http://www.mdpi.com/journal/viruses Latest open access articles published in Viruses at http://www.mdpi.com/journal/viruses/ http://www.mdpi.com/1999-4915/2/3/731/ Rift Valley fever virus (RVFV) is a human and livestock pathogen endemic to sub-Saharan Africa. We have developed a T7-dependent system for the efficient production of RVFV-like particles (RVF-VLPs) based on the virulent ZH-501 strain of RVFV. The RVF-VLPs are capable of performing a single round of infection, allowing for the study of viral replication, assembly, and infectivity. We demonstrate that these RVF-VLPs are antigenically indistinguishable from authentic RVFV and respond similarly to a wide array of known and previously unknown chemical inhibitors. This system should be useful for screening for small molecule inhibitors of RVFV replication. http://www.mdpi.com/1999-4915/2/3/731/ Thu, 18 Mar 2010 00:00:00 CET Viruses 2010-03-18 2 3 Article 731 747 1999-4915 A Novel System for Identification of Inhibitors of Rift Valley Fever Virus Replication 2010-03-18 doi: 10.3390/v2030731 Piper Gerrard http://www.mdpi.com/1999-4915/2/3/710/ Bacteriophage O1 is a Myoviridae A1 group member used historically for identifying Salmonella. Sequencing revealed a single, linear, 86,155-base-pair genome with 39% average G+C content, 131 open reading frames, and 22 tRNAs. Closest protein homologs occur in Erwinia amylovora phage φEa21-4 and Escherichia coli phage wV8. Proteomic analysis indentified structural proteins: Gp23, Gp36 (major tail protein), Gp49, Gp53, Gp54, Gp55, Gp57, Gp58 (major capsid protein), Gp59, Gp63, Gp64, Gp67, Gp68, Gp69, Gp73, Gp74 and Gp77 (tail fiber). Based on phage-host codon differences, 7 tRNAs could affect translation rate during infection. Introns, holin-lysin cassettes, bacterial toxin homologs and host RNA polymerase-modifying genes were absent. http://www.mdpi.com/1999-4915/2/3/710/ Tue, 09 Mar 2010 00:00:00 CET Viruses 2010-03-09 2 3 Article 710 730 1999-4915 Complete Genomic Sequence of Bacteriophage Felix O1 2010-03-09 doi: 10.3390/v2030710 Jean M. Whichard Lee A. Weigt Douglas J. Borris Ling Ling Li Qing Zhang Vivek Kapur F. William Pierson Erika J. Lingohr Yi-Min She Andrew M. Kropinski Nammalwar Sriranganathan http://www.mdpi.com/1999-4915/2/3/692/ More than 170 million patients worldwide are chronically infected with hepatitis C virus (HCV). Prevalence rates range from 0.5% in Northern European countries to 28% in some areas of Egypt. HCV is hepatotropic, and in many countries chronic hepatitis C is a leading cause of liver disease including fibrosis, cirrhosis and hepatocellular carcinoma. HCV persists in 50–85% of infected patients, and once chronic infection is established, spontaneous clearance is rare. HCV is a member of the Flaviviridae family, in which it forms its own genus. Many lines of evidence suggest that the HCV life cycle displays many differences to that of other Flaviviridae family members. Some of these differences may be due to the close interaction of HCV with its host’s lipid and particular triglyceride metabolism in the liver, which may explain why the virus can be found in association with lipoproteins in serum of infected patients. This review focuses on the molecular events underlying the HCV cell entry process and the respective roles of cellular co-factors that have been implied in these events. These include, among others, the lipoprotein receptors low density lipoprotein receptor and scavenger receptor BI, the tight junction factors occludin and claudin-1 as well as the tetraspanin CD81. We discuss the roles of these cellular factors in HCV cell entry and how association of HCV with lipoproteins may modulate the cell entry process. http://www.mdpi.com/1999-4915/2/3/692/ Mon, 08 Mar 2010 00:00:00 CET Viruses 2010-03-08 2 3 Review 692 709 1999-4915 Recent Advances in Hepatitis C Virus Cell Entry 2010-03-08 doi: 10.3390/v2030692 Birke Bartosch Jean Dubuisson http://www.mdpi.com/1999-4915/2/2/676/ The flavivirus genus includes viruses with a remarkable ability to produce disease on a large scale. The expansion and increased endemicity of dengue and West Nile viruses in the Americas exemplifies their medical and epidemiological importance. The rapid detection of viral infection and induction of the innate antiviral response are crucial to determining the outcome of infection. The intracellular pathogen receptors RIG-I and MDA5 play a central role in detecting flavivirus infections and initiating a robust antiviral response. Yet, these viruses are still capable of producing acute illness in humans. It is now clear that flaviviruses utilize a variety of mechanisms to modulate the interferon response. The non-structural proteins of the various flaviviruses reduce expression of interferon dependent genes by blocking phosphorylation, enhancing degradation or down-regulating expression of major components of the JAK/STAT pathway. Recent studies indicate that interferon modulation is an important factor in the development of severe flaviviral illness. This suggests that an increased understanding of viral-host interactions will facilitate the development of novel therapeutics to treat these viral infections and improved biological models to study flavivirus pathogenesis. http://www.mdpi.com/1999-4915/2/2/676/ Tue, 23 Feb 2010 00:00:00 CET Viruses 2010-02-23 2 2 Review 676 691 1999-4915 How Flaviviruses Activate and Suppress the Interferon Response 2010-02-23 doi: 10.3390/v2020676 Jorge L. Muñoz-Jordán Brenda L. Fredericksen http://www.mdpi.com/1999-4915/2/2/655/ Arboviruses are maintained in a natural cycle that requires blood-sucking arthropod and vertebrate hosts. Arboviruses are believed to persistently infect their arthropod host without overt pathology and cause acute infection with viremia in their vertebrate host. We have focused on elucidating how a specific arbovirus, Rift Valley fever (RVF) virus, causes cytopathic effect in cells derived from vertebrates and non-cytopathic infection in cells derived from arthropods. We demonstrate that the vertebrate virulence factor, NSs, is functional in arthropod cells but is expressed at significantly lower levels in infected arthropod versus infected vertebrate cells. http://www.mdpi.com/1999-4915/2/2/655/ Wed, 17 Feb 2010 00:00:00 CET Viruses 2010-02-17 2 2 Article 655 675 1999-4915 Restriction of Rift Valley Fever Virus Virulence in Mosquito Cells 2010-02-17 doi: 10.3390/v2020655 Valerie M. Vaughn Cale C. Streeter David J. Miller Sonja R. Gerrard http://www.mdpi.com/1999-4915/2/2/639/ West-Central Africa is an epicenter of the HIV pandemic; endemic to Cameroon are HIV-1 viruses belonging to all (sub)subtypes and numerous Circulating Recombinant Forms (CRFs). The rural villages of Cameroon harbor many strains of HIV-1, though these areas are not as well monitored as the urban centers. In the present study, 82 specimens obtained in 2000 and 2001 from subjects living in the rural villages of the South and West Regions of Cameroon were subtyped in gag, pol, and env and compared to 90 specimens obtained in 2006–2008 in the same regions, in order to analyze HIV-1 evolution in these rural areas. It was found that in the South Region, the proportion of unique recombinant forms (URFs) remained constant (~40%), while the amount of URFs containing fragments of a CRF increased by 25%. (Sub)subtypes A1, F2, H, and K, and CRF09_cpx, identified in 2000 and 2001, were replaced by CRFs 01_AE, 13_cpx, 14_BG, and 18_cpx in 2006–2008. In the West Region, (sub)subtypes A2, C, G, and H, and CRFs 01_AE and 09_cpx, identified in 2000–2001, were replaced by sub-subtype A1 and CRFs 25_cpx and 37_cpx in 2006–2008. The proportion of URFs in the West Region dropped significantly over the time period by 43%. In both Regions, the proportion of CRF02_AG increased at all loci. These findings demonstrate that the evolution of HIV-1 is distinct for each endemic region, and suggests that the proportion of URFs containing CRF fragments is increasing as the genetic identity of the virus continues to shift dramatically. This highlights the concern that subtype-specific vaccines may not be relevant in Cameroon, and that the distribution of viral diversity in these regions of Cameroon must be carefully monitored. http://www.mdpi.com/1999-4915/2/2/639/ Fri, 12 Feb 2010 00:00:00 CET Viruses 2010-02-12 2 2 Article 639 654 1999-4915 The Evolution of HIV-1 Diversity in Rural Cameroon and its Implications in Vaccine Design and Trials 2010-02-12 doi: 10.3390/v2020639 Rebecca Powell Denis Barengolts Luzia Mayr Phillipe Nyambi http://www.mdpi.com/1999-4915/2/2/606/ HIV-1 Reverse Transcriptase (HIV-1 RT) has been the target of numerous approved anti-AIDS drugs that are key components of Highly Active Anti-Retroviral Therapies (HAART). It remains the target of extensive structural studies that continue unabated for almost twenty years. The crystal structures of wild-type or drug-resistant mutant HIV RTs in the unliganded form or in complex with substrates and/or drugs have offered valuable glimpses into the enzyme’s folding and its interactions with DNA and dNTP substrates, as well as with nucleos(t)ide reverse transcriptase inhibitor (NRTI) and non-nucleoside reverse transcriptase inhibitor (NNRTIs) drugs. These studies have been used to interpret a large body of biochemical results and have paved the way for innovative biochemical experiments designed to elucidate the mechanisms of catalysis and drug inhibition of polymerase and RNase H functions of RT. In turn, the combined use of structural biology and biochemical approaches has led to the discovery of novel mechanisms of drug resistance and has contributed to the design of new drugs with improved potency and ability to suppress multi-drug resistant strains. http://www.mdpi.com/1999-4915/2/2/606/ Thu, 11 Feb 2010 00:00:00 CET Viruses 2010-02-11 2 2 Review 606 638 1999-4915 Structural Aspects of Drug Resistance and Inhibition of HIV-1 Reverse Transcriptase 2010-02-11 doi: 10.3390/v2020606 Kamalendra Singh Bruno Marchand Karen A. Kirby Eleftherios Michailidis Stefan G. Sarafianos http://www.mdpi.com/1999-4915/2/2/601/ Commentary on Pais-Correia, A.M.; Sachse, M.; Guadagnini, S.; Robbiati, V.; Lasserre, R.; Gessain, A.; Gout, O.; Alcover, A.; Thoulouze, M.I. Biofilm-like extracellular viral assemblies mediate HTLV-1 cell-to-cell transmission at virological synapses. Nat. Med. 2010, 16, 83-89. http://www.mdpi.com/1999-4915/2/2/601/ Wed, 10 Feb 2010 00:00:00 CET Viruses 2010-02-10 2 2 Commentary 601 605 1999-4915 Surface Transmission or Polarized Egress? Lessons Learned from HTLV Cell-to-Cell Transmission 2010-02-10 doi: 10.3390/v2020601 Jing Jin Nathan Sherer Walther Mothes http://www.mdpi.com/1999-4915/2/2/574/ The C-C chemokine receptor type 5 (CCR5) is a key player in HIV infection due to its major involvement in the infection process. Investigations into the role of the CCR5 coreceptor first focused on its binding to the virus and the molecular mechanisms leading to the entry and spread of HIV. The identification of naturally occurring CCR5 mutations has allowed scientists to address the CCR5 molecule as a promising target to prevent or limit HIV infection in vivo. Naturally occurring CCR5-specific antibodies have been found in exposed but uninfected people, and in a subset of HIV seropositive people who show long-term control of the infection. This suggests that natural autoimmunity to the CCR5 coreceptor exists and may play a role in HIV control. Such natural immunity has prompted strategies aimed at achieving anti-HIV humoral responses through CCR5 targeting, which will be described here. http://www.mdpi.com/1999-4915/2/2/574/ Fri, 05 Feb 2010 00:00:00 CET Viruses 2010-02-05 2 2 Review 574 600 1999-4915 CCR5: From Natural Resistance to a New Anti-HIV Strategy 2010-02-05 doi: 10.3390/v2020574 Lucia Lopalco http://www.mdpi.com/1999-4915/2/2/566/ A new series of genetic screens begins to illuminate the interaction between influenza virus and the infected cell. http://www.mdpi.com/1999-4915/2/2/566/ Fri, 05 Feb 2010 00:00:00 CET Viruses 2010-02-05 2 2 Commentary 566 573 1999-4915 A Host of Factors Regulating Influenza Virus Replication 2010-02-05 doi: 10.3390/v2020566 Andrew Mehle Jennifer A. Doudna http://www.mdpi.com/1999-4915/2/2/547/ Elicitation of antibodies with potent and broad neutralizing activity against HIV by immunization remains a challenge. Several monoclonal antibodies (mAbs) isolated from humans with HIV-1 infection exhibit such activity but vaccine immunogens based on structures containing their epitopes have not been successful for their elicitation. All known broadly neutralizing mAbs (bnmAbs) are immunoglobulin (Ig) Gs (IgGs) and highly somatically hypermutated which could impede their elicitation. Ig Ms (IgMs) are on average significantly less divergent from germline antibodies and are relevant for the development of vaccine immunogens but are underexplored compared to IgGs. Here we describe the identification and characterization of several human IgM-derived mAbs against HIV-1 which were selected from a large phage-displayed naive human antibody library constructed from blood, lymph nodes and spleens of 59 healthy donors. These antibodies bound with high affinity to recombinant envelope glycoproteins (gp140s, Envs) of HIV-1 isolates from different clades. They enhanced or did not neutralize infection by some of the HIV-1 primary isolates using CCR5 as a coreceptor but neutralized all CXCR4 isolates tested although weakly. One of these antibodies with relatively low degree of somatic hypermutation was more extensively characterized. It bound to a highly conserved region partially overlapping with the coreceptor binding site and close to but not overlapping with the CD4 binding site. These results suggest the existence of conserved structures that could direct the immune response to non-neutralizing or even enhancing antibodies which may represent a strategy used by the virus to escape neutralizing immune responses. Further studies will show whether such a strategy plays a role in HIV infection of humans, how important that role could be, and what the mechanisms of infection enhancement are. The newly identified mAbs could be used as reagents to further characterize conserved non-neutralizing, weakly neutralizing or enhancing epitopes and modify or remove them from candidate vaccine immunogens. http://www.mdpi.com/1999-4915/2/2/547/ Thu, 04 Feb 2010 00:00:00 CET Viruses 2010-02-04 2 2 Article 547 565 1999-4915 Cross-Reactive Human IgM-Derived Monoclonal Antibodies that Bind to HIV-1 Envelope Glycoproteins 2010-02-04 doi: 10.3390/v2020547 Weizao Chen Zhongyu Zhu Huaxin Liao Gerald V. Quinnan Christopher C. Broder Barton F. Haynes Dimiter S. Dimitrov http://www.mdpi.com/1999-4915/2/2/532/ Influenza vaccine manufacturers require antigenically relevant vaccine viruses that have good manufacturing properties and are safe to use. In developing pandemic vaccine viruses, reverse genetics has been employed as a rational approach that can also be used effectively to attenuate the highly virulent H5N1 virus and at the same time place the H5 HA and N1 NA on a background of PR8, a virus that has been used over many decades to provide high yielding vaccine viruses. Reverse genetics has also been used successfully alongside classical reassorting techniques in the development of (swine flu) pandemic A(H1N1)v vaccine viruses. http://www.mdpi.com/1999-4915/2/2/532/ Tue, 02 Feb 2010 00:00:00 CET Viruses 2010-02-02 2 2 Review 532 546 1999-4915 Developing Vaccines to Combat Pandemic Influenza 2010-02-02 doi: 10.3390/v2020532 