- Thomas S. Postler ORCID:orcid.org/0000-0002-3558-90841,
- Martin Beer ORCID:orcid.org/0000-0002-0598-52542,
- Bradley J. Blitvich ORCID:orcid.org/0000-0002-9857-57553,
- Jens Bukh ORCID:orcid.org/0000-0002-7815-48064,5,
- Xavier de Lamballerie ORCID:orcid.org/0000-0001-7895-27206,
- J. Felix Drexler ORCID:orcid.org/0000-0002-3509-02327,
- Allison Imrie ORCID:orcid.org/0000-0003-4715-66628,
- Amit Kapoor ORCID:orcid.org/0000-0002-8117-73479,10,
- Galina G. Karganova (Карганова Галина Григорьевна) ORCID:orcid.org/0000-0002-8901-620611,
- Philippe Lemey ORCID:orcid.org/0000-0003-2826-535312,
- Volker Lohmann ORCID:orcid.org/0000-0001-8719-760813,
- Peter Simmonds ORCID:orcid.org/0000-0002-7964-470014,
- Donald B. Smith ORCID:orcid.org/0000-0002-2876-531814,
- Jack T. Stapleton ORCID:orcid.org/0000-0002-2302-905515,16 &
- …
- Jens H. Kuhn ORCID:orcid.org/0000-0002-7800-604517
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Abstract
This review provides a summary of the recently ratified changes to genus and species nomenclature within the virus familyFlaviviridae along with reasons for these changes. First, it was considered that the vernacular terms “flaviviral”, “flavivirus”, and “flaviviruses” could under certain circumstances be ambiguous due to the same word stem “flavi” in the taxon namesFlaviviridae andFlavivirus; these terms could either have referred to all viruses classified in the familyFlaviviridae or only to viruses classified in the included genusFlavivirus. To remove this ambiguity, the genus nameFlavivirus was changed toOrthoflavivirus by the International Committee on Taxonomy of Viruses (ICTV). Second, all species names in the family were changed to adhere to a newly ICTV-mandated binomial format (e.g.,Orthoflavivirus zikaense,Hepacivirus hominis) similar to nomenclature conventions used for species elsewhere in biology. It is important to note, however, that virus names remain unchanged. Here we outline the revised taxonomy of the familyFlaviviridae as approved by the ICTV in April 2023.
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Introduction
The familyFlaviviridae encompasses four genera and 89 species [1]. The International Committee on Taxonomy of Viruses (ICTV) [5] recently made a number of changes to the names of genera and species in the family. This review describes these changes and the reasons for them. As a guide for those working in the flavivirus field, we also provide a comprehensive list of the previous and new nomenclature for each species and their viruses.
New genus nameOrthoflavivirus
The genusFlavivirus within the familyFlaviviridae was established for a large number of arthropod-borne viruses (e.g., dengue viruses and Zika virus) that are high-consequence human and veterinary pathogens [6]. The genus nameFlavivirus contained the word stem “flavi”, which is also used for the family name. Therefore, the vernacular terms “flaviviral”, “flavivirus”, and “flaviviruses” were ambiguous, as these words might have referred to all members of the family (viruses of the generaFlavivirus,Hepacivirus,Pegivirus, andPestivirus) or only to those of the genusFlavivirus.
To preclude this potential confusion, a taxonomic proposal (TaxoProp 2022.007S.A.Flaviviridae_1genren_sprenamed) was submitted to the ICTV in 2022. It proposed that the genusFlavivirus be renamedOrthoflavivirus, which roughly translates to “true flaviviruses” or “flavivirusessensu stricto”. This proposal was approved by the ICTV Executive Committee in late 2022 and ratified by the ICTV in April 2023 [2,9]. Consequently, the terms “flaviviral”, “flavivirus”, and “flaviviruses” should be used to refer to the collective members of the familyFlaviviridae, whereas the terms “orthoflaviviral”, “orthoflavivirus”, and “orthoflaviviruses” should be used for viruses of the genusOrthoflavivirus (all orthoflaviviruses are flaviviruses, but not all flaviviruses are orthoflaviviruses).
