MicroRNA-mediated interactions between host andhepatitis C virus

Micro RNAs(mi RNAs) are small noncoding RNAs. More than 2500 mature mi RNAs are detected in plants, animals and several types of viruses. Hepatitis C virus(HCV), which is a positive-sense, singlestranded RNA virus, does not encode viral mi RNA. However, HCV infection alters the expression of host mi RNAs, either in cell culture or in patients with liver disease progression, such as liver fibrosis, cirrhosis, and hepatocellular carcinoma. In turn, host mi RNAs regulate HCV life cycle through directly binding to HCV RNAs or indirectly targeting cellular m RNAs. Increasing evidence demonstrates that mi RNAs are one of the centered factors in the interaction network between virus and host. The competitive viral and host RNA hypothesis proposes a latent cross-regulation pattern between host m RNAs and HCV RNAs. High loads of HCV RNA sequester and de-repress host mi RNAs from their normal host targets and thus disturb host gene expression, indicating a means of adaptation for HCV to establish a persistent infection. Some special mi RNAs are closely correlated with liver-specific disease progression and the changed levels of mi RNAs are even higher sensitivity and specificity than those of traditional proteins. Therefore, some of them can serve as novel diagnostic/prognostic biomarkers in HCVinfected patients with liver diseases. They are also attractive therapeutic targets for development of new anti-HCV agents.

SARS-CoV-2 encoded microRNAs are involved in the process of virus infection and host immune response

The outbreak of COVID-19 caused by SARS-CoV-2 is spreading worldwide,with the pathogenesis mostly unclear.Both virus and host-derived microRNA(miRNA)play essential roles in the pathology of virus infection.This study aims to uncover the mechanism for SARS-CoV-2 pathogenicity from the perspective of miRNA.We scanned the SARS-CoV-2 genome for putative miRNA genes and miRNA targets and conducted in vivo experiments to validate the virus-encoded miRNAs and their regulatory role on the putative targets.One of such virus-encoded miRNAs,MR147-3p,was overexpressed that resulted in significantly decreased transcript levels of all of the predicted targets in human,i.e.,EXOC7,RAD9A,and TFE3 in the virus-infected cells.The analysis showed that the immune response and cytoskeleton organization are two of the most notable biological processes regulated by the infection-modulated miRNAs.Additionally,the genomic mutation of SARS-CoV-2 contributed to the changed miRNA repository and targets,suggesting a possible role of miRNAs in the attenuated phenotype of SARS-CoV-2 during its evolution.This study provided a comprehensive view of the miRNA-involved regulatory system during SARS-CoV-2 infection,indicating possible antiviral therapeutics against SARS-CoV-2 through intervening miRNA regulation.

Host preference of the major strains of Plum pox virus--Opinions based on regional and world-wide sequence data

Plum pox virus（PPV）causes sharka-the most serious viral disease of stone fruit trees.PPV is wide spread in Europe and Mediterranean Basin,its incidence has been further approved in Asia and both Americas.Nine PPV strains have been recognized until now（PPV-D,PPV-M,PPV-Rec,PPV-EA,PPV-C,PPV-T,PPV-W,PPV-CR,and PPV-An）,forming molecularly distinct entities,however,only partially differentiable by their biological or epidemiological properties.The most strict virus-host linkages under natural conditions have been detected for strains naturally infecting cherries（PPV-C and PPV-CR）.However,although less stringent but still clear host preference is observed also for three epidemiologically most important strains（PPV-D/plum/apricot,PPV-M/peach,and PPV-Rec/plum）.So far no genetic marker has been mapped in the PPV genome,which responsibility for the host specificity/preference could be explicitly demonstrated.In this review,we focus on the host preference of three major PPV strains as evidenced by analysis of an extensive dataset of PPV isolates of Slovak and world-wide origin.Together,we discuss several performed relevant experiments and further possible research procedures aimed to better understand the genetic determinants and mechanisms of the host preference of this potyvirus.

