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Grimwood RM, Reyes EMR, Cooper J, Welch J, Taylor G, Makan T, Lim L, Dubrulle J, McInnes K, Holmes EC, Geoghegan JL. From islands to infectomes: host-specific viral diversity among birds across remote islands. BMC Ecol Evol 2024; 24:84. [PMID: 38926829 PMCID: PMC11209962 DOI: 10.1186/s12862-024-02277-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2024] [Accepted: 06/23/2024] [Indexed: 06/28/2024] Open
Abstract
BACKGROUND Accelerating biodiversity loss necessitates monitoring the potential pathogens of vulnerable species. With a third of New Zealand's avifauna considered at risk of extinction, a greater understanding of the factors that influence microbial transmission in this island ecosystem is needed. We used metatranscriptomics to determine the viruses, as well as other microbial organisms (i.e. the infectomes), of seven bird species, including the once critically endangered black robin (Petroica traversi), on two islands in the remote Chatham Islands archipelago, New Zealand. RESULTS We identified 19 likely novel avian viruses across nine viral families. Black robins harboured viruses from the Flaviviridae, Herpesviridae, and Picornaviridae, while introduced starlings (Sturnus vulgaris) and migratory seabirds (Procellariiformes) carried viruses from six additional viral families. Potential cross-species virus transmission of a novel passerivirus (family: Picornaviridae) between native (black robins and grey-backed storm petrels) and introduced (starlings) birds was also observed. Additionally, we identified bacterial genera, apicomplexan parasites, as well as a novel megrivirus linked to disease outbreaks in other native New Zealand birds. Notably, island effects were outweighed by host taxonomy as a significant driver of viral composition, even among sedentary birds. CONCLUSIONS These findings underscore the value of surveillance of avian populations to identify and minimise escalating threats of disease emergence and spread in these island ecosystems. Importantly, they contribute to our understanding of the potential role of introduced and migratory birds in the transmission of microbes and associated diseases, which could impact vulnerable island-endemic species.
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Affiliation(s)
- Rebecca M Grimwood
- Department of Microbiology and Immunology, University of Otago, Dunedin, 9016, New Zealand
| | - Enzo M R Reyes
- Department of Conservation/Te Papa Atawhai, Nelson, New Zealand
| | - Jamie Cooper
- Department of Conservation/Te Papa Atawhai, Nelson, New Zealand
| | - Jemma Welch
- Department of Conservation/Te Papa Atawhai, Nelson, New Zealand
| | - Graeme Taylor
- Department of Conservation/Te Papa Atawhai, Nelson, New Zealand
| | - Troy Makan
- Department of Conservation/Te Papa Atawhai, Nelson, New Zealand
| | - Lauren Lim
- School of Medical Sciences, The University of Sydney, Sydney, NSW, 2006, Australia
| | - Jérémy Dubrulle
- Department of Microbiology and Immunology, University of Otago, Dunedin, 9016, New Zealand
| | - Kate McInnes
- Department of Conservation/Te Papa Atawhai, Nelson, New Zealand
| | - Edward C Holmes
- School of Medical Sciences, The University of Sydney, Sydney, NSW, 2006, Australia
| | - Jemma L Geoghegan
- Department of Microbiology and Immunology, University of Otago, Dunedin, 9016, New Zealand.
- Institute of Environmental Science and Research, Wellington, 5018, New Zealand.
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2
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Nuñez LFN, Chacón RD, da Costa AC, Santander-Parra SH, da Costa Pereira Innocentini R, Sánchez-Llatas CJ, Cea-Callejo P, Ichillumpa SV, Astolfi Ferreira CS, Marques de Sá LR, Piantino Ferreira AJ. Detection and Molecular Characterization of Chicken Parvovirus and Chicken Megrivirus in Layer Breeders Affected by Intestinal Dilatation Syndrome. Avian Pathol 2024:1-28. [PMID: 38916258 DOI: 10.1080/03079457.2024.2372486] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/26/2024]
Abstract
Intestinal dilatation syndrome (IDS) is a segmental enteropathy characterized by dilatation of the junction of the ileum and jejunum (Meckel's diverticulum). IDS severely affects the poultry industry by causing a chronic and irreversible drop in egg laying, reducing feed conversion efficiency, and increasing the mortality rate. The clinical and pathological features of IDS in white laying hens were described, and viral molecular and metagenomic research was conducted. The 50- to 60-day-old chickens presented pale mucosa, apathy, depression, ruffled feathers, and diarrhoea, accompanied by a 20% loss in fertile egg production, 20% culling of birds, and 5% mortality. The main findings at necropsy were marked intestinal dilatation with intestinal stasis, a narrow distal jejunum in the region of Meckel's diverticulum, and undigested food. Microscopic analysis revealed marked atrophic lymphoplasmacytic and heterophilic enteritis with hyperplastic crypts, ulceration, and heterophilic and lymphoplasmacytic perineuritis. The molecular assays consistently detected the presence of chicken parvovirus in the three segments of the intestine, pancreas, and proventriculus, as well as chicken megrivirus in the intestinal contents. Marked atrophic enteritis with perineuritis and intestinal stasis are associated with clinical manifestations of poor intestinal absorption and secondary bacterial infection. Our data provide useful information about IDS and highlight the importance of further studies to determine the specific role of each detected virus in this syndrome.RESEARCH HIGHLIGHTS IDS presented pathognomonic dilatation of the jejunum up to Meckel's diverticulum.IDS caused weight loss, decreased egg production, and increased culling and mortality.Chicken parvovirus (ChPV) was consistently detected through PCR assays.Chicken megrivirus (ChMV) was consistently detected through viral metagenomics.
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Affiliation(s)
- Luis Fabian N Nuñez
- Facultad de Ciencias de la Salud, Carrera de Medicina Veterinaria, Universidad de Las Américas (UDLA), Quito, Ecuador
| | - Ruy D Chacón
- Laboratory of Avian Diseases, School of Veterinary Medicine and Animal Science, Department of Pathology, University of São Paulo, São Paulo, Brazil
| | | | - Silvana H Santander-Parra
- Facultad de Ciencias de la Salud, Carrera de Medicina Veterinaria, Universidad de Las Américas (UDLA), Quito, Ecuador
| | | | - Christian J Sánchez-Llatas
- Faculty of Biology, Department of Genetics, Physiology, and Microbiology, Complutense University of Madrid, Madrid, Spain
| | - Pablo Cea-Callejo
- Faculty of Biology, Department of Genetics, Physiology, and Microbiology, Complutense University of Madrid, Madrid, Spain
| | - Stefhany Valdeiglesias Ichillumpa
- Laboratorio de Fisiología Molecular, Instituto de Investigación en Ganadería y Biotecnología, Facultad de Ingeniería Zootecnista, Agronegocios y Biotecnología, Universidad Nacional Toribio Rodríguez de Mendoza de Amazonas (UNTRM), Amazonas, Peru
| | - Claudete S Astolfi Ferreira
- Laboratory of Avian Diseases, School of Veterinary Medicine and Animal Science, Department of Pathology, University of São Paulo, São Paulo, Brazil
| | - Lilian Rose Marques de Sá
- Laboratory of Diagnostic and Environmental Pathology, School of Veterinary Medicine and Animal Science, Department of Pathology, University of São Paulo, São Paulo, Brazil
| | - Antonio J Piantino Ferreira
- Laboratory of Avian Diseases, School of Veterinary Medicine and Animal Science, Department of Pathology, University of São Paulo, São Paulo, Brazil
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3
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Li Y, Zhang L, Wang L, Li J, Zhao Y, Liu F, Wang Q. Structure and function of type IV IRES in picornaviruses: a systematic review. Front Microbiol 2024; 15:1415698. [PMID: 38855772 PMCID: PMC11157119 DOI: 10.3389/fmicb.2024.1415698] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2024] [Accepted: 05/13/2024] [Indexed: 06/11/2024] Open
Abstract
The Picornaviridae is a family of icosahedral viruses with single-stranded, highly diverse positive-sense RNA genomes. Virions consist of a capsid, without envelope, surrounding a core of RNA genome. A typical genome of picornavirus harbors a well-conserved and highly structured RNA element known as the internal ribosome entry site (IRES), functionally essential for viral replication and protein translation. Based on differences in their structures and mechanisms of action, picornaviral IRESs have been categorized into five types: type I, II, III, IV, and V. Compared with the type IV IRES, the others not only are structurally complicated, but also involve multiple initiation factors for triggering protein translation. The type IV IRES, often referred to as hepatitis C virus (HCV)-like IRES due to its structural resemblance to the HCV IRES, exhibits a simpler and more compact structure than those of the other four. The increasing identification of picornaviruses with the type IV IRES suggests that this IRES type seems to reveal strong retention and adaptation in terms of viral evolution. Here, we systematically reviewed structural features and biological functions of the type IV IRES in picornaviruses. A comprehensive understanding of the roles of type IV IRESs will contribute to elucidating the replication mechanism and pathogenesis of picornaviruses.
