In the last decade, the emergence of variant strains of avian reovirus (ARV) has caused enormous economic impact in the poultry industry across Canada and USA. ARVs are non-enveloped viruses with ten segments of double-stranded RNA genome. So far, only six genotyping cluster groups are identified worldwide based on sequence analysis of the σC protein encoded by the S1 segment. In this study, we performed deep next generation whole-genome sequencing and analysis of twelve purified ARVs isolated from Saskatchewan, Canada. The viruses represent different genotyping cluster. A genome-wide sequence divergence of up to 25 per cent was observed between the virus isolates with a comparable and contrasting evolutionary history. The proportion of synonymous single-nucleotide variations (sSNVs) was higher than the non-synonymous (ns) SNVs across all the genomic segments. Genomic segment S1 was the most variable as compared with the other genes followed by segment M2. Evidence of positive episodic/diversifying selection was observed at different codon positions in the σC protein sequence, which is the genetic marker for the classification of ARV genotypes. In addition, the N-terminus of σC protein had a persuasive diversifying selection, which was not detected in other genomic segments. We identified only four ARV genotypes based on the most variable σC gene sequence. However, a different pattern of phylogenetic clustering was observed with concatenated whole-genome sequences. Together with the accumulation of point mutations, multiple re-assortment events appeared as mechanisms of ARV evolution. For the first time, we determined the mean rate of molecular evolution of ARVs, which was computed as 2.3 × 10⁻³ substitution/site/year. In addition, widespread geographic intermixing of ARVs was observed between Canada and USA, and between different countries of the world. In conclusion, the study provides a comprehensive analysis of the complete genome of different genotyping clusters of ARVs including their molecular rate of evolution and spatial distribution. The new findings in this study can be utilized for the development of effective vaccines and other control strategies against ARV-induced arthritis/tenosynovitis in the poultry industry worldwide.

Newly emerging arthrotropic avian reoviruses (ARVs) are genetically divergent, antigenically heterogeneous, and economically costly. Nevertheless, the mechanism of emerging ARV-induced disease pathogenesis and potential differences in virulence between virus genotypes have not been adequately addressed. In this study, the life cycle of ARV, including the formation of cytoplasmic ARV neo-organelles, paracrystalline structures, and virus release mechanisms, were characterized in the infected host cell by transmission electron microscopy (TEM). In addition, progressive changes in the structure of infected cells were investigated by time-lapse and field emission scanning electron (FE-SE) microscopy. ARVs from the four genotypic cluster groups included in the study caused gross and microscopic lesions in the infected birds. Marked infiltration of γδT cells, CD4⁺ and CD8⁺ T lymphocytes were observed in ARV infected tendon tissues starting day 3 post-infection. The ARV variant from genotype cluster-2 triggered significantly high trafficking of IFN-γ producing CD8⁺ T lymphocytes in tendon tissues and concomitantly showed high morbidity and severe disease manifestations. In contrast, the ARV variant from genotype cluster-4 was less virulent, caused milder disease, and accompanied less infiltration of IFN-γ producing CD8⁺ T cells. Interestingly, when we blunted antiviral immune responses using clodronate liposomes (which depletes antigen-presenting cells) or cyclosporin (which inhibits cytokine production that regulates T-cell proliferation), significantly lower IFN-γ producing CD8⁺ T cells infiltrated into tendon tissues, resulting in reduced tendon tissues apoptosis and milder disease manifestations. In summary, these data suggest that the degree of ARV virulence and tenosynovitis/arthritis are potentially directly associated with the ability of the virus to traffic massive infiltration of cytotoxic CD8⁺ T cells into the infected tissues. Moreover, the ability to traffic cytotoxic CD8⁺ T cells into infected tendon tissues and the severity of tenosynovitis differ between variants from different ARV genotype cluster groups. However, more than one virus isolate per genotype group needs to be tested to further confirm the association of pathogenicity with genotype. These findings can be used to further examine the interaction of viral and cellular pathways which are essential for the pathogenesis of the disease at the molecular level and to develop effective disease control strategies.

