Taxonomic expansion and reorganization of Flaviviridae
Flaviviridae is a family of non-segmented positive-sense RNA viruses that includes major pathogens such as hepatitis C virus, dengue viruses and yellow fever virus. Recent large-scale metagenomic surveys have identified many RNA viruses related to members of this family, such as orthoflaviviruses an...
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| Vydáno v: | Nature microbiology Ročník 10; číslo 11; s. 3026 |
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| Hlavní autoři: | , , , , , , , , , , , , , |
| Médium: | Journal Article |
| Jazyk: | angličtina |
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England
01.11.2025
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| ISSN: | 2058-5276, 2058-5276 |
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| Abstract | Flaviviridae is a family of non-segmented positive-sense RNA viruses that includes major pathogens such as hepatitis C virus, dengue viruses and yellow fever virus. Recent large-scale metagenomic surveys have identified many RNA viruses related to members of this family, such as orthoflaviviruses and pestiviruses. These viruses diverge by having different genome lengths and configurations, and host range. Here we performed an analysis of RNA-directed RNA polymerase (RdRP) hallmark gene sequences of flaviviruses and 'flavi-like' viruses. We uncovered four divergent clades and multiple lineages that are congruent with phylogenies of their helicase genes, protein profile hidden Markov model profiles, and evolutionary relationships based on predicted RdRP protein structures. These results support their classification into three families (Flaviviridae, Pestiviridae and Hepaciviridae) and 12 genera in the established order Amarillovirales, with groupings correlating with genome properties and host range. This taxonomy provides a framework for future evolutionary studies on this important viral family. |
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| AbstractList | Flaviviridae is a family of non-segmented positive-sense RNA viruses that includes major pathogens such as hepatitis C virus, dengue viruses and yellow fever virus. Recent large-scale metagenomic surveys have identified many RNA viruses related to members of this family, such as orthoflaviviruses and pestiviruses. These viruses diverge by having different genome lengths and configurations, and host range. Here we performed an analysis of RNA-directed RNA polymerase (RdRP) hallmark gene sequences of flaviviruses and 'flavi-like' viruses. We uncovered four divergent clades and multiple lineages that are congruent with phylogenies of their helicase genes, protein profile hidden Markov model profiles, and evolutionary relationships based on predicted RdRP protein structures. These results support their classification into three families (Flaviviridae, Pestiviridae and Hepaciviridae) and 12 genera in the established order Amarillovirales, with groupings correlating with genome properties and host range. This taxonomy provides a framework for future evolutionary studies on this important viral family.Flaviviridae is a family of non-segmented positive-sense RNA viruses that includes major pathogens such as hepatitis C virus, dengue viruses and yellow fever virus. Recent large-scale metagenomic surveys have identified many RNA viruses related to members of this family, such as orthoflaviviruses and pestiviruses. These viruses diverge by having different genome lengths and configurations, and host range. Here we performed an analysis of RNA-directed RNA polymerase (RdRP) hallmark gene sequences of flaviviruses and 'flavi-like' viruses. We uncovered four divergent clades and multiple lineages that are congruent with phylogenies of their helicase genes, protein profile hidden Markov model profiles, and evolutionary relationships based on predicted RdRP protein structures. These results support their classification into three families (Flaviviridae, Pestiviridae and Hepaciviridae) and 12 genera in the established order Amarillovirales, with groupings correlating with genome properties and host range. This taxonomy provides a framework for future evolutionary studies on this important viral family. Flaviviridae is a family of non-segmented positive-sense RNA viruses that includes major pathogens such as hepatitis C virus, dengue viruses and yellow fever virus. Recent large-scale metagenomic surveys have