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Affiliation(s)
- Yan Li
- College of Veterinary Medicine, Qingdao Agricultural University, Qingdao, China
- Qingdao Center for Animal Disease Control and Prevention, Qingdao, China
| | - Lei Zhang
- Shandong New Hope Liuhe Group Co., Ltd., Qingdao, China
| | - Ling Wang
- University Hospital, Qingdao Agricultural University, Qingdao, China
| | - Jing Li
- Market Supervision Administration of Huangdao District, Qingdao, China
| | - Yanwei Zhao
- College of Veterinary Medicine, Qingdao Agricultural University, Qingdao, China
| | - Fuxiao Liu
- College of Veterinary Medicine, Qingdao Agricultural University, Qingdao, China
| | - Qianqian Wang
- College of Veterinary Medicine, Qingdao Agricultural University, Qingdao, China
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4
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Zhang J, Fu H, Chen C, Jiang J, Lin Y, Jiang B, Lin L, Hu Q, Wan C. Rapid detection of pigeon Megrivirus using TaqMan real-time PCR technology. Poult Sci 2023; 102:103027. [PMID: 37651775 PMCID: PMC10480624 DOI: 10.1016/j.psj.2023.103027] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2023] [Revised: 08/09/2023] [Accepted: 08/09/2023] [Indexed: 09/02/2023] Open
Abstract
Megriviruses have been identified from fecal samples in wild pigeons in Hong Kong (China) and Hungary. In this study, the genomic sequences of pigeon Megriviruses (PiMeVs) were downloaded from GenBank and compared. Based on the genetic comparison results, a pair of primers and TaqMan probe were designed based on the conserved sequences of the 3C gene (located in the P3 gene coding region), and a TaqMan real-time PCR method (TaqMan-qPCR) was established. The standard curve of the TaqMan-qPCR had an axial intercept of 39.74 and a slope of -3.2475 with a linear correlation (R2) of 1.00 and an efficiency of 103.2%. No cross-amplification signal was found from other pigeon viruses (such as avian influenza virus, pigeon paramyxovirus type I, pigeon torque teno virus, pigeon adenovirus, and pigeon circovirus). The limit of detection concentration was 53.6 copies/μL. The intra- and interassay results were less than 1.0% based on the reproducibility test. Furthermore, field samples investigation by the established TaqMan-qPCR method showed that positive signals can be found from racing pigeon fecal samples and embryos. Thus, our data suggested that this visible TaqMan-qPCR method is sensitive, specific, and reproducible. Moreover, we first confirmed the presence of pigeon Megrivirus infection in racing pigeon embryos, indicating that the virus may be vertically transmitted. This study provides a reference basis for further understanding the epidemiology of PiMeVs.
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Affiliation(s)
- Jinpeng Zhang
- Institute of Animal Husbandry and Veterinary Medicine, Fujian Academy of Agricultural Sciences, Fuzhou 350013, China
| | - Huanru Fu
- School of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Cuiteng Chen
- Institute of Animal Husbandry and Veterinary Medicine, Fujian Academy of Agricultural Sciences, Fuzhou 350013, China
| | - Jinxiu Jiang
- Institute of Animal Husbandry and Veterinary Medicine, Fujian Academy of Agricultural Sciences, Fuzhou 350013, China
| | - Yusheng Lin
- Institute of Animal Husbandry and Veterinary Medicine, Fujian Academy of Agricultural Sciences, Fuzhou 350013, China
| | - Bin Jiang
- Institute of Animal Husbandry and Veterinary Medicine, Fujian Academy of Agricultural Sciences, Fuzhou 350013, China
| | - Lin Lin
- Institute of Animal Husbandry and Veterinary Medicine, Fujian Academy of Agricultural Sciences, Fuzhou 350013, China
| | - Qilin Hu
- Institute of Animal Husbandry and Veterinary Medicine, Fujian Academy of Agricultural Sciences, Fuzhou 350013, China
| | - Chunhe Wan
- Institute of Animal Husbandry and Veterinary Medicine, Fujian Academy of Agricultural Sciences, Fuzhou 350013, China; Fujian Key Laboratory for Avian Diseases Control and Prevention/Fujian Key Laboratory of Animal Genetics and Breeding/Fujian Animal Diseases Control Technology Development Centre, Fuzhou 350013, China.
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5
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Wierenga JR, Grimwood RM, Taylor HS, Hunter S, Argilla LS, Webster T, Lim L, French R, Schultz H, Jorge F, Bostina M, Burga L, Swindells-Wallace P, Holmes EC, McInnes K, Morgan KJ, Geoghegan JL. Total infectome investigation of diphtheritic stomatitis in yellow-eyed penguins (Megadyptes antipodes) reveals a novel and abundant megrivirus. Vet Microbiol 2023; 286:109895. [PMID: 37890432 DOI: 10.1016/j.vetmic.2023.109895] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2023] [Revised: 10/15/2023] [Accepted: 10/19/2023] [Indexed: 10/29/2023]
Abstract
First identified in 2002, diphtheritic stomatitis (DS) is a devastating disease affecting yellow-eyed penguins (Megadyptes antipodes, or hoiho in te reo Māori). The disease is associated with oral lesions in chicks and has caused significant morbidity and mortality. DS is widespread among yellow-eyed penguin chicks on mainland New Zealand yet appears to be absent from the subantarctic population. Corynebacterium spp. have previously been suspected as causative agents yet, due to inconsistent cultures and inconclusive pathogenicity, their role in DS is unclear. Herein, we used a metatranscriptomic approach to identify potential causative agents of DS by revealing the presence and abundance of all viruses, bacteria, fungi and protozoa - together, the infectome. Oral and cloacal swab samples were collected from presymptomatic, symptomatic and recovered chicks along with a control group of healthy adults. Two novel viruses from the Picornaviridae were identified, one of which - yellow-eyed penguin megrivirus - was highly abundant in chicks irrespective of health status but not detected in healthy adults. Tissue from biopsied oral lesions also tested positive for the novel megrivirus upon PCR. We found no overall clustering among bacteria, protozoa and fungi communities at the genus level across samples, although Paraclostridium bifermentans was significantly more abundant in oral microbiota of symptomatic chicks compared to other groups. The detection of a novel and highly abundant megrivirus has sparked a new line of inquiry to investigate its potential association with DS.
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Affiliation(s)
- Janelle R Wierenga
- Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand; Wildbase, School of Veterinary Science, Massey University, New Zealand
| | - Rebecca M Grimwood
- Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand
| | - Harry S Taylor
- Biodiversity Group, Department of Conservation/Te Papa Atawhai, New Zealand; Diagnostic and Surveillance Services, Biosecurity New Zealand, Ministry for Primary Industries, New Zealand
| | - Stuart Hunter
- Wildbase, School of Veterinary Science, Massey University, New Zealand
| | - Lisa S Argilla
- Wildlife Hospital, Dunedin, Otago Polytechnic School of Veterinary Nursing, New Zealand
| | | | - Lauren Lim
- Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand
| | - Rebecca French
- Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand
| | - Hendrik Schultz
- Biodiversity Group, Department of Conservation/Te Papa Atawhai, New Zealand
| | - Fátima Jorge
- Otago Micro and Nano Imaging, University of Otago, Dunedin, New Zealand
| | - Mihnea Bostina
- Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand
| | - Laura Burga
- Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand
| | | | - Edward C Holmes
- Sydney Institute for Infectious Diseases, School of Medical Sciences, The University of Sydney, Australia
| | - Kate McInnes
- Biodiversity Group, Department of Conservation/Te Papa Atawhai, New Zealand
| | - Kerri J Morgan
- Wildbase, School of Veterinary Science, Massey University, New Zealand
| | - Jemma L Geoghegan
- Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand; Institute of Environmental Science and Research, Wellington, New Zealand.
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6
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Fomsgaard AS, Tahas SA, Spiess K, Polacek C, Fonager J, Belsham GJ. Unbiased Virus Detection in a Danish Zoo Using a Portable Metagenomic Sequencing System. Viruses 2023; 15:1399. [PMID: 37376698 DOI: 10.3390/v15061399] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2023] [Revised: 06/16/2023] [Accepted: 06/16/2023] [Indexed: 06/29/2023] Open
Abstract
Metagenomic next-generation sequencing (mNGS) is receiving increased attention for the detection of new viruses and infections occurring at the human-animal interface. The ability to actively transport and relocate this technology enables in situ virus identification, which could reduce response time and enhance disease management. In a previous study, we developed a straightforward mNGS procedure that greatly enhances the detection of RNA and DNA viruses in human clinical samples. In this study, we improved the mNGS protocol with transportable battery-driven equipment for the portable, non-targeted detection of RNA and DNA viruses in animals from a large zoological facility, to simulate a field setting for point-of-incidence virus detection. From the resulting metagenomic data, we detected 13 vertebrate viruses from four major virus groups: (+)ssRNA, (+)ssRNA-RT, dsDNA and (+)ssDNA, including avian leukosis virus in domestic chickens (Gallus gallus), enzootic nasal tumour virus in goats (Capra hircus) and several small, circular, Rep-encoding, ssDNA (CRESS DNA) viruses in several mammal species. More significantly, we demonstrate that the mNGS method is able to detect potentially lethal animal viruses, such as elephant endotheliotropic herpesvirus in Asian elephants (Elephas maximus) and the newly described human-associated gemykibivirus 2, a human-to-animal cross-species virus, in a Linnaeus two-toed sloth (Choloepus didactylus) and its enclosure, for the first time.