James S. Robertson Othmar G. Engelhardt http://www.mdpi.com/1999-4915/2/2/503/ Most of the current knowledge on antiretroviral (ARV) drug development and resistance is based on the study of subtype B of HIV-1, which only accounts for 10% of the worldwide HIV infections. Cumulative evidence has emerged that different HIV types, groups and subtypes harbor distinct biological properties, including the response and susceptibility to ARV. Recent laboratory and clinical data highlighting such disparities are summarized in this review. Variations in drug susceptibility, in the emergence and selection of specific drug resistance mutations, in viral replicative capacity and in the dynamics of resistance acquisition under ARV selective pressure are discussed. Clinical responses to ARV therapy and associated confounding factors are also analyzed in the context of infections by distinct HIV genetic variants. http://www.mdpi.com/1999-4915/2/2/503/ Tue, 02 Feb 2010 00:00:00 CET Viruses 2010-02-02 2 2 Review 503 531 1999-4915 HIV Genetic Diversity and Drug Resistance 2010-02-02 doi: 10.3390/v2020503 André F. Santos Marcelo A. Soares http://www.mdpi.com/1999-4915/2/2/468/ Covalent modification with polyethylene glycol (PEG), a non-toxic polymer used in food, cosmetic and pharmaceutical preparations for over 60 years, can profoundly influence the pharmacokinetic, pharmacologic and toxciologic profile of protein and peptide-based therapeutics. This review summarizes the history of PEGylation and PEG chemistry and highlights the value of this technology in the context of the design and development of recombinant viruses for gene transfer, vaccination and diagnostic purposes. Specific emphasis is placed on the application of this technology to the adenovirus, the most potent viral vector with the most highly characterized toxicity profile to date, in several animal models. http://www.mdpi.com/1999-4915/2/2/468/ Mon, 01 Feb 2010 00:00:00 CET Viruses 2010-02-01 2 2 Review 468 502 1999-4915 PEGylated Adenoviruses: From Mice to Monkeys 2010-02-01 doi: 10.3390/v2020468 Piyanuch Wonganan Maria A. Croyle http://www.mdpi.com/1999-4915/2/2/435/ Currently, there are more than 30 million people infected with HIV-1 and thousands more are infected each day. Vaccination is the single most effective mechanism for prevention of viral disease, and after more than 25 years of research, one vaccine has shown somewhat encouraging results in an advanced clinical efficacy trial. A modified intent-to-treat analysis of trial results showed that infection was approximately 30% lower in the vaccine group compared to the placebo group. The vaccine was administered using a heterologous prime-boost regimen in which both target antigens and delivery vehicles were changed during the course of inoculations. Here we examine the complexity of heterologous prime-boost immunizations. We show that the use of different delivery vehicles in prime and boost inoculations can help to avert the inhibitory effects caused by vector-specific immune responses. We also show that the introduction of new antigens into boost inoculations can be advantageous, demonstrating that the effect of ‘original antigenic sin’ is not absolute. Pre-clinical and clinical studies are reviewed, including our own work with a three-vector vaccination regimen using recombinant DNA, virus (Sendai virus or vaccinia virus) and protein. Promising preliminary results suggest that the heterologous prime-boost strategy may possibly provide a foundation for the future prevention of HIV-1 infections in humans. http://www.mdpi.com/1999-4915/2/2/435/ Mon, 01 Feb 2010 00:00:00 CET Viruses 2010-02-01 2 2 Review 435 467 1999-4915 Heterologous Prime-Boost HIV-1 Vaccination Regimens in Pre-Clinical and Clinical Trials 2010-02-01 doi: 10.3390/v2020435 Scott A. Brown Sherri L. Surman Robert Sealy Bart G. Jones Karen S. Slobod Kristen Branum Timothy D. Lockey Nanna Howlett Pamela Freiden Patricia Flynn Julia L. Hurwitz http://www.mdpi.com/1999-4915/2/2/413/ RNA replicons are derived from either positive- or negative-strand RNA viruses. They represent disabled virus vectors that are not only avirulent, but also unable to revert to virulence. Due to autonomous RNA replication, RNA replicons are able to drive high level, cytosolic expression of recombinant antigens stimulating both the humoral and the cellular branch of the immune system. This review provides an update on the available literature covering influenza virus vaccines based on RNA replicons. The pros and cons of these vaccine strategies will be discussed and future perspectives disclosed. http://www.mdpi.com/1999-4915/2/2/413/ Fri, 29 Jan 2010 00:00:00 CET Viruses 2010-01-29 2 2 Review 413 434 1999-4915 RNA Replicons - A New Approach for Influenza Virus Immunoprophylaxis 2010-01-29 doi: 10.3390/v2020413 Gert Zimmer http://www.mdpi.com/1999-4915/2/2/395/ Cystic fibrosis (CF) is a chronic autosomic recessive syndrome, caused by mutations in the CF Transmembrane Conductance Regulator (CFTR) gene, a chloride channel expressed on the apical side of the airway epithelial cells. The lack of CFTR activity brings a dysregulated exchange of ions and water through the airway epithelium, one of the main aspects of CF lung disease pathophysiology. Lentiviral (LV) vectors, of the Retroviridae family, show interesting properties for CF gene therapy, since they integrate into the host genome and allow long-lasting gene expression. Proof-of-principle that LV vectors can transduce the airway epithelium and correct the basic electrophysiological defect in CF mice has been given. Initial data also demonstrate that LV vectors can be repeatedly administered to the lung and do not give rise to a gross inflammatory process, although they can elicit a T cell-mediated response to the transgene. Future studies will clarify the efficacy and safety profile of LV vectors in new complex animal models with CF, such as ferrets and pigs. http://www.mdpi.com/1999-4915/2/2/395/ Fri, 29 Jan 2010 00:00:00 CET Viruses 2010-01-29 2 2 Review 395 412 1999-4915 Lentiviral Vectors and Cystic Fibrosis Gene Therapy 2010-01-29 doi: 10.3390/v2020395 Stefano Castellani Massimo Conese http://www.mdpi.com/1999-4915/2/2/372/ Nucleoside reverse transcriptase (RT) inhibitors of HIV block viral replication through the ability of HIV RT to incorporate chain-terminating nucleotide analogs during viral DNA synthesis. Once incorporated, the chain-terminating residue must be removed before DNA synthesis can continue. Removal can be accomplished by the excision activity of HIV RT, which catalyzes the transfer of the 3'-terminal residue on the blocked DNA chain to an acceptor substrate, probably ATP in most infected cells. Mutations of RT that enhance excision activity are the most common cause of resistance to 3'-azido-3'-deoxythymidine (AZT) and exhibit low-level cross-resistance to most other nucleoside RT inhibitors. The resistance to AZT is suppressed by a number of additional mutations in RT, most of which were identified because they conferred resistance to other RT inhibitors. Here we review current understanding of the biochemical mechanisms responsible for increased or decreased excision activity due to these mutations. http://www.mdpi.com/1999-4915/2/2/372/ Thu, 28 Jan 2010 00:00:00 CET Viruses 2010-01-28 2 2 Review 372 394 1999-4915 The Role of Nucleotide Excision by Reverse Transcriptase in HIV Drug Resistance 2010-01-28 doi: 10.3390/v2020372 Antonio J. Acosta-Hoyos Walter A. Scott http://www.mdpi.com/1999-4915/2/2/334/ Cardiovascular disease represents the most common cause of mortality in the developed world but, despite two decades of promising pre-clinical research and numerous clinical trials, cardiovascular gene transfer has so far failed to demonstrate convincing benefits in the clinical setting. In this review we discuss the various targets which may be suitable for cardiovascular gene therapy and the viral vectors which have to date shown the most potential for clinical use. We conclude with a summary of the current state of clinical cardiovascular gene therapy and the key trials which are ongoing. http://www.mdpi.com/1999-4915/2/2/334/ Wed, 27 Jan 2010 00:00:00 CET Viruses 2010-01-27 2 2 Review 334 371 1999-4915 Development of Viral Vectors for Use in Cardiovascular Gene Therapy 2010-01-27 doi: 10.3390/v2020334 Paul D. Williams Parisa Ranjzad Salik J. Kakar Paul A. Kingston http://www.mdpi.com/1999-4915/2/1/314/ Autophagy is an evolutionarily conserved cellular degradation pathway involving the digestion of intracellular components via the lysosomal pathway. The autophagic pathway constitutively maintains cellular homeostasis by recycling cytoplasmic organelles and proteins, but it is also stimulated by environmental stress conditions, such as starvation, oxidative stress, and the accumulation of misfolded proteins. It also acts as a cellular defense mechanism against microorganisms by contributing to both the innate and adaptive immunity, and by eliminating intracellular pathogens (xenophagy). There is growing evidence that host cells try to control Herpesvirus infections by activating the autophagic machinery. However, it is well-known that Herpesviruses are smart pathogens and several, such as HSV-1, HCMV and HHV-8, are known to have developed numerous defense strategies for evading the host’s immune response. Inhibition of the antiviral autophagic mechanism has also been reported. Autophagy has also been shown to enhance the major histocompatibility complex presentation of at least two viral proteins, the EBVencoded EBNA-1 and the HSV-1 encoded gB. In this review, we present an overview of recent advances in our understanding of the complex interplay between autophagy and Herpesviruses. http://www.mdpi.com/1999-4915/2/1/314/ Tue, 26 Jan 2010 00:00:00 CET Viruses 2010-01-26 2 1 Review 314 333 1999-4915 Herpesviruses and Autophagy: Catch Me If You Can! 2010-01-26 doi: 10.3390/v2010314 Yolaine Cavignac Audrey Esclatine http://www.mdpi.com/1999-4915/2/1/298/ Tumor suppressor p53 is widely known as ‘the guardian of the genome’ due to its ability to prevent the emergence of transformed cells by the induction of cell cycle arrest and apoptosis. However, recent studies indicate that p53 is also a direct transcriptional target of type I interferons (IFNs) and thus, it is activated by these cytokines upon viral infection. p53 has been shown to contribute to virus-induced apoptosis, therefore dampening the ability of a wide range of viruses to replicate and spread. Interestingly, recent studies also indicate that several IFN-inducible genes such as interferon regulatory factor 9 (IRF9), IRF5, IFN-stimulated gene 15 (ISG15) and toll-like receptor 3 (TLR3) are in fact, p53 direct transcriptional targets. These findings indicate that p53 may play a key role in antiviral innate immunity by both inducing apoptosis in response to viral infection, and enforcing the type I IFN response, and provide a new insight into the evolutionary reasons why many viruses encode p53 antagonistic proteins. http://www.mdpi.com/1999-4915/2/1/298/ Fri, 22 Jan 2010 00:00:00 CET Viruses 2010-01-22 2 1 Review 298 313 1999-4915 Dual Role of p53 in Innate Antiviral Immunity 2010-01-22 doi: 10.3390/v2010298 Carmen Rivas Stuart A. Aaronson Cesar Munoz-Fontela http://www.mdpi.com/1999-4915/2/1/283/ It is well known that mucosal tissues contain the largest surface area of the human body and are the front line of natural host defense against various pathogens. In fact, more than 80% of infectious disease pathogens probably gain entry into the susceptible human hosts through open mucosal surfaces. Human immunodeficiency virus type one (HIV-1), a mainly sexually transmitted virus, also primarily targets the vaginal and gastrointestinal mucosa as entry sites for viral transmission, seeding, replication and amplification. Since HIV-1 establishes its early replication in vaginal or rectal mucosal tissues, the induction of sufficient mucosal immunity at the initial site of HIV-1 transmission becomes essential for a protective vaccine. However, despite the fact that current conventional vaccine strategies have remained unsuccessful in preventing HIV-1 infection, sufficient financial support and resources have yet to be given to develop a vaccine able to elicit protective mucosal immunity against sexual transmissions. Interestingly, Chinese ancestors invented variolation through intranasal administration about one thousand years ago, which led to the discovery of a successful smallpox vaccine and the final eradication of the disease. It is the hope for all mankind that the development of a mucosal AIDS vaccine will ultimately help control the AIDS pandemic. In order to discover an effective mucosal AIDS vaccine, it is necessary to have a deep understanding of mucosal immunology and to test various mucosal vaccination strategies. http://www.mdpi.com/1999-4915/2/1/283/ Fri, 22 Jan 2010 00:00:00 CET Viruses 2010-01-22 2 1 Review 283 297 1999-4915 The Development of an AIDS Mucosal Vaccine 2010-01-22 doi: 10.3390/v2010283 Xian Tang Zhiwei Chen http://www.mdpi.com/1999-4915/2/1/262/ The members of the filoviruses are recognized as some of the most lethal viruses affecting human and non-human primates. The only two genera of the Filoviridae family, Marburg virus (MARV) and Ebola virus (EBOV), comprise the main etiologic agents of severe hemorrhagic fever outbreaks in central Africa, with case fatality rates ranging from 25 to 90%. Fatal outcomes have been associated with a late and dysregulated immune response to infection, very likely due to the virus targeting key host immune cells, such as macrophages and dendritic cells (DCs) that are necessary to mediate effective innate and adaptive immune responses. Despite major progress in the development of vaccine candidates for filovirus infections, a licensed vaccine or therapy for human use is still not available. During the last ten years, important progress has been made in understanding the molecular mechanisms of filovirus pathogenesis. Several lines of evidence implicate the impairment of the host interferon (IFN) antiviral innate immune response by MARV or EBOV as an important determinant of virulence. In vitro and in vivo experimental infections with recombinant Zaire Ebola virus (ZEBOV), the best characterized filovirus, demonstrated that the viral protein VP35 plays a key role in inhibiting the production of IFN-α/β. Further, the action of VP35 is synergized by the inhibition of cellular responses to IFN-α/β by the minor matrix viral protein VP24. The dual action of these viral proteins may contribute to an efficient initial virus replication and dissemination in the host. Noticeably, the analogous function of these viral proteins in MARV has not been reported. Because the IFN response is a major component of the innate immune response to virus infection, this chapter reviews recent findings on the molecular mechanisms of IFN-mediated antiviral evasion by filovirus infection. http://www.mdpi.com/1999-4915/2/1/262/ Thu, 21 Jan 2010 00:00:00 CET Viruses 2010-01-21 2 1 Review 262 282 1999-4915 Evasion of the Interferon-Mediated Antiviral Response by Filoviruses 2010-01-21 doi: 10.3390/v2010262 Washington B. Cárdenas http://www.mdpi.com/1999-4915/2/1/244/ Numerous human genetic and acquired diseases could be corrected or ameliorated if viruses are harnessed to safely and effectively deliver therapeutic genes to diseased cells and tissues in vivo. Innate immune and inflammatory response represents one of the key stumbling blocks during the development of