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Meng F, Dong X, Hu T, Chang S, Fan J, Zhao P, Cui Z. A deep sequencing reveals significant diversity among dominant variants and evolutionary dynamics of avian leukosis viruses in two infectious ecosystems. BMC Vet Res 2016; 12:287. [PMID: 27993149 PMCID: PMC5168851 DOI: 10.1186/s12917-016-0902-6] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2016] [Accepted: 11/29/2016] [Indexed: 11/22/2022] Open
Abstract
Background As a typical retrovirus, the evolution of Avian leukosis virus subgroup J (ALV-J) in different infectious ecosystems is not characterized, what we know is there are a cloud of diverse variants, namely quasispecies with considerable genetic diversity. This study is to explore the selection of infectious ecosystems on dominant variants and their evolutionary dynamics of ALV-J between DF1 cells and specific-pathogen-free (SPF) chickens. High-throughput sequencing platforms provide an approach for detecting quasispecies diversity more fully. Results An average of about 20,000 valid reads were obtained from two variable regions of gp85 gene and LTR-U3 region from each sample in different infectious ecosystems. The top 10 dominant variants among ALV-J from chicken plasmas, DF1 cells and liver tumor were completely different from each other. Also there was a difference of shannon entropy and global selection pressure values (ω) in different infectious ecosystems. In the plasmas of two chickens, a large portion of quasispecies contained a 3-peptides “LSD” repeat insertion that was only less than 0.01% in DF1 cell culture supernatants. In parallel studies, the LTR-U3 region of ALV-J from the chicken plasmas demonstrated more variants with mutations in their transcription regulatory elements than those from DF1 cells. Conclusions Our data taken together suggest that the molecular epidemiology based on isolated ALV-J in cell culture may not represent the true evolution of virus in chicken flocks in the field. The biological significance of the “LSD” insert and mutations in LTR-U3 needs to be further studied. Electronic supplementary material The online version of this article (doi:10.1186/s12917-016-0902-6) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Fanfeng Meng
- College of Veterinary Medicine, Shandong Agricultural University, Taian, 271018, China
| | - Xuan Dong
- College of Veterinary Medicine, Shandong Agricultural University, Taian, 271018, China
| | - Tao Hu
- Institute of Pathogen Biology, Taishan Medical College, Taian, Shandong, China
| | - Shuang Chang
- College of Veterinary Medicine, Shandong Agricultural University, Taian, 271018, China
| | - Jianhua Fan
- Poultry lnstitute, Chinese Academy of Agricultural Sciences, Yangzhou, Jiangsu, China
| | - Peng Zhao
- College of Veterinary Medicine, Shandong Agricultural University, Taian, 271018, China.
| | - Zhizhong Cui
- College of Veterinary Medicine, Shandong Agricultural University, Taian, 271018, China.
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Cunha MV, Inácio J, Freimanis G, Fusaro A, Granberg F, Höper D, King DP, Monne I, Orton R, Rosseel T. Next-generation sequencing in veterinary medicine: how can the massive amount of information arising from high-throughput technologies improve diagnosis, control, and management of infectious diseases? Methods Mol Biol 2014; 1247:415-36. [PMID: 25399113 PMCID: PMC7123048 DOI: 10.1007/978-1-4939-2004-4_30] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
The development of high-throughput molecular technologies and associated bioinformatics has dramatically changed the capacities of scientists to produce, handle, and analyze large amounts of genomic, transcriptomic, and proteomic data. A clear example of this step-change is represented by the amount of DNA sequence data that can be now produced using next-generation sequencing (NGS) platforms. Similarly, recent improvements in protein and peptide separation efficiencies and highly accurate mass spectrometry have promoted the identification and quantification of proteins in a given sample. These advancements in biotechnology have increasingly been applied to the study of animal infectious diseases and are beginning to revolutionize the way that biological and evolutionary processes can be studied at the molecular level. Studies have demonstrated the value of NGS technologies for molecular characterization, ranging from metagenomic characterization of unknown pathogens or microbial communities to molecular epidemiology and evolution of viral quasispecies. Moreover, high-throughput technologies now allow detailed studies of host-pathogen interactions at the level of their genomes (genomics), transcriptomes (transcriptomics), or proteomes (proteomics). Ultimately, the interaction between pathogen and host biological networks can be questioned by analytically integrating these levels (integrative OMICS and systems biology). The application of high-throughput biotechnology platforms in these fields and their typical low-cost per information content has revolutionized the resolution with which these processes can now be studied. The aim of this chapter is to provide a current and prospective view on the opportunities and challenges associated with the application of massive parallel sequencing technologies to veterinary medicine, with particular focus on applications that have a potential impact on disease control and management.
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Affiliation(s)
- Mónica V. Cunha
- Instituto Nacional de Investigação Agrária e Veterinária, IP and Centro de Biologia Ambiental, Faculdade de Ciências, Universidade de Lisboa, Lisbon, Portugal
| | - João Inácio
- Instituto Nacional de Investigação Agrária e Veterinária, IP, Lisboa, Portugal and School of Pharmacy and Biomolecular Sciences, University of Brighton, Brighton, United Kingdom
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Waltzek TB, Cortés-Hinojosa G, Wellehan JFX, Gray GC. Marine mammal zoonoses: a review of disease manifestations. Zoonoses Public Health 2012; 59:521-35. [PMID: 22697432 PMCID: PMC7477081 DOI: 10.1111/j.1863-2378.2012.01492.x] [Citation(s) in RCA: 67] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Marine mammals evoke strong public affection as well as considerable scientific interest. However, the resultant close contact with marine wildlife poses human health risks, including traumatic injury and zoonotic disease transmission. The majority of zoonotic marine mammal diseases result in localized skin infections in man that resolve spontaneously or with appropriate medical therapy. However, other marine mammal zoonoses, if left untreated, induce life‐threatening systemic diseases that could pose public health risks. As the number of zoonotic diseases rises, the diagnosis of and treatment for these emerging pathogens pose special challenges requiring the expertise of physicians, veterinarians and wildlife biologists. Here, we provide a comprehensive review of the bacterial, viral and fungal marine mammal zoonotic diseases that we hope will be utilized by public health professionals, physicians, veterinarians and wildlife biologists to better understand, diagnose and prevent marine mammal zoonotic diseases.
