Metagenomic characterisation of avian parvoviruses and picornaviruses from Australia wild ducks

Authors: Jessy Vibin, Anthony Chamings, Marcel Klassen, Tarka Raj Bhatta and Soren Alexandersen.


Ducks can shed and disseminate viruses and thus play a role in cross-species transmission. In the current study, we detected and characterised various avian parvoviruses and picornaviruses from wild Pacific black ducks, Chestnut teals, Grey teals and Wood ducks sampled at multiple time points from a single location using metagenomics. We characterised 46 different avian parvoviruses belonging to three different genera Dependoparvovirus, Aveparvovirus and Chaphamaparvovirus, and 11 different avian picornaviruses tentatively belonging to four different genera SicinivirusAnativirusMegrivirus and Aalivirus. Most of these viruses were genetically different from other currently known viruses from the NCBI dataset. The study showed that the abundance and number of avian picornaviruses and parvoviruses varied considerably throughout the year, with the high number of virus reads in some of the duck samples highly suggestive of an active infection at the time of sampling. The detection and characterisation of several parvoviruses and picornaviruses from the individual duck samples also suggests co-infection, which may lead to the emergence of novel viruses through possible recombination. Therefore, as new and emerging diseases evolve, it is relevant to explore and monitor potential animal reservoirs in their natural habitat.


SOURCE: Scientific Reports  2020; 10, 12800.

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Detection and characterisation of canine astrovirus, canine parvovirus and canine papillomavirus in puppies using next generation sequencing

Authors: Tarka Raj BhattaAnthony ChamingsJessy Vibin & Soren Alexandersen

Source: Scientific Reports 9, Article number: 4602 (2019)

Brief summary of the paper: Gastroenteritis in young animals is a clinical presentation with many infectious and non- infectious aetiologies. We used next generation sequencing (NGS) to investigate the possible infectious causes of gastroenteritis in puppies from a dog kennel in Victoria, Australia.

The near complete genome of a canine astrovirus was obtained from pooled faecal samples, and was found to be 94.7% identical with a canine astrovirus detected in the United Kingdom in 2012. The phylogenetic analysis of the capsid gene found similarities to those of canine astroviruses identified in Italy in 2005 and in UK and Hungary in 2012, but distant from that of a canine astrovirus previously identified in Australia in 2012.

Thus, different serotypes of canine astrovirus are likely circulating in Australia. The close relationship to European astroviruses also suggested that there had been recent movements of ancestor canine astroviruses between Australia and Europe.

NGS also detected other infections in the puppies including several canine papillomaviruses and a canine parvovirus (vaccine strain) as well as a very low level of campylobacter. Canine astrovirus was the probable cause of diarrhoea in these puppies, with the possible involvement of campylobacter bacteria. NGS was effective as a non-targeted method to determine the likely infectious cause of gastroenteritis.

World “One Health” Day 2018

Join GCEID and the partner organisations in celebrating World One Health day.  “One Health” is a multidisciplinary approach to managing infectious diseases in people, animals and the environment. This event will showcase how researchers in Geelong are undertaking collaborative research to protect people, animals and the environment from infectious diseases.
When: Thursday 15 November 2018 between 10am and 3pm
This is an open house event, please feel free to drop in at any point throughout the day

Where: St Mary’s Building, 190 Myers Street, Geelong, 3220

All welcome at this free event.

  • Morning session: Research Talks (10-11:45am)
  • Lunch Session: Meet the researchers (noon-1:15pm)
  • Afternoon session: Showcasing the work of AAHL and Barwon Health in infectious disease control (1:30-3pm)

Please click here for Program details

Please feel free to drop in to one, two or all three sessions!  To ensure adequate catering you can register at eventbrite


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

Authors: Jessy Vibin, Anthony Chamings, Fiona Collier, Marcel Klaassen, Tiffanie M. Nelson & Soren Alexandersen

SourceScientific Reportsvolume 8, Article number: 8686 (2018)

Brief summary of the paper: 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.

Is Australia as protected from potentially serious host-jumping virus outbreaks as previously thought?

A GCEID team has discovered coronaviruses in Australia’s wild birds, showing the nation is not as isolated from potentially serious host-jumping virus outbreaks as previously thought. The researchers, led by the Geelong Centre for Emerging Infectious Diseases (GCEID), has discovered that two different types of coronaviruses are present in Australian wild birds. The discovery marks an important step in building scientists’ understanding of this family of viruses, which have a history of being able to jump into new host species and cause disease.

Read more on this @ Deakin Invenio: Virus discovery in Australian wild birds

The study is the first to demonstrate the presence of coronaviruses in Australian wild birds, and was published in “Nature: Scientific Reports”. See below for more details:

Authors: Anthony Chamings, Tiffanie M. Nelson, Jessy Vibin, Michelle Wille, Marcel Klaassen & Soren Alexandersen

Source: Scientific Reports, Volume 8, Article number: 5980 (2018)

Brief summary of the paper: We evaluated the presence of coronaviruses by PCR in 918 Australian wild bird samples collected during 2016–17. Coronaviruses were detected in 141 samples (15.3%) from species of ducks, shorebirds and herons and from multiple sampling locations.

Sequencing of selected positive samples found mainly gammacoronaviruses, but also some deltacoronaviruses. The detection rate of coronaviruses was improved by using multiple PCR assays, as no single assay could detect all coronavirus positive samples. Sequencing of the relatively conserved Orf1 PCR amplicons found that Australian duck gammacoronaviruses were similar to duck gammacoronaviruses around the world.

Some sequenced shorebird gammacoronaviruses belonged to Charadriiformes lineages, but others were more closely related to duck gammacoronaviruses. Australian duck and heron deltacoronaviruses belonged to lineages with other duck and heron deltacoronaviruses, but were almost 20% different in nucleotide sequence to other deltacoronavirus sequences available. Deltacoronavirus sequences from shorebirds formed a lineage with a deltacoronavirus from a ruddy turnstone detected in the United States.

Given that Australian duck gammacoronaviruses are highly similar to those found in other regions, and Australian ducks rarely come into contact with migratory Palearctic duck species, we hypothesise that migratory shorebirds are the important vector for moving wild bird coronaviruses into and out of Australia.