Molecular Microbiology Research, 2025, Vol.15, No.1, 10-17 http://microbescipublisher.com/index.php/mmr 13 4.3 Co-expression network construction and key gene screening To figure out which genes play a leading role in the immune response, the researchers established a co-expression network. In goat models, genes like TNF, IL-6, and CCL20 are at the center of the network, indicating that they are critical in the entire immune response (Li et al., 2019). The network also reveals the association between miRNA and mRNA. For example, cfa-let-7a may regulate Thrombospondin 1, thereby affecting cell death and immune response (Pang et al., 2020). Through this network analysis, we can not only pick out some key genes as potential intervention targets, but also better understand the interaction between the virus and the host during infection. 5 Viral Suppression of Immune Response Mechanisms 5.1 Strategies of FMDV to evade immune surveillance Foot-and-mouth disease virus (FMDV) is not easy to deal with, it uses various methods to avoid host immune monitoring. The most common method is to "silence" some important immune-related genes. These genes are originally used by the body to fight viruses, but viruses can reduce their expression. Studies in pigs have found that some genes related to immune responses are downregulated after infection, which may be exactly the effect FMDV wants (Jarczak et al., 2019). In addition, the virus will focus on certain signaling pathways, such as ribosome-related pathways, which interfere with the normal operation of the entire immune system by interrupting these mechanisms. 5.2 Analysis of interferon signaling pathway inhibition 5.2.1 Mechanisms by which the virus suppresses the expression of interferon-stimulated genes (ISGs) Interferon is a natural tool used by the body to deal with viruses, while ISGs are genes activated under the influence of interferon signals. But FMDV will make trouble and prevent these genes from being expressed. Some studies have found that after viral infection, many immune genes that should have been upregulated were downregulated (Lüet al., 2018). Viruses may achieve this by interfering with some key transcription factors or signaling molecules. 5.2.2 Molecular pathways by which FMDV suppresses type I interferon (IFN-α/β) production FMDV not only suppresses ISGs, it also prevents the production of interferon itself. For example, viruses can affect the expression of receptors such as TLR7 and RIG-I. They were originally responsible for identifying viral RNA and then initiating the process of interferon production (Lin, 2024). Once these receptors are interfered with, the entire antiviral pathway will "fail" and the virus will spread more easily. 5.2.3 STAT1/STAT2 signaling blockade and immune evasion STAT1 and STAT2 are the "downstream executors" of interferon responses. Once FMDV cuts this signal chain, ISGs cannot be activated and the entire anti-viral process will be stopped (Zhao et al., 2017). This is also one of the common strategies used by the virus to evade epidemics and stabilize infections. 5.3 Effects of viral proteins on immune modulators The proteins of FMDV itself will also directly affect the host's immune regulation. For example, the RNA polymerase used for viral replication is encoded by the 3Dpol gene. If siRNA is used specifically to target this gene, it can effectively reduce the number of viruses. In some transgenic goats, the amount of virus replication decreased significantly after expressing this siRNA. At the same time, the expression of molecules related to immunomodulation such as TLR7, RIG-I, and TRAF6 has also changed (Nahas et al., 2021). This shows that viral proteins can indirectly control the host's immune response by affecting these key molecules. 6 Case Study Analysis 6.1 Investigation of FMD outbreaks in goats in a specific region Foot-and-mouth disease (FMD) is highly contagious and can affect even-unged animals like goats. Understanding the epidemic situation in a certain area will help judge how the virus spreads and what impact it has. Taking India as an example, although there are vaccinations in the local area, there are still many reports of the epidemic
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