Overexpression of Histone Deacetylase 6 Enhances Resistance to Porcine Reproductive and Respiratory Syndrome Virus in Pigs

Unravelling the impact of epigenetic mechanisms on offspring growth, production, reproduction and disease susceptibility

Epigenetic mechanisms, such as DNA methylation, histone modifications and non-coding RNA molecules, play a critical role in gene expression and regulation in livestock species, influencing development, reproduction and disease resistance. DNA methylation patterns silence gene expression by blocking transcription factor binding, while histone modifications alter chromatin structure and affect DNA accessibility. Livestock-specific histone modifications contribute to gene expression and genome stability. Non-coding RNAs, including miRNAs, piRNAs, siRNAs, snoRNAs, lncRNAs and circRNAs, regulate gene expression post-transcriptionally. Transgenerational epigenetic inheritance occurs in livestock, with environmental factors impacting epigenetic modifications and phenotypic traits across generations. Epigenetic regulation revealed significant effect on gene expression profiling that can be exploited for various targeted traits like muscle hypertrophy, puberty onset, growth, metabolism, disease resistance and milk production in livestock and poultry breeds. Epigenetic regulation of imprinted genes affects cattle growth and metabolism while epigenetic modifications play a role in disease resistance and mastitis in dairy cattle, as well as milk protein gene regulation during lactation. Nutri-epigenomics research also reveals the influence of maternal nutrition on offspring's epigenetic regulation of metabolic homeostasis in cattle, sheep, goat and poultry. Integrating cyto-genomics approaches enhances understanding of epigenetic mechanisms in livestock breeding, providing insights into chromosomal structure, rearrangements and their impact on gene regulation and phenotypic traits. This review presents potential research areas to enhance production potential and deepen our understanding of epigenetic changes in livestock, offering opportunities for genetic improvement, reproductive management, disease control and milk production in diverse livestock species.

Cleavage of HDAC6 to dampen its antiviral activity by nsp5 is a common strategy of swine enteric coronaviruses

HDAC6, a structurally and functionally unique member of the histone deacetylase (HDAC) family, is an important host factor that restricts viral infection. The broad-spectrum antiviral activity of HDAC6 makes it a potent antiviral agent. Previously, we found that HDAC6 functions to antagonize porcine deltacoronavirus (PDCoV), an emerging enteropathogenic coronavirus with zoonotic potential. However, the final outcome is typically a productive infection that materializes as cells succumb to viral infection, indicating that the virus has evolved sophisticated mechanisms to combat the antiviral effect of HDAC6. Here, we demonstrate that PDCoV nonstructural protein 5 (nsp5) can cleave HDAC6 at glutamine 519 (Q519), and cleavage of HDAC6 was also detected in the context of PDCoV infection. More importantly, the anti-PDCoV activity of HDAC6 was damaged by nsp5 cleavage. Mechanistically, the cleaved HDAC6 fragments (amino acids 1-519 and 520-1159) lost the ability to degrade PDCoV nsp8 due to their impaired deacetylase activity. Furthermore, nsp5-mediated cleavage impaired the ability of HDAC6 to activate RIG-I-mediated interferon responses. We also tested three other swine enteric coronaviruses (transmissible gastroenteritis virus, porcine epidemic diarrhea virus, and swine acute diarrhea syndrome-coronavirus) and found that all these coronaviruses have adopted similar mechanisms to cleave HDAC6 in both an overexpression system and virus-infected cells, suggesting that cleavage of HDAC6 is a common strategy utilized by swine enteric coronaviruses to antagonize the host's antiviral capacity. Together, these data illustrate how swine enteric coronaviruses antagonize the antiviral function of HDAC6 to maintain their infection, providing new insights to the interaction between virus and host.IMPORTANCEViral infections and host defenses are in constant opposition. Once viruses combat or evade host restriction, productive infection is achieved. HDAC6 is a broad-spectrum antiviral protein that has been demonstrated to inhibit many viruses, including porcine deltacoronavirus (PDCoV). However, whether HDAC6 is reciprocally targeted and disabled by viruses remains unclear. In this study, we used PDCoV as a model and found that HDAC6 is targeted and cleaved by nsp5, a viral 3C-like protease. The cleaved HDAC6 loses its deacetylase activity as well as its ability to degrade viral proteins and activate interferon responses. Furthermore, this cleavage mechanism is shared among other swine enteric coronaviruses. These findings shed light on the intricate interplay between viruses and HDAC6, highlighting the strategies employed by viruses to evade host antiviral defenses.