High-throughput RNA interference screens integrative analysis: Towards a comprehensive understanding of the virus-host interplay

Viruses are extremely heterogeneous entities; the size and the nature of their genetic information, as well as the strategies employed to amplify and propagate their genomes, are highly variable. However, as obligatory intracellular parasites, replication of all viruses relies on the host cell. Having co-evolved with their host for several million years, viruses have developed very sophisticated strategies to hijack cellular factors that promote virus uptake, replication, and spread. Identification of host cell factors(HCFs) required for these processes is a major challenge for researchers, but it enables the identification of new, highly selective targets for anti viral therapeutics. To this end, the establishment of platforms enabling genome-wide high-throughput RNA interference(HT-RNAi) screens has led to the identification of several key factors involved in the viral lifecycle. A number of genome-wide HT-RNAi screens have been performed for major human pathogens. These studies enable first inter-viral comparisons related to HCF requirements. Although several cellular functions appear to be uniformly required for the life cycle of most viruses tested(such as the proteasome and the Golgi-mediated secretory pathways), some factors, like the lipid kinase Phosphatidylinositol 4-kinase Ⅲα in the case of hepatitis C virus, are selectively required for individual viruses. However, despite the amount of data available, we are still far away from a comprehensive understanding of the interplay between viruses and host factors. Major limitations towards this goal are the low sensitivity and specificity of such screens, resulting in limited overlap between different screens performed with the same virus. This review focuses on how statistical and bioinformatic analysis methods applied to HTRNAi screens can help overcoming these issues thus increasing the reliability and impact of such studies.

MicroRNAs as Important Players in Host-hepatitis B Virus Interactions

Hepatitis B virus (HBV) infection,a major public health problem,causes acute and chronic hepatitis that is often complicated by liver cirrhosis and hepatocellular carcinoma.The pathogenic mechanisms of HBV-related liver disease are not well understood,and the current licensed therapies are not effective in permanently clearing virus from the circulation.In recent years,the role of micro-ribonucleic acids (miRNAs) in HBV infection has attracted great interest.Cellular miRNAs can influence HBV replication directly by binding to HBV transcripts and indirectly by targeting cellular factors relevant to the HBV life cycle.They are also involved in the regulation of cellular genes and signaling pathways that have critical roles in HBV pathogenesis.HBV infection,in turn,can trigger changes in cellular miRNA expression that are associated with distinctive miRNA expression profiles depending on the phase of liver disease.These alterations in miRNA expression have been linked to disease progression and hepatocarcinogenesis.We provide here an up to date review regarding the field of miRNAs and HBV interplay and highlight the potential utility of miRNAs as diagnostic biomarkers and therapeutic targets for the management of HBV-related liver disease.

Competitive virus and host RNAs： the interplay of a hidden virus and host interaction

During virus infection, viral RNAs and mRNAs function as blueprints for viral protein synthesis and possibly as pathogen-associated molecular patterns （PAMPs） in innate immunity. Here, considering recent research progress in microRNAs （miRNAs） and competitive endogenous RNAs （ceRNAs）, we speculate that viral RNAs act as sponges and can sequester endogenous miRNAs within infected cells, thus cross-regulating the stability and translational efficiency of host mRNAs with shared miRNA response elements. This cross-talk and these reciprocal interactions between viral RNAs and host mRNAs are termed ＂competitive viral and host RNAs＂ （cvhRNAs）. We further provide recent experimental evidence for the existence of cvhRNAs networks in hepatitis B virus （HBV）, as well as Her- pesvirus saimiri （HVS）, lytic murine cytomegalovirus （MCMV） and human cytomegalovirus （HCMV） infec- tions. In addition, the cvhRNA hypothesis also pre- dicts possible cross-regulation between host and other viruses, such as hepatitis C virus （HCV）, HIV, influenza virus, human papillomaviruses （HPV）. Since the interaction between miRNAs and viral RNAs also inevitably leads to repression of viral RNA function, we speculate that virus may evolve either to employ cvhRNA networks or to avoid miRNA targeting for optimal fitness within the host. CvhRNA networks may therefore play a fundamental role in the regulation of viral replication, infection establishment, and viral pathogenesis.

