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Ortigas-Vasquez A, Pandey U, Renner D, Bowen C, Baigent SJ, Dunn J, Cheng H, Yao Y, Read AF, Nair V, Kennedy DA, Szpara ML. Comparative Analysis of Multiple Consensus Genomes of the Same Strain of Marek's Disease Virus Reveals Intrastrain Variation. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.09.04.556264. [PMID: 37732198 PMCID: PMC10508761 DOI: 10.1101/2023.09.04.556264] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/22/2023]
Abstract
Current strategies to understand the molecular basis of Marek's disease virus (MDV) virulence primarily consist of cataloguing divergent nucleotides between strains with different phenotypes. However, each MDV strain is typically represented by a single consensus genome despite the confirmed existence of mixed viral populations. To assess the reliability of single-consensus interstrain genomic comparisons, we obtained two additional consensus genomes of vaccine strain CVI988 (Rispens) and two additional consensus genomes of the very virulent strain Md5 by sequencing viral stocks and cultured field isolates. In conjunction with the published genomes of CVI988 and Md5, this allowed us to perform 3-way comparisons between consensus genomes of the same strain. We found that consensus genomes of CVI988 can vary in as many as 236 positions involving 13 open reading frames (ORFs). In contrast, we found that Md5 genomes varied only in 11 positions involving a single ORF. Phylogenomic analyses showed all three Md5 consensus genomes clustered closely together, while also showing that CVI988 GenBank.BAC diverged from CVI988 Pirbright.lab and CVI988 USDA.PA.field . Comparison of CVI988 consensus genomes revealed 19 SNPs in the unique regions of CVI988 GenBank.BAC that were not present in either CVI988 Pirbright.lab or CVI988 USDA.PA.field . Finally, we evaluated the genomic heterogeneity of CVI988 and Md5 populations by identifying positions with >2% read support for alternative alleles in two ultra-deeply sequenced samples. We were able to confirm that both populations of CVI988 and Md5 were mixed, exhibiting a total of 29 and 27 high-confidence minor variant positions, respectively. We did not find any evidence of minor variants in the positions corresponding to the 19 SNPs in the unique regions of CVI988 GenBank.BAC . Taken together, our findings confirm that consensus genomes of the same strain of MDV can vary and suggest that multiple consensus genomes per strain are needed in order to maximize the accuracy of interstrain genomic comparisons.
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Sun B, Ni M, Liu H, Liu D. Viral intra-host evolutionary dynamics revealed via serial passage of Japanese encephalitis virus in vitro. Virus Evol 2023; 9:veac103. [PMID: 37205166 PMCID: PMC10185921 DOI: 10.1093/ve/veac103] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2022] [Revised: 10/04/2022] [Accepted: 03/21/2023] [Indexed: 12/02/2023] Open
Abstract
Analyses of viral inter- and intra-host mutations could better guide the prevention and control of infectious diseases. For a long time, studies on viral evolution have focused on viral inter-host variations. Next-generation sequencing has accelerated the investigations of viral intra-host diversity. However, the theoretical basis and dynamic characteristics of viral intra-host mutations remain unknown. Here, using serial passages of the SA14-14-2 vaccine strain of Japanese encephalitis virus (JEV) as the in vitro model, the distribution characteristics of 1,788 detected intra-host single-nucleotide variations (iSNVs) and their mutated frequencies from 477 deep-sequenced samples were analyzed. Our results revealed that in adaptive (baby hamster kidney (BHK)) cells, JEV is under a nearly neutral selection pressure, and both non-synonymous and synonymous mutations represent an S-shaped growth trend over time. A higher positive selection pressure was observed in the nonadaptive (C6/36) cells, and logarithmic growth in non-synonymous iSNVs and linear growth in synonymous iSNVs were observed over time. Moreover, the mutation rates of the NS4B protein and the untranslated region (UTR) of the JEV are significantly different between BHK and C6/36 cells, suggesting that viral selection pressure is regulated by different cellular environments. In addition, no significant difference was detected in the distribution of mutated frequencies of iSNVs between BHK and C6/36 cells.
