NE2334: Genetic Bases for Resistance and Immunity to Avian Diseases

(Multistate Research Project)

Status: Active

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SAES-422 Reports

Annual/Termination Reports:

[11/06/2024]

Date of Annual Report: 11/06/2024

Report Information

Annual Meeting Dates: 10/02/2024 - 10/03/2024
Period the Report Covers: 09/24/2023 - 10/03/2024

Participants

Ryan Arsenault, University of Delaware
Lisa Bielke, North Carolina University
Andrew Broadbent, University of Maryland
Paul Cotter, Cotter Laboratory
Rami Dalloul, University of Georgia
Yvonne Dreschsler, Western University of Health Sciences
Gisela F. Erf, University of Arkansas
Rodrigo A. Gallardo, University of California Statewide Administration
Ruediger Hauck, Auburn University
Cari Hearn, Michigan
Keith Jarosinski, University of Illinois
Matthew D. Koci, North Carolina State University
Susan J. Lamont, Iowa State University
Ali Nazmi, Ohio State University
Theros T. Ng, Western University of Health Sciences
Mark S. Parcells, University of Delaware
Ramesh K. Selvaraj, University of Georgia
Brandi Sparling, Western University of Health Sciences
Robert Taylor, Jr., West Virginia University
Huaijun Zhou, University of California, Davis

