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

Parvoviruses under the genus Chaphamaparvovirus (subfamily Hamaparvovirinae) are highly divergent and have recently been identified in many animals. However, the detection and characterisation of parvoviruses in psittacine birds are limited. Therefore, this study reports a novel parvovirus, tentatively named psittaciform chaphamaparvovirus 2 (PsChPV-2) under the genus Chaphamaparvovirus, which was identified in Australian Neophema birds. The PsChPV-2 genome is 4371 bp in length and encompasses four predicted open-reading frames, including two major genes, a nonstructural replicase gene (NS1), and a structural capsid gene (VP1). The NS1 and VP1 genes showed the closest amino acid identities of 56.2% and 47.7%, respectively, with a recently sequenced psittaciform chaphamaparvovirus 1 from a rainbow lorikeet (Trichoglossus moluccanus). Subsequent phylogenetic analyses exhibited that the novel PsChPV-2 is most closely related to other chaphamaparvoviruses of avian origin and has the greatest sequence identity with PsChPV-1 (60.6%). Further systematic investigation is warranted to explore the diversity with many avian-associated parvoviruses likely to be discovered

Characterization of a Novel Complete-Genome Sequence of a Galliform Chaphamaparvovirus from a Free-Range Laying Chicken Clinically Diagnosed with Spotty Liver Disease

This study reports a novel complete genome of galliform chaphamaparvovirus 4, which was detected in the bile of a free-range laying chicken diagnosed with spotty liver disease. The genome was 4,367 bp in length, enclosed by two identical inverted terminal repeats. The detection of this novel chaphamaparvovirus represents a notable concern for the poultry industry in Australia

Complete Mitochondrial Genome Sequence of an Australian Little Crow (Corvus bennetti)

This study reports the complete mitochondrial genome sequence of an Australian little crow (Corvus bennetti). The circular genome has a size of 16,895 bp and contains 13 protein-coding genes, 22 tRNA genes, and two rRNA genes. The study provides a reference mitochondrial genome of a little crow for further molecular studies

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

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

Detection of a Novel Alphaherpesvirus and Avihepadnavirus in a Plantar Papilloma from a Rainbow Lorikeet (Trichoglosis moluccanus)

Cutaneous plantar papillomas are a relatively common lesion of wild psittacine birds in Australia. Next-generation sequencing technology was used to investigate the potential aetiologic agent(s) for a plantar cutaneous papilloma in a wild rainbow lorikeet (Trichoglosis moluccanus). In the DNA from this lesion, two novel viral sequences were detected. The first was the partial sequence of a herpesvirus with the proposed name, psittacid alphaherpesvirus 6, from the Mardivirus genus of the family alphaherpesviruses. This represents the first mardivirus to be detected in a psittacine bird, the first mardivirus to be detected in a wild bird in Australia, and the second mardivirus to be found in a biopsy of an avian cutaneous papilloma. The second virus sequence was a complete sequence of a hepadnavirus, proposed as parrot hepatitis B genotype H (PHBV-H). PHBV-H is the first hepadnavirus to be detected in a wild psittacine bird in Australia. Whether other similar viruses are circulating in wild birds in Australia and whether either of these viruses play a role in the development of the plantar papilloma will require testing of biopsies from similar lesions and normal skin from other wild psittacine birds

On the Spatial Pattern of Input-Output Metrics for a Network Synchronization Process

A graph-theoretic analysis is undertaken for a compendium of input-output (transfer) metrics of a standard discrete-time linear synchronization model, including lp gains, frequency responses, frequency-band energy, and Markov parameters. We show that these transfer metrics exhibit a spatial degradation, such that they are monotonically nonincreasing along vertex cutsets away from an exogenous input. We use this spatial analysis to characterize signal-to-noise ratios (SNRs) in diffusive networks driven by process noise, and to develop a notion of propagation stability for dynamical networks. Finally, the formal results are illustrated through an example

A Novel Pathogenic Avipoxvirus Infecting Vulnerable Cook’s Petrel (Pterodroma cookii) in Australia Demonstrates a High Genomic and Evolutionary Proximity with South African Avipoxviruses

Avipoxviruses are assumed to be restricted to avian hosts and are considered to be important viral pathogens that may impact the conservation of many vulnerable or endangered birds. Recent reports of avipoxvirus-like viruses from reptiles suggest that cross-species transmission may be possible within birds and other species. Most of the avipoxviruses in wild and sea birds remain uncharacterized, and their genetic variability is unclear. Here, cutaneous pox lesions were used to recover a novel, full-length Cook’s petrelpox virus (CPPV) genome from a vulnerable Cook’s petrel (Pterodroma cookii), and this was followed by the detection of immature virions using transmission electron microscopy (TEM). The CPPV genome was 314,065 bp in length and contained 357 predicted open-reading frames (ORFs). While 323 of the ORFs of the CPPV genome had the greatest similarity with the gene products of other avipoxviruses, a further 34 ORFs were novel. Subsequent phylogenetic analyses showed that the CPPV was most closely related to other avipoxviruses that were isolated mostly from South African bird species and demonstrated the highest sequence similarity with a recently isolated flamingopox virus (88.9%) in South Africa. Considering the sequence similarity observed between CPPV and other avipoxviruses, TEM evidence of poxvirus particles, and phylogenetic position, this study concluded that CPPV is a distinct candidate of avipoxviruses

Propagation Stability Concepts for Network Synchronization Processes

A notion of disturbance propagation stability is defined for dynamical network processes, in terms of decrescence of an input-output energy metric along cutsets away from the disturbance source. A characterization of the disturbance propagation notion is developed for a canonical model for synchronization of linearly-coupled homogeneous subsystems. Specifically, propagation stability is equivalenced with the frequency response of a certain local closed-loop model, which is defined from the subsystem model and local network connections, being sub-unity gain. For the case where the subsystem is single-input single-output (SISO), a further simplification in terms of the subsystem's open loop Nyquist plot is obtained. An extension of the disturbance propagation stability concept toward imperviousness of subnetworks to disturbances is briefly developed, and an example focused on networks with planar subsystems is considered

The first complete mitochondrial genome sequence of an Australian raven (Corvus coronoides)

Here, we report the complete mitochondrial genome of an Australian raven (Corvus coronoides). The mitogenome of C. coronoides was characterised as a circular molecule of 16,925 bp in length encoding a typically conserved structure similar to those of other Corvidae. It consisted of 13 protein-coding genes (PCGs), two rRNA genes, and 22 tRNA genes, with all protein-coding sequences commencing with methionine. The lengths of 12S ribosomal RNA and 16S ribosomal RNA were 980 bp and 1600 bp, respectively, and were located between tRNA-Phe and tRNA-Leu. The overall base composition of the mitogenome of C. coronoides was slightly higher AT (56.0%) content than GC (44.0%). A phylogenetic tree using available complete mitogenome sequences of the family Corvidae revealed a close evolutionary relationship of C. coronoides with the now extinct Chatham raven (C. moriorum), a large songbird that was native to the Chatham Islands east of New Zealand

Genome Sequence of a Beak and Feather Disease Virus from an Unusual Novel Host, Australian Boobook Owl (Ninox boobook)

The beak and feather disease virus (BFDV) is a pathogen of psittacine birds. BFDVs infecting nonpsittacine birds remain largely uncharacterized. We report the genome of a BFDV from a boobook owl (Ninox boobook), a nonpsittacine bird. The genome consisted of 1,993 bp containing two major bidirectionally transcribed open reading frames