The European subtype of tick-borne encephalitis virus (TBEV-Eur; species Orthoflavivirus encephalitidis, family Flaviviridae) was the only tick-borne flavivirus present in central Europe known to cause neurologic disease in humans and several animal species. Here, we report a tick-borne flavivirus isolated from Alpine chamois (Rupicapra rupicapra rupicapra) with encephalitis and attached ticks, present over a wide area in the Alps. Cases were detected in 2017 in Salzburg, Austria, and 2023 in Lombardy and Piedmont, Italy. The virus strains exhibit 94.8-97.3% nucleotide identities to each other and are more closely related to Louping ill viruses (LIV; Orthoflavivirus loupingi; 90-92% identities) than to TBEV-Eur (less than 88%). The chamois-derived virus strains, tentatively termed "Alpine chamois encephalitis virus", form a well-supported independent genetic clade with Spanish goat encephalitis virus, clearly separated from other LIV. This supports its designation as a new virus subtype with the proposed shared taxonomic name "Spanish goat and Alpine chamois encephalitis virus subtype" within the species Orthoflavivirus loupingi. The zoonotic potential of this newly identified virus subtype as well as its host range in other animal species including farm animals needs to be further investigated.

Center for Virology Medical University of Vienna 1090 Vienna Austria

Center of Pathobiology Department of Biological Sciences and Pathobiology University of Veterinary Medicine Vienna 1210 Vienna Austria

College of Medicine Mohammed Bin Rashid University of Medicine and Health Sciences Dubai Health Dubai P O Box 505055 United Arab Emirates

Department of Veterinary Sciences University of Pisa 56124 Pisa Italy

Institute for Veterinary Disease Control Mödling Austrian Agency for Health and Food Safety Ltd 2340 Mödling Austria

Institute of Vertebrate Biology Czech Academy of Sciences 60365 Brno Czech Republic

Istituto Zooprofilattico Sperimentale del Piemonte Liguria e Valle d'Aosta 10154 Torino Italy

Istituto Zooprofilattico Sperimentale della Lombardia e dell'Emilia Romagna 25124 Brescia Italy

Istituto Zooprofilattico Sperimentale delle Venezie 35020 Legnaro Italy

Veterinary Practice Reitsam 5450 Werfen Austria

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