HDAC6 Degrades nsp8 of Porcine Deltacoronavirus through Deacetylation and Ubiquitination to Inhibit Viral Replication

Porcine deltacoronavirus (PDCoV) is an emerging swine enteropathogenic coronavirus that has the potential to infect humans. Histone deacetylase 6 (HDAC6) is a unique type IIb cytoplasmic deacetylase with both deacetylase activity and ubiquitin E3 ligase activity, which mediates a variety of cellular processes by deacetylating histone and nonhistone substrates. In this study, we found that ectopic expression of HDAC6 significantly inhibited PDCoV replication, while the reverse effects could be observed after treatment with an HDAC6-specific inhibitor (tubacin) or knockdown of HDAC6 expression by specific small interfering RNA. Furthermore, we demonstrated that HDAC6 interacted with viral nonstructural protein 8 (nsp8) in the context of PDCoV infection, resulting in its proteasomal degradation, which was dependent on the deacetylation activity of HDAC6. We further identified the key amino acid residues lysine 46 (K46) and K58 of nsp8 as acetylation and ubiquitination sites, respectively, which were required for HDAC6-mediated degradation. Through a PDCoV reverse genetics system, we confirmed that recombinant PDCoV with a mutation at either K46 or K58 exhibited resistance to the antiviral activity of HDAC6, thereby exhibiting higher replication compared with wild-type PDCoV. Collectively, these findings contribute to a better understanding of the function of HDAC6 in regulating PDCoV infection and provide new strategies for the development of anti-PDCoV drugs. IMPORTANCE As an emerging enteropathogenic coronavirus with zoonotic potential, porcine deltacoronavirus (PDCoV) has sparked tremendous attention. Histone deacetylase 6 (HDAC6) is a critical deacetylase with both deacetylase activity and ubiquitin E3 ligase activity and is extensively involved in many important physiological processes. However, little is known about the role of HDAC6 in the infection and pathogenesis of coronaviruses. Our present study demonstrates that HDAC6 targets PDCoV-encoded nonstructural protein 8 (nsp8) for proteasomal degradation through the deacetylation at the lysine 46 (K46) and the ubiquitination at K58, suppressing viral replication. Recombinant PDCoV with a mutation at K46 and/or K58 of nsp8 displayed resistance to the antiviral activity of HDAC6. Our work provides significant insights into the role of HDAC6 in regulating PDCoV infection, opening avenues for the development of novel anti-PDCoV drugs.

N-Acetyltransferase 9 Inhibits Porcine Reproductive and Respiratory Syndrome Virus Proliferation by N-Terminal Acetylation of the Structural Protein GP5

