Metagenomic characterisation of avian parvoviruses and picornaviruses from Australian wild ducks

Abstract

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 Sicinivirus , Anativirus , Megrivirus 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.

Metagenomic characterisation of additional and novel avian viruses from Australian wild ducks

“…Avian viruses belonging to virus families other than Parvoviridae and Picornaviridae are described here and were detected and characterised in samples from Pacific black ducks (PBD12.16, PBD05.18 and PBD08.18), Chestnut teals (CT08.18 and CT11.18) and Grey teals (GT11.18) (Table 1 ) . From the Chestnut teal (CT05.18) and Wood duck (WD08.18) samples collected in May and August 2018, respectively, no other avian viruses were detected other than those previously described viruses belonging to Parvoviridae and Picornaviridae 6 .…”

“…We have previously described viruses belonging to the virus families Parvoviridae and Picornaviridae from our duck samples as they had the most abundant virus reads generated 6 . Avian viruses belonging to virus families other than Parvoviridae and Picornaviridae are described here and were detected and characterised in samples from Pacific black ducks (PBD12.16, PBD05.18 and PBD08.18), Chestnut teals (CT08.18 and CT11.18) and Grey teals (GT11.18) (Table 1 ) .…”

“… Sample Avian viruses detected and characterised Pacific black duck PBD12.16 Aviadenovirus (PBDAdV/PBD12.16) Calicivirus (PBDCV/PBD12.16) PBD05.18 Avastrovirus (PBDAstV/PBD05.18) PBD08.18 Avian orthoreovirus (PBDORV/PBD08.18) Rotavirus G (PBDRVG/PBD08.18) Chestnut teal CT08.18 Gammacoronavirus Rotavirus F (CTRVF/CT08.18) CT11.18 Avastrovirus (CTAstV/CT11.18) Grey teal GT11.18 Gyrovirus (GTGV/GT11.18) A total of nine viruses were characterised from the duck samples, of which eight of them are described in the current study in detail. Viruses characterised previously from these duck samples are published earlier 1 , 3 , 4 , 6 . …”

“…Metagenomics of viruses, utilises the power of NGS for the discovery, analysis and characterisation of viruses, thereby enabling virome analysis and providing insight into viruses for which these birds act as a natural reservoir. The use of the metagenomic technique in bird samples can lead to the determination of the virome from an individual bird or a population, and the identification of various novel avian viruses 3 , 5 , 6 . Nevertheless, only a few studies have explored the viruses circulating among wild ducks in Australia 3 – 6 .…”

“…Metagenomics of viruses was carried out to detect and characterise avian viruses present in the sample of Australian wild ducks using a protocol optimised in our laboratory and described earlier 3 . We previously focused on avian parvoviruses and picornaviruses from these duck samples as they were found to be abundant compared to other avian viruses 6 . We also reported a reassorted low pathogenicity H9N2 avian influenza virus with intercontinental gene segments in Chestnut teal samples collected on August 2018 1 .…”