viral-based therapies. In this review, current data on the early innate immune responses to viruses and to the most commonly used gene therapy vectors (using adenovirus and adeno-associated virus) will be discussed. Recent findings in the field may help develop new approaches to moderate these innate immune anti-viral responses and thus improve the safety of viral vectors for human gene therapy applications. http://www.mdpi.com/1999-4915/2/1/244/ Tue, 19 Jan 2010 00:00:00 CET Viruses 2010-01-19 2 1 Review 244 261 1999-4915 Virus Infection Recognition and Early Innate Responses to Non-Enveloped Viral Vectors 2010-01-19 doi: 10.3390/v2010244 Dmitry M. Shayakhmetov http://www.mdpi.com/1999-4915/2/1/213/ Reverse transcription of retroviral genomes into double stranded DNA is a key event for viral replication. The very first stage of HIV reverse transcription, the initiation step, involves viral and cellular partners that are selectively packaged into the viral particle, leading to an RNA/protein complex with very specific structural and functional features, some of which being, in the case of HIV-1, linked to particular isolates. Recent understanding of the tight spatio-temporal regulation of reverse transcription and its importance for viral infectivity further points toward reverse transcription and potentially its initiation step as an important drug target. http://www.mdpi.com/1999-4915/2/1/213/ Mon, 18 Jan 2010 00:00:00 CET Viruses 2010-01-18 2 1 Review 213 243 1999-4915 Initiation of HIV Reverse Transcription 2010-01-18 doi: 10.3390/v2010213 Catherine Isel Chantal Ehresmann Roland Marquet http://www.mdpi.com/1999-4915/2/1/189/ The hepatitis delta virus (HDV) is the smallest known RNA pathogen capable of propagation in the human host and causes substantial global morbidity and mortality. Due to its small size and limited protein coding capacity, HDV is exquisitely reliant upon host cellular proteins to facilitate its transcription and replication. Remarkably, HDV does not encode an RNA-dependent RNA polymerase which is traditionally required to catalyze RNA-templated RNA synthesis. Furthermore, HDV lacks enzymes responsible for post-transcriptional and -translational modification, processes which are integral to the HDV life cycle. This review summarizes the known HDV-interacting proteins and discusses their significance in HDV biology. http://www.mdpi.com/1999-4915/2/1/189/ Mon, 18 Jan 2010 00:00:00 CET Viruses 2010-01-18 2 1 Review 189 212 1999-4915 Interaction of Host Cellular Proteins with Components of the Hepatitis Delta Virus 2010-01-18 doi: 10.3390/v2010189 Valerie Greco-Stewart Martin Pelchat http://www.mdpi.com/1999-4915/2/1/166/ The current pandemic caused by the new influenza A(H1N1) virus of swine origin and the current pandemic threat caused by the highly pathogenic avian influenza A viruses of the H5N1 subtype have renewed the interest in the development of vaccines that can induce broad protective immunity. Preferably, vaccines not only provide protection against the homologous strains, but also against heterologous strains, even of another subtype. Here we describe viral targets and the arms of the immune response involved in protection against influenza virus infections such as antibodies directed against the hemagglutinin, neuraminidase and the M2 protein and cellular immune responses directed against the internal viral proteins. http://www.mdpi.com/1999-4915/2/1/166/ Thu, 14 Jan 2010 00:00:00 CET Viruses 2010-01-14 2 1 Review 166 188 1999-4915 Targets for the Induction of Protective Immunity Against Influenza A Viruses 2010-01-14 doi: 10.3390/v2010166 Rogier Bodewes Albert D.M.E. Osterhaus Guus F. Rimmelzwaan http://www.mdpi.com/1999-4915/2/1/147/ Exogenous retroviruses are subclassified into seven genera and include viruses that cause diseases in humans. The viral Gag and Gag-Pro-Pol polyproteins are processed by the retroviral protease in the last stage of replication and inhibitors of the HIV-1 protease are widely used in AIDS therapy. Resistant mutations occur in response to the drug therapy introducing residues that are frequently found in the equivalent position of other retroviral proteases. Therefore, besides helping to understand the general and specific features of these enzymes, comparative studies of retroviral proteases may help to understand the mutational capacity of the HIV-1 protease. http://www.mdpi.com/1999-4915/2/1/147/ Thu, 14 Jan 2010 00:00:00 CET Viruses 2010-01-14 2 1 Article 147 165 1999-4915 Comparative Studies on Retroviral Proteases: Substrate Specificity 2010-01-14 doi: 10.3390/v2010147 József Tözsér http://www.mdpi.com/1999-4915/2/1/131/ The hepatitis delta virus genome is a small circular RNA, similar to viroids. Although HDV contains a gene, the protein produced (HDAg) is encoded by less than half the genome and possesses no RNA polymerase activity. Because of this limited coding capacity, HDV relies heavily on host functions and on structural features of the viral RNA—very much like viroids. The virus’ use of host RNA editing activity to produce two functionally distinct forms of HDAg is a particularly good example of this reliance. This review covers the mechanisms and control of RNA editing in the HDV replication cycle. http://www.mdpi.com/1999-4915/2/1/131/ Tue, 12 Jan 2010 00:00:00 CET Viruses 2010-01-12 2 1 Review 131 146 1999-4915 RNA Editing and its Control in Hepatitis Delta Virus Replication 2010-01-12 doi: 10.3390/v2010131 Renxiang Chen Sarah D. Linnstaedt John L. Casey http://www.mdpi.com/1999-4915/2/1/111/ The stable insertion of a copy of their genome into the host cell genome is an essential step of the life cycle of retroviruses. The site of viral DNA integration, mediated by the viral-encoded integrase enzyme, has important consequences for both the virus and the host cell. The analysis of retroviral integration site distribution was facilitated by the availability of the human genome sequence, revealing the non-random feature of integration site selection and identifying different favored and disfavored genomic locations for individual retroviruses. This review will summarize the current knowledge about retroviral differences in their integration site preferences as well as the mechanisms involved in this process. http://www.mdpi.com/1999-4915/2/1/111/ Tue, 12 Jan 2010 00:00:00 CET Viruses 2010-01-12 2 1 Review 111 130 1999-4915 Retroviral Integration Site Selection 2010-01-12 doi: 10.3390/v2010111 Sébastien Desfarges Angela Ciuffi http://www.mdpi.com/1999-4915/2/1/107/ Commentary on Byeon, I.J.; Meng, X.; Jung, J.; Zhao, G.; Yang, R.; Ahn, J.; Shi, J.; Concel, J.; Aiken, C.; Zhang, P.; Gronenborn, A.M. Structural convergence between Cryo-EM and NMR reveals intersubunit interactions critical for HIV-1 capsid function. Cell 2009, 139, 780-790. http://www.mdpi.com/1999-4915/2/1/107/ Mon, 11 Jan 2010 00:00:00 CET Viruses 2010-01-11 2 1 Commentary 107 110 1999-4915 Correlative Structural Biology: How to Investigate the Fine Details of Viral Structure 2010-01-11 doi: 10.3390/v2010107 Elizabeth R. Wright http://www.mdpi.com/1999-4915/2/1/78/ Targeted therapy of cancer using oncolytic viruses has generated much interest over the past few years in the light of the limited efficacy and side effects of standard cancer therapeutics for advanced disease. In 2006, the world witnessed the first government-approved oncolytic virus for the treatment of head and neck cancer. It has been known for many years that viruses have the ability to replicate in and lyse cancer cells. Although encouraging results have been demonstrated in vitro and in animal models, most oncolytic viruses have failed to impress in the clinical setting. The explanation is multifactorial, determined by the complex interactions between the tumor and its microenvironment, the virus, and the host immune response. This review focuses on discussion of the obstacles that oncolytic virotherapy faces and recent advances made to overcome them, with particular reference to adenoviruses. http://www.mdpi.com/1999-4915/2/1/78/ Mon, 11 Jan 2010 00:00:00 CET Viruses 2010-01-11 2 1 Review 78 106 1999-4915 Oncolytic Viruses for Cancer Therapy: Overcoming the Obstacles 2010-01-11 doi: 10.3390/v2010078 Han Hsi Wong Nicholas R. Lemoine Yaohe Wang http://www.mdpi.com/1999-4915/2/1/73/ The national HIV seroprevalence in Nigeria has risen steeply from about 3% in 1993 to 5-8% in 2001 and now stands at 4.4%. HIV epidemic continues to be a serious threat to the most populous country in Africa with a population of 140 million, with limited use of antiviral drugs that is taken for life since it only suppresses the virus without completely eliminating the virus or leading to cure. Only a change in social behavior and an affordable vaccine can halt the epidemic in Africa. We report here results of a pilot study on the recruitment strategies, sociodemographic aspects and HIV risk behavior of a cohort of normal volunteers recruited at the University of Jos, Nigeria. Our study recorded a high degree of interest and zeal to participate in HIV vaccine studies by volunteers, and demonstrated the superiority of snowballing over invitation by mail, as a recruitment strategy. A cohort of university students may be particularly suitable for conducting HIV vaccine trials because of the assurance of prospective follow-up for up to four years (time to graduation), and a good understanding of the risks and benefits of participation as outlined in the informed consent. We had 100% retention during a follow-up period of two years. Most importantly, the cohort reflected a relatively low HIV seroprevalence, which gives preventive programs the potential to blunt or halt the epidemic. http://www.mdpi.com/1999-4915/2/1/73/ Mon, 11 Jan 2010 00:00:00 CET Viruses 2010-01-11 2 1 Communication 73 77 1999-4915 Preliminary Report on HIV-1 Vaccine Preparedness in Nigeria: Advantages of Recruiting University Students 2010-01-11 doi: 10.3390/v2010073 Abigail Edubio Simon Agwale Marc Bulterys Dadik Jelpe John Idoko Chris Isichei Ruth Guyit Alash’le Abimiku http://www.mdpi.com/1999-4915/2/1/55/ The ability of a cell to combat an intracellular pathogen requires a mechanism to recognize the threat and elicit a transcriptional response against it. In the context of virus infection, the cell must take measures to inhibit viral replication, meanwhile, convey warning signals to neighboring cells of the imminent threat. This immune response is predominantly mediated by the production of cytokines, notably, interferon beta (IFNβ). IFNβ signaling results in the transcriptional induction of over one hundred antiviral gene products whose timely expression renders infected cells more capable of inhibiting virus replication, while providing the uninfected cells with the reinforcements to generate a less permissive cellular environment. Induction of IFNβ and many aspects of the antiviral response pivot on the function of the IKK and IKK-related kinases. Despite sharing high levels of homology and some degree of functional redundancy, the classic IKK kinases: IKKα and IKKβ, and the IKK-related kinases: TBK1 and IKKε, perform distinct roles in regulating the host antiviral defense. These kinases serve as molecular operators in their cooperative ability to integrate incoming cellular cues and act on a range of essential antiviral transcription factors to reshape the cellular transcriptome during infection. http://www.mdpi.com/1999-4915/2/1/55/ Fri, 08 Jan 2010 00:00:00 CET Viruses 2010-01-08 2 1 Review 55 72 1999-4915 The IKK Kinases: Operators of Antiviral Signaling 2010-01-08 doi: 10.3390/v2010055 Alissa M. Pham Benjamin R. tenOever http://www.mdpi.com/1999-4915/2/1/33/ The diversity of HIV-1 and its propensity to generate escape mutants present fundamental challenges to control efforts, including HIV vaccine design. Intra-host diversification of HIV is determined by immune responses elicited by an HIV-infected individual over the course of the infection. Complex and dynamic patterns of transmission of HIV lead to an even more complex population viral diversity over time, thus presenting enormous challenges to vaccine development. To address inter-patient viral evolution over time, a set of 653 unique HIV-1 subtype C gag sequences were retrieved from the LANL HIV Database, grouped by sampling year as <2000, 2000, 2001–2002, 2003, and 2004–2006, and analyzed for the site-specific frequency of translated amino acid residues. Phylogenetic analysis revealed that a total of 289 out of 653 (44.3%) analyzed sequences were found within 16 clusters defined by aLRT of more than 0.90. Median (IQR) inter-sample diversity of analyzed gag sequences was 8.7% (7.7%; 9.8%). Despite the heterogeneous origins of analyzed sequences, the gamut and frequency of amino acid residues in wild-type Gag were remarkably stable over the last decade of the HIV-1 subtype C epidemic. The vast majority of amino acid residues demonstrated minor frequency fluctuation over time, consistent with the conservative nature of the HIV-1 Gag protein. Only 4.0% (20 out of 500; HXB2 numbering) amino acid residues across Gag displayed both statistically significant (p<0.05 by both a trend test and heterogeneity test) changes in amino acid frequency over time as well as a range of at least 10% in the frequency of the major amino acid. A total of 59.2% of amino acid residues with changing frequency of 10%+ were found within previously identified CTL epitopes. The time of the most recent common ancestor of the HIV-1 subtype C was dated to around 1950 (95% HPD from 1928 to 1962). This study provides evidence for the overall stability of HIV-1 subtype C Gag among viruses circulating in the epidemic over the last decade. However selected sites across HIV-1C Gag with changing amino acid frequency are likely to be under selection pressure at the population level. http://www.mdpi.com/1999-4915/2/1/33/ Thu, 07 Jan 2010 00:00:00 CET Viruses 2010-01-07 2 1 Article 33 54 1999-4915 HIV-1 Subtype C Phylodynamics in the Global Epidemic 2010-01-07 doi: 10.3390/v2010033 Vlad Novitsky Rui Wang Stephen Lagakos Max Essex http://www.mdpi.com/1999-4915/2/1/27/ Commentary on Tawar, R.G.; Duquerroy, S.; Vonrhein, C.; Varela, P.F.; Damier-Piolle, L.; Castagné, N.; MacLellan, K.; Bedouelle, H.; Bricogne, G.; Bhella, D.; Eléouët, J.