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Affiliation(s)
- Bangyao Sun
- School of Medical Laboratory, Weifang Medical University, Baotong West Street, Weifang 261053, China
- CAS Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Chinese Academy of Sciences, Xiaohongshan 44#, Wuhan 430000, China
- Computational Virology Group, Center for Bacteria and Viruses Resources and Bioinformation, Wuhan Institute of Virology, Chinese Academy of Sciences, Xiaohongshan 44#, Wuhan 430000, China
- University of Chinese Academy of Sciences, Yuquan Road 19#, Beijing 100049, China
| | - Ming Ni
- Beijing Institute of Radiation Medicine, Taiping Road 27#, Beijing 100850, China
| | - Haizhou Liu
- Computational Virology Group, Center for Bacteria and Viruses Resources and Bioinformation, Wuhan Institute of Virology, Chinese Academy of Sciences, Xiaohongshan 44#, Wuhan 430000, China
| | - Di Liu
- CAS Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Chinese Academy of Sciences, Xiaohongshan 44#, Wuhan 430000, China
- Computational Virology Group, Center for Bacteria and Viruses Resources and Bioinformation, Wuhan Institute of Virology, Chinese Academy of Sciences, Xiaohongshan 44#, Wuhan 430000, China
- University of Chinese Academy of Sciences, Yuquan Road 19#, Beijing 100049, China
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Identification and Validation of Ikaros (IKZF1) as a Cancer Driver Gene for Marek’s Disease Virus-Induced Lymphomas. Microorganisms 2022; 10:microorganisms10020401. [PMID: 35208856 PMCID: PMC8877892 DOI: 10.3390/microorganisms10020401] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2021] [Revised: 01/24/2022] [Accepted: 01/25/2022] [Indexed: 12/29/2022] Open
Abstract
Marek’s disease virus (MDV) is the causative agent for Marek’s disease (MD), which is characterized by T-cell lymphomas in chickens. While the viral Meq oncogene is necessary for transformation, it is insufficient, as not every bird infected with virulent MDV goes on to develop a gross tumor. Thus, we postulated that the chicken genome contains cancer driver genes; i.e., ones with somatic mutations that promote tumors, as is the case for most human cancers. To test this hypothesis, MD tumors and matching control tissues were sequenced. Using a custom bioinformatics pipeline, 9 of the 22 tumors analyzed contained one or more somatic mutation in Ikaros (IKFZ1), a transcription factor that acts as the master regulator of lymphocyte development. The mutations found were in key Zn-finger DNA-binding domains that also commonly occur in human cancers such as B-cell acute lymphoblastic leukemia (B-ALL). To validate that IKFZ1 was a cancer driver gene, recombinant MDVs that expressed either wild-type or a mutated Ikaros allele were used to infect chickens. As predicted, birds infected with MDV expressing the mutant Ikaros allele had high tumor incidences (~90%), while there were only a few minute tumors (~12%) produced in birds infected with the virus expressing wild-type Ikaros. Thus, in addition to Meq, key somatic mutations in Ikaros or other potential cancer driver genes in the chicken genome are necessary for MDV to induce lymphomas.
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Yehia N, El-Sayed HS, Omar SE, Erfan A, Amer F. Genetic evolution of Marek's disease virus in vaccinated poultry farms. Vet World 2021; 14:1342-1353. [PMID: 34220140 PMCID: PMC8243665 DOI: 10.14202/vetworld.2021.1342-1353] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2020] [Accepted: 04/09/2021] [Indexed: 11/24/2022] Open
Abstract
Background and Aim: The Marek’s disease virus (MDV) is a neoplastic disease causing serious economic losses in poultry production. This study aimed to investigate MDV occurrence in poultry flocks in the Lower Egypt during the 2020 breakout and genetically characterized Meq, gL, and ICP4 genes in field strains of MDV. Materials and Methods: Forty samples were collected from different breeds from eight Egyptian governorates in 2020. All flocks had received a bivalent vaccine (herpesvirus of turkey FC-126 + Rispens CVI988). However, weight loss, emaciation, reduced egg production, paralysis, and rough/raised feather follicles occurred. Samples were collected from feather follicles, liver, spleen, and nerve tissue for diagnosis by polymerase chain reaction. MDV genetic characterization was then performed by sequencing the Meq, gL, and ICP4 genes of five positive samples representing different governorates and breeds. Results: A total of 28 samples were positive for MDV field strains, while two were related to MDV vaccinal strains. All samples tested negative for ALV (A, B, C, D, and J) and REV. Phylogenetic analysis of the Meq gene of sequenced samples revealed that all MDVs were related to the highly virulent European viruses (Gallid herpesvirus 2 ATE and PC12/30) with high amino acid (A.A.) identity 99.2-100%. Alternatively, there was low A.A. identity with the vaccine strains CVI988 and 3004 (up to 82.5%). These results indicate that further investigation of the efficacy of current Egyptian vaccines is required. The Egyptian strains also harbor a specific mutation, allowing clustering into two subgroups (A and B). By mutation analysis of the Meq gene, the Egyptian viruses in our study had R101K, P217A, and E263D mutations present in all Egyptian viruses. Furthermore, R176A and T180A mutations specific to our strains contributed to the high virulence of highly virulent strains. There were no mutations of the gL or ICP4 genes. Conclusion: Further studies should evaluate the protection contributed by current vaccines used in Egypt.