Porcine reproductive and respiratory syndrome virus (PRRSV) is a serious threat to the global swine industry. As a typical immunosuppressive virus, PRRSV has developed a variety of complex mechanisms to escape the host innate immunity. In this study, we uncovered a novel immune escape mechanism of PRRSV infection. Here, we demonstrate for the first time that the endoplasmic reticulum (ER)-resident N-acetyltransferase Nat9 is an important host restriction factor for PRRSV infection. Nat9 inhibited PRRSV proliferation in an acetyltransferase activity-dependent manner. Mechanistically, glycoprotein 5 (GP5) of PRRSV was identified as interacting with Nat9 and being N-terminally acetylated by it, which generates a GP5 degradation signal, promoting the K27-linked-ubiquitination degradation of GP5 to decrease virion assembly. Meanwhile, the expression of Nat9 was inhibited during PRRSV infection. In detail, two transcription factors, ETV5 and SP1, were screened out as the key transcription factors binding to the core promoter region of Nat9, and the PRRSV nonstructural protein 1β (Nsp1β), Nsp4, Nsp9, and nucleocapsid (N) proteins were found to interfere significantly with the expression of ETV5 and SP1, thereby regulating the transcription activity of Nat9 and inhibiting the expression of Nat9. The findings suggest that PRRSV decreases the N-terminal acetylation of GP5 to support virion assembly by inhibiting the expression of Nat9. Taken together, our findings showed that PRRSV has developed complex mechanisms to inhibit Nat9 expression and trigger virion assembly. IMPORTANCE To ensure efficient replication, a virus must hijack or regulate multiple host factors for its own benefit. Understanding virus-host interactions and the molecular mechanisms of host resistance to PRRSV infection is necessary to develop effective strategies to control PRRSV. The N-acetyltransferase Nat9 plays important roles during virus infection. Here, we demonstrate that Nat9 exhibits an antiviral effect on PRRSV proliferation. The GP5 protein of PRRSV is targeted specifically by Nat9, which mediates GP5 N-terminal acetylation and degradation via a ubiquitination-dependent proteasomal pathway. However, PRRSV manipulates the transcription factors ETV5 and SP1 to inhibit the expression of Nat9 and promote virion assembly. Thus, we report a novel function of Nat9 in PRRSV infection and elucidate a new mechanism by which PRRSV can escape the host innate immunity, which may provide novel insights for the development of antiviral drugs.

Anti-microbial host factor HDAC6 is antagonised by the influenza A virus through host caspases and viral PA

Histone deacetylase 6 (HDAC6), through the repertoire of its substrate proteins, plays a critical role in human physiology, and an aberrant function of HDAC6 contributes to various pathophysiological conditions. HDAC6 is also known to be an anti-microbial host factor and has been implicated in restricting or clearing the infection of various human viral and bacterial pathogens. However, the state and the mechanisms of its antagonism in infected cells are not understood. Here, we demonstrate that influenza A virus (IAV) antagonises HDAC6 by recruiting both viral and host components. We found that HDAC6 mRNA expression, and consequently, the HDAC6 polypeptide expression is downregulated in human lung epithelial cells during early stage of IAV infection but can be rescued by depleting the expression of viral polymerase acidic (PA) protein, a subunit of IAV RNA polymerase. In addition, during later stage of the infection, the HDAC6 polypeptide undergoes caspase-mediated cleavage at two sites, generating two cleaved fragments. Both these fragments disappeared when the expression of caspase 3 was depleted in infected cells, whereas only second fragment disappeared when the expression of caspase 6 was depleted. But both fragments disappeared and the level of full-length HDAC6 polypeptide was rescued when the expression of PA was depleted in infected cells. Collectively, these data indicated that IAV antagonises the HDAC6 by decreasing its expression level in infected cells, both at mRNA and polypeptide level via PA gene, which has been implicated in auxiliary functions like degradation of host mRNA and induction of apoptosis.

Generation of PCBP1-deficient pigs using CRISPR/Cas9-mediated gene editing

Classical swine fever virus (CSFV), a classic swine fever pathogen, causes severe economic losses worldwide. Poly (rC)-binding protein 1 (PCBP1), which interacts with N^pro of CSFV, plays a vital role in CSFV growth. We are the first to report the generation of PCBP1-deficient pigs via gene-editing technology. The PCBP1-deficient pigs exhibited normal birth weight and reproductive-performance traits and developed normally. Viral challenge experiments indicated that primary cells isolated from F₀- and F₁-generation pigs exhibited significantly reduced CSFV infection. Additional mechanistic exploration further confirmed that the PCBP1 deficiency-mediated antiviral effect is related to the activation of type I interferon (IFN). Besides showing that a gene-editing strategy could be used to generate PCBP1-deficient pigs, our study introduces a valuable animal model for further investigating the infection mechanisms of CSFV that will help to develop better antiviral solutions.