-F.; Rey, F.A. Crystal structure of a nucleocapsid-like nucleoprotein-RNA complex of respiratory syncytial virus. Science 2009, 326, 1279-1283. http://www.mdpi.com/1999-4915/2/1/27/ Thu, 07 Jan 2010 00:00:00 CET Viruses 2010-01-07 2 1 Commentary 27 32 1999-4915 Nucleoproteins of Negative Strand RNA Viruses; RNA Binding, Oligomerisation and Binding to Polymerase Co-Factor 2010-01-07 doi: 10.3390/v2010027 Rob W. H. Ruigrok Thibaut Crépin http://www.mdpi.com/1999-4915/2/1/1/ Technological advances and increasingly cost-effect methodologies in DNA sequencing and computational analysis are providing genome and proteome data for human adenovirus research. Applying these tools, data and derived knowledge to the development of vaccines against these pathogens will provide effective prophylactics. The same data and approaches can be applied to vector development for gene delivery in gene therapy and vaccine delivery protocols. Examination of several field strain genomes and their analyses provide examples of data that are available using these approaches. An example of the development of HAdV-B3 both as a vaccine and also as a vector is presented. http://www.mdpi.com/1999-4915/2/1/1/ Wed, 06 Jan 2010 00:00:00 CET Viruses 2010-01-06 2 1 Review 1 26 1999-4915 Applying Genomic and Bioinformatic Resources to Human Adenovirus Genomes for Use in Vaccine Development and for Applications in Vector Development for Gene Delivery 2010-01-06 doi: 10.3390/v2010001 Jason Seto Michael P. Walsh Padmanabhan Mahadevan Qiwei Zhang Donald Seto http://www.mdpi.com/1999-4915/1/3/1351/ Since its emergence in South East Asia in 2003, Highly Pathogenic Avian Influenza (HPAI) A/H5N1 has reportedly caused outbreaks in poultry and/or wild birds in 62 countries, of which 24 were in Europe. Interestingly, out of the many genetic clades circulating in Asia, the westward spread of HPAI A/H5N1 to Central Asia, the Middle East, Europe and Africa was dominated by one single clade, namely clade 2.2. In this paper, we review and update through phylogenetic and gene migrational analysis the information concerning the evolution and the molecular epidemiology of HPAI A/H5N1 on the European continent. http://www.mdpi.com/1999-4915/1/3/1351/ Wed, 23 Dec 2009 00:00:00 CET Viruses 2009-12-23 1 3 Review 1351 1363 1999-4915 H5N1 Virus Evolution in Europe—An Updated Overview 2009-12-23 doi: 10.3390/v1031351 Giovanni Cattoli Alice Fusaro Isabella Monne Ilaria Capua http://www.mdpi.com/1999-4915/1/3/1325/ The view that satellite RNAs (satRNAs) and satellite viruses are purely molecular parasites of their cognate helper viruses has changed. The molecular mechanisms underlying the synergistic and/or antagonistic interactions among satRNAs/satellite viruses, helper viruses, and host plants are beginning to be comprehended. This review aims to summarize the recent achievements in basic and practical research, with special emphasis on the involvement of RNA silencing mechanisms in the pathogenicity, population dynamics, and, possibly, the origin(s) of these subviral agents. With further research following current trends, the comprehensive understanding of satRNAs and satellite viruses could lead to new insights into the trilateral interactions among host plants, viruses, and satellites. http://www.mdpi.com/1999-4915/1/3/1325/ Fri, 18 Dec 2009 00:00:00 CET Viruses 2009-12-18 1 3 Review 1325 1350 1999-4915 Satellite RNAs and Satellite Viruses of Plants 2009-12-18 doi: 10.3390/v1031325 Chung-Chi Hu Yau-Heiu Hsu Na-Sheng Lin http://www.mdpi.com/1999-4915/1/3/1295/ The turbulent history of clinical trials in viral gene therapy has taught us important lessons about vector design and safety issues. Much effort was spent on analyzing genotoxicity after somatic integration of therapeutic DNA into the host genome. Based on these findings major improvements in vector design including the development of viral hybrid vectors for somatic integration have been achieved. This review provides a state-of-the-art overview of available hybrid vectors utilizing viruses for high transduction efficiencies in concert with various integration machineries for random and targeted integration patterns. It discusses advantages but also limitations of each vector system. http://www.mdpi.com/1999-4915/1/3/1295/ Tue, 15 Dec 2009 00:00:00 CET Viruses 2009-12-15 1 3 Review 1295 1324 1999-4915 Viral Hybrid Vectors for Somatic Integration - Are They the Better Solution? 2009-12-15 doi: 10.3390/v1031295 Nadine Müther Nadja Noske Anja Ehrhardt http://www.mdpi.com/1999-4915/1/3/1265/ The HIV/AIDS pandemic is one of the most devastating pandemics worldwide. Today, the major route of infection by HIV is sexual transmission. One of the most promising strategies for vaccination against HIV sexual infection is the development of a mucosal vaccine, which should be able to induce strong local and systemic protective immunity. It is believed that both humoral and cellular immune responses are needed for inducing a sterilizing protection against HIV. Recently, passive administration of monoclonal neutralizing antibodies in macaques infected by vaginal challenge demonstrated a crucial role of FcγRs in the protection afforded by these antibodies. This questioned about the role of innate and adaptive immune functions, including ADCC, ADCVI, phagocytosis of opsonized HIV particles and the production of inflammatory cytokines and chemokines, in the mechanism of HIV inhibition in vivo. Other monoclonal antibodies - non-neutralizing inhibitory antibodies - which recognize immunogenic epitopes, have been shown to display potent FcγRs-dependent inhibition of HIV replication in vitro. The potential role of these antibodies in protection against sexual transmission of HIV and their biological relevance for the development of an HIV vaccine therefore need to be determined. This review highlights the potential role of FcγRsmediated innate and adaptive immune functions in the mechanism of HIV protection. http://www.mdpi.com/1999-4915/1/3/1265/ Tue, 15 Dec 2009 00:00:00 CET Viruses 2009-12-15 1 3 Review 1265 1294 1999-4915 Antibody-Mediated Fcγ Receptor-Based Mechanisms of HIV Inhibition: Recent Findings and New Vaccination Strategies 2009-12-15 doi: 10.3390/v1031265 Vincent Holl Maryse Peressin Christiane Moog http://www.mdpi.com/1999-4915/1/3/1240/ In recent studies we and others have identified the cellular proteins PML, hDaxx, and Sp100, which form a subnuclear structure known as nuclear domain 10 (ND10) or PML nuclear bodies (PML-NBs), as host restriction factors that counteract herpesviral infections by inhibiting viral replication at different stages. The antiviral function of ND10, however, is antagonized by viral regulatory proteins (e.g., ICP0 of herpes simplex virus; IE1 of human cytomegalovirus) which induce either a modification or disruption of ND10. This review will summarize the current knowledge on how viral replication is inhibited by ND10 proteins. Furthermore, herpesviral strategies to defeat this host defense mechanism are discussed. http://www.mdpi.com/1999-4915/1/3/1240/ Tue, 15 Dec 2009 00:00:00 CET Viruses 2009-12-15 1 3 Review 1240 1264 1999-4915 Interplay between Herpesvirus Infection and Host Defense by PML Nuclear Bodies 2009-12-15 doi: 10.3390/v1031240 Nina Tavalai Thomas Stamminger http://www.mdpi.com/1999-4915/1/3/1209/ The design, development and clinical success of HIV protease inhibitors represent one of the most remarkable achievements of molecular medicine. This review describes all nine currently available FDA-approved protease inhibitors, discusses their pharmacokinetic properties, off-target activities, side-effects, and resistance profiles. The compounds in the various stages of clinical development are also introduced, as well as alternative approaches, aiming at other functional domains of HIV PR. The potential of these novel compounds to open new way to the rational drug design of human viruses is critically assessed. http://www.mdpi.com/1999-4915/1/3/1209/ Fri, 11 Dec 2009 00:00:00 CET Viruses 2009-12-11 1 3 Review 1209 1239 1999-4915 Current and Novel Inhibitors of HIV Protease 2009-12-11 doi: 10.3390/v1031209 Jana Pokorná Ladislav Machala Pavlína Řezáčová Jan Konvalinka http://www.mdpi.com/1999-4915/1/3/1204/ Timely implementation of antiviral treatment and other public health based responses are dependent on accurate and rapid diagnosis of the novel pandemic influenza A(H1N1) strain. In this study we developed a duplex real-time PCR (RT-PCR) (dFLU-TM) assay for the simultaneous detection of a broad range of influenza A subtypes and specific detection of the novel H1N1 2009 pandemic strain. The assay was compared to the combined results of two previously described monoplex RT-PCR assays using 183 clinical samples and 10 seasonal influenza A isolates. Overall, the results showed that the dFLU-TM RT-PCR method is suitable for detection of influenza A, including the novel H1N1 pandemic strain, in clinical samples. http://www.mdpi.com/1999-4915/1/3/1204/ Wed, 09 Dec 2009 00:00:00 CET Viruses 2009-12-09 1 3 Article 1204 1208 1999-4915 A Novel Duplex Real-Time Reverse-Transcription PCR Assay for the Detection of Influenza A and the Novel Influenza A(H1N1) Strain 2009-12-09 doi: 10.3390/v1031204 Rebecca J. Rockett Seweryn Bialasiewicz David M. Whiley Cheryl Bletchly Cassandra E. Faux Stephen B. Lambert Graeme R. Nimmo Michael D. Nissen Theo P. Sloots http://www.mdpi.com/1999-4915/1/3/1190/ Hendra and Nipah virus, which constitute the genus Henipavirus, are zoonotic paramyxoviruses that have been associated with sporadic outbreaks of severe disease and mortality in humans since their emergence in the late 1990s. Similar to other paramyxoviruses, their ability to evade the host interferon (IFN) response is conferred by the P gene. The henipavirus P gene encodes four proteins; the P, V, W and C proteins, which have all been described to inhibit the antiviral response. Further studies have revealed that these proteins have overlapping but unique properties which enable the virus to block multiple signaling pathways in the IFN response. The best characterized of these is the JAK-STAT signaling pathway which is targeted by the P, V and W proteins via an interaction with the transcription factor STAT1. In addition the V and W proteins can both limit virus-induced induction of IFN but they appear to do this via distinct mechanisms that rely on unique sequences in their C-terminal domains. The ability to generate recombinant Nipah viruses now gives us the opportunity to determine the precise role for each of these proteins and address their contribution to pathogenicity. Additionally, the question of whether these multiple anti-IFN strategies are all active in the different mammalian hosts for henipaviruses, particularly the fruit bat reservoir, warrants further exploration. http://www.mdpi.com/1999-4915/1/3/1190/ Tue, 08 Dec 2009 00:00:00 CET Viruses 2009-12-08 1 3 Review 1190 1203 1999-4915 Henipaviruses Employ a Multifaceted Approach to Evade the Antiviral Interferon Response 2009-12-08 doi: 10.3390/v1031190 Megan L. Shaw http://www.mdpi.com/1999-4915/1/3/1178/ Human rhinoviruses (HRV) are known to cause common cold as well as more complicated respiratory infections. HRV species -A, -B and -C have all been associated with lower respiratory infections and exacerbations of asthma. However, the type distribution of strains connected to different kinds of lower respiratory conditions is not clearly known. We have analysed the presence of HRV in sputum specimens derived from military recruits with and without pre-diagnosed asthma at times of acute respiratory infection (CIAS Study, 2004-2005). The analysis was performed with HRV and HEV real-time RT-PCR assays. Subsequently we studied type distribution of HRV strains by genetic typing in the VP4/VP2 genomic region. In total 146 (38.8%) specimens were HRV-positive and 36 (9.3%) HEV-positive. No difference was found in HRV detection between the asthmatic vs. non-asthmatic patients. Most of the genetically typed strains, 18 (62.1%), belonged to HRV-A, while HRV-B strains constituted five (17.2%) of the HRV-positive strains. HRV-C strain was typed four times from the HRV-positive cases and a HEV-D strain twice. We further typed six HEV positive strains in the partial VP1 region. Three of these belonged to HRV-A and three to HEV-D. HRV-A strains were discovered throughout the study period, while HRV-C strains originated from winter and spring specimens. Interestingly, four out of five typed HRV-B strains originated from the summer season specimens. http://www.mdpi.com/1999-4915/1/3/1178/ Fri, 04 Dec 2009 00:00:00 CET Viruses 2009-12-04 1 3 Communication 1178 1189 1999-4915 All Known Human Rhinovirus Species Are Present in Sputum Specimens of Military Recruits During Respiratory Infection 2009-12-04 doi: 10.3390/v1031178 Carita Savolainen-Kopra Soile Blomqvist Svetlana Kaijalainen Ulla Jounio Raija Juvonen Ari Peitso Annika Saukkoriipi Olli Vainio Tapani Hovi Merja Roivainen http://www.mdpi.com/1999-4915/1/3/1166/ Infectious bronchitis virus (IBV) causes highly contagious respiratory or urogenital tract diseases in chickens. The Maryland 27(Md27) strain was first isolated in 1976 from diseased chicken flocks in the Delmarva Peninsula region. To understand the genetic diversity and phylogenetic relationship of existing strains with Md27, the complete nucleotide sequence of the 3’end coding region (~7.2 kb) of Md27 was determined and compared with other IBV strains and coronaviruses. It has the same S-3-M-5-N-3’ gene order, as is the case of other IBV strains. The spike gene of Md27 exhibits 97% identity with the SE17 strain. There are deletions at the spike gene, non-coding region between M and 5 genes, and at the 3’untranslated region (UTR), which is different from Ark-like strains. Phylogenetic analysis and sequence alignments demonstrate that Md27 is a chimera containing different gene segments that are most closely related to the SE17, Conn and JMK strains. This current study provides evidence for genomic mutations and intergenic recombination that have taken place in the evolution of IBV strain Md27. http://www.mdpi.com/1999-4915/1/3/1166/ Fri, 04 Dec 2009 00:00:00 CET Viruses 2009-12-04 1 3 Article 1166 1177 1999-4915 Complete Nucleotide Analysis of the Structural Genome of the Infectious Bronchitis Virus Strain Md27 Reveals its Mosaic Nature 2009-12-04 doi: 10.3390/v1031166 Arun Ammayappan Vikram N. Vakharia http://www.mdpi.com/1999-4915/1/3/1137/ Retroviruses are RNA viruses that replicate through a DNA intermediate, in a process catalyzed by the viral reverse transcriptase (RT). Although cellular polymerases and host factors contribute to retroviral mutagenesis, the RT errors play a major role in retroviral mutation. RT mutations that affect the accuracy of the viral polymerase have been identified by in vitro analysis of the fidelity of DNA synthesis, by using enzymological (gel-based) and genetic assays (e.g., M13mp2 lacZ forward mutation assays). For several amino acid substitutions, these observations have been confirmed in cell culture using viral vectors. This review provides an update on studies leading to the identification of the major components of the fidelity center in retroviral RTs. http://www.mdpi.com/1999-4915/1/3/1137/ Fri, 04 Dec 2009 00:00:00 CET Viruses 2009-12-04 1 3 Review 1137 1165 1999-4915 Mutation Rates and Intrinsic Fidelity of Retroviral Reverse Transcriptases 2009-12-04 doi: 10.3390/v1031137 Luis Menéndez-Arias http://www.mdpi.com/1999-4915/1/3/1110/ Antiviral inhibitors of HIV-1 protease are a notable success of structure-based drug design and have dramatically improved AIDS therapy. Analysis of the structures and activities of drug resistant protease variants has revealed novel molecular mechanisms of drug resistance and guided the design of tight-binding inhibitors for resistant variants. The plethora of structures reveals distinct molecular mechanisms associated with resistance: mutations that alter the protease interactions with inhibitors or substrates; mutations that alter dimer stability; and distal mutations that transmit changes to the active site. These insights will inform the continuing design of novel antiviral inhibitors targeting resistant strains of HIV. http://www.mdpi.com/1999-4915/1/3/1110/ Thu, 03 Dec 2009 00:00:00 CET Viruses 2009-12-03 1 3 Review 1110 1136 1999-4915 HIV-1 Protease: Structural Perspectives on Drug Resistance 2009-12-03 doi: 10.3390/v1031110 Irene T. Weber Johnson Agniswamy http://www.mdpi.com/1999-4915/1/3/1089/ Recent years’ enzootic spread of highly pathogenic H5N1 virus among poultry and the many lethal zoonoses in its wake has stimulated basic and applied pandemic vaccine research. The quest for an efficacious, affordable and timely accessible pandemic vaccine has been high on the agenda. When a variant H1N1 strain of swine