Large Number Of Viruses Research Articles

Role of RNA chaperones in virus replication

RNA molecules are functionally diverse in part due to their extreme structural flexibility that allows rapid regulation by refolding. RNA folding could be a difficult process as often molecules adopt a spatial conformation that is very stable but not biologically functional, named a kinetic trap. RNA chaperones are non-specific RNA binding proteins that help RNA folding by resolving misfolded structures or preventing their formation. There is a large number of viruses whose genome is RNA that allows some evolutionary advantages, such as rapid genome mutation. On the other hand, regions of the viral RNA genomes can adopt different structural conformations, some of them lacking functional relevance and acting as misfolded intermediates. In fact, for an efficient replication, they often require RNA chaperone activities. There is a growing list of RNA chaperones encoded by viruses involved in different steps of the viral cycle. Also, cellular RNA chaperones have been involved in replication of RNA viruses. This review briefly describes RNA chaperone activities and is focused in the roles that viral or cellular nucleic acid chaperones have in RNA virus replication, particularly in those viruses that require discontinuous RNA synthesis.

Distribution of Human Polyoma- viruses, Adenoviruses, and Hepatitis E Virus in the Environment and in a Drinking-Water Treatment Plant

Large numbers of viruses are excreted in human feces and urine, which even at low concentrations may cause illness when ingested. Some of these viruses have not been traditionally monitored in terms of waterborne diseases and are considered emergent viruses, such as hepatitis E virus (HEV) and JC and BK polyomavirus (JCPyV and BKPyV). The high prevalence of human adenoviruses (HAdV) and polyomaviruses, which both show DNA genomes, in sewage from widely divergent areas has suggested the relevance of evaluating these viruses as possible indicators of viral contamination. The concentration of these viruses was analyzed in sewage and river water and after treatment in a drinking-water treatment plant including chlorination, flocculation, ozonation, and granulate active carbon (GAC) filtration. Samples of GAC-filtered water were collected before a second chlorination treatment. The river used as a source of fresh water presented an average concentration of 2.6 x 10(1) JCPyV and 4 x 10(2) HAdV GC (genome copies)/L. A removal of 2 logarithms (99%) of HAdV and JCPyV was observed in the drinking-water treatment plant. All the GAC-filtered water samples studied contained HAdV, with a mean value of 4.3 HAdV GC/L. HEV strains belonging to genotype 3 were frequently detected in low concentrations in urban sewage and in biosolids or sewage containing swine feces but not in the river water samples studied. The detection of viruses by molecular techniques is useful for genetically describe emergent viruses in community wastewaters and water supplies. Quantification of JCPyV and HAdV using quantitative real-time PCR (QPCR) may be useful for evaluating virus removal efficiency in water treatment plants and as an index of the virological quality of water and of the potential presence of human viruses.

Inhibition of PKR by RNA and DNA viruses

Interferons were the first of the anti-viral innate immune modulators to be characterized, initially characterized solely as anti-viral proteins [reviewed in Le Page, C., Genin, P., Baines, M.G., Hiscott, J., 2000. Inteferon activation and innate immunity. Rev. Immunogenet. 2, 374–386]. As we have progressed in our understanding of the interferons they have taken a more central role in our understanding of innate immunity and its interplay with the adaptive immune response. One of the key players in function of interferon is the interferon-inducible enzyme, protein kinase (PKR, activatable by RNA). The key role played by PKR in the innate response to virus infection is emphasized by the large number of viruses, DNA viruses as well as RNA viruses, whose hosts range from insects to humans, that code for PKR inhibitors. In this review we will first describe activation of PKR and then describe the myriad of ways that viruses inhibit function of PKR.

Evaluation of TV cell line viral susceptibility using conventional cell culture techniques

Abstract Despite the fact that a lot of methods have been developed for rapid virus detection, classic cell culture is still “the golden standard”. The range of viruses that can be isolated and cultured in cell line systems is often limited by the susceptibility of cells to support viral replication. Since the primary cell culture, the best cellular system available to support replication of a large number of viruses, is very expensive and diffcult to obtain, cell lines, which are easier to manipulate, are commonly used for virus growth and isolation. In two previous papers we described the TV cell line initiated by our team from a laryngeal tumor, which harbors human papillomavirus (HPV) gene sequences. In this paper we analyze its capacity to support virus replication. Depending on the virus, different cytopathic effects were produced. Comparison of viral effect observed on this cell line with the effect obtained on other cell lines has been performed. This cell line might be used in the clinical virology laboratory for virus isolation.