Brief Summary of Minutes

Accomplishments

Broadbent Objective 2: We investigated agents and mechanisms affecting poultry immune health, focusing on infectious bursal disease virus (IBDV) and avian reovirus (ARV). Recent work in the Delmarva region identified a novel IBDV variant with mutations in the hypervariable region (HVR) of the capsid gene, particularly four mutations (S254N, S317R, G322E, E323D) that significantly reduce the virus’s neutralization by antibodies targeting the common Delaware-E strain, indicating a potential immune escape variant circulating locally. Additionally, the innovative use of chicken intestinal organoids has provided insight into ARV pathogenesis, revealing that distinct ARV strains elicit different immune responses; for example, an enteritis-causing strain led to elevated inflammatory cytokines and reduced intestinal barrier integrity, highlighting strain-specific immune challenges. These findings enhance understanding of immune evasion and variability in disease outcomes in poultry, aiding in the design of targeted vaccines and treatments. Objective 3. We aim to enhance immune function and disease resistance in poultry by developing and utilizing genetic tools and assays. Researchers have built a novel reverse genetics system and B-cell neutralization assay for antigenic characterization of infectious bursal disease virus (IBDV), enabling precise assessment of how specific mutations in the hypervariable region affect antibody neutralization and revealing that sequence data alone inadequately reflects antigenic differences. In addition, newly established intestinal organoids derived from chickens, turkeys, and ducks are now used to analyze and compare species-specific mucosal immune responses to enteric viruses, supporting efforts to understand interspecies immune variation and improve vaccine efficacy. Cotter Objective 3: This research identifies unique cytological behaviors and mitotic capabilities in thrombocytes and plasmacytes that expand our understanding of avian immune cells. Observations of thrombocyte mitosis, an unusual phenomenon, suggest that fully differentiated thrombocytes may revert to mitotic states under stress. Thrombocytes were also shown to undergo shape changes and cytoplasmic shedding, producing thromboplastids, which parallel erythroplastids in erythrocytes, highlighting adaptive responses. Additionally, plasmacytes were categorized by RNA hue, with derived and dwarf types observed, the latter potentially representing hypodiploid cells linked to truncated IgY production in waterfowl. Finally, the analysis of Mott-type plasmacytes revealed polyploid characteristics and distinct cytoplasmic inclusions (Russell bodies), challenging conventional cell differentiation theories. These findings contribute to understanding immune cell plasticity and potential responses to pathology. Drechsler, Ng, Sparling Objectives: 1: Developing a project on Cluster Homolog Immunoglobulin-like Receptors in the chicken (CHIR). Phylogenetic analysis and re-annotation of CHIR submitted to NCBI. Preliminary data with siRNA shows effects on CHIR-B. Single-cell sequencing of the shell gland shows differences in cellular populations and CHIRs in B2 and B19 haplotypes. Objective 3: Continuation of functional annotation of the chicken genome: RNA-sequencing, ATAC-sequencing, Cut&Taq-sequencing, and whole genome bisulfite sequencing (WGBS) of 20 tissues/cells have been completed. DNA methylome completed for reproductive and intestinal tissues/ peripheral immune cells. RNA seq was completed for all tissues and peripheral blood cells. ATAC seq was completed using a new methodology for better quality and smaller cell populations due to issues with QC previously. ChIP seq with new methodology is close to completion. A supplemental article on the functional annotation of the chicken genome was published in the Journal of Animal Science in 2023. Erf Objective 2. Studies on multifactorial, non-communicable disease using the UCD200/206 disease models, provided new insights into autoimmune pathology and revealed aberrant innate immune responses, especially to Gram+-bacteria, as well as altered primary and secondary, cellular- and humoral-immune responses to live herpesvirus of turkey vaccines in the UCD-scleroderma model. Evaluation of the local (GF-pulp) and systemic (blood) cellular responses, as well as systemic antibody-responses to different formulations, preparations, and dosages of a first and second administration of killed Salmonella vaccines, demonstrated heterophil dominated, T cell-dependent, immune responses. Objective 3: AR maintained and reproduced genetic lines that spontaneously develop autoimmune diseases. AR refined and expanded the use of the growing feather as an in vivo test-tube system to study innate and adaptive immune responses in poultry. The combination of the in vivo test tube with blood sampling proved effective in evaluating the effects of genetic selection and nutrition on innate immune system development and function. Gallardo Objective 3: Understand the pathobiology of IBV causing FLS in laying hens. Hauck Objective 2: This study investigates how infections with coccidia and avian reoviruses (ARV) interact within chicken cell models and influence immune responses. Using chicken embryo liver (CELi), kidney (CEK), and macrophage (HD11) cell lines, cells were inoculated with ARV and analyzed at various time points for viral loads and gene expression changes. Viral loads were highest in CELi cells, with differential gene expression (DEGs) most prominent in HD11 cells at 12 hours, CEK at 8 hours, and CELi at 24 hours post-inoculation. Pathway analysis highlighted cell type-specific responses: organ development in HD11, blood clotting in CEK, and interferon and cytokine signaling in CELi. These findings provide insight into cell-specific immune responses and the molecular interplay between ARV and the host. Hearn Objective 1: Single-cell sequencing has been performed to analyze immune cell composition, infection response and transcriptional regulation of MD-resistant, susceptible and F1 hybrid chickens; animal studies have been performed to identify MHC and non-MHC genetic resistance to IBDV and ILTV infection; large-scale transmission experiments have been performed to analyze influence of vaccination, host genetics, and viral mutation rate on MDV transmission and evolution; flow-sorted samples have been obtained for TCR repertoire sequencing of MHC-congenic chicken CTLs. Objective 2: Polyclonal antisera to chicken PD-1 and PD-L1 have been developed and tested in vivo for effects on MD pathogenesis and survival Objective 3: Single-cell sequencing for a multi-organ chicken immune atlas has been performed and analyzed; RNA probe-based immune cell immunophenotyping is in progress; ADOL genetic chicken lines have been transferred to USNPRC and are being maintained. Jarosinski Objective 1: Cloned and sequenced innate immune genes from MD-resistant and -susceptible chickens. Objective 2: Cloned potential MDV gC interacting partners to test in co-immunoprecipitation assays and tested purinergic receptor expression during MDV infection. Objective 3: We have cloned the putative chicken CR1, CR2, C3, and C4 and generated mAbs for CR1 and CR2. Lamont Objective 1: Progress was made in defining genetic control of response to various pathogens in chickens. Objective 3: ISU chicken genetic lines were reproduced and maintained and shared for collaborative research. Nazmi Objective 3: This study investigates the role of intraepithelial lymphocytes (IEL) in chickens during necrotic enteritis (NE), a condition caused by the co-infection of Eimeria maxima and Clostridium perfringens. Sixty-three specific-pathogen-free chickens were divided into control, Eimeria maxima (EM), and Eimeria maxima + Clostridium perfringens (EM/CP) groups. The EM/CP group exhibited subclinical NE, lower body weight gain, and shorter colon lengths. Significant changes in IEL populations were observed one day after C. perfringens infection, with the EM/CP group showing increased natural IEL subsets. By seven days post-infection, some IEL populations remained elevated. The EM/CP group also had higher levels of pro-inflammatory cytokines in the jejunum, suggesting that these IEL play a crucial protective role in the immune response against C. perfringens during subclinical NE. Parcells Objective 1: From a practical standpoint, we found that vIL8 is a virulence determinant in the context of HVT. Objective 2: We found that BRG1 binds the C-terminus of vv+MDVs and is dependent on the mutations found at specific positions common to mutation (PPPP->P(Q/A)PP) and that this binding confers increased transcriptional activation. Objective 3: We found that EZH2 is constitutively expressed in PBMC and therefore its activity on the MDV genome may be regulated by histone demethylases. Selvaraj Objective 3: A study evaluated the efficacy of two killed Salmonella bacterin vaccine, administered intramuscularly- in layers. The first vaccine had 97% S. typhimurium and 3% Immune Plus® with preservatives and adjuvants. The second vaccine was synthesized with 77% S. typhimurium, 10% Klebsiella strain KP9580, 10% Klebsiella strain KPZBT01, and 3% Immune Plus® with preservatives and adjuvants. These results indicate that the killed bacterin vaccine produces an increase in serum antibody titer and could be a potential viable vaccine candidate against Salmonella infection in layers. Taylor Objective 1.  Individual or pooled DNA having defined alloantigen genotypes analyzed with 600k SNP enabled the identification of systems A, D, E, and I which are C4BPM, CD99, FCAMR, and RHCE, respectively. Systems H and L have been found on chromosomes 24 and 4, respectively. Their gene identification remains in progress. Selection for high (HAS) and low (LAS) antibody response to sheep red blood cells had different impacts on PBL and spleen mRNA expression of cytokines and chemokines. LAS peripheral blood leukocytes had higher IL6 but no difference in IL4, IL10, CXCL8, CCL4, or TGF-4 compared with HAS. HAS spleen cells had higher IL4 and CXCL8 but no difference in IL6, IL10, CCL4, or TGF-4 compared with LAS. Selection for antibody response to sheep red blood cells resulted in different growth patterns and relative weights of the spleen and bursa of Fabricius. HAS spleens grew faster than LAS spleens. LAS bursae were smaller than HAS bursae through 63 days of age. One hundred fifty protein-encoding genes on Chromosome 31 were identified as CHIRs Cluster Homolog of Immunoglobulin-like Receptors (CHIRs). These large transmembrane glycoproteins that direct the immune response include functional groups CHIRA, CHIRB, and CHIRAB which are putatively activating, inhibitory, or dual function, respectively. Over 1000 diverse and rare CHIRs variants associated with differential Marek’s disease response (P < 0.05) emphasize the impact of CHIRs on shaping avian immune responses in diverse contexts. Objective 3: West Virginia University (WVU) maintained genetic stocks are typed at the MHC and other alloantigen systems. The stocks, available for collaborative projects include two inbred lines, four congenic lines and five different line crosses. Alloantisera produced by Dr. W. E. Briles at Northern Illinois University (NIU) are held by WVU. This resource includes 243 alloantisera reacting against 74 different antigens, across most alloantigen systems. Zhou Objective 2: This study examines mucosal immune responses to avian influenza virus (AIV) in the Harderian gland (HG) of two genetically distinct chicken lines: the Fayoumi, which is relatively resistant to AIV, and the Leghorn, which is more susceptible. Chickens from both lines were inoculated with low pathogenic avian influenza (LPAI) H6N2, and various immune parameters were assessed through viral titers, tissue analysis, and flow cytometry. Findings revealed that Fayoumi chickens exhibited a higher percentage of macrophages and less severe symptoms compared to Leghorns by day four post-inoculation. Leghorns had increased MHC class II expression on macrophages and B cells, despite having fewer macrophages overall. Ongoing analyses, including single-cell RNA sequencing and spatial gene expression profiling, aim to identify genetic factors that confer resistance in Fayoumi chickens. Ultimately, this research seeks to enhance understanding of host resilience to AIV, thereby reducing disease impact and improving poultry industry sustainability.