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Affiliation(s)
- T B Waltzek
- Department of Environmental and Global Health, College of Public Health and Health Professions, University of Florida, Gainesville, FL 32611, USA.
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Abstract
Evolution of RNA viruses occurs through disequilibria of collections of closely related mutant spectra or mutant clouds termed viral quasispecies. Here we review the origin of the quasispecies concept and some biological implications of quasispecies dynamics. Two main aspects are addressed: (i) mutant clouds as reservoirs of phenotypic variants for virus adaptability and (ii) the internal interactions that are established within mutant spectra that render a virus ensemble the unit of selection. The understanding of viruses as quasispecies has led to new antiviral designs, such as lethal mutagenesis, whose aim is to drive viruses toward low fitness values with limited chances of fitness recovery. The impact of quasispecies for three salient human pathogens, human immunodeficiency virus and the hepatitis B and C viruses, is reviewed, with emphasis on antiviral treatment strategies. Finally, extensions of quasispecies to nonviral systems are briefly mentioned to emphasize the broad applicability of quasispecies theory.
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Affiliation(s)
- Esteban Domingo
- Centro de Biología Molecular Severo Ochoa (CSIC-UAM), C/ Nicolás Cabrera, Universidad Autónoma de Madrid, Cantoblanco, Madrid, Spain.
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Radford AD, Chapman D, Dixon L, Chantrey J, Darby AC, Hall N. Application of next-generation sequencing technologies in virology. J Gen Virol 2012; 93:1853-1868. [PMID: 22647373 PMCID: PMC3709572 DOI: 10.1099/vir.0.043182-0] [Citation(s) in RCA: 179] [Impact Index Per Article: 14.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
The progress of science is punctuated by the advent of revolutionary technologies that provide new ways and scales to formulate scientific questions and advance knowledge. Following on from electron microscopy, cell culture and PCR, next-generation sequencing is one of these methodologies that is now changing the way that we understand viruses, particularly in the areas of genome sequencing, evolution, ecology, discovery and transcriptomics. Possibilities for these methodologies are only limited by our scientific imagination and, to some extent, by their cost, which has restricted their use to relatively small numbers of samples. Challenges remain, including the storage and analysis of the large amounts of data generated. As the chemistries employed mature, costs will decrease. In addition, improved methods for analysis will become available, opening yet further applications in virology including routine diagnostic work on individuals, and new understanding of the interaction between viral and host transcriptomes. An exciting era of viral exploration has begun, and will set us new challenges to understand the role of newly discovered viral diversity in both disease and health.
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Affiliation(s)
- Alan D Radford
- University of Liverpool, Institute of Infection and Global Health, Leahurst Campus, Chester High Road, Neston, South Wirral CH64 7TE, UK
| | - David Chapman
- Institute for Animal Health, Pirbright Laboratory, Ash Road, Pirbright, Woking, Surrey GU24 0NF, UK
| | - Linda Dixon
- Institute for Animal Health, Pirbright Laboratory, Ash Road, Pirbright, Woking, Surrey GU24 0NF, UK
| | - Julian Chantrey
- University of Liverpool, School of Veterinary Science, Leahurst Campus, Chester High Road, Neston, South Wirral CH64 7TE, UK
| | - Alistair C Darby
- Institute of Integrative Biology, Biosciences Building, Crown Street, University of Liverpool, Liverpool L69 7ZB, UK
| | - Neil Hall
- Institute of Integrative Biology, Biosciences Building, Crown Street, University of Liverpool, Liverpool L69 7ZB, UK
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High levels of genetic variation within core Helicoverpa armigera nucleopolyhedrovirus genes. Virus Genes 2011; 44:149-62. [DOI: 10.1007/s11262-011-0660-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2011] [Accepted: 08/08/2011] [Indexed: 12/11/2022]
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Deuzing I, Fagrouch Z, Groenewoud MJ, Niphuis H, Kondova I, Bogers W, Verschoor EJ. Detection and characterization of two chimpanzee polyomavirus genotypes from different subspecies. Virol J 2010; 7:347. [PMID: 21110837 PMCID: PMC3003640 DOI: 10.1186/1743-422x-7-347] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2010] [Accepted: 11/26/2010] [Indexed: 11/10/2022] Open
Abstract
The complete nucleotide sequences of three chimpanzee polyomavirus genetic variants were determined. Phylogenetic analysis indicated that the viruses form two different genotypes of ChPyV. Comparison with other primate polyomaviruses revealed a putative agnogene, and an unusually long VP1 open reading frame. The transcriptional control regions (TCR) of the viruses were extremely short (155 nucleotides), and highly conserved amongst the genotypes. Analysis of the TCR from different chimpanzee subspecies, and from a series of tissues from five individuals confirmed its genetic stability, and also indicates that double-infections with different genotypes can occur.
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Affiliation(s)
- Ilona Deuzing
- Department of Virology, Biomedical Primate Research Centre (BPRC), Rijswijk, The Netherlands
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