Metagenomic analysis of the turkey gut RNA virus community

Day, J. Michael; Ballard, Linda; Duke, Mary V.; Scheffler, Brian E.; Zsák, László

doi:10.1186/1743-422x-7-313

Cited by 102 publications

(95 citation statements)

References 40 publications

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“…According to the data obtained from all these studies mentioned above, the primary PBV infection could take place between the first weeks of life in birds. Recently, through metagenomic approach, many viruses that were previously characterized as well as new, genetically divergent and novel viruses have been identified including picobirnaviruses [19]. This reveals that the putative turkeyorigin for PBVs is unique among the available PBV sequences so far from different hosts; PBVs are genetically diverse and rapidly evolving worldwide in different hosts.…”

Section: Pbv Infection In Animals Birds and Reptilesmentioning

confidence: 99%

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Animal Picobirnavirus

2014

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Picobirnavirus (PBV) is a small, non-enveloped, bisegmented double-stranded RNA (dsRNA) virus of vertebrate hosts. The name 'Picobirnavirus' derives from the prefix 'pico' (latin for 'small') in reference to the small virion size, plus the prefix 'bi' (latin for 'two') and the word 'RNA' to indicate the nature of the viral genome. The serendipitous discovery of PBV dates back to 1988 from Brazil, when human fecal samples collected during the acute gastroenteritis outbreaks were subjected for routine rotavirus surveillance by polyacrylamide gel electrophoresis (PAGE) and silver straining (S/S). The PAGE gels after silver staining showed a typical 'two RNA band' pattern, and it was identified as Picobirnavirus. Likewise, the feces of wild black-footed pigmy rice rats (Oryzomys nigripes) subjected for PAGE assay by the same research group in Brazil reported the presence of PBV (Pereira et al., J Gen Virol 69:2749-2754. PBVs have been detected in faeces of humans and wide range of animal species with or without diarrhoea, worldwide. The probable role of PBV as either a 'primary diarrhoeal agent' in 'immunocompetent children'; or a 'potential pathogen' in 'immunocompromised individuals' or an 'innocuous virus' in the intestine remains elusive and needs to be investigated despite the numerous reports of the presence of PBV in fecal samples of various species of domestic mammals, wild animals, birds and snakes; our current knowledge of their biology, etiology, pathogenicity or their transmission characteristics remains subtle. This review aims to analyse the veterinary and zoonotic aspects of animal Picobirnavirus infections since its discovery.

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Section: Pbv Infection In Animals Birds and Reptilesmentioning

confidence: 99%

“…It includes, detecting previously characterized viruses, as well as genetically diverse, novel subtypes or genotypes of viruses including picobirnaviruses from different geographical locations around the world [19,22,78,87].…”

Section: Introductionmentioning

confidence: 99%

Animal Picobirnavirus

2014

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“…Also, the impact of these viruses on broiler performance needs to be thoroughly investigated. Although virally induced enteric diseases are economic burden on poultry growers, no single virus has emerged as a likely causative agent so that appropriate prevention and control efforts could be applied (Day et al, 2010). Complete understanding of the contribution of enteric viruses and other pathogens in enteric diseases of chicken still have a long way to go in the development of preventive and control measures.…”

Section: Discussionmentioning

confidence: 99%

Detection and molecular characterization of enteric viruses in enteritis-affected commercial broiler chickens in India

Kaithal¹,

Jindal²,

Kumar³

et al. 2016

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Summary. -A study was conducted to detect and characterize the enteric viruses (chicken astrovirus, avian nephritis virus and avian orthoreovirus) present in flocks of commercial broiler chickens suffering from enteritis in Haryana, India. The intestinal contents were collected from 65 enteritis-affected flocks (cases) and tested by reverse transcription PCR (RT-PCR). Of these 65 cases, 35 (53.80%) were positive for a single virus and 26 (40.00%) for two viruses. The remaining four samples were negative for all three viruses tested. Of the 65 cases, 57 were positive for chicken astrovirus (CAstV) while 30 cases had avian nephritis virus (ANV). None of the cases were positive for orthoreovirus. Comparison of 12 CAstVs of this study with previously published CAstV sequences revealed nucleotide identities ranging from 73.20 to 98.00%. The nucleotide identities ranged between 83.10-95.50% when nine ANVs of this study were compared with previously reported ANV sequences. The amino acid sequences of CAstVs in comparison to previously published sequences revealed certain unique changes. Phylogeny based on polymerase gene revealed that CAstVs and ANVs of this study were under the same monophyletic clade. In conclusion, a large number of broiler chicken flocks experiencing enteritis were positive for CAstV and ANV by RT-PCR. The presence of more than one enteric virus in enteritis-affected flocks and changes at the genetic level in these viruses may affect the severity of disease.Keywords: chicken astrovirus; avian nephritis virus; avian orthoreovirus; broiler chicken; India * Corresponding author. E-mail: nareshjindal1@gmail.com; phone: +91-1662-289323. Abbreviations: ANV = avian nephritis virus; ARV = avian reovirus; CAstV = chicken astrovirus; GI = gastrointestinal; PES = poult enteritis syndrome; RSS = runting and stunting syndrome; RT-PCR = reverse transcription PCR

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“…In the past, efforts have been made to use NGS-based approaches, in particular pyrosequencing, for obtaining genetic data from different viral pathogens, such as HIV; avian leukosis virus; lyssaviruses; enteric viruses, and few arboviruses, including DENV-1 and phleboviruses (Victoria et al, 2009;Bimber et al, 2010;Bishop-Lilly et al, 2010;Day et al, 2010;Hedskog et al, 2010;De Wolf et al, 2011;Schinazi et al, 2011;Abbate et al, 2011;De Benedictis et al, 2011;Palacios et al, 2011).…”

Section: Discussionmentioning

confidence: 99%

Optimization of dengue virus genome assembling using GSFLX 454 pyrosequencing data: evaluation of assembling strategies

Casseb¹,

Cardoso²,

Ramos³

et al. 2012

Genet. Mol. Res.

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ABSTRACT. Currently assembling genomes without reference is one of the most important challenges for bioinformaticists all over the world in an attempt to characterize new organisms. The current study has used two dengue virus type 4 (DENV-4) strains recently isolated in Brazil, which have its genomes sequenced using the GSFLX 454 sequencer (Roche, Life Science) by the pyrosequencing method. The GSFLX 454 data were used for testing different genome assembling strategies. We described a pipeline that was able to recover more than 96% of the sequenced genome in a single run and could be helpful for further assembly attempts of other DENV genomes, as well as other RNA virus-like genomes.

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Metagenomic analysis of the turkey gut RNA virus community

Cited by 102 publications

References 40 publications

Animal Picobirnavirus

Animal Picobirnavirus

Detection and molecular characterization of enteric viruses in enteritis-affected commercial broiler chickens in India

Optimization of dengue virus genome assembling using GSFLX 454 pyrosequencing data: evaluation of assembling strategies

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