Publications

Peer-Reviewed Publications Abraham, M.E., C. I. Robison, P. B. S. Serpa, N. J. Strandberg, M. A. Erasmus, G. S. Fraley, G. F. Erf, and D. M. Karcher. 2024 Cage-free pullets minimally affected by stocking density stressors. Animals (Basel). 14:1513. doi: 10.3390/ani14101513. PMID: 38791730; PMCID: PMC11117258. Ahmed Ali, R.A. Gallardo, F.A. Careem. Comparative pathogenicity of CA1737/04 and Mass infectious bronchitis virus genotypes in laying chickens. Comparative immunology microbiology and infectious diseases. 2023. Frontiers in Veterinary Science. Accepted. Akbar, H., K.W. Jarosinski. 2024. Temporal dynamics of purinergic receptor expression in the lungs of Marek’s disease (MD) virus-infected chickens resistant or susceptible to MD. Viruses. 16(7):1130. doi: 10.3390/v16071130 Al Hakeem, W. G., Cason, E. E., Adams, D., Fathima, S., Shanmugasundaram, R., Lourenco, J., & Selvaraj, R. K. (2024). Characterizing the Effect of Campylobacter jejuni Challenge on Growth Performance, Cecal Microbiota, and Cecal Short-Chain Fatty Acid Concentrations in Broilers. Animals, 14(3), 473. Ana P. da SilvaAF, Rianne ButerB, James MillsC, Remco DijkmanB, Anneke FeberweeB, Robert BecksteadC, Yosef HubermanD, Melina JonasE, Rosana MalenaD, Fernando PaolicchiD, Rodrigo A. GallardoAF Infectious coryza classification, diagnostics, and a comprehensive investigation on the HMTp210 gene of Avibacterium paragallinarum. Avian Dis.2024 Submitted. Beck, C. N., J. Zhao, and G. F. Erf. 2024. Vaccine immunogenicity versus gastrointestinal microbiome status: Implications for poultry production. Appl. Sci Appl. Sci. 14(3), 1240; https://doi.org/10.3390/app14031240 Botchway PK, Amuzu-Aweh EN, Naazie A, Aning GK, Otsyina HR, Saelao P, Wang Y, Zhou H, Dekkers JCM, Lamont SJ, Gallardo RA, Kelly TR, Bunn D, Kayang BB. Genotypic and phenotypic characterisation of three local chicken ecotypes of Ghana based on principal component analysis and body measurements. PLoS One. 2024 Aug 7;19(8):e0308420. doi: 10.1371/journal.pone.0308420. PMID: 39110760; PMCID: PMC11305577. Brandi A. Sparling, Theros T. Ng, Anaid Carlo-Allende, Fiona M. McCarthy, Robert L. Taylor Jr., Yvonne Drechsler. Immunoglobulin-like receptors in chickens: identification, functional characterization, and renaming to cluster homolog of immunoglobulin-like receptors. Poultry Science. 2024 Feb 1;103(2):103292. Cason, E. E., Al Hakeem, W. G., Adams, D., Shanmugasundaram, R., & Selvaraj, R. Al Hakeem, Walid G., et al. "The effect of Campylobacter jejuni challenge on the ileal microbiota and short-chain fatty acids at 28 and 35 days of age." Italian Journal of Animal Science 23.1 (2024): 299-312. Cotter, P. 2024. Avian polyclonal B-cell lymphocytosis – a stress indication or a consequence of infection? p39-41 Proceedings of the 73rd Western Poultry Disease Conference, Apr. 14-17, Salt Lake City UT. Cotter, P. 2024. The cytology of avian monocytosis – a laying hen perspective, pp36-38. Proceedings of the 73rd Western Poultry Disease Conference, Apr 14-17, Salt Lake City UT. Cotter, P. F. 2024. Reticulocytes and related erythroid atypia of ducks - indicators of stress or pathology? 2024 Poultry Science 103:103353 https://doi.org/10.1016/j.psj.2023.103353 Elaina R. Sculley, Edward S. Ricemeyer, Rachel C. Carroll, John Driver, Jacqueline Smith, Jim Kaufman, Cari Hearn, Adam Balic, Paula Chen, Susan Lamont, Skyler Kramer, Yvonne Drechsler, Hans Cheng, Wesley C. Warren. A single-nucleus census of immune and non-immune cell types for the major immune organ systems of chicken. bioRxiv. 2024:2024-08. Falcon, D.M., K. A. Byrne, M. A. Sales, and G. F. Erf. 2024. Spontaneous immunological activities in the target tissue of vitiligo-prone Smyth and vitiligo-susceptible Brown lines of chicken. Front Immunol. 15:1386727. doi: 10.3389/fimmu.2024.1386727. PMID: 38720888; PMCID: PMC11076693. Fathima, S., Al Hakeem, W. G., Shanmugasundaram, R., & Selvaraj, R. K. (2024). Effect of arginine supplementation on the growth performance, intestinal health, and immune responses of broilers during necrotic enteritis challenge. Poultry Science, 103(7), 103815. Fathima, S., Al Hakeem, W. G., Shanmugasundaram, R., Lourenco, J. M., & Selvaraj, R. K. (2024). The effect of supplemental arginine on the gut microbial homeostasis of broilers during sub-clinical necrotic enteritis challenge. Frontiers in Physiology, 15, 1463420. Fulton. J. E., A. M. McCarron, A. R. Lund, W. Drobik-Czwarno, A. Mullen, A. Wolc, J. Szadkowska, C. J. Schmidt and R. L. Taylor, Jr. 2024. The RHCE gene encodes the chicken blood system I. Gen. Sel. Evol. 56:47 <a href="https://doi.org/10.1186/s12711-024-00911-9">https://doi.org/10.1186/s12711-024-00911-9</a> Huaijun Zhou, Isabelle Baltenweck, Jack Dekkers, Rodrigo Gallardo, Boniface B. Kayang, Terra Kelly, Peter L. M. Msoffe, Amandus Muhairwa, James Mushi, Augustine Naazie, Hope R. Otsyina, Emily Ouma, and Susan J. Lamont. Feed the Future Innovation Lab for Genomics to Improve Poultry: a holistic approach to improve indigenous chicken production focusing on resilience to Newcastle disease. World Poultry Science Journal. 