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Panyako PM, Ommeh SC, Kuria SN, Lichoti JK, Musina J, Nair V, Nene V, Oyola SO, Munir M. Metagenomic characterization reveals virus coinfections associated with Newcastle disease virus among poultry in Kenya. J Basic Microbiol 2023; 63:1383-1396. [PMID: 37821414 DOI: 10.1002/jobm.202300390] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2023] [Revised: 09/20/2023] [Accepted: 10/01/2023] [Indexed: 10/13/2023]
Abstract
Newcastle disease (ND) is an endemic viral disease affecting poultry and causing massive economic losses. This cross-sectional purposive study detected coinfections that are associated with the Newcastle disease virus among poultry from selected regions in Kenya. Cloacal (n = 599) and oral-pharyngeal (n = 435) swab samples were collected and pooled into 17 and 15 samples, respectively. A total of 17,034,948 and 7,751,974 paired-end reads with an average of 200 nucleotides were generated from the cloacal and oral-pharyngeal swab samples, respectively. Analysis of the de novo assembled contigs identified 177 and 18 cloacal and oral-pharyngeal contigs, respectively with hits to viral sequences, as determined by BLASTx and BLASTn analyses. Several known and unknown representatives of Coronaviridae, Picobirnaviridae, Reoviridae, Retroviridae, and unclassified Deltavirus were identified in the cloacal swab samples. However, no Newcastle disease virus (family Paramyxoviridae) was detected in the cloacal swabs, although they were detected in the oropharyngeal swabs of chickens sampled in Nairobi, Busia, and Trans Nzoia. Additionally, sequences representative of Paramyxoviridae, Coronaviridae, and Retroviridae were identified in the oral-pharyngeal swab samples. Infectious bronchitis virus and rotavirus were chickens' most prevalent coinfections associated with the Newcastle disease virus. The detection of these coinfections suggests that these viruses are significant threats to the control of Newcastle disease as the Newcastle disease virus vaccines are known to fail because of these coinfections. Therefore, this study provides important information that will help improve disease diagnosis and vaccine development for coinfections associated with the Newcastle disease virus.
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Affiliation(s)
- Philip M Panyako
- Institute for Biotechnology Research, Jomo Kenyatta University of Agriculture and Technology, Nairobi, Kenya
| | - Sheila C Ommeh
- Institute for Biotechnology Research, Jomo Kenyatta University of Agriculture and Technology, Nairobi, Kenya
| | - Stephen N Kuria
- Institute for Biotechnology Research, Jomo Kenyatta University of Agriculture and Technology, Nairobi, Kenya
| | - Jacqueline K Lichoti
- State Department of Livestock, Ministry of Agriculture, Livestock and Fisheries, Nairobi, Kenya
| | - Johns Musina
- Department of Zoology, National Museums of Kenya, Nairobi, Kenya
| | - Venugopal Nair
- Nuffield Department of Medicine, The Jenner Institute, University of Oxford, Oxford, UK
| | - Vish Nene
- International Livestock Research Institute (ILRI), Nairobi, Kenya
| | - Samuel O Oyola
- International Livestock Research Institute (ILRI), Nairobi, Kenya
| | - Muhammad Munir
- Department of Biomedical and Life Sciences, Lancaster University, Lancaster, UK
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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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3
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Ali MZ, Moula MM, Bhuiyan ZA, Giasuddin M, Shin HJ. First Isolation and Molecular Characterization of Chicken Astrovirus and Avian Nephritis Virus in Chickens in Bangladesh. Front Vet Sci 2021; 8:769489. [PMID: 34926641 PMCID: PMC8672296 DOI: 10.3389/fvets.2021.769489] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2021] [Accepted: 11/04/2021] [Indexed: 11/13/2022] Open
Abstract
Chicken astrovirus (CAstV) and avian nephritis virus (ANV) are enteric viruses of poultry and have infected a wide range of poultry species worldwide, causing runting-stunting syndrome (RSS), which requires virus screening and results in serious economic damage. No confirmed cases have been reported from Bangladesh. In the present study, CAstV and ANV were monitored in Bangladesh. We monitored samples for CAstV and ANV and compared their genomic sequences to other reference strains. We found 8/31 flocks (25.8%) were positive for CAstV, 6/31 flocks (19.3%) had mixed infection of CAstV and ANV, and 1 flock (3.2%) was positive for ANV. Only ANV and a combination of CAstV and ANV were found in broilers and broiler breeders, but CAstV was found in all types of chickens. We isolated two of each from CAstV and ANV through specific pathogen-free chicken embryonated eggs via the yolk sac route. Phylogenetic analysis based on the ORF1b conserved region of CAstV and ANV suggested that the locally circulating strain was closely related to the strains isolated from India and Brazil. This report is the first molecular characterization of CAstV and ANV in Bangladesh. This study highlights that CAstV and ANV are circulating in Bangladeshi poultry.
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Affiliation(s)
- Md Zulfekar Ali
- Animal Health Research Division, Bangladesh Livestock Research Institute, Dhaka, Bangladesh
| | | | - Zafar Ahmed Bhuiyan
- Nourish Central Poultry Laboratory, Nourish Poultry and Hatchery Ltd., Dhaka, Bangladesh
| | - Md Giasuddin
- Animal Health Research Division, Bangladesh Livestock Research Institute, Dhaka, Bangladesh
| | - Hyun-Jin Shin
- College of Veterinary Medicine, Chungnam National University, Daejeon, South Korea.,Research Institute of Veterinary Medicine, Chungnam National University, Daejeon, South Korea
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Aruwa CE, Pillay C, Nyaga MM, Sabiu S. Poultry gut health - microbiome functions, environmental impacts, microbiome engineering and advancements in characterization technologies. J Anim Sci Biotechnol 2021; 12:119. [PMID: 34857055 PMCID: PMC8638651 DOI: 10.1186/s40104-021-00640-9] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2021] [Accepted: 10/01/2021] [Indexed: 12/12/2022] Open
Abstract
The gastrointestinal tract (GIT) health impacts animal productivity. The poultry microbiome has functions which range from protection against pathogens and nutrients production, to host immune system maturation. Fluctuations in the microbiome have also been linked to prevailing environmental conditions. Healthy poultry birds possess a natural resistance to infection. However, the exploration of environmental impacts and other relevant factors on poultry growth and health have been underplayed. Since good performance and growth rate are central to animal production, the host-microbiome relationship remains integral. Prior to the emergence of metagenomic techniques, conventional methods for poultry microbiome studies were used and were low-throughput and associated with insufficient genomic data and high cost of sequencing. Fortunately, the advent of high-throughput sequencing platforms have circumvented some of these shortfalls and paved the way for increased studies on the poultry gut microbiome diversity and functions. Here, we give an up-to-date review on the impact of varied environments on microbiome profile, as well as microbiome engineering and microbiome technology advancements. It is hoped that this paper will provide invaluable information that could guide and inspire further studies on the lingering pertinent questions about the poultry microbiome.
