity, Makerere University, Kampala, Uganda
| | - Fedor Korennoy
- Federal Center for Animal Health (FGBI ARRIAH), Vladimir, Russia
| | | | - Barbara Wieland
- Institute of Virology and Immunology (IVI), Switzerland; Department of Infectious Diseases and Pathobiology (DIP), University of Bern, Switzerland
| | - Andres Perez
- College of Veterinary Medicine, University of Minnesota, St. Paul, MN, United States
| | - Henry Kiara
- International Livestock Research Institute, Nairobi, Kenya
| | - Dennis Muhanguzi
- College of Veterinary Medicine, Animal Resources, and Biosecurity, Makerere University, Kampala, Uganda
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2
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Postler TS, Rubino L, Adriaenssens EM, Dutilh BE, Harrach B, Junglen S, Kropinski AM, Krupovic M, Wada J, Crane A, Kuhn JH, Mushegian A, Rūmnieks J, Sabanadzovic S, Simmonds P, Varsani A, Zerbini FM, Callanan J, Draper LA, Hill C, Stockdale SR. Guidance for creating individual and batch latinized binomial virus species names. J Gen Virol 2022; 103. [PMID: 36748479 DOI: 10.1099/jgv.0.001800] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/04/2022] Open
Abstract
The International Committee on Taxonomy of Viruses recently adopted, and is gradually implementing, a binomial naming format for virus species. Although full Latinization of these names remains optional, a standardized nomenclature based on Latinized binomials has the advantage of comparability with all other biological taxonomies. As a language without living native speakers, Latin is more culturally neutral than many contemporary languages, and words built from Latin roots are already widely used in the language of science across the world. Conversion of established species names to Latinized binomials or creation of Latinized binomials de novo may seem daunting, but the rules for name creation are straightforward and can be implemented in a formulaic manner. Here, we describe approaches, strategies and steps for creating Latinized binomials for virus species without prior knowledge of Latin. We also discuss a novel approach to the automated generation of large batches of novel genus and species names. Importantly, conversion to a binomial format does not affect virus names, many of which are created from local languages.
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Affiliation(s)
- Thomas S Postler
- Department of Microbiology & Immunology, Vagelos College of Physicians & Surgeons, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Luisa Rubino
- Consiglio Nazionale delle Ricerche, Istituto per la Protezione Sostenibile delle Piante, Sede Secondaria di Bari, 70126 Bari, Italy
| | | | - Bas E Dutilh
- Institute of Biodiversity, Faculty of Biological Sciences, Cluster of Excellence Balance of the Microverse, Friedrich Schiller University Jena, 07743 Jena, Germany.,Theoretical Biology and Bioinformatics, Department of Biology, Utrecht University, 3584 CH Utrecht, Netherlands
| | - Balázs Harrach
- Veterinary Medical Research Institute, H-1143 Budapest, Hungary
| | - Sandra Junglen
- Institute of Virology, Charité - Universitätsmedizin, corporate member of Free University Berlin, Humboldt-University Berlin, and Berlin Institute of Health, 10117 Berlin, Germany
| | - Andrew M Kropinski
- Departments of Pathobiology, University of Guelph, Guelph, Ontario, N1G 2W1, Canada
| | - Mart Krupovic
- Institut Pasteur, Université Paris Cité, CNRS UMR6047, Archaeal Virology Unit, 75015 Paris, France
| | - Jiro Wada
- Integrated Research Facility at Fort Detrick, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Frederick, MD 21702, USA
| | - Anya Crane
- Integrated Research Facility at Fort Detrick, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Frederick, MD 21702, USA
| | - Jens H Kuhn