2024 https://doi.org/10.1080/00439339.2024.2321350 Honaker, C. F., R. L. Taylor, Jr., F. W. Edens, and P. B. Siegel. 2024. Growth of white Leghorn chicken immune organs after long-term divergent selection for high or low antibody response to sheep red blood cells. Animals 14:1487 https://doi.org/10.3390/ani14101487 J.Lane, E. Chenais, B. Bird, G. Vidal, H. Zhou, G. van Hoy, R.A. Gallardo, A. Roug, W. Smith, T. Kelly. A One Health Approach to Reducing Livestock Disease Prevalence in Developing Countries: Advances, Challenges, and Prospects. Annual Review of Animal Biosciences. Vol 13. In Press. Jayawardena, D., A. Majumder, A. Nazmi, R. Kaur, S. Tyagi, A. Anbazhagan, A. Kumar, S. Saksena, D. Olivares-Villagómez and P. K. Dudeja. 2023. Ion Transport basis of diarrhea, Paneth cell metaplasia and upregulation of mechanosensory pathway in anti-CD40 colitis. Inflammatory Bowel Diseases. XX,1-13. https://doi.org/10.1093/ibd/izae002 Kappari, L., Dasireddy, J. R., Applegate, T. J., Selvaraj, R. K., & Shanmugasundaram, R. (2024). MicroRNAs: exploring their role in farm animal disease and mycotoxin challenges. Frontiers in Veterinary Science, 11, 1372961. Khalid Z, Hauck R (2024): Comparative Transcriptomic Analysis of Chicken-origin Cell Lines following Avian Reovirus Inoculation. In: Proceedings of the 73rd Western Poultry Disease Conference, Salt Lake City, UT. pp 82 – 83. Kim, T, Hearn, C. J. and Heidari, M. Efficacy of Recombinant Marek's Disease Virus Vaccine 301B/1 Expressing Membrane-Anchored Chicken Interleukin-15. Avian Dis. 2024 Jun;68(2):117-128. Majeed, S., S.K. Hamad, B.R. Shah, L. Bielke, A. Nazmi. 2024. Natural intraepithelial lymphocytes populations rise during necrotic enteritis chickens. Frontiers in Immunology. 15:1354701. https://doi.org/10.3389/fimmu.2024.1354701 Mitchell, J., Sutton, K., Elango, J.N., Borowska, D., Perry, F., Lahaye, L., Santin, E., Arsenault, R.J., Vervelde, L. Chicken intestinal organoids: a novel method to measure the mode of action of feed additives. 2024. Frontiers in Immunology. 15, 10.3389/fimmu.2024.1368545 Patria, J.N., Jwander, L., Mbachu, I., Parcells, L., Ladman, B., Trimbert, J., Kaufer, B. B., Tavlarides-Hontz, and Mark S. Parcells. The meq Genes of Nigerian Marek’s Disease Virus (MDV) Field Isolates Contain Mutations Common to Both European and US High Virulence Strains. (in review). Perry, F., Johnson, C.N., Lahaye, L., Santin, E., Korver D.R., Kogut, M.H., Arsenault, R.J. Protected biofactors and antioxidants reduce the negative consequences of virus and cold challenge by modulating immunometabolism via changes in the Interleukin-6 receptor signaling cascade in the liver. 2024. Poultry Science. 103 (9), 104044. <ol start="2023"> <li>Buter, A. Feberwee, Sjaak de Wit, A. Heuvelink, A. P. da Silva, R. A. Gallardo, E. Soriano Vargas, J. Verwey, A. Jung, M. Tödte, R. Dijkman. Molecular characterization of the HMTp210 gene of Avibacterium paragallinarum and the proposition of a new genotyping method as alternative for classical serotyping. 2023. Avian Pathology 52 (5): 362-376 https://doi.org/10.1080/03079457.2023.2239178</li> <li>Jude, A.P. Da Silva, D. Rejmanek, H.L. Shivaprasad, S. Stoute, C. Jerry, R.A. Gallardo. Whole genome sequence of a novel genotype VIII infectious bronchitis virus isolated from California layers in 2021. ASM Microbiology Resource Announcements. 2023. In press.</li> <li>Jude, B. Jordan, A. Muller-Slay, R. Luciano, A. P da Silva, R. A. Gallardo. Mitigation of False Layer Syndrome Through Maternal Antibodies Against Infectious Bronchitis Virus. 2023. Avian Diseases. https://doi.org/10.1637/aviandiseases-D-23-00039</li> </ol> R.M. Abd-Elsalam, S.M. Najimudeen, M.E. Mahmoud, M. Hassan, R.A. Gallardo, M.F. Abdul Careem. Differential impact of Massachusetts, Canadian 4/91 and California 1737 genotypes of infectious bronchitis virus infection on lymphoid orans of chickens. 2024. Viruses. Accepted. DOI: 10.3390/v16030326 Rice, E.S., Alberdi, A., Alfieri, J., Athery, G., Balacco, J.R., Bardou, P., Blackmon, H., Charles, M., Cheng, H.H., Fedrigo, O., Fiddaman, S., Formenti, G., Frantz, L., M. Thomas, G.P., Hearn, C.J., Jarvis, E.D., Klopp, C., Marcos, S., Velez-Irizarry, D., Xu, L., Warren, W.C., Mason, A.S. 2023. A pangenome graph reference of 30 chicken genomes allows genotyping of large and complex structural variants. BMC Biology. 21(267). Rocchi, A. J., J. M Santamaria, C. N. Beck, M. A. Sales, B. M. Hargis, G. Tellez-Isaias, and G. F. Erf. 2023. Immunosuppressive effects of cyclic, environmental heat-stress in broiler chickens: Local and systemic inflammatory responses to intradermal injection of lipopolysaccharide. Vet. Sci. 11:16 <ol start="2023"> <li>Ramsubeik, S. Stoute, R.A. Gallardo, B. Crossley, D. Rejmanek, R. Jude, C. Jerry. Infectious bronchitis virus California variant CA1737 isolated from a commercial layer flock with cystic oviducts and poor external egg quality. Avian Diseases. 2023. 67 (2): 212-218.</li> </ol> Sparling, B. A., T. T. Ng, A. Carlo-Allende, F. M. McCarthy, R. L. Taylor, Jr., and Y. Drechsler. 