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Zhu ZJ, Teng M, Liu Y, Chen FJ, Yao Y, Li EZ, Luo J. Immune escape of avian oncogenic Marek's disease herpesvirus and antagonistic host immune responses. NPJ Vaccines 2024; 9:109. [PMID: 38879650 PMCID: PMC11180173 DOI: 10.1038/s41541-024-00905-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2024] [Accepted: 06/07/2024] [Indexed: 06/19/2024] Open
Abstract
Marek's disease virus (MDV) is a highly pathogenic and oncogenic alpha herpesvirus that causes Marek's disease (MD), which is one of the most important immunosuppressive and rapid-onset neoplastic diseases in poultry. The onset of MD lymphomas and other clinical diseases can be efficiently prevented by vaccination; these vaccines are heralded as the first demonstration of a successful vaccination strategy against a cancer. However, the persistent evolution of epidemic MDV strains towards greater virulence has recently resulted in frequent outbreaks of MD in vaccinated chicken flocks worldwide. Herein, we provide an overall review focusing on the discovery and identification of the strategies by which MDV evades host immunity and attacks the immune system. We have also highlighted the decrease in the immune efficacy of current MD vaccines. The prospects, strategies and new techniques for the development of efficient MD vaccines, together with the possibilities of antiviral therapy in MD, are also discussed.
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Affiliation(s)
- Zhi-Jian Zhu
- College of Biological and Food Engineering & Affiliated Central Hospital, Huanghuai University, Zhumadian, 463000, People's Republic of China
- Institute for Animal Health & UK-China Center of Excellence for Research on Avian Disease, Henan Academy of Agricultural Sciences, Zhengzhou, 450002, People's Republic of China
- Henan Provincial Key Laboratory of Animal Immunology, Henan Academy of Agricultural Sciences, Zhengzhou, 450002, People's Republic of China
- Key Laboratory of Animal Immunology, Ministry of Agriculture and Rural Affairs of the People's Republic of China, Zhengzhou, 450002, People's Republic of China
| | - Man Teng
- Institute for Animal Health & UK-China Center of Excellence for Research on Avian Disease, Henan Academy of Agricultural Sciences, Zhengzhou, 450002, People's Republic of China
- Henan Provincial Key Laboratory of Animal Immunology, Henan Academy of Agricultural Sciences, Zhengzhou, 450002, People's Republic of China
- Key Laboratory of Animal Immunology, Ministry of Agriculture and Rural Affairs of the People's Republic of China, Zhengzhou, 450002, People's Republic of China
| | - Yu Liu
- College of Biological and Food Engineering & Affiliated Central Hospital, Huanghuai University, Zhumadian, 463000, People's Republic of China
| | - Fu-Jia Chen
- College of Biological and Food Engineering & Affiliated Central Hospital, Huanghuai University, Zhumadian, 463000, People's Republic of China
| | - Yongxiu Yao
- The Pirbright Institute & UK-China Centre of Excellence for Research on Avian Diseases, Pirbright, Ash Road, Guildford, Surrey, GU24 0NF, UK
| | - En-Zhong Li
- College of Biological and Food Engineering & Affiliated Central Hospital, Huanghuai University, Zhumadian, 463000, People's Republic of China.
| | - Jun Luo
- Institute for Animal Health & UK-China Center of Excellence for Research on Avian Disease, Henan Academy of Agricultural Sciences, Zhengzhou, 450002, People's Republic of China.
- Henan Provincial Key Laboratory of Animal Immunology, Henan Academy of Agricultural Sciences, Zhengzhou, 450002, People's Republic of China.
- Key Laboratory of Animal Immunology, Ministry of Agriculture and Rural Affairs of the People's Republic of China, Zhengzhou, 450002, People's Republic of China.
- Laboratory of Functional Microbiology and Animal Health, College of Animal Science and Technology, Henan University of Science and Technology, Luoyang, 471003, People's Republic of China.
- Longhu Laboratory, Zhengzhou, 450046, People's Republic of China.
