Human enterovirus group B viruses rely on vimentin dynamics for efficient processing of viral non-structural proteins

We report that several viruses from the human enterovirus group B cause massive vimentin rearrangements during lytic infection. Comprehensive studies suggested that viral protein synthesis was triggering the vimentin rearrangements. Blocking the host cell vimentin dynamics with IDPN did not significantly affect the production of progeny viruses and only moderately lowered the synthesis of structural proteins such as VP1. In contrast, the synthesis of the non-structural proteins 2A, 3C, and 3D was drastically lowered. This led to attenuation of the cleavage of the host cell substrates PABP and G3BP1 and reduced caspase activation, thus leading to prolonged cell survival. Furthermore, the localization of the proteins differed in the infected cells. Capsid protein VP1 was found diffusely around the cytoplasm, whereas 2A and 3D followed vimentin distribution. Based on protein blotting, lower amounts of non-structural proteins did not result from proteasomal degradation, but from lower synthesis without intact vimentin cage structure. In contrast, inhibition of Hsp90 chaperone activity, which regulates P1 maturation, lowered the amount of VP1, but had less effect on 2A. The results suggest that, the vimentin dynamics regulate viral non-structural protein synthesis while having no effect on structural protein synthesis or overall infection efficiency. The results presented here shed new light on differential fate of structural and non-structural proteins of enteroviruses, having consequences on host cell survival. Importance A virus needs the host cell in order to replicate and produce new progeny viruses. For this, the virus takes over the host cell and modifies it to become a factory for viral proteins. Irrespective of the specific virus family, these proteins can be divided into structural and non-structural proteins. Structural proteins are the building blocks for the new progeny virions, whereas the non-structural proteins orchestrate the take-over of the host cell and its functions. Here we have shown a mechanism that viruses exploit in order to regulate the host cell. We show that viral protein synthesis induces vimentin cages, which promote production of specific viral proteins that eventually control apoptosis and the host cell death. This study specifies vimentin as the key regulator of these events and indicates that viral proteins have different fates in the cells depending on their association with vimentin cages.peerReviewe

Antiviral Mechanisms of N-Phenyl Benzamides on Coxsackie Virus A9

Enteroviruses are one of the most abundant groups of viruses infecting humans, and yet there are no approved antivirals against them. To find effective antiviral compounds against enterovirus B group viruses, an in-house chemical library was screened. The most effective compounds against Coxsackieviruses B3 (CVB3) and A9 (CVA9) were CL212 and CL213, two N-phenyl benzamides. Both compounds were more effective against CVA9 and CL213 gave a better EC50 value of 1 µM with high a specificity index of 140. Both drugs were most effective when incubated directly with viruses suggesting that they mainly bound to the virions. A real-time uncoating assay showed that the compounds stabilized the virions and radioactive sucrose gradient as well as TEM confirmed that the viruses stayed intact. A docking assay, taking into account larger areas around the 2-and 3-fold axes of CVA9 and CVB3, suggested that the hydrophobic pocket gives the strongest binding to CVA9 but revealed another binding site around the 3-fold axis which could contribute to the binding of the compounds. Together, our data support a direct antiviral mechanism against the virus capsid and suggest that the compounds bind to the hydrophobic pocket and 3-fold axis area resulting in the stabilization of the virion

Detection of Viral −RNA and +RNA Strands in Enterovirus-Infected Cells and Tissues

The current methods to study the distribution and dynamics of viral RNA molecules inside infected cells are not ideal, as electron microscopy and immunohistochemistry can only detect mature virions, and quantitative real-time PCR does not reveal localized distribution of RNAs. We demonstrated here the branched DNA in situ hybridization (bDNA ISH) technology to study both the amount and location of the emerging −RNA and +RNA during acute and persistent enterovirus infections. According to our results, the replication of the viral RNA started 2–3 h after infection and the translation shortly after at 3–4 h post-infection. The replication hotspots with newly emerging −RNA were located quite centrally in the cell, while the +RNA production and most likely virion assembly took place in the periphery of the cell. We also discovered that the pace of replication of −RNA and +RNA strands was almost identical, and −RNA was absent during antiviral treatments. ViewRNA ISH with our custom probes also showed a good signal during acute and persistent enterovirus infections in cell and mouse models. Considering these results, along with the established bDNA FISH protocol modified by us, the effects of antiviral drugs and the emergence of enterovirus RNAs in general can be studied more effectively

