As a result of the recognition of HCV RNA by the MAVS protein, an innate antiviral response is activated, which is associated with the increased production of interferon and proinflammatory cytokines [37]. These events create an inflammatory environment that attracts innate immune cells (primarily natural killer cells), which destroy infected cells. To avoid being destroyed in the earliest stages of infection, HCV proteins can inhibit antiviral signaling into mitochondria. This signal is initiated by RNA viruses in response to the recognition of dsRNA by the RNA helicase RIG-I, and the subsequent chain of reactions, one of the central roles that is played by the MAVS membrane protein is the directing of the signal to the expression of interferon $\beta$. However, the cleavage of MAVS from the mitochondrial membrane, caused by the NS3/4A HCV protein, disrupts its function and blocks the production of interferon [38]. Thus, blocking the interaction of NS3/4A with MAVS will potentially prevent the development of HCV infection at the earliest stage.

Autophagy is a regulated process of the destruction of damaged or dysfunctional cell organelles. Unutilized damaged cellular structures can act as inducers of inflammation, which is not beneficial for HCV pathogenesis in the acute phase of the infection since the probability of the immune cells detecting the virus and the elimination of infected cells increases. Therefore, the viral apparatus is aimed at enhancing autophagy. Some HCV regulatory proteins are able to induce autophagy through an interaction with autophagy proteins. Thus, it was found that the function of the HCV p7 protein, when bound to the beclin-1 protein, was associated with the initiation of autophagy [39]. Another HCV protein, NS3/4A, is able to interact with mitochondria-associated immune-associated GTPases M (IRGM), which also play a regulatory role in the autophagy process. It is known that HCV proteins activate IRGM-mediated phosphorylation of ULK1, which is one of the initiating factors for triggering autophagy [40]. Other regulatory interactions between HCV proteins and autophagy proteins include the binding of HCV nonstructural protein 5B (NS5B) to autophagy related 5 (ATG5) and autophagy related 12 (ATG12) [41], and of HCV nonstructural protein 5B (NS4B) to Ras-related protein 5 (Rab5), vacuolar protein sorting 34 (Vps34), and beclin-1 [42]. It has also been shown that an increase in the expression of the HCV NS5A protein leads to an increase in the expression of the beclin-1 protein [42].

Mitophagy is a particular variant of autophagy and is aimed at removing damaged and dysfunctional mitochondria. Since “unhealthy” mitochondria are a source of ROS that initiate inflammation and apoptosis, their removal is a favorable factor for maintaining the initial population of HCV virions in infected hepatocytes. Mitophagy has been shown to increase with HCV infection [38]. It was demonstrated that HCV activates the expression of Parkin and Pink1, which are key enzymes in mitophagy, and also induces mitochondrial translocation of Parkin, which was the initial stage of mitophagy [43]. It is also known that NS5A HCV proteins cause the mitochondrial translocation of Parkin [44]. The HCV proteins responsible for increasing the expression of mitophagy proteins have not yet been identified, which also forms a promising direction for future research.

The processes of mitochondrial fission and fusion in hepatocytes are aimed at redistributing mitochondrial content and establishing a balance in the number of mitochondria. Both processes are aimed at maintaining a high-quality composition of mitochondria, however, in the case of fission, two smaller mitochondria are formed from one mitochondrion, and in the case of fusion, one elongated mitochondria is formed from two individuals. HCV enhances mitochondrial fission, and since mitochondrial fission often precedes mitophagy, its increase during acute HCV infection was discussed in the previous section. Furthermore, in addition to evading the immune response, the activation of mitochondrial fission can be caused by an increase in the intensity of metabolism. An increased number of mitochondria can “work for the virus”, supplying energy for the assembly of new virions. It was shown that HCV induced the phosphorylation and translocation of the Drp1 (mitochondrial fission protein) to the mitochondrial membrane, which was necessary to initiate mitochondrial fission [45]. HCV is able to inhibit mitochondrial fusion, which is associated with mtDNA depletion [46]. Importantly, the balance between fission and fusion is critical for stabilizing mtDNA copy number and maintaining a healthy liver function [47]. Drp1 is a target for HCV but the question remains regarding whether HCV proteins can directly affect this target.

Like many other viruses, HCV redirects energy metabolism from oxidative phosphorylation to glycolysis. This is performed so that it can quickly use the cell’s energy resources, in a short time, for processes associated with RNA replication, translation of HCV proteins, and virion assembly. Thus, it was found that the expression of the key protein subunits in the ETC complexes: mitochondrially Encoded NADH: Ubiquinone Oxidoreductase Core Subunit 1,3,4,4L (MT-ND1), (MT-ND3), (MT-ND4), and (MT-ND4L) of complex I and MT-CO2 of complex IV decreased in 6 days after the onset of HCV replication [48]. ATP synthase was also found to be downregulated in 4 weeks after the onset of the infection [48]. An increase in the expression and activity of key glycolysis enzymes during HCV infection has also been noted [48]. Thus, the activity of hexokinase increased as a result of an interaction between this enzyme and the HCV NS5A protein [49]. Therefore, inhibition of this metabolic shift by creating drugs that prevent the interaction between HCV proteins and the enzymes involved in oxidative phosphorylation and glycolysis can potentially slow down the reproduction of HCV.

