Immune Escape Strategies By Viruses

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Introduction

Viruses are considered as extremely successful predators as they can replicate and control the host cell synthesizing machinery. Viruses have coevolved with their hosts and thus have limited pathogenicity in any immunocompromised natural host.

Viruses can exist in two forms:

Extra cellular virion particles
Intracellular genomes.

Virions are more resistant to physical stress than genomes but are susceptible to humoral immune control. Nevertheless, to exist as a species, virus replication and transfer to a new host are essential. Virus is on borderline between living and nonliving. The response of evasion of the antiviral immune system is critical for the replication of viruses and spread. Viruses have different strategies to evade dghIFN induction and the signaling to avoid the antiviral mechanisms of the host innate immune system.

In fact some of the viruses will have utilizing the multiple strategies to evade an antiviral innate immune signaling, as it’s seen with a hepatitis C virus. Evasion strategies followed by viruses:

The strategies follow are as under are as under:

1. Evasion or Targeting of Porcine Reproductive and Respiratory Syndrome Virus

Viruses have developed several ways to evade detection by PRRs. Many RNA viruses replicate in the cytoplasm where they are sensed by cytoplasmic Porcine Reproductive and Respiratory Syndrome Virus:

MDA5 and RIG-I. In contrast, most of the DNA viruses will replicating within the nucleus and also can be sensed in the nucleus or in the cytoplasm by IFI16 or cGAS, respectively. Thus to avoid the detection by the host innate the immune system at their sites of replication, viruses will have to be evolved by several of the evasion strategies.

For example

Hepatitis C virus, the positive-sense single-stranded, RNA virus, dengue virus, replicates in the cytoplasm where its dsRNA would be expected to be detected by the cytoplasmic RNA sensor proteins RIG-I and MDA5 to induce type I IFN. However, new work has revealed that DenV induces membrane modifications that sequester the DenV RNA away from RIG-I and MDA5, resulting in poor induction of type I IFN. It has been known for some time that hepatitis C virus (HCV), which like Dengue Virus is in the Flaviviridae family of viruses, similarly induces membrane rearrangements to house its replication machinery. Interestingly, it has now been suggested that similar to Dengue Virus , hepatitis C virus induced membrane rearrangement prevents recognition of hepatitis C virus , RNA by RIG-I .Indeed, a study by Neufeldt, showed hepatitis C virus that co-opts host nuclear pore complex proteins (NPC) to the membranous web to regulate protein transport into the replication complex. As viral proteins have cryptic nuclear localization signals they can relocalize to these sites of replication; however, as RIG-I does not, it is excluded from the sites of replication. Intriguingly, addition of a nuclear localization signal to RIG-I, allows it to sense hepatitis C virus. RNA and activate IFN induction, suggesting that the NPC at the membranous web acts as a regulator to determine the proteins that can access the membranous web. This is the first demonstration that sequestered viral replication within rearranged cytoplasmic membranes actively prevents PRR sensing of viral RNA and the subsequent induction of IFN.

The PRRs RIG-I and MDA5 are frequently inhibited by viruses to prevent activation of IFN. These proteins are activated by specific PAMPs, with RIG-I recognizing ssRNA that contains a 5′ triphosphate as well as short double-stranded (ds) RNA molecules, and MDA5 sensing longer dsRNA molecules (reviewed in [3]). Enteroviruses, including poliovirus (PV), coxsackievirus B3 (CVB3), and enterovirus 71 (EV-D71), are positive-sense ssRNA viruses sensed in the cytoplasm by MDA5 and RIG-I. These enteroviruses encode two proteases, 2Apro and 3Cpro, required for viral polyprotein processing. However, 2Apro and 3Cpro have also been shown to cleave MDA5 and RIG-I, respectively. This demonstrates that enteroviruses have converged on common strategies to evade multiple PRRs during infection further supporting the fact that PRR sensing is critical for limiting viral replication and spread.