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Affiliation(s)
- Christiana Eleojo Aruwa
- Department of Biotechnology and Food Science, Faculty of Applied Sciences, Durban University of Technology, P.O. Box 1334, Durban, 4000, South Africa
| | - Charlene Pillay
- Department of Biotechnology and Food Science, Faculty of Applied Sciences, Durban University of Technology, P.O. Box 1334, Durban, 4000, South Africa
| | - Martin M Nyaga
- Next Generation Sequencing Unit, Division of Virology, Faculty of Heath Sciences, University of the Free State, Bloemfontein, South Africa
| | - Saheed Sabiu
- Department of Biotechnology and Food Science, Faculty of Applied Sciences, Durban University of Technology, P.O. Box 1334, Durban, 4000, South Africa.
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Islam MR, Martinez-Soto CE, Lin JT, Khursigara CM, Barbut S, Anany H. A systematic review from basics to omics on bacteriophage applications in poultry production and processing. Crit Rev Food Sci Nutr 2021:1-33. [PMID: 34609270 DOI: 10.1080/10408398.2021.1984200] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
The growing human population is currently facing an unprecedented challenge on global food production and sustainability. Despite recognizing poultry as one of the most successful and rapidly growing food industries to address this challenge; poultry health and safety remain major issues that entail immediate attention. Bacterial diseases including colibacillosis, salmonellosis, and necrotic enteritis have become increasingly prevalent during poultry production. Likewise, outbreaks caused by consumption of undercooked poultry products contaminated with zoonotic bacterial pathogens such as Salmonella, Campylobacter and Listeria, are a serious public health concern. With antimicrobial resistance problem and restricted use of antibiotics in food producing animals, bacteriophages are increasingly recognized as an attractive natural antibacterial alternative. Bacteriophages have recently shown promising results to treat diseases in poultry, reduce contamination of carcasses, and enhance the safety of poultry products. Omics technologies have been successfully employed to accurately characterize bacteriophages and their genes/proteins important for interaction with bacterial hosts. In this review, the potential of using lytic bacteriophages to mitigate the risk of major poultry-associated bacterial pathogens are explored. This study also explores challenges associated with the adoption of this technology by industries. Furthermore, the impact of omics approaches on studying bacteriophages, their host interaction and applications is discussed.
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Affiliation(s)
- Md Rashedul Islam
- Guelph Research and Development Centre, Agriculture and Agri-Food Canada, Guelph, Ontario, Canada
| | - Carlos E Martinez-Soto
- Guelph Research and Development Centre, Agriculture and Agri-Food Canada, Guelph, Ontario, Canada.,Department of Food Science, University of Guelph, Guelph, Ontario, Canada
| | - Janet T Lin
- Guelph Research and Development Centre, Agriculture and Agri-Food Canada, Guelph, Ontario, Canada
| | - Cezar M Khursigara
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario, Canada
| | - Shai Barbut
- Department of Food Science, University of Guelph, Guelph, Ontario, Canada
| | - Hany Anany
- Guelph Research and Development Centre, Agriculture and Agri-Food Canada, Guelph, Ontario, Canada.,Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario, Canada.,Department of Food Science, University of Guelph, Guelph, Ontario, Canada
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6
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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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7
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François S, Pybus OG. Towards an understanding of the avian virome. J Gen Virol 2020; 101:785-790. [PMID: 32519942 PMCID: PMC7641393 DOI: 10.1099/jgv.0.001447] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2020] [Accepted: 05/21/2020] [Indexed: 02/06/2023] Open
Abstract
The last two decades have seen the rise of viromics, the study of viral communities through the detection and characterization of virus genome sequences. Here we systematically review and summarize the scope and limitations of our current understanding of avian viromes, in both domesticated and wild-bird populations. We compare this viromic work to the broader literature on avian prokaryotic microbiomes, and highlight the growing importance of structured sampling and experimental design for testing explanatory hypotheses. We provide a number of recommendations for sample collection and preliminary data analysis to guide the development of avian viromics. Avian viromes have the potential to inform disease surveillance in poultry and improve our understanding of the risk of zoonotic viruses to human health.
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Affiliation(s)
| | - Oliver G Pybus
- Department of Zoology, University of Oxford, UK
- Department of Pathobiology and Population Sciences, Royal Veterinary College London, UK
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Wan X, Xu L, Sun X, Li H, Yan F, Han R, Li H, Li Z, Tian Y, Liu X, Kang X, Wang Z, Wang Y. Gut microbiota profiles of commercial laying hens infected with tumorigenic viruses. BMC Vet Res 2020; 16:218. [PMID: 32600312 PMCID: PMC7324990 DOI: 10.1186/s12917-020-02430-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2019] [Accepted: 06/15/2020] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Studies have shown that some viral infections cause structural changes in the intestinal microflora, but little is known about the effects of tumorigenic viral infection on the intestinal microflora of chickens. RESULTS A 29-week commercial layer flock positive for avian leukosis virus-J (ALV-J), Marek's disease virus (MDV) and avian reticuloendotheliosis virus (REV) was selected, and fresh fecal samples were collected and examined for the composition of the gut microflora by Illumina sequencing of the V3-V4 region of the 16S rRNA gene. The operational taxonomic units (OTUs) of the fecal microbiota differentiated the chickens infected with only ALV-J and those coinfected with ALV-J and MDV or REV from infection-negative chickens. The enrichment and diversity of cloacal microflora in chickens infected with ALV-J alone were slightly different from those in the infection-negative chickens. However, the diversity of cloacal microflora was significantly increased in chickens coinfected with both ALV-J and MDV or REV. CONCLUSIONS The intestinal microbiota was more strongly disturbed in chickens after coinfection with ALV-J and MDV or REV than after infection with ALV-J alone, and there may be underlying mechanisms by which the capacity for the stabilization of the intestinal flora was impaired due to viral infection and tumorigenesis.
