In this chapter, the authors review how the adaptive immune response protects against the attack of pathogens, describing the major types of lymphocytes, B and T cells, and the different forms of immune protection they provide. They discuss how best to deliver vaccines using adjuvants and delivery platforms, how to differentiate vaccinated from infected animals, how to assess protection after vaccination, and the features of active, passive, and herd immunity. It is important for vaccines to induce the type of immunity able to neutralize the pathogen: antibody and/or cell-mediated immunity. Emergency vaccination using DIVA vaccines could be an important control tool for disease outbreaks in densely populated livestock areas. DIVA vaccination might also limit the number of culled animals in the process of disease eradication, thereby enhancing public acceptance of disease control measures and limiting economic damage. Therefore, the DIVA concept is recommended for inclusion in any new vaccine development.

Foot and mouth disease (FMD) is a highly contagious and economically important viral disease of domestic cloven-hoofed animals including cattle, buffaloes, goats, sheep, pigs, and more than 100 wildlife species. This chapter provides a review on FMD vaccines, vaccination strategy, application, and effectiveness of vaccination programs. Immune responses can be subdivided broadly into two parts: innate and adaptive immunity. Purchasing vaccines in most cases follows tendering procedures with information provided by the tenderer and manufacturers. These procedures are fully described in the FMD vaccination and postvaccination monitoring guidelines. Vaccination strategies for the control of FMD depend on the objectives of the control program and the epidemiology of infection. Additionally, quality assurance and quality control testing of finished products by independent vaccine quality control centers should be the common practice prior to the batch release.

This chapter considers different vaccination strategies and important concepts for monitoring vaccine performance in the field, including vaccine coverage, herd immunity, and vaccine effectiveness studies. Where infectious agents are endemic, with a high risk of exposure to infection, vaccination may be used to protect individual groups or animals from disease on a risk basis. The process of vaccination involves multiple decisions and activities. Problems can arise due to poor strategy, inadequate implementation, or changes in the pathogen or the livestock industry. The advantages of vaccine efficacy studies include rigorous controls for biases by sex/age, etc., as study individuals are randomly allocated into groups. Furthermore, they require recording of vaccination status and include a prospective, active monitoring phase for AR, including laboratory confirmation of the infectious status/outcome of interest and vaccine immunogenicity. Measuring vaccination coverage and postvaccination immunity are two key indicators establishing that vaccination has been applied correctly.

Coronavirus infection induces the unfolded protein response (UPR), a cellular signalling pathway composed of three branches, triggered by unfolded proteins in the endoplasmic reticulum (ER) due to high ER load. We have used RNA sequencing and ribosome profiling to investigate holistically the transcriptional and translational response to cellular infection by murine hepatitis virus (MHV), often used as a model for the Betacoronavirus genus to which the recently emerged SARS-CoV-2 also belongs. We found the UPR to be amongst the most significantly up-regulated pathways in response to MHV infection. To confirm and extend these observations, we show experimentally the induction of all three branches of the UPR in both MHV- and SARS-CoV-2-infected cells. Over-expression of the SARS-CoV-2 ORF8 or S proteins alone is itself sufficient to induce the UPR. Remarkably, pharmacological inhibition of the UPR greatly reduced the replication of both MHV and SARS-CoV-2, revealing the importance of this pathway for successful coronavirus replication. This was particularly striking when both IRE1α and ATF6 branches of the UPR were inhibited, reducing SARS-CoV-2 virion release (~1,000-fold). Together, these data highlight the UPR as a promising antiviral target to combat coronavirus infection.

Mosquitoes are known as important vectors of many arthropod-borne (arbo)viruses causing disease in humans. These include dengue (DENV) and Zika (ZIKV) viruses. The exogenous small interfering (si)RNA (exo-siRNA) pathway is believed to be the main antiviral defense in arthropods, including mosquitoes. During infection, double-stranded RNAs that form during viral replication and infection are cleaved by the enzyme Dicer 2 (Dcr2) into virus-specific 21 nt vsiRNAs, which are subsequently loaded into Argonaute 2 (Ago2). Ago2 then targets and subsequently cleaves complementary RNA sequences, resulting in degradation of the target viral RNA. Although various studies using silencing approaches have supported the antiviral activity of the exo-siRNA pathway in mosquitoes, and despite strong similarities between the siRNA pathway in the Drosophila melanogaster model and mosquitoes, important questions remain unanswered. The antiviral activity of Ago2 against different arboviruses has been previously demonstrated. However, silencing of Ago2 had no effect on ZIKV replication, whereas Dcr2 knockout enhanced its replication. These findings raise the question as to the role of Ago2 and Dcr2 in the control of arboviruses from different viral families in mosquitoes. Using a newly established Ago2 knockout cell line, alongside the previously reported Dcr2 knockout cell line, we investigated the impact these proteins have on the modulation of different arboviral infections. Infection of Ago2 knockout cell line with alpha- and bunyaviruses resulted in an increase of viral replication, but not in the case of ZIKV. Analysis of small RNA sequencing data in the Ago2 knockout cells revealed a lack of methylated siRNAs from different sources, such as acute and persistently infecting viruses-, TE- and transcriptome-derived RNAs. The results confirmed the importance of the exo-siRNA pathway in the defense against arboviruses, but highlights variability in its response to different viruses and the impact the siRNA pathway proteins have in controlling viral replication. Moreover, this established Ago2 knockout cell line can be used for functional Ago2 studies, as well as research on the interplay between the RNAi pathways.

Picornavirus capsids are assembled from 60 copies of a capsid precursor via a pentameric assembly intermediate or ‘pentamer’. Upon completion of virion assembly, a maturation event induces a final cleavage of the capsid precursor to create the capsid protein VP4, which is essential for capsid stability and entry into new cells. For the picornavirus foot-and-mouth disease virus (FMDV), intact capsids are temperature and acid-labile and can disassemble into pentamers. During disassembly, capsid protein VP4 is lost, presumably altering the structure and properties of the resulting pentamers. The purpose of this study was to compare the characteristics of recombinant “assembly” and “disassembly” pentamers. We generated recombinant versions of these different pentamers containing an engineered cleavage site to mimic the maturation cleavage. We compared the sedimentation and antigenic characteristics of these pentamers using sucrose density gradients and reactivity with an antibody panel. Pentamers mimicking the assembly pathway sedimented faster than those on the disassembly pathway suggesting that for FMDV, in common with other picornaviruses, assembly pentamers sediment at 14S whereas only pentamers on the disassembly pathway sediment at 12S. The reactivity with anti-VP4 antibodies was reduced for the 12S pentamers, consistent with the predicted loss of VP4. Reactivity with other antibodies was similar for both pentamers suggesting that major antigenic features may be preserved between the VP4 containing assembly pentamers and the disassembly pentamers lacking VP4.