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Affiliation(s)
- Nahed Yehia
- Reference Laboratory for Veterinary Quality Control on Poultry Production, Animal Health Research Institute, Agricultural Research Center, Dokki, Giza 12618, Egypt
| | - Hemat S El-Sayed
- Department of Poultry Diseases, Benha Provincial Laboratory, Animal Health Research Institute, Agricultural Research Center, Giza, Egypt
| | - Sabry E Omar
- Department of Poultry Diseases, Benha Provincial Laboratory, Animal Health Research Institute, Agricultural Research Center, Giza, Egypt
| | - Ahmed Erfan
- Reference Laboratory for Veterinary Quality Control on Poultry Production, Animal Health Research Institute, Agricultural Research Center, Dokki, Giza 12618, Egypt
| | - Fatma Amer
- Reference Laboratory for Veterinary Quality Control on Poultry Production, Animal Health Research Institute, Agricultural Research Center, Dokki, Giza 12618, Egypt
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Kuny CV, Bowen CD, Renner DW, Johnston CM, Szpara ML. In vitro evolution of herpes simplex virus 1 (HSV-1) reveals selection for syncytia and other minor variants in cell culture. Virus Evol 2020; 6:veaa013. [PMID: 32296542 PMCID: PMC7151645 DOI: 10.1093/ve/veaa013] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
The large dsDNA virus herpes simplex virus 1 (HSV-1) is considered to be genetically stable, yet it can rapidly evolve in response to strong selective pressures such as antiviral treatment. Deep sequencing has revealed that clinical and laboratory isolates of this virus exist as populations that contain a mixture of minor alleles or variants, similar to many RNA viruses. The classic virology approach of plaque purifying virus creates a genetically homogenous population, but it is not clear how closely this represents the mixed virus populations found in nature. We sought to study the evolution of mixed versus highly purified HSV-1 populations in controlled cell culture conditions, to examine the impact of this genetic diversity on evolution. We found that a mixed population of HSV-1 acquired more genetic diversity and underwent a more dramatic phenotypic shift than a plaque-purified population, producing a viral population that was almost entirely syncytial after just ten passages. At the genomic level, adaptation and genetic diversification occurred at the level of minor alleles or variants in the viral population. Certain genetic variants in the mixed viral population appeared to be positively selected in cell culture, and this shift was also observed in clinical samples during their first passages in vitro. In contrast, the plaque-purified viral population did not appear to change substantially in phenotype or overall quantity of minor allele diversity. These data indicate that HSV-1 is capable of evolving rapidly in a given environment, and that this evolution is facilitated by diversity in the viral population.
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Affiliation(s)
- Chad V Kuny
- Departments of Biology, and Biochemistry and Molecular Biology, The Huck Institutes of the Life Sciences, and Center for Infectious Disease Dynamics, Pennsylvania State University, University Park, PA, USA
| | - Christopher D Bowen
- Departments of Biology, and Biochemistry and Molecular Biology, The Huck Institutes of the Life Sciences, and Center for Infectious Disease Dynamics, Pennsylvania State University, University Park, PA, USA
| | - Daniel W Renner
- Departments of Biology, and Biochemistry and Molecular Biology, The Huck Institutes of the Life Sciences, and Center for Infectious Disease Dynamics, Pennsylvania State University, University Park, PA, USA
| | - Christine M Johnston
- Department of Medicine, University of Washington, Seattle, WA, USA
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Moriah L Szpara
- Departments of Biology, and Biochemistry and Molecular Biology, The Huck Institutes of the Life Sciences, and Center for Infectious Disease Dynamics, Pennsylvania State University, University Park, PA, USA
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6
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Dunn JR, Black Pyrkosz A, Steep A, Cheng HH. Identification of Marek's disease virus genes associated with virulence of US strains. J Gen Virol 2019; 100:1132-1139. [PMID: 31184569 DOI: 10.1099/jgv.0.001288] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
Marek's disease virus (MDV) is the most well-cited example of vaccine-driven virulence evolution. MDV induces a lymphoproliferative disease in chickens, which is currently controlled by widespread vaccination of flocks. Unfortunately, Marek's disease (MD) vaccines, while effective in preventing tumours, do not prevent viral replication and mutation, which has been hypothesized as the major driving force for increased MDV virulence of field strains during the past 40 years in US commercial flocks. To limit future virulence increases, there is interest in characterizing MDV strain genomes collected over the years and associating genetic variations with variation in virulence. In this study, we characterized 70 MDV genomes with known virulence by complete or targeted DNA sequencing, and identified genetic variants that showed association with virulence. Our results revealed a number of MDV genes as would be expected for a complex trait. In addition, phylogenetic analysis revealed a clear separation of strains that varied by virulence. Interestingly, high virulence isolates from the same farms persisted over years despite eradication attempts, which has implications on control efforts. Given the growing ability to bioengineer the MDV genome, it should be feasible to experimentally test whether these individual variants influence virulence markers alone or combinations. Once validated, these markers may provide an alternative to live bird testing for evaluating virulence of new MDV field strains.