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Boeren M, Meysman P, Laukens K, Ponsaerts P, Ogunjimi B, Delputte P. T cell immunity in HSV-1- and VZV-infected neural ganglia. Trends Microbiol 2023; 31:51-61. [PMID: 35987880 DOI: 10.1016/j.tim.2022.07.008] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Revised: 07/20/2022] [Accepted: 07/21/2022] [Indexed: 11/17/2022]
Abstract
Herpesviruses hijack the MHC class I (MHC I) and class II (MHC II) antigen-presentation pathways to manipulate immune recognition by T cells. First, we illustrate herpes simplex virus-1 (HSV-1) and varicella-zoster virus (VZV) MHC immune evasion strategies. Next, we describe MHC-T cell interactions in HSV-1- and VZV- infected neural ganglia. Although studies on the topic are scarce, and use different models, most reports indicate that neuronal HSV-1 infection is mainly controlled by CD8+ T cells through noncytolytic mechanisms, whereas VZV seems to be largely controlled through CD4+ T cell-specific immune responses. Autologous human stem-cell-derived in vitro models could substantially aid in elucidating these neuroimmune interactions and are fit for studies on both herpesviruses.
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Affiliation(s)
- Marlies Boeren
- Laboratory of Microbiology, Parasitology and Hygiene (LMPH), University of Antwerp, Antwerp, Belgium; Laboratory of Experimental Hematology (LEH), Vaccine and Infectious Disease Institute (VAXINFECTIO), University of Antwerp, Antwerp, Belgium; Antwerp Center for Translational Immunology and Virology (ACTIV), Vaccine and Infectious Disease Institute, University of Antwerp, Antwerp, Belgium
| | - Pieter Meysman
- Antwerp Unit for Data Analysis and Computation in Immunology and Sequencing (AUDACIS), Antwerp, Belgium; Adrem Data Lab, Department of Computer Science, University of Antwerp, Antwerp, Belgium; Biomedical Informatics Research Network Antwerp (biomina), University of Antwerp, Antwerp, Belgium
| | - Kris Laukens
- Antwerp Unit for Data Analysis and Computation in Immunology and Sequencing (AUDACIS), Antwerp, Belgium; Adrem Data Lab, Department of Computer Science, University of Antwerp, Antwerp, Belgium; Biomedical Informatics Research Network Antwerp (biomina), University of Antwerp, Antwerp, Belgium
| | - Peter Ponsaerts
- Laboratory of Experimental Hematology (LEH), Vaccine and Infectious Disease Institute (VAXINFECTIO), University of Antwerp, Antwerp, Belgium
| | - Benson Ogunjimi
- Antwerp Center for Translational Immunology and Virology (ACTIV), Vaccine and Infectious Disease Institute, University of Antwerp, Antwerp, Belgium; Antwerp Unit for Data Analysis and Computation in Immunology and Sequencing (AUDACIS), Antwerp, Belgium; Centre for Health Economics Research & Modeling Infectious Diseases (CHERMID), Vaccine & Infectious Disease Institute (VAXINFECTIO), University of Antwerp, Antwerp, Belgium; Department of Paediatrics, Antwerp University Hospital, Antwerp, Belgium
| | - Peter Delputte
- Laboratory of Microbiology, Parasitology and Hygiene (LMPH), University of Antwerp, Antwerp, Belgium; Infla-med, University of Antwerp, Antwerp, Belgium.
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The Marek's Disease Virus Unique Gene MDV082 Is Dispensable for Virus Replication but Contributes to a Rapid Disease Onset. J Virol 2021; 95:e0013121. [PMID: 34011541 DOI: 10.1128/jvi.00131-21] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Abstract
Marek's disease virus (MDV) is a highly oncogenic alphaherpesvirus of chickens that causes lymphomas in various organs. Most MDV genes are conserved among herpesviruses, while others are unique to MDV and may contribute to pathogenesis and/or tumor formation. High transcript levels of the MDV-specific genes MDV082, RLORF11, and SORF6 were recently detected in lytically infected cells; however, it remained elusive if the respective proteins are expressed and if they play a role in MDV pathogenesis. In this study, we first addressed if these proteins are expressed by inserting FLAG tags at their N or C termini. We could demonstrate that among the three genes tested, MDV082 is the only gene that encodes a protein and is expressed very late in MDV plaques in vitro. To investigate the role of this novel MDV082 protein in MDV pathogenesis, we generated a recombinant virus that lacks expression of the MDV082 protein. Our data revealed that the MDV082 protein contributes to the rapid onset of Marek's disease but is not essential for virus replication, spread, and tumor formation. Taken together, this study sheds light on the expression of MDV-specific genes and unravels the role of the late protein MDV082 in MDV pathogenesis. IMPORTANCE MDV is a highly oncogenic alphaherpesvirus that causes Marek's disease in chickens. The virus causes immense economic losses in the poultry industry due to the high morbidity and mortality, but also the cost of the vaccination. MDV encodes over 100 genes that are involved in various processes of the viral life cycle. Functional characterization of MDV genes is an essential step toward understanding the complex virus life cycle and MDV pathogenesis. Here, we have identified a novel protein encoded by MDV082 and two potential noncoding RNAs (RLORF11 and SORF6). The novel MDV082 protein is not needed for efficient MDV replication and tumor formation. However, our data demonstrate that the MDV082 protein is involved in the rapid onset of Marek's disease.
