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Open Access Publications from the University of California

Scholarly Works (35 results)

  • Thesis
  • Peer Reviewed
UC Davis Electronic Theses and Dissertations (2024)

Currently, Avian Hepatitis E virus (aHEV) has emerged as a significant concern within the poultry industry, leading to elevated mortality rates characterized by enlarged livers and spleens in affected flocks. The pathological progression involves hepatic lipidosis, exudate release into the coelomic cavity, and eventual liver fracture accompanied by hemorrhages. Despite its impact, there remains a notable dearth of comprehensive information on the pathobiology and epidemiology of the virus and associated disease. This study focused on aHEV infections in commercial layers, its seroprevalence, virus isolation, designing a new diagnostic tool for detection of viral RNA, and the identification of circulating genotypes. Utilizing a commercial ELISA test, we observed approximately 30% seropositivity among all collected serum samples. In addition, we detected a positive correlation between aHEV titers and the age of the birds. Regarding viral load distribution, gallbladders exhibited the highest loads compared to the livers and spleens. The genotyping strategy was able to detect genotype 2 viruses, and for the first time in the U.S. identified genotype 3, which has significantly altered the previously established epidemiological understanding of this virus in the country. Despite efforts to isolate the virus in SPF eggs, our results were not successful. In conclusion, all these findings highlight the importance of continuing aHEV research to strengthen control strategies in the poultry sector.

    • Thesis
    • Peer Reviewed
    UC Davis Electronic Theses and Dissertations (2022)

    Avian reoviruses are recognized for their genetic variability. The emergence of pathogenic variant strains causes negative impacts to the poultry industry worldwide. The disease prevention is based on the use of live classical and inactivated autogenous vaccines, however, they have a limited effect against the circulating variants, so they require a frequent update. The current molecular classification methods use the partial S1 gene that encodes the סC protein, but different genotypes do not always correlate with pathogenicity and sometimes induce a deficient cross-protection. Therefore, investigation of other variable genes and correlations between pathogenicity and antigenicity of variant strains is crucial for a better classification method. The present investigation focuses on the molecular, pathogenic, and antigenic characterization of emerging avian reovirus variant strains. This research is divided into three chapters. In the first chapter, we did a molecular characterization based on the S1 gene of 85 avian reoviruses obtained from the California outbreak and we did a whole-genome characterization of a portion of them. The characterized reoviruses were categorized in six genotypic clusters. We detected a shift in cluster representation throughout time occurred. According to the whole genome analyses, our results suggested that the L3, M2 and S1 genes accounted for most of the variability of these viruses. In chapter two we investigated the pathogenicity within the same S1 genotypic cluster variants. The genomes of two variant strains and a classical strain belonging to the same S1 genotype one were compared. Additionally, these strains were used in a challenge experiment involving inoculated and horizontally exposed specific-pathogen-free chickens. The whole-genome sequence analysis of the three strains revealed nucleotide identity differences in the L3, M2, and S1 genes. In addition, the variant strains indicated nucleotide identities differences in the S4 gene, despite having high homologies in all other genes. The challenge experiments showed that variant and classical strains replicated differently in tendons, hearts and duodena of the challenged and exposed chickens and caused dissimilar pathologic lesions and lymphoid depletion degrees in bursas and thymi of the challenged chickens. Because we consider that it is critical to associate genetic changes with the pathogenicity and antigenicity of variant strains in the selection of autogenous vaccines, in chapter three, we explored the association between the genetic and antigenic characteristics of 29 avian reoviruses, including conventional and variant strains using genetic and antigenic cartography. We detected high variation in terms of antigenicity which was not strongly correlated with the genetic composition of variable genes. The information generated in the present investigation contributes to the understanding of the epidemiology and pathobiology of avian reoviruses variant strains. In addition, it provides insights on how other genes besides S1 add variability in the diverse avian reovirus phenotypes.

