Psittacid Adenovirus-2 infection in the critically endangered orange-bellied parrot (Neophema chrysogastor): A key threatening process or an example of a host-adapted virus?

Temporal Loss of Genome-Wide and Immunogenetic Diversity in a Near-Extinct Parrot

Loss of genetic diversity threatens a species' adaptive potential and long-term resilience. Predicted to be extinct by 2038, the orange-bellied parrot (Neophema chrysogaster) is a critically endangered migratory bird threatened by numerous viral, bacterial and fungal diseases. The species has undergone multiple population crashes, reaching a low of three wild-born females and 13 males in 2016, and is now represented by only a single wild population and individuals in the captive breeding program. Here we used our high-quality long-read reference genome, and contemporary (N = 19) and historical (N = 16) resequenced genomes from as early as 1829, to track the long-term genomic erosion and immunogenetic diversity decline in this species. 62% of genomic diversity was lost between historical (mean autosomal heterozygosity = 0.00149 ± 0.000699 SD) and contemporary (0.00057 ± 0.000026) parrots. A greater number and length of runs of homozygosity in contemporary samples were also observed. A temporal reduction in the number of alleles at Toll-like receptor genes was found (historical average alleles = 5.78 ± 2.73; contemporary = 3.89 ± 2.10), potentially exacerbating disease susceptibility in the contemporary population. Of particular concern is the new threat of avian influenza strain (HPAI) to Australia. We discuss the conservation implications of our findings and propose that hybridisation and synthetic biology may be required to address the catastrophic loss of genetic diversity that has occurred in this species in order to prevent extinction.

High prevalence and genetic heterogeneity of adenoviruses at a psittacine breeding facility

A polymerase chain reaction (PCR) survey was performed at an amateur parrot breeding facility in Italy to investigate the presence and molecular characteristics of adenoviruses. Eighty psittacine birds, belonging to seven parrot species, were sampled by cloacal swabs; in addition, 15 livers were collected from specimens that were found dead. Seventy-two out of 95 samples collected were positive for adenoviruses, with a prevalence rate of 75.8%. All seven psittacine species tested positive for at least one genus of the family Adenoviridae; notably, adenoviral infection was found for the first time in the hooded parrot (Psephotellus dissimilis). Based on the sequences and phylogenetic analysis, 57 sequences were psittacine adenovirus 2, seven sequences were duck adenovirus 1 and two sequences were identified as psittacine adenovirus 5. The six remaining sequences showed low nucleotide and amino acid identity with the reference strains of accepted species or types, revealing the presence of novel adenoviruses belonging to the genera Aviadenovirus, Barthadenovirus and Siadenovirus. There were identical adenovirus sequences in both apparently healthy and dead birds suggesting that further investigation into the role and impact of these viruses on the health of psittacine birds is warranted.

Characterisation of a novel aviadenovirus associated with disease in tawny frogmouths (Podargus strigoides)

Aviadenoviruses are widespread in wild birds but rarely cause disease in nature. However, when naïve species are exposed to poultry or aviaries, aviadenoviruses can lead to disease outbreaks. This study characterised a novel aviadenovirus infection in a native Australian bird, the tawny frogmouth (Podargus strigoides) during an outbreak investigation. The identified complete genome of aviadenovirus, named tawny frogmouth aviadenovirus A (TwAviAdV-A) was 41,175 bp in length containing 52 putative genes. TwAviAdV-A exhibits the common aviadenovirus genomic organisation but with a notable monophyletic subclade in the phylogeny. The TwAviAdV-A virus was hepatotrophic and the six frogmouths presented to the wildlife hospitals in South Eastern Queensland most commonly exhibited regurgitation (in four frogmouths). Three were died or euthanized, two recovered, and one showed no signs. The detection of TwAviAdV-A in frogmouths coming into care re-emphasizes the need for strict biosecurity protocols in wildlife hospitals and care facilities.

Case Series of Disseminated Xanthogranulomatosis in Red-crowned Parakeets (Cyanoramphus novaezelandiae) with Detection of Psittacine Adenovirus 2 (PsAdV-2)

Simple Summary

Lipometabolic disorders, such as xanthogranulomatosis, are common diseases in avian medicine. Various manifestations of lipometabolic disorders and risk factors for acquiring lipometabolic diseases have been described in the past years. Xanthogranulomas are usually limited to the skin and supposed to be associated with traumatic or inflammatory injuries in that area. Disseminated xanthogranulomatosis, appearing simultaneously in several internal organs, has been recently described in psittacine birds, the cause of the diseases was not known. Here, we describe a case series of disseminated xanthogranulomatosis in another psittacine species, the Red-crowned Parakeet (Cyanoramphus novaezelandiae) and a possible association with a concurrent psittacine adenovirus 2 (PsAdV-2) infection. Viral infections that trigger lipometabolic diseases have been described in human medicine in some species of small animals and in chickens. PsAdV-2- infections are widely distributed in avian species. A possible association between PsAdV-2- infections and lipometabolic diseases in the Red-crowned Parakeet should be considered. Individual birds and flocks with both or either of these diseases should be carefully examined and monitored.