Variant avian reoviruses (ARVs) are economically important emerging pathogens of poultry, which mainly affect young broiler chickens and cause significant production losses. Currently, there are no effective commercial vaccines available for control and prevention of emerging variant ARVs. In this study, monovalent inactivated adjuvated (20% Emulsigen D) broiler breeder vaccines containing antigens from ARV genotype cluster (C) group -2, -4, -5, or -6, and a multivalent vaccine containing antigens from all the four indicated genotypic cluster groups were developed and evaluated for their efficacy in protecting broiler progenies against homologous or heterologous ARV challenge. The use of monovalent or multivalent inactivated vaccines in a prime-boost immunization strategy induced the production of ARV specific antibodies in broiler breeders. The maternal antibodies were effectively transferred to broiler progenies. Broiler progenies obtained from immunized breeders demonstrated milder clinical symptoms and reduced gross and histopathological lesions after homologous ARV challenge. More severe gross and histological lesions were observed in challenged progenies from unvaccinated broiler breeders. However, cross protection was not observed when either of the monovalent-vaccine groups were challenged with a heterologous virus. In addition, the progenies from the unvaccinated ARV challenged control or heterologous ARV challenged vaccinated groups had significantly reduced body weight gain (p < 0.01) than the unchallenged-control, challenged-multivalent, or homologous ARV-challenged monovalent vaccine groups. However, homologous ARV challenged progenies in the multivalent or monovalent vaccine groups had similar body weight gain as the control unchallenged group with significantly reduced viral load (p < 0.01) in the gastrocnemius tendon tissue. This study indicates that broad-spectrum protection of broiler progenies from variant ARV infections is feasible through the development of multivalent vaccines after proper characterization, selection and incorporation of multiple antigens based on circulating ARV genotypes in targeted regions.

In the past, we demonstrated that oligodeoxynucleotides containing CpG motifs (CpG-ODN) mimicking bacterial DNA, stimulate the innate immune system of neonatal broiler chickens and protect them against Escherichia coli and Salmonella Typhimurium (S. Typhimurium) septicemia. The first line of innate immune defense mechanism is formed by heterophils and plays a critical protective role against bacterial septicemia in avian species. Therefore, the objectives of this study were 1) to explore the kinetics of CpG-ODN mediated antibacterial mechanisms of heterophils following single or twice administration of CpG-ODN in neonatal broiler chickens and 2) to investigate the kinetics of the immunoprotective efficacy of single versus twice administration of CpG-ODN against S. Typhimurium septicemia. In this study, we successfully developed and optimized flow cytometry-based assays to measure phagocytosis, oxidative burst, and degranulation activity of heterophils. Birds that received CpG-ODN had significantly increased (p < 0.05) phagocytosis, oxidative burst, and degranulation activity of heterophils as early as 24 h following CpG-ODN administration. Twice administration of CpG-ODN significantly increased the phagocytosis activity of heterophils. In addition, our newly developed CD107a based flow cytometry assay demonstrated a significantly higher degranulation activity of heterophils following twice than single administration of CpG-ODN. However, the oxidative burst activity of heterophils was not significantly different between birds that received CpG-ODN only once or twice. Furthermore, delivery of CpG-ODN twice increased immunoprotection against S. Typhimurium septicemia compared to once but the difference was not statistically significant. In conclusion, we demonstrated enhanced bactericidal activity of heterophils after administration of CpG-ODN to neonatal broiler chickens. Further investigations will be required to identify other activated innate immune cells and the specific molecular pathways associated with the CpG-ODN mediated activation of heterophils.

Establishing beneficial microbiota in chickens earlier in life is advantageous for optimum production and health. This study was conducted to investigate the colonization of probiotics in the intestines of specific pathogen free chicken embryos using a coarse spray of probiotics on incubating eggs to accelerate the establishment of a healthy jejunal microbiota in neonatal chickens. Enterococcus faecalis were sprayed on incubating eggs on 12, 15 and/or 17 days of embryonation (DOE) to explore the optimum day(s) needed for colonization. Colonization was confirmed by direct culture and whole genome sequencing of intestinal contents of embryos. Colonization was best observed when probiotics were sprayed on two separate days - 15 and 17 DOE. Further, effects of coarse spray of E. faecalis, Ligilactobacillus salivarius, Lactobacillus plantarum, Bifidobacterium pullorum subsp. gallinarum, and Pediococcus acidilactici on incubating eggs individually or as a mixture in jejunal microbiota were assessed at 2, 10, 20, and 30 days post hatch (DPH) using 16S rRNA amplicon sequencing. Coarse spray application of L. salivarius, L. plantarum and the mixture of probiotics lead to significantly faster convergence trajectories towards a mature reference profile [represented by 30 DPH with no probiotics delivery (negative control)], compared to groups that received probiotics by the oral route. Beta diversity analysis showed the largest separation between groups at 2 DPH. Over 10, 20, and 30 DPH, all communities gradually converged, with the group that received the sprayed probiotic mixture retaining a unique profile for the longest period. The group that received the sprayed probiotic mixture consistently outperformed the negative control group and the group given oral probiotics on 2 DPH at both species and genus levels in terms of richness. This confirms the beneficial effect of a probiotic mixture spray compared to natural colonization or short-term oral application. In conclusion, spray application of probiotics as a coarse spray is an industry feasible technique and noninvasive method for introducing probiotics to chicken embryos leading to a rapid establishment of healthy jejunal microbial composition.