We are analyzing https://link.springer.com/article/10.1186/s13099-016-0113-5.

Title:
Duck gut viral metagenome analysis captures snapshot of viral diversity | Gut Pathogens
Description:
Background Ducks (Anas platyrhynchos) an economically important waterfowl for meat, eggs and feathers; is also a natural reservoir for influenza A viruses. The emergence of novel viruses is attributed to the status of co-existence of multiple types and subtypes of viruses in the reservoir hosts. For effective prediction of future viral epidemic or pandemic an in-depth understanding of the virome status in the key reservoir species is highly essential. Methods To obtain an unbiased measure of viral diversity in the enteric tract of ducks by viral metagenomic approach, we deep sequenced the viral nucleic acid extracted from cloacal swabs collected from the flock of 23 ducks which shared the water bodies with wild migratory birds. Result In total 7,455,180 reads with average length of 146 bases were generated of which 7,354,300 reads were de novo assembled into 24,945 contigs with an average length of 220 bases and the remaining 100,880 reads were singletons. The duck virome were identified by sequence similarity comparisons of contigs and singletons (BLASTx E score, <10−3) against viral reference database. Numerous duck virome sequences were homologous to the animal virus of the Papillomaviridae family; and phages of the Caudovirales, Inoviridae, Tectiviridae, Microviridae families and unclassified phages. Further, several duck virome sequences had homologous with the insect viruses of the Poxviridae, Alphatetraviridae, Baculoviridae, Densovirinae, Iflaviridae and Dicistroviridae families; and plant viruses of the Secoviridae, Virgaviridae, Tombusviridae and Partitiviridae families, which reflects the diet and habitation of ducks. Conclusion This study increases our understanding of the viral diversity and expands the knowledge about the spectrum of viruses harboured in the enteric tract of ducks.
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Keywords {🔍}

viral, pubmed, sequences, viruses, article, duck, virome, google, scholar, gut, central, cas, virus, papillomavirus, analysis, ducks, influenza, diversity, species, avian, metagenomic, related, protein, acid, reads, sequence, similarity, animal, insect, fig, virol, open, tract, dna, phylogenetic, genome, papillomaviruses, gene, plos, data, including, reservoir, enteric, birds, contigs, family, plant, study, host, bat,

Topics {✒️}

ashwin ashok raut neighbor-joining method based article download pdf a-tail adapter ligation putative duck-origin papillomavirus central indian state duck-specific sequence identified central agricultural university ncbi short-read archive rupam dutta preliminary view full-length papillomavirus genome duck gut virome viral nucleic acid fecal viral flora rna viral community balanced salt solution generation sequencing duck origin papillomavirus eukaryotic virus-related sequences privacy choices/manage cookies illumina miseq platform van doorslaer viral nucleic acids duck viral sequences article fawaz double strand cdna complete genome sequencing deeper sequencing methods partial genomes sequences full access uncultured viral community creative commons license duck virome sequences methods ethics statement related viral species contig sequence related current viral database viral protein database viral reference database economically important waterfowl pcr amplification highly divergent nature full genome sequences de novo assembled emerging viral diseases viral protein sequences high-density farm highly species specific sequence similarity comparisons

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         description:Ducks (Anas platyrhynchos) an economically important waterfowl for meat, eggs and feathers; is also a natural reservoir for influenza A viruses. The emergence of novel viruses is attributed to the status of co-existence of multiple types and subtypes of viruses in the reservoir hosts. For effective prediction of future viral epidemic or pandemic an in-depth understanding of the virome status in the key reservoir species is highly essential. To obtain an unbiased measure of viral diversity in the enteric tract of ducks by viral metagenomic approach, we deep sequenced the viral nucleic acid extracted from cloacal swabs collected from the flock of 23 ducks which shared the water bodies with wild migratory birds. In total 7,455,180 reads with average length of 146 bases were generated of which 7,354,300 reads were de novo assembled into 24,945 contigs with an average length of 220 bases and the remaining 100,880 reads were singletons. The duck virome were identified by sequence similarity comparisons of contigs and singletons (BLASTx E score, <10−3) against viral reference database. Numerous duck virome sequences were homologous to the animal virus of the Papillomaviridae family; and phages of the Caudovirales, Inoviridae, Tectiviridae, Microviridae families and unclassified phages. Further, several duck virome sequences had homologous with the insect viruses of the Poxviridae, Alphatetraviridae, Baculoviridae, Densovirinae, Iflaviridae and Dicistroviridae families; and plant viruses of the Secoviridae, Virgaviridae, Tombusviridae and Partitiviridae families, which reflects the diet and habitation of ducks. This study increases our understanding of the viral diversity and expands the knowledge about the spectrum of viruses harboured in the enteric tract of ducks.
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      description:Ducks (Anas platyrhynchos) an economically important waterfowl for meat, eggs and feathers; is also a natural reservoir for influenza A viruses. The emergence of novel viruses is attributed to the status of co-existence of multiple types and subtypes of viruses in the reservoir hosts. For effective prediction of future viral epidemic or pandemic an in-depth understanding of the virome status in the key reservoir species is highly essential. To obtain an unbiased measure of viral diversity in the enteric tract of ducks by viral metagenomic approach, we deep sequenced the viral nucleic acid extracted from cloacal swabs collected from the flock of 23 ducks which shared the water bodies with wild migratory birds. In total 7,455,180 reads with average length of 146 bases were generated of which 7,354,300 reads were de novo assembled into 24,945 contigs with an average length of 220 bases and the remaining 100,880 reads were singletons. The duck virome were identified by sequence similarity comparisons of contigs and singletons (BLASTx E score, <10−3) against viral reference database. Numerous duck virome sequences were homologous to the animal virus of the Papillomaviridae family; and phages of the Caudovirales, Inoviridae, Tectiviridae, Microviridae families and unclassified phages. Further, several duck virome sequences had homologous with the insect viruses of the Poxviridae, Alphatetraviridae, Baculoviridae, Densovirinae, Iflaviridae and Dicistroviridae families; and plant viruses of the Secoviridae, Virgaviridae, Tombusviridae and Partitiviridae families, which reflects the diet and habitation of ducks. This study increases our understanding of the viral diversity and expands the knowledge about the spectrum of viruses harboured in the enteric tract of ducks.
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         Parasitology
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      name:OIE Reference Laboratory for Avian Influenza, ICAR-National Institute of High Security Animal Diseases, Bhopal, India
      name:OIE Reference Laboratory for Avian Influenza, ICAR-National Institute of High Security Animal Diseases, Bhopal, India
      name:OIE Reference Laboratory for Avian Influenza, ICAR-National Institute of High Security Animal Diseases, Bhopal, India
      name:OIE Reference Laboratory for Avian Influenza, ICAR-National Institute of High Security Animal Diseases, Bhopal, India
      name:OIE Reference Laboratory for Avian Influenza, ICAR-National Institute of High Security Animal Diseases, Bhopal, India
      name:College of Veterinary Sciences and Animal Husbandry, Central Agricultural University, Aizawl, India
      name:Laboratory of Immunology, Department of Biological Sciences, Indian Institute of Science Education and Research, Bhopal, India
      name:OIE Reference Laboratory for Avian Influenza, ICAR-National Institute of High Security Animal Diseases, Bhopal, India
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