Neurotropic Tick-Borne Flavivirus in Alpine Chamois (Rupicapra rupicapra rupicapra), Austria, 2017, Italy, 2023

Abstract

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.

Keywords: Alpine chamois; Flaviviridae; Ixodes ricinus; Rupicapra rupicapra; Spanish goat encephalitis virus; encephalitis; flavivirus; louping ill virus; neurotropic; tick-borne encephalitis virus.

Figure 1

Location of the three cases of Alpine chamois encephalitis virus infections in Austria and northern Italy, indicated by red dots. The straight line distances between the cases were 390 km [case 1 (Salzburg) and 2 (Piedmont)], 334 km [case 1 (Salzburg) and 3 (Lombardy)], and 66 km [case 2 (Piedmont) and 3 (Lombardy)], respectively.

Figure 2

Histological sections from the brain of case 1. (A) Nonpurulent leptomeningitis: Slight lymphoplasmohistiocytic infiltrate (*); (B–D) Nonpurulent encephalitis; (B): Slight lymphoplasmohistiocytic perivascular infiltrate (*); (C) Two glial nodules in brain stem (*); (D) Glial shrubbery in the cerebellum (*). Microphoto, H&E, bar (A) = 100 µm, bars (B–D) = 180 µm.

Figure 3

Maximum likelihood phylogenetic tree of the complete genomes of Alpine chamois encephalitis viruses and other TBEV, LIV, and LIV-like sequences constructed using the IQtree software and the GTR + F+I + G4 model according to BIC and a bootstrap of 1000 replicates. Sequences investigated in this study are shown in blue. The sequences of Spanish sheep encephalitis virus, Greek goat encephalitis virus, and Turkish sheep encephalitis virus are highlighted in yellow, and the sequence of Spanish goat encephalitis virus is highlighted in turquoise.

Figure 4

SSE similarity plots over the whole genome sequences between the Alpine chamois encephalitis viruses (ACEV) from Austria and Italy, the Spanish goat encephalitis virus (SGEV), and the reference strains of tick-borne encephalitis virus European subtype (TBEV-Eur) and Louping ill virus (LIV). Tick and chamois virus sequences for Piedmont and Lombardy are tagged as a group. Similarity plots were generated using SSE version 1.2 using a sliding window of 600 and a step size of 100 nucleotides. The percentage of identities (y-axis) between 50 and 100% is shown over the whole genome alignment (x-axis).

Figure 5

Structural alignment of the E protein. The secondary structure elements are defined based on an ESPript algorithm and are labeled as in a previous report on the LIV structure (PDB no. 6J5C) and are presented on top (Spiral lines indicate helices, arrows represent β strands and TT letters turns). The Arabic numerals 1–6 indicate cysteine residues that pair to form disulfide bonds. Lines above the sequences indicate domains I (red), II (yellow), and III (blue), as well as the fusion peptide loop (pink) and the dI/dIII and dIII/stem linkers (purple). Austrian and Italian ACEV strains are shown in a box.

Figure 6

Map of Europe. Location of the three cases of Alpine chamois encephalitis virus infections in Austria and Northern Italy and approximate location of the cases of Spanish goat encephalitis virus infections in the Principality of Asturias (capital: Oviedo) in Northwestern Spain are displayed. The approximate straight line distance between cases of Alpine chamois encephalitis virus and Spanish goat encephalitis virus infections (for the latter, the exact location was not published) is between 1170 km (Piedmont case, Oviedo) and 1550 km (Salzburg case, Oviedo). The base map shapefile was obtained from the Geographic Information System of the EU Commission via the Eurostat webpage—the 2021 version at 20 M resolution showing NUTS level 3 regions—and annotated in QGIS v.3.4.15.