Phenotypic Characterization of Recombinant Marek's Disease Virus in Live Birds Validates Polymorphisms Associated with Virulence.

Marek's disease (MD) is a highly infectious lymphoproliferative disease in chickens with a significant economic impact. Mardivirus gallidalpha 2, also known as Marek's disease virus (MDV), is the causative pathogen and has been categorized based on its virulence rank into four pathotypes: mild (m), virulent (v), very virulent (vv), and very virulent plus (vv+). A prior comparative genomics study suggested that several single-nucleotide polymorphisms (SNPs) and genes in the MDV genome are associated with virulence, including nonsynonymous (ns) SNPs in eight open reading frames (ORF): UL22, UL36, UL37, UL41, UL43, R-LORF8, R-LORF7, and ICP4. To validate the contribution of these nsSNPs to virulence, the vv+MDV strain 686 genome was modified by replacing nucleotides with those observed in the vMDV strains. Pathogenicity studies indicated that these substitutions reduced the MD incidence and increased the survival of challenged birds. Furthermore, using the best-fit pathotyping method to rank the virulence, the modified vv+MDV 686 viruses resulted in a pathotype similar to the vvMDV Md5 strain. Thus, these results support our hypothesis that SNPs in one or more of these ORFs are associated with virulence but, as a group, are not sufficient to result in a vMDV pathotype, suggesting that there are additional variants in the MDV genome associated with virulence, which is not surprising given this complex phenotype and our previous finding of additional variants and SNPs associated with virulence.

A pangenome graph reference of 30 chicken genomes allows genotyping of large and complex structural variants.

BACKGROUND: The red junglefowl, the wild outgroup of domestic chickens, has historically served as a reference for genomic studies of domestic chickens. These studies have provided insight into the etiology of traits of commercial importance. However, the use of a single reference genome does not capture diversity present among modern breeds, many of which have accumulated molecular changes due to drift and selection. While reference-based resequencing is well-suited to cataloging simple variants such as single-nucleotide changes and short insertions and deletions, it is mostly inadequate to discover more complex structural variation in the genome. METHODS: We present a pangenome for the domestic chicken consisting of thirty assemblies of chickens from different breeds and research lines. RESULTS: We demonstrate how this pangenome can be used to catalog structural variants present in modern breeds and untangle complex nested variation. We show that alignment of short reads from 100 diverse wild and domestic chickens to this pangenome reduces reference bias by 38%, which affects downstream genotyping results. This approach also allows for the accurate genotyping of a large and complex pair of structural variants at the K feathering locus using short reads, which would not be possible using a linear reference. CONCLUSIONS: We expect that this new paradigm of genomic reference will allow better pinpointing of exact mutations responsible for specific phenotypes, which will in turn be necessary for breeding chickens that meet new sustainability criteria and are resilient to quickly evolving pathogen threats.

Targeted Ablation of Exon 2 of the Avian Leukosis Virus-A (ALV-A) Receptor Gene in a Chicken Fibroblast Cell Line by CRISPR Abrogates ALV-A Infection.

The U.S. Department of Agriculture Avian Disease and Oncology Laboratory currently relies on live birds of specific genetic backgrounds for producing chicken-embryo fibroblasts that are used for the diagnosis and subtyping of field isolates associated with avian leukosis virus (ALV) outbreaks. As an alternative to maintaining live animals for this purpose, we are currently developing cell lines capable of achieving the same result by ablation of the entry receptors utilized by ALV strains. We used CRISPR-Cas9 on the cell fibroblast-derived cell line DF-1 to disrupt the tva gene, which encodes the receptor required for binding and entry of ALV-A into cells. We ultimately identified seven DF-1 clones that had biallelic and homozygous indels at the Cas9 target site, exon 2 of tva. When tested in vitro for their ability to host ALV-A, the five clones that had frameshift mutations that disrupted the Tva protein were unable to support ALV-A replication. This result clearly demonstrates that modified cell lines can be used as part of a battery of tests to determine ALV subtype for isolate characterization, thus eliminating the need for live birds.