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Affiliation(s)
- Anna S Fomsgaard
- Department of Virus & Microbiological Special Diagnostics, Statens Serum Institut, 5 Artillerivej, 2300 Copenhagen, Denmark
- Department of Veterinary and Animal Sciences, University of Copenhagen, 4 Stigboejlen, 1870 Frederiksberg, Denmark
| | | | - Katja Spiess
- Department of Virus & Microbiological Special Diagnostics, Statens Serum Institut, 5 Artillerivej, 2300 Copenhagen, Denmark
| | - Charlotta Polacek
- Department of Virus & Microbiological Special Diagnostics, Statens Serum Institut, 5 Artillerivej, 2300 Copenhagen, Denmark
| | - Jannik Fonager
- Department of Virus & Microbiological Special Diagnostics, Statens Serum Institut, 5 Artillerivej, 2300 Copenhagen, Denmark
| | - Graham J Belsham
- Department of Veterinary and Animal Sciences, University of Copenhagen, 4 Stigboejlen, 1870 Frederiksberg, Denmark
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7
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Yan T, Li G, Zhou D, Hu L, Hao X, Li R, Wang G, Cheng Z. Long read sequencing revealed proventricular virome of broiler chicken with transmission viral proventriculitis. BMC Vet Res 2022; 18:253. [PMID: 35768837 PMCID: PMC9241223 DOI: 10.1186/s12917-022-03339-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2021] [Accepted: 06/07/2022] [Indexed: 11/20/2022] Open
Abstract
Background Transmissible viral proventriculitis (TVP) causes significant economic loss to the poultry industry. However, the exact causative agents are obscure. Here we examine the virome of proventriculus from specified pathogen free (SPF) chickens that reproduced by infection of proventricular homogenate from broiler chicken with TVP using long read sequencing of the Pacific Biosciences RSII platform. The normal SPF chickens were used as control. Results Our investigation reveals a virome of proventriculitis, including three Gyrovirus genera of the Aneloviridae: Gyrovirus homsa1 (GyH1) (also known as Gyrovirus 3, GyV3) (n = 2662), chicken anemia virus (CAV) (n = 482) and Gyrovirus galga1 (GyG1) (also known as avian Gyrovirus 2, AGV2) (n = 11); a plethora of novel CRESS viral genomes (n = 26) and a novel genomovirus. The 27 novel viruses were divided into three clusters. Phylogenetic analysis showed that the GyH1 strain was more closely related to the strains from chicken (MG366592) than mammalian (human and cat), the GyG1 strain was closely related to the strains from cat in China (MK089245) and from chicken in Brazil (HM590588), and the CAV strain was more closely related to the strains from Germany (AJ297684) and United Kingdom (U66304) than that previously found in China. Conclusion In this study, we revealed that Gyrovirus virome showed high abundance in chickens with TVP, suggesting their potential role in TVP, especially GyH1. This study is expected to contribute to the knowledge of the etiology of TVP. Supplementary Information The online version contains supplementary material available at 10.1186/s12917-022-03339-9.
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Affiliation(s)
- Tianxing Yan
- Present Address: College of Veterinary Medicine, Shandong Agricultural University, Shandong Provence, Tai'an, 271018, China
| | - Gen Li
- Present Address: College of Veterinary Medicine, Shandong Agricultural University, Shandong Provence, Tai'an, 271018, China.,College of Veterinary Medicine, Qingdao Agricultural University, Qingdao, 266000, China
| | - Defang Zhou
- Present Address: College of Veterinary Medicine, Shandong Agricultural University, Shandong Provence, Tai'an, 271018, China
| | - Liping Hu
- Animal Epidemic Prevention and Control Center of Shandong Province, Jinan, China
| | - Xiaojing Hao
- Animal Husbandry and Veterinary Research Institute of Qingdao, Qingdao, China
| | - Ruiqi Li
- Present Address: College of Veterinary Medicine, Shandong Agricultural University, Shandong Provence, Tai'an, 271018, China
| | - Guihua Wang
- Present Address: College of Veterinary Medicine, Shandong Agricultural University, Shandong Provence, Tai'an, 271018, China
| | - Ziqiang Cheng
- Present Address: College of Veterinary Medicine, Shandong Agricultural University, Shandong Provence, Tai'an, 271018, China.
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8
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Kubacki J, Qi W, Fraefel C. Differential Viral Genome Diversity of Healthy and RSS-Affected Broiler Flocks. Microorganisms 2022; 10:microorganisms10061092. [PMID: 35744610 PMCID: PMC9231120 DOI: 10.3390/microorganisms10061092] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Revised: 05/18/2022] [Accepted: 05/23/2022] [Indexed: 01/17/2023] Open
Abstract
The intestinal virus community contributes to health and disease. Runting and stunting syndrome (RSS) is associated with enteric viruses and leads to economic losses in the poultry industry. However, many viruses that potentially cause this syndrome have also been identified in healthy animals. To determine the difference in the virome of healthy and diseased broilers, samples from 11 healthy and 17 affected broiler flocks were collected at two time points and analyzed by Next-Generation Sequencing. Virus genomes of Parvoviridae, Astroviridae, Picornaviridae, Caliciviridae, Reoviridae, Adenoviridae, Coronaviridae, and Smacoviridae were identified at various days of poultry production. De novo sequence analysis revealed 288 full or partial avian virus genomes, of which 97 belonged to the novel genus Chaphamaparvovirus. This study expands the knowledge of the diversity of enteric viruses in healthy and RSS-affected broiler flocks and questions the association of some viruses with the diseases.
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Affiliation(s)
- Jakub Kubacki
- Institute of Virology, Vetsuisse Faculty, University of Zurich, 8057 Zurich, Switzerland;
- Correspondence:
| | - Weihong Qi
- Functional Genomics Center Zurich, 8057 Zurich, Switzerland;
| | - Cornel Fraefel
- Institute of Virology, Vetsuisse Faculty, University of Zurich, 8057 Zurich, Switzerland;
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9
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Shan T, Yang S, Wang H, Wang H, Zhang J, Gong G, Xiao Y, Yang J, Wang X, Lu J, Zhao M, Yang Z, Lu X, Dai Z, He Y, Chen X, Zhou R, Yao Y, Kong N, Zeng J, Ullah K, Wang X, Shen Q, Deng X, Zhang J, Delwart E, Tong G, Zhang W. Virome in the cloaca of wild and breeding birds revealed a diversity of significant viruses. MICROBIOME 2022; 10:60. [PMID: 35413940 PMCID: PMC9001828 DOI: 10.1186/s40168-022-01246-7] [Citation(s) in RCA: 27] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/04/2021] [Accepted: 02/16/2022] [Indexed: 06/01/2023]
Abstract
BACKGROUND Wild birds may harbor and transmit viruses that are potentially pathogenic to humans, domestic animals, and other wildlife. RESULTS Using the viral metagenomic approach, we investigated the virome of cloacal swab specimens collected from 3182 birds (the majority of them wild species) consisting of > 87 different species in 10 different orders within the Aves classes. The virus diversity in wild birds was higher than that in breeding birds. We acquired 707 viral genomes from 18 defined families and 4 unclassified virus groups, with 265 virus genomes sharing < 60% protein sequence identities with their best matches in GenBank comprising new virus families, genera, or species. RNA viruses containing the conserved RdRp domain with no phylogenetic affinity to currently defined virus families existed in different bird species. Genomes of the astrovirus, picornavirus, coronavirus, calicivirus, parvovirus, circovirus, retrovirus, and adenovirus families which include known avian pathogens were fully characterized. Putative cross-species transmissions were observed with viruses in wild birds showing > 95% amino acid sequence identity to previously reported viruses in domestic poultry. Genomic recombination was observed for some genomes showing discordant phylogenies based on structural and non-structural regions. Mapping the next-generation sequencing (NGS) data respectively against the 707 genomes revealed that these viruses showed distribution pattern differences among birds with different habitats (breeding or wild), orders, and sampling sites but no significant differences between birds with different behavioral features (migratory and resident). CONCLUSIONS The existence of a highly diverse virome highlights the challenges in elucidating the evolution, etiology, and ecology of viruses in wild birds. Video Abstract.