      Cover page: Molecular, Pathogenic, and Antigenic Characterization of Emerging Avian Reovirus Variant Strains
      • Article
      • Peer Reviewed
      UC Davis Previously Published Works (2020)
      The chicken immune system has provided an immense contribution to basic immunology knowledge by establishing major landmarks and discoveries that defined concepts widely used today. One of many special features on chickens is the presence of a compact and simple major histocompatibility complex (MHC). Despite its simplicity, the chicken MHC maintains the essential counterpart genes of the mammalian MHC, allowing for a strong association to be detected between the MHC and resistance or susceptibility to infectious diseases. This association has been widely studied for several poultry infectious diseases, including infectious bronchitis. In addition to the MHC and its linked genes, other non-MHC loci may play a role in the mechanisms underlying such resistance. It has been reported that innate immune responses, such as macrophage function and inflammation, might be some of the factors driving resistance or susceptibility, consequently influencing the disease outcome in an individual or a population. Information about innate immunity and genetic resistance can be helpful in developing effective preventative measures for diseases such as infectious bronchitis, to which a systemic antibody response is often not associated with disease protection. In this review, we summarize the importance of the chicken MHC in poultry disease resistance, particularly to infectious bronchitis virus (IBV) infections and the role played by innate immunity and inflammation on disease outcome. We highlight how future studies focusing on the MHC and non-MHC genes can potentially bring clarity to observed resistance in some chicken B haplotype lines.
        Cover page: The Chicken MHC: Insights into Genetic Resistance, Immunity, and Inflammation Following Infectious Bronchitis Virus Infections
        • Article
        • Peer Reviewed
        UC Davis Previously Published Works (2017)
        Live virus vaccines are commonly used in poultry production, particularly in broilers. Massive application and generation of a protective local mucosal and humoral immunity with no adverse effects is the main goal for this strategy. Live virus vaccines can be improved by adding adjuvants to boost mucosal innate and adaptive responses. In a previous study we showed that diatomaceous earth (DE) can be used as adjuvant in inactivated vaccines. The aim of this study was to test DE as adjuvant in an Ark-DPI live infectious bronchitis virus (IBV) vaccine after ocular or spray application. Titrating the virus alone or after addition of DE showed that DE had no detrimental effect on the vaccine virus. However, adding DE to the vaccine did not induce higher IgG titers in the serum and IgA titers in tears. It also did not affect the frequency of CD4+ T cells, CD8+ T cells and monocytes/macrophages in the blood and the spleen determined by flow cytometry. In addition, protection generated against IBV homologous challenges, measured by viral load in tears, respiratory signs and histopathology in tracheas, did not vary when DE was present in the vaccine formulation. Finally, we confirmed through our observations that Ark vaccines administered by hatchery spray cabinet elicit weaker immune responses and protection against an IBV homologous challenge compared to the same vaccine delivered via ocular route.
          Cover page: The effect of diatomaceous earth in live, attenuated infectious bronchitis vaccine, immune responses, and protection against challenge
          • Article
          • Peer Reviewed
          UC Davis Previously Published Works (2016)
          Runting stunting syndrome (RSS) is a disease condition that affects broilers and causes impaired growth and poor feed conversion because of enteritis characterized by pale and distended small intestines with watery contents. The etiology of the disease is multifactorial, and a large variety of viral agents have been implicated. Here we describe the detection and isolation of an infectious bronchitis virus (IBV) -like coronavirus from the intestines of a flock of 60,000 14-day-old brown/red broiler chicks. The birds showed typical clinical signs of RSS including stunting and uneven growth. At necropsy, the small intestines were pale and distended with watery contents. Histopathology of the intestines revealed increased cellularity of the lamina propria, blunting of villi, and cystic changes in the crypts. Negative stain electron microscopy of the intestinal contents revealed coronavirus particles. Transmission electron microscopy of the intestine confirmed coronavirus in the cytoplasm of enterocytes. Using immunohistochemistry (IHC), IBV antigen was detected in the intestinal epithelial cells as well as in the proventriculus and pancreas. There were no lesions in the respiratory system, and no IBV antigen was detected in trachea, lung, air sac, conjunctiva, and cecal tonsils. A coronavirus was isolated from the intestine of chicken embryos but not from the allantoic sac inoculated with the intestinal contents of the broiler chicks. Sequencing of the S1 gene showed nucleic acid sequence identities of 93.8% to the corresponding region of IBV California 99 and of 85.7% to IBV Arkansas. Nucleic acid sequence identities to other IBV genotypes were lower. The histopathologic lesions in the intestines were reproduced after experimental infection of specific-pathogen-free chickens inoculated in the conjunctiva and nares. Five days after infection, six of nine investigated birds showed enteritis associated with IBV antigen as detected by IHC. In contrast to the field infection, birds in the experimental group showed clear respiratory signs and lesions in the upper respiratory tract. The results suggest a broader tissue tropism of this isolate, which might be related to the mutations in the S1 gene.
            • Article
            • Peer Reviewed
            UC Davis Previously Published Works (2022)
            Infectious bronchitis virus (IBV) is a highly variable RNA virus that affects chickens worldwide. Due to its inherited tendency to suffer point mutations and recombination events during viral replication, emergent IBV strains have been linked to nephropathogenic and reproductive disease that are more severe than typical respiratory disease, leading, in some cases, to mortality, severe production losses, and/or unsuccessful vaccination. QX and DMV/1639 strains are examples of the above-mentioned IBV evolutionary pathway and clinical outcome. In this study, our purpose was to systematically compare whole genomes of QX and DMV strains looking at each IBV gene individually. Phylogenetic analyses and amino acid site searches were performed in datasets obtained from GenBank accounting for all IBV genes and using our own relevant sequences as a basis. The QX dataset studied is more genetically diverse than the DMV dataset, partially due to the greater epidemiological diversity within the five QX strains used as a basis compared to the four DMV strains from our study. Historically, QX strains have emerged and spread earlier than DMV strains in Europe and Asia. Consequently, there are more QX sequences deposited in GenBank than DMV strains, assisting in the identification of a larger pool of QX strains. It is likely that a similar evolutionary pattern will be observed among DMV strains as they develop and spread in North America.
              Cover page: Infectious Bronchitis Virus: A Comprehensive Multilocus Genomic Analysis to Compare DMV/1639 and QX Strains
              • Article
              • Peer Reviewed
              UC Davis Previously Published Works (2018)