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Affiliation(s)
- Xianhua Wan
- College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zhengzhou, 450000 China
| | - Laipeng Xu
- College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zhengzhou, 450000 China
| | - Xiangli Sun
- College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zhengzhou, 450000 China
| | - Hui Li
- College of Environmental and Resource Sciences, Henan Agricultural University, Zhengzhou, 450000 China
| | - Fengbin Yan
- College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zhengzhou, 450000 China
- Henan Research Center of Germplasm Resources for Poultry, Zhengzhou, 450002 China
| | - Ruili Han
- College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zhengzhou, 450000 China
- Henan Research Center of Germplasm Resources for Poultry, Zhengzhou, 450002 China
| | - Hong Li
- College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zhengzhou, 450000 China
- Henan Research Center of Germplasm Resources for Poultry, Zhengzhou, 450002 China
| | - Zhuanjian Li
- College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zhengzhou, 450000 China
- Henan Research Center of Germplasm Resources for Poultry, Zhengzhou, 450002 China
| | - Yadong Tian
- College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zhengzhou, 450000 China
- Henan Research Center of Germplasm Resources for Poultry, Zhengzhou, 450002 China
| | - Xiaojun Liu
- College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zhengzhou, 450000 China
- Henan Research Center of Germplasm Resources for Poultry, Zhengzhou, 450002 China
| | - Xiangtao Kang
- College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zhengzhou, 450000 China
- Henan Research Center of Germplasm Resources for Poultry, Zhengzhou, 450002 China
| | - Zhenya Wang
- Key Laboratory of “Runliang” Antiviral Medicines Research and Development, Institute of Drug Discovery & Development, Zhengzhou University, Zhengzhou, 450001 China
| | - Yanbin Wang
- College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zhengzhou, 450000 China
- Henan Research Center of Germplasm Resources for Poultry, Zhengzhou, 450002 China
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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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Yuan L, Hensley C, Mahsoub HM, Ramesh AK, Zhou P. Microbiota in viral infection and disease in humans and farm animals. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2020; 171:15-60. [PMID: 32475521 PMCID: PMC7181997 DOI: 10.1016/bs.pmbts.2020.04.005] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
The influence of the microbiota on viral infection susceptibility and disease outcome is undisputable although varies among viruses. The purpose of understanding the interactions between microbiota, virus, and host is to identify practical, effective, and safe approaches that target microbiota for the prevention and treatment of viral diseases in humans and animals, as currently there are few effective and reliable antiviral therapies available. The initial step for achieving this goal is to gather clinical evidences, focusing on the viral pathogens-from human and animal studies-that have already been shown to interact with microbiota. The subsequent step is to identify mechanisms, through experimental evidences, to support the development of translational applications that target microbiota. In this chapter, we review evidences of virus infections altering microbiota and of microbiota enhancing or suppressing infectivity, altering host susceptibility to certain viral diseases, and influencing vaccine immunogenicity in humans and farm animals.
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Affiliation(s)
- Lijuan Yuan
- Department of Biomedical Sciences and Pathobiology, Virginia-Maryland College of Veterinary Medicine, Virginia Polytechnic Institute and State University, Blacksburg, VA, United States; Integrated Life Science Building, Blacksburg, VA, United States.
| | - Casey Hensley
- Department of Biomedical Sciences and Pathobiology, Virginia-Maryland College of Veterinary Medicine, Virginia Polytechnic Institute and State University, Blacksburg, VA, United States; Integrated Life Science Building, Blacksburg, VA, United States
| | - Hassan M Mahsoub
- Department of Biomedical Sciences and Pathobiology, Virginia-Maryland College of Veterinary Medicine, Virginia Polytechnic Institute and State University, Blacksburg, VA, United States; Integrated Life Science Building, Blacksburg, VA, United States
| | - Ashwin K Ramesh
- Department of Biomedical Sciences and Pathobiology, Virginia-Maryland College of Veterinary Medicine, Virginia Polytechnic Institute and State University, Blacksburg, VA, United States; Integrated Life Science Building, Blacksburg, VA, United States
| | - Peng Zhou
- Department of Biomedical Sciences and Pathobiology, Virginia-Maryland College of Veterinary Medicine, Virginia Polytechnic Institute and State University, Blacksburg, VA, United States; Integrated Life Science Building, Blacksburg, VA, United States
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Betancourt L, Hume M, Rodríguez F, Nisbet D, Sohail MU, Afanador-Tellez G. Effects of Colombian oregano essential oil (Lippia origanoides Kunth) and Eimeria species on broiler production and cecal microbiota. Poult Sci 2019; 98:4777-4786. [PMID: 30995320 DOI: 10.3382/ps/pez193] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2018] [Accepted: 03/21/2019] [Indexed: 12/16/2022] Open
Abstract
The gut microbiota has an important effect on poultry health and production. The aim of this study was to evaluate the effect of Colombian oregano (COO), Lippia origanoides Kunth, essential oil supplementation on broiler chicken performance and their cecal bacterial microbiome by 16S-based sequencing. Essential oil was extracted by steam distillation and analyzed by Gas chromatography/mass spectrometry. Two COO levels in feed, 0 ppm control (C) and 100 ppm (O), were evaluated in 2 groups of broilers either unchallenged (U) or challenged (E) with a viable attenuated Eimeria (coccidia) oocyte vaccine. Four treatments, UC, UO, EC, and EO, were distributed among 720 one-day-old male Ross broilers randomly placed in 24 pens. Cecal contents DNA was extracted and pyrosequencing was performed following a standard procedure. Pyrosequencing data were processed, and sequence reads were phylogenetically classified. Similarity of membership and structure in the communities were calculated. At the end of the study, the greatest COO effect was found in coccidia-challenged broilers, with an OE body weight of 1,889 ± 52.4 g with respect to 1,799 ± 36.2 g for CE (P < 0.01). Broiler cecal samples were consistent in that phylum Firmicutes and class Clostridia were highly prevalent; COO had no effect on these taxa levels between the 4 treatments (P > 0.05). A positive correlation (P < 0.01) was observed between the Firmicutes:Bacteriodetes phyla ratio against body weight at 35 D of age. This study provided both positive and negative correlations between broiler body weight against some bacterial groups identified, offering perspectives regarding bacterial groups and their impact on host health and metabolism. Lippia origanoides Kunth high thymol content showed a beneficial effect on body weight and the feed conversion ratio in broilers under coccidia challenge.