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Kozdruń W, Samanta Niczyporuk J, Styś-Fijoł N. Marek’s Disease Is a Threat for Large Scale Poultry Production. Vet Med Sci 2021. [DOI: 10.5772/intechopen.98939] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022] Open
Abstract
Marek’s disease (MD) is one of the widespread infectious diseases that causes huge losses in large-scale poultry production. This is due to weight loss, poorer feed conversion and an increased number of deaths among infected birds. The etiological agent is a Marek’s disease virus (MDV) belonging to the Herpesviridae family. It is mainly described in poultry, however, it is also found in geese. There are three MDV serotypes, and four patotypes within serotype 1. Currently, Marek’s disease is very rare in its classical form. There are non-specific clinical symptoms, and anatomopathological changes are mainly observed in the liver, spleen and the reproductive system. This may be due to the evolution in the pathogenicity of MDV field strains over the past several decades. The presence of MDV and number of molecular diagnostic tests based on the detection of viral nucleic acids and viral proteins is already found in birds that have several weeks old. Laboratory diagnostics are based mainly on molecular biology (mainly PCR) methods. The only relatively effective method instead of biosecurity measures, of preventing MD is prophylactic vaccination of 1-day-old chickens or in ovo vaccination. Nevertheless, Marek’s disease is still recorded in poultry flocks around the world, with estimated losses reaching several million dollars.
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Latest Insights into Unique Open Reading Frames Encoded by Unique Long (UL) and Short (US) Regions of Marek's Disease Virus. Viruses 2021; 13:v13060974. [PMID: 34070255 PMCID: PMC8225041 DOI: 10.3390/v13060974] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2021] [Revised: 05/20/2021] [Accepted: 05/21/2021] [Indexed: 12/27/2022] Open
Abstract
Marek’s disease virus (MDV) is an oncogenic avian alphaherpesvirus whose genome consists of unique long (UL) and short (US) regions that are flanked by inverted repeat regions. More than 100 open reading frames (ORFs) have been annotated in the MDV genome, and are involved in various aspects of MDV biology and pathogenesis. Within UL and US regions of MDV, there are several unique ORFs, some of which have recently been shown to be important for MDV replication and pathogenesis. In this review, we will summarize the current knowledge on these ORFs and compare their location in different MDV strains.
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Structure and function of the porcine TAP protein and its inhibition by the viral immune evasion protein ICP47. Int J Biol Macromol 2021; 178:514-526. [PMID: 33662419 DOI: 10.1016/j.ijbiomac.2021.02.196] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2020] [Revised: 02/22/2021] [Accepted: 02/25/2021] [Indexed: 11/22/2022]
Abstract
The binding mode to TAP (i.e., the peptide transporter associated with antigen processing) from a viral peptide thus far has been unknown in the field of antiviral immunity, but an interfering mode from a virus-encoded TAP inhibitor has been well documented with respect to blocking the TAP function. In the current study, we predicted the structure of the pig TAP transporter and its inhibition complex by the small viral protein ICP47 of the herpes simplex virus (HSV) encoded by the TAP inhibitor to exploit inhibition of the TAP transporter as the host's immune evasion strategy. We found that the hot spots (residues Leu5, Tyr22, and Leu51) on the ICP47 inhibitor interface tended to prevail over the favored Leu and Tyr, which contributed to significant functional binding at the C-termini recognition principle of the TAP. We further characterized the specificity determinants of the peptide transporter from the pig TAP by the ICP47 inhibitor effects and multidrug TmrAB transporter from the Thermus thermophillus and its immunity regarding its structural homolog of the pig TAP. The specialized structure-function relationship from the pig TAP exporter could provide insight into substrate specificity of the unique immunological properties from the host organism. The TAP disarming capacity from all five viral inhibitors (i.e., the five virus-encoded TAP inhibitors of ICP47, UL49.5, U6, BNLF2a, and CPXV012 proteins) was linked to the infiltration of the TAP functional structure in an unstable conformation and the mounting susceptibility caused by the host's TAP polymorphism. It is anticipated that the functional characterization of the pig TAP transporter based on the pig genomic variants will lead to additional insights into the genotype and single nucleotide polymorphism (SNP) in relation to antiviral resistance and disease susceptibility.
