Creating Disease Resistant Chickens: A Viable Solution to Avian Influenza?

Financial impacts of a housing order on commercial free range egg layers in response to highly pathogenic avian influenza

Recent annual outbreaks of Highly Pathogenic Avian Influenza (HPAI) have led to mandatory housing orders on commercial free-range flocks. Indefinite periods of housing, after poultry have had access to range, could have production and financial consequences for free range egg producers. The impact of these housing orders on the performance of commercial flocks is seldom explored at a business level, predominantly due to the paucity of commercially sensitive data. The aim of this paper is to assess the financial and production impacts of a housing order on commercial free-range egg layers. We use a unique data set showing week by week performance of layers gathered from 9 UK based farms over the period 2020-2022. These data cover an average of 100,000 laying hens and include two imposed housing orders, in 2020/2021 and in 2021/22. We applied a random intercept linear regression to assess impacts on physical outputs and inputs, bird mortality and the impacts on revenue, feed costs and margin over feed cost. Feed use and feed costs per bird increased during the housing order which is a consequence of increased control over diet intake in housed compared to ranged birds. An increase in revenue was also found, ostensibly due to a higher proportion of large eggs produced, leading to a higher margin over feed cost. Overall, these large commercial poultry sheds were able to mitigate some of the potential adverse economic effects of housing orders. Potential negative impacts may occur dependant on the duration of the housing order and those farms with less control over their input costs.

Comparative Investigation of Coincident Single Nucleotide Polymorphisms Underlying Avian Influenza Viruses in Chickens and Ducks

Avian influenza is a severe viral infection that has the potential to cause human pandemics. In particular, chickens are susceptible to many highly pathogenic strains of the virus, resulting in significant losses. In contrast, ducks have been reported to exhibit rapid and effective innate immune responses to most avian influenza virus (AIV) infections. To explore the distinct genetic programs that potentially distinguish the susceptibility/resistance of both species to AIV, the investigation of coincident SNPs (coSNPs) and their differing causal effects on gene functions in both species is important to gain novel insight into the varying immune-related responses of chickens and ducks. By conducting a pairwise genome alignment between these species, we identified coSNPs and their respective effect on AIV-related differentially expressed genes (DEGs) in this study. The examination of these genes (e.g., CD74, RUBCN, and SHTN1 for chickens and ABCA3, MAP2K6, and VIPR2 for ducks) reveals their high relevance to AIV. Further analysis of these genes provides promising effector molecules (such as IκBα, STAT1/STAT3, GSK-3β, or p53) and related key signaling pathways (such as NF-κB, JAK/STAT, or Wnt) to elucidate the complex mechanisms of immune responses to AIV infections in both chickens and ducks.

Modification of surface glycan by expression of beta-1,4-N-acetyl-galactosaminyltransferase (B4GALNT2) confers resistance to multiple viruses infection in chicken fibroblast cell

Introduction

Infectious viruses in poultry, such as avian influenza virus (AIV) and Newcastle disease virus (NDV), are one of the most major threats to the poultry industry, resulting in enormous economic losses. AIVs and NDVs preferentially recognize α-2,3-linked sialic acid to bind to target cells. The human beta-1,4-N-acetyl-galactosaminyltransferase 2 (B4GALNT2) modifies α-2,3-linked sialic acid-containing glycan by transferring N-acetylgalactosamine to the sub-terminal galactose of the glycan, thus playing a pivotal role in preventing viruses from binding to cell surfaces. However, chickens lack a homolog of the B4GALNT2 gene.

Methods

Here, we precisely tagged the human B4GALNT2 gene downstream of the chicken GAPDH so that the engineered cells constitutively express the human B4GALNT2. We performed a lectin binding assay to analyze the modification of α-2,3-linked sialic acid-containing glycan by human B4GALNT2. Additionally, we infected the cells with AIV and NDV and compared cell survivability, viral gene transcription, and viral titer using the WST-1 assay, RT-qPCR and TCID50 assay, respectively.