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Affiliation(s)
- Tongling Shan
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, 200241, China
| | - Shixing Yang
- School of Medicine, Jiangsu University, Zhenjiang, 212003, Jiangsu, China
| | - Haoning Wang
- School of Geography and Tourism, Harbin University, Harbin, 150886, Heilongjiang, China
- Key Laboratory of Wildlife diseases and Biosecurity Management of Heilongjiang Province, Harbin, 150886, Heilongjiang, China
| | - Hao Wang
- Department of Clinical Laboratory, The Affiliated Huai'an Hospital of Xuzhou Medical University, Huai'an, 223002, Jiangsu, China
| | - Ju Zhang
- School of Medicine, Jiangsu University, Zhenjiang, 212003, Jiangsu, China
| | - Ga Gong
- Animal Science College, Tibet Agriculture and Animal Husbandry University, Nyingchi, 860000, Tibet, China
| | - Yuqing Xiao
- School of Medicine, Jiangsu University, Zhenjiang, 212003, Jiangsu, China
| | - Jie Yang
- School of Medicine, Jiangsu University, Zhenjiang, 212003, Jiangsu, China
| | - Xiaolong Wang
- Wildlife and Protected Area College/Center of Conservation Medicine and Ecological Safety Northeast Forestry University, Harbin, 150006, Heilongjiang, China
| | - Juan Lu
- School of Medicine, Jiangsu University, Zhenjiang, 212003, Jiangsu, China
| | - Min Zhao
- School of Medicine, Jiangsu University, Zhenjiang, 212003, Jiangsu, China
| | - Zijun Yang
- School of Medicine, Jiangsu University, Zhenjiang, 212003, Jiangsu, China
| | - Xiang Lu
- School of Medicine, Jiangsu University, Zhenjiang, 212003, Jiangsu, China
| | - Ziyuan Dai
- School of Medicine, Jiangsu University, Zhenjiang, 212003, Jiangsu, China
| | - Yumin He
- School of Medicine, Jiangsu University, Zhenjiang, 212003, Jiangsu, China
| | - Xu Chen
- School of Medicine, Jiangsu University, Zhenjiang, 212003, Jiangsu, China
| | - Rui Zhou
- School of Medicine, Jiangsu University, Zhenjiang, 212003, Jiangsu, China
| | - Yuxin Yao
- School of Medicine, Jiangsu University, Zhenjiang, 212003, Jiangsu, China
| | - Ning Kong
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, 200241, China
| | - Jian Zeng
- School of Medicine, Jiangsu University, Zhenjiang, 212003, Jiangsu, China
| | - Kalim Ullah
- School of Medicine, Jiangsu University, Zhenjiang, 212003, Jiangsu, China
| | - Xiaochun Wang
- School of Medicine, Jiangsu University, Zhenjiang, 212003, Jiangsu, China
| | - Quan Shen
- School of Medicine, Jiangsu University, Zhenjiang, 212003, Jiangsu, China
| | - Xutao Deng
- Vitalant Research Institute, San Francisco, CA, 94118, USA
| | - Jianmin Zhang
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, 510642, Guangdong, China
| | - Eric Delwart
- Vitalant Research Institute, San Francisco, CA, 94118, USA
- Department of Laboratory Medicine, University of California San Francisco, San Francisco, CA, 94118, USA
| | - Guangzhi Tong
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, 200241, China.
- Jiangsu Co-Innovation Center for the Prevention and Control of Important Animal Infectious Disease and Zoonose, Yangzhou University, Yangzhou, 225009, Jiangsu, China.
| | - Wen Zhang
- School of Medicine, Jiangsu University, Zhenjiang, 212003, Jiangsu, China.
- International Center for Genomics Research, Jiangsu University, Zhenjiang, 212013, Jiangsu, China.
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10
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Kim SH, Kwon YK, Park CK, Kim HR. Identification of Campylobacter jejuni and Chlamydia psittaci from cockatiel (Nymphicus hollandicus) using metagenomics. BMC Genomics 2021; 22:797. [PMID: 34742232 PMCID: PMC8571871 DOI: 10.1186/s12864-021-08122-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2021] [Accepted: 10/25/2021] [Indexed: 11/10/2022] Open
Abstract
Background In July 2015, the carcasses of 11 cockatiels were submitted for disease diagnosis to the Avian Disease Division of the Animal and Plant Quarantine Agency of Korea. The cockatiels, which appeared dehydrated and underweight, had exhibited severe diarrhea and 22 % mortality over 2 weeks. Traditional diagnosis did not reveal the causes of these symptoms. Methods We conducted metagenomics analysis on intestines and livers from the dead cockatiels using Illumina high-throughput sequencing. To obtain more accurate and longer contigs, which are required for further genetic characterization, we compared the results of three de novo assembly tools (metaSPAdes, MEGAHIT, and IDBA-UD). Results Sequence reads of Campylobacter jejuni (C. jejuni) and Chlamydia psittaci (C. psittaci) were present in most of the cockatiel samples. Either of these bacteria could cause the reported symptoms in psittaciformes. metaSPAdes (ver.3.14.1) identified the 1152 bp flaA gene of C. jejuni and the 1096 bp ompA gene of C. psittaci. Genetic analysis revealed that flaA of C. jejuni was recombinant between C. jejuni and Campylobacter coli, and that ompA of C. psittaci isolated from cockatiel was closely related to strains isolated from humans. Conclusions C. jejuni and C. psittaci were detected in cockatiels in the Republic of Korea using metagenomic analysis. This approach is useful for understanding pathogens of pet birds. Three de novo assemblers were compared to obtain accurate contigs from large quantities of reads, and sequences of C. jejuni and C. psittaci generated by metaSPAdes were analyzed.
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Affiliation(s)
- Si-Hyeon Kim
- Avian Disease Division, Animal and Plant Quarantine Agency, 177 Hyeoksin 8-ro, Gyeongsangbuk-do, 39660, Gimcheon-si, Republic of Korea
| | - Yong-Kuk Kwon
- Avian Disease Division, Animal and Plant Quarantine Agency, 177 Hyeoksin 8-ro, Gyeongsangbuk-do, 39660, Gimcheon-si, Republic of Korea
| | - Choi-Kyu Park
- Animal Disease Intervention Center, College of Veterinary Medicine, Kyungpook National University, 41566, Daegu, Republic of Korea
| | - Hye-Ryoung Kim
- Avian Disease Division, Animal and Plant Quarantine Agency, 177 Hyeoksin 8-ro, Gyeongsangbuk-do, 39660, Gimcheon-si, Republic of Korea.
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11
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Kim HR, Jang I, Kim SH, Kwon YK. Viral Metagenomic Analysis of Japanese Quail ( Coturnix japonica) with Enteritis in the Republic of Korea. Avian Dis 2021; 65:40-45. [PMID: 34339120 DOI: 10.1637/aviandiseases-d-20-00081] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2020] [Accepted: 08/27/2020] [Indexed: 11/05/2022]
Abstract
We performed viral metagenomics analysis of Japanese quail affected with enteritis to elucidate the viral etiology. Metagenomics generated 21,066,442 sequence reads via high-throughput sequencing, with a mean length of 136 nt. Enrichment in viral sequences suggested that at least three viruses were present in quail samples. Coronavirus and picornavirus were identified and are known as pathogens causing quail enteritis that match the observed morphology. Abundant reads of coronavirus from quail samples yielded four fragment sequences exhibiting six genomes of avian coronavirus. Sequence analysis showed that this quail coronavirus was related to turkey coronavirus and chicken infectious bronchitis virus. Quail picornavirus 8177 bp in size was identified and was similar to the QPV1/HUN/01 virus detected in quails without clinical symptoms in Hungary with 84.6% nucleotide and 94.6% amino acid identity. Our results are useful for understanding the genetic diversity of quail viruses. Further studies must be performed to determine whether quail coronavirus and quail picornavirus are pathogens of the digestive tract of quails.
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Affiliation(s)
- Hye-Ryoung Kim
- Avian Disease Division, Animal and Plant Quarantine Agency, Gimcheon-si, Gyeongsangbuk-do, 39660, Republic of Korea,
| | - Il Jang
- Avian Disease Division, Animal and Plant Quarantine Agency, Gimcheon-si, Gyeongsangbuk-do, 39660, Republic of Korea
| | - Si-Hyeon Kim
- Avian Disease Division, Animal and Plant Quarantine Agency, Gimcheon-si, Gyeongsangbuk-do, 39660, Republic of Korea
| | - Yong-Kuk Kwon
- Avian Disease Division, Animal and Plant Quarantine Agency, Gimcheon-si, Gyeongsangbuk-do, 39660, Republic of Korea
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12
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Hauck R, Stoute S, Senties-Cue CG, Guy JS, Shivaprasad HL. A Retrospective Study of Transmissible Viral Proventriculitis in Broiler Chickens in California: 2000-18. Avian Dis 2021; 64:525-531. [PMID: 33570104 DOI: 10.1637/aviandiseases-d20-00057] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2020] [Accepted: 07/17/2020] [Indexed: 11/05/2022]
Abstract
Transmissible viral proventriculitis (TVP) is a disease of chickens, mostly in broilers of 2-8 wk of age. Chicken proventricular necrosis virus (CPNV), a birnavirus, is the etiologic agent. Characteristic gross lesions are enlargement, atony, and pallor of the proventriculus. Cases diagnosed in California between 2000 and 2018 (n = 477), originating from 93 different farms representing all major companies in the region, were analyzed. Frequency of cases varied widely between years, with no recognizable seasonality. The flocks were between 6 and 61 days of age; the average age was 34.0 days, and the median age was 35 days. In 166 cases, between 6.3% and 100% of the submitted birds had gross lesions in the proventriculus. The most common findings were enlarged or dilated proventriculi, thickened walls, and pale or mottled serosal appearance. Histopathologically, inflammation of the glands was the most frequent finding. Other lesions included necrosis, hyperplasia, or both conditions of the glandular epithelium; dilated glands; and occasionally fibrin deposition, fibrosis, and hemorrhages. Twenty-three proventriculi from six cases were tested by immunohistochemistry for the presence of CPNV antigen; 21 stained positive. In 209 cases, birds also had lesions in the bursa fabricii attributed to infectious bursal disease, but with no significant difference in the mean percentage of birds with gross lesions in the proventriculus between cases with or without lesions in the bursa fabricii. The results show that TVP is a common disease of broiler flocks in California and confirms that CPNV is the likely causative agent.