Nota de investigación- La ablación dirigida del exón 2 del gene del receptor del virus de la leucosis aviar A (ALV-A) en una línea celular de fibroblastos de pollo mediante CRISPR anula la infección por ALV-A. El Laboratorio de Oncología y Enfermedades Aviares del Departamento de Agricultura de los Estados Unidos. actualmente depende de aves vivas con antecedentes genéticos específicos para producir fibroblastos de embrión de pollo que se utilizan para el diagnóstico y la subtipificación de aislamientos de campo asociados con brotes del virus de la leucosis aviar (ALV). Como alternativa al mantenimiento de animales vivos para este propósito, actualmente se están desarrollando líneas celulares capaces de lograr el mismo resultado mediante la ablación de los receptores de entrada utilizados por las cepas ALV. Se utilizó el método repeticiones palindrómicas cortas agrupadas y regularmente interespaciadas o CRISPR-Cas9 en la línea celular DF-1 derivada de fibroblastos para interrumpir el gene Tva, que codifica el receptor requerido para la unión y entrada de ALV-A en las células. Finalmente, se identificaron siete clones de DF-1 que tenían inserciones y deleciones (indeles) bialélicos y homocigóticos en el sitio blanco Cas9, exón 2 del gene tva. Cuando se probó in vitro su capacidad para albergar ALV-A, los cinco clones que tenían mutaciones que involucraban al marco de lectura y que interrumpieron la proteína Tva no pudieron admitir la replicación de ALVA. Este resultado demuestra claramente que las líneas celulares modificadas se pueden utilizar como parte de una batería de pruebas para determinar el subtipo de ALV para la caracterización de los aislamientos, eliminando así la necesidad de aves vivas.

The immune cell landscape and response of Marek's disease resistant and susceptible chickens infected with Marek's disease virus.

Genetically resistant or susceptible chickens to Marek's disease (MD) have been widely used models to identify the molecular determinants of these phenotypes. However, these prior studies lacked the basic identification and understanding of immune cell types that could be translated toward improved MD control. To gain insights into specific immune cell types and their responses to Marek's disease virus (MDV) infection, we used single-cell RNA sequencing (scRNAseq) on splenic cells from MD resistant and susceptible birds. In total, 14,378 cells formed clusters that identified various immune cell types. Lymphocytes, specifically T cell subtypes, were the most abundant with significant proportional changes in some subtypes upon infection. The largest number of differentially expressed genes (DEG) response was seen in granulocytes, while macrophage DEGs differed in directionality by subtype and line. Among the most DEG in almost all immune cell types were granzyme and granulysin, both associated with cell-perforating processes. Protein interactive network analyses revealed multiple overlapping canonical pathways within both lymphoid and myeloid cell lineages. This initial estimation of the chicken immune cell type landscape and its accompanying response will greatly aid efforts in identifying specific cell types and improving our knowledge of host response to viral infection.

Contribution of the TCRß Repertoire to Marek's Disease Genetic Resistance in the Chicken.

Marek's disease (MD) is a lymphoproliferative disease of chickens induced by Marek's disease virus (MDV), an oncogenic α-herpesvirus. MDV has increased in virulence, prompting continued efforts in both improved vaccines and enhanced genetic resistance. Model pairs of genetically MD-resistant and MD-susceptible chickens that were either MHC-matched or MHC-congenic allowed characterization of T cell receptor (TCR) repertoires associated with MDV infection. MD-resistant chickens showed higher usage of Vß-1 TCRs than susceptible chickens in both the CD8 and CD4 subsets in the MHC-matched model, and in the CD8 subset only in the MHC-congenic model, with a shift towards Vß-1+ CD8 cells during MDV infection. Long and short read sequencing identified divergent TCRß loci between MHC-matched MD-resistant and MD-susceptible chickens, with MD-resistant chickens having more TCR Vß1 genes. TCR Vß1 CDR1 haplotype usage in MD-resistant x MD-susceptible F1 birds by RNAseq indicated that the most commonly used CDR1 variant was unique to the MD-susceptible line, suggesting that selection for MD resistance in the MHC-matched model optimized the TCR repertoire away from dominant recognition of one or more B2 haplotype MHC molecules. Finally, TCR downregulation during MDV infection in the MHC-matched model was strongest in the MD-susceptible line, and MDV reactivation downregulated TCR expression in a tumor cell line.

Fast-forwarding evolution-Accelerated adaptation in a proofreading-deficient hypermutator herpesvirus.