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Affiliation(s)
- John R Dunn
- Avian Disease and Oncology Laboratory, Agricultural Research Service, United States Department of Agriculture, 4279 E. Mount Hope Road, East Lansing, MI, 48823, USA
| | - Alexis Black Pyrkosz
- Avian Disease and Oncology Laboratory, Agricultural Research Service, United States Department of Agriculture, 4279 E. Mount Hope Road, East Lansing, MI, 48823, USA
| | - Alec Steep
- Avian Disease and Oncology Laboratory, Agricultural Research Service, United States Department of Agriculture, 4279 E. Mount Hope Road, East Lansing, MI, 48823, USA.,Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, MI, 48824, USA
| | - Hans H Cheng
- Avian Disease and Oncology Laboratory, Agricultural Research Service, United States Department of Agriculture, 4279 E. Mount Hope Road, East Lansing, MI, 48823, USA
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He L, Li J, Zhang Y, Luo J, Cao Y, Xue C. Phylogenetic and molecular epidemiological studies reveal evidence of recombination among Marek's disease viruses. Virology 2018; 516:202-209. [PMID: 29407378 DOI: 10.1016/j.virol.2018.01.019] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2017] [Revised: 01/24/2018] [Accepted: 01/25/2018] [Indexed: 01/09/2023]
Abstract
Marek's disease has brought enormous loss in chicken production worldwide and the increasing virulence of Marek's disease virus (MDV) became a severe problem. To better understand the genetic basis underlying, a Chinese MDV strain HNGS101 isolated from immunized chickens was sequenced. Phylogenetic analysis implied that HNGS101 showed more relatedness to Eurasian strains than GaHV-2 circulating in North America. Recombination networks analysis showed the evidence of recombination among MDV strains, and several recombination events in the UL and US region were found. Further analysis indicated that the HNGS101 strain seemed to be generated by the recombination of the earliest Eurasian strains and North American strains in the US region, which may be responsible for the MD outbreaks in China. In summary, this study demonstrates recombination events among MDV strains [corrected], which may shed light on the mechanism of virulence enhancement.
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Affiliation(s)
- Liangliang He
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou 510006, China
| | - Jie Li
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou 510006, China; School of Biology and Food Engineering, Changshu Institute of Technology, Changshu 215500, China
| | - Yun Zhang
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou 510006, China
| | - Jun Luo
- Key Laboratory of Animal Immunology of the Ministry of Agriculture, Henan Provincial Key Laboratory of Animal Immunology, Henan Academy of Agricultural Sciences, Zhengzhou 450002, China; College of Animal Science and Technology, Henan University of Science and Technology, Luoyang 471003, China
| | - Yongchang Cao
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou 510006, China
| | - Chunyi Xue
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou 510006, China.
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8
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Kim SC, Won YH, Park JS, Jeon JS, Ahn JH, Song MJ, Shin OS, Lee CH. Vaccine-type mutations identified in Varicella zoster virus passaged in cell culture. Virus Res 2017; 245:62-68. [PMID: 29242077 DOI: 10.1016/j.virusres.2017.12.004] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2017] [Revised: 12/08/2017] [Accepted: 12/08/2017] [Indexed: 10/18/2022]
Abstract
Varicella-zoster virus (VZV) is a causative agent for chickenpox and shingles. Comparative genomic sequence analysis of clinical and vaccine strains suggested potential sites responsible for attenuation. In this study, low and high passages of two VZV clinical strains cultured in human fibroblast cells were compared for genomic DNA sequences and growth characteristics. Mutations were detected at 187 and 162 sites in the strain YC01 and YC02, respectively. More than 86% of mutations were found in open reading frames, and ORF62 exhibited highest frequency of mutations. T to C and A to G transitions accounted for more 90% of all possible substitutions. Forty mutations were common to two strains, including 27 in ORF62. Mutations found in attenuated vaccine strains were also detected at 7 positions. Both high and low passage strains were infectious and grew similarly in human fibroblast cells. In guinea pig cells, however, high passage strain remained infectious while low passage strain lost infectivity. This study may provide new insight into the attenuating mutations associated with in vitro passaging of VZV.