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Reduced CSFV infection in PCBP1-deficient cells is related to activated ISGs expression

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PCBP1-deficient pigs were successfully generated via gene-editing technology

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Primary cells isolated from PCBP1-deficient pigs exhibited reduced CSFV infection

Porcine Deltacoronavirus Infection Cleaves HDAC2 to Attenuate Its Antiviral Activity

Protein acetylation plays an important role during virus infection. Thus, it is not surprising that viruses always evolve elaborate mechanisms to regulate the functions of histone deacetylases (HDACs), the essential transcriptional and epigenetic regulators for deacetylation. Porcine deltacoronavirus (PDCoV), an emerging enteropathogenic coronavirus, causes severe diarrhea in suckling piglets and has the potential to infect humans. In this study, we found that PDCoV infection inhibited cellular HDAC activity. By screening the expressions of different HDAC subfamilies after PDCoV infection, we unexpectedly found that HDAC2 was cleaved. Ectopic expression of HDAC2 significantly inhibited PDCoV replication, while the reverse effects could be observed after treatment with an HDAC2 inhibitor (CAY10683) or the knockdown of HDAC2 expression by specific siRNA. Furthermore, we demonstrated that PDCoV-encoded nonstructural protein 5 (nsp5), a 3C-like protease, was responsible for HDAC2 cleavage through its protease activity. Detailed analyses showed that PDCoV nsp5 cleaved HDAC2 at glutamine 261 (Q261), and the cleaved fragments (amino acids 1 to 261 and 262 to 488) lost the ability to inhibit PDCoV replication. Interestingly, the Q261 cleavage site is highly conserved in HDAC2 homologs from other mammalian species, and the nsp5s encoded by seven tested mammalian coronaviruses also cleaved HDAC2, suggesting that cleaving HDAC2 may be a common strategy used by different mammalian coronaviruses to antagonize the antiviral role of HDAC2. IMPORTANCE As an emerging porcine enteropathogenic coronavirus that possesses the potential to infect humans, porcine deltacoronavirus (PDCoV) is receiving increasing attention. In this work, we found that PDCoV infection downregulated cellular histone deacetylase (HDAC) activity. Of particular interest, the viral 3C-like protease, encoded by the PDCoV nonstructural protein 5 (nsp5), cleaved HDAC2, and this cleavage could be observed in the context of PDCoV infection. Furthermore, the cleavage of HDAC2 appears to be a common strategy among mammalian coronaviruses, including the emerging severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), to antagonize the antiviral role of HDAC2. To our knowledge, PDCoV nsp5 is the first identified viral protein that can cleave cellular HDAC2. Results from our study provide new targets to develop drugs combating coronavirus infection.

Enhancing Animal Disease Resistance, Production Efficiency, and Welfare through Precise Genome Editing

The major goal of animal breeding is the genetic enhancement of economic traits. The CRISPR/Cas system, which includes nuclease-mediated and base editor mediated genome editing tools, provides an unprecedented approach to modify the mammalian genome. Thus, farm animal genetic engineering and genetic manipulation have been fundamentally revolutionized. Agricultural animals with traits of interest can be obtained in just one generation (and without long time selection). Here, we reviewed the advancements of the CRISPR (Clustered regularly interspaced short palindromic repeats)/Cas (CRISPR associated proteins) genome editing tools and their applications in animal breeding, especially in improving disease resistance, production performance, and animal welfare. Additionally, we covered the regulations on genome-edited animals (GEAs) and ways to accelerate their use. Recommendations for how to produce GEAs were also discussed. Despite the current challenges, we believe that genome editing breeding and GEAs will be available in the near future.

Current and prospective control strategies of influenza A virus in swine

BACKGROUND

Influenza A Viruses (IAV) are endemic pathogens of significant concern in humans and multiple keystone livestock species. Widespread morbidity in swine herds negatively impacts animal welfare standards and economic performance whilst human IAV pandemics have emerged from pigs on multiple occasions. To combat the rising prevalence of swine IAV there must be effective control strategies available.