2024. Identification, functional characterization, and renaming of the chicken homologue of immunoglobulin-like receptors to cluster homologue of immunoglobulin-like receptors. Poult. Sci. 103:103292 <a href="https://doi.org/10.1016/j.psj.2023.103292">https://doi.org/10.1016/j.psj.2023.103292</a> Stearns, R., K. Bowen, R. L. Taylor, Jr., J. S. Moritz, K. Matak, J. Tou, A. Freshour, J. Jaczynski, T. Boltz, X. Li, and C. Shen. 2024. Microbial profile of broiler carcasses processed at a university scale mobile poultry processing unit. Poult. Sci. 103:103576 https://doi.org/10.1016/j.psj.2024.103576 Swaggerty, C. L., C. F. Honaker, P. B. Siegel, M. H. Kogut, R. C. Anderson, C. M. Ashwell, and R. L. Taylor, Jr. 2024. Chickens selected for high and low antibody responses to sheep red blood cells influences cytokine and chemokine expression in peripheral blood leukocytes and splenic tissue. Poult. Sci. 103:103972 https://doi.org/10.1016/j.psj.2024.103972 Tsaxra, J.B., Abolnik, C., Chengula, A.A., Mushi, J.R., Msoffe, P.L.M, Muhairwa, A.P. Phiri, T., Jude, R., Chouicha, N., Mollel, E.L., Zhou, H., Gallardo, R. Kelly, T.R. 2024. Spatiotemporal Patterns of Distribution and Risk Factors for Newcastle Disease Virus Among Chickens in a Tanzania Live Bird Market. Transboundary and Emerging Diseases, vol. 2024, Article ID 5597050, 9 pages, 2024. https://doi.org/10.1155/2024/5597050. Tsaxra, J.B., Abolnik, C., Kelly, T.R. Chengula, A.A., Mushi, J.R., Msoffe, P.L.M, Muhairwa, A.P. Phiri, T., Jude, R., Chouicha, N., Mollel, E.L., Zhou, H., Gallardo, R.. Molecular characterization of Newcastle disease virus obtained from Mawenzi live bird market in Morogoro, Tanzania in 2020–2021. Braz J Microbiol (2023). https://doi.org/10.1007/s42770-023-01159-z Veronica Nguyen, Simone Stoute, Shayne Ramsubeik, Ian Miller, Carmen Jerry, Charles Corsiglia, and Rodrigo A. Gallardo. Epidemiological patterns of the infectious coryza outbreak in California 2016-2022. Avian Diseases. ** Accepted **. Wang, L., T. Xie, X. Zhou, G. Yang, Z. Guo, Y. Zhao, Y. Huang, S. J. Lamont, X. Lan 2023. LncIRF1 promotes chicken resistance to ALV-J Infection. 3 Biotech DOI: 10.1007/s13205-023-03773-y Wang, Y., P. Saelao, G. Chanthavixay, R. A. Gallardo, A. Wolc, J. E. Fulton, J. C. Dekkers, S. J. Lamont, T. R. Kelly, H. Zhou. 2024. Genomic regions and candidate genes affecting response to heat stress with Newcastle virus infection in commercial layers chicks using chicken 600K SNP array. Int. J. Mol. Sci. 2024, 25(5), 2640; https://doi.org/10.3390/ijms25052640. Xu H, Vega-Rodriguez W, Campos V., Jarosinski KW. 2024. mRNA splicing of UL44 and secretion of Alphaherpesvirinae glycoprotein C (gC) is conserved among the Mardiviruses. Viruses. 16(5);782. doi:10.3390/v16050782 <ol start="2024"> <li>Wang, P.Saelao, G. Chanthavixay, R.A. Gallardo, A, Wolc, J.E. Fulton, J.M. Dekkers, S.J. Lamont, T.R. Kelly, H. Zhou. Genomic regions and candidate genes affecting the response to heat stress with Newcastle virus infection in comercial layers chicks by using chicken 600K SNP array. 2024. International Journal of Molecular Sciences. DOI: 10.3390/ijms25052640</li> </ol> Yvonne Drechsler, Theros T. Ng, Brandi A. Sparling, R. D. Hawkins. 177 Functional Annotation of an Array of Immune Cells and Various Tissues in the Chicken. Journal of Animal Science. 2023 Nov 1;101(Supplement_2):24-5. Zhang, L., Xie, Q., Chang, S., Ai, Y., Dong, K., Zhang, H. 2024. Epigenetic factor microRNAs likely mediate vaccine protection efficacy against lymphomas in response to tumor virus infection in chickens through target gene involved signaling pathways. Veterinary Sciences. 11(4):139. Zhou, H. I. Baltenweck, J. C.M. Dekkers, R. Gallardo, B. B. Kayang, T. Kelly, P.L.M. Msoffe, A. Muhairwa, J. Mushi, A. Naazie., Otsyina, H.R., E. Ouma, S. J. Lamont. 2024. Feed the Future Innovation Lab for Genomics to Improve Poultry: A Holistic Approach to Improve Indigenous Chicken Production Focusing on Resilience to Newcastle Disease. World’s Poultry Science Journal. DOI: 10.1080/00439339.2024.2321350. Zhou, H., I. Baltenweck, J. Dekkers, R. Gallardo, B.B. Kayang, T. Kelly, P. L. M. Msoffe, A. Muhairwa, J. Mushi, A. Naazie, H. R. Otsyina, E. Ouma, S. J. Lamont. 2024. Feed the Future Innovation Lab for Genomics to Improve Poultry: A Holistic Approach to Improve Indigenous Chicken Production Focusing on Resilience to Newcastle Disease. World’s Poultry Science Journal. 80:2, 273-297, DOI: 10.1080/00439339.2024.2321350   Abstracts Anaid Carlo-Allende, Brandi A. Sparling, Yvonne Drechsler. RNA-interference: role of Ig-like receptor B in chicken macrophage response to AIV and Salmonella. College of Veterinary Medicine 2024 Research Day, Western University of Health Sciences, Pomona, CA. March 25th, 2024. Anderson, A., C. N. Beck, J. M. Santamaria, J. T. Lee, R. Adhikari, S. Rochell, and G. F. Erf. 2024. Influence of dietary arginine level on local and systemic leukocyte populations and inflammatory cytokine expression in response to intradermal injection of lipopolysaccharide in broilers. Poult. Sci. 439P. Arsenault, R.J. The Commensal vs. Control: Salmonella in Broilers. International Association for Food Protection Annual Meeting. 