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

Wei-Shan Chang1,2,3 John-Sebastian Eden1,2,3,4 Jane Hall5 Mang Shi1,2,3 Karrie Rose5,6 Edward C Holmes7,2,3
Affiliations 7 institutions
  1. Marie Bashir Institute for Infectious Diseases and Biosecurity, University of Sydney, Sydney, New South Wales, Australia.
  2. School of Life and Environmental Sciences, University of Sydney, Sydney, New South Wales, Australia.
  3. School of Medical Sciences, University of Sydney, Sydney, New South Wales, Australia.
  4. Centre for Virus Research, Westmead Institute for Medical Research, Westmead, New South Wales, Australia.
  5. Australian Registry of Wildlife Health, Taronga Conservation Society Australia, Mosman, New South Wales, Australia.
  6. College of Public Health, Medical and Veterinary Sciences, James Cook University, Townsville, Queensland, Australia.
  7. Marie Bashir Institute for Infectious Diseases and Biosecurity, University of Sydney, Sydney, New South Wales, Australia [email protected].
PMID 32581107 2020 J Virol eng epublish
PubMed DOI Browse context

Article

Publication summary

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 spillover 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 metatranscriptomic approach, combined with clinical investigation and histopathology, we identified a number of novel viruses from the families <i>Astroviridae, Adenoviridae, Picornaviridae, Polyomaviridae, Paramyxoviridae, Parvoviridae</i>, and <i>Circoviridae</i> 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 reverse transcription (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 <i>Corvidae</i> and <i>Artamidae</i> families and neuropathology in members of the <i>Psittaculidae</i> 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.<b>IMPORTANCE</b> 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.

birds evolution metatranscriptomics neurological syndrome paresis wildlife Metagenome Transcriptome Adenoviridae Animals Animals, Wild Astroviridae Australia Bird Diseases Birds Circoviridae Cities DNA Virus Infections

Structured evidence records

Evidence records

9 total
Zoonotic Surveillance 5 records
Zoonotic Surveillance Extraction confidence 0.95
Key finding

Metatranscriptomic analysis revealed multiple viral families in urban Australian wild birds, indicating diverse viral presence in these hosts.

Virus
Astroviridae
Location
Australia urban Australian, Australia
Supporting text

Using a bulk and unbiased metatranscriptomic 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.

Method
metatranscriptomic sequencing; RT-PCR; clinical investigation; histopathology
Sample type
RNA from diseased birds; tissue
Geographic raw
urban Australian
Country inferred
Australia
Zoonotic Surveillance Extraction confidence 0.95
Key finding

Metatranscriptomic analysis revealed multiple viral families in urban Australian wild birds, indicating diverse viral presence in these hosts.

Virus
Adenoviridae
Location
Australia urban Australian, Australia
Supporting text

Using a bulk and unbiased metatranscriptomic 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.

Method
metatranscriptomic sequencing; RT-PCR; clinical investigation; histopathology
Sample type
RNA from diseased birds; tissue
Geographic raw
urban Australian
Country inferred
Australia
Zoonotic Surveillance Extraction confidence 0.95
Key finding

Metatranscriptomic analysis revealed multiple viral families in urban Australian wild birds, indicating diverse viral presence in these hosts.

Location
Australia urban Australian, Australia
Supporting text

Using a bulk and unbiased metatranscriptomic 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.

Method
metatranscriptomic sequencing; RT-PCR; clinical investigation; histopathology
Sample type
RNA from diseased birds; tissue
Geographic raw
urban Australian
Country inferred
Australia
Zoonotic Surveillance Extraction confidence 0.95
Key finding

Metatranscriptomic analysis revealed multiple viral families in urban Australian wild birds, indicating diverse viral presence in these hosts.

Location
Australia urban Australian, Australia
Supporting text

Using a bulk and unbiased metatranscriptomic 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.

Method
metatranscriptomic sequencing; RT-PCR; clinical investigation; histopathology
Sample type
RNA from diseased birds; tissue
Geographic raw
urban Australian
Country inferred
Australia
Zoonotic Surveillance Extraction confidence 0.95
Key finding

Metatranscriptomic analysis revealed multiple viral families in urban Australian wild birds, indicating diverse viral presence in these hosts.

Location
Australia urban Australian, Australia
Supporting text

Using a bulk and unbiased metatranscriptomic 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.

Method
metatranscriptomic sequencing; RT-PCR; clinical investigation; histopathology
Sample type
RNA from diseased birds; tissue
Geographic raw
urban Australian
Country inferred
Australia
Genomic Evolution 3 records
Genomic Evolution Extraction confidence 0.60
Key finding

Metatranscriptomic sequencing and phylogenetic classification revealed multiple novel viruses from several families in Australian urban wild birds showing paresis symptoms.

Virus
Astroviridae
Host
Aves
Location
Not specified
Supporting text

Using a bulk and unbiased metatranscriptomic 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.

Analysis methods
metatranscriptomic sequencing; phylogenetic analysis
Genomic Evolution Extraction confidence 0.60
Key finding

Genetic and phylogenetic analyses characterized novel adenoviruses found in Australian urban wild birds with paresis.

Virus
Adenoviridae
Host
Aves
Location
Not specified
Supporting text

MeSH terms include 'Adenoviridae / genetics' and 'Phylogeny', indicating genome sequencing and phylogenetic analysis of adenoviruses detected in these birds.

Analysis methods
genome sequencing; phylogenetic analysis
Genomic Evolution Extraction confidence 0.60
Key finding

Paramyxoviruses identified in wild birds were genetically sequenced and positioned within existing phylogenetic lineages.

Host
Aves
Location
Not specified
Supporting text

MeSH terms 'Paramyxoviridae / genetics' and 'Phylogeny' support that paramyxovirus sequences were genetically analyzed and phylogenetically classified.

Analysis methods
genome sequencing; phylogenetic analysis
Reservoir Ecology 1 records
Reservoir Ecology Extraction confidence 0.80
Key finding

Urban wild birds in Australia serve as natural reservoirs for multiple viral families.

Virus
Not specified
Host
Aves
Location
Australia Australian urban environments, Australia
Supporting text

Wild birds are major natural reservoirs and potential dispersers of a variety of infectious diseases.

Method
metagenomic sequencing; metatranscriptomic analysis; RT-PCR confirmation; clinical investigation; histopathology
Sample type
RNA from diseased birds
Geographic raw
Australian urban environments
Country inferred
Australia