origin emerged as a pandemic virus, it surprised many, as this subtype is well-known to man as a seasonal virus. This review will cover some difficult vaccine questions, such as the immunological challenges, the new production platforms, and the limited supply and global equity issues. http://www.mdpi.com/1999-4915/1/3/1089/ Thu, 03 Dec 2009 00:00:00 CET Viruses 2009-12-03 1 3 Review 1089 1109 1999-4915 Pandemic Influenza Vaccines – The Challenges 2009-12-03 doi: 10.3390/v1031089 Lars R. Haaheim Abdullah S. Madhun Rebecca Cox http://www.mdpi.com/1999-4915/1/3/1073/ Hepatitis C virus (HCV) establishes a persistent infection in more than 70% of infected individuals. This striking ability to evade the powerful innate immune system results from viral interference occurring at several levels of the interferon (IFN) system. There is strong evidence from cell culture experiments that HCV can inhibit the induction of IFNβ by cleaving important proteins in the virus sensory pathways of cells such as MAVS and TRIF. There is also evidence that HCV interferes with IFNα signaling through the Jak-STAT pathway, and that HCV proteins target IFN effector systems such as protein kinase R (PKR). These in vitro findings will have to be confirmed in clinical trials investigating the molecular mechanisms of HCV interference with the innate immune system in liver samples. http://www.mdpi.com/1999-4915/1/3/1073/ Mon, 30 Nov 2009 00:00:00 CET Viruses 2009-11-30 1 3 Review 1073 1088 1999-4915 HCV Innate Immune Responses 2009-11-30 doi: 10.3390/v1031073 Markus H. Heim http://www.mdpi.com/1999-4915/1/3/1057/ The Non-Structural 1 (NS1) protein is a multifactorial protein of type A influenza viruses that plays an important role in the virulence of the virus. A large amount of what we know about this protein has been obtained from studies using human influenza isolates and, consequently, the human NS1 protein. The current global interest in avian influenza, however, has highlighted a number of sequence and functional differences between the human and avian NS1. This review discusses these differences in addition to describing potential uses of NS1 in the management and control of avian influenza outbreaks. http://www.mdpi.com/1999-4915/1/3/1057/ Thu, 26 Nov 2009 00:00:00 CET Viruses 2009-11-26 1 3 Review 1057 1072 1999-4915 A Closer Look at the NS1 of Influenza Virus 2009-11-26 doi: 10.3390/v1031057 William G. Dundon Ilaria Capua http://www.mdpi.com/1999-4915/1/3/1035/ Rotavirus is a primary cause of severe dehydrating gastroenteritis in infants and young children. The virus is sensitive to the antiviral effects triggered by the interferon (IFN)-signaling pathway, an important component of the host cell innate immune response. To counteract these effects, rotavirus encodes a nonstructural protein (NSP1) that induces the degradation of proteins involved in regulating IFN expression, such as members of the IFN regulatory factor (IRF) family. In some instances, NSP1 also subverts IFN expression by causing the degradation of a component of the E3 ubiquitin ligase complex responsible for activating NF-κB. By antagonizing multiple components of the IFN-induction pathway, NSP1 aids viral spread and contributes to rotavirus pathogenesis. http://www.mdpi.com/1999-4915/1/3/1035/ Tue, 24 Nov 2009 00:00:00 CET Viruses 2009-11-24 1 3 Review 1035 1056 1999-4915 Rotavirus Antagonism of the Innate Immune Response 2009-11-24 doi: 10.3390/v1031035 Michelle M. Arnold John T. Patton http://www.mdpi.com/1999-4915/1/3/1022/ Dendritic cells (DC) are major players in both innate and adaptive immune responses against influenza virus. These immune responses, as well as the important interface between the innate and adaptive systems, are orchestrated by specialized subsets of DC, including conventional steady-state DC, migratory DC and plasmacytoid DC. The characteristics and efficacy of the responses are dependent on the relative activity of these DC subsets, rendering DC crucial for the development of both naïve and memory immune responses. However, due to their critical role, DC also contribute to the immunopathological processes observed during acute influenza, such as that caused by the pathogenic H5N1 viruses. Therein, the role of different DC subsets in the induction of interferon type I, proinflammatory cytokine and chemokine responses is important for the outcome of interaction between the virus and host immune defences. The present review will present current knowledge on this area, relating to the importance of DC activity for the induction of efficacious humoral and cell-mediated immune responses. This will include the main viral elements associated with the triggering or inhibition of DC activation. Finally, the current knowledge on understanding how differences in various vaccines influence the manner of immune defence induction will be presented. http://www.mdpi.com/1999-4915/1/3/1022/ Tue, 24 Nov 2009 00:00:00 CET Viruses 2009-11-24 1 3 Review 1022 1034 1999-4915 Dendritic Cells in Innate and Adaptive Immune Responses against Influenza Virus 2009-11-24 doi: 10.3390/v1031022 Artur Summerfield Kenneth C. McCullough http://www.mdpi.com/1999-4915/1/3/1003/ The family Bunyaviridae contains more than 350 viruses that are distributed throughout the world. Most members of the family are transmitted by arthopods, and several cause disease in man, domesticated animals and crop plants. Despite being recognized as an emerging threat, details of the virulence mechanisms employed by bunyaviruses are scant. In this article we summarise the information currently available on how these viruses are able to establish infection when confronted with a powerful antiviral interferon system. http://www.mdpi.com/1999-4915/1/3/1003/ Mon, 23 Nov 2009 00:00:00 CET Viruses 2009-11-23 1 3 Review 1003 1021 1999-4915 Bunyaviruses and the Type I Interferon System 2009-11-23 doi: 10.3390/v1031003 Richard M. Elliott Friedemann Weber http://www.mdpi.com/1999-4915/1/3/979/ Immune responses against HSV-1 and HSV-2 are complex and involve a delicate interplay between innate signaling pathways and adaptive immune responses. The innate response to HSV involves the induction of type I IFN, whose role in protection against disease is well characterized in vitro and in vivo. Cell types such as NK cells and pDCs contribute to innate anti-HSV responses in vivo. Finally, the adaptive response includes both humoral and cellular components that play important roles in antiviral control and latency. This review summarizes the innate and adaptive effectors that contribute to susceptibility, immune control and pathogenesis of HSV, and highlights the delicate interplay between these two important arms of immunity. http://www.mdpi.com/1999-4915/1/3/979/ Wed, 18 Nov 2009 00:00:00 CET Viruses 2009-11-18 1 3 Review 979 1002 1999-4915 Innate and Adaptive Immune Responses to Herpes Simplex Virus 2009-11-18 doi: 10.3390/v1030979 Tracy Chew Kathryne E. Taylor Karen L. Mossman http://www.mdpi.com/1999-4915/1/3/939/ One of the most common viral infections in humans is caused by herpes simplex virus (HSV). It can easily be treated with nucleoside analogues (e.g., acyclovir), but resistant strains are on the rise. Naturally occurring antimicrobial peptides have been demonstrated to possess antiviral activity against HSV. New evidence has also indicated that these host defence peptides are able to selectively stimulate the innate immune system to fight of infections. This review will focus on the anti-HSV activity of such peptides (both natural and synthetic), describe their mode of action and their clinical potential. http://www.mdpi.com/1999-4915/1/3/939/ Wed, 18 Nov 2009 00:00:00 CET Viruses 2009-11-18 1 3 Review 939 964 1999-4915 Therapeutic Approaches Using Host Defence Peptides to Tackle Herpes Virus Infections 2009-11-18 doi: 10.3390/v1030939 Håvard Jenssen http://www.mdpi.com/1999-4915/1/3/965/ Apoptosis is triggered as an intrinsic defense against numerous viral infections. Almost every virus encodes apoptotic modulators, and the herpes simplex viruses (HSV) are no exception. During HSV infection, there is an intricate balance between pro- and anti-apoptotic factors that delays apoptotic death until the virus has replicated. Perturbations in the apoptotic balance can cause premature cell death and have the potential to dramatically alter the outcome of infection. Recently, certain cellular genes have been shown to regulate sensitivity to HSV-dependent apoptosis. This review summarizes current knowledge of the cellular genes that impact the apoptotic balance during HSV infection. http://www.mdpi.com/1999-4915/1/3/965/ Wed, 18 Nov 2009 00:00:00 CET Viruses 2009-11-18 1 3 Review 965 978 1999-4915 Cellular Players in the Herpes Simplex Virus Dependent Apoptosis Balancing Act 2009-11-18 doi: 10.3390/v1030965 Marie L. Nguyen John A. Blaho http://www.mdpi.com/1999-4915/1/3/920/ Groups of rhesus macaques that had previously been immunized with HIV-1 envelope (env) peptides and first generation adenovirus serotype 5 (FG-Ad5) vaccines expressing the same peptides were immunized intramuscularly three times with helperdependent adenovirus (HD-Ad) vaccines expressing only the HIV-1 envelope from JRFL. No gag, pol, or other SHIV genes were used for vaccination. One group of the FG-Ad5-immune animals was immunized three times with HD-Ad5 expressing env. One group was immunized by serotype-switching with HD-Ad6, HD-Ad1, and HD-Ad2 expressing env. Previous work demonstrated that serum antibody levels against env were significantly higher in the serotype-switched group than in the HD-Ad5 group. In this study, neutralizing antibody and T cell responses were compared between the groups before and after rectal challenge with CCR5-tropic SHIV-SF162P3. When serum samples were assayed for neutralizing antibodies, only weak activity was observed. T cell responses against env epitopes were higher in the serotype-switched group. When these animals were challenged rectally with SHIV-SF162P3, both the Ad5 and serotype-switch groups significantly reduced peak viral loads 2 to 10-fold 2 weeks after infection. Peak viral loads were significantly lower for the serotype-switched group as compared to the HD-Ad5-immunized group. Viral loads declined over 18 weeks after infection with some animals viremia reducing nearly 4 logs from the peak. These data demonstrate significant mucosal vaccine effects after immunization with only env antigens. These data also demonstrate HD-Ad vectors are a robust platform for vaccination. http://www.mdpi.com/1999-4915/1/3/920/ Tue, 10 Nov 2009 00:00:00 CET Viruses 2009-11-10 1 3 Article 920 938 1999-4915 Protection against Mucosal SHIV Challenge by Peptide and Helper-Dependent Adenovirus Vaccines 2009-11-10 doi: 10.3390/v1030920 Eric A. Weaver Pramod N. Nehete Bharti P. Nehete Stephanie J. Buchl Donna Palmer David C. Montefiori Philip Ng K. Jagannadha Sastry Michael A. Barry http://www.mdpi.com/1999-4915/1/3/895/ Defective interfering (DI) RNAs are subviral RNAs produced during multiplication of RNA viruses by the error-prone viral replicase. DI-RNAs are parasitic RNAs that are derived from and associated with the parent virus, taking advantage of viral-coded protein factors for their multiplication. Recent advances in the field of DI RNA biology has led to a greater understanding about generation and evolution of DI-RNAs as well as the mechanism of symptom attenuation. Moreover, DI-RNAs are versatile tools in the hands of virologists and are used as less complex surrogate templates to understand the biology of their helper viruses. The ease of their genetic manipulation has resulted in rapid discoveries on cis-acting RNA replication elements required for replication and recombination. DI-RNAs have been further exploited to discover host factors that modulate Tomato bushy stunt virus replication, as well as viral RNA recombination. This review discusses the current models on generation and evolution of DI-RNAs, the roles of viral and host factors in DI-RNA replication, and the mechanisms of disease attenuation. http://www.mdpi.com/1999-4915/1/3/895/ Tue, 10 Nov 2009 00:00:00 CET Viruses 2009-11-10 1 3 Review 895 919 1999-4915 Defective Interfering RNAs: Foes of Viruses and Friends of Virologists 2009-11-10 doi: 10.3390/v1030895 Kunj B. Pathak Peter D. Nagy http://www.mdpi.com/1999-4915/1/3/873/ There is ample evidence that synthesis of HIV-1 proviral DNA from the viral RNA genome during reverse transcription requires host factors. However, only a few cellular proteins have been described in detail that affect reverse transcription and interact with reverse transcriptase (RT). HIV-1 integrase is an RT binding protein and a number of IN-binding proteins including INI1, components of the Sin3a complex, and Gemin2 affect reverse transcription. In addition, recent studies implicate the cellular proteins HuR, AKAP149, and DNA topoisomerase I in reverse transcription through an interaction with RT. In this review we will consider interactions of reverse transcription complex with viral and cellular factors and how they affect the reverse transcription process. http://www.mdpi.com/1999-4915/1/3/873/ Tue, 10 Nov 2009 00:00:00 CET Viruses 2009-11-10 1 3 Review 873 894 1999-4915 Reverse Transcriptase and Cellular Factors: Regulators of HIV-1 Reverse Transcription 2009-11-10 doi: 10.3390/v1030873 Kylie Warren David Warrilow Luke Meredith David Harrich http://www.mdpi.com/1999-4915/1/3/852/ Hepatocarcinogenesis is a complex process that remains still partly understood. That might be explained by the multiplicity of etiologic factors, the genetic/epigenetic heterogeneity of tumors bulks and the ignorance of the liver cell types that give rise to tumorigenic cells that have stem cell-like properties. The DNA stress induced by hepatocyte turnover, inflammation and maybe early oncogenic pathway activation and sometimes viral factors, leads to DNA damage response which activates the key tumor suppressive checkpoints p53/p21Cip1 and p16INK4a/pRb responsible of cell cycle arrest and cellular senescence as reflected by the cirrhosis stage. Still obscure mechanisms, but maybe involving the Wnt signaling and Twist proteins, would allow pre-senescent hepatocytes to bypass senescence, acquire immortality by telomerase reactivation and get the last genetic/epigenetic hits necessary for cancerous transformation. Among some of the oncogenic pathways that might play key driving roles in hepatocarcinogenesis, c-myc and the Wnt/β-catenin signaling seem of particular interest. Finally, antiproliferative and apoptosis deficiencies involving TGF-β, Akt/PTEN, IGF2 pathways for instance are prerequisite for cancerous transformation. Of evidence, not only the transformed liver cell per se but the facilitating microenvironment is of fundamental importance for tumor bulk growth and metastasis. http://www.mdpi.com/1999-4915/1/3/852/ Mon, 09 Nov 2009 00:00:00 CET Viruses 2009-11-09 1 3 Review 852 872 1999-4915 Molecular Mechanisms Underlying Hepatocellular Carcinoma 2009-11-09 doi: 10.3390/v1030852 Philippe Merle Christian Trepo http://www.mdpi.com/1999-4915/1/3/832/ Like many animal viruses, those of the Rhabdoviridae family, are able to antagonize the type I interferon response and cause disease in mammalian hosts. Though these negative-stranded RNA viruses are very simple and code for as few as five proteins, they have been seen to completely abrogate the type I interferon response early in infection. In this review, we will discuss the viral organization and type I interferon evasion of rhabdoviruses, focusing