Change to species names in the familyFlaviviridae
In March 2021, the ICTV ratified TaxoProp 2018.001G.R.binomial_species, which requires all species names to follow a new codified rule:
"A species name shall consist of only two distinct word components separated by a space. The first word component shall begin with a capital letter and be identical in spelling to the name of the genus to which the species belongs. The second word component shall not contain any suffixes specific for taxa of higher ranks. The entire species name (both word components) shall be italicized" [3,7].
The purpose of this rule is to differentiate more clearly the name of a virus from the name of the species (taxon) to which it is assigned by using the standardized genus + species epithet format found elsewhere in biological taxonomy nomenclature [8]. For orthoflaviviruses, this change was particularly relevant because most species names were the same as the virus names, apart from the orthography; e.g., yellow fever virus was a member of the speciesYellow fever virus, a situation that created confusion.
The new binomial rule required all names of species previously included in the genusFlavivirus to adhere to the format “Orthoflavivirus xxxxxx”, in which “xxxxxx” represents a single word. At the same time, the opportunity was taken to abandon the single-letter species epithets used for names of species included in the generaHepacivirus, Pegivirus, andPestivirus and instead establish a consistent naming format within the familyFlaviviridae. New species names were proposed according to guidance outlined by Postler et al. [4] in the same proposal that addressed the genus name issue (TaxoProp 2022.007S.A.Flaviviridae_1genren_sprenamed). Tables 1,2,3 and 4 list the current taxonomy of the familyFlaviviridae, including the prior species names as a reference; Table 5 provides guidance for applying the updated nomenclature in manuscripts.
As with species-renaming proposals elsewhere in virus taxonomy, it should be stressed that these changes to the names of virus species have no influence on the names of the viruses classified within them. Thus, for instance, the virus name “Zika virus” and its abbreviation “ZIKV” remain unchanged even though the species,Zika virus, was renamedOrthoflavivirus zikaense. Similarly, hepatitis C virus (HCV) remains the same, whereas the species was renamedHepacivirus hominis.
Conclusion
We hope this description of the modifications and replacements of genus and species names is of value by both explaining the reasons for the nomenclature changes and providing a useful reference list for those working in the field. The ICTV Online Report chapter on the familyFlaviviridae has also been updated with the new genus and species names [6].
Data availability
Not applicable.
References
International Committee on Taxonomy of Viruses (ICTV) (2023) Virus taxonomy: 2022 Release (MSL #38).https://talk.ictvonline.org/taxonomy/. Accessed 17 July 2023
International Committee on Taxonomy of Viruses (ICTV) (2023) Approved proposals.https://ictv.global/files/proposals/approved. Accessed 17 July 2023
International Committee on Taxonomy of Viruses (ICTV) (2023) ICTV Code. The International Code of Virus Classification and Nomenclature (ICVCN). March 2021.https://ictv.global/about/code. Accessed 17 July 2023
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 (2022) Guidance for creating individual and batch latinized binomial virus species names. J Gen Virol 103:001800
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Simmonds P, Becher P, Bukh J, Gould EA, Meyers G, Monath T, Muerhoff S, Pletnev A, Rico-Hesse R, Smith DB, Stapleton JT, ICTV Report Consortium (2017) ICTV virus taxonomy profile:Flaviviridae. J Gen Virol 98:2–3
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 (2021) 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 166:2633–2648
Zerbini FM, Siddell SG, Mushegian AR, Walker PJ, Lefkowitz EJ, Adriaenssens EM, Alfenas-Zerbini P, Dutilh BE, García ML, Junglen S, Krupovic M, Kuhn JH, Lambert AJ, Łobocka M, Oksanen HM, Robertson DL, Rubino L, Sabanadzovic S, Simmonds P, Suzuki N, Van Doorslaer K, Vandamme AM, Varsani A (2022) Differentiating between viruses and virus species by writing their names correctly. Arch Virol 167:1231–1234
Zerbini FM, Siddell SG, Lefkowitz EJ, Mushegian AR, Adriaenssens EM, Alfenas-Zerbini P, Dempsey DM, Dutilh BE, García ML, Hendrickson RC, Junglen S, Krupovic M, Kuhn JH, Lambert AJ, Łobocka M, Oksanen HM, Orton RJ, Robertson DL, Rubino L, Sabanadzovic S, Simmonds P, Smith DB, Suzuki N, Van Dooerslaer K, Vandamme A-M, Varsani A (2023) Changes to virus taxonomy and the ICTV Statutes ratified by the International Committee on Taxonomy of Viruses (2023). Arch Virol 168:175
Acknowledgements
We thank Anya Crane (NIH NIAID DCR IRF-Frederick) for critically editing the manuscript.