2024, July 14-17, Long Beach, CA. Arsenault, R.J. The Immune System, Disease Resistance, and Performance in Production Animals. Kemin Intestinal Health Symposium. 2023, October 4-5, New Orleans, LA.Impact of two novel Salmonella bacterin vaccines on broiler chicken immunity and performance. 2024. Asghar Sedaghat, Walid Ghazi Al Hakeem , Shahna Fathima , Syamily Shaji , Parimal Sheth, and Ramesh Selvaraj. (2024). Beck, C. N., J. M. Santamaria, R. Perera, and G. F. Erf. 2023. Leukocyte profiles in blood, spleen, liver, and cecal tonsils following a multi-step commercial Salmonella vaccination program in White Leghorn chicks. IPSF. M15. Beck, C. N., J. M. Santamaria, R. Perera, and G. F. Erf. 2024. Intradermal administration of Salmonella Typhimurium in non-sensitized and sensitized specific pathogen-free White Leghorn chicks results in qualitatively different local inflammatory responses. Poult. Sci. 151. Beck, C. N., J. M. Santamaria, R. Perera, J. Zhao, and G. F. Erf. 2024. Commercial Salmonella vaccination programs influence cecal pouch microbiome and alter cecal tonsil T cell levels in specific pathogen-free White Leghorn chicks. Poult. Sci. 399P. Brandi A. Sparling, Yvonne Drechsler. (2024). Exploring Ig-like receptor gene polymorphisms and their relation to disease resistance in the chicken [Talk]. Plant and Animal Genome Conference XXXI, Poultry 1, San Diego, CA. January 12-17, 2024. Dunn, J., Mays, J., Hearn, C., Cheng, H., Chase-Topping, M., Lycett, S., Doeschl-Wilson, A.LUS-UK Collab: Influence of vaccines, host genetics, and mutation rates on the evolution of infectious diseases. CRWAD. 2024, January 21-24, Chicago, IL. Facchetti v Assumpcao, A., V. Caputi, C. M. Ashwell, C. F. Honaker, A. M. Donoghue, P. B. Siegel, R. L. Taylor Jr, and J. M. Lyte. 2024. Cecal antibody concentrations of White Leghorn chickens selected for divergent blood antibody titer response to sheep red blood cells. Poult. Sci. 103(Suppl. 1):148 abstract 297 Fathima, S., Al Hakeem, W., Shah, B., Shanmugasundaram, R., & Selvaraj, R. (2024). Effect of arginine supplementation on production performance and inflammatory response in broilers during necrotic enteritis challenge. International Poultry Science Forum. He, Y., R. L Taylor Jr., H. Zhang, C. M Ashwell, K. Zhao and J. Song. 2024. Transgenerational epigenetic inheritance and poultry health. PAG 31, San Diego, Jan. 11-17, 2024 https://pag.confex.com/pag/31/meetingapp.cgi/Paper/53871 Hoangvi Le, Brandi A. Sparling, Yvonne Drechsler, Theros T. Ng. Oral Presentation. Targeted RNA in situ hybridization to determine the spatial expression of the Cluster Homolog of Immunoglobulin-like Receptors (CHIR) in the chicken intestine after coccidia vaccine challenge. Poultry Science Association Conference, Louisville, KY. July 15th to July 18th, 2024. Hoangvi Le, Brandi A. Sparling, Yvonne Drechsler, Theros T. Ng. Targeted RNA in situ hybridization to determine the spatial expression of the Cluster Homolog of Immunoglobulin-like Receptors (CHIR) in the chicken intestine after coccidia vaccine challenge. College of Veterinary Jarosinski KW. Marek’s Disease Virus UL13, Virion Protein US10, and Cellular LY6E in Horizontal Transmission. 104th Meeting of the Conference of Research Workers in Animal Disease. Chicago, IL, Jan 21-23, 2024 Jarosinski KW. The role of the conserved alphaherpesvirus glycoprotein C in host-to-host transmission. 104th Meeting of the Conference of Research Workers in Animal Disease. Chicago, IL, Jan 21-23, 2024. Lowman, Z. S., K. A. Estes, C. M. Ashwell, and R. L. Taylor, Jr. 2024. Shell quality and egg mineral content from commercial W-36 laying hens supplemented with KeyShure plus zinc and manganese. Poult. Sci. 103(Suppl. 1): 234-235 abstract 513P Majeed, S., B.R. Shah, S.K. Hamad, N. Khalid, A. Nazmi. 2024. Natural intraepithelial lymphocytes respond to necrotic enteritis in chickens. CFAES Research Poster Forum, Colombus, Ohio, USA. Mark Parcells, Joseph Patria, Luka Jwander, Ifeoma Mbachu, Levi Parcells, Brian Ladman, Jakob Trimbert, Benedikt Kaufer, Phaedra Tavlarides-Hontz. The Mutations in the Sequences of the Meq Gene of Nigerian Marek’s Disease Virus (MDV) Field Strains Show Point Mutations Common to European and US High Virulence Strains. Proceedings of the 14th International Symposium on Marek’s Disease and Avian Herpesviruses. p. 26. St. Louis, MO. July 12-14, 2024 Mark Parcells, Joshua Miller, Justin Cueva2, Joseph Patria, Andele Conradie, Benedikt Kaufer, Phaedra Tavlarides-Hontz. Expression versus Replication of Marek’s Disease Viruses of Different Pathotypes: High Virulence MDVs Show Increased Genome Expression Relative to Virus Genome Replication in an REV-transformed Chicken T-cell Line Model for Latency. Proceedings of the 14th International Symposium on Marek’s Disease and Avian Herpesviruses. p. 50. St. Louis, MO. July 12-14, 2024 Mark Parcells, Justin Cueva, Nicholas Egan, Imane Assakhi, Phaedra Tavlarides-Hontz. Sequential Interactions of Marek’s Disease Virus Meq Proteins with Polycomb Repressive Complex Proteins During Latency Establishment. Proceedings of the 14th International Symposium on Marek’s Disease and Avian Herpesviruses. p. 44. St. Louis, MO. July 12-14, 2024 Nazmi, A., S. Majeed, S.K. Hamad, B.R. Shah, L. Bielke. 