SCRV has strong virulence and can spread horizontally or vertically through water, aerosols, animal bites, insect vector or plant trauma or transplantation (Kuzmin et al., 2009). SCRV belongs to the genus Perhabdovirus and has more than 94% homology with SHVV, MoARV, CrERV and CHRV (Liu et al., 2015, Ou et al., 2013, Liu et al., 2019a, Luo et al., 2013). After infection with the virus of this genus, the symptoms of the fish are drowsiness, enlargement of the abdomen, and bleeding from the liver, spleen and skin (Ma et al., 2013, Ou et al., 2013, Luo et al., 2013, Huang et al., 2021). Therefore, these viruses may be different strains of the same virus. In order to study the interaction between SCRV and the host, host-specific gene expression changes were revealed through SCRV infected E11 cells transcriptome analysis. These findings highlight the dynamic nature of host-virus interactions and their important implications for disease management strategies, and have far-reaching implications for the exploration of potential hosts of SCRV.
A total of 29,894 unigenes were found via the Illumina HiSeq X Ten sequencing (Table 2). Ke et al. studied 24-hour responses that obtained approximately 20,000 unigenes by infection with the Siniperca chuatsi skin cell (SCSC) line (Ke et al., 2022). Liu et al. predicted 93,372 unigenes by transcriptional analysis of SHVV-infected SSN-1 cells at two different time points (Liu et al., 2019b). Compared to the results of other studies, this study similarly found a wealth of stitching data. There were 4137 DEGs consisting of 2189 upregulated and 1948 downregulated genes compared to the uninfected group when compared with the non-infected group (Fig. 4A). These were further confirmed by qRT-PCR. GO analysis showed that the most abundant category was “cellular process” in the biological process subclass. The top categories were “cell” and “cell part” in the biological process subclass. The most abundant category was “binding” in the molecular function subclass (Fig. 5). Cell, cell part, and organelle make up the largest percentage of cell component. It can be speculated that immune cells initiate an innate immune response when a pathogen infects a host, activating the first line of defense of the host immune system. KEGG enrichment analysis indicated that all DEGs were annotated to 223 signaling pathways (Fig. 6). These DEGs were involved in many immune-related pathways, such as Toll-like receptor signaling pathway, complement and coagulation cascades, TNF signaling pathway, TGF-beta signaling pathway, p53 signaling pathway, fanconi anemia pathway. Similarly, Zhao et al. showed that when IHNV infects rainbow trout gonadal cells (RTG-2), a large number of immune-related pathways in KEGG were mobilized (Zhao et al., 2022). Chen et al. studied that most of the identified DEGs were significantly associated with immune response-regulating signaling pathway when red-spotted grouper nervous necrosis virus (RGNNV) infected SSN-1 cells (Chen et al., 2017). Analysis of the immune pathways associated with viral infection is essential for the molecular mechanisms of SCRV-infected E11 cells.
Further, the DEGs activated 31 canonical immune-related KEGG pathways, including MAPK signaling pathway, PI3K-Akt signaling pathway, Endocytosis, Apoptosis. In this study, more than 23 DEGs were respectively enriched in these categories (Table 3). MAPK signaling pathway is the core pathway of intracellular regulatory network, which is closely related to inflammation and immunity (Zhu et al., 2024). When SHVV infects SSN-1 cells, the MAPK signaling pathway was also activated (Liu et al., 2019b). The PI3K-Akt signaling pathway, like the MAPK signaling pathway, is an important pathway for membrane receptor signaling to intracellular transduction, which regulates apoptosis, growth, and the expression of some important genes (Wu et al., 2021). In addition, endocytic trafficking affects sophisticated cellular properties, including cell polarity and collective cell migration. There is a strong relevance with apoptosis and cancer immunity (Sigismund et al., 2021). In short, most the immune-related pathways were activated in this study. Innate immunity is made up of a series of germ cell coding receptors called pattern recognition receptors (PRRs), whose function is to act as an inducer of host defense mechanisms to recognize pathogen associated molecular patterns (PAMPs) or damage associated molecular patterns (DAMPs) that are considered the most basic forms of host defense present in plants and animals (Ausubel, 2005, Tang et al., 2012). Various PRRs, such as NOD-like receptors (NLRs), RIG-I-like receptors (RLRs), and Toll-like receptors (TLRs) are key receptors mediating innate immunity (Table 3). RLRs plays a vital role in establishing innate natural immunity against viruses, inducing the production of interferon and pro-inflammatory cytokines through RLR cascade signaling. TLRs can recognize a variety of molecularly related molecules, resist pathogen invasion, and play a role in inflammation, cell regulation, survival, and proliferation. (Gay et al., 2014). NLRs can recognize pathogenic molecular patterns of viruses, regulate the formation of inflammatory bodies, and induce the generation of IL-1β and IL-18, thereby participating in the inflammatory response (Pashenkov et al., 2019). Consequently, these receptors detect pathogen invasion and initiate their respective mediated immune pathways to produce immune responses to resist it when SCRV infected E11 cells. The enrichment of signaling pathways lays a foundation for understanding the immune mechanisms of SCRV infection in different hosts.
In conclusion, the transcriptomic profiling results of SCRV infected E11 cells announced the interaction mechanism between the virus and the host, which was helpful to find potential hosts for SCRV and provided valuable clues for the study of SCRV infection.