D. WÜTHRICH^1,2, C.L. BOUJON³, L. TRUCHET³, S. SELIMOVIC-HAMZA^2,3, I.G. BOUZALAS³, R. BRUGGMANN¹, T. SEUBERLICH<sup>3

1</sup>Interfaculty Bioinformatics Unit, University of Bern and Swiss Institute of Bioinformatics, 3001 Bern, Switzerland; , ²Graduate School for Cellular and Biomedical Sciences, University of Bern, 3001 Bern, Switzerland, ³NeuroCenter, Division of Neurological Sciences, Vetsuisse Faculty, University of Bern, Bern, Switzerland

Non-suppurative encephalitis is one of the most frequent pathological diagnosis in cattle with neurological disease, but there is a gap in the knowledge on disease-associated pathogens. In order to identify viruses that are associated with non-suppurative encephalitis in cattle, we established a viral metagenomics based analysis pipeline for virus detection and discovery. RNA and DNA libraries were prepared from brain tissue samples of diseased cattle and subjected to Illumina next-generation-sequencing (NGS). Collected sequence reads were (i) mapped to a reference virus genome database for the detection of known viruses and (ii) assembled to contigs and searched for similarities to viral proteins in order to identify novel viruses. We found parainfluenza virus 5, bovine polyomavirus 2 (BoPV-2 SF), ovine herpesvirus 2 and bovine herpesvirus 6 (BHV-6) in a proportion of the affected cattle. In addition we discovered two novel bovine astroviruses (BoAstV CH13 and BoAstV CH15) as well as a putative new bovine betaretrovirus (1, 2). In case-control studies using PCR protocols and in-situ RNA hybridization BoAstV-CH13, BoPV-2 SF and BoHV-6 were statistically associated with the disease. Retrospective studies indicate that BoAstV CH13 is present in brain tissues of around one quarter of cattle with virus encephalitis of unknown etiology and that astroviruses have been involved in the pathogenesis of this disease entity since the mid-20th century. These data expand our knowledge on encephalitis-associated pathogens in cattle and point to the value of NGS in resolving complex infection scenarios in a clinical disease setting.

1. Bouzalas IG, Wüthrich D, Walland J, Drögemüller C, Zurbriggen A, Vandevelde M, Oevermann A, Bruggmann R, Seuberlich T. J Clin Microbiol 2014;52:3318–24.
2. Seuberlich T, Wüthrich D, Selimovic-Hamza S, Drögemüller C, Oevermann A, Bruggmann R, Bouzalas I. Emerg Microbes Infect 2016; 5(1):e5.