Abstract

Xanthogranulomatosis is a common dermatological disease in birds. This form of inflammation, possibly associated with lipometabolic disorders, can also be seen in visceral organs, which as yet has only rarely been described in avian medicine. In general, diseases related to impaired lipid metabolism are frequently reported in avian medicine, with hepatic steatosis and atherosclerosis being the most common. In human medicine, infectious agents—especially some strains of adenovirus—were implicated in contributing to lipometabolic disorders; this has also been described for chicken. Here, a case series of six Red-crowned Parakeets (Cyanoramphus novaezelandiae) is presented, all cases being characterized by psittacine adenovirus 2 (PsAdV-2) infection with or without disseminated xanthogranulomatosis. The affected individuals were examined alive by clinical examination. Total body radiographs were taken of two birds, haematology and blood biochemistry results were achieved in one bird. The birds either died immediately after clinical presentation or within two days, two individuals were euthanized due to worsening of their clinical condition. All birds underwent a post-mortem examination. While four birds were finally diagnosed with disseminated xanthogranulomatosis, all six individuals had large eosinophilic intranuclear inclusion bodies in the epithelial cells of the collecting ducts of the kidney and tested positive for PsAdV-2. Further examinations are needed to clarify to what extent PsAdV-2 might elicit lipometabolic disease in birds, or psittacines in general, and, in particular, the Red-crowned Parakeet.

Adenoviruses in Avian Hosts: Recent Discoveries Shed New Light on Adenovirus Diversity and Evolution

While adenoviruses cause infections in a wide range of vertebrates, members of the genus Atadenovirus, Siadenovirus, and Aviadenovirus predominantly infect avian hosts. Several recent studies on avian adenoviruses have encouraged us to re-visit previously proposed adenovirus evolutionary concepts. Complete genomes and partial DNA polymerase sequences of avian adenoviruses were extracted from NCBI and analysed using various software. Genomic analyses and constructed phylogenetic trees identified the atadenovirus origin from an Australian native passerine bird in contrast to the previously established reptilian origin. In addition, we demonstrated that the theories on higher AT content in atadenoviruses are no longer accurate and cannot be considered as a species demarcation criterion for the genus Atadenovirus. Phylogenetic reconstruction further emphasised the need to reconsider siadenovirus origin, and we recommend extended studies on avian adenoviruses in wild birds to provide finer evolutionary resolution.

First detection of Psittacid alphaherpesvirus 5 and coinfection with beak and feather disease virus in naturally infected captive ringneck parakeets (Psittacula krameri) in Brazil

This study describes a case report in captive rose-ringed parakeets (Psittacula krameri) that developed clinical signs and eventually died after introducing new birds without quarantine. Bronchopneumonia and airsacculitis with syncytial cells associated with intranuclear inclusion bodies were found. Herpesvirus was detected in lungs and liver by PCR, and a nearly complete genome sequence of a Psittacid alphaherpesvirus 5 was obtained from the lung of a bird. Metagenomic analysis also identified beak and feather disease virus in the same samples. The study also highlights the importance of quarantine for avoiding the introduction of new diseases in captive aviaries.

Genomic characterization of psittacine adenovirus 2, a siadenovirus identified in a moribund African grey parrot (Psittacus erithacus)

Here, we report the complete genome sequence of psittacine adenovirus 2 from a moribund African grey parrot (Psittacus erithacus) with neurological signs and systemic inflammation. The complete siadenovirus genome is 25,386 bp in size. The results of genetic and phylogenetic analyses support its classification as a member of a novel species within the genus Siadenovirus. This study represents the first report of the genome sequence of an adenovirus from an African grey parrot.

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.