2024. Natural intraepithelial lymphocytes are critical intestinal defense against necrotic enteritis in chickens. American Association of Immunologist Annual Meeting, Chicago, USA. Niraula, A., R. L. Taylor, Jr., J. E. Fulton, and R. A. Dalloul. 2024. Major histocompatibility complex B15 haplotype and alloantigen types D and E exhibit association with resistance traits to coccidiosis challenge in chickens. 2024 Int. Poult. Scientific Forum p.52 abstract T161 Optimizing Protein Sources in Reduced-Protein Diets to Improve the Immune Responses During Coccidiosis in Broiler Chickens. Revathi Shanmugasundaram, Adeleye Ajao, Shana Fathima, Adelumola Oladeinde, Ramesh Selvaraj, Todd Applegate, and Oluyinka Olukosi. 2024. International Poultry Science Forum. Santamaria, J. M., C. N. Beck, R. Perera, and G. F. Erf. 2024. Immunogenic differences in primary immune response profiles to electron beam irradiated and formalin-inactivated Salmonella vaccines in pullets. Poult. Sci. 152. Santamaria, J. M., C. N. Beck, S. Orlowski, M. Maqueda, W. G. Bottje, and G. F. Erf. 2023. Local and systemic inflammatory responses to Gram- and Gram+ bacterial cell wall components in broiler lines selected for water-efficiency: insights from the dual-window approach. IPSF. M16. Santamaria, J. M., C. N. Beck, S. Orlowski, M. Maqueda, W. G. Bottje, and G. F. Erf. 2024. Selection of broiler breeder lines for improved water efficiency does not negatively affect innate and adaptive immune responses to intradermal injection of Salmonella-killed vaccine or lipopolysaccharide. Poult. Sci. 401P. Shah, B.K., S. Majeed, N. Khalid, A. Nazmi. 2024. In-ovo administration of osteopontin into chicken eggs: hatchability, chick quality, growth, and intestinal development. CFAES Research Poster Forum, Colombus, Ohio, USA. Shelby Ferrier, Hoangvi Le, Brandi A. Sparling, Yvonne Drechsler, Theros T. Ng. Investigate CHIR genes on chromosome 31 in Line N and Line P chicken lines. College of Veterinary Medicine 2024 Research Day, Western University of Health Sciences, Pomona, CA. March 25th, 2024. Shelby Ferrier, Hoangvi Le, Brandi A. Sparling, Yvonne Drechsler, Theros T. Ng: Investigate CHIR genes on chromosome 31 in Line N and Line P chicken lines. Poultry Science Association Conference, Louisville, KY. July 15th to July 18th, 2024. Taylor, R. L., Jr., A. M. McCarron, A. R. Lund, W. Drobik-Czwarno, A. Mullen, A. Wolc, J. Szadkowska, C. J. Schmidt and J. E. Fulton. 2024. The RHCE gene encodes the novel chicken blood alloantigen system I. Poult. Sci. 103(Suppl. 1):147 abstract 295 The Role of Exosomes in Marek's Disease Virus-mediated Immunosuppression and Immunity. Sohee Lee*, Yaw Kobia Mwodor, Shannon Modla, Ken Pendarvis, Phaedra Tavlarides-Hontz, Ryan J. Arsenault, and Mark S. Parcells. 96th Annual Northeastern Conference on Avian Diseases, p. 63, Penn State, Sept. 18 – 19, 2024 Sohee Lee, Yaw Kobia Mwodor, Shannon Modla, Ken Pendarvis, Phaedra Tavlarides-Hontz, Ryan J. Arsenault, Mark S. Parcells. The Role of Exosomes in Coordination of Immune Responses and Marek's disease virus- mediated Immune Suppression. Proceedings of the 14th International Symposium on Marek’s Disease and Avian Herpesviruses. p. 31. St. Louis, MO. July 12-14, 2024 The Marek’s disease virus (MDV) Meq Oncoprotein of vv+MDVs Specifically Binds the Chromatin Modifier BRG1 and Increases Meq Transcriptional Activity. Joseph Patria, Meilyn Farnell, Tiana Saldana, Phaedra Tavlarides-Hontz, and Mark Parcells. Proceedings of the 14th International Symposium on Marek’s Disease and Avian Herpesviruses. p. 25. St. Louis, MO. July 12-14, 2024 The Marek’s disease virus (MDV) Meq Oncoprotein of vv+MDVs Specifically Binds the Chromatin Modifier BRG1 and Increases Meq Transcriptional Activity. Joseph Patria, Meilyn Farnell, Tiana Saldana, Phaedra Travlarides-Hontz, and Mark S. Parcells. 96th Annual Northeastern Conference on Avian Diseases, p. 62, Penn State, Sept. 18 – 19, 2024 Uribe-Diaz, S., A. I. Omolewu, J. M. Santamaria, C. N. Beck, C. N. Vuong, G. Tellez-Isaias, G. F. Erf, B. M. Hargis, and Y. M. Kwon. 2024 Evaluation of the cellular immune response initiated by DNA aptamer-based experimental Salmonella vaccine complex using the growing feather pulp cutaneous test in broiler chickens. Poult. Sci. 153. Velez-Irizarry, D., Hearn, C. Characterizing the Single-cell Immune Landscape of Marek’s Disease Viral Infection Across Different Genetic Backgrounds Using Single-Cell RNA Sequencing. 14th International Symposium on Marek’s Disease and Avian Herpesviruses. 2024, July 12-14, St. Louis, MO. Velez-Irizarry, D., Hearn, C. Dissecting Immune Cell-Types Allele-Specific Expression in Response to Marek’s Disease Viral Infection. 14th International Symposium on Marek’s Disease and Avian Herpesviruses. 2024, July 12-14, St. Louis, MO.