Results

We validated human B4GALNT2 successfully modified α-2,3-linked sialic acid-containing glycan in chicken DF-1 cells. Following viral infection, we showed that human B4GALNT2 reduced infection of two AIV subtypes and NDV at 12-, 24-, and 36-hours post-infection. Moreover, cells expressing human B4GALNT2 showed significantly higher cell survivability compared to wild-type DF-1 cells, and viral gene expression was significantly reduced in the cells expressing human B4GALNT2.

Discussion

Collectively, these results suggest that artificially expressing human B4GALNT2 in chicken is a promising strategy to acquire broad resistance against infectious viruses with a preference for α-2,3-linked sialic acids such as AIV and NDV.

Strategies for the Generation of Gene Modified Avian Models: Advancement in Avian Germline Transmission, Genome Editing, and Applications

Avian models are valuable for studies of development and reproduction and have important implications for food production. Rapid advances in genome-editing technologies have enabled the establishment of avian species as unique agricultural, industrial, disease-resistant, and pharmaceutical models. The direct introduction of genome-editing tools, such as the clustered regularly interspaced short palindromic repeats (CRISPR) system, into early embryos has been achieved in various animal taxa. However, in birds, the introduction of the CRISPR system into primordial germ cells (PGCs), a germline-competent stem cell, is considered a much more reliable approach for the development of genome-edited models. After genome editing, PGCs are transplanted into the embryo to establish germline chimera, which are crossed to produce genome-edited birds. In addition, various methods, including delivery by liposomal and viral vectors, have been employed for gene editing in vivo. Genome-edited birds have wide applications in bio-pharmaceutical production and as models for disease resistance and biological research. In conclusion, the application of the CRISPR system to avian PGCs is an efficient approach for the production of genome-edited birds and transgenic avian models.

Genome centric engineering using ZFNs, TALENs and CRISPR-Cas9 systems for trait improvement and disease control in Animals

Livestock is an essential life commodity in modern agriculture involving breeding and maintenance. The farming practices have evolved mainly over the last century for commercial outputs, animal welfare, environment friendliness, and public health. Modifying genetic makeup of livestock has been proposed as an effective tool to create farmed animals with characteristics meeting modern farming system goals. The first technique used to produce transgenic farmed animals resulted in random transgene insertion and a low gene transfection rate. Therefore, genome manipulation technologies have been developed to enable efficient gene targeting with a higher accuracy and gene stability. Genome editing (GE) with engineered nucleases-Zinc finger nucleases (ZFNs) and transcription activator-like effector nucleases (TALENs) regulates the targeted genetic alterations to facilitate multiple genomic modifications through protein-DNA binding. The application of genome editors indicates usefulness in reproduction, animal models, transgenic animals, and cell lines. Recently, CRISPR/Cas system, an RNA-dependent genome editing tool (GET), is considered one of the most advanced and precise GE techniques for on-target modifications in the mammalian genome by mediating knock-in (KI) and knock-out (KO) of several genes. Lately, CRISPR/Cas9 tool has become the method of choice for genome alterations in livestock species due to its efficiency and specificity. The aim of this review is to discuss the evolution of engineered nucleases and GETs as a powerful tool for genome manipulation with special emphasis on its applications in improving economic traits and conferring resistance to infectious diseases of animals used for food production, by highlighting the recent trends for maintaining sustainable livestock production.