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Affiliation(s)
- Seok Cheon Kim
- Department of Microbiology, Chungbuk National University, Cheongju, South Korea
| | - Youn Hee Won
- Department of Microbiology, Chungbuk National University, Cheongju, South Korea
| | - Ji Seon Park
- Department of Microbiology, Chungbuk National University, Cheongju, South Korea
| | - Jeong Seon Jeon
- Department of Microbiology, Chungbuk National University, Cheongju, South Korea
| | - Jin Hyun Ahn
- Department of Molecular Cell Biology, Sungkyunkwan University School of Medicine, Suwon, South Korea
| | - Moon Jung Song
- Department of Biosystems and Biotechnology, Division of Biotechnology, College of Life Sciences and Biotechnology, Korea University, Seoul, South Korea
| | - Ok Sarah Shin
- Department of Biomedical Sciences, College of Medicine, Korea University, Seoul, South Korea
| | - Chan Hee Lee
- Department of Microbiology, Chungbuk National University, Cheongju, South Korea.
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Dunn JR, Reddy SM, Niikura M, Nair V, Fulton JE, Cheng HH. Evaluation and Identification of Marek's Disease Virus BAC Clones as Standardized Reagents for Research. Avian Dis 2017; 61:107-114. [DOI: 10.1637/0005-2086-61.1.107] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Affiliation(s)
- John R. Dunn
- United States Department of Agriculture, Agricultural Research Service, U.S. National Poultry Research Center, Avian Disease and Oncology Laboratory, East Lansing, MI 48823
| | - Sanjay M. Reddy
- College of Veterinary Medicine & Biomedical Sciences, Texas A&M University, College Station, TX 77843
| | | | - Venugopal Nair
- Pirbright Institute, Pirbright, Surrey, GU24 0NF, United Kingdom
| | | | - Hans H. Cheng
- United States Department of Agriculture, Agricultural Research Service, U.S. National Poultry Research Center, Avian Disease and Oncology Laboratory, East Lansing, MI 48823
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Hildebrandt E, Dunn JR, Cheng HH. Addition of a UL5 helicase-primase subunit point mutation eliminates bursal-thymic atrophy of Marek's disease virus ∆Meq recombinant virus but reduces vaccinal protection. Avian Pathol 2016; 44:254-8. [PMID: 25968878 DOI: 10.1080/03079457.2015.1041366] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
Marek's disease virus (MDV) is an oncogenic alphaherpesvirus and the causative agent of Marek's disease (MD), characterized by immunosuppression, paralysis, nerve enlargement and induction of T-cell lymphomas in chickens. Despite widespread usage of vaccines since the 1970s to control MD, more virulent field strains of MDV have emerged that overcome vaccinal protection, necessitating the development of new and more protective MD vaccines. The ∆Meq virus, a recombinant Md5 strain MDV lacking the viral oncogene Meq, is one candidate MD vaccine with great potential but unfortunately it also causes bursal-thymic atrophy (BTA) in maternal antibody negative chickens, raising concerns that impede commercial use as a vaccine. Previously, we identified a point mutation within UL5 that reduced in vivo replication in attenuated viruses. We proposed that introduction of the UL5 point mutation into the ∆Meq virus would reduce in vivo replication and eliminate BTA yet potentially retain high protective abilities. In birds, the ∆Meq+UL5 recombinant MDV had reduced replication compared to the original ∆Meq virus, while weights of lymphoid organs indicated that ∆Meq+UL5 did not induce BTA, supporting the hypothesis that reduction of in vivo replication would also abolish BTA. Vaccine trials of the ∆Meq+UL5 virus compared to other ∆Meq-based viruses and commercial vaccines show that, while the ∆Meq+UL5 does provide vaccinal protection, this protection was also reduced compared to the original ∆Meq virus. Therefore, it appears that a very delicate balance is required between levels of replication able to induce high vaccinal protection, yet not so high as to induce BTA.
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Affiliation(s)
- Evin Hildebrandt
- a Genetics Program , Michigan State University , East Lansing , MI , USA
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11
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Marek's disease vaccines: Current status, and strategies for improvement and development of vector vaccines. Vet Microbiol 2016; 206:113-120. [PMID: 28038868 DOI: 10.1016/j.vetmic.2016.11.024] [Citation(s) in RCA: 58] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2016] [Revised: 11/19/2016] [Accepted: 11/23/2016] [Indexed: 11/24/2022]
Abstract
Marek's disease (MD) is a lymphoproliferative viral disease of chickens, which has been controlled through vaccination since 1969. MD vaccines protect against tumors but do not provide sterilizing immunity, and thus it is generally believed that their use has contributed to increase virulence of field strains with the ability to cause MD in vaccinated chickens. Traditional methods of developing vaccines, like cell culture attenuation, have proved unsuccessful for the development of improved vaccines to protect against highly virulent MD virus (MDV) field strains. With the advent of recombinant DNA technology, it is now possible to study MDV gene function and develop rational vaccines that protect against highly pathogenic strains. In addition, the long term protection conferred by MD vaccines, their excellent safety profile, their efficacy when administered early (at hatch or in ovo), and their ability to overcome maternal antibodies, has made MDV an excellent candidate vector to protect not only against MD but also against other important viral poultry diseases. In this review we will discuss the current status of MD vaccines and their use as vector vaccines to control important viral poultry diseases.
