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Secondary and tertiary RNA structures play key roles in genome replication of single stranded positive sense RNA viruses. Complex, functional structures are particularly abundant in the untranslated regions of picornaviruses, where they are involved in initiation of translation, priming of new strand synthesis and genome circularisation. The 5′ UTR of foot-and-mouth disease virus (FMDV) is predicted to include ac.360 nucleotide-long stem-loop, termed the short (S) fragment. This structure is highly conserved and essential for viral replication, but the precise function(s) are unclear. Here, we used selective 2′ hydroxyl acetylation analysed by primer extension (SHAPE) to experimentally-determine aspects of the structure, alongside comparative genomic analyses to confirm structure conservation from a wide range of field isolates. To examine its role in virus replication, we introduced a series of deletions to the distal and proximal regions of the stem loop. These truncations affected genome replication in a size-dependent and, in some cases, host cell-dependent manner. Furthermore, during passage of viruses incorporating the largest tolerated deletion from the proximal region of the S fragment stem loop, an additional mutation was selected in the viral RNA-dependent RNA polymerase, 3Dpol, which influenced the function of the enzyme. These data suggest that the S fragment and 3Dpolinteract in the formation of the FMDV replication complex.

BK polyomavirus (BKPyV) is a common opportunistic pathogen and the causative agent of several diseases in transplant patients and the immunosuppressed. Despite its importance, aspects of the virus lifecycle such as how the virus exits an infected cells, remain poorly understood. The late region of the BKPyV genome encodes an auxillery protein called agnoprotein. We and others have shown that agnoprotein is an essential factor in virus release, and the loss of agnoprotein results in an accumulation of virus particles within the nucleus of an infected cell. The functions of agnoprotein necessary for this egress phenotype are not known. Here we demonstrate that agnoprotein shows properties associated with viroporins, a group of virus-encoded membrane spanning proteins that play key roles in virus infection and release. We demonstrate that agnoprotein oligomerises and perturbs membranes in cells. The development of a novel recombinant agnoprotein expression system permitted the identification of the first small molecules targeting agnoprotein. These compounds abrogated agnoprotein viroporin activity in vitro and reduced virus release, indicating that viroporin activity contributes to the phenotype observed in agnoprotein knockout viruses. The identification of channel activity should enhance the future understanding of the physiological function of agnoprotein and could represent an important target for antiviral intervention.

Foot-and-mouth-disease virus (FMDV), the etiological agent responsible for foot-and-mouth disease (FMD), is a member of the genusAphthoviruswithin thePicornavirusfamily. In common with all picornaviruses, replication of the single-stranded positive-sense RNA genome involves synthesis of a negative-sense complementary strand that serves as a template for the synthesis of multiple positive-sense progeny strands. We have previously employed FMDV replicons to examine viral RNA and protein elements essential to replication, however, the factors affecting differential strand production remain unknown. Replicon-based systems require transfection of high levels of RNA, which can overload sensitive techniques such as qPCR preventing discrimination of specific strands. Here, we describe a method in which replicating RNA is labelledin vivowith 5-ethynyl uridine. The modified base is then linked to a biotin tag using click chemistry, facilitating purification of newly synthesised viral genomes or anti-genomes from input RNA. This selected RNA can then be amplified by strand-specific qPCR, thus enabling investigation of the consequences of defined mutations on the relative synthesis of negative-sense intermediate and positive-strand progeny RNAs. We apply this new approach to investigate the consequence of mutation of viralcis-acting replication elements and provide direct evidence for their roles in negative-strand synthesis.

The enterovirus (EV) genus includes a number of important human and animal pathogens. EV-A71, EV-D68, poliovirus (PV), and coxsackievirus (CV) outbreaks have affected millions worldwide causing a range of upper respiratory, skin, neuromuscular diseases, including acute flaccid myelitis, and hand-foot-and-mouth disease. There are no FDA-approved anti-viral therapeutics for these enteroviruses. In this study, we describe novel broad spectrum anti-viral compounds targeting the conserved non-structural viral protein 2C that have low micro-molar to nanomolar IC50 values. The selection of resistant mutants resulted in amino acid substitutions in the viral capsid protein, implying a role for 2C in capsid assembly, as has been seen in PV. The assembly and encapsidation stages of the viral life cycle are not fully understood and the inhibitors reported here could be useful probes in understanding these processes.