Myxovirus resistance (Mx) Gene Diversity in Avian Influenza Virus Infections

Avian influenza viruses (AIVs) pose threats to animal and human health. Outbreaks from the highly pathogenic avian influenza virus (HPAIV) in indigenous chickens in Bangladesh are infrequent. This could be attributed to the Myxovirus resistance (Mx) gene. To determine the impact of Mx gene diversity on AIV infections in chicken, we assessed the Mx genes, AIVs, and anti-AIV antibodies. DNA from blood cells, serum, and cloacal swab samples was isolated from non-vaccinated indigenous chickens and vaccinated commercial chickens. Possible relationships were assessed using the general linear model (GLM) procedure. Three genotypes of the Mx gene were detected (the resistant AA type, the sensitive GG type, and the heterozygous AG type). The AA genotype (0.48) was more prevalent than the GG (0.19) and the AG (0.33) genotypes. The AA genotype was more prevalent in indigenous than in commercial chickens. A total of 17 hemagglutinating viruses were isolated from the 512 swab samples. AIVs were detected in two samples (2/512; 0.39%) and subtyped as H1N1, whereas Newcastle disease virus (NDV) was detected in the remaining samples. The viral infections did not lead to apparent symptoms. Anti-AIV antibodies were detected in 44.92% of the samples with levels ranging from 27.37% to 67.65% in indigenous chickens and from 26% to 87.5% in commercial chickens. The anti-AIV antibody was detected in 40.16%, 65.98%, and 39.77% of chickens with resistant, sensitive, and heterozygous genotypes, respectively. The genotypes showed significant association (p < 0.001) with the anti-AIV antibodies. The low AIV isolation rates and high antibody prevalence rates could indicate seroconversion resulting from exposure to the virus as it circulates. Results indicate that the resistant genotype of the Mx gene might not offer anti-AIV protection for chickens.

Dual Host and Pathogen RNA-Seq Analysis Unravels Chicken Genes Potentially Involved in Resistance to Highly Pathogenic Avian Influenza Virus Infection

Highly pathogenic avian influenza viruses (HPAIVs) cause severe systemic disease and high mortality rates in chickens, leading to a huge economic impact in the poultry sector. However, some chickens are resistant to the disease. This study aimed at evaluating the mechanisms behind HPAIV disease resistance. Chickens of different breeds were challenged with H7N1 HPAIV or clade 2.3.4.4b H5N8 HPAIV, euthanized at 3 days post-inoculation (dpi), and classified as resistant or susceptible depending on the following criteria: chickens that presented i) clinical signs, ii) histopathological lesions, and iii) presence of HPAIV antigen in tissues were classified as susceptible, while chickens lacking all these criteria were classified as resistant. Once classified, we performed RNA-Seq from lung and spleen samples in order to compare the transcriptomic signatures between resistant and susceptible chickens. We identified minor transcriptomic changes in resistant chickens in contrast with huge alterations observed in susceptible chickens. Interestingly, six differentially expressed genes were downregulated in resistant birds and upregulated in susceptible birds. Some of these genes belong to the NF-kappa B and/or mitogen-activated protein kinase signaling pathways. Among these six genes, the serine protease-encoding gene PLAU was of particular interest, being the most significantly downregulated gene in resistant chickens. Expression levels of this protease were further validated by RT-qPCR in a larger number of experimentally infected chickens. Furthermore, HPAIV quasi-species populations were constructed using 3 dpi oral swabs. No substantial changes were found in the viral segments that interact with the innate immune response and with the host cell receptors, reinforcing the role of the immune system of the host in the clinical outcome. Altogether, our results suggest that an early inactivation of important host genes could prevent an exaggerated immune response and/or viral replication, conferring resistance to HPAIV in chickens.

Genome editing of avian species: implications for animal use and welfare

Avian species are used as model systems in research and have contributed to ground-breaking concepts in developmental biology, immunology, genetics, virology, cancer and cell biology. The chicken in particular is an important research model and an agricultural animal as a major contributor to animal protein resources for the global population. The development of genome editing methods, including CRISPR/Cas9, to mediate germline engineering of the avian genome will have important applications in biomedical, agricultural and biotechnological activities. Notably, these precise genome editing tools have the potential to enhance avian health and productivity by identifying and validating beneficial genetic variants in bird populations. Here, we present a concise description of the existing methods and current applications of the genome editing tools in bird species, focused on chickens, with attention on animal use and welfare issues for each of the techniques presented.