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12
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Machida Y, Murata S, Matsuyama-Kato A, Isezaki M, Taneno A, Sakai E, Konnai S, Ohashi K. Isolation and purification of Gallid herpesvirus 2 strains currently distributed in Japan. J Vet Med Sci 2016; 79:115-122. [PMID: 27725354 PMCID: PMC5289247 DOI: 10.1292/jvms.16-0329] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023] Open
Abstract
Gallid herpesvirus 2 (GaHV-2) causes malignant lymphomas in chickens (Marek’s disease, MD). Although MD is controlled through vaccination
efforts, field isolates of GaHV-2 have increased in virulence worldwide and even cause MD in vaccinated chickens. GaHV-2 strains are classified into four
categories (mild, virulent, very virulent and very virulent +) based on the virulence exhibited in experimental infection in unvaccinated or MD-vaccinated
susceptible chickens. Although MD cases are sporadically reported in Japan, the recent field strains of GaHV-2 in Japan have not been characterized. During
isolation of recent field strains by using primary chicken kidney cell cultures, a method classically used for GaHV-2 isolation, vaccine strains were
simultaneously isolated. Therefore, it is necessary to separate vaccine strains to characterize the virulence and pathogenicity of the GaHV-2 strains currently
distributed in Japan. In this study, we prepared cell suspensions from the spleens of MD-symptomatic chickens, inoculated day-old-chicks and isolated GaHV-2
strains by primary chicken kidney cell cultures at 2−3 weeks post inoculation. The isolated strains were passaged several times on chicken embryo fibroblast
cells, and PCR analysis revealed that the isolated strains were not contaminated with vaccine strains. Moreover, the contaminant vaccine strains were completely
removed by the purification of plaques observed in chicken kidney cells. These procedures are necessary to isolate GaHV-2 field strains from vaccine strains in
order to carry out future studies to characterize these strains and glean insights into GaHV-2 virulence and pathogenicity.
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Affiliation(s)
- Yuka Machida
- Department of Disease Control, Graduate School of Veterinary Medicine, Hokkaido University, Kita-18, Nishi-9, Kita-ku, Sapporo 060-0818, Japan
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13
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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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14
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Lv H, Zhang Y, Sun G, Bao K, Gao Y, Qi X, Cui H, Wang Y, Li K, Gao L, Pan Q, Wang X, Liu C. Genetic evolution of Gallid herpesvirus 2 isolated in China. INFECTION GENETICS AND EVOLUTION 2016; 51:263-274. [PMID: 27112385 DOI: 10.1016/j.meegid.2016.04.027] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/04/2016] [Revised: 04/20/2016] [Accepted: 04/21/2016] [Indexed: 01/12/2023]
Abstract
Gallid herpesvirus 2 (GaHV-2), which causes Marek's disease in chickens and has caused extensive economic losses, has recently evolved increased virulence in China. To better understand the genetic basis of the pathogenic characteristics changed and increased virulence, we sequenced the genomes of six new GaHV-2 strains (LCC, LTS, WC/1203, JL/1404, CC/1409, and HS/1412) isolated from chickens with failed immunisation as well as one previously isolated Chinese GaHV-2 strain, J-1. Based on a multiple sequence alignment, several characteristic point mutations were detected in the open reading frames of the Chinese isolates. In addition, two deletions and an insertion were identified at the unique short region and terminal repeat short region junctions in Chinese isolates, and the insertion was a characteristic of the new Chinese isolates. According to a phylogenetic analysis, the GaHV-2 genome diverged substantially over the last two decades in China. Based on the internal repeat long region, the new isolates were closely related to very virulent or very virulent plus strains. Additionally, the new Chinese isolates diverged from the previously isolated strains J-1 and 814. In conclusion, our results provide evidence that Chinese GaHV-2 strains contain characteristic sequences, especially the new isolates. The observed genetic divergence in the new Chinese GaHV-2 strains over the last two decades may be related to observed changes in pathogenic characteristics and virulence.
