A novel group of avian astroviruses from Neotropical passerine birds broaden the diversity and host range of Astroviridae

Fernández-Correa, Izaskun; Truchado, Daniel A.; Gómez-Lucı́a, Esperanza; Doménech, Ana; Pérez‐Tris, Javier; Schmidt‐Chanasit, Jonas; Cadar, Dániel; Benı́tez, Laura

doi:10.1038/s41598-019-45889-3

Cited by 29 publications

(34 citation statements)

References 50 publications

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“…Viruses of the family Astroviridae infect multiple mammalian species, including humans, and also avian species and are most commonly associated with gastroenteritis and, rarely, neurological symptoms. A number of novel divergent astroviruses in wild birds have recently been discovered through metagenomic surveillance ( 63 – 65 ). Many avian astroviruses, including avian nephritis virus, duck and turkey astroviruses, and duck hepatitis virus 2, have considerable economic impact on the poultry industry, and these viruses are widely distributed in wild birds ( 66 ).…”

Section: Discussionmentioning

confidence: 99%

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

Chang

Eden

Hall

et al. 2020

J Virol

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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.

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Section: Discussionmentioning

confidence: 99%

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

Chang

Eden

Hall

et al. 2020

J Virol

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“…Astrovirus infection is most commonly associated with gastroenteritis, and rarely neurological symptoms. A number of novel divergent novel astroviruses in wild birds have recently been discovered through metagenomic surveillance (61–63). Many avian astroviruses, including avian nephritis virus, duck and turkey astroviruses and duck hepatitis virus 2, have considerable economic impact on the poultry industry and these viruses are widely distributed in wild birds (62).…”

Section: Discussionmentioning

confidence: 99%

Meta-transcriptomic analysis of virus diversity in urban wild birds with paretic disease

Chang

Eden

Hall

et al. 2020

Preprint

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29Wild birds are major natural reservoirs and potential dispersers of a variety of infectious 30 diseases. As such, it is important to determine the diversity of viruses they carry and use this 31 information to help understand the potential risks of spill-over to humans, domestic animals, and 32 other wildlife. We investigated the potential viral causes of paresis in long-standing, but 33 undiagnosed disease syndromes in wild Australian birds. RNA from diseased birds was extracted 34 and pooled based on tissue type, host species and clinical manifestation for metagenomic 35 sequencing. Using a bulk and unbiased meta-transcriptomic approach, combined with careful 36 clinical investigation and histopathology, we identified a number of novel viruses from the 37 families Astroviridae, Picornaviridae, Polyomaviridae, Paramyxoviridae, Parvoviridae, 38 Flaviviridae, and Circoviridae in common urban wild birds including Australian magpies, 39 magpie lark, pied currawongs, Australian ravens, and rainbow lorikeets. In each case the 40 presence of the virus was confirmed by RT-PCR. These data revealed a number of candidate 41 viral pathogens that may contribute to coronary, skeletal muscle, vascular and neuropathology in 42 birds of the Corvidae and Artamidae families, and neuropathology in members of the 43 Psittaculidae. The existence of such a diverse virome in urban avian species highlights the 44 importance and challenges in elucidating the etiology and ecology of wildlife pathogens in urban 45 environments. This information will be increasingly important for managing disease risks and 46 conducting surveillance for potential viral threats to wildlife, livestock and human health. More 47

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“…In Nouragues, the families Polycipiviridae and Reoviridae represented, by far, the main families of animal viruses (70.3% and 28.1% respectively; Figure 1). Nevertheless, sequences from the families Astroviridae, Anelloviridae and Picornaviridae were also present and we were able to obtain the complete genomes of four different astroviruses, a novel gyrovirus (these viruses have been fully described elsewhere, see Fernandez-Correa et al 2019 and Truchado et al 2019 [31,32]) and a novel picornavirus (Table 1). Identity values were relatively high in general for contigs of putative avian viruses in Nouragues (>60%; Table 1) but these identities were lower when analyzing complete genomes.…”

Section: Composition Of Nouragues/la Herrería Cloacal Viromesmentioning

confidence: 98%

“…Similarity and possible recombination events along the amino acid sequence of ORF1 of the different members of the Hepeviridae family were examined using RAT (https://omictools.com/rat-tool) and the region beyond the polymerase of unknown function was analyzed using Phyre2 in search of similarity to known protein motifs [30]. In this study, we include data of the complete genomes of four different astroviruses (Passerine astrovirus-1-4; PasAstV-1-4) and a novel gyrovirus (gyrovirus 11; GyV11) that have been fully described elsewhere [31,32], as they were retrieved from these metagenomic analyses.…”

Section: Genomic Analysis Of the Novel Virusesmentioning

confidence: 99%

Comparative Metagenomics of Palearctic and Neotropical Avian Cloacal Viromes Reveal Geographic Bias in Virus Discovery

et al. 2020

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Our understanding about viruses carried by wild animals is still scarce. The viral diversity of wildlife may be best described with discovery-driven approaches to the study of viral diversity that broaden research efforts towards non-canonical hosts and remote geographic regions. Birds have been key organisms in the transmission of viruses causing important diseases, and wild birds are threatened by viral spillovers associated with human activities. However, our knowledge of the avian virome may be biased towards poultry and highly pathogenic diseases. We describe and compare the fecal virome of two passerine-dominated bird assemblages sampled in a remote Neotropical rainforest in French Guiana (Nouragues Natural Reserve) and a Mediterranean forest in central Spain (La Herrería). We used metagenomic data to quantify the degree of functional and genetic novelty of viruses recovered by examining if the similarity of the contigs we obtained to reference sequences differed between both locations. In general, contigs from Nouragues were significantly less similar to viruses in databases than contigs from La Herrería using Blastn but not for Blastx, suggesting that pristine regions harbor a yet unknown viral diversity with genetically more singular viruses than more studied areas. Additionally, we describe putative novel viruses of the families Picornaviridae, Reoviridae and Hepeviridae. These results highlight the importance of wild animals and remote regions as sources of novel viruses that substantially broaden the current knowledge of the global diversity of viruses.

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A novel group of avian astroviruses from Neotropical passerine birds broaden the diversity and host range of Astroviridae

Cited by 29 publications

References 50 publications

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

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

Meta-transcriptomic analysis of virus diversity in urban wild birds with paretic disease

Comparative Metagenomics of Palearctic and Neotropical Avian Cloacal Viromes Reveal Geographic Bias in Virus Discovery

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