- Integrated Research Facility at Fort Detrick, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Frederick, MD 21702, USA
| | - Arcady Mushegian
- Division of Molecular and Cellular Biosciences, National Science Foundation, Alexandria, VA 22314, USA
| | - Jānis Rūmnieks
- Latvian Biomedical Research and Study Centre, Riga, LV-1067, Latvia
| | - Sead Sabanadzovic
- Department of Biochemistry, Molecular Biology, Entomology and Plant Pathology, Mississippi State University, Mississippi State, MS 39762, USA
| | - Peter Simmonds
- Nuffield Department of Experimental Medicine, University of Oxford, Peter Medawar Building, Oxford, OX1 3SY, UK
| | - Arvind Varsani
- The Biodesign Center for Fundamental and Applied Microbiomics, School of Life Sciences, Center for Evolution and Medicine, Arizona State University, Tempe, AZ 85287-4701, USA.,Structural Biology Research Unit, Department of Integrative Biomedical Sciences, University of Cape Town, Cape Town, South Africa
| | - F Murilo Zerbini
- Departamento de Fitopatologia/BIOAGRO, Universidade Federal de Viçosa, Viçosa, MG 36570-900, Brazil
| | - Julie Callanan
- APC Microbiome Ireland, University College Cork, Cork, T12 YT20, Ireland
| | - Lorraine A Draper
- APC Microbiome Ireland, University College Cork, Cork, T12 YT20, Ireland
| | - Colin Hill
- APC Microbiome Ireland, University College Cork, Cork, T12 YT20, Ireland
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Walker PJ, Siddell SG, Lefkowitz EJ, Mushegian AR, Adriaenssens EM, Alfenas-Zerbini P, Davison AJ, Dempsey DM, Dutilh BE, García ML, Harrach B, Harrison RL, Hendrickson RC, Junglen S, Knowles NJ, Krupovic M, Kuhn JH, Lambert AJ, Łobocka M, Nibert ML, Oksanen HM, Orton RJ, Robertson DL, Rubino L, Sabanadzovic S, Simmonds P, Smith DB, Suzuki N, Van Dooerslaer K, Vandamme AM, Varsani A, Zerbini FM. Changes to virus taxonomy and to the International Code of Virus Classification and Nomenclature ratified by the International Committee on Taxonomy of Viruses (2021). Arch Virol 2021; 166:2633-2648. [PMID: 34231026 DOI: 10.1007/s00705-021-05156-1] [Citation(s) in RCA: 196] [Impact Index Per Article: 65.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
This article reports the changes to virus taxonomy approved and ratified by the International Committee on Taxonomy of Viruses (ICTV) in March 2021. The entire ICTV was invited to vote on 290 taxonomic proposals approved by the ICTV Executive Committee at its meeting in October 2020, as well as on the proposed revision of the International Code of Virus Classification and Nomenclature (ICVCN). All proposals and the revision were ratified by an absolute majority of the ICTV members. Of note, ICTV mandated a uniform rule for virus species naming, which will follow the binomial 'genus-species' format with or without Latinized species epithets. The Study Groups are requested to convert all previously established species names to the new format. ICTV has also abolished the notion of a type species, i.e., a species chosen to serve as a name-bearing type of a virus genus. The remit of ICTV has been clarified through an official definition of 'virus' and several other types of mobile genetic elements. The ICVCN and ICTV Statutes have been amended to reflect these changes.
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Affiliation(s)
- Peter J Walker
- School of Chemistry and Molecular Biosciences, The University of Queensland, St Lucia, QLD, 4072, Australia
| | - Stuart G Siddell
- School of Cellular and Molecular Medicine, Faculty of Life Sciences, University of Bristol, University Walk, Bristol, BS8 1TD, UK
| | - Elliot J Lefkowitz
- Department of Microbiology, University of Alabama at Birmingham (UAB), BBRB 276, 845 19th St South, Birmingham, AL, 35294-2170, USA
| | - Arcady R Mushegian
- Division of Molecular and Cellular Biosciences, National Science Foundation, 2415 Eisenhower Avenue, Alexandria, VA, 22314, USA.