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Affiliation(s)
- Liliana Betancourt
- Facultad de Medicina Veterinaria y de Zootecnia, Universidad Nacional de Colombia, Bogotá 11001, Colombia
| | - Michael Hume
- United States Department of Agriculture, ARS, FFSRU, College Station, TX 250047, USA
| | | | - David Nisbet
- United States Department of Agriculture, ARS, FFSRU, College Station, TX 250047, USA
| | - Muhammad Umar Sohail
- Government College University, Faisalabad, Pakistan to Qatar University Biomedical Research Center, Doha 2713, Qatar
| | - Germán Afanador-Tellez
- Facultad de Medicina Veterinaria y de Zootecnia, Universidad Nacional de Colombia, Bogotá 11001, Colombia
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12
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Astrovirus and the microbiome. Curr Opin Virol 2019; 37:10-15. [PMID: 31163291 DOI: 10.1016/j.coviro.2019.05.002] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2019] [Revised: 04/26/2019] [Accepted: 05/02/2019] [Indexed: 11/22/2022]
Abstract
Although astroviruses are most commonly associated with acute gastrointestinal illness in humans, their ability to infect a broad range of hosts and cause a spectrum of disease makes them widespread and complex pathogens. The precise mechanisms that dictate the course of astrovirus disease have not been studied extensively but are likely driven by multifactorial host-microbe interactions. Recent insights from studies of animal astrovirus infections have revealed both beneficial and detrimental effects for the host. However, further in-depth studies are needed to fully explore the consequences of astrovirus-induced changes in the gut microenvironment as well as the role of the microbiota in astrovirus infection.
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13
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Wohlgemuth N, Honce R, Schultz-Cherry S. Astrovirus evolution and emergence. INFECTION, GENETICS AND EVOLUTION : JOURNAL OF MOLECULAR EPIDEMIOLOGY AND EVOLUTIONARY GENETICS IN INFECTIOUS DISEASES 2019; 69:30-37. [PMID: 30639546 PMCID: PMC7106029 DOI: 10.1016/j.meegid.2019.01.009] [Citation(s) in RCA: 69] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/17/2018] [Revised: 01/09/2019] [Accepted: 01/10/2019] [Indexed: 12/19/2022]
Abstract
Astroviruses are small, non-enveloped, positive-sense, single-stranded RNA viruses that belong to the Astroviridae family. Astroviruses infect diverse hosts and are typically associated with gastrointestinal illness; although disease can range from asymptomatic to encephalitis depending on the host and viral genotype. Astroviruses have high genetic variability due to an error prone polymerase and frequent recombination events between strains. Once thought to be species specific, recent evidence suggests astroviruses can spread between different host species, although the frequency with which this occurs and the restrictions that regulate the process are unknown. Recombination events can lead to drastic evolutionary changes and contribute to cross-species transmission events. This work reviews the current state of research on astrovirus evolution and emergence, especially as it relates to cross-species transmission and recombination of astroviruses.
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Affiliation(s)
- Nicholas Wohlgemuth
- Department of Infectious Diseases, St. Jude Children's Research Hospital, Memphis, TN 38105, United States
| | - Rebekah Honce
- Department of Infectious Diseases, St. Jude Children's Research Hospital, Memphis, TN 38105, United States; Department of Microbiology, Immunology, and Biochemistry, University of Tennessee Health Science Center, Memphis, TN 38105, United States
| | - Stacey Schultz-Cherry
- Department of Infectious Diseases, St. Jude Children's Research Hospital, Memphis, TN 38105, United States.
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14
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Genomic Sequence of a Megrivirus Strain Identified in Laying Hens in Brazil. Microbiol Resour Announc 2019; 8:MRA01438-18. [PMID: 30701237 PMCID: PMC6346186 DOI: 10.1128/mra.01438-18] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2018] [Accepted: 12/18/2018] [Indexed: 12/05/2022] Open
Abstract
A new strain of chicken megrivirus was identified in fecal samples of layer chickens in a commercial flock in Minas Gerais, Brazil. It is most closely related to the family Picornaviridae, genus Megrivirus, species Melegrivirus A, and has an overall nucleotide identity of up to 85.1% with other megrivirus strains. A new strain of chicken megrivirus was identified in fecal samples of layer chickens in a commercial flock in Minas Gerais, Brazil. It is most closely related to the family Picornaviridae, genus Megrivirus, species Melegrivirus A, and has an overall nucleotide identity of up to 85.1% with other megrivirus strains.
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15
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Lima DA, Cibulski SP, Tochetto C, Varela APM, Finkler F, Teixeira TF, Loiko MR, Cerva C, Junqueira DM, Mayer FQ, Roehe PM. The intestinal virome of malabsorption syndrome-affected and unaffected broilers through shotgun metagenomics. Virus Res 2018; 261:9-20. [PMID: 30543873 DOI: 10.1016/j.virusres.2018.12.005] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2018] [Revised: 12/06/2018] [Accepted: 12/08/2018] [Indexed: 01/19/2023]
Abstract
Malabsorption syndrome (MAS) is an economically important disease of young, commercially reared broilers, characterized by growth retardation, defective feather development and diarrheic faeces. Several viruses have been tentatively associated to such syndrome. Here, in order to examine potential associations between enteric viruses and MAS, the faecal viromes of 70 stool samples collected from diseased (n = 35) and healthy (n = 35) chickens from seven flocks were characterized and compared. Following high-throughput sequencing, a total of 8,347,319 paired end reads, with an average of 231 nt, were generated. Through analysis of de novo assembled contigs, 144 contigs > 1000 nt were identified with hits to eukaryotic viral sequences, as determined by GenBank database. A number of known and unknown representatives of Adenoviridae, Anelloviridae, Astroviridae, Caliciviridae, Circoviridae, Parvoviridae, Picobirnaviridae, Picornaviridae and Reoviridae, as well as novel uncharacterized CRESS-DNA viruses, were identified. However, the distribution of sequence reads of viral genomes identified in diseased or healthy birds revealed no statistically significant differences. These findings indicate no association between the occurrence of MAS and enteric viruses. The viral genomes reported in the present study, including a variety of novel viruses, seem part of the normal intestinal microbiota of chickens.