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Affiliation(s)
- Rüdiger Hauck
- Department of Pathobiology and Department of Poultry Science, Auburn University, Auburn, AL 36849
| | - Simone Stoute
- California Animal Health and Food Safety Laboratory System, Turlock Branch, University of California Davis, Davis, CA 95380
| | - C Gabriel Senties-Cue
- California Animal Health and Food Safety Laboratory System, Turlock Branch, University of California Davis, Davis, CA 95380
| | - James S Guy
- Department of Population Health and Pathobiology, College of Veterinary Medicine, North Carolina State University, Raleigh, NC 27606
| | - H L Shivaprasad
- California Animal Health and Food Safety Laboratory System, Tulare Branch, University of California Davis, Davis, CA 93274
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13
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Leão PA, Amaral CI, Santos WHM, Moreira MVL, de Oliveira LB, Costa EA, Resende M, Wenceslau R, Ecco R. Retrospective and prospective studies of transmissible viral proventriculitis in broiler chickens in Brazil. J Vet Diagn Invest 2021; 33:605-610. [PMID: 33769146 DOI: 10.1177/10406387211004106] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
We investigated the occurrence and pathologic findings of transmissible viral proventriculitis (TVP) associated with the chicken proventricular necrosis virus (CPNV) in commercial broiler chickens in southeastern Brazil. Seventy-three broilers, 25-36 d old, with a history of reduced growth, were referred to our veterinary pathology services from 2013 to 2017. Broilers were clinically examined, weighed, and euthanized for postmortem examination. Broilers of different ages with proventricular histologic lesions were positive for CPNV by RT-PCR; however, the intensity of histologic lesions was higher among 33-d-old animals, and viral RNA detection was more frequent among those that were 28 d old. In the proventriculi of 35 of 73 (48%) broilers, lesions were characterized by glandular epithelial necrosis, lymphoplasmacytic and histiocytic infiltrates, and metaplasia of glandular epithelium to ductal epithelium. In 24 of 73 (36%) broilers with histologic TVP-compatible lesions, CPNV was detected by RT-PCR for the viral protein 1 (VP1) gene. Broilers with histologic lesions were lighter than expected compared to the Cobb 500 standard weight. TVP has not been reported previously in broiler chickens in Brazil, to our knowledge.
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Affiliation(s)
- Philipe A Leão
- Departments of Veterinary Clinic and Surgery, Veterinary School, Universidade Federal de Minas Gerais-UFMG, Belo Horizonte, Minas Gerais, Brazil
| | - Camila I Amaral
- Departments of Veterinary Clinic and Surgery, Veterinary School, Universidade Federal de Minas Gerais-UFMG, Belo Horizonte, Minas Gerais, Brazil
| | - Willian H M Santos
- Departments of Veterinary Clinic and Surgery, Veterinary School, Universidade Federal de Minas Gerais-UFMG, Belo Horizonte, Minas Gerais, Brazil
| | - Matheus V L Moreira
- Departments of Veterinary Clinic and Surgery, Veterinary School, Universidade Federal de Minas Gerais-UFMG, Belo Horizonte, Minas Gerais, Brazil
| | - Leticia B de Oliveira
- Departments of Veterinary Clinic and Surgery, Veterinary School, Universidade Federal de Minas Gerais-UFMG, Belo Horizonte, Minas Gerais, Brazil
| | - Erica A Costa
- Preventive Veterinary Medicine, Veterinary School, Universidade Federal de Minas Gerais-UFMG, Belo Horizonte, Minas Gerais, Brazil
| | - Mauricio Resende
- Preventive Veterinary Medicine, Veterinary School, Universidade Federal de Minas Gerais-UFMG, Belo Horizonte, Minas Gerais, Brazil
| | - Raphael Wenceslau
- Departments of Veterinary Clinic and Surgery, Veterinary School, Universidade Federal de Minas Gerais-UFMG, Belo Horizonte, Minas Gerais, Brazil
| | - Roselene Ecco
- Departments of Veterinary Clinic and Surgery, Veterinary School, Universidade Federal de Minas Gerais-UFMG, Belo Horizonte, Minas Gerais, Brazil
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14
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Śmiałek M, Gesek M, Dziewulska D, Niczyporuk JS, Koncicki A. Transmissible Viral Proventriculitis Caused by Chicken ProVentricular Necrosis Virus Displaying Serological Cross-Reactivity with IBDV. Animals (Basel) 2020; 11:ani11010008. [PMID: 33374720 PMCID: PMC7822447 DOI: 10.3390/ani11010008] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2020] [Revised: 12/17/2020] [Accepted: 12/20/2020] [Indexed: 11/16/2022] Open
Abstract
Transmissible viral proventriculitis (TVP) of chickens is manifested in decreased body weight gains, poor feed conversion and weight diversity. Although TVP etiology has not been defined, a Birnaviridae family member, named chicken proventricular necrosis virus (CPNV) is considered as a potential factor of a disease. This study was undertaken in order to reproduce TVP and to evaluate its etiology. Broiler chickens of the TVP-infected group were inoculated with TVP positive proventriculi homogenate on the 24th day of life. Samples were collected, on infection day and 14 days post-infection (dpi). The 14 dpi anatomo- and histopathological evaluation, revealed that we have succeeded to reproduce TVP. TVP-infected birds gained 30.38% less body weight. In the TVP-infected group a seroconversion against picornaviruses, fowl adenoviruses (FAdV) and infectious bursal disease viruses (IBDV) was recorded with an ELISA test. Using RT-PCR and PCR, CPNV was detected in proventriculi and FAdV in spleens and livers of infected birds, 14 dpi. Our study supports that CPNV is involved in the development of TVP. We did not record the presence of IBDV in TVP or control birds, despite our recording of a seroconversion against IBDV in TVP infected birds. CPNV and IBDV belong to the same family, which allows us to assume serological cross-reactivity between them. The role of FAdV needs further evaluation.
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Affiliation(s)
- Marcin Śmiałek
- Department of Avian Disease, Faculty of Veterinary Medicine, University of Warmia and Mazury, ul. Oczapowskiego 13/14, 10-719 Olsztyn, Poland; (D.D.); (A.K.)
- Correspondence:
| | - Michał Gesek
- Department of Pathological Anatomy, Faculty of Veterinary Medicine, University of Warmia and Mazury, ul. Oczapowskiego 13, 10-719 Olsztyn, Poland;
| | - Daria Dziewulska
- Department of Avian Disease, Faculty of Veterinary Medicine, University of Warmia and Mazury, ul. Oczapowskiego 13/14, 10-719 Olsztyn, Poland; (D.D.); (A.K.)
| | - Jowita Samanta Niczyporuk
- Department of Poultry Diseases, National Veterinary Research Institute in Puławy, 57 Partyzantów Avenue, 24-100 Puławy, Poland;
| | - Andrzej Koncicki
- Department of Avian Disease, Faculty of Veterinary Medicine, University of Warmia and Mazury, ul. Oczapowskiego 13/14, 10-719 Olsztyn, Poland; (D.D.); (A.K.)
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15
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Genome Sequences of Seven Megrivirus Strains from Chickens in The Netherlands. Microbiol Resour Announc 2020; 9:9/47/e01207-20. [PMID: 33214312 PMCID: PMC7679105 DOI: 10.1128/mra.01207-20] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Abstract
We report seven chicken megrivirus genome sequences identified in chicken fecal samples from a broiler farm in the Netherlands. The sequences were determined using metagenomic sequencing and would expand our understanding of the genome diversity of megriviruses. We report seven chicken megrivirus genome sequences identified in chicken fecal samples from a broiler farm in The Netherlands. The sequences were determined using metagenomic sequencing and would expand our understanding of the genome diversity of megriviruses.
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16
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Yan T, Li G, Zhou D, Yang X, Hu L, Cheng Z. Novel Cyclovirus Identified in Broiler Chickens With Transmissible Viral Proventriculitis in China. Front Vet Sci 2020; 7:569098. [PMID: 33134354 PMCID: PMC7550471 DOI: 10.3389/fvets.2020.569098] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2020] [Accepted: 08/18/2020] [Indexed: 11/30/2022] Open
Abstract
In October 2018, an outbreak of transmissible viral proventriculitis (TVP) occurred in 30-day-old commercial broiler chickens on a farm in Weifang, China. TVP, an infectious viral disease characterized by runting and stunting, is associated with many viruses, and has a significant economic impact on the global poultry industry. TVP is diagnosed according to clinical symptoms, gross and histological lesions, and negative PCR results for pathogenic bacteria, avian leukosis virus subgroup J, Marek's disease virus, reticuloendotheliosis virus, infectious bursa disease virus, avian reovirus, chicken anemia virus, infectious bronchitis virus, chicken proventricular necrosis virus, gyrovirus 3 and chicken circovirus. To further detect the possible causative pathogens of TVP, we used PacBio third-generation sequencing to examine proventricular samples. A dominant abundance of the novel cyclovirus (CyCV), chCyCV-SDAU-1, was identified in broilers with TVP. The complete chCyCV-SDAU-1 genome was verified via inverse PCR, was 1936 bp long, and consisted of Rep, Cp, and two intergenic regions. Phylogenetic tree analysis showed that chCyCV-SDAU-1 formed an independent branch with other cycloviruses. The homology of chCyCV-SDAU-1 with 20 others known cycloviruses was < 40%. Retrospective investigation showed that the CyCV infection rate in the broilers with TVP was 80% (16/20), while no CyCV was found in healthy chickens. In conclusion, a novel CyCV was identified in chickens with TVP, though its role in this disease is unclear.