MAIN BODY

The most basic form of IAV control on swine farms is through good animal husbandry practices and high animal welfare standards. To control inter-herd transmission, biosecurity considerations such as quarantining of pigs and implementing robust health and safety systems for workers help to reduce the likelihood of swine IAV becoming endemic. Closely complementing the physical on-farm practices are IAV surveillance programs. Epidemiological data is critical in understanding regional distribution and variation to assist in determining an appropriate response to outbreaks and understanding the nature of historical swine IAV epidemics and zoonoses. Medical intervention in pigs is restricted to vaccination, a measure fraught with the intrinsic difficulties of mounting an immune response against a highly mutable virus. It is the best available tool for controlling IAV in swine but is far from being a perfect solution due to its unreliable efficacy and association with an enhanced respiratory disease. Because IAV generally has low mortality rates there is a reticence in the uptake of vaccination. Novel genetic technologies could be a complementary strategy for IAV control in pigs that confers broad-acting resistance. Transgenic pigs with IAV resistance are useful as models, however the complexity of these reaching the consumer market limits them to research models. More promising are gene-editing approaches to prevent viral exploitation of host proteins and modern vaccine technologies that surpass those currently available.

CONCLUSION

Using the suite of IAV control measures that are available for pigs effectively we can improve the economic productivity of pig farming whilst improving on-farm animal welfare standards and avoid facing the extensive social and financial costs of a pandemic. Fighting 'Flu in pigs will help mitigate the very real threat of a human pandemic emerging, increase security of the global food system and lead to healthier pigs.

Impacts of Epigenetic Processes on the Health and Productivity of Livestock

The dynamic changes in the epigenome resulting from the intricate interactions of genetic and environmental factors play crucial roles in individual growth and development. Numerous studies in plants, rodents, and humans have provided evidence of the regulatory roles of epigenetic processes in health and disease. There is increasing pressure to increase livestock production in light of increasing food needs of an expanding human population and environment challenges, but there is limited related epigenetic data on livestock to complement genomic information and support advances in improvement breeding and health management. This review examines the recent discoveries on epigenetic processes due to DNA methylation, histone modification, and chromatin remodeling and their impacts on health and production traits in farm animals, including bovine, swine, sheep, goat, and poultry species. Most of the reports focused on epigenome profiling at the genome-wide or specific genic regions in response to developmental processes, environmental stressors, nutrition, and disease pathogens. The bulk of available data mainly characterized the epigenetic markers in tissues/organs or in relation to traits and detection of epigenetic regulatory mechanisms underlying livestock phenotype diversity. However, available data is inadequate to support gainful exploitation of epigenetic processes for improved animal health and productivity management. Increased research effort, which is vital to elucidate how epigenetic mechanisms affect the health and productivity of livestock, is currently limited due to several factors including lack of adequate analytical tools. In this review, we (1) summarize available evidence of the impacts of epigenetic processes on livestock production and health traits, (2) discuss the application of epigenetics data in livestock production, and (3) present gaps in livestock epigenetics research. Knowledge of the epigenetic factors influencing livestock health and productivity is vital for the management and improvement of livestock productivity.

Quantitative Proteomic Analysis of Global Protein Acetylation in PRRSV-Infected Pulmonary Alveolar Macrophages

Porcine reproductive and respiratory syndrome (PRRS), caused by PRRS virus (PRRSV), is a serious viral disease affecting global swine industry. Due to the lack of effective vaccines, new antiviral strategies to compensate for the inefficacy of available vaccines are urgently required. Lysine acetylation, as an important post-translational modification during infection, plays a key regulatory role in host antiviral responses. In this study, the global acetylome is profiled using acetylation specific antibody-based enrichment and tandem mass tag label high-affinity purification liquid chromatography-mass spectrometry in PRRSV-infected pulmonary alveolar macrophages (PAMs). As a result, 3731 lysine acetylation sites on 1421 cellular proteins are identified. Bioinformatics analysis of the different acetylated proteins revealed their involvement in various biological processes, including the host immune response and energy metabolism. These findings will contribute to the understanding of PRRSV pathogenesis and identify new cellular targets for anti-PPRSV therapeutics.