Both RIG-I and MDA5 require a coordinated set of events to go from their inactive to active state. One of the steps to activate RIG-I and MDA5 includes removal of inhibitory phosphorylation marks by the protein phosphatases PP1α and PP1γ. The negative-sense ssRNA viruses, measles virus (MV) and Nipah virus, both inhibit MDA5 activation through the actions of their V protein. The V protein, which acts as an IFN antagonist, binds PP1α and PP1γ to prevent the dephosphorylation of MDA5 specifically during infection. MV also utilizes a second strategy to prevent PP1α/γ dephosphorylation of MDA5. This strategy involves activation of a DC-SIGN signaling pathway that activates Raf1 kinase for activation of the PP1 inhibitor 1, which blocks PP1α/γ action

Full activation of RIG-I requires the actions of a set of proteins, including TRIM25, RIPLET. All of these proteins are targeted by viruses to prevent their activation. Both TRIM25 and RIPLET are E3 ubiquitin ligases that ubiquitinate RIG-I with K63-linked ubiquitin chains for its full activation. However, the negative-sense ssRNA virus, influenza virus, which is sensed by RIG-I, evades the actions of both TRIM25 and Riplet. The viral NS1 protein binds to both TRIM25 and Riplet in a species-specific manner. This prevents the activation of RIG-I during infection leading to a decreased induction of IFN. Recently, it was shown that the HCV NS3-4A protease complex, which has long been known to cleave MAVS and TRIF. The 14-3-3ɛ protein, which binds to RIG-I to mediate translocation of RIG-I from the cytoplasm to interact with MAVS at intracellular membranes, is also inhibited by viruses. The 14-3-3ɛ protein binds proteins like RIG-I that contain phosphorylated serine or threonine at an Rxx (pS/pT) xP motif. Interestingly, the NS3 proteases of both DenV and West Nile virus (WNV) bind to 14-3-3ɛ via a phosphomimetic RxEP motif, suggesting that NS3 competitively inhibits RIG-I binding to 14-3-3ɛ, thus blocking translocation to MAVS to prevent induction of antiviral innate immunity.

Viruses also evade sensing by PRRs by encoding proteins that protect the viral nucleic acids from sensors. The cytoplasmic PRR cGAS senses viral DNA in the cytoplasm. During HIV-1 and HIV-2 infection, the viral complementary DNA (cDNA) within the virion is sensed by cGAS after infection. However, the HIV-1 but not HIV-2 cDNA is protected within the viral capsid until it is transported into the nucleus for replication. The mechanism behind this protection is due to affinity of the HIV-1, but not HIV-2, capsid with the host protein cycophilin A (CypA) which stabilizes the viral capsid to prevent exposure of the viral cDNA to cGAS in the cytoplasm. In addition to cGAS, viruses target IFI16, which senses DNA viruses that replicate in the nucleus. In particular, the herpes simplex virus-1 (HSV-1) immediate early protein ICP0 has E3 ubiquitin ligase activity that ubiquitinates IFI16, resulting in its degradation by the ubiquitin proteasome and loss of IFN induction.

2. Targeting of adaptor proteins and their kinases

In addition to using viral proteases to cleave PRRs, as described above, viruses also utilize their proteases to target the downstream signaling molecules in antiviral innate immune pathways. In particular, the NS3-4A protease of HCV blocks antiviral signaling by cleaving at least three innate immune signaling molecules. The HCV NS3-4A protease prevents activation of the transcription factor IRF3 and induction of IFN by cleaving the signaling adaptor protein MAVS. The NS3-4A protease can also cleave TRIF, an adaptor protein for TLR3, a protein that senses viral dsRNA in the endosome. Finally, as described above, NS3-4A also cleaves RIPLET. As the HCV NS3-4A protease cleaves two molecules in the RIG-I signaling pathway (both RIPLET and MAVS), this suggests that either the virus is ensuring that the RIG-I pathway is inhibited or that RIPLET may have additional functions within innate immunity besides activating RIG-I.

Since MAVS activation coordinates IFN-induction by both RIG-I and MDA5, it is not surprising that viruses often target MAVS or proteins that regulate its function. In addition to HCV, the positive-sense RNA viruses, porcine reproductive and respiratory syndrome virus (PRRSV) and EV-D71, use the nsp4 cysteine protease and 2Apro, respectively, to cleave MAVS during infection. The Dengue Virus protease NS2B3 cleaves the mitofusins, MFN1 and MFN2, known to be positive (MFN1) or negative (MFN2) regulators of MAVS function. Therefore, as their cleavage in DenV-infected cells results in increased virus replication, it suggests that cleavage of MFN1 (vs MFN2) is required to prevent the antiviral response in Dengue Virus infected cells.