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Evasion of the Cell-Mediated Immune Response by Alphaherpesviruses. Viruses 2020; 12:v12121354. [PMID: 33256093 PMCID: PMC7761393 DOI: 10.3390/v12121354] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2020] [Revised: 11/25/2020] [Accepted: 11/25/2020] [Indexed: 12/17/2022] Open
Abstract
Alphaherpesviruses cause various diseases and establish life-long latent infections in humans and animals. These viruses encode multiple viral proteins and miRNAs to evade the host immune response, including both innate and adaptive immunity. Alphaherpesviruses evolved highly advanced immune evasion strategies to be able to replicate efficiently in vivo and produce latent infections with recurrent outbreaks. This review describes the immune evasion strategies of alphaherpesviruses, especially against cytotoxic host immune responses. Considering these strategies, it is important to evaluate whether the immune evasion mechanisms in cell cultures are applicable to viral propagation and pathogenicity in vivo. This review focuses on cytotoxic T lymphocytes (CTLs), natural killer cells (NK cells), and natural killer T cells (NKT cells), which are representative immune cells that directly damage virus-infected cells. Since these immune cells recognize the ligands expressed on their target cells via specific activating and/or inhibitory receptors, alphaherpesviruses make several ligands that may be targets for immune evasion. In addition, alphaherpesviruses suppress the infiltration of CTLs by downregulating the expression of chemokines at infection sites in vivo. Elucidation of the alphaherpesvirus immune evasion mechanisms is essential for the development of new antiviral therapies and vaccines.
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Boone AC, Käser T, Cortes AL, Kulkarni RR, López de Juan Abad BA, Villalobos T, Esandi J, Perozo F, Lemiere S, Gimeno IM. In ovo vaccination with herpesvirus of turkey enhances innate and cellular responses in meat-type chickens: Effect of vaccine dose and strain. Vaccine 2020; 38:4837-4845. [PMID: 32505441 DOI: 10.1016/j.vaccine.2020.05.050] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2020] [Revised: 05/11/2020] [Accepted: 05/17/2020] [Indexed: 01/31/2023]
Abstract
In ovo vaccination with herpesvirus of turkey (HVT) or recombinant HVT (rHVT) is commonly used in meat-type chickens. Previous studies showed that in ovo vaccination with HVT enhances innate, cellular, and humoral immune responses in egg-type chicken embryos. This study evaluated if in ovo vaccination with HVT hastens immunocompetence of commercial meat-type chickens and optimized vaccination variables (dose and strain of HVT) to accelerate immunocompetence. A conventional HVT vaccine was given at recommended dose (RD), HVT-RD = 6080 plaque forming units (PFU), double-dose (2x), half-dose (1/2), or quarter-dose (1/4). Two rHVTs were given at RD: rHVT-A = 7380 PFU, rHVT-B = 8993 PFU. Most, if not all, treatments enhanced splenic lymphoproliferation with Concanavalin A and increased the percentage of granulocytes at day of age. Dose had an effect and HVT-RD was ideal. An increase of wing-web thickness after exposure to phytohemagglutinin-L was only detected after vaccination with HVT-RD. Furthermore, compared to sham-inoculated chickens, chickens in the HVT-RD had an increased percentage of CD3+ T cells and CD4+ T-helper cells, and increased expression of major histocompatibility complex (MHC)-II on most cell subsets (CD45+ cells, non-T leukocytes, T cells and the CD8+ and T cell receptor γδ T-cell subsets). Other treatments (HVT-1/2 and rHVT-B) share some of these features but differences were not as remarkable as in the HVT-RD group. Expression of MHC-I was reduced, compared to sham-inoculated chickens, in most of the cell phenotypes evaluated in the HVT-RD, HVT-2x and rHVT-A groups, while no effect was observed in other treatments. The effect of in ovo HVT on humoral immune responses (antibody responses to keyhole limpet hemocyanin and to a live infectious bronchitis/Newcastle disease vaccine) was minimal. Our study demonstrates in ovo vaccination with HVT in meat-type chickens can accelerate innate and adaptive immunity and we could optimize such effect by modifying the vaccine dose.