| | | | - Poliane Alfenas-Zerbini
- Departamento de Microbiologia, Universidade Federal de Viçosa, Viçosa, MG, 36570-000, Brazil
| | - Andrew J Davison
- MRC-University of Glasgow Centre for Virus Research, Sir Michael Stoker Building, 464 Bearsden Road, Glasgow, G61 1QH, UK
| | - Donald M Dempsey
- Department of Microbiology, University of Alabama at Birmingham (UAB), BBRB 276, 845 19th St South, Birmingham, AL, 35294-2170, USA
| | - Bas E Dutilh
- Theoretical Biology and Bioinformatics, Department of Biology, Utrecht University, Padualaan 8, Room Z-509, 3584 CH, Utrecht, The Netherlands
| | - María Laura García
- Instituto de Biotecnología y Biología Molecular, CCT-La Plata, CONICET, UNLP, calles 47 y 115 (1900), La Plata, Buenos Aires, Argentina
| | - Balázs Harrach
- Veterinary Medical Research Institute, Hungária krt. 21, H-1143, Budapest, Hungary
| | - Robert L Harrison
- Invasive Insect Biocontrol and Behavior Laboratory, USDA-ARS, 10300 Baltimore Avenue, Bldg 007 Barc-West, Beltsville, MD, 20705, USA
| | - R Curtis Hendrickson
- Department of Microbiology, University of Alabama at Birmingham (UAB), BBRB 276, 845 19th St South, Birmingham, AL, 35294-2170, USA
| | - Sandra Junglen
- Institute of Virology, Charité-Universitätsmedizin, corporate member of Free University Berlin, Humboldt-University Berlin, and Berlin Institute of Health, Germany, Berlin, Germany
| | - Nick J Knowles
- The Pirbright Institute, Ash Road, Pirbright, GU24 0NF, Surrey, UK
| | - Mart Krupovic
- Department of Microbiology, Institut Pasteur, 25 rue du Dr Roux, 75015, Paris, France
| | - Jens H Kuhn
- NIH/NIAID/DCR/Integrated Research Facility at Fort Detrick (IRF-Frederick), B-8200 Research Plaza, Fort Detrick, Frederick, MD, 21702, USA
| | - Amy J Lambert
- Division of Vector-Borne Diseases, National Center for Emerging and Zoonotic Infectious Diseases, Centers for Disease Control and Prevention, Fort Collins, CO, 80521, USA
| | - Małgorzata Łobocka
- Institute of Biochemistry and Biophysics of the Polish Academy of Sciences, 02-106, Warsaw, Poland
| | - Max L Nibert
- Department of Microbiology, Harvard Medical School, 77 Ave Louis Pasteur, Boston, MA, 02115, USA
| | - Hanna M Oksanen
- Molecular and Integrative Biosciences Research Programme, Faculty of Biological and Environmental Sciences, University of Helsinki, Viikinkaari 9, FI-00014, Helsinki, Finland
| | - Richard J Orton
- MRC-University of Glasgow Centre for Virus Research, Sir Michael Stoker Building, 464 Bearsden Road, Glasgow, G61 1QH, UK
| | - David L Robertson
- MRC-University of Glasgow Centre for Virus Research, Sir Michael Stoker Building, 464 Bearsden Road, Glasgow, G61 1QH, UK
| | - Luisa Rubino
- Istituto per la Protezione Sostenibile delle Piante, CNR, UOS Bari, Via Amendola 165/A, 70126, Bari, Italy
| | - Sead Sabanadzovic
- Department of Biochemistry, Molecular Biology, Entomology and Plant Pathology, Mississippi State University, 100 Old Hwy 12 Mail Stop 9775, Mississippi State, MS, 39762, USA
| | - Peter Simmonds
- Nuffield Department of Medicine, University of Oxford, Peter Medawar Building, South Parks Road, Oxford, OX1 3SY, UK
| | - Donald B Smith
- Nuffield Department of Medicine, University of Oxford, Peter Medawar Building, South Parks Road, Oxford, OX1 3SY, UK
| | - Nobuhiro Suzuki
- Institute of Plant Science and Resources, Okayama University, Kurashiki, Okayama, 710-0046, Japan
| | - Koenraad Van Dooerslaer
- School of Animal and Comparative Biomedical Sciences, Department of Immunobiology, BIO5 Institute, and University of Arizona Cancer Center, Tucson, AZ, 85721, USA
| | - Anne-Mieke Vandamme
- KU Leuven, Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, Clinical and Epidemiological Virology, Institute for the Future, 3000, Leuven, Belgium.,Center for Global Health and Tropical Medicine, Unidade de Microbiologia, Instituto de Higiene e Medicina Tropical, Universidade Nova de Lisboa, Rua da Junqueira, 100, 1349-008, Lisboa, Portugal
| | - Arvind Varsani
