Induction of antiviral and cell mediated immune responses significantly reduce viral load in an acute foot-and-mouth disease virus infection in cattle

MHC-I pathway disruption by viruses: insights into immune evasion and vaccine design for animals

Among various pathogens, viruses pose significant threats to the livestock and poultry industry, resulting in substantial annual costs due to production losses and vaccination. The MHC-I presentation pathway is a crucial surveillance mechanism for preventing viral infections. Consequently, many viruses have evolved sophisticated strategies to inhibit the presentation of viral peptides by MHC-I to CD8+ T-cells, thereby evading the immune system. Understanding the mechanisms that suppress the MHC-I pathway and identifying specific binding peptides are essential for comprehending viral immune evasion and developing effective animal vaccines. This review summarizes the viral strategies for evading immune recognition, including the inhibition of MHC-I molecules synthesis, degradation, transport, and assembly, which affect MHC-I surface expression during viral infections. We also present evidence that MHC-I surface expression is frequently lost during numerous viral infections in livestock and poultry and offer new insights into the underlying mechanisms through which viruses inactivate the MHC-I antigen presentation pathway. Collectively, these advanced findings on viral evasion from the MHC-I pathway could inform the development of more effectives strategies to restore immunological control over viral infections and improve vaccines for the livestock and poultry industry.

Comparative Transcriptomics Analysis of Foot-and-Mouth Disease Virus-Infected Cell Model Systems

The highly contagious FMDV is the agent responsible for foot-and-mouth disease, significantly impacting animals with cloven hooves and incurring substantial economic losses globally. The FMDV genome, composed of single-stranded RNA, consists of approximately 8500 nucleotides and harbors a single open reading frame (ORF) encoding both structural and non-structural proteins vital for the virus's pathogenicity and replication. BHK-21 (baby hamster kidney) cells are the optimal cell line for FMDV culture due to their robust viral replication ability and high infection susceptibility. The insufficient elucidation of the host response to FMDV hampers progress towards the establishment of precise therapeutic interventions. To fill this void in understanding, samples from FMDV-challenged and control BHK-21 cells were systematically procured, with comprehensive transcriptome sequencing subsequently undertaken to delineate the gene expression landscapes of each group. A total of 4018 differentially expressed genes were identified, of which 2044 were downregulated and 1974 were upregulated. The data indicate that FMDV infection significantly enhances transcription initiation in BHK-21. According to GO and KEGG enrichment analysis, FMDV affects a number of immune-related processes as well as the movement of chemicals within cells. In the analysis of the protein-protein interaction network, Fos, Flt3lg, Rpl22l1, Ifi35, Ep300, and Rps16 emerged as pivotal hub proteins, underscoring their significant roles within the cellular interactome. The RT-qPCR experiment of Lgfb5, Ler2, Vgll3, and Ahr verified that the DEGs' expression profiles matched the results of the RNA-seq investigation. The study's findings have enhanced our understanding of the molecular pathways underlying FMDV pathogenesis and host interactions. Furthermore, the identification of key genes could serve as potential targets for therapeutic strategies and diagnostic tools, thereby enhancing control measures for livestock foot-and-mouth disease and mitigating its economic impact.

Ruminant livestock TR V(D)J genes and CDR3 repertoire

Ruminant livestock exhibit certain immune characteristics that make them valuable models for studying T cell receptor diversity and immune responses. This resistance is attributed to their well-developed immune system, comprising both innate and adaptive components. In this review, we delve into the intricate workings of the immune system of ruminant livestock, focusing on innate immunity and adaptive immunity. Specifically, we discuss the TR V(D)J genes (including TRB, TRG, and TRA/D chain) and the characteristics of the complementary determining region 3 (CDR3) repertoire in bovine and ovine species, shedding light on the diversity and functionality of the T-cell receptor(TCR) repertoire in these species. Understanding the distinct features of these germline genes and CDR3 repertoires is essential for unraveling the complexities of immune responses in ruminant livestock. Lastly, we outline future prospects in this field, emphasizing the importance of further research to enhance our understanding of ruminant livestock immunity and its potential applications in disease management, vaccine development, and breeding strategies.