on vesicular stomatitis virus (VSV) and rabies virus (RABV). Despite their structural similarities, VSV and RABV have completely different mechanisms by which they avert the host immune response. VSV relies on the matrix protein to interfere with host gene transcription and nuclear export of anti-viral mRNAs. Alternatively, RABV uses its phosphoprotein to interfere with IRF-3 phosphorylation and STAT1 signaling. Understanding the virus-cell interactions and viral proteins necessary to evade the immune response is important in developing effective vaccines and therapeutics for this viral family. http://www.mdpi.com/1999-4915/1/3/832/ Mon, 09 Nov 2009 00:00:00 CET Viruses 2009-11-09 1 3 Review 832 851 1999-4915 Interferon Response and Viral Evasion by Members of the Family Rhabdoviridae 2009-11-09 doi: 10.3390/v1030832 Elizabeth J. Faul Douglas S. Lyles Matthias J. Schnell http://www.mdpi.com/1999-4915/1/3/818/ Hepatitis delta virus (HDV) is a distant relative of plant viroids in the animal world. Similar to plant viroids, HDV replicates its circular RNA genome using a double rolling-circle mechanism. Nevertheless, the production of hepatitis delta antigen (HDAg), which is indispensible for HDV replication, is a unique feature distinct from plant viroids, which do not encode any protein. Here the HDV RNA replication cycle is reviewed, with emphasis on the function of HDAg in modulating RNA replication and the nature of the enzyme involved. http://www.mdpi.com/1999-4915/1/3/818/ Fri, 06 Nov 2009 00:00:00 CET Viruses 2009-11-06 1 3 Review 818 831 1999-4915 Hepatitis Delta Virus RNA Replication 2009-11-06 doi: 10.3390/v1030818 Chung-Hsin Tseng Michael M. C. Lai http://www.mdpi.com/1999-4915/1/3/802/ Several human monoclonal antibodies (hmAbs) and antibody fragments, including the best characterized in terms of structure-function b12 and Fab X5, exhibit relatively potent and broad HIV-1 neutralizing activity. However, the elicitation of b12 or b12-like antibodies in vivo by vaccine immunogens based on the HIV-1 envelope glycoprotein (Env) has not been successful. B12 is highly divergent from the closest corresponding germline antibody while X5 is less divergent. We have hypothesized that the relatively high degree of specific somatic hypermutations may preclude binding of the HIV-1 envelope glycoprotein (Env) to closest germline antibodies, and that identifying antibodies that are intermediates in the pathways to maturation could help design novel vaccine immunogens to guide the immune system for their enhanced elicitation. In support of this hypothesis we have previously found that a germline-like b12 (monovalent and bivalent scFv as an Fc fusion protein or IgG) lacks measurable binding to an Env as measured by ELISA with a sensitivity in the μM range [1]; here we present evidence confirming and expanding these findings for a panel of Envs. In contrast, a germline-like scFv X5 bound Env with high (nM) affinity. To begin to explore the maturation pathways of these antibodies we identified several possible b12 intermediate antibodies and tested their neutralizing activity. These intermediate antibodies neutralized only some HIV-1 isolates and with relatively weak potency. In contrast, germline-like scFv X5 neutralized a subset of the tested HIV-1 isolates with comparable efficiencies to that of the mature X5. These results could help explain the relatively high immunogenicity of the coreceptor binding site on gp120 and the abundance of CD4-induced (CD4i) antibodies in HIV-1-infected patients (X5 is a CD4i antibody) as well as the maturation pathway of X5. They also can help identify antigens that can bind specifically to b12 germline and intermediate antibodies that together with Envs could be used as a conceptually novel type of candidate vaccines. Such candidate vaccines based on two or more immunogens could help guiding the immune system through complex maturation pathways for elicitation of antibodies that are similar or identical to antibodies with known properties. http://www.mdpi.com/1999-4915/1/3/802/ Fri, 06 Nov 2009 00:00:00 CET Viruses 2009-11-06 1 3 Article 802 817 1999-4915 Maturation Pathways of Cross-Reactive HIV-1 Neutralizing Antibodies 2009-11-06 doi: 10.3390/v1030802 Xiaodong Xiao Weizao Chen Yang Feng Dimiter S. Dimitrov http://www.mdpi.com/1999-4915/1/3/780/ Since its initial description as an HIV-1 integrase (IN) interactor seven years ago, LEDGF has become one of the best-characterized host factors involved in viral replication. Results of intensive studies in several laboratories indicated that the protein serves as a targeting factor for the lentiviral DNA integration machinery, and accounts for the characteristic preference of Lentivirus to integrate within active transcription units. The IN-LEDGF interaction has been put forward as a promising target for antiretroviral drug development and as a potential tool to improve safety of lentiviral vectors for use in gene therapy. Additionally, as a natural ligand of lentiviral IN proteins, LEDGF has been successfully used in structural biology studies of retroviral DNA integration. This review focuses on the structural aspects of the IN-LEDGF interaction and their functional consequences. http://www.mdpi.com/1999-4915/1/3/780/ Fri, 06 Nov 2009 00:00:00 CET Viruses 2009-11-06 1 3 Review 780 801 1999-4915 The Interaction Between Lentiviral Integrase and LEDGF: Structural and Functional Insights 2009-11-06 doi: 10.3390/v1030780 Stephen Hare Peter Cherepanov http://www.mdpi.com/1999-4915/1/3/760/ The major immediate-early (IE) gene of human cytomegalovirus (CMV) is believed to have a decisive role in acute infection and its activity is an important indicator of viral reactivation from latency. Although a variety of gene products are expressed from this region, the 72-kDa IE1 and the 86-kDa IE2 nuclear phosphoproteins are the most abundant and important. Both proteins have long been recognized as promiscuous transcriptional regulators. More recently, a critical role of the IE1 and IE2 proteins in counteracting nonadaptive host cell defense mechanisms has been revealed. In this review we will briefly summarize the available literature on IE1- and IE2-dependent mechanisms contributing to CMV evasion from intrinsic and innate immune responses. http://www.mdpi.com/1999-4915/1/3/760/ Thu, 05 Nov 2009 00:00:00 CET Viruses 2009-11-05 1 3 Review 760 779 1999-4915 The Human Cytomegalovirus Major Immediate-Early Proteins as Antagonists of Intrinsic and Innate Antiviral Host Responses 2009-11-05 doi: 10.3390/v1030760 Christina Paulus Michael Nevels http://www.mdpi.com/1999-4915/1/3/737/ Herpes simplex virus (HSV), a human pathogenic virus, has evolved several strategies to evade the production and function of interferons (IFNs) and cytokines generated by the innate immune system to restrict the virus. Equilibrium exists between the virus and the immune response, and a shift in this delicate balance either restricts the virus or enhances virus spread and tissue damage. Therefore, understanding of the cytokine response generated after HSV infection and the underlying virus-cell interactions is essential to improve our understanding of viral pathogenesis. This review summarizes the current knowledge on induction and evasion of the innate immune response by HSV. http://www.mdpi.com/1999-4915/1/3/737/ Thu, 05 Nov 2009 00:00:00 CET Viruses 2009-11-05 1 3 Review 737 759 1999-4915 Activation and Evasion of Innate Antiviral Immunity by Herpes Simplex Virus 2009-11-05 doi: 10.3390/v1030737 Jesper Melchjorsen Sampsa Matikainen Søren R. Paludan http://www.mdpi.com/1999-4915/1/3/713/ Integration of a reverse transcribed DNA copy of the HIV viral genome into the host chromosome is essential for virus replication. This process is catalyzed by the virally encoded protein integrase. The catalytic activities, which involve DNA cutting and joining steps, have been recapitulated in vitro using recombinant integrase and synthetic DNA substrates. Biochemical and biophysical studies of these model reactions have been pivotal in advancing our understanding of mechanistic details for how IN interacts with viral and target DNAs, and are the focus of the present review. http://www.mdpi.com/1999-4915/1/3/713/ Thu, 05 Nov 2009 00:00:00 CET Viruses 2009-11-05 1 3 Review 713 736 1999-4915 HIV-1 Integrase-DNA Recognition Mechanisms 2009-11-05 doi: 10.3390/v1030713 Jacques J. Kessl Christopher J. McKee Jocelyn O. Eidahl Nikolozi Shkriabai Ari Katz Mamuka Kvaratskhelia http://www.mdpi.com/1999-4915/1/3/689/ Coronaviruses infect many species of animal including humans, causing acute and chronic diseases of many organ systems. Murine coronavirus, mouse hepatitis virus (MHV) infection of the mouse, provides animal models for the study of central nervous system disease, including encephalitis and demyelinating diseases such as Multiple Sclerosis and for hepatitis. While there are many studies of the adaptive immune response to MHV, there has until recently been scant information on the type I interferon (IFN) response to MHV. The relationship between MHV and the IFN-α/β response is paradoxical. While the type I IFN response is a crucial aspect of host defense against MHV in its natural host, there is little if any induction of IFN following infection of mouse fibroblast cell lines in vitro. Furthermore, MHV is relatively resistant to the antiviral effects of IFN-α/β in mouse fibroblast cell lines and in human 293T cells. MHV can, under some circumstances, compromise the antiviral effects of IFN signaling. The nucleocapsid protein as well as the nsp1 and nsp3 proteins of MHV has been reported to have IFN antagonist activity. However, in primary cell types such as plasmacytoid dendritic cells (pDC) and macrophages, IFN is induced by MHV infection and an antiviral state is established. Other primary cell types such as neurons, astrocytes and hepatocytes fail to produce IFN following infection and, in vivo, likely depend on IFN produced by pDCs and macrophages for protection from MHV. Thus MHV induction of IFN-α/β and the ability to induce an antiviral state in response to interferon is extremely cell type dependent. IFN induced protection from MHV pathogenesis likely requires the orchestrated activities of several cell types, however, the cell types involved in limiting MHV replication may be different in the liver and in the immune privileged CNS. http://www.mdpi.com/1999-4915/1/3/689/ Wed, 04 Nov 2009 00:00:00 CET Viruses 2009-11-04 1 3 Review 689 712 1999-4915 Murine Coronavirus Cell Type Dependent Interaction with the Type I Interferon Response 2009-11-04 doi: 10.3390/v1030689 Kristine M. Rose Susan R. Weiss http://www.mdpi.com/1999-4915/1/3/678/ The WU polyomavirus (WUPyV) is a novel member of the family Polyomaviridae recently detected in respiratory tract specimens by shotgun sequencing. Intriguingly, viral genome has been detected in 0.4% to 11.5% of respiratory tract specimens from children with respiratory disease. The levels of co-infection with established respiratory viruses were in the range between 30.8% and 91.7%. Moreover, some studies report detection of WUPyV in stool or serum. So far, WUPyV infections can not be distinguished from other viral infections by means of clinical symptoms. Respiratory tract disease like pneumonia or bronchitis is frequently observed in patients harbouring WUPyV. Detection of viremia suggests systemic infections. However, the available data do not prove WUPyV to be a human pathogen. Further investigations are necessary. http://www.mdpi.com/1999-4915/1/3/678/ Wed, 04 Nov 2009 00:00:00 CET Viruses 2009-11-04 1 3 Review 678 688 1999-4915 WU Polyomavirus (WUPyV): A Recently Detected Virus Causing Respiratory Disease? 2009-11-04 doi: 10.3390/v1030678 Michael Kleines Martin Häusler Alexander Krüttgen Simone Scheithauer http://www.mdpi.com/1999-4915/1/3/657/ Although polypurine tract (PPT)-primed initiation of plus-strand DNA synthesis in retroviruses and LTR-containing retrotransposons can be accurately duplicated, the molecular details underlying this concerted series of events remain largely unknown. Importantly, the PPT 3’ terminus must be accommodated by ribonuclease H (RNase H) and DNA polymerase catalytic centers situated at either terminus of the cognate reverse transcriptase (RT), and in the case of the HIV-1 enzyme, ~70Å apart. Communication between RT and the RNA/DNA hybrid therefore appears necessary to promote these events. The crystal structure of the HIV-1 RT/PPT complex, while informative, positions the RNase H active site several bases pairs from the PPT/U3 junction, and thus provides limited information on cleavage specificity. To fill the gap between biochemical and crystallographic approaches, we review a multidisciplinary approach combining chemical probing, mass spectrometry, NMR spectroscopy and single molecule spectroscopy. Our studies also indicate that nonnucleoside RT inhibitors affect enzyme orientation, suggesting initiation of plus-strand DNA synthesis as a potential therapeutic target. http://www.mdpi.com/1999-4915/1/3/657/ Wed, 04 Nov 2009 00:00:00 CET Viruses 2009-11-04 1 3 Review 657 677 1999-4915 Revisiting Plus-Strand DNA Synthesis in Retroviruses and Long Terminal Repeat Retrotransposons: Dynamics of Enzyme: Substrate Interactions 2009-11-04 doi: 10.3390/v1030657 Daniele Fabris John P. Marino Stuart F. J. Le Grice http://www.mdpi.com/1999-4915/1/3/647/ HCoV-NL63 is a recently identified respiratory virus. Its pathogenesis has not been fully unraveled because an animal model is currently lacking. Here we examined whether rhesus macaques encounter HCoV-NL63 infections during life, by examining the levels of antibodies to HCoV-NL63 in time. The animals were followed for 7 up till 19 years, and in three animals we observed a steep rise in antibodies during follow up, indicative of a natural infection with HCoV-NL63. http://www.mdpi.com/1999-4915/1/3/647/ Fri, 30 Oct 2009 00:00:00 CET Viruses 2009-10-30 1 3 Communication 647 656 1999-4915 Seroconversion to HCoV-NL63 in Rhesus Macaques 2009-10-30 doi: 10.3390/v1030647 Ronald Dijkman H. Lie Mulder Lynne Rumping Ilse Kraaijvanger Martin Deijs Maarten F. Jebbink Ernst J. Verschoor Lia van der Hoek http://www.mdpi.com/1999-4915/1/3/630/ Epidemiological studies have provided overwhelming evidence for a causal role of chronic HBV infection in the development of hepatocellular carcinoma (HCC), but the molecular mechanisms underlying virally-induced tumorigenesis remain largely debated. In the absence of a dominant oncogene encoded by the HBV genome, indirect roles have been proposed, including insertional activation of cellular oncogenes by HBV DNA integration, induction of genetic instability by viral integration or by the regulatory protein HBx, and long term effects of viral proteins in enhancing immune-mediated liver disease. In this chapter, we discuss different models of HBV-mediated liver cell transformation based on animal systems of hepadnavirus infection as well as functional studies in hepatocyte and hepatoma cell lines. These studies might help identifying the cellular effectors connecting HBV infection and liver cell transformation. http://www.mdpi.com/1999-4915/1/3/630/ Fri, 30 Oct 2009 00:00:00 CET Viruses 2009-10-30 1 3 Article 630 646 1999-4915 Liver Cell Transformation in Chronic HBV Infection 2009-10-30 doi: 10.3390/v1030630 Shirine Benhenda Delphine Cougot Christine Neuveut Marie Annick Buendia http://www.mdpi.com/1999-4915/1/3/594/ Since its emergence onto the gene therapy scene nearly 25 years ago, the replication-defective Herpes