              Background

              Newcastle disease virus, in its most pathogenic form, threatens the livelihood of rural poultry farmers where there is a limited infrastructure and service for vaccinations to prevent outbreaks of the virus. Previously reported studies on the host response to Newcastle disease in chickens have not examined the disease under abiotic stressors, such as heat, which commonly experienced by chickens in regions such as Africa. The objective of this study was to elucidate the underlying biological mechanisms that contribute to disease resistance in chickens to the Newcastle disease virus while under the effects of heat stress.

              Results

              Differential gene expression analysis identified genes differentially expressed between treated and non-treated birds across three time points (2, 6, and 10 days post-infection) in Fayoumi and Leghorn birds. Across the three time points, Fayoumi had very few genes differentially expressed between treated and non-treated groups at 2 and 6 days post-infection. However, 202 genes were differentially expressed at 10 days post-infection. Alternatively, Leghorn had very few genes differentially expressed at 2 and 10 days post-infection but had 167 differentially expressed genes at 6 days post-infection. Very few differentially expressed genes were shared between the two genetic lines, and pathway analysis found unique signaling pathways specific to each genetic line. Fayoumi had significantly lower viral load, higher viral clearance, higher anti-NDV antibody levels, and fewer viral transcripts detected compared to Leghorns. Fayoumis activated immune related pathways including SAPK/JNK and p38 MAPK signaling pathways at earlier time points, while Leghorn would activate these same pathways at a later time. Further analysis revealed activation of the GP6 signaling pathway that may be responsible for the susceptible Leghorn response.