The Australian Biosecurity Genomic Database: a new resource for high-throughput sequencing analysis based on the National Notifiable Disease List of Terrestrial Animals

The Australian Biosecurity Genomic Database (ABGD) is a curated collection of reference viral genome sequences based on the Australian National Notifiable Disease List of Terrestrial Animals. It was created to facilitate the screening of high-throughput sequencing (HTS) data for the potential presence of viruses associated with notifiable disease. The database includes a single verified sequence (the exemplar species sequence, where relevant) for each of the 60 virus species across 21 viral families that are associated with or cause these notifiable diseases, as recognized by the World Organisation for Animal Health. The open-source ABGD on GitHub provides usage guidance documents and is intended to support building a culture in Australian HTS communities that promotes the use of quality-assured, standardized, and verified databases for Australia's national biosecurity interests. Future expansion of the database will include the addition of more strains or subtypes for highly variable viruses, viruses causing diseases of aquatic animals, and genomes of other types of pathogens associated with notifiable diseases, such as bacteria. Database URL: https://github.com/ausbiopathgenDB/AustralianBiosecurityGenomicDatabase.

Strong selection signatures for Aleutian disease tolerance acting on novel candidate genes linked to immune and cellular responses in American mink (Neogale vison)

Aleutian disease (AD) is a multi-systemic infectious disease in American mink (Neogale vison) caused by Aleutian mink disease virus (AMDV). This study aimed to identify candidate regions and genes underlying selection for response against AMDV using whole-genome sequence (WGS) data. Three case-control selection signatures studies were conducted between animals (N = 85) producing high versus low antibody levels against AMDV, grouped by counter immunoelectrophoresis (CIEP) test and two enzyme-linked immunosorbent assays (ELISA). Within each study, selection signals were detected using fixation index (FST) and nucleotide diversity (θπ ratios), and validated by cross-population extended haplotype homozygosity (XP-EHH) test. Within- and between-studies overlapping results were then evaluated. Within-studies overlapping results indicated novel candidate genes related to immune and cellular responses (e.g., TAP2, RAB32), respiratory system function (e.g., SPEF2, R3HCC1L), and reproduction system function (e.g., HSF2, CFAP206) in other species. Between-studies overlapping results identified three large segments under strong selection pressure, including two on chromosome 1 (chr1:88,770-98,281 kb and chr1:114,133-120,473) and one on chromosome 6 (chr6:37,953-44,279 kb). Within regions with strong signals, we found novel candidate genes involved in immune and cellular responses (e.g., homologous MHC class II genes, ITPR3, VPS52) in other species. Our study brings new insights into candidate regions and genes controlling AD response.

Analysis of runs of homozygosity of cattle living in different climate zones

Aim of this study was to analyze the distribution and characteristics of runs of homozygosity in Bos taurus taurus and Bos taurus indicus breeds, as well as their crosses, farmed all around the world. With this aim in view, we used single-nucleotide polymorphisms (SNP) genotypes for 3,263 cattle belonging to 204 different breeds. After quality control, 23,311 SNPs were retained for the analysis. Animals were divided into seven different groups: 1) continental taurus, 2) temperate taurus, 3) temperate indicus, 4) temperate composite, 5) tropical taurus, 6) tropical indicus, and 7) tropical composite. The climatic zones were created according to the latitude of the breeds' country of origin: i) continental, latitude ≥ 45°; ii) temperate, 45°< Latitude >23.26°; iii) tropics, latitude ≤ 23.26°. Runs of homozygosity were computed as 15 SNPs spanning in at least 2 Mb; number of ROH per animal (nROH), average ROH length (meanMb), and ROH-based inbreeding coefficients (FROH) were also computed. Temperate indicus showed the largest nROH, whereas Temperate taurus the lowest value. Moreover, the largest meanMb was observed for Temperate taurus, whereas the lowest value for Tropics indicus. Temperate indicus breeds showed the largest FROH values. Genes mapped in the identified ROH were reported to be associated with the environmental adaptation, disease resistance, coat color determinism, and production traits. Results of the present study confirmed that runs of homozygosity could be used to identify genomic signatures due to both artificial and natural selection.