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Affiliation(s)
- Allison C Boone
- North Carolina State University, College of Veterinary Medicine, 1060 William Moore Drive, Raleigh, NC 27607, United States; Rollins Animal Disease Diagnostic Laboratory, 2101 Blue Ridge Road, Raleigh, NC 27607, United States.
| | - Tobias Käser
- North Carolina State University, College of Veterinary Medicine, 1060 William Moore Drive, Raleigh, NC 27607, United States.
| | - Aneg L Cortes
- North Carolina State University, College of Veterinary Medicine, 1060 William Moore Drive, Raleigh, NC 27607, United States.
| | - Raveendra R Kulkarni
- North Carolina State University, College of Veterinary Medicine, 1060 William Moore Drive, Raleigh, NC 27607, United States.
| | - Blanca A López de Juan Abad
- North Carolina State University, College of Veterinary Medicine, 1060 William Moore Drive, Raleigh, NC 27607, United States.
| | - Tarsicio Villalobos
- Zoetis-International Biodevices and Automation, 1040 Swabia Ct, Durham, NC 27703, United States.
| | - Javier Esandi
- Zoetis-International Biodevices and Automation, 1040 Swabia Ct, Durham, NC 27703, United States.
| | - Francisco Perozo
- Boehringer Ingelheim Animal Health, Binger Strasse 173, 55216 Ingelheim, Germany.
| | - Stephane Lemiere
- Boehringer Ingelheim Animal Health, Binger Strasse 173, 55216 Ingelheim, Germany.
| | - Isabel M Gimeno
- North Carolina State University, College of Veterinary Medicine, 1060 William Moore Drive, Raleigh, NC 27607, United States.
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Sadigh Y, Tahiri-Alaoui A, Spatz S, Nair V, Ribeca P. Pervasive Differential Splicing in Marek's Disease Virus can Discriminate CVI-988 Vaccine Strain from RB-1B Very Virulent Strain in Chicken Embryonic Fibroblasts. Viruses 2020; 12:E329. [PMID: 32197378 PMCID: PMC7150913 DOI: 10.3390/v12030329] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2020] [Revised: 03/07/2020] [Accepted: 03/10/2020] [Indexed: 12/13/2022] Open
Abstract
Marek's disease is a major scourge challenging poultry health worldwide. It is caused by the highly contagious Marek's disease virus (MDV), an alphaherpesvirus. Here, we showed that, similar to other members of its Herpesviridae family, MDV also presents a complex landscape of splicing events, most of which are uncharacterised and/or not annotated. Quite strikingly, and although the biological relevance of this fact is unknown, we found that a number of viral splicing isoforms are strain-specific, despite the close sequence similarity of the strains considered: very virulent RB-1B and vaccine CVI-988. We validated our findings by devising an assay that discriminated infections caused by the two strains in chicken embryonic fibroblasts on the basis of the presence of some RNA species. To our knowledge, this study is the first to accomplish such a result, emphasizing how relevant a comprehensive picture of the viral transcriptome is to fully understand viral pathogenesis.
