ena-STUDY-UNIVERSITY OF BERN-30-01-2019-15:02:19:411-106
Discovery of novel astrovirus genotype species in small ruminants
Astroviruses (AstV) are single-stranded, positive-sense RNA viruses with a genome length between 6.2 and 7.8 kb, which includes three open reading frames (ORF). ORF1a encodes together with ORF1b and via a translational ribosomal frameshift mechanism the non-structural proteins, while ORF2 encodes the capsid protein precursor. Enterotropic astroviruses are best known for causing diarrhoea in humans and are also found in many other mammals; in those, the relevance in gastroenteritis remains unclear. Recently described neurotropic astroviruses showed associations with encephalitis in humans as well as in other mammals. In Switzerland two neurotropic astroviruses were identified in cattle, bovine astrovirus CH13 (BoAstV-CH13) and -CH15 (BoAstV-CH15), as well as one in a sheep, named ovine astrovirus CH16 (OvAstV-CH16). OvAstV-CH16 shows a high similarity to BoAstV-CH15, which strengthens the hypothesis of an interspecies transmission. In humans, astroviruses associated with encephalitis were found also in human stool samples, suggesting that in these patients the infection spreads from the gastrointestinal tract to the brain under certain conditions, such as immunosuppression. Whether a similar pathogenesis occurs in ruminants remains unknown. The aim of this study was 1) the discovery and analyzation of so far unknown astroviruses in small ruminants and other ruminant like species' feces samples, 2) the investigation of the potential occurence of neurotropic astroviruses in feces samples and 3) the examination of a potential interspecies transmission of astroviruses.Therefore RNA extraction out of 164 fecal samples from different ruminant species, including sheep, goats, alpacas, llamas, deer, ibex, chamois, bison and giraffe was perfomed and all samples were screened on neurotropic as well as on various astroviruses using PCR. Positive tested samples were submitted to next generation sequencing (NGS). After quality trimming and host-gene-removal the remaining data was de novo assembled. The generated sequences were compared to nucleotide, amino acid databases, virus properties were identified, and phylogenetic analyses as well as recombination analysis were performed.The excretion of neurotropic astroviruses in small ruminants' feces could not be demonstrated, but on the other hand, this work suggests the first identification of astroviruses in goats and the discovery of multiple new genetic variants as well as novel genotype-species in small ruminants. Additionally, multiple putative recombination events in four of five newly discovered full-length genome sequences were predicted. The high genetic similarity and predicted recombinations between some of these astroviruses suggest interspecies transmission events.
Astroviruses (AstV) are single-stranded, positive-sense RNA viruses with a genome length between 6.2 and 7.8 kb, which includes three open reading frames (ORF). ORF1a encodes together with ORF1b and via a translational ribosomal frameshift mechanism the non-structural proteins, while ORF2 encodes the capsid protein precursor. Enterotropic astroviruses are best known for causing diarrhoea in humans and are also found in many other mammals; in those, the relevance in gastroenteritis remains unclear. Recently described neurotropic astroviruses showed associations with encephalitis in humans as well as in other mammals. In Switzerland two neurotropic astroviruses were identified in cattle, bovine astrovirus CH13 (BoAstV-CH13) and -CH15 (BoAstV-CH15), as well as one in a sheep, named ovine astrovirus CH16 (OvAstV-CH16). OvAstV-CH16 shows a high similarity to BoAstV-CH15, which strengthens the hypothesis of an interspecies transmission. In humans, astroviruses associated with encephalitis were found also in human stool samples, suggesting that in these patients the infection spreads from the gastrointestinal tract to the brain under certain conditions, such as immunosuppression. Whether a similar pathogenesis occurs in ruminants remains unknown. The aim of this study was 1) the discovery and analyzation of so far unknown astroviruses in small ruminants and other ruminant like species' feces samples, 2) the investigation of the potential occurence of neurotropic astroviruses in feces samples and 3) the examination of a potential interspecies transmission of astroviruses.Therefore RNA extraction out of 164 fecal samples from different ruminant species, including sheep, goats, alpacas, llamas, deer, ibex, chamois, bison and giraffe was perfomed and all samples were screened on neurotropic as well as on various astroviruses using PCR. Positive tested samples were submitted to next generation sequencing (NGS). After quality trimming and host-gene-removal the remaining data was de novo assembled. The generated sequences were compared to nucleotide, amino acid databases, virus properties were identified, and phylogenetic analyses as well as recombination analysis were performed.The excretion of neurotropic astroviruses in small ruminants' feces could not be demonstrated, but on the other hand, this work suggests the first identification of astroviruses in goats and the discovery of multiple new genetic variants as well as novel genotype-species in small ruminants. Additionally, multiple putative recombination events in four of five newly discovered full-length genome sequences were predicted. The high genetic similarity and predicted recombinations between some of these astroviruses suggest interspecies transmission events.