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Background Newcastle disease virus (NDV) is a threat to poultry production worldwide. A better understanding of mechanisms of resistance and susceptibility to this virus will improve measures for NDV prevention and control. Males and females from resistant Fayoumi and susceptible Leghorn lines were either challenged with a lentogenic strain of the virus or given a mock infection at 3 weeks of age. The lung transcriptomes generated by RNA-seq were studied using contrasts across the challenged and nonchallenged birds, the two lines, and three time points post-infection, and by using Weighted Gene Co-expression Network Analysis (WGNCA). Results Genetic line and sex had a large impact on the lung transcriptome. When contrasting the challenged and nonchallenged birds, few differentially expressed genes (DEG) were identified within each line at 2, 6, and 10 days post infection (dpi), except for the more resistant Fayoumi line at 10 dpi, for which several pathways were activated and inhibited at this time. The interaction of challenge and line at 10 dpi significantly impacted 131 genes (False Discovery Rate (FDR) <0.05), one of which was PPIB . Many DEG were identified between the Fayoumi and Leghorns. The number of DEG between the two lines in the challenged birds decreased over time, but increased over time in the nonchallenged birds. The nonchallenged Fayoumis at 10 dpi showed enrichment of immune type cells when compared to 2 dpi, suggesting important immune related development at this age. These changes between 10 and 2 dpi were not identified in the challenged Fayoumis. The energy allocated to host defense may have interrupted normal lung development. WGCNA identified important modules and driver genes within those modules that were associated with traits of interest, several of which had no known associated function. Conclusions The lines’ unique response to NDV offers insights into the potential means of their resistance and susceptibility. The lung transcriptome shows a unique response to lentogenic NDV compared to a previous study on the trachea of the same birds. It is important to analyze multiple tissues in order to best understand the chicken’s overall response to NDV challenge and improve strategies to combat this devastating disease.

Enhancing genetic resistance of chickens to Newcastle Disease Virus (NDV) provides a promising way to improve poultry health, and to alleviate poverty and food insecurity in developing countries. In this study, two inbred chicken lines with different responses to NDV, Fayoumi and Leghorn, were challenged with LaSota NDV strain at 21 days of age. Through transcriptome analysis, gene expression in spleen at 2 and 6 days post-inoculation was compared between NDV-infected and control groups, as well as between chicken lines. At a false discovery rate <0.05, Fayoumi chickens, which are relatively more resistant to NDV, showed fewer differentially expressed genes (DEGs) than Leghorn chickens. Several interferon-stimulated genes were identified as important DEGs regulating immune response to NDV in chicken. Pathways predicted by IPA analysis, such as \"EIF-signaling\", \"actin cytoskeleton organization nitric oxide production\" and \"coagulation system\" may contribute to resistance to NDV in Fayoumi chickens. The identified DEGs and predicted pathways may contribute to differential responses to NDV between the two chicken lines and provide potential targets for breeding chickens that are more resistant to NDV.

Behind each eye of the chicken resides a unique lymph tissue, the Harderian gland, for which RNA sequencing (RNA-seq) analysis is novel. We characterized the response of this tissue to Newcastle disease virus (NDV) in two inbred lines with different susceptibility to NDV across three time points. Three-week-old relatively resistant (Fayoumi) and relatively susceptible (Leghorn) birds were inoculated with a high-titered (10 7 EID 50 ) La Sota strain of NDV via an oculonasal route. At 2, 6, and 10 days post infection (dpi) Harderian glands were collected and analyzed via RNA-seq. The Fayoumi had significantly more detectable viral transcripts in the Harderian gland at 2 dpi than the Leghorn, but cleared the virus by 6 dpi. At all three time points, few genes were declared differentially expressed (DE) between the challenged and nonchallenged birds, except for the Leghorns at 6 dpi, and these DE genes were predicted to activate an adaptive immune response. Relative to the Leghorn, the Fayoumi was predicted to activate more immune pathways in both challenged and nonchallenged birds suggesting a more elevated immune system in the Fayoumis under homeostatic conditions. Overall, this study helped characterize the function of this important tissue and its response to NDV.

Newcastle disease virus (NDV) is a threat to the global poultry industry, but particularly for smallholder farmers in low- and middle-income countries. Previous reports suggest that some breeds of chickens are less susceptible to NDV infection, however, the mechanisms contributing to this are unknown. We here examined the comparative transcriptional responses of innate immune genes to NDV infection in inbred sublines of the Fayoumi and Leghorn breeds known to differ in their relative susceptibility to infection as well as at the microchromosome bearing the major histocompatability complex (MHC) locus. The analysis identified a set of five core genes, Mx1 , IRF1 , IRF7 , STAT1 , and SOCS1 , that are up-regulated regardless of subline. Several genes were differentially expressed in a breed- or subline-dependent manner. The breed-dependent response involved TLR3 , NOS2 , LITAF , and IFIH1 in the Fayoumi versus IL8 , CAMP , and CCL4 in the Leghorn. Further analysis identified subline-dependent differences in the pro-inflammatory response within the Fayoumi breed that are likely influenced by the MHC. These results have identified conserved, breed-dependent, and subline-dependent innate immune responses to NDV infection in chickens, and provide a strong framework for the future characterization of the specific roles of genes and pathways that influence the susceptibility of chickens to NDV infection.

Newcastle disease virus (NDV) has devastating impacts on poultry throughout the world. The inbred Fayoumi and Leghorn chicken lines, previously characterized as relatively resistant and susceptible, respectively, to various pathogens were utilized to characterize host response to the NDV vaccine and identify potential genes and pathways associated with NDV resistance. Three-week-old chicks were inoculated with La Sota NDV (challenged) or PBS (nonchallenged) via the oculonasal route. At 2, 6, and 10 days post infection (dpi), approximately one-third of the birds within each line and challenge group were euthanized for tissue collection. At 2 and 6 dpi, lachrymal fluid was collected from all birds for viral quantification using qPCR. At 0 and 10 dpi, serum was collected from all birds to quantify NDV antibody levels using ELISA. The transcriptome response in tracheal epithelial cells, lungs, and Harderian glands from four birds per treatment group (line, dpi, and challenge group; 48 birds total) was analyzed using RNA-seq. These three tissues chosen for their location near the site of infection. A separate study analyzed mean survival time after challenge with velogenic NDV. These studies found the Fayoumi and Leghorn chickens were relatively resistant and susceptible, respectively to lentogenic and velogenic NDV, based on lachrymal fluid viral load, antibody levels, and within-tissue viral transcript counts detected by RNA-seq after the lentogenic challenge, and survival analysis after a velogenic challenge. The trachea, lung, and Harderian gland RNA-seq data were analyzed individually and jointly to gain a more comprehensive understanding of the impact of lentogenic NDV challenge using differential expression and co-expression analyses. The tissues with detectable viral transcripts, trachea and Harderian gland, activated T cell related pathways after challenge. The challenge had the largest impact on the trachea transcriptome, based on principal component analysis and numbers of differentially expressed genes. In the lung and Harderian gland, especially, the two lines had distinct responses to the virus. The combined tissue analysis revealed clusters of co-expressed genes that were correlated with important factors like line, challenge status, and dpi. Overall, EIF2 signaling, mTOR signaling, collagen related genes, and TNFSF13B / TNFRSF13B were identified as potential candidate genes and pathways related to NDV resistance. Further studies are required to determine and confirm how these genes and pathways impact NDV resistance.