- The Biodesign Center for Fundamental and Applied Microbiomics, School of Life Sciences, Center for Evolution and Medicine, Arizona State University, P.O. Box 874701, Tempe, AZ, 85287-4701, USA
| | - Francisco Murilo Zerbini
- Departamento de Fitopatologia/BIOAGRO, Universidade Federal de Viçosa, Viçosa, MG, 36570-900, Brazil
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Dutuze MF, Ingabire A, Gafarasi I, Uwituze S, Nzayirambaho M, Christofferson RC. Identification of Bunyamwera and Possible Other Orthobunyavirus Infections and Disease in Cattle during a Rift Valley Fever Outbreak in Rwanda in 2018. Am J Trop Med Hyg 2020; 103:183-189. [PMID: 32314686 PMCID: PMC7356447 DOI: 10.4269/ajtmh.19-0596] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
In 2018, a large outbreak of Rift Valley fever (RVF)–like illness in cattle in Rwanda and surrounding countries was reported. From this outbreak, sera samples from 157 cows and 28 goats suspected to be cases of RVF were tested to confirm or determine the etiology of the disease. Specifically, the hypothesis that orthobunyaviruses—Bunyamwera virus (BUNV), Batai virus (BATV), and Ngari virus (NRIV)—were co-circulating and contributed to RVF-like disease was tested. Using reverse transcriptase-polymerase chain reaction (RT-PCR), RVFV RNA was detected in approximately 30% of acutely ill animals, but in all cases of hemorrhagic disease. Seven cows with experienced abortion had positive amplification and visualization by gel electrophoresis of all three segments of either BUNV or BATV, and three of these were suggested to be coinfected with BUNV and BATV. On sequencing, five of these seven cows were conclusively positive for BUNV. However, in several other animals, sequencing was successful for some but not all segments of targeted viruses BUNV and BATV. In addition, there was evidence of RVFV–orthobunyavirus coinfection, through RT-PCR/gel electrophoresis and subsequent Sanger sequencing. In no cases were we able to definitely identify the specific coinfecting viral species. This is the first time evidence for orthobunyavirus circulation has been molecularly confirmed in Rwanda. Furthermore, RT-PCR results suggest that BUNV and BATV may coinfect cattle and that RVFV-infected animals may be coinfected with other orthobunyaviruses. Finally, we confirm that BUNV and, perhaps, other orthobunyaviruses were co-circulating with RVFV and contributed to the burden of disease attributed to RVFV in Rwanda.
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Affiliation(s)
- Marie Fausta Dutuze
- College of Agriculture and Animal Sciences and Veterinary Medicine, University of Rwanda, Kigali, Rwanda.,School of Veterinary Medicine, Louisiana State University, Baton Rouge, Louisiana
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6
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Siddell SG, Walker PJ, Lefkowitz EJ, Mushegian AR, Dutilh BE, Harrach B, Harrison RL, Junglen S, Knowles NJ, Kropinski AM, Krupovic M, Kuhn JH, Nibert ML, Rubino L, Sabanadzovic S, Simmonds P, Varsani A, Zerbini FM, Davison AJ. Binomial nomenclature for virus species: a consultation. Arch Virol 2020; 165:519-525. [PMID: 31797129 PMCID: PMC7026202 DOI: 10.1007/s00705-019-04477-6] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
Abstract
The Executive Committee of the International Committee on Taxonomy of Viruses (ICTV) recognizes the need for a standardized nomenclature for virus species. This article sets out the case for establishing a binomial nomenclature and presents the advantages and disadvantages of different naming formats. The Executive Committee understands that adopting a binomial system would have major practical consequences, and invites comments from the virology community before making any decisions to change the existing nomenclature. The Executive Committee will take account of these comments in deciding whether to approve a standardized binomial system at its next meeting in October 2020. Note that this system would relate only to the formal names of virus species and not to the names of viruses.