In the initial phase of HCV infection, it is advantageous for the virus to maximize progeny within the infected cell by using its resources. To do this, HCV implements a variety of ways to block cell apoptosis from being initiated. One of these ways is to enhance mitophagy, as described above. Furthermore, HCV is able to directly inhibit apoptosis. Thus, in the study [50], it was shown that the HCV E2 protein reduced the level of cytochrome C and blocked its release from mitochondria, which reduced apoptosis in HCV-infected cells. Hence, reducing the interaction of these proteins may be an effective strategy to reduce the persistence of HCV. Mitochondrial and other cellular targets of HCV during the acute phase of infection are summarized in Table 1.

In the chronic phase, HCV actively spreads and infects new hepatocytes. In the newly infected cells, HCV can also inhibit apoptosis to create a larger number of virions; however, for HCV to spread further, contrastingly, activates apoptosis of the hepatocytes. It should be noted that the death of hepatocytes during HCV infection occurs mainly as a result of exposure to leukocytes and not the cytopathic effect of HCV. In a study [51] using hepatocyte cell culture, it was demonstrated that the hepatitis C core protein activated the mitochondrial apoptosis pathway through the opportunistic activation of caspase 8. Another study that used a cell culture model demonstrated that the HCV structural protein E2 was able to induce mitochondrial-dependent apoptosis, which is the opposite of the effect shown in Section 4.1.5., and can be associated with both the level of E2 expression and the cellular factors that can modulate its activity in different ways [14]. HCV infection is associated with an increase in oxidative stress and with changes in intramitochondrial Ca${}^{2+}$ (mt-Ca${}^{2+)}$ homeostasis. The overexpression of specific HCV proteins (mainly the core protein) leads to an increase in ROS production, which accompanies other mitochondrial dysfunctions [52]. The disease development in patients with chronic hepatitis C is modeled on the level of oxidative change and the mt-Ca${}^{2+}$ load. Thus, low levels of ROS and oxidative stress, which are dependent on mt-Ca${}^{2+}$, activate a survival-promoting adaptive response and a proliferative adaptive response via redox signaling [53]. It was shown that various HCV proteins could inhibit ETC complex I, which led to an increase in ROS production and an increase in oxidative stress in the cell [54]. Elevated levels of ROS are initiating signals that trigger apoptosis. Thus, an increase in the apoptosis of hepatocytes leads to the growth of DAMPs (damage-associated molecular patterns), which form as a result of the destruction of cells and biomolecules under oxidative stress. This further stimulates inflammation and the subsequent healing reaction, which, when spreading throughout the damaged liver, can lead to the development of fibrosis and cirrhosis.

As it was described in Section 4.1.4., the main metabolic change in acute HCV infection is associated with a shift in energy production, from oxidative phosphorylation to glycolysis. In the chronic phase, HCV continues to use cellular resources, including its energy substrates, which are necessary for RNA replication, the translation of HCV proteins, and capsid assembly. Rapid glycolysis, in this situation, remains the preferred way of obtaining energy. In the chronic phase of infection, the number of cells with preferential glycolysis increases, which is a similar situation to the Warburg effect in cancer cells. Additionally, HCV proteins are able to activate the HIF-1 hypoxia transcription factor, which increases the expression of glycolytic enzymes [55]. Plastic metabolism is also activated and occurs through the pentose phosphate pathway, whose increase is also observed during tumor development [48]. In addition, HCV proteins can directly affect cell proliferation. Thus, the HCV E2 protein can activate the MAPK/ERK signaling pathway, which leads to increased hepatocyte proliferation [56]. The HCV NS5B protein is able to bind to the retinoblastoma (Rb) protein, which also leads to increased hepatocyte proliferation [57]. It is known that HCV proteins are able to modulate the transcription of 15 genes associated with the regulation of cell proliferation, including genes involved in the Wnt/$\beta$-catenin signaling pathway [58]. All these factors increase the risk of developing hepatocellular carcinoma (HCC), which is one of the most severe complications of HCV infection. The presence of mitochondrial dysfunction in HCC cells, revealed in the form of the deactivation of ETC enzymes [59], can serve as evidence of a metabolic shift toward glycolysis, via the HCV protein effect on mitochondrial ETC proteins. A change in carbohydrate metabolism leads to the accumulation of a number of metabolites, such as acyl-CoA, which is also an intermediate participant in triglyceride synthesis reactions, leading to the progressive formation of lipid droplets [60]. In addition, the formation of lipid droplets is directly enhanced by HCV proteins: Core and NS5A. This process is important for the assembly and release of HCV virions from infected cells [61]. Other factors, such as the activation of HIF-1 and sterol regulatory element binding protein (SREBP-1c), whose activity increases during HCV infection, may enhance the de novo lipogenesis. Other factors causing lipid metabolism disorders occur through the modulation of ANGPTL3 transcription, via the HCV core protein and a decrease in PPAR-$\alpha$ transcription that occurs as a result of an exposure to the non-structural (NSP) HCV proteins, which leads to a decrease in the fatty acid $\beta$-oxidation [61]. Overall, this may explain the development of steatosis, which is also one of the complications of a chronic HCV infection [55]. Mitochondrial and other cellular targets of HCV that occur during the chronic phase of infection are summarized in Table 2.