Antiviral functionalization of cellulose using tannic acid and tannin-rich extracts

Due to seasonally appearing viruses and several outbreaks and present pandemic, we are surrounded by viruses in our everyday life. In order to reduce viral transmission, functionalized surfaces that inactivate viruses are in large demand. Here the endeavor was to functionalize cellulose-based materials with tannic acid (TA) and tannin-rich extracts by using different binding polymers to prevent viral infectivity of both non-enveloped coxsackievirus B3 (CVB3) and enveloped human coronavirus OC43 (HCoV-OC43). Direct antiviral efficacy of TA and spruce bark extract in solution was measured: EC50 for CVB3 was 0.12 and 8.41  μg/ml and for HCoV-OC43, 78.16 and 95.49  μg/ml, respectively. TA also led to an excellent 5.8- to 7-log reduction of severe acute respiratory syndrome coronavirus 2 (SARSCoV-2) virus infectivity. TA functionalized materials reduced infectivity already after 5-min treatment at room temperature. All the tested methods to bind TA showed efficacy on paperboard with 0.1 to 1% (w/v) TA concentrations against CVB3 whereas material hydrophobicity decreased activities. Specific signatures for TA and HCoV-OC43 were discovered by Raman spectroscopy and showed clear co-localization on the material. qPCR study suggested efficient binding of CVB3 to the TA functionalized cellulose whereas HCoV-OC43 was flushed out from the surfaces more readily. In conclusion, the produced TA-materials showed efficient and broadly acting antiviral efficacy. Additionally, the co-localization of TA and HCoV-OC43 and strong binding of CVB3 to the functionalized cellulose demonstrates an interaction with the surfaces. The produced antiviral surfaces thus show promise for future use to increase biosafety and biosecurity by reducing pathogen persistence

Novel activities of safe-in-human broad-spectrum antiviral agents

Abstract According to the WHO, there is an urgent need for better control of viral diseases. Re-positioning existing safe-in-human antiviral agents from one viral disease to another could play a pivotal role in this process. Here, we reviewed all approved, investigational and experimental antiviral agents, which are safe in man, and identified 59 compounds that target at least three viral diseases. We tested 55 of these compounds against eight different RNA and DNA viruses. We found novel activities for dalbavancin against echovirus 1, ezetimibe against human immunodeficiency virus 1 and Zika virus, as well as azacitidine, cyclosporine, minocycline, oritavancin and ritonavir against Rift valley fever virus. Thus, the spectrum of antiviral activities of existing antiviral agents could be expanded towards other viral diseases.Peer reviewe

Vemurafenib Inhibits Acute and Chronic Enterovirus Infection by Affecting Cellular Kinase Phosphatidylinositol 4-Kinase Type IIIb

Enteroviruses are one of the most abundant viruses causing mild to serious acute infections in humans and also contributing to chronic diseases like type 1 diabetes. Presently, there are no approved antiviral drugs against enteroviruses. Here, we studied the potency of vemurafenib, an FDA-Approved RAF kinase inhibitor for treating BRAFV600E mutant-related melanoma, as an antiviral against enteroviruses. We showed that vemurafenib prevented enterovirus translation and replication at low micromolar dosage in an RAF/MEK/ERK-independent manner. Vemurafenib was effective against group A, B, and C enteroviruses, as well as rhinovirus, but not parechovirus or more remote viruses such as Semliki Forest virus, adenovirus, and respiratory syncytial virus. The inhibitory effect was related to a cellular phosphatidylinositol 4-kinase type IIIb (PI4KB), which has been shown to be important in the formation of enteroviral replication organelles. Vemurafenib prevented infection efficiently in acute cell models, eradicated infection in a chronic cell model, and lowered virus amounts in pancreas and heart in an acute mouse model. Altogether, instead of acting through the RAF/MEK/ERK pathway, vemurafenib affects the cellular PI4KB and, hence, enterovirus replication, opening new possibilities to evaluate further the potential of vemurafenib as a repurposed drug in clinical care. IMPORTANCE Despite the prevalence and medical threat of enteroviruses, presently, there are no antivirals against them. Here, we show that vemurafenib, an FDA-Approved RAF kinase inhibitor for treating BRAFV600E mutant-related melanoma, prevents enterovirus translation and replication. Vemurafenib shows efficacy against group A, B, and C enteroviruses, as well as rhinovirus, but not parechovirus or more remote viruses such as Semliki Forest virus, adenovirus, and respiratory syncytial virus. The inhibitory effect acts through cellular phosphatidylinositol 4-kinase type IIIb (PI4KB), which has been shown to be important in the formation of enteroviral replication organelles. Vemurafenib prevents infection efficiently in acute cell models, eradicates infection in a chronic cell model, and lowers virus amounts in pancreas and heart in an acute mouse model. Our findings open new possibilities to develop drugs against enteroviruses and give hope for repurposing vemurafenib as an antiviral drug against enteroviruses