Simplex Virus Type-1 (HSV-1) amplicon has gained significance as a versatile gene transfer platform due to its extensive transgene capacity, widespread cellular tropism, minimal immunogenicity, and its amenability to genetic manipulation. Herein, we detail the recent advances made with respect to the design of the HSV amplicon, its numerous in vitro and in vivo applications, and the current impediments this virus-based gene transfer platform faces as it navigates a challenging path towards future clinical testing. http://www.mdpi.com/1999-4915/1/3/594/ Thu, 29 Oct 2009 00:00:00 CET Viruses 2009-10-29 1 3 Review 594 629 1999-4915 Herpes Virus Amplicon Vectors 2009-10-29 doi: 10.3390/v1030594 Suresh de Silva William J. Bowers http://www.mdpi.com/1999-4915/1/3/574/ Paramyxovirinae, a subfamily of Paramyxoviridae, are negative strand RNA viruses comprised of many important human and animal pathogens, which share a high degree of genetic and structural homology. The accessory proteins expressed from the P/V/C gene are major factors in the pathogenicity of the viruses, because of their ability to abrogate various facets of type I interferon (IFN) induction and signaling. Most of the paramyxoviruses exhibit a commonality in their ability to antagonize innate immunity by blocking IFN induction and the Jak/STAT pathway. However, the manner in which the accessory proteins inhibit the pathway differs among viruses. Similarly, there are variations in the capability of the viruses to counteract intracellular detectors (RNA helicases, mda-5 and RIG-I). Furthermore, a functional specificity in the antagonism of the IFN response has been reported, suggesting that specificity in the circumvention of innate immunity restricts viral host range. Available evidence indicates that paramyxoviruses employ specific strategies to antagonize the IFN response of their specific hosts, which is one of the major factors that determine viral pathogenicity and host range. http://www.mdpi.com/1999-4915/1/3/574/ Wed, 28 Oct 2009 00:00:00 CET Viruses 2009-10-28 1 3 Review 574 593 1999-4915 Antagonism of Innate Immunity by Paramyxovirus Accessory Proteins 2009-10-28 doi: 10.3390/v1030574 Raychel Chambers Toru Takimoto http://www.mdpi.com/1999-4915/1/3/545/ Type-I interferons (IFN-I) play an important role in the innate immune response to several retroviruses. They seem to be effective in controlling the in vivo infection, though many of the clinical signs of retroviral infection may be due to their continual presence which over-stimulates the immune system and activates apoptosis. IFN-I not only affect the immune system, but also operate directly on virus replication. Most data suggest that the in vitro treatment with IFN-I of retrovirus infected cells inhibits the final stages of virogenesis, avoiding the correct assembly of viral particles and their budding, even though the mechanism is not well understood. However, in some retroviruses IFN-I may also act at a previous stage as some retroviral LTRs posses sequences homologous to the IFNstimulated response element (ISRE). When stimulated, ISREs control viral transcription. HIV-1 displays several mechanisms for evading IFN-I, such as through Tat and Nef. Besides IFN-α and IFN-β, some other type I IFN, such as IFN-τ and IFN-ω, have potent antiviral activity and are promising treatment drugs. http://www.mdpi.com/1999-4915/1/3/545/ Tue, 27 Oct 2009 00:00:00 CET Viruses 2009-10-27 1 3 Review 545 573 1999-4915 Effect of Type-I Interferon on Retroviruses 2009-10-27 doi: 10.3390/v1030545 Esperanza Gómez-Lucía Victorio M. Collado Guadalupe Miró Ana Doménech http://www.mdpi.com/1999-4915/1/3/523/ The interferon-induced double-stranded (ds)RNA-dependent protein kinase (PKR) limits viral replication by an eIF2α-mediated block of translation. Although many negative-strand RNA viruses activate PKR, the responsible RNAs have long remained elusive, as dsRNA, the canonical activator of PKR, has not been detected in cells infected with such viruses. In this review we focus on the activating RNA molecules of different virus families, in particular the negative-strand RNA viruses. We discuss the recently identified non-canonical activators 5’-triphosphate RNA and the vRNP of influenza virus and give an update on strategies of selected RNA and DNA viruses to prevent activation of PKR. http://www.mdpi.com/1999-4915/1/3/523/ Tue, 27 Oct 2009 00:00:00 CET Viruses 2009-10-27 1 3 Review 523 544 1999-4915 Activation of the Antiviral Kinase PKR and Viral Countermeasures 2009-10-27 doi: 10.3390/v1030523 Bianca Dauber Thorsten Wolff http://www.mdpi.com/1999-4915/1/3/510/ A virulent recombinant HSV lacking the diploid γ134.5 gene (Δγ134.5) have been investigated over the last two decades both for anti-tumor therapy and as vaccine vectors. The first generation vectors, while safe, are incapable of sustained replication in the majority of treated patients. An interferon inducible host antiviral kinase, protein kinase R (PKR), limits late viral protein synthesis and replication of Δγ134.5 viruses. This review describes the development of new Δγ134.5 vectors, through serial passage selection and direct viral genome engineering, which demonstrate selective PKR evasion in targeted cells and improved viral replication without restoring neurovirulence. http://www.mdpi.com/1999-4915/1/3/510/ Thu, 22 Oct 2009 00:00:00 CEST Viruses 2009-10-22 1 3 Review 510 522 1999-4915 Spontaneous and Engineered Compensatory HSV Mutants that Counteract the Host Antiviral PKR Response 2009-10-22 doi: 10.3390/v1030510 Amish C. Shah Jacqueline N. Parker Masako Shimamura Kevin A. Cassady http://www.mdpi.com/1999-4915/1/3/484/ One year of interferon therapy inhibits HBV replication in one third of the patients whereas long-term administration of oral nucleos(t)ide analogues is efficient in most of them, as long as early treatment adaptation in patients with partial virological response and resistance is provided. Following the demonstration of a more potent antiviral effect in terms of sustained virological response (SVR) rates, Pegylated-IFN coupled with Ribavirin has become the standard treatment for chronic hepatitis C, with nearly 65% of all treated patients achieving a SVR. Long-term suppression of HBV and eradication of HCV would halt the progression of chronic hepatitis to cirrhosis, hepatocellular carcinoma and liver decompensation. http://www.mdpi.com/1999-4915/1/3/484/ Thu, 22 Oct 2009 00:00:00 CEST Viruses 2009-10-22 1 3 Review 484 509 1999-4915 HBV and HCV Therapy 2009-10-22 doi: 10.3390/v1030484 Pietro Lampertico Alessio Aghemo Mauro Viganò Massimo Colombo http://www.mdpi.com/1999-4915/1/3/460/ Host resistance to infection depends on the efficiency with which innate immune responses keep the infectious agent in check. Innate immunity encompasses components with sensing, signaling and effector properties. These elements with nonredundant functions are encoded by a set of host genes, the resistome. Here, we review our findings concerning the resistome. We have screened randomly mutagenized mice for susceptibility to a natural opportunistic pathogen, the mouse cytomegalovirus. We found that some genes with initially no obvious functions in innate immunity may be critical for host survival to infections, falling into a newly defined category of genes of the resistome. http://www.mdpi.com/1999-4915/1/3/460/ Tue, 20 Oct 2009 00:00:00 CEST Viruses 2009-10-20 1 3 Review 460 483 1999-4915 Identification of Mouse Cytomegalovirus Resistance Loci by ENU Mutagenesis 2009-10-20 doi: 10.3390/v1030460 Karine Crozat Philippe Georgel http://www.mdpi.com/1999-4915/1/3/441/ Assays to simultaneously detect multiple potential agents of bioterrorism are limited. Two multiplex PCR and RT-PCR enzyme hybridization assays (mPCR-EHA, mRT-PCR-EHA) were developed to simultaneously detect many of the CDC category “A” bioterrorism agents. The “Bio T” DNA assay was developed to detect: Variola major (VM), Bacillus anthracis (BA), Yersinia pestis (YP), Francisella tularensis (FT) and Varicella zoster virus (VZV). The “Bio T” RNA assay (mRT-PCR-EHA) was developed to detect: Ebola virus (Ebola), Lassa fever virus (Lassa), Rift Valley fever (RVF), Hantavirus Sin Nombre species (HSN) and dengue virus (serotypes 1-4). Sensitivity and specificity of the 2 assays were tested by using genomic DNA, recombinant plasmid positive controls, RNA transcripts controls, surrogate (spiked) clinical samples and common respiratory pathogens. The analytical sensitivity (limit of detection (LOD)) of the DNA asssay for genomic DNA was 1×100~1×102 copies/mL for BA, FT and YP. The LOD for VZV whole organism was 1×10-2 TCID50/mL. The LOD for recombinant controls ranged from 1×102~1×103copies/mL for BA, FT, YP and VM. The RNA assay demonstrated LOD for RNA transcript controls of 1×104~1×106 copies/mL without extraction and 1×105~1×106 copies/mL with extraction for Ebola, RVF, Lassa and HSN. The LOD for dengue whole organisms was ~1×10-4 dilution for dengue 1 and 2, 1×104 LD50/mL and 1×102 LD50/mL for dengue 3 and 4. The LOD without extraction for recombinant plasmid DNA controls was ~1×103 copies/mL (1.5 input copies/reaction) for Ebola, RVF, Lassa and HSN. No cross-reactivity of primers and probes used in both assays was detected with common respiratory pathogens or between targeted analytes. Clinical sensitivity was estimated using 264 surrogate clinical samples tested with the BioT DNA assay and 549 samples tested with the BioT RNA assay. The clinical specificity is 99.6% and 99.8% for BioT DNA assay and BioT RNA assay, respectively. The surrogate sensitivities of these two assays were 100% (95%CI 83-100) for FT, BA (pX02), YP, VM, VZV, dengue 2,3,4 and 95% (95%CI 75-100) for BA (pX01) and dengue 1 using spiked clinical specimens. The specificity of both BioT multiplex assays on spiked specimens was 100% (95% CI 99-100). Compared to other available assays (culture, serology, PCR, etc.) both the BioT DNA mPCR-EHA and BioT RNA mRT-PCR-EHA are rapid, sensitive and specific assays for detecting many category “A” Bioterrorism agents using a standard thermocycler. http://www.mdpi.com/1999-4915/1/3/441/ Tue, 20 Oct 2009 00:00:00 CEST Viruses 2009-10-20 1 3 Article 441 459 1999-4915 Simultaneous Detection of CDC Category "A" DNA and RNA Bioterrorism Agents by Use of Multiplex PCR & RT-PCR Enzyme Hybridization Assays 2009-10-20 doi: 10.3390/v1030441 Jie He Andrea J. Kraft Jiang Fan Meredith Van Dyke Lihua Wang Michael E. Bose Marilyn Khanna Jacob A. Metallo Kelly J. Henrickson http://www.mdpi.com/1999-4915/1/3/420/ Investigating and assigning gene functions of herpesviruses is a process, which profits from consistent technical innovation. Cloning of bacterial artificial chromosomes encoding herpesvirus genomes permits nearly unlimited possibilities in the construction of genetically modified viruses. Targeted or randomized screening approaches allow rapid identification of essential viral proteins. Nevertheless, mapping of essential genes reveals only limited insight into function. The usage of dominant-negative (DN) proteins has been the tool of choice to dissect functions of proteins during the viral life cycle. DN proteins also facilitate the analysis of host-virus interactions. Finally, DNs serve as starting-point for design of new antiviral strategies. http://www.mdpi.com/1999-4915/1/3/420/ Mon, 19 Oct 2009 00:00:00 CEST Viruses 2009-10-19 1 3 Review 420 440 1999-4915 Dominant-Negative Proteins in Herpesviruses – From Assigning Gene Function to Intracellular Immunization 2009-10-19 doi: 10.3390/v1030420 Hermine Mühlbach Christian A. Mohr Zsolt Ruzsics Ulrich H. Koszinowski http://www.mdpi.com/1999-4915/1/3/383/ Type-I interferons (IFN-I) are cytokines essential for vertebrate antiviral defense, including against herpesviruses. IFN-I have potent direct antiviral activities and also mediate a multiplicity of immunoregulatory functions, which can either promote or dampen antiviral adaptive immune responses. Plasmacytoid dendritic cells (pDCs) are the professional producers of IFN-I in response to many viruses, including all of the herpesviruses tested. There is strong evidence that pDCs could play a major role in the initial orchestration of both innate and adaptive antiviral immune responses. Depending on their activation pattern, pDC responses may be either protective or detrimental to the host. Here, we summarize and discuss current knowledge regarding pDC implication in the physiopathology of mouse and human herpesvirus infections, and we discuss how pDC functions could be manipulated in immunotherapeutic settings to promote health over disease. http://www.mdpi.com/1999-4915/1/3/383/ Wed, 14 Oct 2009 00:00:00 CEST Viruses 2009-10-14 1 3 Review 383 419 1999-4915 Plasmacytoid Dendritic Cells and the Control of Herpesvirus Infections 2009-10-14 doi: 10.3390/v1030383 Thomas Baranek Nicolas Zucchini Marc Dalod http://www.mdpi.com/1999-4915/1/3/362/ During the co-evolution of cytomegalovirus (CMV) and natural killer (NK) cells, each has evolved specific tactics in an attempt to prevail. CMV has evolved multiple immune evasion mechanisms to avoid detection by NK cells and other immune cells, leading to chronic infection. Meanwhile, the host has evolved virus-specific receptors to counter these evasion strategies. The natural selection of viral genes and host receptors allows us to observe a unique molecular example of "survival of the fittest", as virus and immune cells try to out-maneuver one another or for the virus to achieve détente for optimal dissemination in the population. http://www.mdpi.com/1999-4915/1/3/362/ Tue, 13 Oct 2009 00:00:00 CEST Viruses 2009-10-13 1 3 Review 362 382 1999-4915 The Natural Selection of Herpesviruses and Virus-Specific NK Cell Receptors 2009-10-13 doi: 10.3390/v1030362 Joseph C. Sun Lewis L. Lanier http://www.mdpi.com/1999-4915/1/3/335/ Highly Pathogenic Avian Influenza (HPAI) H5N1 virus is an ongoing public health and socio-economic challenge, particularly in South East Asia. H5N1 is now endemic in poultry in many countries, and represents a major pandemic threat. Here, we describe the evolution of H5N1 virus in South East Asia, the reassortment events leading to high genetic diversity in the region, and factors responsible for virus spread. The virus has evolved with genetic variations affecting virulence, drug-resistance, and adaptation to new host species. The constant surveillance of these changes is of primary importance in the global efforts of the scientific community. http://www.mdpi.com/1999-4915/1/3/335/ Tue, 06 Oct 2009 00:00:00 CEST Viruses 2009-10-06 1 3 Review 335 361 1999-4915 A(H5N1) Virus Evolution in South East Asia 2009-10-06 doi: 10.3390/v1030335 Ramona Alikiiteaga Gutiérrez Monica Jane Naughtin Srey Viseth Horm Sorn San Philippe Buchy http://www.mdpi.com/1999-4915/1/2/317/ Viroids, due to their small size and lack of protein-coding capacity, must rely essentially on their hosts for replication. Intriguingly, viroids have evolved the ability to replicate in two cellular organella, the nucleus (family Pospiviroidae) and the chloroplast (family Avsunviroidae). Viroid replication proceeds through an RNA-based rolling-circle mechanism with three steps that, with some variations, operate in both polarity strands: i) synthesis of longer-than-unit strands catalyzed by either the nuclear RNA polymerase II or a nuclear-encoded chloroplastic RNA polymerase, in both instances redirected to transcribe RNA templates, ii) cleavage to unit-length, which in the family Avsunviroidae is mediated by hammerhead ribozymes embedded in both polarity