Impact Statements

Broadbent Objective 2: It is important to identify novel variants of IBDV that are currently circulating, to determine whether vaccines should be updated. We identified a novel variant in the Delmarva region and demonstrated that 4 mutations present in the HVR led to a reduction in antibody binding. This information will be valuable to companies making IBDV vaccines. Objective 3: It is difficult to assess whether an ARV isolated from a chicken with enteritis is the primary cause, or whether it is a bystander infection not contributing to the enteritis. It may be possible to use primary organoids to screen isolates to evaluate if they cause enteritis or not. The organoids can also be used to study the mucosal immune response of the avian intestine to infection with enteric viruses.
Cotter Objective 3: A demonstration of thrombocyte mitosis is the first report of a property of a cell now known to be important in innate and acquired immunity.
Drechsler, Ng, Sparling Objective 1: Establishing the role of chicken immunoglobulin-like receptors will benefit agricultural and human research. This study will further understand immunoglobulin-like receptors in disease resistance in MHC-defined chickens, providing producers with genetic biomarkers for enhanced immunity against diseases through selective breeding. Objective 3: Functionally annotating the chicken genome will benefit research on agricultural animals. Uncovering the location of regulatory elements and determining their interactions will provide the necessary framework to understand how regulatory networks govern gene expression and how genetic and environmental influences alter these networks to impact animal growth, health, and disease susceptibility or resistance.
Erf Objective 2: Association of altered innate responses with autoimmune disease development and immunopathology provides insight into the regulation and function of the immune system in poultry. Studies on cellular and humoral responses to vaccines and vaccine components is important for the development of effective and safe vaccines. Understanding the influence of nutrition and environmental conditions on immune system development and function improves poultry production and health management. Objective 3: The autoimmune disease-prone Smyth, UCD-200/206 and Obese strain chickens are important genetic models to study the cause-effect relationship between genetic susceptibility, immune function, and environmental factors in multifactorial, non-communicable diseases affecting poultry and humans. The growing feather “in vivo test-tube” system together with blood sampling is an effective, minimally invasive two-window approach for the simultaneous examination of cellular and systemic immune responses, over time, in an individual.
Gallardo Objective 3: The understanding of the origin of FLS in laying hens gives us insights on the use of antibodies early in the chick’s life, to prevent the clinical issue.
Hauck Objective 2: A better understanding of how different cell types respond to infection with ARV is the first step in the identification of biomarkers for ARV infections. It is laying the groundwork for future experiments into the pathogenesis of ARV infections that will allow a more targeted testing of intervention methods.
Hearn Objective 1: Mechanisms of MHC- and non-MHC genetic resistance to poultry pathogens are being examined at the levels of immune cell composition, transcriptional regulation, and receptor diversity, and effects on disease response and pathogen transmission are being studied, which will aid development of both genetic and vaccine-based disease control methods. Objective 2: Determining the effects of the PD-1/PD-L1 T cell signaling pathway on MD pathology may offer novel targets for genetic resistance or new vaccine adjuvantation platforms. Objective 3: Development of a chicken immune cell atlas, RNA-based methods for bioassaying immune cell markers, and maintenance of critical genetic stocks will aid basic and applied avian immunology research needed to meet ongoing poultry disease challenges.
Jarosinski Objective 1: Identifying cellular interacting partners for MDV gC could significantly impact vaccine design and therapies to prevent MDV infection. Objective 2: Identifying a cell receptor would have a major impact on controlling MD. Objective 3: Understanding the mechanisms involved in how avian herpesviruses (pathogenic and vaccines) transmit from chicken to chicken will help generate better vaccines and the genetic selection of chicken lines.
Lamont Objective 1: Identification of structural and functional genetic variants associated with differential responses to pathogens laid the foundation for future studies and for genetic selection to improve disease resistance in poultry. Objective 3: Continued research with ISU chicken genetic lines was enabled.
Nazmi Objective 3: Our results indicate that innate immune cells (iCD8a and non-T cells (CD3neg IEL) and innate-like immune cells (TCRgd and TCRabCD8aa IEL) play a crucial role in protecting the mucosal barrier against NE induced by C. perfringens.
Parcells Objective 1: Understanding the genetic basis of disease resistance in poultry, particularly in the context of Marek's disease (MD) is significant. By characterizing the role of exosomes in immune suppression and vaccine responses, as well as investigating the effects of specific genes like SATB1 and vIL8 on vaccine efficacy, this research provides valuable insights into how genetic factors influence disease outcomes. Ultimately, these findings could guide the development of more effective vaccines and breeding strategies to enhance disease resistance in poultry populations. Objective 2: It is crucial for advancing our understanding of how environmental, dietary, and physiological factors influence the immune development and disease resistance of poultry. By investigating the role of splice variant-derived Meq proteins in Marek’s disease virus (MDV) pathogenesis and the evolutionary mechanisms behind MDV virulence, this research sheds light on the fundamental processes that affect disease susceptibility. These insights could inform the development of targeted strategies to enhance immune function and resilience in poultry, ultimately improving disease management and production efficiency in the industry. Objective 3: to enhance poultry production efficiency by developing methodologies and reagents that assess immune function and disease resistance. Cloning and expressing key chicken genes will provide vital tools for studying immune responses and protein interactions. This will support genetic selection efforts, leading to improved disease resilience and productivity in poultry.
Selvaraj Objective 3: Developed a killed vaccine, that will not cause liver disease in layers, for Salmonella.
Taylor Objective 1: Identifying alloantigen genes, their products as well as their associations with economic traits will facilitate genetic improvement and benefit stakeholders. Objective 3: Defined genetic stocks will enhance discovery of gene products that have direct or indirect impact important commercial traits.
Zhou Objective 2: We identified genetic variants associated with enhanced resistance to AI, which will have a significant impact on the poultry industry.