Comparative Investigation of Gene Regulatory Processes Underlying Avian Influenza Viruses in Chicken and Duck

Simple Summary

Avian influenza poses a great risk to gallinaceous poultry, while mallard ducks can withstand most virus strains. To date, the mechanisms underlying the susceptibility of chicken and the effective immune response of duck have not been completely understood. In this study, our aim is to investigate the transcriptional gene regulation governing the expression of important avian-influenza-induced genes and to reveal the master regulators stimulating an effective immune response after virus infection in ducks while dysfunctioning in chicken.

Abstract

The avian influenza virus (AIV) mainly affects birds and not only causes animals’ deaths, but also poses a great risk of zoonotically infecting humans. While ducks and wild waterfowl are seen as a natural reservoir for AIVs and can withstand most virus strains, chicken mostly succumb to infection with high pathogenic avian influenza (HPAI). To date, the mechanisms underlying the susceptibility of chicken and the effective immune response of duck have not been completely unraveled. In this study, we investigate the transcriptional gene regulation underlying disease progression in chicken and duck after AIV infection. For this purpose, we use a publicly available RNA-sequencing dataset from chicken and ducks infected with low-pathogenic avian influenza (LPAI) H5N2 and HPAI H5N1 (lung and ileum tissues, 1 and 3 days post-infection). Unlike previous studies, we performed a promoter analysis based on orthologous genes to detect important transcription factors (TFs) and their cooperation, based on which we apply a systems biology approach to identify common and species-specific master regulators. We found master regulators such as EGR1, FOS, and SP1, specifically for chicken and ETS1 and SMAD3/4, specifically for duck, which could be responsible for the duck’s effective and the chicken’s ineffective immune response.

A Genetically Engineered Commercial Chicken Line Is Resistant to Highly Pathogenic Avian Leukosis Virus Subgroup J

Viral diseases remain a major concern for animal health and global food production in modern agriculture. In chickens, avian leukosis virus subgroup J (ALV-J) represents an important pathogen that causes severe economic loss. Until now, no vaccine or antiviral drugs are available against ALV-J and strategies to combat this pathogen in commercial flocks are desperately needed. CRISPR/Cas9 targeted genome editing recently facilitated the generation of genetically modified chickens with a mutation of the chicken ALV-J receptor Na+/H+ exchanger type 1 (chNHE1). In this study, we provide evidence that this mutation protects a commercial chicken line (NHE1ΔW38) against the virulent ALV-J prototype strain HPRS-103. We demonstrate that replication of HPRS-103 is severely impaired in NHE1ΔW38 birds and that ALV-J-specific antigen is not detected in cloacal swabs at later time points. Consistently, infected NHE1ΔW38 chickens gained more weight compared to their non-transgenic counterparts (NHE1W38). Histopathology revealed that NHE1W38 chickens developed ALV-J typical pathology in various organs, while no pathological lesions were detected in NHE1ΔW38 chickens. Taken together, our data revealed that this mutation can render a commercial chicken line resistant to highly pathogenic ALV-J infection, which could aid in fighting this pathogen and improve animal health in the field.

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.

Animal science Down Under: a history of research, development and extension in support of Australia’s livestock industries