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Affiliation(s)
- Diane A Lima
- Laboratório de Virologia, Departamento de Microbiologia, Imunologia e Parasitologia, Instituto de Ciências Básicas da Saúde (ICBS), Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, RS, Brazil.
| | - Samuel P Cibulski
- Laboratório de Virologia, Faculdade de Veterinária, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, Brazil
| | - Caroline Tochetto
- Laboratório de Virologia, Departamento de Microbiologia, Imunologia e Parasitologia, Instituto de Ciências Básicas da Saúde (ICBS), Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, RS, Brazil
| | - Ana Paula M Varela
- Laboratório de Virologia, Departamento de Microbiologia, Imunologia e Parasitologia, Instituto de Ciências Básicas da Saúde (ICBS), Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, RS, Brazil
| | - Fabrine Finkler
- Laboratório de Virologia, Departamento de Microbiologia, Imunologia e Parasitologia, Instituto de Ciências Básicas da Saúde (ICBS), Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, RS, Brazil
| | - Thais F Teixeira
- Laboratório de Virologia, Departamento de Microbiologia, Imunologia e Parasitologia, Instituto de Ciências Básicas da Saúde (ICBS), Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, RS, Brazil
| | - Márcia R Loiko
- Laboratório de Virologia, Departamento de Microbiologia, Imunologia e Parasitologia, Instituto de Ciências Básicas da Saúde (ICBS), Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, RS, Brazil
| | - Cristine Cerva
- Laboratório de Biologia Molecular, Instituto de Pesquisas Veterinárias Desidério Finamor (IPVDF), Eldorado do Sul, RS, Brazil
| | - Dennis M Junqueira
- Centro Universitário Ritter dos Reis - UniRitter, Health Science Department, Porto Alegre, RS, Brazil
| | - Fabiana Q Mayer
- Laboratório de Biologia Molecular, Instituto de Pesquisas Veterinárias Desidério Finamor (IPVDF), Eldorado do Sul, RS, Brazil
| | - Paulo M Roehe
- Laboratório de Virologia, Departamento de Microbiologia, Imunologia e Parasitologia, Instituto de Ciências Básicas da Saúde (ICBS), Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, RS, Brazil
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16
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Wille M, Eden JS, Shi M, Klaassen M, Hurt AC, Holmes EC. Virus-virus interactions and host ecology are associated with RNA virome structure in wild birds. Mol Ecol 2018; 27:5263-5278. [PMID: 30375075 PMCID: PMC6312746 DOI: 10.1111/mec.14918] [Citation(s) in RCA: 57] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2018] [Revised: 10/11/2018] [Accepted: 10/18/2018] [Indexed: 12/13/2022]
Abstract
Little is known about the factors that shape the ecology of RNA viruses in nature. Wild birds are an important case in point, as other than influenza A virus, avian samples are rarely tested for viruses, especially in the absence of overt disease. Using bulk RNA-sequencing ("meta-transcriptomics"), we revealed the viral diversity present in Australian wild birds through the lens of the ecological factors that may determine virome structure and abundance. A meta-transcriptomic analysis of four Anseriformes (waterfowl) and Charadriiformes (shorebird) species sampled in temperate and arid Australia revealed the presence of 27 RNA virus genomes, 18 of which represent newly described species. The viruses identified included a previously described gammacoronavirus and influenza A viruses. Additionally, we identified novel virus species from the families Astroviridae, Caliciviridae, Reoviridae, Rhabdoviridae, Picobirnaviridae and Picornaviridae. We noted differences in virome structure that reflected underlying differences in location and influenza A infection status. Red-necked Avocets (Recurvirostra novaehollandiae) from Australia's arid interior possessed the greatest viral diversity and abundance, markedly higher than individuals sampled in temperate Australia. In Ruddy Turnstones (Arenaria interpres) and dabbling ducks (Anas spp.), viral abundance and diversity were higher and more similar in hosts that were positive for influenza A infection compared to those that were negative for this virus, despite samples being collected on the same day and from the same location. This study highlights the extent and diversity of RNA viruses in wild birds and lays the foundation for understanding the factors that determine virome structure in wild populations.
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Affiliation(s)
- Michelle Wille
- WHO Collaborating Centre for Reference and Research on Influenza, The Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
| | - John-Sebastian Eden
- Marie Bashir Institute for Infectious Diseases and Biosecurity, Charles Perkins Centre, School of Life and Environmental Sciences and Sydney Medical School, The University of Sydney, Sydney, New South Wales, Australia.,The Westmead Institute for Medical Research, Centre for Virus Research, Sydney, New South Wales, Australia
| | - Mang Shi
- Marie Bashir Institute for Infectious Diseases and Biosecurity, Charles Perkins Centre, School of Life and Environmental Sciences and Sydney Medical School, The University of Sydney, Sydney, New South Wales, Australia
| | - Marcel Klaassen
- Centre for Integrative Ecology, Deakin University, Geelong, Victoria, Australia
| | - Aeron C Hurt
- WHO Collaborating Centre for Reference and Research on Influenza, The Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
| | - Edward C Holmes
- Marie Bashir Institute for Infectious Diseases and Biosecurity, Charles Perkins Centre, School of Life and Environmental Sciences and Sydney Medical School, The University of Sydney, Sydney, New South Wales, Australia
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17
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Nuñez LFN, Parra SHS, De la Torre D, Catroxo MH, Buim MR, Chacon RV, Ferreira CSA, Piantino Ferreira AJ. Isolation of avian nephritis virus from chickens showing enteric disorders. Poult Sci 2018; 97:3478-3488. [PMID: 30239960 PMCID: PMC6142861 DOI: 10.3382/ps/pey207] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Runting-stunting syndrome (RSS) is one of the diseases associated with many detected viruses. In Brazil, there were reports of several enteric disease outbreaks in chickens in which avian nephritis virus (ANV) was detected; however, the role of ANV in the outbreaks and whether the virus was a causative agent of these cases of enteric diseases were not determined. The aim of this study was to isolate ANV in specific pathogen-free (SPF) chicken embryonated eggs (CEE) from the enteric contents of chickens showing signs of RSS. For this purpose, 22 samples of chicken enteric contents that were positive only for ANV were inoculated into 7 and 14-day-old SPF-CEE via the yolk sac route and incubated for 5 d, with a total of 3 passages. Virus isolation was confirmed by the presence of embryo injuries, detection of viral RNA by RT-PCR, and visualization of viral particles using electron microscopy. Therefore, the 7-day-old inoculated embryos showed dwarfism, gelatinous consistency, hemorrhage, and edema in the embryos, whereas the 14-day-old did not show any alteration. Viral RNA was detected in the embryos of both ages of inoculation, and the same viral particles were visualized. The embryos from the mock group showed no alteration and were negative for all the tests. The viral cDNA was sequenced, and the molecular and phylogenetic analyses showed that the Brazilian isolates are more related with the ANV-1 serotype group; the sequences of these isolates showed a high percentage of nucleotide (86.4 to 94.9%) and amino acid (92.3 to 98.7%) similarity with other sequences from China, Japan, Australia, and the United States that belong to this serotype previously classified group. In this study, we isolated 8 samples of ANV in SPF-CEE from enteric content samples from chickens with RSS. In doing so, we showed the pathological injuries to the embryo caused by the virus and the molecular characterization of a part of the ORF 1b gene of the virus.