Genomic Characterisation of a Highly Divergent Siadenovirus (Psittacine Siadenovirus F) from the Critically Endangered Orange-Bellied Parrot (Neophema chrysogaster)

Siadenoviruses have been detected in wild and captive birds worldwide. Only nine siadenoviruses have been fully sequenced; however, partial sequences for 30 others, many of these from wild Australian birds, are also described. Some siadenoviruses, e.g., the turkey siadenovirus A, can cause disease; however, most cause subclinical infections. An example of a siadenovirus causing predominately subclinical infections is psittacine siadenovirus 2, proposed name psittacine siadenovirus F (PsSiAdV-F), which is enzootic in the captive breeding population of the critically endangered orange-bellied parrot (OBP, Neophema chrysogaster). Here, we have fully characterised PsSiAdV-F from an OBP. The PsSiAdV-F genome is 25,392 bp in length and contained 25 putative genes. The genome architecture of PsSiAdV-F exhibited characteristics similar to members within the genus Siadenovirus; however, the novel PsSiAdV-F genome was highly divergent, showing highest and lowest sequence similarity to skua siadenovirus A (57.1%) and psittacine siadenovirus D (31.1%), respectively. Subsequent phylogenetic analyses of the novel PsSiAdV-F genome positioned the virus into a phylogenetically distinct sub-clade with all other siadenoviruses and did not show any obvious close evolutionary relationship. Importantly, the resulted tress continually demonstrated that novel PsSiAdV-F evolved prior to all known members except the frog siadenovirus A in the evolution and possibly the ancestor of the avian siadenoviruses. To date, PsSiAdV-F has not been detected in wild parrots, so further studies screening PsSiAdV-F in wild Australian parrots and generating whole genome sequences of siadenoviruses of Australian native passerine species is recommended to fill the siadenovirus evolutionary gaps.

Histopathologic Changes, Ultrastructure, and Molecular Characterization of an Adenovirus in a Sun Conure (Aratinga solstitialis)

In this case report, we describe the pathologic changes and the ultrastructural and molecular characteristics of an adenovirus in a sun conure (Aratinga solstitialis) that presented with a history of sudden death. On histologic examination, there was multifocal hepatic and splenic necrosis. Within some hepatocytes and unidentified cells in the spleen, renal interstitial fibroblasts, and ovarian stroma were intranuclear amphophilic inclusion bodies. Electron microscopy of affected tissue showed intranuclear icosahedral viral particles with an inner capsid (29.2-33.8 nm in diameter) and an outer capsid (70.2-71.7 nm in diameter). Next-generation sequencing and BLAST analysis of complementary DNA synthesized from RNA extracted from formalin-fixed tissues showed an adenovirus, designated sun conure adenovirus (SCAdv). A DNA in situ hybridization (ISH) probe, constructed from the SCAdv and similar sequences from GenBank, was also positive in the intranuclear inclusion bodies, whereas standard ISH for psittacine adenovirus 1 was negative. These results show that ancillary diagnostic testing, such as next-generation sequencing, even using formalin-fixed, paraffin-embedded tissues, along with ISH, can be useful in identifying additional, unknown viruses that show similar pathology to commonly known viruses but do not show up as positive on routine diagnostic tests.

Opportunistic sampling of wild native and invasive birds reveals a rich diversity of adenoviruses in Australia

Little is known about the diversity of adenoviruses in wild birds and how they have evolved and are maintained in complex ecosystems. In this study, 409 samples were collected from woodland birds caught for banding (droppings), birds submitted to a wildlife hospital (droppings and tissues), silver gulls (droppings or tissues), and feral pigeons (Columbia livia; oral, cloacal swabs, or tissues) from the Greater Sydney area in NSW, Australia. Additional samples were from native pigeons and doves (swabs) presented to the Healesville Sanctuary, VIC, Australia. Samples were screened for adenovirus DNA using degenerate primers and polymerase chain reaction. Adenovirus sequences were detected in eighty-three samples representing thirty-five novel amino acid sequences. Fourteen novel sequences were atadenoviruses, seven were aviadenoviruses, twelve were siadenoviruses, and one was a mastadenovirus. Sequences from passerine birds were predominately found to form a single lineage within the atadenoviruses, a second lineage in the siadenoviruses, and a third smaller aviadenovirus lineage. These viruses appeared to have co-evolved with a diverse group of woodland birds that share similar habitat. Evidence for host/virus co-evolution in some viruses and a wide host range in others was observed. A high prevalence of adenovirus infection was found in rainbow lorikeets (Trichoglossus haematodus), galahs (Eolophus roseicapilla), and sulphur-crested cockatoos (Cacatua galerita). Sequences were either identical to or mapped to already established lineages in the Aviadenovirus, Siadenovirus, and Atadenovirus genera, suggesting a possible origin of the psittacine adenoviruses in ancestral Australian psittacine birds. The sequences of passerine and psittacine origin provided insight into diversity and structure of the Atadenovirus genus and demonstrated for the first-time viruses of passerine origin in the Aviadenovirus genus. Four unrelated adenovirus sequences were found in silver gull samples (Chroicocephalus novaehollandiae), including one of pigeon origin, suggesting environmental virus exposure. Three pigeon adenovirus types were detected in feral pigeons and infection prevalence was high. Evidence for host switching between invasive species and native species and native species and invasive species was documented. A variant of a murine adenovirus was detected in kidney tissue from two bird species suggesting mouse to bird transmission.