Association of miRNA-122-binding site polymorphism at the interleukin-1 a gene and its interaction with hepatitis B virus mutations with hepatocellular carcinoma risk

This study was designed to investigate the contribution of miRNA-122-binding site polymorphism at the IL-1A gene and its multiplicative interactions with hepatitis B virus （HBV） mutations in the risk of hepatocellular carcinoma （HCC）. A total of 1021 healthy controls, 302 HBV surface antigen （HBsAg） seroclearance subjects, and 2011 HBsAg-positive subjects （including 1021 HCC patients） were enrolled in this study. Quantitative PCR was used to genotype rs3783553. HBV mutations were determined by direct sequencing. Multivariate logistic regression analyses were performed to test the associations of rs3783553, mutations, and their interactions with the risk of HCC. No significant association was found between rs3783553 and the risk of HCC among healthy controls, HBsAg seroclearance subjects, HBsAg-positive subjects without HCC, and all controls. Additionally, rs3783553 was not significantly associated with chronic HBV infection, liver cirrhosis, HBV e antigen seroconversion, abnormal alanine aminotransferase, and high viral load （ 〉 10^4 copies/ml）. However, the TTCA insertion allele of rs3783553 was significantly associated with an increased frequency of HBV C7A mutation compared with homozygous TTCA deletion carriers [（del/ins ＋ ins/ins） vs. del/del, adjusted odds ratio （OR）= 1.48, 95% confidence interval （CI）= 1.09-2.02, P = 0.013]. Multiplicative interaction of rs3783553 with HBV preS deletion significantly reduced the risk of HCC in males, with an adjusted OR of 0.64 （95% CI = 0.42-0.98; P = 0.041） after age and HBV genotype were adjusted. Although rs3783553 did not significantly affect genetic susceptibility to HBV-related HCC, its variant allele may predispose the host to selecting HBV C7A mutation during evolution and significantly reduce the risk of HCC caused by HBV preS deletion. This study provides an insight into the complex host-virus interaction in HBV-induced hepatocarcinogenesis and is helpful in determining HBsAg-positive subjects who are likely to develop HCC.

Virus/host cell interactions:From structure to medical implication

The first event in viral infection is the attachment of a virus to specific receptors on the host cell surface. This will trigger conformational changes of the viral surface protein. For

Proteomics Profiling of Host Cell Response via Protein Expression and Phosphorylation upon Dengue Virus Infection

Dengue virus(DENV)infection is a worldwide public health threat.To date,the knowledge about the pathogenesis and progression of DENV infection is still limited.Combining global profiling based on proteomic analysis together with functional verification analysis is a powerful strategy to investigate the interplay between the virus and host cells.In the present study,quantitative proteomics has been applied to evaluate host responses(as indicated by altered proteins and modifications)in human cells(using K562 cell line)upon DENV-2 infection,as DENV-2 spreads most widely among all DENV serotypes.Comparative analysis was performed to define differentially expressed proteins in the infected cells compared to the mock-control,and it revealed critical pathogen-induced changes covering a broad spectrum of host cellular compartments and processes.We also discovered more dramatic changes(>20%,160 regulated phosphoproteins)in protein phosphorylation compared to protein expression(14%,321 regulated proteins).Most of these proteins/phosphoproteins were involved in transcription regulation,RNA splicing and processing,immune system,cellular response to stimulus,and macromolecule biosynthesis.Western blot analysis was also performed to confirm the proteomic data.Potential roles of these altered proteins were discussed.The present study provides valuable large-scale protein-related information for elucidating the functional emphasis of host cell proteins and their post-translational modifications in virus infection,and also provides insight and protein evidence for understanding the general pathogenesis and pathology of DENV.

Recent advances in the identification of the host factors involved in dengue virus replication

Dengue virus(DENV) belongs to the genus Flavivirus of the family Flaviviridae and it is primarily transmitted via Aedes aegypti and Aedes albopictus mosquitoes. The life cycle of DENV includes attachment, endocytosis, protein translation, RNA synthesis, assembly, egress, and maturation.Recent researches have indicated that a variety of host factors, including cellular proteins and micro RNAs, positively or negatively regulate the DENV replication process. This review summarizes the latest findings(from 2014 to 2016) in the identification of the host factors involved in the DENV life cycle and Dengue infection.