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Affiliation(s)
- Luis Fabian N Nuñez
- Department of Pathology, School of Veterinary Medicine, University of São Paulo (USP), Av. Prof. Dr. Orlando M. Paiva, 87, CEP 05508-270, São Paulo, SP, Brazil.,School of Veterinary Medicine, Central University of Ecuador, Quito EC170521, Ecuador
| | - Silvana H Santander Parra
- Department of Pathology, School of Veterinary Medicine, University of São Paulo (USP), Av. Prof. Dr. Orlando M. Paiva, 87, CEP 05508-270, São Paulo, SP, Brazil
| | - David De la Torre
- Department of Pathology, School of Veterinary Medicine, University of São Paulo (USP), Av. Prof. Dr. Orlando M. Paiva, 87, CEP 05508-270, São Paulo, SP, Brazil.,School of Veterinary Medicine, Central University of Ecuador, Quito EC170521, Ecuador
| | - Marcia H Catroxo
- Laboratory of Electron Microscopy, Center for Research and Development of Animal Health, Instituto Biológico, Av. Cons. Rodrigues Alves, 1252, 04014-002, São Paulo, SP, Brazil
| | - Marcos R Buim
- Laboratory of Avian Diseases, Instituto Biológico, Av. Gaspar Ricardo, 1700, CEP 17690-000, Bastos, SP, Brazil, and
| | - Ruy V Chacon
- Department of Pathology, School of Veterinary Medicine, University of São Paulo (USP), Av. Prof. Dr. Orlando M. Paiva, 87, CEP 05508-270, São Paulo, SP, Brazil
| | - Claudete S Astolfi Ferreira
- Department of Pathology, School of Veterinary Medicine, University of São Paulo (USP), Av. Prof. Dr. Orlando M. Paiva, 87, CEP 05508-270, São Paulo, SP, Brazil
| | - Antonio J Piantino Ferreira
- Department of Pathology, School of Veterinary Medicine, University of São Paulo (USP), Av. Prof. Dr. Orlando M. Paiva, 87, CEP 05508-270, São Paulo, SP, Brazil
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18
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Boros Á, Polgár B, Pankovics P, Fenyvesi H, Engelmann P, Phan TG, Delwart E, Reuter G. Multiple divergent picobirnaviruses with functional prokaryotic Shine-Dalgarno ribosome binding sites present in cloacal sample of a diarrheic chicken. Virology 2018; 525:62-72. [PMID: 30245195 DOI: 10.1016/j.virol.2018.09.008] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2018] [Revised: 09/07/2018] [Accepted: 09/13/2018] [Indexed: 01/09/2023]
Abstract
Picobirnaviruses (PBVs) of family Picobirnaviridae have bisegmented (S1 and S2 segments), double-stranded RNA genomes. In this study a total of N = 12 complete chicken PBVs (ChPBV) segments (N = 5 of S1 and N = 7 of S2, Acc. Nos.: MH425579-90) were determined using viral metagenomic and RT-PCR techniques from a single cloacal sample of a diarrheic chicken. The identified ChPBV segments are unrelated to each other and distant from all of the currently known PBVs. In silico sequence analyses revealed the presence of conserved prokaryotic Shine-Dalgarno-like (SD-like) sequences upstream of the three presumed open reading frames (ORFs) of the S1 and a single presumed ORF of the S2 segments. According to the results of expression analyses in E. coli using 6xHis-tagged recombinant ChPBV segment 1 construct and Western blot these SD-like sequences are functional in vivo suggesting that S1 of study PBVs can contain three ORFs and supporting the bacteriophage-nature of PBVs.
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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, Pécs, Hungary
| | - Beáta Polgár
- Department of Medical Microbiology and Immunology, Medical School, University of Pécs, Pécs, 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, Pécs, Hungary
| | - Hajnalka Fenyvesi
- 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, Pécs, Hungary
| | - Péter Engelmann
- Department of Immunology and Biotechnology, Clinical Center, Medical School, University of Pécs, Pécs, 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
- Department of Medical Microbiology and Immunology, Medical School, University of Pécs, Pécs, Hungary.
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19
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Nuñez LF, Santander-Parra SH, Chaible L, De la Torre DI, Buim MR, Murakami A, Zaidan Dagli ML, Astolfi-Ferreira CS, Piantino Ferreira AJ. Development of a Sensitive Real-Time Fast-qPCR Based on SYBR ® Green for Detection and Quantification of Chicken Parvovirus (ChPV). Vet Sci 2018; 5:vetsci5030069. [PMID: 30044371 PMCID: PMC6163237 DOI: 10.3390/vetsci5030069] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2018] [Revised: 07/17/2018] [Accepted: 07/19/2018] [Indexed: 12/29/2022] Open
Abstract
Many viruses have been associated with runting and stunting syndrome (RSS). These viral infections mainly affect young chickens, causing apathy, depression, ruffled feathers, cloacal pasting, and diarrhea. Chicken Parvovirus (ChPV) is such an infection and has been detected in chickens showing signs of enteric diseases worldwide. Therefore, the present study aims to develop a sensitive real-time fast-qPCR assay based on SYBR® Green for detection and quantification of ChPV. A 561-bp non-structural (NS) gene was amplified and cloned, and a pair of primers was designed based on conserved nucleotide sequences on the NS gene of ChPV, the intercalating DNA reagent SYBR® Green was employed, and the Fast mode of a thermocycler was used. The assay detects 109 to 101 copies of the genome (CG). The limit of detection (LoD) was estimated to five CG, and the limit of quantification (LoQ) was estimated at ten CG. The standard curve efficiency was 101.94%, and the melting curve showed a unique clean peak and a melting temperature of 79.3 °C. The assay was specific to amplify the ChPV NS gene, and no amplification was shown from other viral genomes or in the negative controls. A total of 141 samples were tested using the assay, of which 139 samples were found positive. The highest CG value of ChPV was 5.7 × 106 CG/uL of DNA without apparent clinical signs of enteric disturbance, and 4.6 × 106 CG/uL DNA were detected in chickens with RSS.
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Affiliation(s)
- Luis F Nuñez
- Department of Pathology, School of Veterinary Medicine, University of São Paulo (USP), Av. Prof. Dr. Orlando M. Paiva, 87, CEP 05508-270 São Paulo, Brazil.