Pigs Overexpressing Porcine β-Defensin 2 Display Increased Resilience to Glaesserella parasuis Infection

As the causative agent of Glässer’s disease, Glaesserella (Haemophilus) parasuis has led to serious economic losses to the swine industry worldwide. Due to the low cross-protection of vaccines and increasing antimicrobial resistance of G. parasuis, it is important to develop alternative approaches to prevent G. parasuis infection. Defensins are host defense peptides that have been suggested to be promising substitutes for antibiotics in animal production, while porcine β-defensin 2 (PBD-2) is a potent antimicrobial peptide discovered in pigs. Our previous study generated transgenic (TG) pigs overexpressing PBD-2, which displayed enhanced resistance to Actinobacillus pleuropneumoniae. In this study, the antibacterial activities of PBD-2 against G. parasuis are determined in vitro and in the TG pig model. The concentration-dependent bactericidal activity of synthetic PBD-2 against G. parasuis was measured by bacterial counting. Moreover, after being infected with G. parasuis via a cohabitation challenge model, TG pigs overexpressing PBD-2 displayed significantly milder clinical signs and less severe gross pathological changes than their wild-type (WT) littermates. The TG pigs also exhibited alleviated lung and brain lesions, while bacterial loads in the lung and brain tissues of the TG pigs were significantly lower than those of the WT pigs. Additionally, lung and brain homogenates from TG pigs possessed enhanced antibacterial activity against G. parasuis when compared with those from the WT pigs. Altogether, these proved that overexpression of PBD-2 could also endow pigs with increased resilience to G. parasuis infection, which further confirmed the potential of using the PBD-2 coding gene to develop disease-resistant pigs and provided a novel strategy to combat G. parasuis as well.

Improvement of Disease Resistance in Livestock: Application of Immunogenomics and CRISPR/Cas9 Technology

Disease occurrence adversely affects livestock production and animal welfare, and have an impact on both human health and public perception of food-animals production. Combined efforts from farmers, animal scientists, and veterinarians have been continuing to explore the effective disease control approaches for the production of safe animal-originated food. Implementing the immunogenomics, along with genome editing technology, has been considering as the key approach for safe food-animal production through the improvement of the host genetic resistance. Next-generation sequencing, as a cutting-edge technique, enables the production of high throughput transcriptomic and genomic profiles resulted from host-pathogen interactions. Immunogenomics combine the transcriptomic and genomic data that links to host resistance to disease, and predict the potential candidate genes and their genomic locations. Genome editing, which involves insertion, deletion, or modification of one or more genes in the DNA sequence, is advancing rapidly and may be poised to become a commercial reality faster than it has thought. The clustered regulatory interspaced short palindromic repeats (CRISPR)/CRISPR-associated protein 9 (Cas9) [CRISPR/Cas9] system has recently emerged as a powerful tool for genome editing in agricultural food production including livestock disease management. CRISPR/Cas9 mediated insertion of NRAMP1 gene for producing tuberculosis resistant cattle, and deletion of CD163 gene for producing porcine reproductive and respiratory syndrome (PRRS) resistant pigs are two groundbreaking applications of genome editing in livestock. In this review, we have highlighted the technological advances of livestock immunogenomics and the principles and scopes of application of CRISPR/Cas9-mediated targeted genome editing in animal breeding for disease resistance.