Insect transmission of plant viruses： Multilayered interactions optimize viral propagation

By serving as vectors of transmission, insects play a key role in the infection cycle of many plant viruses. Viruses use sophisticated transmission strategies to overcome the spatial barrier separating plants and the impediment imposed by the plant cell wall. Interactions among insect vectors, viruses, and host plants mediate transmission by integrating all organizational levels, from molecules to populations. Best-examined on the molecular scale are two basic transmission modes wherein virus-vector interactions have been well characterized. Whereas association of virus particles with specific sites in the vector＇s mouthparts or in alimentary tract regions immediately posterior to them is required for noncirculative transmission, the cycle of particles through the vector body is necessary for circulative transmission. Virus transmission is also determined by interactions that are associated with changes in vector feeding behaviors and with alterations in plant host＇s morphology and/or metabolism that favor the attraction or deterrence of vectors. A recent concept in virus-host-vector interactions proposes that when vectors land on infected plants, vector elicitors and effectors ＂inform＂ the plants of the confluence of interacting entities and trigger signaling pathways and plant defenses. Simultaneously, the plant responses may also influence virus acquisition and inoculation by vectors. Over- all, a picture is emerging where transmission depends on multilayered virus-vector-host interactions that define the route of a virus through the vector, and on the manipulation of the host and the vector. These interactions guarantee virus propagation until one or more of the interactants undergo changes through evolution or are halted by environmental interventions.

Integrated analysis of miRNAs and transcriptomes in Aedes albopictus midgut reveals the differential expression profiles of immune-related genes during dengue virus serotype-2 infection

Mosquito microRNAs （miRNAs） are involved in host-virus interaction, and have been reported to be altered by dengue virus （DENV） infection in Aedes albopictus （Diptera： Culicidae）. However, little is known about the molecular mechanisms of Aedes albopictus midgut--the first organ to interact with DENV--involved in its resistance to DENV. Here we used high-throughput sequencing to characterize miRNA and messenger RNA （mRNA） expression patterns in Aedes albopictus midgut in response to dengue virus serotype 2. A total of three miRNAs and 777 mRNAs were identified to be differentially expressed upon DENV infection. For the mRNAs, we identified 198 immune-related genes and 31 of them were differentially expressed. Gene Ontology and Kyoto Encyclopedia of Genes and Genomes enrichment analyses also showed that the differentially expressed immune-related genes were involved in immune response. Then the differential expression patterns of six immune-related genes and three miRNAs were confirmed by real-time reverse transcription polymerase chain reaction. Furthermore, seven known miRNA-mRNA interaction pairs were identified by aligning our two datasets. These analyses of miRNA and mRNA transcriptomes provide valuable information for uncovering the DENV response genes and provide a basis for future study of the resistance mechanisms in Aedes albopictus midgut.

<i>Imperata yellow mottle virus</i>: An Emerging Threat to Maize, Sorghum and Pearl Millet in Burkina Faso

Imperata yellow mottle caused by Imperata yellow mottle virus (IYMV) of the genus Sobemovirus was first characterized on Imperata cylindrical and Zea mays in Burkina Faso. The disease has been reported in several localities of the country but its ecology and epidemiology are poorly known. In particular, only I. cylindrical and maize have been reported within IYMV host range. The aim of this study was to investigate the experimental host range of the virus. Mechanical inoculation of a mixture of four IYMV isolates to 18 plant species, including four crops (maize, rice, sorghum and pearl millet) and 14 wild grasses showed clear mottle symptoms in maize, sorghum and pearl millet and two wild grass species (Setaria verticillata and Rottboellia exaltata). Symptom development was confirmed by Enzyme-linked immunosorbent assay and reverse transcription–polymerase chain reaction (RT-PCR). Infection of crop species by IYMV depended on cultivars tested. Therefore, proportions of positive cultivars were 16/36 in maize, 4/10 in sorghum and 4/9 in pearl millet, respectively. Studies on virus-host interactions using individual virus isolates showed two pathogenic patterns. Three out of the four isolates tested infected all plant species and cultivars. In contrast, the fourth IYMV isolate could infect only one maize cultivar. These results expand the previously known host range of IYMV from two to five species, indicating a narrow host range. Among the new characterized host species, sorghum and pearl millet are important cereal crops. Therefore, Imperata yellow motte disease is a potential threat for the cereal crop production and its ecology and epidemiology should be thoroughly investigated.

