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

Abstract

Emerging viral pathogens are a significant concern, with potential consequences for human, animal and environmental health. Over the past several decades, many novel viruses have been found in animals, including birds, and often pose a significant threat to vulnerable species. However, despite enormous interest in virus research, little is known about virus communities (viromes) in Australian Neophema birds. Therefore, this study was designed to characterise the viromes of Neophema birds and track the evolutionary relationships of recently emerging psittacine siadenovirus F (PsSiAdV-F) circulating in the critically endangered, orange-bellied parrot (OBP, Neophema chrysogaster), using a viral metagenomic approach. This study identified 16 viruses belonging to the families Adenoviridae, Circoviridae, Endornaviridae, Picobirnaviridae and Picornaviridae. In addition, this study demonstrated a potential evolutionary relationship of a PsSiAdV-F sequenced previously from the critically endangered OBP. Strikingly, five adenoviral contigs identified in this study show the highest identities with human adenovirus 2 and human mastadenovirus C. This highlights an important and unexpected aspects of the avian virome and warrants further studies dedicated to this subject. Finally, the findings of this study emphasise the importance of testing birds used for trade or in experimental settings for potential pathogens to prevent the spread of infections.

Characterization of a Near-Complete Genome Sequence of a Chaphamaparvovirus from an Australian Boobook Owl (Ninox boobook)

“…They encode two genes: a nonstructural replicase gene (NS) and a capsid (VP) gene ( 2 , 3 ). ChPVs are likely to be widespread in nature and have been detected in the feces of birds ( 4 – 6 ) and mammals ( 7 ); a ChPV causes renal disease in laboratory mice ( 8 ). Recently, two novel ChPVs (psittacine chaphamaparvovirus 1 and 2 [PsChPV-1 and PsChPV-2, respectively]) was detected in the liver of rainbow lorikeets ( Trichoglossus moluccanus ) ( 9 ) and fecal materials of Neophema birds ( 10 ) in Australia.…”

“…DNA was extracted using the PureLink genomic DNA minikit (Invitrogen, CA, USA). The library was prepared using an Illumina DNA prep kit (San Diego, CA, USA), starting with 250 ng DNA ( 6 ). The quality and quantity of the prepared library were assessed by the Australian Genome Research Facility (AGRF), Melbourne, Australia, and the library was sequenced using the Illumina NovaSeq sequencing platform, generating 150-bp paired-end reads.…”

Molecular and Phylogenetic Characterisation of a Highly Divergent Novel Parvovirus (Psittaciform Chaphamaparvovirus 2) in Australian Neophema Parrots

“…Eliminating likely impurities, such as host cells, bacteria, food particles, and free nucleic acids, from the faecal samples, followed by virus particle enrichment, was performed under the stated methods [16,17], with minor variations. Briefly, the faecal materials were aseptically resuspended and vigorously homogenised in sterile phosphate-buffered saline (PBS; 1:10) and centrifuged at 2500× g for 90 min at 4 • C. The supernatant was filtered using a 0.80 µm syringe filter, and the filtrate was processed downstream.…”

Molecular characterisation of a novel pathogenic avipoxvirus from an Australian little crow (Corvus bennetti) directly from the clinical sample

“…A total of 250 ng of extracted genomic DNA was used to prepare the library using the protocol adapted previously using the Illumina DNA Prep (Illumina, San Diego, CA, USA) 40 . The quality and quantity of the prepared library was assessed using an Agilent Tape Station (Agilent Technologies) by the Genomic Platform, La Trobe University.…”