Generation of Marker-Free pbd-2 Knock-in Pigs Using the CRISPR/Cas9 and Cre/loxP Systems

Porcine β-defensin 2 (PBD-2), expressed by different tissues of pigs, is a multifunctional cationic peptide with antimicrobial, immunomodulatory and growth-promoting abilities. As the latest generation of genome-editing tool, CRISPR/Cas9 system makes it possible to enhance the expression of PBD-2 in pigs by site-specific knock-in of pbd-2 gene into the pig genome. In this study, we aimed to generate marker-free pbd-2 knock-in pigs using the CRISPR/Cas9 and Cre/loxP systems. Two copies of pbd-2 gene linked by a T2A sequence were inserted into the porcine Rosa26 locus through CRISPR/Cas9-mediated homology-directed repair. The floxed selectable marker gene neoR, used for G418 screening of positive cell clones, was removed by cell-penetrating Cre recombinase with a recombination efficiency of 48.3%. Cloned piglets were produced via somatic cell nuclear transfer and correct insertion of pbd-2 genes was confirmed by PCR and Southern blot. Immunohistochemistry and immunofluorescence analyses indicated that expression levels of PBD-2 in different tissues of transgenic (TG) piglets were significantly higher than those of their wild-type (WT) littermates. Bactericidal assays demonstrated that there was a significant increase in the antimicrobial properties of the cell culture supernatants of porcine ear fibroblasts from the TG pigs in comparison to those from the WT pigs. Altogether, our study improved the protein expression level of PBD-2 in pigs by site-specific integration of pbd-2 into the pig genome, which not only provided an effective pig model to study the anti-infection mechanisms of PBD-2 but also a promising genetic material for the breeding of disease-resistant pigs.

Disease resistance for different livestock species

This chapter deals with progress in disease resistance for the livestock population species-wise and describes the progress that occurred globally. Certain genes were identified for mastitis resistance and the strategies for genomic control of mastitis are discussed. Gene-edited tuberculosis-resistant cattle were developed for the first time with CRISPR/Cas 9 technology with NRAMP gene insert. Similarly studies are in progress for the development of trypanosomiasis-resistant cattle at ILRI. Genomic insights were discussed for disease resistance for goat against gastrointestinal nematode infestation, coccidiosis, peste des petits ruminants, and scrapie. Similarly genomic resistance was also discussed for sheep, discussing the mechanism of disease resistance with MHC, antibody and T cell response, cytokines, and receptors. Genes identified for bacterial diarrhoeal resistance as K88, F18 (an intestinal receptor) for resistance to bacterial infection in pig. Gene-edited pigs were developed against porcine reproductive and respiratory syndrome and transmissible gastroenteritis caused by corona virus using CRISPR/Cas9 technology. Insights on the omics technologies developed and studied were discussed for livestock species. Genomic control on various diseases of poultry is discussed as salmonellosis, avian influenza, Marek’s disease, Newcastle disease with advanced genomic and allied techniques for its control as RNA interference, flow cytometry, quantitative polymerase chain reaction, transcriptomics, etc. A new concept on natural antibodies was discussed.

Genetic Markers Associated with Field PRRSV-Induced Abortion Rates

In gilts and sows, the more severe clinical manifestation of porcine reproductive and respiratory syndrome virus (PRRSV) occurs in late gestation and can result in up to a 40% abortion incidence. Despite the known genetic component in resilience to PRRSV, there is scarce information regarding the abortive outcome of this disease. We tested the relationship between eight molecular markers (six from published studies and two identified in the present study in the HDAC6 gene) and the probability of abortion during a PRRSV outbreak, using data from two commercial Landrace x Large White sow farms with an incidence of abortion of 35% and 17%. From the markers tested, USP18_-1533G>A did not segregate in these populations, and CD163_c.3534C>T and HDAC6_g.2360C>T did not affect the abortion rate. In contrast, the minor allele of two markers in SSC4 (WUR1000125 in GBP1 and rs340943904 in GBP5), which lower viremia in growing pigs, and the major alleles of CD163_rs1107556229 and HDAC6_rs325981825 were associated with a lower probability of abortion during PRRSV outbreaks. The more striking result was for the MX1 gene, where the odds ratio of aborting versus not aborting was nine times lower in the sows homozygous for a 275-bp insertion than in the other genotypes. Interactions between markers were not relevant. All together, we bring here the first evidence that mutations in the host genome can predispose or protect from complete reproductive failure in sows infected with PRRSV.