Host Cell Calpains Can Cleave Structural Proteins from the Enterovirus Polyprotein

Enteroviruses are small RNA viruses that cause diseases with various symptoms ranging from mild to severe. Enterovirus proteins are translated as a single polyprotein, which is cleaved by viral proteases to release capsid and nonstructural proteins. Here, we show that also cellular calpains have a potential role in the processing of the enteroviral polyprotein. Using purified calpains 1 and 2 in an in vitro assay, we show that addition of calpains leads to an increase in the release of VP1 and VP3 capsid proteins from P1 of enterovirus B species, detected by western blotting. This was prevented with a calpain inhibitor and was dependent on optimal calcium concentration, especially for calpain 2. In addition, calpain cleavage at the VP3-VP1 interface was supported by a competition assay using a peptide containing the VP3-VP1 cleavage site. Moreover, a mass spectrometry analysis showed that calpains can cleave this same peptide at the VP3-VP1 interface, the cutting site being two amino acids aside from 3C’s cutting site. Furthermore, we show that calpains cannot cleave between P1 and 2A. In conclusion, we show that cellular proteases, calpains, can cleave structural proteins from enterovirus polyprotein in vitro. Whether they assist polyprotein processing in infected cells remains to be shown

Cellular and viral factors promoting efficient enterovirus uncoating and replication

Enteroviruses are small non-enveloped RNA viruses, which belong to the family of picornaviruses. Although most of the diseases that enteroviruses cause are symptomless or mild, enteroviruses are the most common viruses infecting humans. In addition, enteroviruses can cause more severe diseases such as encephalitis or myocarditis. Despite their prevalence, there are no antivirals on the market against these viruses, and vaccines have been developed only against couple of serotypes. For antiviral development, it is crucial to obtain detailed information about factors that contribute to efficient infection. Thus, this thesis focuses on viral and host cell factors that promote the infection of enterovirus B species after cell entry. In the first study, we characterized a new echovirus 1 particle during infection, likely a novel form of an uncoating intermediate. This particle was more open compared to the native virus, but still contained VP4 protein, and was able to bind to a receptor and cause infection. The second part of the thesis focused on steps after RNA release, namely translation and replication. First, we showed that in addition to viral proteases, cellular calpain proteases can cleave structural proteins from the enteroviral polyprotein, suggesting that calpains might contribute to proteolytic processing during infection. This was shown in an in-vitro study, where calpains released capsid proteins from the P1 precursor. Second, we showed that translation of enteroviral proteins induced the rearrangement of cellular intermediate filament, vimentin. Vimentin cages associated with components of endoplasmic reticulum and Golgi, as well as with replicating viral RNA and non-structural, but not structural proteins. Furthermore, inhibition of vimentin dynamics resulted in lower production of the non-structural compared to structural proteins, indicating that enteroviral proteins can be produced differently, depending on their association with vimentin cages. Keywords: Calpain; enterovirus; polyprotein processing; replication; translation; uncoating; vimentinEnterovirukset ovat pieniä vaipattomia RNA viruksia, jotka kuuluvat pikornaviruksiin. Vaikka enterovirukset useimmiten aiheuttavat oireettomia tai lieviä tauteja, ne ovat myös yleisin ihmisiä infektoiva virusryhmä. Lisäksi joissakin tapauksissa enterovirukset voivat aiheuttaa myös vakavampia tauteja kuten enkefaliittia tai myokardiittia. Vaikka enterovirusinfektiot ovat yleisiä, näitä viruksia vastaan ei ole lääkitystä ja rokote on kehitetty ainoastaan muutamalle serotyypille. Viruslääkkeiden kehittelyn tärkein lähtökohta on ymmärtää tehokkaaseen infektioon vaikuttavat tekijät yksityiskohtaisesti. Niinpä tässä väitöskirjassa keskityttiin tutkimaan virus- ja solutekijöitä, jotka edistävät tehokasta enterovirus B -lajin infektiota sisäänmenovaiheen jälkeen. Ensimmäisessä osatyössä kuvailimme uuden echovirus 1 partikkelin, joka todennäköisesti on välimuotopartikkeli, joka syntyy infektion aikana viruksen avautuessa. Tämä partikkeli oli rakenteeltaan avonaisempi verrattuna natiiviin virukseen, mutta sisälsi kuitenkin VP4 proteiinin, pystyi sitoutumaan reseptoriin ja aiheutti infektion soluissa. Seuraavissa osatöissä keskityimme infektiovaiheisiin RNA:n vapautumisen jälkeen, translaatioon ja replikaatioon. Ensiksi osoitimme in-vitro kokeilla, että viruksen omien proteaasien lisäksi myös solun kalpaiinit pystyivät prosessoimaan enteroviruksen polyproteiinia alueelta, joka sisälsi viruksen rakenneproteiinit. Seuraavaksi osoitimme, että virusproteiinien translaatio sai aikaan muutoksia solun välimuotoisia säikeitä muodostavassa vimentiiniproteiinissa. Syntyneeseen vimentiinihäkkiin kertyi solun endoplasmakalvoston ja Golgin laitteen rakenteita, sekä viruksen RNA ja ei-rakenteelliset proteiinit, mutta ei rakenneproteiineja. Lisäksi vimentiinihäkin muodostumisen estäminen johti ei-rakenteellisten proteiinien heikompaan tuottoon verrattuna rakenneproteiineihin, mikä osoitti, että vimentiinirakenne on tärkeä tiettyjen enteroviruksen proteiinien tuotossa. Avainsanat: Enterovirus; kalpaiini; polyproteiinin prosessointi; replikaatio; translaatio, vimentiini, viruksen avautumine

