Viral metagenomics investigation into viral gastroenteritis in pigs Hungary.. Novel astroviruses in the gastrointestinal tract of Suidae (Sus scrofa domesticus)

Astroviruses within porcine hosts show a remarkable diversity and are known to cause both mild and severe gastroenteritis. During an outbreak of suspected viral gastroenteritis in production pig farms in Hungary in 2011 a number of samples were collected and screened for common viral agents of gastroenteritis, including astroviruses. Lacking conclusive results a subset of the samples were subjected to viral metagenomics to discern putative new viral agents. Viral metagenomics aims at charaterising the virome, the complete viral genomic material of a sample. By enrichment of the viral fraction of the microbiome and high throughput sequencing the genetic material of the virome is charaterised, this data is then classified by bioinforamtic methods. Several known agents of gastroenteritis were classified from the initial viral metagenomics screening and two samples harbouring previously unknown astroviruses as well as several other enteric viruses. Within this article the two new astrovirses are presented (Partial and full genome sequence as well as annotation and phylogenetic analysis) as well as the metagenomics classification of the virome within the two samples. These results shed provide information about previously unknown strains of astrovirus 4 as well as insight into the complex viral community of the porcine gastrointestinal tract.