The 3-Deaza and 7-Deaza Derivatives of 5'-Amino-5'-deoxy-5'-noraristeromycin

The 3-deaza and 7-deaza derivatives of 5'-amino-5'-deoxy-5'-noraristeromycin (6 and 7, respectively) have been prepared from the common starting material (+)-(1R,4S)-4-hydroxycyclopent-2-en-1-yl acetate (8). Two Pd(0)-catalyzed allylic substitution reactions afforded the desired azide intermediates, 12 and 16, which were transformed to target compounds by standard procedures. These compounds were evaluated against a large number of viruses and found to be inactive except for weak effect against hepatitis B virus: 6, EC50 4.7 μM (3TC EC50 0.056 μM); 7, EC50 4.8 μM (3TC EC50 0.063 μM).

Assessing influenza-related mortality: Comment on Zucs et al.

Assessing influenza-related mortality: Comment on Zucs et al.

Amino substituted derivatives of 5′-amino-5′-deoxy-5′-noraristeromycin

The potent antiviral potential of 5′-amino-5′-deoxy-5′-noraristeromycin ( 2) is limited by associated toxicity. To seek derivatives of 2 that circumvent this undesirable property, three amino substituted derivatives (acetyl, 3; formyl, 4; and methyl, 5) of 2 have been prepared in 4–7 steps from the same intermediate, (1 S,4 R)-4-(6-chloropurin-9-yl)cyclopent-2-en-1-ol ( 6). Key steps involved an improved Pd(0)-catalyzed allylic azidation and a novel Pd(0)-catalyzed allylic amidation. The three target compounds were evaluated against a large number of viruses and found to be inactive except for a very weak effect of 5 on human cytomegalovirus, varicella zoster virus, and Epstein–Barr virus. There was also no noteworthy cytotoxicity associated with the new derivatives. Thus, these results indicate variation of the cyclopentyl amine of 2 does not offer a means to improve upon its antiviral potential.

The portal protein plays essential roles at different steps of the SPP1 DNA packaging process

A large number of viruses use a specialized portal for entry of DNA to the viral capsid and for its polarized exit at the beginning of infection. These families of viruses assemble an icosahedral procapsid containing a portal protein oligomer in one of its 12 vertices. The viral ATPase (terminase) interacts with the portal vertex to form a powerful molecular motor that translocates DNA to the procapsid interior against a steep concentration gradient. The portal protein is an essential component of this DNA packaging machine. Characterization of single amino acid substitutions in the portal protein gp6 of bacteriophage SPP1 that block DNA packaging identified sequential steps in the packaging mechanism that require its action. Gp6 is essential at early steps of DNA packaging and for DNA translocation to the capsid interior, it affects the efficiency of DNA packaging, it is a central component of the headful sensor that determines the size of the packaged DNA molecule, and is essential for closure of the portal pore by the head completion proteins to prevent exit of the DNA encapsidated. Functional regions of gp6 necessary at each step are identified within its primary structure. The similarity between the architecture of portal oligomers and between the DNA packaging strategies of viruses using portals strongly suggests that the portal protein plays the same roles in a large number of viruses.

5′-Amino-5′-deoxyaristeromycin and its antiviral properties

An efficient, three-step synthesis of 5′-amino-5′-deoxyaristeromycin (5), from a protected form of aristeromycin (6), is described. Compound 5 was evaluated against a large number of viruses. It showed weak activity towards vaccinia, herpes simplex virus 2, and cytomegalovirus. No other activity was observed. Compound 5 displayed some cytotoxicity towards the host cell lines human foreskin fibroblast, Daudi, and human T-lymphocyte (CEM).

