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

Abstract

Birds, notably wild ducks, are reservoirs of pathogenic and zoonotic viruses such as influenza viruses and coronaviruses. In the current study, we used metagenomics to detect and characterise avian DNA and RNA viruses from wild Pacific black ducks, Chestnut teals and Grey teals collected at different time points from a single location. We characterised a likely new species of duck aviadenovirus and a novel duck gyrovirus. We also report what, to the best of our knowledge, is the first finding of an avian orthoreovirus from Pacific black ducks and a rotavirus F from Chestnut teals. Other viruses characterised from the samples from these wild ducks belong to the virus families Astroviridae, Caliciviridae and Coronaviridae. Some of the viruses may have potential cross-species transmissibility, while others indicated a wide genetic diversity of duck viruses within a genus. The study also showed evidence of potential transmission of viruses along the East Asian—Australasian Flyway; potentially facilitated by migrating shorebirds. The detection and characterisation of several avian viruses not previously described, and causing asymptomatic but potentially also symptomatic infections suggest the need for more virus surveillance studies for pathogenic and potential zoonotic viruses in wildlife reservoirs.

Metagenomic detection and characterisation of multiple viruses in apparently healthy Australian Neophema birds

“…The findings of non-avian host-associated viruses detected in this study were endornavirus and picornavirus, which agree with the previous reports by others, where a large number of non-avian associated viruses were detected in Australian birds 11 , 12 . Some aspects of this case are difficult to explain fully without conducting ethically debatable experimental virus-transmission experiments.…”

“…Birds may serve as reservoirs, intermediate hosts or transporters of parasites and pathogens 11 , 12 , 55 . The similarity of some of the detected sequences of the avian and non-avian host-associated RNA viruses to the viruses that were characterised in China (e.g., Endornaviridae ) 13 , and Belgium (e.g., Picobirnaviridae ), highlights that birds may harbour a diverse range of viruses that need to be investigated further.…”

“…Using viral metagenomic or meta-transcriptomic approaches, picornaviruses were previously reported in wild birds without understanding any pathology they may cause 11 , 12 , 56 , 57 . However, information on picornaviruses harboured by apparently healthy captive birds is scarce.…”

Torque teno virus from Korean domestic swine farms, 2017–2018

“…Of the remaining ORFs, putative ORF2 of M265 contained the well‐observed motifs of Wx 7 Hx 3 CxCx 5 H in TTVs while a cluster of Leucine rich regions followed by Serine rich regions in C‐terminus were observed in the present strains. These features are highly conserved in other Anelloviruses (Vibin et al., 2020). As far as our knowledge, this is the first time the strains belonging to Alphaternovirus were detected and studied.…”

Meta-transcriptomic analysis of the virome and microbiome of the invasive Indian myna (Acridotheres tristis) in Australia

“…Metagenomic sequencing has greatly increased our understanding of viral diversity and cryptic pathogens in wildlife [ 18 ]. For example, metagenomic studies of seemingly healthy avian species have revealed a diverse array of novel avian picornaviruses and caliciviruses from ducks, penguins, cranes and lorikeets [ [19] , [20] , [21] , [22] , [23] , [24] ] with no clear disease association. Importantly, characterizing the virome of highly invasive species through metagenomics can provide a better understanding of the potential ecological consequences and microbial interplay between introduced and native species in an urban bird community [ 25 ].…”