- School of Veterinary Medicine, Central University of Ecuador, Jeronimo Leiton s/n, EC170521 Quito, Ecuador.
| | - Silvana H Santander-Parra
- Department of Pathology, School of Veterinary Medicine, University of São Paulo (USP), Av. Prof. Dr. Orlando M. Paiva, 87, CEP 05508-270 São Paulo, Brazil.
| | - Lucas Chaible
- Department of Pathology, School of Veterinary Medicine, University of São Paulo (USP), Av. Prof. Dr. Orlando M. Paiva, 87, CEP 05508-270 São Paulo, Brazil.
| | - David I De la Torre
- Department of Pathology, School of Veterinary Medicine, University of São Paulo (USP), Av. Prof. Dr. Orlando M. Paiva, 87, CEP 05508-270 São Paulo, Brazil.
- School of Veterinary Medicine, Central University of Ecuador, Jeronimo Leiton s/n, EC170521 Quito, Ecuador.
| | - Marcos R Buim
- Biological Institute, Av. Gaspar Ricardo, 1700, CEP 17690-000 Bastos, Brazil.
| | - Alexandre Murakami
- Department of Pathology, School of Veterinary Medicine, University of São Paulo (USP), Av. Prof. Dr. Orlando M. Paiva, 87, CEP 05508-270 São Paulo, Brazil.
| | - Maria Lucia Zaidan Dagli
- Department of Pathology, School of Veterinary Medicine, University of São Paulo (USP), Av. Prof. Dr. Orlando M. Paiva, 87, CEP 05508-270 São Paulo, Brazil.
| | - Claudete S Astolfi-Ferreira
- Department of Pathology, School of Veterinary Medicine, University of São Paulo (USP), Av. Prof. Dr. Orlando M. Paiva, 87, CEP 05508-270 São Paulo, Brazil.
| | - Antonio J Piantino Ferreira
- Department of Pathology, School of Veterinary Medicine, University of São Paulo (USP), Av. Prof. Dr. Orlando M. Paiva, 87, CEP 05508-270 São Paulo, Brazil.
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20
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Enteric Virus Diversity Examined by Molecular Methods in Brazilian Poultry Flocks. Vet Sci 2018; 5:vetsci5020038. [PMID: 29596389 PMCID: PMC6024555 DOI: 10.3390/vetsci5020038] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2018] [Revised: 03/26/2018] [Accepted: 03/26/2018] [Indexed: 02/04/2023] Open
Abstract
Enteric viruses play an important role in the Brazilian poultry industry due to the economic impact of resulting low yields of broilers, layers, and breeders. The most common enteric viruses affecting commercial flocks in Brazil include Fowl Adenovirus of group I (FAdV-I), Chicken Parvovirus (ChPV), Chicken Astrovirus (CAstV), Avian Nephritis Virus (ANV), Infectious Bronchitis Virus (IBV), Avian Reovirus (AReo), and Avian Rotavirus (ARtV). The aim of this study was to identify single and multiple infections using data obtained from 270 samples from eleven Brazilian states, corresponding to the period between 2010 and 2017. This was accompanied by an analysis of the relationship between the age of birds, clinical signs, and geographical distribution, using Polymerase Chain Reaction (PCR) and Reverse Transcription-PCR (RT-PCR) techniques. Twenty-five profiles of virus combinations were detected. Single infections were encountered in 86.3% of samples, and multiple infections were present in the remaining 13.7%. Both single and multiple infections affected all kinds of commercial chickens with digestive problems, stunting syndrome, decreases in egg and meat production, increased mortality, and respiratory signs. FAdV-I, ChPV, CAstV, ANV, and ARtV were mostly detected in young broilers, in contrast with IBV, which was detected in hens from one to greater than 51 weeks of age. These results exhibit the complexity of enteric diseases and the still poorly understood role of each pathogen as a unique etiological agent.
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21
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Lin HH, Liao YC. drVM: a new tool for efficient genome assembly of known eukaryotic viruses from metagenomes. Gigascience 2017; 6:1-10. [PMID: 28369462 PMCID: PMC5466706 DOI: 10.1093/gigascience/gix003] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2016] [Accepted: 01/15/2017] [Indexed: 11/29/2022] Open
Abstract
Background: Virus discovery using high-throughput next-generation sequencing has become more commonplace. However, although analysis of deep next-generation sequencing data allows us to identity potential pathogens, the entire analytical procedure requires competency in the bioinformatics domain, which includes implementing proper software packages and preparing prerequisite databases. Simple and user-friendly bioinformatics pipelines are urgently required to obtain complete viral genome sequences from metagenomic data. Results: This manuscript presents a pipeline, drVM (detect and reconstruct known viral genomes from metagenomes), for rapid viral read identification, genus-level read partition, read normalization, de novo assembly, sequence annotation, and coverage profiling. The first two procedures and sequence annotation rely on known viral genomes as a reference database. drVM was validated via the analysis of over 300 sequencing runs generated by Illumina and Ion Torrent platforms to provide complete viral genome assemblies for a variety of virus types including DNA viruses, RNA viruses, and retroviruses. drVM is available for free download at: https://sourceforge.net/projects/sb2nhri/files/drVM/ and is also assembled as a Docker container, an Amazon machine image, and a virtual machine to facilitate seamless deployment. Conclusions: drVM was compared with other viral detection tools to demonstrate its merits in terms of viral genome completeness and reduced computation time. This substantiates the platform's potential to produce prompt and accurate viral genome sequences from clinical samples.
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22
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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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23
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Smyth VJ. A Review of the Strain Diversity and Pathogenesis of Chicken Astrovirus. Viruses 2017; 9:v9020029. [PMID: 28208602 PMCID: PMC5332948 DOI: 10.3390/v9020029] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2017] [Revised: 01/25/2017] [Accepted: 01/25/2017] [Indexed: 12/25/2022] Open
Abstract
Although a relatively recently emerged virus, identified only in 2004 as a separate species of avian astrovirus, chicken astrovirus (CAstV) has been associated with poor growth of broiler flocks, enteritis and diarrhea and is a candidate pathogen in cases of runting stunting syndrome. More recently CAstV has been implicated in cases of two other diseases of broilers as the sole etiological agent, namely severe kidney disease of young broilers with visceral gout and the “White Chicks” hatchery disease. Examination of the strains of CAstV associated with the two latter diseases reveals they are closely related genetically. This review will discuss the pathogenesis of CAstV in relation to strain diversity and the effects of vertical versus horizontal transmission, virus load, co-infections and age of bird at infection, all factors that may impact upon disease severity.