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Affiliation(s)
- Stuart G. Siddell
- School of Cellular and Molecular Medicine, Faculty of Life Sciences, University of Bristol, University Walk, Bristol, BS8 1TD UK
| | - Peter J. Walker
- School of Biological Sciences, The University of Queensland, Saint Lucia, QLD 4072 Australia
| | - Elliot J. Lefkowitz
- Department of Microbiology, University of Alabama at Birmingham (UAB), BBRB 276, 845 19th ST South, Birmingham, AL 35294-2170 USA
| | - Arcady R. Mushegian
- Division of Molecular and Cellular Biosciences, National Science Foundation, 2415 Eisenhower Avenue, Alexandria, VA 22314 USA
| | - Bas E. Dutilh
- Theoretical Biology and Bioinformatics, Department of Biology, Utrecht University, Padualaan 8, Room N-604, 3584 CH Utrecht, The Netherlands
- Centre for Molecular and Biomolecular Informatics, Radboud University Medical Center (Radboudumc), Geert Grooteplein 26, 6525 GA Nijmegen, The Netherlands
| | - Balázs Harrach
- Institute for Veterinary Medical Research, Centre for Agricultural Research, Hungária krt. 21, Budapest, 1143 Hungary
| | - Robert L. Harrison
- Invasive Insect Biocontrol and Behavior Laboratory, USDA-ARS, 10300 Baltimore Avenue, Bldg 007 BARC-West, Beltsville, MD 20705 USA
| | - Sandra Junglen
- Institute of Virology, Charité-Universitätsmedizin, Corporate Member of Free University Berlin, Humboldt-University Berlin, Berlin, Germany
- Berlin Institute of Health, Berlin, Germany
| | - Nick J. Knowles
- The Pirbright Institute, Ash Road, Pirbright, Surrey, GU24 0NF UK
| | - Andrew M. Kropinski
- Department of Food Science, University of Guelph, Guelph, ON N1G 2W1 Canada
- Department of Pathobiology, University of Guelph, Guelph, ON N1G 2W1 Canada
| | - Mart Krupovic
- Department of Microbiology, Institut Pasteur, 25 rue du Dr Roux, 75015 Paris, France
| | - Jens H. Kuhn
- National Institutes of Health, National Institute of Allergy and Infectious Diseases, Division of Clinical Research, Integrated Research Facility at Fort Detrick (IRF-Frederick), B-8200 Research Plaza, Fort Detrick, Frederick, MD 21702 USA
| | - Max L. Nibert
- Department of Microbiology, Blavatnik Institute, Harvard Medical School, 77 Ave Louis Pasteur, Boston, MA 02115 USA
| | - Luisa Rubino
- Istituto per la Protezione Sostenibile delle Piante, CNR, Sede Secondaria di Bari, Via Amendola 165/A, 70126 Bari, Italy
| | - Sead Sabanadzovic
- Department of Biochemistry, Molecular Biology, Entomology and Plant Pathology, Mississippi State University, 100 Old Hwy 12 Mail Stop 9775, Mississippi State, MS 39762 USA
| | - Peter Simmonds
- Nuffield Department of Experimental Medicine, University of Oxford, Peter Medawar Building, South Parks Road, Oxford, OX1 3PS UK
| | - Arvind Varsani
- The Biodesign Center for Fundamental and Applied Microbiomics, School of Life Sciences, Center for Evolution and Medicine, Arizona State University, P.O. Box 874701, Tempe, AZ 85287-4701 USA
| | - Francisco Murilo Zerbini
- Departamento de Fitopatologia/BIOAGRO, Universidade Federal de Viçosa, Viçosa, MG 36570-900 Brazil
| | - Andrew J. Davison
- MRC-University of Glasgow Centre for Virus Research, Sir Michael Stoker Building, 464 Bearsden Road, Glasgow, G61 1QH UK
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7
