Virome analysis suggests deltacoronaviruses and picornaviruses as a probable cause of severe intestinal disease on three quail farms

Abstract Background Quail farming is increasingly popular mainly due to higher market interest in meat and eggs. However, quails are susceptible to several common poultry viral infections, especially in intensive farming systems. Enteric viruses in poultry can cause significant economic losses, particularly in young birds. Mixed viral infections often exacerbate disease severity. Gamma and deltacoronaviruses are known causes of enteritis in quails, although infections with coronaviruses as well as picornaviruses may be also asymptomatic. Advanced diagnostic tools like next-generation sequencing (NGS) and metagenomics have improved understanding of these infections, yet knowledge gaps persist, and new viruses are continually being identified. Results Three outbreaks of enteritis with high mortality in quail farms were investigated using NGS with a metagenomic approach. We found that coronaviruses, picornaviruses (anativiruses) and parvoviruses were highly abundant in samples from investigated outbreaks. Viruses belonging to the families Adenoviridae, Astroviridae and Flaviviridae were less abundant and not present in all samples. Coronaviruses and picornaviruses were detected in all outbreaks, while parvovirus was detected only in one. The complete genomes of three quail deltacoronaviruses, three quail anativiruses and one quail chaphamaparvovirus were determined by NGS. Phylogenetic analysis revealed that the coronavirus and anativirus strains from this study were closely related to the other relevant quail virus strains. As for chaphamaparvovirus, this is the first report of this virus in quails. Conclusions The data from this study indicates the presence of numerous viruses in samples from quails with enteritis that have been overlooked by standard diagnostic approaches but could have played a role in the development of enteritis. These results may support further analysis of virome in healthy quails and in those with different clinical signs.