Funding
This work was supported in part through Laulima Government Solutions, LLC, prime Contract No. HHSN272201800013C with the U.S. National Institute of Allergy and Infectious Diseases (NIAID). J.H.K. performed this work as an employee of Tunnell Government Services (TGS), a subcontractor of Laulima Government Solutions, LLC, under Contract No. HHSN272201800013C. The views and conclusions contained in this document are those of the authors and should not be interpreted as necessarily representing the official policies, either expressed or implied, of the U.S. Department of Health and Human Services or of the institutions and companies affiliated with the authors.
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Authors and Affiliations
Vaccine Design and Development Laboratory, International AIDS Vaccine Initiative, Brooklyn, NY, USA
Thomas S. Postler
Institute of Diagnostic Virology, Friedrich-Loeffler-Institut, Greifswald, Insel Riems, Germany
Martin Beer
Department of Veterinary Microbiology and Preventive Medicine, College of Veterinary Medicine, Iowa State University, Ames, IA, USA
Bradley J. Blitvich
Copenhagen Hepatitis C Program (CO-HEP), Department of Infectious Diseases, Copenhagen University Hospital Hvidovre, Hvidovre, Denmark
Jens Bukh
CO-HEP, Department of Immunology and Microbiology, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
Jens Bukh
Unité des Virus Émergents (Aix-Marseille Univ-IRD 190-Inserm 1207), Marseille, France
Xavier de Lamballerie
Institute of Virology, Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, Berlin, Germany
J. Felix Drexler
School of Biomedical Sciences, University of Western Australia, Nedlands, WA, Australia
Allison Imrie
Center for Vaccines and Immunity, The Research Institute at Nationwide Children’s Hospital, Columbus, OH, USA
Amit Kapoor
Department of Pediatrics, College of Medicine and Public Health, The Ohio State University, Columbus, OH, USA
Amit Kapoor
Laboratory of Biology of Arboviruses, FSASI “Chumakov Federal Scientific Center for Research and Development of Immune-and-Biological Products of RAS” (Chumakov Institute of Poliomyelitis and Viral Encephalitides), Moscow, Russia
Galina G. Karganova (Карганова Галина Григорьевна)
Department of Microbiology, Immunology and Transplantation, Rega Institute, KU Leuven, Leuven, Belgium
Philippe Lemey
Department of Infectious Diseases, Molecular Virology, Heidelberg University, Heidelberg, Germany
Volker Lohmann
Nuffield Department of Medicine, University of Oxford, Oxford, UK
Peter Simmonds & Donald B. Smith
Medicine Service, Iowa City Veterans Administration Healthcare, Iowa City, IA, USA
Jack T. Stapleton
Departments of Internal Medicine, Microbiology and Immunology, University of Iowa, Iowa City, IA, USA
Jack T. Stapleton
Integrated Research Facility at Fort Detrick (IRF-Frederick), Division of Clinical Research (DCR), National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health (NIH), B-8200 Research Plaza, Fort Detrick, Frederick, MD, 21702, USA
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Martin Beer, Bradley J. Blitvich, Jens Bukh, Xavier de Lamballerie, J. Felix Drexler, Allison Imrie, Amit Kapoor, Galina G. Karganova, Philippe Lemey, Volker Lohmann, Peter Simmonds, Donald B. Smith, Jack T. Stapleton: The members of the 2020–2023 International Committee on Taxonomy of Viruses (ICTV)Flaviviridae Study Group.
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Postler, T.S., Beer, M., Blitvich, B.J.et al. Renaming of the genusFlavivirus toOrthoflavivirus and extension of binomial species names within the familyFlaviviridae.Arch Virol168, 224 (2023). https://doi.org/10.1007/s00705-023-05835-1
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