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Affiliation(s)
- Tianxing Yan
- College of Veterinary Medicine, Shandong Agricultural University, Tai'an, China
| | - Gen Li
- College of Veterinary Medicine, Shandong Agricultural University, Tai'an, China.,College of Veterinary Medicine, Qingdao Agricultural University, Qingdao, China
| | - Defang Zhou
- College of Veterinary Medicine, Shandong Agricultural University, Tai'an, China
| | - Xiaoxia Yang
- Hospital of Shandong Agricultural University, Tai'an, China
| | - Liping Hu
- Animal Epidemic Prevention and Control Center of Shandong Province, Jinan, China
| | - Ziqiang Cheng
- College of Veterinary Medicine, Shandong Agricultural University, Tai'an, China
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17
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Kim HR, Kwon YK, Jang I, Bae YC. Viral metagenomic analysis of chickens with runting-stunting syndrome in the Republic of Korea. Virol J 2020; 17:53. [PMID: 32293477 PMCID: PMC7157833 DOI: 10.1186/s12985-020-01307-z] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2019] [Accepted: 02/27/2020] [Indexed: 12/27/2022] Open
Abstract
Background and aims Runting-stunting syndrome (RSS) in chickens, also known as malabsorption syndrome, which is characterized by mild to severe enteritis and diagnosed through typical histopathologic examination as well as clinical signs, results in considerable economic losses. Despite the many studies carried out over decades to determine the etiologic agents of RSS involved in the disease, several outbreaks remained without the elucidation of, potentially multiple, etiologies involved. Methods We performed comparative analysis of viral metagenomes from four chicken flocks affected with RSS using next-generation sequencing. Primers for the detection of chicken enteric viruses were designed from the sequencing data obtained with metagenomics. Multiplex reverse transcription–polymerase chain reaction (PCR) and PCR were performed to detect a variety of etiological agents previously described in natural cases of RSS. Results The most abundant viral families identified in this study were Astroviridae, Picornaviridae, Parvoviridae, Caliciviridae, Reoviridae and Picobirnaviridae. Chicken astrovirus sequences were present in all four samples, suggesting an association between chicken astrovirus and RSS and chicken astrovirus as a candidate pathogen responsible for RSS. Picobirnavirus and the newly identified chapparvovirus were found in chickens in the Republic of Korea for the first time, and the genetic diversity of enteric viruses and viral communities was showed. Conclusions Chicken astrovirus was consistently detected in broilers affected with RSS and the result of this study may contribute to knowledge of enteric diseases and viruses in chickens.
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Affiliation(s)
- Hye-Ryoung Kim
- Animal and Plant Quarantine Agency, 177 Hyeoksin 8-ro, Gimcheon-si, Gyeongsangbuk-do, 39660, Republic of Korea.
| | - Yong-Kuk Kwon
- Animal and Plant Quarantine Agency, 177 Hyeoksin 8-ro, Gimcheon-si, Gyeongsangbuk-do, 39660, Republic of Korea
| | - Il Jang
- Animal and Plant Quarantine Agency, 177 Hyeoksin 8-ro, Gimcheon-si, Gyeongsangbuk-do, 39660, Republic of Korea
| | - You-Chan Bae
- Animal and Plant Quarantine Agency, 177 Hyeoksin 8-ro, Gimcheon-si, Gyeongsangbuk-do, 39660, Republic of Korea
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18
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Virus Metagenomics in Farm Animals: A Systematic Review. Viruses 2020; 12:v12010107. [PMID: 31963174 PMCID: PMC7019290 DOI: 10.3390/v12010107] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2019] [Revised: 01/12/2020] [Accepted: 01/14/2020] [Indexed: 02/07/2023] Open
Abstract
A majority of emerging infectious diseases are of zoonotic origin. Metagenomic Next-Generation Sequencing (mNGS) has been employed to identify uncommon and novel infectious etiologies and characterize virus diversity in human, animal, and environmental samples. Here, we systematically reviewed studies that performed viral mNGS in common livestock (cattle, small ruminants, poultry, and pigs). We identified 2481 records and 120 records were ultimately included after a first and second screening. Pigs were the most frequently studied livestock and the virus diversity found in samples from poultry was the highest. Known animal viruses, zoonotic viruses, and novel viruses were reported in available literature, demonstrating the capacity of mNGS to identify both known and novel viruses. However, the coverage of metagenomic studies was patchy, with few data on the virome of small ruminants and respiratory virome of studied livestock. Essential metadata such as age of livestock and farm types were rarely mentioned in available literature, and only 10.8% of the datasets were publicly available. Developing a deeper understanding of livestock virome is crucial for detection of potential zoonotic and animal pathogens and One Health preparedness. Metagenomic studies can provide this background but only when combined with essential metadata and following the “FAIR” (Findable, Accessible, Interoperable, and Reusable) data principles.
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19
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Kaszab E, Doszpoly A, Lanave G, Verma A, Bányai K, Malik YS, Marton S. Metagenomics revealing new virus species in farm and pet animals and aquaculture. GENOMICS AND BIOTECHNOLOGICAL ADVANCES IN VETERINARY, POULTRY, AND FISHERIES 2020. [PMCID: PMC7149329 DOI: 10.1016/b978-0-12-816352-8.00002-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 10/31/2022]
Abstract
Viral metagenomics is slowly taking over the traditional and widely used molecular techniques for the investigation of pathogenic viruses responsible for illness and inflicting great economic burden on the farm animal industry. Owing to the continued improvements in sequencing technologies and the dramatic reduction of per base costs of sequencing the use of next generation sequencing have been key factors in this progress. Discoveries linked to viral metagenomics are expected to be beneficial to the field of veterinary medicine starting from the development of better diagnostic assays to the design of new subunit vaccines with minimal investments. With these achievements the research has taken a giant leap even toward the better healthcare of animals and, as a result, the animal sector could be growing at an unprecedented pace.
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20
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Grau-Roma L, Schock A, Nofrarías M, Ali Wali N, de Fraga AP, Garcia-Rueda C, de Brot S, Majó N. Retrospective study on transmissible viral proventriculitis and chicken proventricular necrosis virus (CPNV) in the UK. Avian Pathol 2019; 49:99-105. [PMID: 31591909 DOI: 10.1080/03079457.2019.1677856] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
Chicken proventricular necrosis virus (CPNV) is a recently described birnavirus, which has been proposed to be the cause of transmissible viral proventriculitis (TVP). The understanding of the epidemiology of both the virus and the disease is very limited. A retrospective investigation on TVP and CPNV in broiler chicken submissions from the UK from between 1994 and 2015 was performed with the aims of assessing the longitudinal temporal evolution of TVP and CPNV, and to review the histological proventricular lesions in the studied chickens. Ninety-nine of the 135 included submissions (73.3%) fulfilled the TVP-diagnostic criteria, while the remaining 36 submissions (26.7%) displayed only lymphocytic proventriculitis (LP). The first detection of CPNV by PCR dated from 2009. Results showed a rise in the number of both TVP and positive CPNV RT-PCR submissions from 2009 with a peak in 2013, suggesting that they may be an emerging or re-emerging disease and pathogen, respectively. Twenty-two out of the 99 submissions displaying TVP lesions (22%) and four out of the 36 (11%) submissions with LP gave positive CPNV RT-PCR results, further supporting the association between CPNV and TVP and confirming that CPNV is present in a low proportion of proventriculi that do not fulfil the TVP-diagnostic criteria. In addition, intranuclear inclusion bodies were observed in 22 of the submissions with TVP. The vast majority of these cases (21 of 22, 96%) gave negative CPNV RT-PCR results, raising the question of whether a virus other than CPNV is responsible for some of these TVP-affected cases.RESEARCH HIGHLIGHTSTVP and CPNV have been present in British broilers since at least 1994 and 2009, respectively.TVP and CPNV seem to be an emerging and re-emerging disease and pathogen, respectively.CPNV was detected in proventriculi with both TVP and LP-lesions.Viruses other than CPNV may be responsible for some TVP-affected cases.
