Openly accessible

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

Vibin, Jessy, Chamings, Anthony, Collier, Fiona, Klaassen, Marcel, Nelson, Tiffanie M and Alexandersen, Soren 2018, Metagenomics detection and characterisation of viruses in faecal samples from Australian wild birds, Scientific reports, vol. 8, no. 1, pp. 1-23, doi: 10.1038/s41598-018-26851-1.

Attached Files
Name Description MIMEType Size Downloads
vibin-metagenomicsdetection-2018.pdf Published version application/pdf 1.76MB 3

Title Metagenomics detection and characterisation of viruses in faecal samples from Australian wild birds
Author(s) Vibin, Jessy
Chamings, AnthonyORCID iD for Chamings, Anthony orcid.org/0000-0002-7762-4757
Collier, Fiona
Klaassen, MarcelORCID iD for Klaassen, Marcel orcid.org/0000-0003-3907-9599
Nelson, Tiffanie MORCID iD for Nelson, Tiffanie M orcid.org/0000-0002-5341-312X
Alexandersen, SorenORCID iD for Alexandersen, Soren orcid.org/0000-0002-5039-3178
Journal name Scientific reports
Volume number 8
Issue number 1
Article ID 8686
Start page 1
End page 23
Total pages 23
Publisher Nature Publishing Group
Place of publication London, Eng.
Publication date 2018-06-06
ISSN 2045-2322
2045-2322
Keyword(s) Science & Technology
Multidisciplinary Sciences
Science & Technology - Other Topics
COMPLETE MITOCHONDRIAL GENOME
AVIAN PARAMYXOVIRUSES
GENETIC DIVERSITY
MUSCOVY DUCK
VIROME
CORONAVIRUSES
PATHOGENICITY
SUBSTITUTIONS
REPLICATION
HEPATITIS
Summary 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.
Language eng
DOI 10.1038/s41598-018-26851-1
Field of Research 110399 Clinical Sciences not elsewhere classified
HERDC Research category C1 Refereed article in a scholarly journal
Copyright notice ©2018, The Authors
Free to Read? Yes
Use Rights Creative Commons Attribution licence
Persistent URL http://hdl.handle.net/10536/DRO/DU:30109652

Document type: Journal Article
Collections: School of Medicine
Open Access Collection
Connect to link resolver
 
Unless expressly stated otherwise, the copyright for items in DRO is owned by the author, with all rights reserved.

Every reasonable effort has been made to ensure that permission has been obtained for items included in DRO. If you believe that your rights have been infringed by this repository, please contact drosupport@deakin.edu.au.

Versions
Version Filter Type
Citation counts: TR Web of Science Citation Count  Cited 0 times in TR Web of Science
Scopus Citation Count Cited 0 times in Scopus
Google Scholar Search Google Scholar
Access Statistics: 12 Abstract Views, 4 File Downloads  -  Detailed Statistics
Created: Sat, 23 Jun 2018, 03:15:32 EST

Every reasonable effort has been made to ensure that permission has been obtained for items included in DRO. If you believe that your rights have been infringed by this repository, please contact drosupport@deakin.edu.au.