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Affiliation(s)
- Yashar Sadigh
- Avian Viral Oncogenesis, The Pirbright Institute, Ash Road, Woking GU24 0NF, UK;
| | - Abdessamad Tahiri-Alaoui
- Clinical BioManufacturing Facility, The Jenner Institute, University of Oxford, Old Road, Headington, Oxford OX3 7JT, UK;
| | - Stephen Spatz
- US National Poultry Research Center, 934 College Station Road, Athens, GA 30605, USA;
| | - Venugopal Nair
- Avian Viral Oncogenesis, The Pirbright Institute, Ash Road, Woking GU24 0NF, UK;
| | - Paolo Ribeca
- Integrative Biology and Bioinformatics, The Pirbright Institute, Ash Road, Woking GU24 0NF, UK
- Biomathematics and Statistics Scotland (BioSS), James Clerk Maxwell Building, Peter Guthrie Tait Road, The King’s Buildings, Edinburgh EH9 3FD, UK
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The Transcriptional Landscape of Marek's Disease Virus in Primary Chicken B Cells Reveals Novel Splice Variants and Genes. Viruses 2019; 11:v11030264. [PMID: 30884829 PMCID: PMC6466439 DOI: 10.3390/v11030264] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2019] [Revised: 03/12/2019] [Accepted: 03/13/2019] [Indexed: 12/14/2022] Open
Abstract
Marek's disease virus (MDV) is an oncogenic alphaherpesvirus that infects chickens and poses a serious threat to poultry health. In infected animals, MDV efficiently replicates in B cells in various lymphoid organs. Despite many years of research, the viral transcriptome in primary target cells of MDV remained unknown. In this study, we uncovered the transcriptional landscape of the very virulent RB1B strain and the attenuated CVI988/Rispens vaccine strain in primary chicken B cells using high-throughput RNA-sequencing. Our data confirmed the expression of known genes, but also identified a novel spliced MDV gene in the unique short region of the genome. Furthermore, de novo transcriptome assembly revealed extensive splicing of viral genes resulting in coding and non-coding RNA transcripts. A novel splicing isoform of MDV UL15 could also be confirmed by mass spectrometry and RT-PCR. In addition, we could demonstrate that the associated transcriptional motifs are highly conserved and closely resembled those of the host transcriptional machinery. Taken together, our data allow a comprehensive re-annotation of the MDV genome with novel genes and splice variants that could be targeted in further research on MDV replication and tumorigenesis.
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Li Y, Niu M, Zou Q. ELM-MHC: An Improved MHC Identification Method with Extreme Learning Machine Algorithm. J Proteome Res 2019; 18:1392-1401. [DOI: 10.1021/acs.jproteome.9b00012] [Citation(s) in RCA: 42] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Affiliation(s)
- Yanjuan Li
- School of Information and Computer Engineering, Northeast Forestry University, Harbin 150040, China
| | - Mengting Niu
- School of Information and Computer Engineering, Northeast Forestry University, Harbin 150040, China
| | - Quan Zou
- Institute of Fundamental and Frontier Sciences, University of Electronic Science and Technology of China, Chengdu 610054, China
- Center for Informational Biology, University of Electronic Science and Technology of China, Chengdu 610054, China
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12
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Boodhoo N, Gurung A, Sharif S, Behboudi S. Marek's disease in chickens: a review with focus on immunology. Vet Res 2016; 47:119. [PMID: 27894330 PMCID: PMC5127044 DOI: 10.1186/s13567-016-0404-3] [Citation(s) in RCA: 98] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2016] [Accepted: 11/03/2016] [Indexed: 12/15/2022] Open
Abstract
Marek's disease (MD), caused by Marek's disease virus (MDV), is a commercially important neoplastic disease of poultry which is only controlled by mass vaccination. Importantly, vaccines that can provide sterile immunity and inhibit virus transmission are lacking; such that vaccines are only capable of preventing neuropathy, oncogenic disease and immunosuppression, but are unable to prevent MDV transmission or infection, leading to emergence of increasingly virulent pathotypes. Hence, to address these issues, developing more efficacious vaccines that induce sterile immunity have become one of the important research goals for avian immunologists today. MDV shares very close genomic functional and structural characteristics to most mammalian herpes viruses such as herpes simplex virus (HSV). MD also provides an excellent T cell lymphoma model for gaining insights into other herpesvirus-induced oncogenesis in mammals and birds. For these reasons, we need to develop an in-depth knowledge and understanding of the host-viral interaction and host immunity against MD. Similarly, the underlying genetic variation within different chicken lines has a major impact on the outcome of infection. In this review article, we aim to investigate the pathogenesis of MDV infection, host immunity to MD and discuss areas of research that need to be further explored.
