Metatranscriptomic Analysis of Virus Diversity in Urban Wild Birds with Paretic Disease

Abstract

Wild birds are major natural reservoirs and potential dispersers of a variety of infectious diseases. As such, it is important to determine the diversity of viruses they carry and use this information to help understand the potential risks of spill-over to humans, domestic animals, and other wildlife. We investigated the potential viral causes of paresis in long-standing, but undiagnosed, disease syndromes in wild Australian birds. RNA from diseased birds was extracted and pooled based on tissue type, host species and clinical manifestation for metagenomic sequencing. Using a bulk and unbiased meta-transcriptomic approach, combined with clinical investigation and histopathology, we identified a number of novel viruses from the families Astroviridae, Adenoviridae, Picornaviridae, Polyomaviridae, Paramyxoviridae, Parvoviridae, and Circoviridae in common urban wild birds including Australian magpies, magpie larks, pied currawongs, Australian ravens, and rainbow lorikeets. In each case the presence of the virus was confirmed by RT-PCR. These data revealed a number of candidate viral pathogens that may contribute to coronary, skeletal muscle, vascular and neuropathology in birds of the Corvidae and Artamidae families, and neuropathology in members of the Psittaculidae. The existence of such a diverse virome in urban avian species highlights the importance and challenges in elucidating the etiology and ecology of wildlife pathogens in urban environments. This information will be increasingly important for managing disease risks and conducting surveillance for potential viral threats to wildlife, livestock and human health. IMPORTANCE Wildlife naturally harbor a diverse array of infectious microorganisms and can be a source of novel diseases in domestic animals and human populations. Using unbiased RNA sequencing we identified highly diverse viruses in native birds from Australian urban environments presenting with paresis. This research included the clinical investigation and description of poorly understood recurring syndromes of unknown etiology: clenched claw syndrome, and black and white bird disease. As well as identifying a range of potentially disease-causing viral pathogens, this study describes methods that can effectively and efficiently characterize emergent disease syndromes in free ranging wildlife, and promotes further surveillance for specific pathogens of potential conservation and zoonotic concern.

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

“…Evidence that this ancestoral species may have been a primitive Australian parrot includes the observation that PsSiAdV-F has only been detected in psittacine species where it causes predominantly subclinical infections and is widespread in captive populations of at least three species of Australian parrot: the orange-bellied parrot, the scarlet-chested parrot ( Neophema splendida ), and the Bourke’s parrot ( Neopsephotus bourkii ) [ 12 , 13 ]. Additionally, there is an extensive diversity of siadenoviruses present in wild and captive native Australian passerine species, and viruses belonging to the more recently evolved siadenovirus clade containing the psittacine siadenovirus E have also been detected in wild Australian psittacine birds [ 5 , 8 , 45 ]. Ultimate proof that PsSiAdV-F originated in Australian psittacine birds will require that it be identified in a wild Australian psittacine species, and to date, surveys of wild psittacine birds in Australia have not detected it yet [ 4 , 7 ].…”

Unbiased Characterization of the Microbiome and Virome of Questing Ticks

“…Indeed, in theory RNA-seq can be used to identify any infecting microorganism within a sample. Similarly, metagenomic methods have been used to identify novel pathogens both in humans and in animals ( Edridge et al, 2019a , b ; Chang et al, 2020 ).…”

Meta-transcriptomic discovery of a divergent circovirus and a chaphamaparvovirus in captive reptiles with proliferative respiratory syndrome

“…Although a ChPV was previously identified in crocodile feces [36], it is possible that this virus originated in the tilapia fish fed to these crocodiles. Our documentation of a diarrhea and sudden death in puppies [62], and a novel lorikeet chaphamaparvovirus coinfected with psittacine circovirus (beak and feather disease virus) in wild birds has been described [63]. Recently, a similar coexistence of Tasmanian devil-associated circovirus and chaphamaparvovirus was identified in a Tasmania devil metagenomic virome study, but with no disease association [64].…”