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Affiliation(s)
- Hongchao Lv
- Division of Avian Infectious Diseases, State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, the Chinese Academy of Agricultural Sciences, Harbin 150001, PR China
| | - Yanping Zhang
- Division of Avian Infectious Diseases, State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, the Chinese Academy of Agricultural Sciences, Harbin 150001, PR China
| | - Guorong Sun
- Division of Avian Infectious Diseases, State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, the Chinese Academy of Agricultural Sciences, Harbin 150001, PR China
| | - Keyan Bao
- Division of Avian Infectious Diseases, State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, the Chinese Academy of Agricultural Sciences, Harbin 150001, PR China
| | - Yulong Gao
- Division of Avian Infectious Diseases, State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, the Chinese Academy of Agricultural Sciences, Harbin 150001, PR China
| | - Xiaole Qi
- Division of Avian Infectious Diseases, State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, the Chinese Academy of Agricultural Sciences, Harbin 150001, PR China
| | - Hongyu Cui
- Division of Avian Infectious Diseases, State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, the Chinese Academy of Agricultural Sciences, Harbin 150001, PR China
| | - Yongqiang Wang
- Division of Avian Infectious Diseases, State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, the Chinese Academy of Agricultural Sciences, Harbin 150001, PR China
| | - Kai Li
- Division of Avian Infectious Diseases, State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, the Chinese Academy of Agricultural Sciences, Harbin 150001, PR China
| | - Li Gao
- Division of Avian Infectious Diseases, State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, the Chinese Academy of Agricultural Sciences, Harbin 150001, PR China
| | - Qing Pan
- Division of Avian Infectious Diseases, State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, the Chinese Academy of Agricultural Sciences, Harbin 150001, PR China
| | - Xiaomei Wang
- Division of Avian Infectious Diseases, State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, the Chinese Academy of Agricultural Sciences, Harbin 150001, PR China.
| | - Changjun Liu
- Division of Avian Infectious Diseases, State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, the Chinese Academy of Agricultural Sciences, Harbin 150001, PR China.
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15
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Hildebrandt E, Dunn JR, Cheng HH. The Mut UL5-I682R Marek's Disease Virus with a Single Nucleotide Mutation Within the Helicase-Primase Subunit Gene not only Reduces Virulence but also Provides Partial Vaccinal Protection Against Marek's Disease. Avian Dis 2015; 59:94-7. [PMID: 26292541 DOI: 10.1637/10929-090314-reg] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
Marek's disease virus (MDV) is an oncogenic herpesvirus that afflicts chickens with the disease known as Marek's disease (MD). This virus induces tumors, nerve lesions, immunosuppression, and death of affected birds. Vaccines are the primary control method for MD but, due to the periodic evolution of field strains, it is necessary to explore the development of new MD vaccines. MD vaccines are often attenuated MDV strains generated through serial passage in vitro. We previously used experimental evolution of MDV to provide a better understanding of the genetic basis of attenuation. During complete genome sequencing of evolved MDV populations, we identified a point mutation within the UL5 helicase-primase gene and created a UL5 recombinant virus that significantly reduced disease incidence by 89%-100%. To determine if experimental evolution also identifies mutations that provide protective qualities as potential vaccine candidates, we tested the UL5 recombinant virus as a vaccine and compared its protection to commercial herpesvirus of turkey (HVT) and bivalent (HVT + SB-1) vaccines. Both commercial vaccines resulted in higher protection against MD than did the UL5 recombinant virus, although the UL5 virus did provide protection against developing MD in 46%-70% of birds challenged. This indicates that a mutation within the UL5 helicase-primase gene not only reduces virulence but also confers protection against challenge with virulent MDV, providing support that not only can experimental evolution identify candidate mutations involved in attenuation but can also identify potential candidates for use in vaccine development.
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16
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Hildebrandt E, Dunn JR, Cheng HH. Characterizing in vivo stability and potential interactions of a UL5 helicase-primase mutation previously shown to reduce virulence and in vivo replication of Marek's disease virus. Virus Res 2015; 203:1-3. [PMID: 25828576 DOI: 10.1016/j.virusres.2015.03.011] [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: 12/10/2014] [Revised: 03/19/2015] [Accepted: 03/20/2015] [Indexed: 10/23/2022]
Abstract
The unpredictable yet recurrent emergence of more virulent field strains of Marek's disease virus (MDV) in Marek's disease (MD) vaccinated flocks of chickens has prompted concerns regarding the sustainability of MD vaccines. A single non-synonymous point mutation (I682R) within the UL5 helicase-primase unit was shown to reduce virulence by over 90%. Considering in vitro attenuation is commonly used to generate MD vaccines, this result prompted further characterization of this mutation, particularly to better understand the potential of point mutations for use in vaccine development. Incorporation of a second non-synonymous point mutation (UL46-Q117R; tegument) found at high frequencies in the same attenuated MDV as the UL5 mutation did not further reduce virulence compared to the single UL5 mutation alone. Furthermore, when the UL5-containing MDV was serially passed three times in vivo, the resulting viruses did not show increases in replication or virulence, and no revertant viruses could be detected. This suggests that point mutations that reduce fitness and in vivo replication may be more stable than initially anticipated, which may alleviate some concerns regarding rationally designed MD vaccines based upon point mutations.
