The Viruses of Wild Pigeon Droppings

Phan, Tung Gia; Vo, Nguyen Phung; Boros, Ákos; Pankovics, Péter; Reuter, Gábor; Li, Olive T. W.; Wang, Chunling; Deng, Xutao; Poon, Leo L. M.; Delwart, Eric

doi:10.1371/journal.pone.0072787

Cited by 114 publications

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“…In June 2014, faecal samples were collected from wild birds of prey, from 11 common kestrels (Falco tinnunculus) and 7 red-footed falcons (F. vespertinus) from Gara (46°03 '28.77"N 19°02'38.50"E) and Kardoskút (46°50'43.30"N 20°64'32.92"E) (Phan et al, 2013). Viral-particle protected nucleic acids were extracted using QIAamp spin-column technique (Qiagen) and subjected to a viral metagenomic analysis using sequence independent random amplification (Victoria et al, 2009).…”

Section: Methodsmentioning

confidence: 99%

“…Viral-particle protected nucleic acids were extracted using QIAamp spin-column technique (Qiagen) and subjected to a viral metagenomic analysis using sequence independent random amplification (Victoria et al, 2009). Viral cDNA library was constructed by Nextera XT DNA Library Preparation Kit (Illumina) and then sequenced on MiSeq Illumina platform according to the manufacturer's instruction, and as described previously (Phan et al, 2013). The acquired reads were trimmed; de-novo assembled and analyzed using an in-house pipeline (Phan et al, 2013).…”

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confidence: 99%

“…Viral cDNA library was constructed by Nextera XT DNA Library Preparation Kit (Illumina) and then sequenced on MiSeq Illumina platform according to the manufacturer's instruction, and as described previously (Phan et al, 2013). The acquired reads were trimmed; de-novo assembled and analyzed using an in-house pipeline (Phan et al, 2013). The reads and contigs greater than 100-bp were compared to the GenBank protein database (BlastX).…”

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Ljungan/Sebokele-like picornavirus in birds of prey, common kestrel ( Falco tinnunculus ) and red-footed falcon ( F. vespertinus )

Pankovics

Boros

Mátics

et al. 2017

Infection, Genetics and Evolution

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(www.picornaviridae.com, Adams et al., 2017). Human parechoviruses are important pathogens in humans especially in infants and young children and are associated with a wide spectrum and severity of diseases (Harvala et al., 2010). Ljungan and Sebokele viruses are thought to be rodent-borne viruses. Ljungan virus was first isolated from bank voles in Sweden (Niklasson & Le Duc, 1984) and it has been suggested to be the zoonotic etiological agent of myocarditis, type-1 diabetes mellitus and possibly other human diseases (Niklasson et al., 1998; Niklasson et al., 2007). Sebokele virus was originally isolated in 1972 fromAfrican wood mice (Digoutte and Germain, 1985; Joffret et al., 2013). Recently, Ljungan virus was also detected in wild birds, in gull species in Japan (Mitake et al., 2016).In general, picornaviruses are small, non-enveloped viruses with single-stranded, positive-sense, 7.2-10.1 kb-long polyadenylated genomic RNA. Picornaviral genomes have a common organization pattern: viral polyprotein coding single open reading frame (ORF) (except for the genus Dicipivirus which has two ORFs separated by an untranslated region) is flanked by the highly structured 5′ and 3′ untranslated regions (UTRs) (Knowles et al., 2012).The picornavirus genomes consist of essential secondary RNA structures functioning as a cisacting RNA sequences e.g. internal ribosomal entry site (IRES) (Martínez-Salas et al., 2015) and cis-acting replication element (cre) (Tolf et al., 2009). Generally, the viral polyprotein (VP) processed to form three or four capsid monomer proteins (VP0-VP3-VP1 or VP4-VP2-VP3-VP1), and at least seven non-structural proteins: 2A-2B-2C-3A-3B-3C-3D; however, differences occur in picornaviruses of different genera. The numbers of the cleaved individual ACCEPTED MANUSCRIPTA C C E P T E D M A N U S C R I P T Birds are well known reservoirs of numerous viral pathogens such as avian influenza virus, West Nile virus and Japanese encephalitis virus in humans (Reed et al., 2003).However, compared to the ten thousands of known bird species, rather few picornaviruses have been described from avian sources, often from faecal samples, and most of these have been identified in the last decade from domestic birds (Boros et al., 2013; Boros et al., 2014b). Birds have the potential also to serve as powerful biomonitors and can be used to survey for factors that may pose both public and wildlife health concerns (Pollack et al., 2017).In this study, a novel member of the genus Parechovirus was detected and characterized from faecal samples of birds of prey, a picornavirus related to Ljungan and Sebokele viruses. Materials and MethodsIn June 2014, faecal samples were collected from wild birds of prey, from 11 common kestrels (Falco tinnunculus) and 7 red-footed falcons (F. vespertinus) from Gara (46°03 '28.77"N 19°02'38.50"E) and Kardoskút (46°50'43.30"N 20°64'32.92"E) (Phan et al., 2013). Viral-particle protected nucleic acids were extracted using QIAamp spin-column technique (Qiagen) and subjected to a viral metage...

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Section: Methodsmentioning

confidence: 99%

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Ljungan/Sebokele-like picornavirus in birds of prey, common kestrel ( Falco tinnunculus ) and red-footed falcon ( F. vespertinus )

Pankovics

Boros

Mátics

et al. 2017

Infection, Genetics and Evolution

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“…To decipher the RNA virus community from turkey flocks experiencing enteric disease, Day et al (2010) analyzed turkey gut RNA virus metagenomics and demonstrated the presence of turkey-origin members of the Picornavirales, and the genus Caliciviridae, and the turkey picobirnaviruses. In order to better understand the viruses shed by pigeons, Phan et al (2013) characterized enteric virome in droppings from wild pigeons and identified sequences of novel aviparvovirus, picornaviruses and described group G rotavirus from pigeons.…”

Section: Virus Discovery and Viral Metagenomicsmentioning

confidence: 99%

Next generation sequencing technologies: Tool to study avian virus diversity

Kapgate¹,

Barbuddhe²,

Kumanan³

2015

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Summary. -Increased globalisation, climatic changes and wildlife-livestock interface led to emergence of novel viral pathogens or zoonoses that have become serious concern to avian, animal and human health. High biodiversity and bird migration facilitate spread of the pathogen and provide reservoirs for emerging infectious diseases. Current classical diagnostic methods designed to be virus-specific or aim to be limited to group of viral agents, hinder identifying of novel viruses or viral variants. Recently developed approaches of next-generation sequencing (NGS) provide culture-independent methods that are useful for understanding viral diversity and discovery of novel virus, thereby enabling a better diagnosis and disease control. This review discusses the different possible steps of a NGS study utilizing sequence-independent amplification, high-throughput sequencing and bioinformatics approaches to identify novel avian viruses and their diversity. NGS lead to the identification of a wide range of new viruses such as picobirnavirus, picornavirus, orthoreovirus and avian gamma coronavirus associated with fulminating disease in guinea fowl and is also used in describing viral diversity among avian species. The review also briefly discusses areas of viral-host interaction and disease associated causalities with newly identified avian viruses.

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“…typhimurium [33,[42][43][44] and viral infections (transmitted by mosquitoes feeding on infected birds) [45,46]. Not only are the pigeon keepers/breeders/ fanciers at risk to develop the above diseases, but also member of their families who reside with them [24] and are exposed to bird droppings or feather dust.…”

Section: Introductionmentioning

confidence: 99%