Introduction. Foot-and-mouth disease (FMD) is a highly contagious and economically devastating viral disease of livestock and is endemic in much of Asia, including Pakistan. Vaccination is used to control disease outbreaks and sensitive diagnostic methods which can differentiate infected animals from vaccinated animals (DIVA) are essential for monitoring the effectiveness of disease control programmes. Tests based on the detection of the non-structural protein (NSP) 3ABC are reliable indicators of virus replication in infected and vaccinated populations. Hypothesis/Gap statement. Diagnosis of FMD is expensive using commercial ELISA kits, yet is essential for controlling this economically-important disease. Aim. The development of a low-cost diagnostic ELISA, using protein made in Escherichia coli . Methodology. In this study, the viral precursor protein 3ABC (r3ABC) was expressed in E. coli , solubilised using detergent and purified using nickel affinity chromatography. The fusion protein contained an attenuating mutation in the protease and a SUMO tag. It was characterised by immunoblotting and immunoprecipitation, which revealed antigenicity against virus-specific polyclonal sera. Using r3ABC, an indirect ELISA was developed and evaluated using field sera from healthy/naïve, vaccinated and infected animals. Results. The diagnostic sensitivity and specificity of the r3ABC in-house ELISA were 95.3 and 96.3% respectively. The ELISA was validated through comparison with the commercially available ID Screen FMD NSP competition kit. Results indicated good concordance rates on tested samples and high agreement between the two tests. Conclusion. The ELISA described here can effectively differentiate between infected and vaccinated animals and represents an important low cost tool for sero-surveillance and control of FMD in endemic settings.

Merkel cell carcinoma (MCC) is an aggressive skin cancer with high rates of recurrence and metastasis. Merkel cell polyomavirus (MCPyV) is associated with the majority of MCC cases. MCPyV-induced tumourigenesis is largely dependent on the expression of the small tumour antigen (ST). Recent findings implicate MCPyV ST expression in the highly metastatic nature of MCC by promoting cell motility and migration, through differential expression of cellular proteins that lead to microtubule destabilisation, filopodium formation and breakdown of cell–cell junctions. However, the molecular mechanisms which dysregulate these cellular processes are yet to be fully elucidated. Here, we demonstrate that MCPyV ST expression activates p38 MAPK signalling to drive cell migration and motility. Notably, MCPyV ST-mediated p38 MAPK signalling occurs through MKK4, as opposed to the canonical MKK3/6 signalling pathway. In addition, our results indicate that an interaction between MCPyV ST and the cellular phospatase subunit PP4C is essential for its effect on p38 MAPK signalling. These results provide novel opportunities for the treatment of metastatic MCC given the intense interest in p38 MAPK inhibitors as therapeutic agents.

Following internalisation viruses have to escape the endocytic pathway and deliver their genomes to initiate replication. Members of thePolyomaviridaetransit through the endolysosomal network and through the endoplasmic reticulum (ER), from which heavily degraded capsids escape into the cytoplasm prior to nuclear entry. Acidification of endosomes and ER entry are essential in the lifecycle of polyomaviruses, however many mechanistic requirements are yet to be elucidated. Alteration of endocytic pH relies upon the activity of ion channels. Using two polyomaviruses with differing capsid architecture, namely Simian virus 40 (SV40) and Merkel cell polyomavirus (MCPyV), we firstly describe methods to rapidly quantify infection using an IncuCyte ZOOM instrument, prior to investigating the role of K+and Ca2+channels during early stages of infection. Broad spectrum inhibitors identified that MCPyV, but not SV40, is sensitive to K+channel modulation. In contrast, both viruses are restricted by the broad spectrum Ca2+channel inhibitor verapamil, however specific targeting of transient or long lasting Ca2+channel subfamilies had no detrimental effect. Further investigation revealed that tetrandrine blockage of two-pore channels (TPCs), the activity of which is essential for endolysosomal-ER fusion, ablates infectivity of both MCPyV and SV40 by preventing disassembly of the capsid, which is required for the exposure of minor capsid protein nuclear signals necessary for nuclear transport. This study therefore identifies a novel target to restrict the entry of polyomaviruses.IMPORTANCEPolyomaviruses establish ubiquitous, asymptomatic infection in their host. However, in the immunocompromised these viruses can cause a range of potentially fatal diseases. Through the use of SV40 and MCPyV, two polyomaviruses with different capsid organisation, we have investigated the role of ion channels during infection. Here, we show that Ca2+channel activity is essential for both polyomaviruses and that MCPyV is also sensitive to K+channel blockage, highlighting new mechanistic requirements of ion channels during polyomavirus infection. In particular, tetrandrine blockage of endolysosomal-ER fusion is highlighted as an essential modulator of both SV40 and MCPyV. Given that the role of ion channels in disease have been well characterised, there is a large panel of clinically available therapeutics that could be repurposed to restrict persistent polyomavirus infection and may ultimately prevent polyomavirus-associated disease.

