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We are analyzing https://animalmicrobiome.biomedcentral.com/articles/10.1186/s42523-025-00428-6.

Title:
Virome analysis suggests deltacoronaviruses and picornaviruses as a probable cause of severe intestinal disease on three quail farms | Animal Microbiome | Full Text
Description:
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. 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. 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.
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Keywords {🔍}

quail, pubmed, article, google, scholar, viruses, virus, cas, strains, enteritis, detected, avian, picornaviruses, birds, dcov, analysis, viral, phylogenetic, coronaviruses, central, quails, outbreaks, samples, chaphamaparvovirus, study, genome, sequence, genbank, virome, strain, table, reads, sequences, slovenia, disease, poultry, ngs, anativirus, quaildcov, tree, deltacoronaviruses, complete, support, infections, found, present, animals, sample, species, rna,

Topics {✒️}

springer nature electronic supplementary material estimate maximum-likelihood phylogenies author information authors additional information publisher bayesian information criterion data availability covaris m220 focused-ultrasonicator research core funding state privacy rights abbreviations ngs background quails anativirus strain quail/slo/628 − 15/2015 anativirus strain quail/slo/56 − 18/2018 anativirus strain quail/slo/70 − 18/2018 materials sharing privacy choices/manage cookies bmc genomics rss-affected broiler flocks van der hoek authors scientific editing open reading frames pénzes jj common histopathological findings anaerobic culture methods oropesa-olmedo da intestinal content samples complete picornavirus polyprotein quail picornavirus strains conclusion woo pcy maximum likelihood method pheasant chaphamaparvovirus strain extracted nucleic acid smart model selection bmc picornavirus sequences obtained quail deltacoronavirus strains intensive farming systems lowest common ancestor rna viral community sensitive protein alignment parvovirus sequences obtained article kuhar day jm eukaryote viral community quail anativirus strains lima da genbank rights

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         headline:Virome analysis suggests deltacoronaviruses and picornaviruses as a probable cause of severe intestinal disease on three quail farms
         description: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. 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. 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.
         datePublished:2025-05-31T00:00:00Z
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      headline:Virome analysis suggests deltacoronaviruses and picornaviruses as a probable cause of severe intestinal disease on three quail farms
      description: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. 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. 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.
      datePublished:2025-05-31T00:00:00Z
      dateModified:2025-05-31T00:00:00Z
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      name:Institute for microbiology and parasitology, Veterinary Faculty, University of Ljubljana, Ljubljana, Slovenia
      name:Institute of poultry, birds, small mammals and reptiles, Veterinary Faculty, University of Ljubljana, Ljubljana, Slovenia
      name:Institute of poultry, birds, small mammals and reptiles, Veterinary Faculty, University of Ljubljana, Ljubljana, Slovenia
      name:Institute of poultry, birds, small mammals and reptiles, Veterinary Faculty, University of Ljubljana, Ljubljana, Slovenia
      name:Institute for microbiology and parasitology, Veterinary Faculty, University of Ljubljana, Ljubljana, Slovenia
      name:Institute of Food Safety, Feed and Environment, Veterinary Faculty, University of Ljubljana, Ljubljana, Slovenia

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