strands, while in the family Pospiviroidae the oligomeric RNAs provide the proper conformation but not the catalytic activity, and iii) circularization. The host RNA polymerases, most likely assisted by additional host proteins, start transcription from specific sites, thus implying the existence of viroid promoters. Cleavage and ligation in the family Pospiviroidae is probably catalyzed by an RNase III-like enzyme and an RNA ligase able to circularize the resulting 5’ and 3’ termini. Whether a chloroplastic RNA ligase mediates circularization in the family Avsunviroidae, or this reaction is autocatalytic, remains an open issue. http://www.mdpi.com/1999-4915/1/2/317/ Mon, 14 Sep 2009 00:00:00 CEST Viruses 2009-09-14 1 2 Review 317 334 1999-4915 Viroid Replication: Rolling-Circles, Enzymes and Ribozymes 2009-09-14 doi: 10.3390/v1020317 Ricardo Flores María-Eugenia Gas Diego Molina-Serrano María-Ángeles Nohales Alberto Carbonell Selma Gago Marcos De la Peña José-Antonio Daròs http://www.mdpi.com/1999-4915/1/2/298/ Despite the non-coding nature of their small RNA genomes, the visible symptoms of viroid infection resemble those associated with many plant virus diseases. Recent evidence indicates that viroid-derived small RNAs acting through host RNA silencing pathways play a key role in viroid pathogenicity. Host responses to viroid infection are complex, involving signaling cascades containing host-encoded protein kinases and crosstalk between hormonal and defense-signaling pathways. Studies of viroid-host interaction in the context of entire biochemical or developmental pathways are just beginning, and many working hypotheses have yet to be critically tested. http://www.mdpi.com/1999-4915/1/2/298/ Thu, 10 Sep 2009 00:00:00 CEST Viruses 2009-09-10 1 2 Review 298 316 1999-4915 Viroid Pathogenicity: One Process, Many Faces 2009-09-10 doi: 10.3390/v1020298 Robert A. Owens Rosemarie W. Hammond http://www.mdpi.com/1999-4915/1/2/276/ The precise role of adaptive immune responses in the clinical outcome of HCV infection is still only partially defined. Recent studies suggest that viral-host cell interactions during the acute phase of infection are essential for viral clearance or progression into chronic HCV infection. This review focuses on different aspects of the adaptive immune responses as determinants of the different outcomes of HCV infection, clearance or persistent infection, and outlines current concepts of HCV evasion strategies. Unravelling these important mechanisms of virus-host interaction will contribute to the development of novel strategies to prevent and control HCV infection. http://www.mdpi.com/1999-4915/1/2/276/ Tue, 08 Sep 2009 00:00:00 CEST Viruses 2009-09-08 1 2 Review 276 297 1999-4915 Adaptive Immunity to Hepatitis C Virus 2009-09-08 doi: 10.3390/v1020276 Mirjam B. Zeisel Samira Fafi-Kremer Eric Robinet François Habersetzer Thomas f. Baumert Françoise Stoll-Keller http://www.mdpi.com/1999-4915/1/2/255/ Bovine herpesvirus 1 (BoHV-1) infected cell protein 0 (bICP0) is an important transcriptional regulatory protein that stimulates productive infection. In transient transfection assays, bICP0 also inhibits interferon dependent transcription. bICP0 can induce degradation of interferon stimulatory factor 3 (IRF3), a cellular transcription factor that is crucial for activating beta interferon (IFN-β) promoter activity. Recent studies also concluded that interactions between bICP0 and IRF7 inhibit trans-activation of IFN-β promoter activity. The C3HC4 zinc RING (really important new gene) finger located near the amino terminus of bICP0 is important for all known functions of bICP0. A recombinant virus that contains a single amino acid change in a well conserved cysteine residue of the C3HC4 zinc RING finger of bICP0 grows poorly in cultured cells, and does not reactivate from latency in cattle confirming that the C3HC4 zinc RING finger is crucial for viral growth and pathogenesis. A bICP0 deletion mutant does not induce plaques in permissive cells, but induces autophagy in a cell type dependent manner. In summary, the ability of bICP0 to stimulate productive infection, and repress IFN dependent transcription plays a crucial role in the BoHV-1 infection cycle. http://www.mdpi.com/1999-4915/1/2/255/ Mon, 07 Sep 2009 00:00:00 CEST Viruses 2009-09-07 1 2 Review 255 275 1999-4915 Regulation of Innate Immune Responses by Bovine Herpesvirus 1 and Infected Cell Protein 0 (bICP0) 2009-09-07 doi: 10.3390/v1020255 Clinton Jones http://www.mdpi.com/1999-4915/1/2/241/ We suggest that viroids are trapped into adaptive peaks as the result of adaptive constraints. The first one is imposed by the necessity to fold into packed structures to escape from RNA silencing. This creates antagonistic epistases, which make future adaptive trajectories contingent upon the first mutation and slow down the rate of adaptation. This second constraint can only be surpassed by increasing genetic redundancy or by recombination. Eigen’s paradox imposes a limit to the increase in genome complexity in the absence of mechanisms reducing mutation rate. Therefore, recombination appears as the only possible route to evolutionary innovation in viroids. http://www.mdpi.com/1999-4915/1/2/241/ Wed, 02 Sep 2009 00:00:00 CEST Viruses 2009-09-02 1 2 Review 241 254 1999-4915 Evolutionary Constraints to Viroid Evolution 2009-09-02 doi: 10.3390/v1020241 Santiago F. Elena Gustavo Gómez José-Antonio Daròs http://www.mdpi.com/1999-4915/1/2/222/ In the 1970s and 1980s it became increasingly clear that blood transfusions could induce a form of chronic hepatitis that could not be ascribed to any of the viruses known to cause liver inflammation. In 1989, the hepatitis C virus (HCV) was discovered and found to be the major causative agent of these infections. Because of its narrow ropism, the in vivo study of this virus was, especially in the early days, limited to the chimpanzee. In the past decade, several alternative animal models have been created. In this review we review these novel animal models and their contribution to our current understanding of the biology of HCV. http://www.mdpi.com/1999-4915/1/2/222/ Wed, 02 Sep 2009 00:00:00 CEST Viruses 2009-09-02 1 2 Review 222 240 1999-4915 HCV Animal Models: A Journey of More than 30 Years 2009-09-02 doi: 10.3390/v1020222 Philip Meuleman Geert Leroux-Roels http://www.mdpi.com/1999-4915/1/2/210/ Viroids are noncoding RNAs that infect plants. In order to establish systemic infection, these RNAs must traffic from an initially infected host cell into neighboring cells and ultimately throughout a whole plant. Recent studies have identified structural motifs in a viroid that are required for trafficking, enabling further studies on the mechanisms of their function. Some cellular proteins interact with viroids in vivo and may play a role in viroid trafficking, which can now be directly tested by using a virus-induced gene silencing system that functions efficiently in plant species from which these factors were identified. This review discusses these recent advances, unanswered questions and the use of viroid infection as an highly productive model to elucidate mechanisms of RNA trafficking that is of broad biological significance. http://www.mdpi.com/1999-4915/1/2/210/ Tue, 01 Sep 2009 00:00:00 CEST Viruses 2009-09-01 1 2 Review 210 221 1999-4915 Viroid Intercellular Trafficking: RNA Motifs, Cellular Factors and Broad Impacts 2009-09-01 doi: 10.3390/v1020210 Ryuta Takeda Biao Ding http://www.mdpi.com/1999-4915/1/2/185/ Hepatitis B virus (HBV) is a major cause of liver disease. HBV primarily infects hepatocytes by a still poorly understood mechanism. After an endocytotic process, the nucleocapsids are released into the cytoplasm and the relaxed circular rcDNA genome is transported towards the nucleus where it is converted into covalently closed circular cccDNA. Replication of the viral genome occurs via an RNA pregenome (pgRNA) that binds to HBV polymerase (P). P initiates pgRNA encapsidation and reverse transcription inside the capsid. Matured, rcDNA containing nucleocapsids can re-deliver the RC-DNA to the nucleus, or be secreted via interaction with the envelope proteins as progeny virions. http://www.mdpi.com/1999-4915/1/2/185/ Tue, 01 Sep 2009 00:00:00 CEST Viruses 2009-09-01 1 2 Review 185 209 1999-4915 HBV Life Cycle: Entry and Morphogenesis 2009-09-01 doi: 10.3390/v1020185 Stephanie Schädler Eberhard Hildt http://www.mdpi.com/1999-4915/1/2/166/ The internal FECV→FIPV mutation theory and three of its correlates were tested in four sibs/half-sib kittens, a healthy contact cat, and in four unrelated cats that died of FIP at geographically disparate regions. Coronavirus from feces and extraintestinal FIP lesions from the same cat were always >99% related in accessory and structural gene sequences. SNPs and deletions causing a truncation of the 3c gene product were found in almost all isolates from the diseased tissues of the eight cats suffering from FIP, whereas most, but not all fecal isolates from these same cats had intact 3c genes. Other accessory and structural genes appeared normal in both fecal and lesional viruses. Deliterious mutations in the 3c gene were unique to each cat, indicating that they did not originate in one cat and were subsequently passed horizontally to the others. Compartmentalization of the parental and mutant forms was not absolute; virus of lesional type was sometimes found in feces of affected cats and virus identical to fecal type was occasionally identified in diseased tissues. Although 3c gene mutants in this study were not horizontally transmitted, the parental fecal virus was readily transmitted by contact from a cat that died of FIP to its housemate. There was a high rate of mutability in all structural and accessory genes both within and between cats, leading to minor genetic variants. More than one variant could be identified in both diseased tissues and feces of the same cat. Laboratory cats inoculated with a mixture of two closely related variants from the same FIP cat developed disease from one or the other variant, but not both. Significant genetic drift existed between isolates from geographically distinct regions of the Western US. http://www.mdpi.com/1999-4915/1/2/166/ Wed, 26 Aug 2009 00:00:00 CEST Viruses 2009-08-26 1 2 Article 166 184 1999-4915 Significance of Coronavirus Mutants in Feces and Diseased Tissues of Cats Suffering from Feline Infectious Peritonitis 2009-08-26 doi: 10.3390/v1020166 Niels C. Pedersen Hongwei Liu Kimberly A. Dodd Patricia A. Pesavento http://www.mdpi.com/1999-4915/1/2/144/ Studies in patients and chimpanzees that spontaneously clear Hepatitis C Virus (HCV) have demonstrated that natural immunity to the virus is induced during primary infections and that this immunity can be cross protective. These discoveries led to optimism regarding prophylactic HCV vaccines and a number of studies in the chimpanzee model have been performed, all of which resulted in modified infections after challenge but did not always prevent persistence of the virus. Therapeutic vaccine strategies have also been pursued in an effort to reduce the costs and side effects associated with anti-viral drug treatment. This review summarizes the studies performed thus far in both patients and chimpanzees for prophylactic and therapeutic vaccination, assesses the progress made and future perspectives. http://www.mdpi.com/1999-4915/1/2/144/ Wed, 12 Aug 2009 00:00:00 CEST Viruses 2009-08-12 1 2 Review 144 165 1999-4915 Prophylactic and Therapeutic Vaccination against Hepatitis C Virus (HCV): Developments and Future Perspectives 2009-08-12 doi: 10.3390/v1020144 Marian E. Major http://www.mdpi.com/1999-4915/1/2/126/ The persistent infection with hepatitis C virus is a major cause of chronic liver disease worldwide. However, the morbidity associated with hepatitis C virus widely varies and depends on several host-related cofactors, such as age, gender, alcohol consumption, body weight, and co-infections. The objective of this review is to discuss three of these cofactors: steatosis, insulin resistance and oxidative stress. Although all may occur independently of HCV, a direct role of HCV infection in their pathogenesis has been reported. This review summarizes the current understanding and potential molecular pathways by which HCV contributes to their development. http://www.mdpi.com/1999-4915/1/2/126/ Tue, 11 Aug 2009 00:00:00 CEST Viruses 2009-08-11 1 2 Review 126 143 1999-4915 Hepatitis C Virus Infection: Molecular Pathways to Steatosis, Insulin Resistance and Oxidative Stress 2009-08-11 doi: 10.3390/v1020126 Sophie Clément Stéphanie Pascarella Francesco Negro http://www.mdpi.com/1999-4915/1/2/104/ The natural history of hepatitis C virus (HCV) infection is determined by a complex interplay between host genetic, immunological and viral factors. This review highlights genes involved in innate and adaptive immune responses associated with different outcomes of HCV infection. For example, an association of HCV clearance with certain HLA alleles has been demonstrated. The mechanisms responsible for these associations have been linked to specific T cell responses for some particular alleles (e.g., HLA-B27). Genetic associations involved in T cell regulation and function further underline the role of the adaptive immune response in the natural history of HCV infection. In addition, some genes involved in innate NK cell responses demonstrate the complex interplay between components of the immune system necessary for a successful host response to HCV infection. http://www.mdpi.com/1999-4915/1/2/104/ Wed, 05 Aug 2009 00:00:00 CEST Viruses 2009-08-05 1 2 Review 104 125 1999-4915 Role of Host Genetic Factors in the Outcome of Hepatitis C Virus Infection 2009-08-05 doi: 10.3390/v1020104 Bertram Bengsch Robert Thimme Hubert E. Blum http://www.mdpi.com/1999-4915/1/2/91/ The successful control of HBV infection requires an efficient expansion of distinct elements of the adaptive immune system (B cells, helper and cytotoxic T cells) that, due to the hepatotropic nature of HBV, need to operate in the liver parenchyma. In this respect, we will discuss broad features of HBV immunity in patients with resolved or chronic HBV infection and analyze how the liver environment can directly modulate HBV-immunity. http://www.mdpi.com/1999-4915/1/2/91/ Mon, 27 Jul 2009 00:00:00 CEST Viruses 2009-07-27 1 2 Review 91 103 1999-4915 HBV-Specific Adaptive Immunity 2009-07-27 doi: 10.3390/v1020091 Antonio Bertoletti Anthony T. Tan Adam J. Gehring http://www.mdpi.com/1999-4915/1/2/84/ The sequence-independent single primer amplification (SISPA) method was performed to identify a virus in 17 clinical respiratory samples producing uncharacterized cytopathic effects in LLC-MK2 cells. Sequence analysis of 600-1600 bp amplicons allowed the identification of six viruses (one influenza C, two parechovirus-3 and three cardioviruses). Genomic sequences of the cardioviruses showed similarities with those of the recently-described Saffold virus strain although significant variation was present in the viral surface EF and CD loops. These results demonstrate the usefulness of SISPA for identifying emerging viruses and also known viruses not easily identified by standard virological methods. http://www.mdpi.com/1999-4915/1/2/84/ Fri, 17 Jul 2009 00:00:00 CEST Viruses 2009-07-17 1 2 Article 84 90 1999-4915 Molecular Characterization of Viruses from Clinical Respiratory Samples Producing Unidentified Cytopathic Effects in Cell Culture 2009-07-17 doi: 10.3390/v1020084 Yacine Abed Guy Boivin