MicroRNA-135a Modulates Hepatitis C Virus Genome Replication through Downregulation of Host Antiviral Factors

Cellular microRNAs(miRNAs) have been shown to modulate HCV infection via directly acting on the viral genome or indirectly through targeting the virus-associated host factors. Recently we generated a comprehensive map of HCV–miRNA interactions through genome-wide miRNA functional screens and transcriptomics analyses. Many previously unappreciated cellular miRNAs were identified to be involved in HCV infection, including miR-135a, a human cancerrelated miRNA. In the present study, we investigated the role of miR-135a in regulating HCV life cycle and showed that it preferentially enhances viral genome replication. Bioinformatics-based integrative analyses and subsequent functional assays revealed three antiviral host factors, including receptor interacting serine/threonine kinase 2(RIPK2), myeloid differentiation primary response 88(MYD88), and C-X-C motif chemokine ligand 12(CXCL12), as bona fide targets of miR-135a. These genes have been shown to inhibit HCV infection at the RNA replication stage. Our data demonstrated that repression of key host restriction factors mediated the proviral effect of miR-135a on HCV propagation. In addition,miR-135a hepatic abundance is upregulated by HCV infection in both cultured hepatocytes and human liver, likely mediating a more favorable environment for viral replication and possibly contributing to HCV-induced liver malignancy.These results provide novel insights into HCV–host interactions and unveil molecular pathways linking miRNA biology to HCV pathogenesis.

MicroRNAs may solve the mystery of chronic hepatitis B virus infection

Hepatitis B virus(HBV)infection is a global public health problem that causes persistent liver diseases such as chronic hepatitis,cirrhosis,and hepatocellular carcinoma.A large amount of people die annually from HBV infection.However,the pathogenesises of the HBV-related diseases are ill defined and the therapeutic strategies for the diseases are less than optimum.The recently discovered microRNAs(miRNAs)are tiny noncoding RNAs that regulate gene expression primarily at the post-transcriptional level by binding to mRNAs.miRNAs contribute to a variety of physiological and pathological processes.A number of miRNAs have been found to play a pivotal role in the host-virus interaction including host-HBV interaction.Numerous studies have indicated that HBV infection could change the cellular miRNA expression patterns and different stages of HBV associated disease have displayed distinctive miRNA profiles.Furthermore,the differential expressed miRNAs have been found involved in the progression of HBV-related diseases,for instance some miRNAs are involved in liver tumorigenesis and tumor metastasis.Studies have also shown that the circulating miRNA in serum or plasma might be a very useful biomarker for the diagnosis and prognosis of HBV-related diseases.In addition,miRNA-based therapy strategies have attracted increasing attention,indicating a promising future in the treatment of HBV-related diseases.

Life cycle and pathogenesis of hepatitis D virus:A review

Hepatitis D virus(HDV) is a defective RNA virus which requires the help of hepatitis B virus(HBV) virus for its replication and assembly of new virions. HDV genome contains only one actively transcribed open reading frame which encodes for two isoforms of hepatitis delta antigen. Post-translational modifications of small and large delta antigens(S-HDAg and L-HDAg) involving phosphorylation and isoprenylation respectively con- fer these antigens their specific properties. S-HDAg is required for the initiation of the viral genome replica- tion, whereas L-HDAg serves as a principal inhibitor of replication and is essential for the assembly of new virion particles. Immune mediation has usually been implicated in HDV-associated liver damage. The patho- genesis of HDV mainly involves interferon-α signaling inhibition, HDV-specific T-lymphocyte activation and cytokine responses, and tumor necrosis factor-alpha and nuclear factor kappa B signaling. Due to limited protein coding capacity, HDV makes use of host cel- lular proteins to accomplish their life cycle processes, including transcription, replication, post-transcriptional and translational modifications. This intimate host- pathogen interaction significantly alters cell proteome and is associated with an augmented expression of pro-inflammatory, growth and anti-apoptotic factorswhich explains severe necroinflammation and increased cell survival and an early progression to hepatocellular carcinoma in HDV patients. The understanding of the process of viral replication, HBV-HDV interactions, and etio-pathogenesis of the severe course of HDV infection is helpful in identifying the potential therapeutic targets in the virus life cycle for the prophylaxis and treatment of HDV infection and complications.