Diseases of the Avian Urinary System

Diseases of the renal system can be caused by infectious and noninfectious processes. Creating a relevant differential diagnosis for kidney disease in the live or dead bird requires a structured approach where the list of differentials is narrowed based on the signalment of the bird; its history, including its diet and management; physical findings; and other diagnostic findings. This article aims to provide the reader not only a list of the diseases that occur in birds but also the guidelines on when a disease should be considered in a differential.

Vidovszky M, Rossi JL, Vicentini F, Harrach B, L. Kaján G. Identification of two novel adenoviruses in smooth-billed ani and tropical screech owl

Avian adenoviruses (AdVs) are a very diverse group of pathogens causing diseases in poultry and wild birds. Wild birds, endangered by habitat loss and habitat fragmentation in the tropical forests, are recognised to play a role in the transmission of various AdVs. In this study, two novel, hitherto unknown AdVs were described from faecal samples of smooth-billed ani and tropical screech owl. The former was classified into genus Aviadenovirus, the latter into genus Atadenovirus, and both viruses most probably represent new AdV species as well. These results show that there is very limited information about the biodiversity of AdVs in tropical wild birds, though viruses might have a major effect on the population of their hosts or endanger even domesticated animals. Surveys like this provide new insights into the diversity, evolution, host variety, and distribution of avian AdVs.

Adenoviruses across the animal kingdom: a walk in the zoo

Adenoviruses (AdVs) infect representatives of numerous species from almost every major vertebrate class, albeit their incidence shows great variability. AdVs infecting birds, reptiles, and bats are the most common and diverse, whereas only one AdV has been so far isolated both from fish and amphibians. The family Adenoviridae is divided into five genera, each corresponding to an independent evolutionary lineage that supposedly coevolved with its respective vertebrate hosts. Members of genera Mastadenovirus and Aviadenovirus seem to infect exclusively mammals and birds, respectively. The genus Ichtadenovirus includes the single known AdV from fish. The majority of AdVs in the genus Atadenovirus originated from squamate reptiles (lizards and snakes), but also certain mammalian and avian AdVs are classified within this genus. The genus Siadenovirus contains the only AdV isolated from frog, along with numerous avian AdVs. In turtles, members of a sixth AdV lineage have been discovered, pending official recognition as an independent genus. The most likely scenario for AdV evolution includes long-term cospeciation with the hosts, as well as occasional switches between closely or, rarely, more distantly related hosts.

A survey of a mixed species aviary provides new insights into the pathogenicity, diversity, evolution, host range, and distribution of psittacine and passerine adenoviruses

A Bourke's parrot (Neopsephotus bourkii) originating from an aviary in Australia, containing two species of parrots, five species of finch and a species of dove, was presented for necropsy. The Bourke's parrot died from gastritis caused by Macrorhabdus ornithogaster, but also had an interstitial nephritis and ureteritis with adenovirus-like inclusion bodies within collecting duct epithelial cells. The adenovirus causing the lesions was shown to be Psittacine adenovirus-2 (PsAdV-2) using a PCR assay specific for adenoviruses and sequencing of amplicons. A survey of droppings from other birds in the aviary using the same PCR assay with amplicon sequencing found a high prevalence of infection of PsAdV-2 in Bourke's and scarlet-chested parrots (Neophema splendida). PsAdV-2 was also present in droppings from a Namaqua dove (Oena capensis). Gouldian finches (Erythrura gouldiae), red-billed firefinches (Lagonosticta senegala), and red-throated parrot finches (Erythrura psittacea) were shedding Gouldian finch adenovirus-1 (GFAdV-1). Two novel adenoviruses, an atadenovirus and a siadenovirus, were detected in the droppings from long-tailed finches (Poephila acuticauda). Kidney tissue from three of four scarlet-chested parrots submitted for necropsy from a second aviary were also positive for PsAdv-2. These findings and previously reported findings of widespread PsAdv-2 infection in captive orange-bellied parrots (Neophemia chrysogaster) raise the possibility that PsAdV-2 is enzootic in Australian aviculture. This represents the first report of GFAdV-1 in Australia and first identification of infection in finch species other than the Gouldian finch. Identification of two novel adenoviruses in long-tailed finches suggests that other novel adenoviruses are circulating in other finch species. RESEARCH HIGHLIGHTS Psittacine adenovirus-2 was present in high prevalence in two Australian aviaries. Gouldian finch adenovirus-1 (GFAdV-1) was detected in Australia for the first time. The host range of GFAdV-1 host range was expanded to other finch species. Novel atadenovirus and siadenovirus were detected in Estrildid finches.