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Affiliation(s)
- Nitish Boodhoo
- The Pirbright Institute, Ash Road, Pirbright, Woking, Surrey, GU24 0NF, UK
| | - Angila Gurung
- The Pirbright Institute, Ash Road, Pirbright, Woking, Surrey, GU24 0NF, UK
| | - Shayan Sharif
- Department of Pathobiology, Ontario Veterinary College, University of Guelph, Guelph, ON, Canada
| | - Shahriar Behboudi
- The Pirbright Institute, Ash Road, Pirbright, Woking, Surrey, GU24 0NF, UK.
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Pandey U, Bell AS, Renner DW, Kennedy DA, Shreve JT, Cairns CL, Jones MJ, Dunn PA, Read AF, Szpara ML. DNA from Dust: Comparative Genomics of Large DNA Viruses in Field Surveillance Samples. mSphere 2016; 1:e00132-16. [PMID: 27747299 PMCID: PMC5064450 DOI: 10.1128/msphere.00132-16] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2016] [Accepted: 08/25/2016] [Indexed: 12/12/2022] Open
Abstract
The intensification of the poultry industry over the last 60 years facilitated the evolution of increased virulence and vaccine breaks in Marek's disease virus (MDV-1). Full-genome sequences are essential for understanding why and how this evolution occurred, but what is known about genome-wide variation in MDV comes from laboratory culture. To rectify this, we developed methods for obtaining high-quality genome sequences directly from field samples without the need for sequence-based enrichment strategies prior to sequencing. We applied this to the first characterization of MDV-1 genomes from the field, without prior culture. These viruses were collected from vaccinated hosts that acquired naturally circulating field strains of MDV-1, in the absence of a disease outbreak. This reflects the current issue afflicting the poultry industry, where virulent field strains continue to circulate despite vaccination and can remain undetected due to the lack of overt disease symptoms. We found that viral genomes from adjacent field sites had high levels of overall DNA identity, and despite strong evidence of purifying selection, had coding variations in proteins associated with virulence and manipulation of host immunity. Our methods empower ecological field surveillance, make it possible to determine the basis of viral virulence and vaccine breaks, and can be used to obtain full genomes from clinical samples of other large DNA viruses, known and unknown. IMPORTANCE Despite both clinical and laboratory data that show increased virulence in field isolates of MDV-1 over the last half century, we do not yet understand the genetic basis of its pathogenicity. Our knowledge of genome-wide variation between strains of this virus comes exclusively from isolates that have been cultured in the laboratory. MDV-1 isolates tend to lose virulence during repeated cycles of replication in the laboratory, raising concerns about the ability of cultured isolates to accurately reflect virus in the field. The ability to directly sequence and compare field isolates of this virus is critical to understanding the genetic basis of rising virulence in the wild. Our approaches remove the prior requirement for cell culture and allow direct measurement of viral genomic variation within and between hosts, over time, and during adaptation to changing conditions.
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Affiliation(s)
- Utsav Pandey
- Department of Biochemistry and Molecular Biology, Center for Infectious Disease Dynamics, and the Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, Pennsylvania, USA
| | - Andrew S. Bell
- Center for Infectious Disease Dynamics, Departments of Biology and Entomology, Pennsylvania State University, University Park, Pennsylvania, USA
| | - Daniel W. Renner
- Department of Biochemistry and Molecular Biology, Center for Infectious Disease Dynamics, and the Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, Pennsylvania, USA
| | - David A. Kennedy
- Center for Infectious Disease Dynamics, Departments of Biology and Entomology, Pennsylvania State University, University Park, Pennsylvania, USA
| | - Jacob T. Shreve
- Department of Biochemistry and Molecular Biology, Center for Infectious Disease Dynamics, and the Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, Pennsylvania, USA
| | - Chris L. Cairns
- Center for Infectious Disease Dynamics, Departments of Biology and Entomology, Pennsylvania State University, University Park, Pennsylvania, USA
| | - Matthew J. Jones
- Center for Infectious Disease Dynamics, Departments of Biology and Entomology, Pennsylvania State University, University Park, Pennsylvania, USA
| | - Patricia A. Dunn
- Department of Veterinary and Biomedical Sciences, Pennsylvania State University, University Park, Pennsylvania, USA
| | - Andrew F. Read
- Center for Infectious Disease Dynamics, Departments of Biology and Entomology, Pennsylvania State University, University Park, Pennsylvania, USA
| | - Moriah L. Szpara