Architecture and biogenesis of plus-strand RNA virus replication factories

Plus-strand RNA virus replication occurs in tight association with cytoplasmic host cell membranes. Both, viral and cellular factors cooperatively generate distinct organelle-like structures, designated viral replication factories. This compartmentalization allows coordination of the different steps of the viral replication cycle, highly efficient genome replication and protection of the viral RNA from cellular defense mechanisms. Electron tomography studies conducted during the last couple of years revealed the three dimensional structure of numerous plus-strand RNA virus replication compartments and highlight morphological analogies between different virus families. Based on the morphology of virusinduced membrane rearrangements, we propose two separate subclasses: the invaginated vesicle/spherule type and the double membrane vesicle type. This review discusses common themes and distinct differences in the architecture of plus-strand RNA virus-induced membrane alterations and summarizes recent progress that has been made in understanding the complex interplay between viral and co-opted cellular factors in biogenesis and maintenance of plus-strand RNA virus replication factories.

Reprogramming the host: Modification of cell functions upon viral infection

Viruses and their hosts have co-evolved for million years. In order to successfully replicate their genome, viruses need to usurp the biosynthetic machinery of the host cell. Depending on the complexity and the nature of the genome, replication might involve or not a relatively large subset of viral products, in addition to a number of host cell factors, and take place in several subcellular compartments, including the nucleus,the cytoplasm, as well as virus-induced, rearranged membranes. Therefore viruses need to ensure the correct subcellular localization of their effectors and to be capable of disguising from the cellular defensive mechanisms. In addition, viruses are capable of exploiting host cell activities, by modulating their post-translational modification apparatus, resulting in profound modifications in the function of cellular and viral products. Not surprisingly infection of host cells by these parasites can lead to alterations of cellular differentiation and growing properties, with important pathogenic consequences. In the present hot topic highlight entitled "Reprogramming the host: modification of cell functions upon viral infection", a number of leading virologists and cell biologist thoroughly describe recent advances in our understanding of how viruses modulate cellular functions to achieve successful replication and propagation at the expenses of human cells.

Virus-Encoded MicroRNAs Reveal How Ranavirus Interacts with Amphibian Immune Defense

Ranaviruses are harmful viruses that infect amphibians, fish, and reptiles, and have caused particularly devastating declines in amphibian populations. One particular type of ranavirus, called Frog Virus 3 (FV3), has been extensively studied due to its prevalence and impact on amphibians. Previous research has primarily focused on the virus’s genes, but little attention has been given to the non-coding regions of its genome. This article reviews recent studies that reveal the ability of ranaviruses, including FV3, to encode microRNA (miRNA), a type of regulatory RNA. These viral miRNAs play a crucial role in suppressing frog immune genes, modulating the virus-host interaction, and promoting viral infection. Understanding how ranaviruses use miRNAs to control disease progression is essential for addressing the health threat they pose to wildlife and ecosystems.

Label-free quantitative proteomics reveals fibrinopeptide B and heparin cofactorⅡas potential serum biomarkers in respiratory syncytial virus-infected mice treated with Qingfei oral liquid formula

Respiratory syncytial virus(RSV) is a leading cause of acute lower respiratory tract infections. Qingfei oral liquid(QFOL), a traditional Chinese medicine, is widely used in clinical treatment for RSV-induced pneumonia. The present study was designed to reveal the potential targets and mechanism of action for QFOL by exploring its influence on the host cellular network following RSV infection. We investigated the serum proteomic changes and potential biomarkers in an RSV-infected mouse pneumonia model treated with QFOL. Eighteen BALB/c mice were randomly divided into three groups: RSV pneumonia model group(M), QFOL-treated group(Q) and the control group(C). Serum proteomes were analyzed and compared using a label-free quantitative LC-MS/MS approach. A total of 172 protein groups, 1009 proteins, and 1073 unique peptides were successfully identified. 51 differentially expressed proteins(DEPs) were identified(15 DEPs when M/C and 43 DEPs when Q/M; 7 DEPs in common). Classification and interaction network showed that these proteins participated in various biological processes including immune response, blood coagulation, complement activation, and so forth. Particularly, fibrinopeptide B(FpB) and heparin cofactor Ⅱ(HCII) were evaluated as important nodes in the interaction network, which was closely involved in coagulation and inflammation. Further, the Fp B level was increased in Group M but decreased in Group Q, while the HCII level exhibited the opposite trend. These findings not only indicated FpB and HCII as potential biomarkers and targets of QFOL in the treatment of RSV pneumonia, but also suggested a regulatory role of QFOL in the RSV-induced disturbance of coagulation and inflammation-coagulation interactions.