              Conclusions

              The findings in this study confirmed our hypothesis that the Fayoumi line was more resistant to Newcastle disease virus infection compared to the Leghorn line. Within line and interaction analysis demonstrated substantial differences in response patterns between the two genetic lines that was not observed from the within line contrasts. This study has provided novel insights into the transcriptome response of the Harderian gland tissue during Newcastle disease virus infection while under heat stress utilizing a unique resistant and susceptible model.
                Cover page: Novel insights into the host immune response of chicken Harderian gland tissue during Newcastle disease virus infection and heat treatment
                • Article
                • Peer Reviewed
                UC Davis Previously Published Works (2022)
                In May 2018, an outbreak of virulent Newcastle disease (vND) affected backyard and commercial premises in Southern California. The re-occurrence of these outbreaks since the 1970s suggests that some poultry communities may not have reliable and stable resources available regarding biosecurity and disease prevention. Therefore, staff at the University of California, Davis (UCD) School of Veterinary Medicine (SVM), and the California Department of Food and Agriculture (CDFA) began organizing educational events and learning more about the gamefowl breeder community through a needs assessment exercise, during which local feedstores and neighborhoods were also visited. Focus groups were organized with breeders in various cities within the regional quarantine area, established by the CDFA during the vND outbreak. The focus groups were aimed at creating open communication networks with gamefowl breeders in the affected area, as well as to learn about their current sources of information, learning preferences, and current management practices. With the input from gamefowl breeders, as well as funding and input from the CDFA and the United States Department of Agriculture (USDA), a quality assurance program called the "Gamefowl Wellness Program" was established. Educational content was created and published through the UCD Gamefowl Wellness Program poultry health website. Additionally, with the help of the CDFA, the USDA, and pharmaceutical companies, Newcastle disease vaccines and training for their application were provided to feedstores with gamefowl breeder clientele. Nurturing trust with these poultry communities allowed us to receive the information needed to develop effective outreach strategies that could better serve them. Responding to community concerns might be a way to garner the trust necessary to prevent or at least promptly detect foreign animal disease outbreaks.
                  Cover page: Outreach Efforts to Prevent Newcastle Disease Outbreaks in Southern California
                  • Article
                  • Peer Reviewed
                  UC Davis Previously Published Works (2020)
                  Disease has large negative impacts on poultry production. A more comprehensive understanding of host-pathogen interaction can lead to new and improved strategies to maintain health. In particular, host genetic factors can lead to a more effective response to pathogens, hereafter termed resistance. Fayoumi and Leghorn chicken lines have demonstrated relative resistance and susceptibility, respectively, to the Newcastle disease virus (NDV) vaccine strain and many other pathogens. This biological model was used to better understand the host response to a vaccine strain of NDV across three tissues and time points, using RNA-seq. Analyzing the Harderian gland, trachea, and lung tissues together using weighted gene co-expression network analysis (WGCNA) identified important genes that were co-expressed and associated with parameters including: genetic line, days post-infection (dpi), challenge status, sex, and tissue. Pathways and driver genes, such as EIF2AK2, MPEG1, and TNFSF13B, associated with challenge status, dpi, and genetic line were of particular interest as candidates for disease resistance. Overall, by jointly analyzing the three tissues, this study identified genes and gene networks that led to a more comprehensive understanding of the whole animal response to lentogenic NDV than that obtained by analyzing the tissues individually.
                    Cover page: Novel Combined Tissue Transcriptome Analysis After Lentogenic Newcastle Disease Virus Challenge in Inbred Chicken Lines of Differential Resistance
                    • Article
                    • Peer Reviewed
                    UC Davis Previously Published Works (2023)
                    Herein, we report the complete genome for an avian infectious bronchitis virus isolated from cecal tonsils of California layers in 2021. This whole-genome sequence belongings to genotype GVIII, previously classified as a unique variant.
                      Cover page: Whole-genome sequence of a genotype VIII infectious bronchitis virus isolated from California layer chickens in 2021.
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