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Calisher CH, Briese T, Brister JR, Charrel RN, Dürrwald R, Ebihara H, Fulhorst CF, Gāo GF, Groschup MH, Haddow AD, Hyndman TH, Junglen S, Klempa B, Klingström J, Kropinski AM, Krupovic M, LaBeaud AD, Maes P, Nowotny N, Nunes MRT, Payne SL, Radoshitzky SR, Rubbenstroth D, Sabanadzovic S, Sasaya T, Stenglein MD, Varsani A, Wahl V, Weaver SC, Zerbini FM, Vasilakis N, Kuhn JH. Strengthening the Interaction of the Virology Community with the International Committee on Taxonomy of Viruses (ICTV) by Linking Virus Names and Their Abbreviations to Virus Species. Syst Biol 2019; 68:828-839. [PMID: 30597118 PMCID: PMC6701456 DOI: 10.1093/sysbio/syy087] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2018] [Revised: 12/16/2018] [Accepted: 11/19/2018] [Indexed: 01/09/2023] Open
Abstract
The International Committee on Taxonomy of Viruses (ICTV) is tasked with classifying viruses into taxa (phyla to species) and devising taxon names. Virus names and virus name abbreviations are currently not within the ICTV's official remit and are not regulated by an official entity. Many scientists, medical/veterinary professionals, and regulatory agencies do not address evolutionary questions nor are they concerned with the hierarchical organization of the viral world, and therefore, have limited use for ICTV-devised taxa. Instead, these professionals look to the ICTV as an expert point source that provides the most current taxonomic affiliations of viruses of interests to facilitate document writing. These needs are currently unmet as an ICTV-supported, easily searchable database that includes all published virus names and abbreviations linked to their taxa is not available. In addition, in stark contrast to other biological taxonomic frameworks, virus taxonomy currently permits individual species to have several members. Consequently, confusion emerges among those who are not aware of the difference between taxa and viruses, and because certain well-known viruses cannot be located in ICTV publications or be linked to their species. In addition, the number of duplicate names and abbreviations has increased dramatically in the literature. To solve this conundrum, the ICTV could mandate listing all viruses of established species and all reported unclassified viruses in forthcoming online ICTV Reports and create a searchable webpage using this information. The International Union of Microbiology Societies could also consider changing the mandate of the ICTV to include the nomenclature of all viruses in addition to taxon considerations. With such a mandate expansion, official virus names and virus name abbreviations could be catalogued and virus nomenclature could be standardized. As a result, the ICTV would become an even more useful resource for all stakeholders in virology.
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Affiliation(s)
- Charles H Calisher
- Arthropod-borne and Infectious Diseases Laboratory, Department of Microbiology, Immunology and Pathology, College of Veterinary Medicine and Biomedical Sciences, Colorado State University, 3195 Rampart Rd., Delivery Code 1690, Foothills Campus, Fort Collins, CO 80523-1692, USA
| | - Thomas Briese
- Department of Epidemiology, Center for Infection and Immunity, Mailman School of Public Health, Columbia University, 722 West 168 St., New York, NY 10032, USA
| | - J Rodney Brister
- National Center for Biotechnology, National Library of Medicine, National Institutes of Health, 8600 Rockville Pike, Bethesda, MD 27102, USA
| | - Rémi N Charrel
- Unité des Virus Emergents (Faculté de Médecine, Université Aix-Marseille—IRD 190—Inserm 1207—IHU Méditerranée Infection), Marseille, France
| | - Ralf Dürrwald
- Department of Infectious Diseases, Robert Koch-Institut, Postfach 65 02 61, D-13302 Berlin, Germany
| | - Hideki Ebihara
- Department of Molecular Medicine, Mayo Clinic, Guggenheim Building, 18th Floor, 200 First St. SW, Rochester, MN 55905, USA
| | - Charles F Fulhorst