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Affiliation(s)
- Llorenç Grau-Roma
- School of Veterinary Medicine and Science (SVMS), University of Nottingham, Loughborough, UK.,Institute of Animal Pathology, University of Bern, Bern, Switzerland
| | - Alex Schock
- Avian Pathology, Animal and Plant Health Agency (APHA), Penicuik, UK
| | - Miquel Nofrarías
- IRTA, Centre de Recerca en Sanitat Animal (CReSA, IRTA-UAB), Barcelona, Spain
| | - Nabil Ali Wali
- IRTA, Centre de Recerca en Sanitat Animal (CReSA, IRTA-UAB), Barcelona, Spain
| | - Aline Padilha de Fraga
- Laboratório de Diagnóstico Molecular, Universidade Luterana do Brasil, Rio Grande do Sul, Brazil
| | | | - Simone de Brot
- School of Veterinary Medicine and Science (SVMS), University of Nottingham, Loughborough, UK.,Institute of Animal Pathology, University of Bern, Bern, Switzerland
| | - Natalia Majó
- IRTA, Centre de Recerca en Sanitat Animal (CReSA, IRTA-UAB), Barcelona, Spain.,Departament de Sanitat i Anatomia Animals, Universitat Autònoma de Barcelona, Barcelona, Spain
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21
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Li G, Yuan S, He M, Zhao M, Hao X, Song M, Zhang L, Qiao C, Huang L, Zhang L, Li C, Wang G, Cheng Z. Emergence of gyrovirus 3 in commercial broiler chickens with transmissible viral proventriculitis. Transbound Emerg Dis 2018; 65:1170-1174. [DOI: 10.1111/tbed.12927] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2018] [Revised: 05/04/2018] [Accepted: 05/23/2018] [Indexed: 11/27/2022]
Affiliation(s)
- Gen Li
- College of Veterinary Medicine; Shandong Agricultural University; Tai'an China
| | - Shiyu Yuan
- College of Veterinary Medicine; Shandong Agricultural University; Tai'an China
| | - Menglian He
- College of Veterinary Medicine; Shandong Agricultural University; Tai'an China
- Department of Animal Science and Technology; Vocational-technical school of Husbandry and Veterinary Medicine; Weifang China
| | - Manda Zhao
- Department of Animal Science and Technology; Vocational-technical school of Husbandry and Veterinary Medicine; Weifang China
| | - Xiaojing Hao
- Qindao husbandry and Veterinary Institute; Qingdao China
| | - Minxun Song
- Poultry Institute of Shandong Agricultural Science Academy; Jinan China
| | - Lingjuan Zhang
- Animal Diseases Control and Prevention Center in Penglai; Yantai China
| | | | - Libo Huang
- College of Veterinary Medicine; Shandong Agricultural University; Tai'an China
| | - Li Zhang
- College of Veterinary Medicine; Shandong Agricultural University; Tai'an China
| | - Chengui Li
- College of Veterinary Medicine; Shandong Agricultural University; Tai'an China
| | - Guihua Wang
- College of Veterinary Medicine; Shandong Agricultural University; Tai'an China
| | - Ziqiang Cheng
- College of Veterinary Medicine; Shandong Agricultural University; Tai'an China
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22
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Bodewes R. Novel viruses in birds: Flying through the roof or is a cage needed? Vet J 2018; 233:55-62. [PMID: 29486880 DOI: 10.1016/j.tvjl.2017.12.023] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2017] [Revised: 09/28/2017] [Accepted: 12/28/2017] [Indexed: 01/17/2023]
Abstract
Emerging viral diseases continue to have a major global impact on human beings and animals. To be able to take adequate measures in case of an outbreak of an emerging disease, rapid detection of the causative agent is a crucial first step. In this review, various aspects of virus discovery are discussed, with a special focus on recently discovered viruses in birds. Novel viruses with a potential major impact have been discovered in domestic and wild bird species in recent years using various virus discovery methods. Only a few studies report the detection of novel viruses in endangered bird species, although increased knowledge about viruses circulating in these species is important. Additional studies focusing on the exact role of a novel virus in disease and on the impact of a novel virus on bird populations are often lacking. Intensive collaboration between different disciplines is needed to obtain useful information about the role of these novel viruses.
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Affiliation(s)
- R Bodewes
- Department of Farm Animal Health, Faculty of Veterinary Medicine, Utrecht University, Utrecht, The Netherlands.
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23
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Boros Á, Pankovics P, Mátics R, Adonyi Á, Bolba N, Phan TG, Delwart E, Reuter G. Genome characterization of a novel megrivirus-related avian picornavirus from a carnivorous wild bird, western marsh harrier (Circus aeruginosus). Arch Virol 2017; 162:2781-2789. [PMID: 28500443 DOI: 10.1007/s00705-017-3403-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2017] [Accepted: 04/04/2017] [Indexed: 11/29/2022]
Abstract
In this study, the complete genome of a novel picornavirus called harrier picornavirus 1 (HaPV-1) strain harrier/MR-01/HUN/2014 (KY488458) was sequenced and analysed from a cloacal sample of a threatened, carnivorous wild bird, western marsh harrier (Circus aeruginosus). HaPV-1 was detectable from 2 of the 3 samples from harriers. HaPV-1 is phylogenetically related to megriviruses (genus Megrivirus) from domestic chicken, turkey and duck, showing a similar genome organization pattern; it also has an avian picornavirus-like "Unit A" motif in the 3' UTR. Unlike the type-IV internal ribosomal entry site (IRES) of megriviruses, HaPV-1 is predicted to contain a type-II-like IRES, suggesting modular exchange of IRES elements between picornavirus genomes.
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Affiliation(s)
- Ákos Boros
- Regional Laboratory of Virology, National Reference Laboratory of Gastroenteric Viruses, ÁNTSZ Regional Institute of State Public Health Service, Pécs, Hungary.,Department of Medical Microbiology and Immunology, Medical School, University of Pécs, Szigeti út 12, Pécs, 7624, Hungary
| | - Péter Pankovics
- Regional Laboratory of Virology, National Reference Laboratory of Gastroenteric Viruses, ÁNTSZ Regional Institute of State Public Health Service, Pécs, Hungary.,Department of Medical Microbiology and Immunology, Medical School, University of Pécs, Szigeti út 12, Pécs, 7624, Hungary
| | - Róbert Mátics
- Hungarian Nature Research Society (HuNaReS), Ajka, Hungary.,Department of Pathophysiology, University of Pécs Medical Center, Pécs, Hungary
| | - Ádám Adonyi
- Regional Laboratory of Virology, National Reference Laboratory of Gastroenteric Viruses, ÁNTSZ Regional Institute of State Public Health Service, Pécs, Hungary
| | - Nóra Bolba
- Regional Laboratory of Virology, National Reference Laboratory of Gastroenteric Viruses, ÁNTSZ Regional Institute of State Public Health Service, Pécs, Hungary.,Department of Medical Microbiology and Immunology, Medical School, University of Pécs, Szigeti út 12, Pécs, 7624, Hungary
| | - Tung Gia Phan
- Blood Systems Research Institute, San Francisco, CA, USA.,University of California, San Francisco, CA, USA
| | - Eric Delwart
- Blood Systems Research Institute, San Francisco, CA, USA.,University of California, San Francisco, CA, USA
| | - Gábor Reuter
- Regional Laboratory of Virology, National Reference Laboratory of Gastroenteric Viruses, ÁNTSZ Regional Institute of State Public Health Service, Pécs, Hungary. .,Department of Medical Microbiology and Immunology, Medical School, University of Pécs, Szigeti út 12, Pécs, 7624, Hungary.
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24
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Lima DA, Cibulski SP, Finkler F, Teixeira TF, Varela APM, Cerva C, Loiko MR, Scheffer CM, Dos Santos HF, Mayer FQ, Roehe PM. Faecal virome of healthy chickens reveals a large diversity of the eukaryote viral community, including novel circular ssDNA viruses. J Gen Virol 2017; 98:690-703. [PMID: 28100302 DOI: 10.1099/jgv.0.000711] [Citation(s) in RCA: 46] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
This study is focused on the identification of the faecal virome of healthy chickens raised in high-density, export-driven poultry farms in Brazil. Following high-throughput sequencing, a total of 7743 de novo-assembled contigs were constructed and compared with known nucleotide/amino acid sequences from the GenBank database. Analyses with blastx revealed that 279 contigs (4 %) were related to sequences of eukaryotic viruses. Viral genome sequences (total or partial) indicative of members of recognized viral families, including Adenoviridae, Caliciviridae, Circoviridae, Parvoviridae, Picobirnaviridae, Picornaviridae and Reoviridae, were identified, some of those representing novel genotypes. In addition, a range of circular replication-associated protein encoding DNA viruses were also identified. The characterization of the faecal virome of healthy chickens described here not only provides a description of the viruses encountered in such niche but should also represent a baseline for future studies comparing viral populations in healthy and diseased chicken flocks. Moreover, it may also be relevant for human health, since chickens represent a significant proportion of the animal protein consumed worldwide.