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Affiliation(s)
- Victoria J Smyth
- Agri-Food and Biosciences Institute, Stormont Laboratory, Stoney Road, Belfast, BT4 3SD, UK.
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24
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Devaney R, Trudgett J, Trudgett A, Meharg C, Smyth V. A metagenomic comparison of endemic viruses from broiler chickens with runting-stunting syndrome and from normal birds. Avian Pathol 2016; 45:616-629. [PMID: 27215546 PMCID: PMC7113909 DOI: 10.1080/03079457.2016.1193123] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Runting-stunting syndrome (RSS) in broiler chickens is an enteric disease that causes significant economic losses to poultry producers worldwide due to elevated feed conversion ratios, decreased body weight during growth, and excessive culling. Of specific interest are the viral agents associated with RSS which have been difficult to fully characterize to date. Past research into the aetiology of RSS has implicated a wide variety of RNA and DNA viruses however, to date, no individual virus has been identified as the main agent of RSS and the current opinion is that it may be caused by a community of viruses, collectively known as the virome. This paper attempts to characterize the viral pathogens associated with 2–3-week-old RSS-affected and unaffected broiler chickens using next-generation sequencing and comparative metagenomics. Analysis of the viromes identified a total of 20 DNA and RNA viral families, along with 2 unidentified categories, comprised of 31 distinct viral genera and 7 unclassified genera. The most abundant viral families identified in this study were the Astroviridae, Caliciviridae, Picornaviridae, Parvoviridae, Coronaviridae, Siphoviridae, and Myoviridae. This study has identified historically significant viruses associated with the disease such as chicken astrovirus, avian nephritis virus, chicken parvovirus, and chicken calicivirus along with relatively novel viruses such as chicken megrivirus and sicinivirus 1 and will help expand the knowledge related to enteric disease in broiler chickens, provide insights into the viral constituents of a healthy avian gut, and identify a variety of enteric viruses and viral communities appropriate for further study.
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Affiliation(s)
- Ryan Devaney
- a School of Biological Sciences, Queens University Belfast , Belfast , UK
| | | | - Alan Trudgett
- a School of Biological Sciences, Queens University Belfast , Belfast , UK
| | - Caroline Meharg
- a School of Biological Sciences, Queens University Belfast , Belfast , UK
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25
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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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26
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Oakley BB, Kogut MH. Spatial and Temporal Changes in the Broiler Chicken Cecal and Fecal Microbiomes and Correlations of Bacterial Taxa with Cytokine Gene Expression. Front Vet Sci 2016; 3:11. [PMID: 26925404 PMCID: PMC4759570 DOI: 10.3389/fvets.2016.00011] [Citation(s) in RCA: 114] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2015] [Accepted: 02/04/2016] [Indexed: 12/31/2022] Open
Abstract
To better understand the ecology of the poultry gastrointestinal (GI) microbiome and its interactions with the host, we compared GI bacterial communities by sample type (fecal or cecal), time (1, 3, and 6 weeks posthatch), and experimental pen (1, 2, 3, or 4), and measured cecal mRNA transcription of the cytokines IL18, IL1β, and IL6, IL10, and TGF-β4. The microbiome was characterized by sequencing of 16S rRNA gene amplicons, and cytokine gene expression was measured by a panel of quantitative-PCR assays targeting mRNAs. Significant differences were observed in the microbiome by GI location (fecal versus cecal) and bird age as determined by permutational MANOVA and UniFrac phylogenetic hypothesis tests. At 1-week posthatch, bacterial genera significantly over-represented in fecal versus cecal samples included Gallibacterium and Lactobacillus, while the genus Bacteroides was significantly more abundant in the cecum. By 6-week posthatch, Clostridium and Caloramator (also a Clostridiales) sequence types had increased significantly in the cecum and Lactobacillus remained over-represented in fecal samples. In the ceca, the relative abundance of sequences classified as Clostridium increased by ca. 10-fold each sampling period from 0.1% at 1 week to 1% at 3 week and 18% at 6 week. Increasing community complexity through time were observed in increased taxonomic richness and diversity. IL18 and IL1β significantly (p < 0.05, pairwise t-tests) increased to maximum mean expression levels 1.5 fold greater at week 3 than 1, while IL6 significantly decreased to 0.8- and 0.5-fold expression at 3- and 6-week posthatch, respectively relative to week 1. Transcription of pro-inflammatory cytokines was generally negatively correlated with the relative abundance of various members of the phylum Firmicutes and positively correlated with Proteobacteria. Correlations of the microbiome with specific cytokine mRNA transcription highlight the importance of the GI microbiome for bird health and productivity and may be a successful high-throughput strategy to identify bacterial taxa with specific immune-modulatory properties.
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Affiliation(s)
- Brian B Oakley
- College of Veterinary Medicine, Western University of Health Sciences , Pomona, CA , USA
| | - Michael H Kogut
- United States Department of Agriculture, Agricultural Research Service, Southern Plains Area Research Center , College Station, TX , USA
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27
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A diarrheic chicken simultaneously co-infected with multiple picornaviruses: Complete genome analysis of avian picornaviruses representing up to six genera. Virology 2016; 489:63-74. [DOI: 10.1016/j.virol.2015.12.002] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2015] [Revised: 11/24/2015] [Accepted: 12/03/2015] [Indexed: 12/23/2022]
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28
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Wellehan • JF, Lierz • M, Phalen • D, Raidal • S, Styles • DK, Crosta • L, Melillo • A, Schnitzer • P, Lennox • A, Lumeij JT. Infectious disease. CURRENT THERAPY IN AVIAN MEDICINE AND SURGERY 2016. [PMCID: PMC7158187 DOI: 10.1016/b978-1-4557-4671-2.00011-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/04/2022]
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29
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Gan D, Liu N, Han CP, Wu J, Feng Z, Jin W, Wang ZY. Advances in research of metavirus in inflammatory bowel disease. Shijie Huaren Xiaohua Zazhi 2015; 23:3882-3887. [DOI: 10.11569/wcjd.v23.i24.3882] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Inflammatory bowel disease (IBD) is a chronic relapsing disease of the gastrointestinal tract. Ulcerative colitis and Crohn's disease are two main forms. With the development of metavirus technique in recent years, the latest research shows that virus is the second largest species in the intestine. The enteric virome may have a direct effect on the intestinal immunological functions, and the intestinal bacteriophages can affect the human gut bacteria and change the enteric internal environment. Therefore, the research focused on the enteric virome may help clarify the aetiological causes of IBD. In this review, we discuss the relationships between intestinal virus, intestinal flora, and the pathogenesis of IBD.
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