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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Published in:Nature microbiology Vol. 10; no. 11; p. 3026
Main Authors: Simmonds, Peter, Butković, Anamarija, Grove, Joe, Mayne, Richard, Mifsud, Jonathon C O, Beer, Martin, Bukh, Jens, Drexler, J Felix, Kapoor, Amit, Lohmann, Volker, Smith, Donald B, Stapleton, Jack T, Vasilakis, Nikos, Kuhn, Jens H
Format: Journal Article
Language:English
Published: England 01.11.2025
Subjects:
Evolution, Molecular
Flaviviridae - classification
Flaviviridae - enzymology
Flaviviridae - genetics
Genome, Viral
Host Specificity
Phylogeny
RNA Helicases - genetics
RNA-Dependent RNA Polymerase - genetics
Viral Proteins - genetics
ISSN:2058-5276, 2058-5276
Online Access:Get more information
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Summary: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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ISSN:2058-5276
2058-5276
DOI:10.1038/s41564-025-02134-0