Studies have highlighted the essential nature of a group of small, highly hydrophobic, membrane embedded, channel-forming proteins in the life cycles of a growing number of RNA viruses. These viroporins mediate the flow of ions and a range of solutes across cellular membranes and are necessary for manipulating a myriad of host processes. As such they contribute to all stages of the virus life cycle. Recent discoveries have identified proteins encoded by the small DNA tumor viruses that display a number of viroporin like properties. This review article summarizes the recent developments in our understanding of these novel viroporins; describes their roles in the virus life cycles and in pathogenesis and speculates on their potential as targets for anti-viral therapeutic intervention.

Cell motility and migration is a complex, multistep, and multicomponent process intrinsic to progression and metastasis. Motility is dependent on the activities of integrin receptors and Rho family GTPases, resulting in the remodeling of the actin cytoskeleton and formation of various motile actin-based protrusions. Merkel cell carcinoma (MCC) is an aggressive skin cancer with a high likelihood of recurrence and metastasis. Merkel cell polyomavirus (MCPyV) is associated with the majority of MCC cases, and MCPyV-induced tumorigenesis largely depends on the expression of the small tumor antigen (ST). Since the discovery of MCPyV, a number of mechanisms have been suggested to account for replication and tumorigenesis, but to date, little is known about potential links between MCPyV T antigen expression and the metastatic nature of MCC. Previously, we described the action of MCPyV ST on the microtubule network and how it impacts cell motility and migration. Here, we demonstrate that MCPyV ST affects the actin cytoskeleton to promote the formation of filopodia through a mechanism involving the catalytic subunit of protein phosphatase 4 (PP4C). We also show that MCPyV ST-induced cell motility is dependent upon the activities of the Rho family GTPases Cdc42 and RhoA. In addition, our results indicate that the MCPyV ST-PP4C interaction results in the dephosphorylation of β1 integrin, likely driving the cell motility pathway. These findings describe a novel mechanism by which a tumor virus induces cell motility, which may ultimately lead to cancer metastasis, and provides opportunities and strategies for targeted interventions for disseminated MCC. IMPORTANCE Merkel cell polyomavirus (MCPyV) is the most recently discovered human tumor virus. It causes the majority of cases of Merkel cell carcinoma (MCC), an aggressive skin cancer. However, the molecular mechanisms implicating MCPyV-encoded proteins in cancer development are yet to be fully elucidated. This study builds upon our previous observations, which demonstrated that the MCPyV ST antigen enhances cell motility, providing a potential link between MCPyV protein expression and the highly metastatic nature of MCC. Here, we show that MCPyV ST remodels the actin cytoskeleton, promoting the formation of filopodia, which is essential for MCPyV ST-induced cell motility, and we also implicate the activity of specific Rho family GTPases, Cdc42 and RhoA, in these processes. Moreover, we describe a novel mechanism for the activation of Rho-GTPases and the cell motility pathway due to the interaction between MCPyV ST and the cellular phosphatase catalytic subunit PP4C, which leads to the specific dephosphorylation of β1 integrin. These findings may therefore provide novel strategies for therapeutic intervention for disseminated MCC.