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Affiliation(s)
- Evin Hildebrandt
- Genetics Program, Michigan State University, East Lansing, MI 48824, United States; USDA, ARS, Avian Disease and Oncology Laboratory, East Lansing, MI 48823, United States
| | - John R Dunn
- USDA, ARS, Avian Disease and Oncology Laboratory, East Lansing, MI 48823, United States
| | - Hans H Cheng
- USDA, ARS, Avian Disease and Oncology Laboratory, East Lansing, MI 48823, United States.
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17
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Hearn C, Preeyanon L, Hunt HD, York IA. An MHC class I immune evasion gene of Marek׳s disease virus. Virology 2014; 475:88-95. [PMID: 25462349 DOI: 10.1016/j.virol.2014.11.008] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2014] [Revised: 10/30/2014] [Accepted: 11/04/2014] [Indexed: 11/18/2022]
Abstract
Marek׳s disease virus (MDV) is a widespread α-herpesvirus of chickens that causes T cell tumors. Acute, but not latent, MDV infection has previously been shown to lead to downregulation of cell-surface MHC class I (Virology 282:198-205 (2001)), but the gene(s) involved have not been identified. Here we demonstrate that an MDV gene, MDV012, is capable of reducing surface expression of MHC class I on chicken cells. Co-expression of an MHC class I-binding peptide targeted to the endoplasmic reticulum (bypassing the requirement for the TAP peptide transporter) partially rescued MHC class I expression in the presence of MDV012, suggesting that MDV012 is a TAP-blocking MHC class I immune evasion protein. This is the first unique non-mammalian MHC class I immune evasion gene identified, and suggests that α-herpesviruses have conserved this function for at least 100 million years.
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Affiliation(s)
- Cari Hearn
- Department of Comparative Medicine & Integrative Biology, Michigan State University, East Lansing, MI, USA
| | - Likit Preeyanon
- Department of Microbiology & Molecular Genetics, Michigan State University, East Lansing, MI, USA
| | - Henry D Hunt
- Department of Microbiology & Molecular Genetics, Michigan State University, East Lansing, MI, USA; United States Department of Agriculture, Agriculture Research Service, Avian Disease and Oncology Laboratory, 4279 East Mount Hope Road, East Lansing, MI 48823, USA
| | - Ian A York
- Department of Microbiology & Molecular Genetics, Michigan State University, East Lansing, MI, USA.
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18
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The ORF012 gene of Marek's disease virus type 1 produces a spliced transcript and encodes a novel nuclear phosphoprotein essential for virus growth. J Virol 2014; 89:1348-63. [PMID: 25392220 DOI: 10.1128/jvi.02687-14] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
UNLABELLED Marek's disease virus (MDV), an alphaherpesvirus, is the causative agent of a lethal disease in chickens characterized by generalized nerve inflammation and rapid lymphoma development. The extensive colinearity of the MDV genome with those of related herpesviruses has eased functional characterization of many MDV genes. However, MDV carries a number of unique open reading frames (ORFs) that have not yet been investigated regarding their coding potentials and the functions of their products. Among these unique ORFs are two putative ORFs, ORF011 and ORF012, which are found at the extreme left end of the MDV unique long region. Using reverse transcriptase PCR, we showed that ORF011 and ORF012 are not individual genes but form a single gene through mRNA splicing of a small intron, resulting in the novel ORF012. We generated an ORF012-null virus using an infectious clone of MDV strain RB-1B. The deletion virus had a marked growth defect in vitro and could not be passaged in cultured cells, suggesting an essential role for the ORF012 product in virus replication. Further studies revealed that protein 012 (p012) localized to the nucleus in transfected and infected cells, and we identified by site-directed mutagenesis and green fluorescent protein (GFP) reporter fusion assays a nuclear localization signal (NLS) that was mapped to a 23-amino-acid sequence at the protein's C terminus. Nuclear export was blocked using leptomycin B, suggesting a potential role for p012 as a nuclear/cytoplasmic shuttling protein. Finally, p012 is phosphorylated at multiple residues, a modification that could possibly regulate its subcellular distribution. IMPORTANCE Marek's disease virus (MDV) causes a devastating oncogenic disease in chickens with high morbidity and mortality. The costs for disease prevention reach several billion dollars annually. The functional investigation of MDV genes is necessary to understand its complex replication cycle, which eventually could help us to interfere with MDV and herpesviral pathogenesis. We have identified a previously unidentified phosphoprotein encoded by MDV ORF012. We were able to show experimentally that predicted splicing of the gene based on bioinformatics data does indeed occur during replication. The newly identified p012 is essential for MDV replication and localizes to the nucleus due to the presence of a transferable nuclear localization signal at its C terminus. Our results also imply that p012 could constitute a nucleocytoplasmic shuttle protein, a feature that could prove interesting and important.
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