identified many RNA viruses related to members of this family, such as orthoflaviviruses and pestiviruses. These viruses diverge by having different genome lengths and configurations, and host range. Here we performed an analysis of RNA-directed RNA polymerase (RdRP) hallmark gene sequences of flaviviruses and 'flavi-like' viruses. We uncovered four divergent clades and multiple lineages that are congruent with phylogenies of their helicase genes, protein profile hidden Markov model profiles, and evolutionary relationships based on predicted RdRP protein structures. These results support their classification into three families (Flaviviridae, Pestiviridae and Hepaciviridae) and 12 genera in the established order Amarillovirales, with groupings correlating with genome properties and host range. This taxonomy provides a framework for future evolutionary studies on this important viral family. |
| Author | Drexler, J Felix Kapoor, Amit Lohmann, Volker Smith, Donald B Stapleton, Jack T Mayne, Richard Vasilakis, Nikos Simmonds, Peter Bukh, Jens Grove, Joe Beer, Martin Mifsud, Jonathon C O Butković, Anamarija Kuhn, Jens H |
| Author_xml | – sequence: 1 givenname: Peter orcidid: 0000-0002-7964-4700 surname: Simmonds fullname: Simmonds, Peter email: peter.simmonds@utu.fi, peter.simmonds@utu.fi organization: Institute of Biomedicine, University of Turku, Turku, Finland. peter.simmonds@utu.fi – sequence: 2 givenname: Anamarija surname: Butković fullname: Butković, Anamarija organization: Archaeal Virology Unit, Institut Pasteur, Université Paris Cité, CNRS UMR6047, Paris, France – sequence: 3 givenname: Joe orcidid: 0000-0001-5390-7579 surname: Grove fullname: Grove, Joe organization: MRC-University of Glasgow Centre for Virus Research, Glasgow, UK – sequence: 4 givenname: Richard orcidid: 0000-0003-1915-4993 surname: Mayne fullname: Mayne, Richard organization: Nuffield Department of Medicine, University of Oxford, Oxford, UK – sequence: 5 givenname: Jonathon C O orcidid: 0000-0001-8934-9193 surname: Mifsud fullname: Mifsud, Jonathon C O organization: Sydney Institute for Infectious Diseases, School of Medical Sciences, The University of Sydney, Sydney, New South Wales, Australia – sequence: 6 givenname: Martin orcidid: 0000-0002-0598-5254 surname: Beer fullname: Beer, Martin organization: Institute of Diagnostic Virology, Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Greifswald-Insel Riems, Germany – sequence: 7 givenname: Jens orcidid: 0000-0002-7815-4806 surname: Bukh fullname: Bukh, Jens organization: Copenhagen Hepatitis C Program (CO-HEP), Department of Infectious Diseases, Copenhagen University Hospital, Hvidovre, and Department of Immunology and Microbiology, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark – sequence: 8 givenname: J Felix orcidid: 0000-0002-3509-0232 surname: Drexler fullname: Drexler, J Felix organization: Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Institute of Virology, Berlin, Germany – sequence: 9 givenname: Amit orcidid: 0000-0002-8117-7347 surname: Kapoor fullname: Kapoor, Amit organization: Center for Vaccines and Immunity, The Research Institute at Nationwide Children's Hospital, Columbus, OH, USA – sequence: 10 givenname: Volker orcidid: 0000-0001-8719-7608 surname: Lohmann fullname: Lohmann, Volker organization: Department of Infectious Diseases, Molecular Virology, Heidelberg University, Heidelberg, Germany – sequence: 11 givenname: Donald B surname: Smith fullname: Smith, Donald B organization: Nuffield Department of Medicine, University of Oxford, Oxford, UK – sequence: 12 givenname: Jack T orcidid: 0000-0002-2302-9055 surname: Stapleton fullname: Stapleton, Jack T organization: Departments of Internal Medicine, Microbiology and Immunology, University of Iowa and Iowa City VA Healthcare, Iowa City, IA, USA – sequence: 13 givenname: Nikos orcidid: 0000-0002-0708-3289 surname: Vasilakis fullname: Vasilakis, Nikos organization: Department of Pathology and Center for Vector-Borne and Zoonotic Diseases, University of Texas Medical Branch, Galveston, TX, USA – sequence: 14 givenname: Jens H orcidid: 0000-0002-7800-6045 surname: Kuhn fullname: Kuhn, Jens H email: jenshkuhn@comcast.net organization: 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, USA. jenshkuhn@comcast.net |
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| Title | Taxonomic expansion and reorganization of Flaviviridae |
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