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Newcastle disease is an acute highly contagious disease, responsible for serious economic losses to poultry industry worldwide particularly in disease endemic regions such as Pakistan. Subsequent to evolution, with the passage of time, novel genotypes and sub-genotypes are emerging worldwide raising concerns on efficacy of vaccine strains and, therefore ascertain candidate vaccines that can provide protection much better than those used before. Now a day, with the advancement in reverse genetics system, efforts are ongoing to construct a vaccine strain that, beside specific immunity, may have the potential to enhance innate immunity and therefore a better use against a viral infection. A much has been elucidated about clinical pathogenicity of NDVs of different pathotypes and genotypes in their susceptible hosts (e.g., chickens); nevertheless, corresponding to innate immune response, there is a paucity of data regarding comparative assessment of transcriptome profile in birds challenged with NDVs of varying pathogenicity to better unleash a comparative rate of expression of differentially expressed genes (DEGs) and their subsequent use in the development of novel vaccines through reverse genetics system. Therefore, the current study was conducted to 1) determine biologic, genomic and genotypic characterization of NDV strains isolated from waterfowl and pigeon independently, 2) a clinico-pathological assessment of these strains in chickens and pigeons and, 3) a comparative assessment of innate immune response-related genes that become either up-regulated or down-regulated upon exposure to NDV strains of varying pathogenicity in chicken using Illumia HiSeq-2500. Biological, genomic and genotypic analysis categorized the Anseriformes-originated NDV isolate as velogenic strain (sub-genotype VIIi) whereas pigeon-originated NDV isolate as mesogenic strain (sub-genotype VIm). Infectious potential of velogenic and mesogenic NDV strains was assessed in broiler chickens and pigeons, separately. For each of virus exposure, variations in the severity and duration of infection were observed among challenged and contact chickens and pigeons. Chicken were found more susceptible to velogenic strain while pigeons were found more susceptible to mesogenic strain. Comparative transcriptome analysis revealed expression profile of innate immune response-related genes in lungs and spleen tissues of chickens infected with velogenic and mesogenic strains. Following Gene Ontology (GO) enrichment and Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis, a total of 109 DEGs were commonly expressed in tissue samples (lung-A, spleen-A, lung-P and spleen-P). Genes associated with metabolic and cellular processes such as innate immune system associated signalling pathways, RIG-I, Toll-like, NF-Kappa β and MAPK signalling pathways for activation of interferonstimulated genes (ISGs) were more abundant. DAVID-based annotation classified these 109 genes into five major categories that included interferon stimulatory genes (ISGs) (n = 37), lymphoid tissue innate immunity (n = 30), inflammatory responses associated genes (n = 29), genes for regulation of adaptive immune components (n = 12) and toll like receptor (n = 1). While comparing lung tissues (lung-A vs lung-P), analysis revealed a significant variation in expression of 101 of 109 DEGs, whereas, 106 DEGs had significant variations in expression for spleen tissues (spleen-A vs spleen-P). Out of 109 DEGs, for lung tissue, six genes (CD22, CR2, FOXS1, ITGA6, KMTSE, LYST, USP15 and USP33) had a non-significant difference in rate of expression while it was three genes (IL15, KLHL13, MKO7) for spleen tissue. Hence, post-infection with NDVs of varying pathogenicity, study highlights differential expression of innate immunity related genes where a candidate gene could be selected to construct vaccine strains through reverse genetics system with cumulative potential to enhance immunity and combat challenge from field viruses in the future.
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