- Department of Biochemistry and Molecular Biology, Center for Infectious Disease Dynamics, and the Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, Pennsylvania, USA
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Miller MM, Taylor RL. Brief review of the chicken Major Histocompatibility Complex: the genes, their distribution on chromosome 16, and their contributions to disease resistance. Poult Sci 2016; 95:375-92. [PMID: 26740135 PMCID: PMC4988538 DOI: 10.3382/ps/pev379] [Citation(s) in RCA: 98] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2015] [Accepted: 11/11/2015] [Indexed: 12/25/2022] Open
Abstract
Nearly all genes presently mapped to chicken chromosome 16 (GGA 16) have either a demonstrated role in immune responses or are considered to serve in immunity by reason of sequence homology with immune system genes defined in other species. The genes are best described in regional units. Among these, the best known is the polymorphic major histocompatibility complex-B (MHC-B) region containing genes for classical peptide antigen presentation. Nearby MHC-B is a small region containing two CD1 genes, which encode molecules known to bind lipid antigens and which will likely be found in chickens to present lipids to specialized T cells, as occurs with CD1 molecules in other species. Another region is the MHC-Y region, separated from MHC-B by an intervening region of tandem repeats. Like MHC-B, MHC-Y is polymorphic. It contains specialized class I and class II genes and c-type lectin-like genes. Yet another region, separated from MHC-Y by the single nucleolar organizing region (NOR) in the chicken genome, contains olfactory receptor genes and scavenger receptor genes, which are also thought to contribute to immunity. The structure, distribution, linkages and patterns of polymorphism in these regions, suggest GGA 16 evolves as a microchromosome devoted to immune defense. Many GGA 16 genes are polymorphic and polygenic. At the moment most disease associations are at the haplotype level. Roles of individual MHC genes in disease resistance are documented in only a very few instances. Provided suitable experimental stocks persist, the availability of increasingly detailed maps of GGA 16 genes combined with new means for detecting genetic variability will lead to investigations defining the contributions of individual loci and more applications for immunogenetics in breeding healthy poultry.
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Affiliation(s)
- Marcia M Miller
- Beckman Research Institute, City of Hope, Department of Molecular and Cellular Biology, Duarte, CA 91010
| | - Robert L Taylor
- Division of Animal and Nutritional Sciences, West Virginia University, Morgantown, WV 26506
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Identification of non-essential loci within the Meleagrid herpesvirus 1 genome. Virol J 2015; 12:130. [PMID: 26307059 PMCID: PMC4550065 DOI: 10.1186/s12985-015-0362-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2015] [Accepted: 08/17/2015] [Indexed: 11/23/2022] Open
Abstract
Background Meleagrid herpesvirus 1 (MeHV-1) infectious bacterial artificial chromosomes (iBACs) are ideal vectors for the development of recombinant vaccines for the poultry industry. However, the full potential of iBACS as vectors can only be realised after thorough genetic characterisation, including identification of those genetic locations that are non-essential for virus replication. Generally, transposition has proven to be a highly effective strategy for rapid and efficient mutagenesis of iBAC clones. The current study describes the characterisation of 34 MeHV-1 mutants containing transposon insertions within the pMeHV1-C18 iBAC genome. Methods Tn5 and MuA transposition methods were used to generate a library of 76 MeHV-1 insertion mutants. The capacity of each mutant to facilitate the recovery of infectious MeHV-1 was determined by the transfection of clone DNA into chicken embryo fibroblasts. Results Attempts to recover infectious virus from the modified clones identified 14 genetic locations that were essential for MeHV-1 replication in cell culture. Infectious MeHV-1 was recovered from the remaining 14 intragenic insertion mutants and six intergenic insertion mutants, suggesting that the respective insertion locations are non-essential for MeHV-1 replication in cell culture. Conclusions The essential and non-essential designations for those MeHV-1 genes characterised in this study were generally in agreement with previous reports for other herpesviruses homologues. However, the requirement for the mardivirus-specific genes LORF4A and LORF5 are reported for the first time. These findings will help direct future work on the development of recombinant poultry vaccines using MeHV-1 as a vector by identifying potential transgene insertion sites within the viral genome. Electronic supplementary material The online version of this article (doi10.1186/s12985-015-0362-9) contains supplementary material, which is available to authorized users.
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