Evolution relies on the availability of genetic diversity for fitness-based selection. However, most deoxyribonucleic acid (DNA) viruses employ DNA polymerases (Pol) capable of exonucleolytic proofreading to limit mutation rates during DNA replication. The relative genetic stability produced by high-fidelity genome replication can make studying DNA virus adaptation and evolution an intensive endeavor, especially in slowly replicating viruses. Here, we present a proofreading-impaired Pol mutant (Y547S) of Marek's disease virus that exhibits a hypermutator phenotype while maintaining unimpaired growth in vitro and wild-type (WT)-like pathogenicity in vivo. At the same time, mutation frequencies observed in Y547S virus populations are 2-5-fold higher compared to the parental WT virus. We find that Y547S adapts faster to growth in originally non-permissive cells, evades pressure conferred by antiviral inhibitors more efficiently, and is more easily attenuated by serial passage in cultured cells compared to WT. Our results suggest that hypermutator viruses can serve as a tool to accelerate evolutionary processes and help identify key genetic changes required for adaptation to novel host cells and resistance to antiviral therapy. Similarly, the rapid attenuation achieved through adaptation of hypermutators to growth in cell culture enables identification of genetic changes underlying attenuation and virulence, knowledge that could practically exploited, e.g. in the rational design of vaccines.

Identification and Validation of Ikaros (IKZF1) as a Cancer Driver Gene for Marek's Disease Virus-Induced Lymphomas.

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.

Vaccinal Efficacy of Recombinant Marek's Disease Vaccine 301B/1 Expressing Chicken Interleukin-15.

Marek's disease (MD) vaccine does not provide sterilizing immunity that prevents subsequent MD virus (MDV) replication and shedding in vaccinated birds. It is hypothesized that cell-mediated immunity is critical to control the virus replication in chickens because MDV exists in cell-associated forms in the host. To improve the MD vaccine efficacy, particularly cell-mediated immunity, we constructed recombinant v301B/1-IL-15, an MDV serotype 2 vaccine strain 301B/1 expressing chicken interleukin-15 (IL-15), a cytokine which promotes T-cell proliferation and enhances T-cell responses. We examined the vaccine efficacy of v301B/1-IL-15 given as a bivalent MD vaccine in combination with turkey herpesvirus (HVT) against a very virulent MDV challenge. The expression of IL-15 did not interfere with virus stability and the growth of recombinant v301B/1-IL-15. However, the protective efficacy of v301B/1-IL-15 was not significantly different from that of v301B/1, the parental virus used to construct v301B/1-IL-15. Shedding of challenge virus was slightly reduced at Day 21 (16 days postchallenge) in the v301B/1-IL-15 plus HVT vaccinated group, with no statistically significant difference to that of the v301B/1 plus HVT vaccinated group, and thymus atrophy was observed to be less severe in the v301B/1-IL-15 plus HVT vaccinated group. Overall, the protection of v301B/1-IL-15 was not differentiable from v301B/1 against very virulent MDV challenge, but there is no interference with bivalent MD vaccine efficacy.

Eficacia de una vacuna recombinante contra la enfermedad de Marek 301B/1 que expresa a la interleucina-15 del pollo. La vacunación contra la enfermedad de Marek (con las siglas en inglés MD) no proporciona inmunidad esterilizante que evite la posterior replicación y diseminación de este virus (MDV) en las aves vacunadas. Se plantea la hipótesis de que la inmunidad mediada por células es fundamental para controlar la replicación del virus en los pollos porque el virus e Marek existe en formas asociadas a células en el huésped. Para mejorar la eficacia de la vacuna de Marek, particularmente la inmunidad mediada por células, se construyó un el virus recombinante v301B/1-IL-15, que es una cepa vacunal del serotipo 2, 301B/1, que expresa el gene de la interleucina-15 de pollo (IL-15), que es una citocina que promueve la proliferación celular de células T y mejora la respuesta de las células T. Se examinó la eficacia de la vacuna de v301B/1-IL-15 administrada como una vacuna bivalente contra la enfermedad de Marek en combinación con el virus del herpes de pavo (HVT) contra un desafío muy virulento. La expresión de IL-15 no interfirió con la estabilidad del virus y la replicación del virus recombinante v301B/1-IL-15. Sin embargo, la eficacia protectora de v301B/1-IL-15 no fue significativamente diferente de la obtenida con el virus v301B/1, que es el virus progenitor utilizado para construir v301B/1-IL-15. La diseminación del virus de desafío se redujo ligeramente en el día 21 (16 días después del desafío) en el grupo vacunado con v301B/1-IL-15 más HVT, sin diferencias estadísticamente significativas con respecto al grupo vacunado con v301B/1 más HVT, y la atrofia del timo se observó que era menos severa en el grupo vacunado con v301B/1-IL-15 más HVT. En general, la protección conferida por v301B/1-IL-15 no fue distinta de la conferida por v301B/1 contra la exposición al virus de Marek muy virulento, pero no hay interferencia con la eficacia de la vacuna de Marek bivalente.

