Identification of Astrovirus in the virome of the upper and lower respiratory tracts of calves with acute signs of bronchopneumonia

ABSTRACT Bovine Astroviruses (BAstV) are small single-stranded, positive-sense RNA viruses that have been historically associated with the infection of the enteric tract in cattle, causing outbreaks of diarrhea, especially in young immunologically naive calves. Long neglected, BAstV have recently regained interest as they have been associated with several nonsuppurative encephalitis cases in cattle as well as in other species. Yet, the difficulty in isolating the virus in conventional cell cultures prevents a full understanding of BAstV tropism and pathogenesis in this species. Here, we describe the metagenomic identification of BAstV in the respiratory tract of calves affected by respiratory distress in French farms. BastV were prevalently detected in the lower respiratory tract of sick calves; however, molecular testing of further cohorts of respiratory samples highlighted their presence also in nasal swabs. Phylogenetic analyses revealed two divergent clades for neurotropic and enteric BAstV, suggesting that their tropism is likely to be strain-specific. BAstV detected in the respiratory tract of calves with respiratory disease were genetically related to enteric strains already described in cattle in Asia, displaying between 85% and 95% nucleotide identity. In addition, the sequences from France belonged to the clade of BAstV identified in yaks, roe deer, and camelids, underlining the interspecies transmission potential of the virus. More studies are warranted to understand if BAstV have a potential role in the onset of bovine respiratory disease. IMPORTANCE Astroviruses (AstV) are known suspects of enteric disease in humans and livestock. Recently, AstV have been linked to encephalitis in immunocompromised patients and other animals, such as cattle, minks, and swine. In our study, we also identified AstV in the respiratory samples of calves with signs of bronchopneumonia, suggesting that their tropism could be even broader. We obtained one bovine AstV (BAstV) complete genome sequence by next-generation sequencing and showed that respiratory and enteric AstV from different species formed a divergent genetic cluster with AstV isolated from encephalitis cases, indicating that tropism might be strain-specific. These data provide further insight into understanding the biology of these understudied pathogens and suggest BAstV as a potential new candidate for bovine respiratory disease. Astroviruses (AstV) are known suspects of enteric disease in humans and livestock. Recently, AstV have been linked to encephalitis in immunocompromised patients and other animals, such as cattle, minks, and swine. In our study, we also identified AstV in the respiratory samples of calves with signs of bronchopneumonia, suggesting that their tropism could be even broader. We obtained one bovine AstV (BAstV) complete genome sequence by next-generation sequencing and showed that respiratory and enteric AstV from different species formed a divergent genetic cluster with AstV isolated from encephalitis cases, indicating that tropism might be strain-specific. These data provide further insight into understanding the biology of these understudied pathogens and suggest BAstV as a potential new candidate for bovine respiratory disease.