Generation of Pigs Resistant to Highly Pathogenic-Porcine Reproductive and Respiratory Syndrome Virus through Gene Editing of CD163

Porcine reproductive and respiratory syndrome (PRRS) is a highly contagious disease and the most economically important disease of the swine industry worldwide. Highly pathogenic-PRRS virus (HP-PRRSV) is a variant of PRRSV, which caused high morbidity and mortality. Scavenger receptor CD163, which contains nine scavenger receptor cysteine-rich (SRCR) domains, is a key entry mediator for PRRSV. A previous study demonstrated that SRCR domain 5 (SRCR5), encoded by exon 7, was essential for PRRSV infection in vitro. Here, we substituted exon 7 of porcine CD163 with the corresponding exon of human CD163-like 1 (hCD163L1) using a CRISPR/Cas9 system combined with a donor vector. In CD163^Mut/Mut pigs, modifying CD163 gene had no adverse effects on hemoglobin-haptoglobin (Hb-Hp) complex clearance or erythroblast growth. In vitro infection experiments showed that the CD163 mutant strongly inhibited HP-PRRSV replication by inhibiting virus uncoating and genome release. Compared to wild-type (WT) pigs in vivo, HP-PRRSV-infected CD163^Mut/Mut pigs showed a substantially decreased viral load in blood and relief from PRRSV-induced fever. While all WT pigs were dead, there of four CD163^Mut/Mut pigs survived and recovered at the termination of the experiment. Our data demonstrated that modifying CD163 remarkably inhibited PRRSV replication and protected pigs from HP-PRRSV infection, thus establishing a good foundation for breeding PRRSV-resistant pigs via gene editing technology.

Livestock 2.0 - genome editing for fitter, healthier, and more productive farmed animals

The human population is growing, and as a result we need to produce more food whilst reducing the impact of farming on the environment. Selective breeding and genomic selection have had a transformational impact on livestock productivity, and now transgenic and genome-editing technologies offer exciting opportunities for the production of fitter, healthier and more-productive livestock. Here, we review recent progress in the application of genome editing to farmed animal species and discuss the potential impact on our ability to produce food.

Histone Deacetylase 2 Is a Component of Influenza A Virus-Induced Host Antiviral Response

Host cells produce variety of antiviral factors that create an antiviral state and target various stages of influenza A virus (IAV) life cycle to inhibit infection. However, IAV has evolved various strategies to antagonize those antiviral factors. Recently, we reported that a member of class I host histone deacetylases (HDACs), HDAC1 possesses an anti-IAV function. Herein, we provide evidence that HDAC2, another class I member and closely related to HDAC1 in structure and function, also possesses anti-IAV properties. In turn, IAV, like HDAC1, dysregulates HDAC2, mainly at the polypeptide level through proteasomal degradation to potentially minimize its antiviral effect. We found that IAV downregulated the HDAC2 polypeptide level in A549 cells in an H1N1 strain-independent manner by up to 47%, which was recovered to almost 100% level in the presence of proteasome-inhibitor MG132. A further knockdown in HDAC2 expression by up to 90% via RNA interference augmented the growth kinetics of IAV in A549 cells by more than four-fold after 24 h of infection. Furthermore, the knockdown of HDAC2 expression decreased the IAV-induced phosphorylation of the transcription factor, Signal Transducer and Activator of Transcription I (STAT1) and the expression of interferon-stimulated gene, viperin in infected cells by 41 and 53%, respectively. The role of HDAC2 in viperin expression was analogous to that of HDAC1, but it was not in the phosphorylation of STAT1. This indicated that, like HDAC1, HDAC2 is a component of IAV-induced host innate antiviral response and performs both redundant and non-redundant functions vis-a-vis HDAC1; however, IAV dysregulates them both in a redundant manner.