About: Metagenomics detection and characterisation of viruses in faecal samples from Australian wild birds

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An Entity of Type : schema:ScholarlyArticle, within Data Space : covidontheweb.inria.fr associated with source document(s)

Attributes	Values
type	Academic Article research paper schema:ScholarlyArticle
isDefinedBy	Covid-on-the-Web dataset
has title	Metagenomics detection and characterisation of viruses in faecal samples from Australian wild birds
Creator	Klaassen, Marcel Alexandersen, Soren Chamings, Anthony Collier, Fiona Vibin, Jessy Nelson, Tiffanie
Source	Medline; PMC
abstract	We present an optimised metagenomics method for detection and characterisation of all virus types including single and double stranded DNA/RNA and enveloped and non-enveloped viruses. Initial evaluation included both spiked and non-spiked bird faecal samples as well as non-spiked human faecal samples. From the non-spiked bird samples (Australian Muscovy duck and Pacific black ducks) we detected 21 viruses, and we also present a summary of a few viruses detected in human faecal samples. We then present a detailed analysis of selected virus sequences in the avian samples that were somewhat similar to known viruses, and had good quality (Q20 or higher) and quantity of next-generation sequencing reads, and was of interest from a virological point of view, for example, avian coronavirus and avian paramyxovirus 6. Some of these viruses were closely related to known viruses while others were more distantly related with 70% or less identity to currently known/sequenced viruses. Besides detecting viruses, the technique also allowed the characterisation of host mitochondrial DNA present and thus identifying host species, while ribosomal RNA sequences provided insight into the “ribosomal activity microbiome”; of gut parasites; and of food eaten such as plants or insects, which we correlated to non-avian host associated viruses.
has issue date	2018-06-06(xsd:dateTime)
bibo:doi	10.1038/s41598-018-26851-1
bibo:pmid	29875375
has license	cc-by
sha1sum (hex)	e5a309be751ae9e2575c3e35edd7f37fa0e99b3d
schema:url	https://doi.org/10.1038/s41598-018-26851-1
resource representing a document's title	Metagenomics detection and characterisation of viruses in faecal samples from Australian wild birds
has PubMed Central identifier	PMC5989203
has PubMed identifier	29875375
schema:publication	Sci Rep
resource representing a document's body	covid:e5a309be751ae9e2575c3e35edd7f37fa0e99b3d#body_text
is schema:about of	named entity 'ribosomal RNA' named entity 'Q20' named entity 'faecal samples' named entity 'viruses' named entity 'host species' named entity 'next-generation sequencing' named entity 'ribosomal' named entity 'viruses' named entity 'Metagenomics' named entity 'Scientific RepoRtS' named entity 'virus' named entity 'metagenomics' named entity 'Hubei' named entity 'non-host' named entity 'Contigs' named entity 'phylogenetic analysis' named entity 'ribosomes' named entity 'faecal samples' named entity 'Codon' named entity 'NCBI' named entity 'bacteriophage' named entity 'Japan' named entity 'Real-time polymerase chain reaction' named entity 'BLASTN' named entity 'virus' named entity 'Emerging Infectious Diseases' named entity 'Ion Torrent' named entity 'viruses' named entity 'nucleotide sequences' named entity 'phylogenetic' named entity 'severe infections' named entity 'mosquitoes' named entity 'virus' named entity 'Gammacoronaviruses' named entity 'Ion Torrent' named entity 'Japan' named entity 'virus' named entity 'virus' named entity 'faecal samples' named entity 'virus' named entity 'nucleotide sequences' named entity 'adenoviruses' named entity 'enteric diseases' named entity 'China' named entity 'Filtration' named entity 'viruses' named entity 'phylogenetic tree' named entity 'consensus sequences' named entity 'pig' named entity 'virus' named entity 'vector' named entity 'virus' named entity 'virus' named entity 'microbiome' named entity 'Hubei' named entity 'SYBR' named entity 'NCBI' named entity 'gammacoronavirus' named entity 'virus' named entity 'downstream processing' named entity 'Thermo Fisher Scientific' named entity 'nucleotides' named entity 'BLAST' named entity 'virus' named entity 'poultry' named entity 'RNA' named entity 'freeze-thaw' named entity 'library preparation' named entity 'APMV' named entity 'metagenomics' named entity 'microbiome' named entity 'genomes' named entity 'virus' named entity 'deltacoronaviruses' named entity 'Ion' named entity 'microbiome'

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