This account of the development and achievements of the animal sciences in Australia is prefaced by a brief history of the livestock industries from 1788 to the present. During the 19th century, progress in industry development was due more to the experience and ingenuity of producers than to the application of scientific principles; the end of the century also saw the establishment of departments of agriculture and agricultural colleges in all Australian colonies (later states). Between the two world wars, the Council for Scientific and Industrial Research was established, including well supported Divisions of Animal Nutrition and Animal Health, and there was significant growth in research and extension capability in the state departments. However, the research capacity of the recently established university Faculties of Agriculture and Veterinary Science was limited by lack of funding and opportunity to offer postgraduate research training. The three decades after 1945 were marked by strong political support for agricultural research, development and extension, visionary scientific leadership, and major growth in research institutions and achievements, partly driven by increased university funding and enrolment of postgraduate students. State-supported extension services for livestock producers peaked during the 1970s. The final decades of the 20th century featured uncertain commodity markets and changing public attitudes to livestock production. There were also important Federal Government initiatives to stabilise industry and government funding of agricultural research, development and extension via the Research and Development Corporations, and to promote efficient use of these resources through creation of the Cooperative Research Centres program. These initiatives led to some outstanding research outcomes for most of the livestock sectors, which continued during the early decades of the 21st century, including the advent of genomic selection for genetic improvement of production and health traits, and greatly increased attention to public interest issues, particularly animal welfare and environmental protection. The new century has also seen development and application of the ‘One Health’ concept to protect livestock, humans and the environment from exotic infectious diseases, and an accelerating trend towards privatisation of extension services. Finally, industry challenges and opportunities are briefly discussed, emphasising those amenable to research, development and extension solutions.

Virus-induced immunosuppression in turkeys (Meleagris gallopavo): A review

Immunosuppression is characterized by a dysfunction of humoral and/or cellular immune response leading to increase of susceptibility to secondary infections, increase of mortality and morbidity, poor productivity, and welfare and vaccination failures. Humoral immune response depression is due to perturbation of soluble factors, as complement and chemokines in innate immunity and antibodies or cytokines in adaptive immunity. At the cellular immune response, immunosuppression is the consequence of the dysfunction of T-cells, B-cells, heterophils, monocytes, macrophages, and natural Killer cells. Immunosuppression in turkeys can be caused by numerous, non-infectious, and infectious agents, having variable pathological and molecular mechanisms. Interactions between them are very complex. This paper reviews the common viruses inducing clinical and sub-clinical immunosuppression in turkeys, and enteric and neoplastic viruses in particular, as well as the interactions among them. The evaluation of immunosuppression is currently based on classical approach; however, new technique such as the microarray technology is being developed to investigate immunological mediator’s genes detection. Controlling of immunosuppression include, in general, biosecurity practices, maintaining appropriate breeding conditions and vaccination of breeders and their progeny. Nevertheless, few vaccines are available against immunosuppressive viruses in turkey’s industry. The development of new control strategies is reviewed.

Genetic determinants of resistance to highly pathogenic avian influenza in chickens

Highly pathogenic avian influenza (HPAI) poses a huge threat to poultry production and also introduces an epidemiological risk in the human population. Thus far, HPAI has been controlled mainly through widespread implementation of biosecurity, and in the case of an outbreak, liquidation of flocks and establishment of protection zones. Alternative strategies for combating HPAI include the use of vaccines, genetic modification, and genetic selection for increased general and specific immunity in birds. These kinds of strategies often require identification of the genes involved in the immune response to the pathogen. Many genes have been identified as potentially associated with differences in the response to HPAI between poultry species and between individuals. Thus far, the most attention has been focused on genes taking part in regulating the innate immune response, which is responsible for preventing infection and limiting the replication and spread of the virus. The most commonly mentioned candidates for layer chickens include interferon-stimulated genes (ISGs) and RIG-I-like receptors. Proteins encoded by genes of the BTLN family, defensins, and proteins involved in apoptosis have also been associated with differences in the response to HPAI. Recent years have seen an increasing number of studies on the genetic determinants of individual differences in the response to HPAI in chickens. Data from HPAI outbreaks in the US in the spring of 2015 and Mexico in the years 2012-2016 have enabled a more precise analysis of this problem. A number of genes have been identified as associated with the immune response, but their specific role in determining the survival of birds requires further study. Preliminary results indicate that genetic determinants of resistance to HPAI are highly complex and can vary depending on the virus strain and the genetic line of birds.