While MAVS is the adaptor for RNA virus sensing, STING is the adaptor for DNA virus sensing via the PRRs cGAS and IFI16. Interestingly, Lau et al. determined that both the adenovirus E1A and human papilloma virus 18 (HPV18) E7 proteins bind to sting to prevent induction of type I IFN upon DNA transfection. Additionally, the Kaposi’s sarcoma-associated herpes virus (KSHV) protein vIRF1 binds to STING and prevents its interactions with TBK1 and IRF3 to block IFN induction. Importantly, this inhibition of IFN induction by KSHV was found to important for reactivation of KSHV from viral latency.

3. Targeting transcription factors

Viruses also directly inhibit transcription factors that act in the IFN induction and response pathways to prevent transcriptional activation of IFNs and interferon-stimulated genes (ISGs) during virus infection. To evade IFN induction, enterovirus 68 (EV-D68) 3Cpro cleaves IRF7 during infection. The human poxvirus, molluscum contagiosum virus (MCV), a DNA virus, also evades IFN induction by using its MC132 protein to recruit the Elongin B/Elongin C/Cullin-5 ubiquitin ligase complex to ubiquitinate and degrade the p65 subunit of NFκB to prevent its activation. To antagonize the transcriptional induction of the IFN response pathway, several viruses directly act on the STAT proteins. Both STAT1 and STAT2 are phosphorylated following IFN signaling thereby promoting their interaction with IRF9 to form the ISGF3 complex that transcriptionally activates ISGs. In particular, the DenV NS5 protein targets STAT2 for degradation, resulting in the ubiquitination and degradation of STAT2. Additionally, the HCV core protein dysregulates STAT1 signaling by increasing the levels of non-phosphorylated STAT1 in the cell. Antagonism of transcription factors by viruses efficiently blocks IFN signaling and ISG induction.

4. Evasion of ISGs

Not surprisingly, viruses have evolved ways to inhibit the antiviral actions of ISGs that are induced by the IFN response pathway. These ISGs have broad mechanisms to confer antiviral activity. In this section, we will focus on how viruses evade the antiviral actions of the ISGs IFIT1 and PKR. The IFIT proteins bind to uncapped RNA to prevent their translation. While many viruses have uncapped RNA and use internal ribosome entry sites for their translation (e.g. HCV), some viruses have evolved ways to cap their RNA to evade IFIT1 recognition. For example, Lassa fever virus and influenza virus snatch caps from host mRNAs. Additionally, many viruses encode proteins that can perform these capping functions. In particular, the WNV NS5 protein contains 2′-Omethyltransferase (2′O-MT) activity to generate a cap 1 structure. This particular cap structure is not sensed by IFIT1 during infection therefore this allows the virus to evade restriction by IFIT. Coronaviruses, positive-sense ssRNA viruses, also encode a 2′O-MT protein, nsp16. Similar to the MT activity of WNV NS5A, the MT activity of nsp16 is required for evasion of IFIT sensing during both murine hepatitis virus and severe acute respiratory syndrome coronavirus infection. Vaccinia virus, a DNA virus that replicates exclusively in the cytoplasm, also has a 2′O-MT and disruption of its activity results in increased susceptibility of vaccinia virus to IFIT protein restriction. Taken together, many viruses evade the actions of IFIT1, demonstrating that IFIT1 has the capacity for potent restriction of viral replication.

The antiviral effector ISG PKR is one of the most common proteins targeted and inactivated by viruses (reviewed in. Activation of this ISG by dsRNA results in PKR auto phosphorylation, dimerization, and phosphorylation of eIF2α leading to decreased protein synthesis due to translational inhibition. This inhibition of translation affects both host and viral mRNAs, which ultimately decreases viral replication.

Example of inhibition of PKR function was described during infection with human cytomegalovirus virus (HCMV), a DNA virus of the herpesvirus family. This virus encodes two proteins, pTRS1 and pIRS1, that antagonize PKR to prevent its auto phosphorylation and subsequent phosphorylation of eIF2α. Importantly, deletion of the viral pTRS1 and pIRS1 proteins leads to decreased expression of viral early and late proteins, resulting in decreased viral replication. This suggests that these proteins are critical for hepatitis C virus to prevent the antiviral activity of PKR for its replication.

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Immune Escape Strategies By Viruses

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