Systematic genome analysis enables long-overdue taxonomic reorganization of genus Orthoflavivirus; potential assignment of over 50 new species

Simmonds, P.; Beer, M.; Bejerman, N.; Bukh, J.; Butkovic, A.; Colmant, A.; Debat, H.; Drexler, J. F.; Kapoor, A.; Kuhn, J. H.; Lohmann, V.; Smith, D. B.; Stapleton, J. T.; Vasilakis, N.

doi:10.64898/2026.10.21.760428

bioRxiv · 10.64898/2026.10.21.760428

Systematic genome analysis enables long-overdue taxonomic reorganization of genus Orthoflavivirus; potential assignment of over 50 new species

Simmonds, P.·Beer, M.·Bejerman, N.·Bukh, J.·Butkovic, A.·Colmant, A.·Debat, H.·Drexler, J. F.·Kapoor, A.·Kuhn, J. H.·Lohmann, V.·Smith, D. B.·Stapleton, J. T.·Vasilakis, N.

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Abstract

Members of the Orthoflavivirus genus in the family Flaviviridae are primarily vector-transmitted RNA viruses infecting humans, other mammals and birds, including major pathogens such as tick borne encephalitis, West Nile, Zika and dengue viruses. Vector-borne flaviviruses are assigned to the Euflavivirus subgenus of orthoflaviviruses, with more divergent largely unclassified insect-specific flaviviruses, including cell fusing agent virus assigned to the second subgenus, Fusivirus. The currently classified 57 orthoflavivirus species have traditionally been assigned descriptively on the basis of their genome and antigenic relatedness, ecology and host and vector tropisms, although many more orthoflavi-like viruses remain unassigned. To investigate whether species might be demarcated using a fixed genetic divergence threshold, we examined distributions of pairwise distances in NS5 and E genes (which encode the RNA-dependent RNA polymerase and envelope protein, respectively) of classified orthoflaviviruses. Demarcation thresholds of 0.1 in the two regions would be most parsimonious with current euflavivirus classification. Exceptions include species in the tick-borne encephalitis virus complex with divergences below the threshold, and dengue virus types currently assigned to a single species that are substantially above. Application of the proposed thresholds would provide the means to establish 25 new euflavivirus and 33 new fusivirus species and reconcile several anomalies and inconsistencies in the current species taxonomy. The use of a species demarcation threshold brings consistency with the classification of viruses in other families. A robust and evolutionarily consistent framework furthermore enables taxonomic assignments of the numerous currently unassigned orthoflaviviruses that lack the phenotypic descriptions required for the current species definition.

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Simmonds, P., Beer, M., Bejerman, N., Bukh, J., Butkovic, A., Colmant, A., Debat, H., Drexler, J. F., Kapoor, A., Kuhn, J. H., Lohmann, V., Smith, D. B., Stapleton, J. T., Vasilakis, N.. 2026-10-26. Systematic genome analysis enables long-overdue taxonomic reorganization of genus Orthoflavivirus; potential assignment of over 50 new species. https://doi.org/10.64898/2026.10.21.760428

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