Real-time Fluorescence Measurement of Enterovirus Uncoating

Viruses need to open, i.e., uncoat, in order to release their genomes for efficient replication and translation. Especially for non-enveloped viruses, such as enteroviruses, the cues leading to uncoating are less well known. The status of the virus has previously been observed mainly by transmission electron microscopy using negative staining, cryo electron microscopy, X-ray crystallography or gradient separation (reviewed in Tuthill et al., 2010, Myllynen et al., 2016, Ruokolainen et al., 2019). However, monitoring of uncoating has been limited by the lack of methods detecting dynamic changes of the virions. Here, we present a real-time fluorescence based protocol, which detects the viral genome (RNA) during various stages of uncoating in vitro, while RNA is still inside the particle that has been expanded before the actual RNA release, and when the RNA has been totally released from the viral particle. Our method allows to explore how various molecular factors may promote or inhibit virus uncoating.peerReviewe

Early entry events in Echovirus 30 infection

Echovirus 30 (E30), a member of the enterovirus B species, is a major cause of viral meningitis, targeting children and adults alike. While it is a frequently isolated enterovirus and the cause of several outbreaks all over the world, suprisingly little is known regarding its entry and replication strategy within cells. In this study, we used E30 Bastianni (E30B) generated from an infectious cDNA clone in order to study early entry events during infection in human RD cells. E30B required the newly discovered Fc echovirus receptor (FcRn) for succesful infection, but not the Coxsackievirus and Adenovirus Receptor (CAR) or Decay-Accelerating Factor (DAF), although an interaction with DAF was observed. Double-stranded RNA replication intermediate was generated between 2 and 3 h post-infection (p.i.). and viral capsid production was initiated between 4 and 5 h p.i. The drugs affecting Rac1 (NSC 23766) and cholesterol (Filipin III) compromised infection, whereas bafilomycin A1, dyngo, U-73122, wortmannin and nocodazole did not, suggesting the virus follows an enterovirus-triggered macropinocytic pathway rather than the clathrin pathway. Colocalization with early endosomes and increased infection due to constitutively active Rab5 expression suggests some overlap and entry to classical early endosomes. Taken together, these results suggest that E30B induces an enterovirus entry pathway, leading to uncoating in early endosomes.peerReviewe