B cells do not play a role in vaccine-mediated immunity against Marek's disease.

BACKGROUND: Marek's disease virus (MDV), a highly oncogenic α-herpesvirus, is the etiological agent of Marek's disease (MD) in chickens. The antiviral activity of vaccine-induced immunity against MD reduces the level of early cytolytic infection, production of cell-free virions in the feather follicle epithelial cells (FFE), and lymphoma formation. Despite the success of several vaccines that have greatly reduced the economic losses from MD, the mechanism of vaccine-induced immunity is poorly understood. METHODS: To provide insight into possible role of B cells in vaccine-mediated protection, we bursectomized birds on day of hatch and vaccinated them eight days later. The birds were challenged 10 days post vaccination with or without receiving adoptive lymphocytes from age-matched control birds prior to inoculation. The study also included vaccinated/challenged and non-vaccinated challenged intact birds. Flowcytometric analysis of PBMN cells were conducted twice post bursectomy to confirm B cell depletion and assess the effect of surgery on T cell population. Immunohistochemical analysis and viral genome copy number assessment in the skin samples at termination was performed to measure the replication rate of MDV in the FFE of the skin tissues of the challenged birds. RESULTS: The non-vaccinated/challenged birds developed typical clinical signs of MD while the vaccinated/challenged and bursectomized, vaccinated/challenged groups with or without adoptive lymphocyte transfer, were fully protected with no sign of transient paralysis, weight loss, or T cell lymphomas. Immunohistochemical analysis and viral genome copy number evaluation in the skin samples revealed that unlike the vaccinated/challenged birds a significant number of virus particles were produced in the FFE of the non-vaccinated/challenged birds at termination. In the bursectomized, vaccinated/challenged groups, only a few replicating virions were detected in the skin of birds that received adoptive lymphocytes prior to challenge. CONCLUSIONS: The study shows that B cells do not play a critical role in MD vaccine-mediated immunity.

Comparison of Marek's Disease Virus Challenge Strains and Bird Types for Vaccine Licensing.

Marek's disease virus (MDV) is an important poultry pathogen that is controlled through widespread vaccination with avirulent and attenuated strains. However, continued evolution of field viruses to higher virulence has required ongoing improvement of available vaccine strains, and these vaccine strains offer an attractive platform for designing recombinant vector vaccines with cross-protection against MDV and additional pathogens. Recent reports of failures in vaccine licensing trials of positive controls to reach appropriately high levels of Marek's disease incidence prompted us to evaluate possible combinations of outbred specific-pathogen-free layer lines and alternative virulent challenge strains that could provide more consistent models for serotype 3 vectored vaccine development. Choice of layer line and virulent MDV challenge strain each contributed to the ability of a challenge model to reach 80% virulence in unvaccinated positive control groups in the majority of trials, without overwhelming serotype 3 vectored vaccine protection in vaccinated groups. Conversely, reducing challenge virus dose by a factor of four, or vaccine dose by half, had no consistent effect across these models. Although MDV strain 617A had the most potential as an alternative to strains that are currently approved for licensing trials, no combination of layer line and challenge virus consistently met the goals for a successful challenge model in all study replicates, indicating that high variability is an inherent difficulty in MDV challenge studies, at least when outbred birds are used.

Artículo regular­Comparación de las cepas de desafío del virus de la enfermedad de Marek y los tipos de aves para la obtención de licencias de vacunas. El virus de la enfermedad de Marek (MDV) es un patógeno importante en la avicultura que se controla mediante la vacunación generalizada con cepas avirulentas y atenuadas. Sin embargo, la evolución continua de los virus de campo hacia una mayor virulencia ha requerido una mejora continua de las cepas vacunales disponibles y estas cepas vacunales ofrecen una plataforma atractiva para diseñar vacunas con vectores recombinantes que induzcan protección cruzada contra el virus de la enfermedad de Marek y patógenos adicionales. Los reportes recientes de fallas en los controles positivos para alcanzar niveles apropiadamente altos de incidencia de la enfermedad de Marek en los ensayos para obtener la licencia de vacunas llevaron a evaluar posibles combinaciones de líneas de postura híbridas libres de patógenos específicos y cepas de desafío virulentas alternativas que podrían proporcionar modelos más consistentes para el desarrollo de vacunas con vectores de serotipo 3. Tanto la elección de la línea de postura como de la cepa de desafío virulenta de Marek contribuyeron a obtener un modelo de desafío con capacidad para alcanzar el 80% de virulencia en grupos controles positivo no vacunados en la mayoría de los ensayos, sin una protección abrumadora de la vacuna con vector de serotipo 3 en los grupos vacunados. Por el contrario, la reducción de la dosis del virus de desafío en un factor de cuatro, o la dosis de vacuna a la mitad, no tuvieron un efecto constante en estos modelos. Aunque la cepa 617A de Marek mostró el mayor potencial como alternativa a las cepas que actualmente están aprobadas para ensayos de licenciar vacunas, ninguna combinación de línea de postura y virus de desafío cumplió consistentemente los objetivos de un modelo de desafío exitoso en todas las réplicas del estudio, lo que indica que la alta variabilidad es una dificultad inherente en los estudios de desafío para la enfermedad de Marek, al menos cuando se utilizan aves híbridas.