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Affiliation(s)
- Diane A Lima
- FEPAGRO Saúde Animal - Instituto de Pesquisas Veterinárias Desidério Finamor (IPVDF), Rio Grande do Sul, Brazil.,Laboratório de Virologia, Departamento de Microbiologia, Imunologia e Parasitologia, Instituto de Ciências Básicas da Saúde (ICBS), Universidade Federal do Rio Grande do Sul (UFRGS), Rio Grande do Sul, Brazil
| | - Samuel P Cibulski
- Laboratório de Virologia, Faculdade de Veterinária, Universidade Federal do Rio Grande do Sul, Rio Grande do Sul, Brazil
| | - Fabrine Finkler
- FEPAGRO Saúde Animal - Instituto de Pesquisas Veterinárias Desidério Finamor (IPVDF), Rio Grande do Sul, Brazil.,Laboratório de Virologia, Departamento de Microbiologia, Imunologia e Parasitologia, Instituto de Ciências Básicas da Saúde (ICBS), Universidade Federal do Rio Grande do Sul (UFRGS), Rio Grande do Sul, Brazil
| | - Thais F Teixeira
- FEPAGRO Saúde Animal - Instituto de Pesquisas Veterinárias Desidério Finamor (IPVDF), Rio Grande do Sul, Brazil.,Laboratório de Virologia, Departamento de Microbiologia, Imunologia e Parasitologia, Instituto de Ciências Básicas da Saúde (ICBS), Universidade Federal do Rio Grande do Sul (UFRGS), Rio Grande do Sul, Brazil
| | - Ana Paula M Varela
- FEPAGRO Saúde Animal - Instituto de Pesquisas Veterinárias Desidério Finamor (IPVDF), Rio Grande do Sul, Brazil.,Laboratório de Virologia, Departamento de Microbiologia, Imunologia e Parasitologia, Instituto de Ciências Básicas da Saúde (ICBS), Universidade Federal do Rio Grande do Sul (UFRGS), Rio Grande do Sul, Brazil
| | - Cristine Cerva
- FEPAGRO Saúde Animal - Instituto de Pesquisas Veterinárias Desidério Finamor (IPVDF), Rio Grande do Sul, Brazil.,Laboratório de Virologia, Departamento de Microbiologia, Imunologia e Parasitologia, Instituto de Ciências Básicas da Saúde (ICBS), Universidade Federal do Rio Grande do Sul (UFRGS), Rio Grande do Sul, Brazil
| | - Márcia R Loiko
- FEPAGRO Saúde Animal - Instituto de Pesquisas Veterinárias Desidério Finamor (IPVDF), Rio Grande do Sul, Brazil.,Laboratório de Virologia, Departamento de Microbiologia, Imunologia e Parasitologia, Instituto de Ciências Básicas da Saúde (ICBS), Universidade Federal do Rio Grande do Sul (UFRGS), Rio Grande do Sul, Brazil
| | - Camila M Scheffer
- FEPAGRO Saúde Animal - Instituto de Pesquisas Veterinárias Desidério Finamor (IPVDF), Rio Grande do Sul, Brazil.,Laboratório de Virologia, Departamento de Microbiologia, Imunologia e Parasitologia, Instituto de Ciências Básicas da Saúde (ICBS), Universidade Federal do Rio Grande do Sul (UFRGS), Rio Grande do Sul, Brazil
| | - Helton F Dos Santos
- FEPAGRO Saúde Animal - Instituto de Pesquisas Veterinárias Desidério Finamor (IPVDF), Rio Grande do Sul, Brazil.,Laboratório de Virologia, Departamento de Microbiologia, Imunologia e Parasitologia, Instituto de Ciências Básicas da Saúde (ICBS), Universidade Federal do Rio Grande do Sul (UFRGS), Rio Grande do Sul, Brazil
| | - Fabiana Q Mayer
- FEPAGRO Saúde Animal - Instituto de Pesquisas Veterinárias Desidério Finamor (IPVDF), Rio Grande do Sul, Brazil
| | - Paulo M Roehe
- FEPAGRO Saúde Animal - Instituto de Pesquisas Veterinárias Desidério Finamor (IPVDF), Rio Grande do Sul, Brazil.,Laboratório de Virologia, Departamento de Microbiologia, Imunologia e Parasitologia, Instituto de Ciências Básicas da Saúde (ICBS), Universidade Federal do Rio Grande do Sul (UFRGS), Rio Grande do Sul, Brazil
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25
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Wang F, Liang T, Liu N, Ning K, Yu K, Zhang D. Genetic characterization of two novel megriviruses in geese. J Gen Virol 2017; 98:607-611. [DOI: 10.1099/jgv.0.000720] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Fumin Wang
- Key Laboratory of Animal Epidemiology and Zoonosis of Ministry of Agriculture, College of Veterinary Medicine, China Agricultural University, Beijing 100193, PR China
| | - Te Liang
- Key Laboratory of Animal Epidemiology and Zoonosis of Ministry of Agriculture, College of Veterinary Medicine, China Agricultural University, Beijing 100193, PR China
| | - Ning Liu
- Key Laboratory of Animal Epidemiology and Zoonosis of Ministry of Agriculture, College of Veterinary Medicine, China Agricultural University, Beijing 100193, PR China
| | - Kang Ning
- Key Laboratory of Animal Epidemiology and Zoonosis of Ministry of Agriculture, College of Veterinary Medicine, China Agricultural University, Beijing 100193, PR China
| | - Kangzhen Yu
- The Ministry of Agriculture of the People’s Republic of China, Beijing 100026, PR China
| | - Dabing Zhang
- Key Laboratory of Animal Epidemiology and Zoonosis of Ministry of Agriculture, College of Veterinary Medicine, China Agricultural University, Beijing 100193, PR China
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26
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Grau-Roma L, Reid K, de Brot S, Jennison R, Barrow P, Sánchez R, Nofrarías M, Clark M, Majó N. Detection of transmissible viral proventriculitis and chicken proventricular necrosis virus in the UK. Avian Pathol 2016; 46:68-75. [PMID: 27400318 DOI: 10.1080/03079457.2016.1207751] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
Increasing evidence suggests that a new birnavirus, named chicken proventricular necrosis virus (CPNV), is the aetiological agent of transmissible viral proventriculitis (TVP). The present work aimed to explore the possible presence of both TVP and CPNV in the UK. Forty-four chickens showing TVP-compatible gross lesions were classified into three groups based on the histological lesions: (i) TVP-affected chickens: lymphocytic infiltration and glandular necrosis (n = 15); (ii) lymphocytic proventriculitis (LP)-affected chickens: lymphocytic infiltration without necrosis (n = 18); and (iii) without proventriculitis (WP): no lymphocytic infiltration or necrosis (n = 11). Nine proventriculi (seven out of 15 corresponding to TVP, and two out of 11 corresponding to LP) were positive for CPNV by reverse transcriptase polymerase chain reaction (RT-PCR). These results support the previously suggested idea of CPNV as causative agent of TVP. Moreover, these data show that CPNV can also be detected in a number of cases with LP, which do not fulfil the histological TVP criteria. Phylogenetic analysis of partial sequences of gene VP1 showed that British CPNV sequences were closer to other European CPNV sequences and might constitute a different lineage from the American CPNV. TVP cases with negative CPNV PCR results may be due to chronic stages of the disease or to the reduced PCR sensitivity on formalin-fixed paraffin-embedded tissues. However, involvement of other agents in some of the cases cannot totally be ruled out. As far as the authors are aware, this is the first peer-reviewed report of TVP as well as of CPNV in the UK, and the first exploratory CPNV phylogenetic study.
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Affiliation(s)
- Llorenç Grau-Roma
- a School of Veterinary Medicine and Science (SVMS) , University of Nottingham (UoN) , Loughborough , UK
| | - Kirsty Reid
- a School of Veterinary Medicine and Science (SVMS) , University of Nottingham (UoN) , Loughborough , UK
| | - Simone de Brot
- a School of Veterinary Medicine and Science (SVMS) , University of Nottingham (UoN) , Loughborough , UK
| | | | - Paul Barrow
- a School of Veterinary Medicine and Science (SVMS) , University of Nottingham (UoN) , Loughborough , UK
| | - Raúl Sánchez
- c IRTA, Centre de Recerca en Sanitat Animal (CReSA, IRTA-UAB) , Barcelona , Spain
| | - Miquel Nofrarías
- c IRTA, Centre de Recerca en Sanitat Animal (CReSA, IRTA-UAB) , Barcelona , Spain
| | - Mike Clark
- a School of Veterinary Medicine and Science (SVMS) , University of Nottingham (UoN) , Loughborough , UK
| | - Natàlia Majó
- c IRTA, Centre de Recerca en Sanitat Animal (CReSA, IRTA-UAB) , Barcelona , Spain.,d Departament de Sanitat i Anatomia Animals , Universitat Autònoma de Barcelona , Barcelona , Spain
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27
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Day JM, Zsak L. Molecular Characterization of Enteric Picornaviruses in Archived Turkey and Chicken Samples from the United States. Avian Dis 2016; 60:500-5. [PMID: 27309295 DOI: 10.1637/11289-092415-resnote] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
Recent metagenomic analyses of the enteric viromes in turkeys and chickens have revealed complex viral communities comprised of multiple viral families. Of particular significance are the novel avian picobirnaviruses (family Picobirnaviridae), multiple genera of tailed phages (family Siphoviridae), and undescribed avian enteric picornaviruses (family Picornaviridae). In addition to these largely undescribed-and therefore relatively poorly understood-poultry enteric viral families, these metagenomic analyses have also revealed the presence of well-known groups of enteric viruses such as the chicken and turkey astroviruses (family Astroviridae) and the avian rotaviruses and reoviruses (family Reoviridae). The order Picornavirales is a group of viruses in flux, particularly among the avian picornaviruses, since several new genera have been described recently based upon community analysis of enteric viromes from poultry and other avian species worldwide. Our previous investigation of the turkey enteric picornaviruses suggests the avian enteric picornaviruses may contribute to the enteric disease syndromes and performance problems often observed in turkeys in the Southeastern United States. This report describes our recent phylogenetic analysis of turkey and chicken enteric samples archived at the Southeast Poultry Research Laboratory from 2004 to present and is a first step in placing these novel avian picornaviruses within the larger Picornaviridae family.
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Affiliation(s)
- J Michael Day
- A USDA/ARS, U.S. National Poultry Research Center, Southeast Poultry Research Laboratory, 934 College Station Road, Athens, GA 30605
| | - Laszlo Zsak
- A USDA/ARS, U.S. National Poultry Research Center, Southeast Poultry Research Laboratory, 934 College Station Road, Athens, GA 30605
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