- Department of Pathology, University of Texas Medical Branch, 301 University Blvd, Galveston, TX 77555-0609, USA
| | - George Fú Gāo
- National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, 155 Changbai Rd., Changping District, Beijing 102206, China
| | - Martin H Groschup
- Institut für Virusdiagnostik, Friedrich-Loeffler-Institut, Südufer 10, 17493 Greifswald-Insel Riems, Germany
| | - Andrew D Haddow
- Department of Virology, United States Army Medical Research Institute of Infectious Diseases, 1425 Porter Street, Fort Detrick, Frederick, MD 21702, USA
| | - Timothy H Hyndman
- College of Veterinary Medicine, School of Veterinary and Life Sciences, Murdoch University, 90 South St., Murdoch, Western Australia 6150, Australia
| | - Sandra Junglen
- Institute of Virology, Charité Universitätsmedizin Berlin, corporate member of Free University Berlin, Humboldt-University Berlin, and Berlin Institute of Health, Germany
- Deutsches Zentrum für Infektionsforschung, Inhoffenstraße 7, 38124 Braunschweig, Germany
| | - Boris Klempa
- Biomedicínske centrum, Virologický ústav, Slovenská Akadémia Vied, Dúbravská cesta 9, 845 05 Bratislava, Slovakia
| | - Jonas Klingström
- Centre for Infectious Medicine, Institutionen för Medicin, Huddinge, Karolinska Institutet, C2:94, Karolinska Universitetssjukhuset, 141 86 Stockholm, Sweden
| | - Andrew M Kropinski
- Department of Food Science, University of Guelph, Guelph, Ontario N1G 2W1, Canada
- Department of Pathobiology, University of Guelph, Guelph, Ontario N1G 2W1, Canada
| | - Mart Krupovic
- Departement of Microbiology, Institut Pasteur, 25 rue du Docteur Roux, 75015 Paris, France
| | - A Desiree LaBeaud
- Division of Infectious Diseases, Department of Pediatrics, Stanford University School of Medicine, 300 Pasteur Dr., G312, Stanford, CA, 94305 USA
| | - Piet Maes
- KU Leuven, Department of Microbiology, Immunology and Transplantation, Rega Institute, Zoonotic Infectious Diseases unit, Herestraat 49 box 1040, BE3000 Leuven, Belgium
| | - Norbert Nowotny
- Institute of Virology, Department of Pathobiology, University of Veterinary Medicine Vienna, Veterinärplatz 1, A-1210 Vienna, Austria
- Department of Basic Medical Sciences, College of Medicine, Mohammed Bin Rashid University of Medicine and Health Sciences, Building 14, Dubai Healthcare City, P.O. Box 505055, Dubai, United Arab Emirates
| | - Márcio Roberto Teixeira Nunes
- Evandro Chagas Institute, Brazilian Ministry of Health, Rodovia Br-316, Km 7 s/n, Levilândia, Ananindeua, Pará, 67030-000, Brazil
| | - Susan L Payne
- Department of Veterinary Pathobiology, College of Veterinary Medicine and Biomedical Sciences, Veterinary Medical Sciences Building, 400 Raymond Stotzer Parkway, Texas A&M University 4467, College Station, TX 77843, USA
| | - Sheli R Radoshitzky
- Molecular and Translational Sciences, United States Army Medical Research Institute of Infectious Diseases, 1425 Porter Street, Fort Detrick, Frederick, MD 21702, USA
| | - Dennis Rubbenstroth
- Institut für Virusdiagnostik, Friedrich-Loeffler-Institut, Südufer 10, 17493 Greifswald-Insel Riems, Germany
- Institut für Virologie, Universitätsklinikum Freiburg, Hermann-Herder-Straße 11, 79104 Freiburg, Germany
| | - Sead Sabanadzovic
- Department of Biochemistry, Molecular Biology, Entomology and Plant Pathology, Mississippi State University, 402 Dorman Hall, Box 9655, Mississippi State, MS 39762, USA
| | - Takahide Sasaya
- Department of Planning and Coordination, National Agriculture and Food Research Organization, 3-1-1 Kannondai, Tsukuba, Ibaraki 305-8517, Japan
| | - Mark D Stenglein
- Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, CO, 80523 USA