Codon Deoptimization of UL54 in meq-Deleted Marek's Disease Vaccine Candidate Eliminates Lymphoid Atrophy but Reduces Vaccinal Protection.

Marek's disease (MD) is an oncogenic, lymphoproliferative, and highly contagious disease of chickens. Its etiologic agent is the alphaherpesvirus Marek's disease virus (MDV, Gallid alphaherpesvirus 2), and it is a chronic and ubiquitous problem for the poultry industry with significant economic impact in the United States and worldwide. We have previously demonstrated that MDV attenuated by dicodon deoptimization of the UL54 gene results in reduced gene product accumulation in vitro, with reduced viral genome copy number upon infection and reduced atrophy of bursa and thymus in vivo as well. In this report we detail our attempts to use the same attenuation strategy on a meq-deleted MDV mutant, rMd5B40ΔMeq. Unlike the wild-type rMd5B40 virus the rMd5B40ΔMeq is no longer oncogenic, but infected birds experience an unacceptable amount of bursa and thymus atrophy (BTA). We produced two meq-deleted MDV recombinants with a dicodon-deoptimized UL54 (rMd5B40ΔMeq/UL54deop1 and -deop2) and tested their tendency to cause BTA and to serve as a protective vaccine. We found that, although dicodon deoptimization of the UL54 gene results in a virus that spares the infected animal from atrophy of the bursa and thymus, the meq-deleted UL54-deoptimized recombinant is also less protective than the meq-deleted virus without UL54 deoptimization, the HVT + SB1 combination vaccine, or the Rispens (CVI988) vaccine.

Attenuation of Marek's disease virus by codon pair deoptimization of a core gene.

Marek's disease virus (MDV) is an oncogenic alphaherpesvirus of Gallus gallus, the domesticated chicken. Control strategies rely upon vaccination with live attenuated viruses of antigenically similar avian herpesviruses or attenuated strains of MDV. Recent studies in other viruses have shown that recoding certain viral genes to employ synonymous but rarely-used codon pairs resulted in viral attenuation. We deoptimized two MDV proteins, UL54/ICP27 and UL49/VP22, and demonstrate that the more severely deoptimized variant of UL54 accumulates significantly less gene product in vitro. Using these UL54 deoptimized mutants, we further demonstrate that animals infected with the UL54-recoded recombinant virus exhibited decreased viral genome copy number in lymphocytes, reduced lymphoid atrophy and reduced tumor incidence. This study demonstrates that codon pair deoptimization of a single viral gene can produce attenuated strains of MDV. This approach may be useful as a rational way of making novel live attenuated virus vaccines for MDV.

Expression of Marek's Disease Virus Oncoprotein Meq During Infection in the Natural Host.

Gallid herpesvirus 2 (Marek's disease virus, MDV) causes lymphoproliferative Marek's disease (MD), and is unique among alphaherpesviruses as the viral genome encodes an oncoprotein, Meq. To elucidate the temporal relationship between Meq expression and the development of MD lymphomas in infected chickens, we generated a virulent recombinant MDV that expresses GFP simultaneously with Meq. By using this virus, we monitored the dynamics of Meq expression in vivo throughout the course of infection. In peripheral blood mononuclear cells, the percentage of Meq-expressing cells dramatically increased in the early latent phase but decreased thereafter. Furthermore, we discovered evidences that indicate some of the infected lymphocytes did not express Meq during the latent phase of MDV pathogenesis. These findings provide the first insight into the temporal relationship between Meq expression and MD progression, and new clues to refine the current MD pathogenesis model.

An MHC class I immune evasion gene of Marek׳s disease virus.

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.