| | - Arvind Varsani
- The Biodesign Center for Fundamental and Applied Microbiomics, School of Life Sciences, Center for Evolution and Medicine, Arizona State University, 727 E. Tyler St., P.O. Box 876101, Tempe, AZ 85287-6101, USA
| | - Victoria Wahl
- National Biodefense Analysis and Countermeasures Center, 8300 Research Plaza, Fort Detrick, Frederick, MD 27102, USA
| | - Scott C Weaver
- Department of Microbiology and Immunology, Institute for Human Infections and Immunity, University of Texas Medical Branch, 301 University Boulevard, Galveston, TX 77555, USA
| | - Francisco Murilo Zerbini
- Departamento de Fitopatologia/BIOAGRO and National Institute of Science and Technology for Plant-Pest Interactions, Universidade Federal de Viçosa, Av. P.H. Rolfs s/n, Viçosa, MG, 36570-900, Brazil
| | - Nikos Vasilakis
- Department of Pathology, Center for Biodefense and Emerging Infectious Diseases, Center for Tropical Diseases, Institute for Human Infection and Immunity, University of Texas Medical Branch, Galveston, TX 77555, USA
| | - Jens H Kuhn
- Integrated Research Facility at Fort Detrick, B-8200 Research Plaza, Fort Detrick, Frederick, MD 27102, USA
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Laenen L, Vergote V, Calisher CH, Klempa B, Klingström J, Kuhn JH, Maes P. Hantaviridae: Current Classification and Future Perspectives. Viruses 2019; 11:v11090788. [PMID: 31461937 PMCID: PMC6784073 DOI: 10.3390/v11090788] [Citation(s) in RCA: 87] [Impact Index Per Article: 17.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2019] [Accepted: 08/23/2019] [Indexed: 01/19/2023] Open
Abstract
In recent years, negative-sense RNA virus classification and taxon nomenclature have undergone considerable transformation. In 2016, the new order Bunyavirales was established, elevating the previous genus Hantavirus to family rank, thereby creating Hantaviridae. Here we summarize affirmed taxonomic modifications of this family from 2016 to 2019. Changes involve the admission of >30 new hantavirid species and the establishment of subfamilies and novel genera based on DivErsity pArtitioning by hieRarchical Clustering (DEmARC) analysis of genomic sequencing data. We outline an objective framework that can be used in future classification schemes when more hantavirids sequences will be available. Finally, we summarize current taxonomic proposals and problems in hantavirid taxonomy that will have to be addressed shortly.
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Affiliation(s)
- Lies Laenen
- KU Leuven, Department of Microbiology and Immunology, Rega Institute for Medical Research, Zoonotic Infectious Diseases Unit, 3000 Leuven, Belgium
- Department of Laboratory Medicine, University Hospitals Leuven, 3000 Leuven, Belgium
| | - Valentijn Vergote
- KU Leuven, Department of Microbiology and Immunology, Rega Institute for Medical Research, Zoonotic Infectious Diseases Unit, 3000 Leuven, Belgium
| | | | - Boris Klempa
- Biomedical Research Center, Slovak Academy of Sciences, 845 05 Bratislava, Slovakia
| | - Jonas Klingström
- Center for Infectious Medicine, Department of Medicine Huddinge, Karolinska Institutet, Karolinska University Hospital, SE-141 86 Stockholm, Sweden
| | - Jens H Kuhn
- Integrated Research Facility at Fort Detrick, National Institute of Allergy and Infectious Diseases, National Institutes of Health, B-8200 Research Plaza, Frederick, MD 21702, USA
| | - Piet Maes
- KU Leuven, Department of Microbiology and Immunology, Rega Institute for Medical Research, Zoonotic Infectious Diseases Unit, 3000 Leuven, Belgium.
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