Specific targeting of a DNA‐binding protein to the SPP1 procapsid by interaction with the portal oligomer

The icosahedral procapsid of tailed bacteriophages is composed of a large number of identical subunits and of minor proteins found in a few copies. Proteins present in a very low copy number are targeted to the viral procapsid by an unknown mechanism. Bacteriophage SPP1 procapsids and mature virions contain two copies of gp7 on average. Gp7 forms stable complexes with the SPP1 portal protein gp6. Deletion of the gp6 carboxyl-terminus and the mutation Y467-->C localized in the same region prevent gp6-gp7 complex formation. Gp7 binds double-stranded and single-stranded DNA. Gp6 competes for this interaction, and purified gp6-gp7 complexes do not bind DNA. Procapsid structures assembled in the absence of gp6 or carrying the mutant gp6 Y467-->C lack gp7. The gp6-gp7 interaction thus targets gp7 to the procapsid where the portal protein is localized asymmetrically at a single vertex of the icosahedral structure. The interaction between the two proteins is disrupted during viral assembly. Proteins homologous to gp6 and gp7 are coded by contiguous genes in a variety of phage genomes from Gram-positive bacteria, suggesting that the gp6-gp7 complex is widespread in this group of phages. Transient association with the portal protein, an essential component of tailed bacteriophages and herpes viruses, provides a novel strategy to target minor proteins to the virion structure that might be operative in a large number of viruses.

9-Deaza-5′-noraristeromycin

9-Deaza-5′-noraristeromycin ( 2) has been prepared in 10 steps from the readily available (+)-(1 R,4 S)-4- t-butyldimethylsilyloxycyclopent-2-en-1-yl acetate. Compound 2 was evaluated against a large number of viruses. No activity was found nor did 2 display cyctotoxicity towards the viral host cells.

Searching for the advantages of virus sex.

Sex (genetic exchange) is a nearly universal phenomenon in biological populations. But this is surprising given the costs associated with sex. For example, sex tends to break apart co-adapted genes, and sex causes a female to inefficiently contribute only half the genes to her offspring. Why then did sex evolve? One famous model poses that sex evolved to combat Muller's ratchet, the mutational load that accrues when harmful mutations drift to high frequencies in populations of small size. In contrast, the Fisher-Muller Hypothesis predicts that sex evolved to promote genetic variation that speeds adaptation in novel environments. Sexual mechanisms occur in viruses, which feature high rates of deleterious mutation and frequent exposure to novel or changing environments. Thus, confirmation of one or both hypotheses would shed light on the selective advantages of virus sex. Experimental evolution has been used to test these classic models in the RNA bacteriophage phi6, a virus that experiences sex via reassortment of its chromosomal segments. Empirical data suggest that sex might have originated in phi6 to assist in purging deleterious mutations from the genome. However, results do not support the idea that sex evolved because it provides beneficial variation in novel environments. Rather, experiments show that too much sex can be bad for phi6; promiscuity allows selfish viruses to evolve and spread their inferior genes to subsequent generations. Here I discuss various explanations for the evolution of segmentation in RNA viruses, and the added cost of sex when large numbers of viruses co-infect the same cell.

3-Benzamido, ureido and thioureidoimidazo[1,2-a]pyridine derivatives as potential antiviral agents.

This work reports the synthesis and the antiviral activities of 3-benzamido, 3-phenylureido and 3-phenylthioureido derivatives in the imidazo[1,2-a]pyridine series. The structure was proven by NMR spectroscopy. The synthesized compounds were evaluated against a large number of viruses. The 3-phenylthioureido derivative 7 showed moderate activity against human cytomegalovirus (HCMV) in vitro. The crystallographic data for 8 are also reported and explain the absence of activity against human immunodeficiency virus (HIV).

Viral gastroenteritis

A large number of viruses can be found in the human intestine. Some (bacteriophages) infect the bacteria present as normal flora and others use the gut as a portal of entry. This review examines the virology, pathogenesis, immunology, epidemiology, clinical features, treatment and prevention of the viral enteropathogens. Rotavirus is undoubtedly the most important, causing an estimated 800,000 deaths each year, especially in developing countries. Recently, an oral live quadrivalent rhesus rotavirus vaccine has been licensed for use in the USA. It has great potential but there are a number of hurdles to be overcome before it can be given to infants in developing countries. Molecular techniques are revolutionizing our understanding of rotavirus pathogenesis, and the tremendous diversity of Caliciviridae and Astroviridae, as well as producing new diagnostic techniques and vaccines.

Can We Explain RNA-Mediated Virus Resistance by Homology-Dependent Gene Silencing?

The use of viral sequences to produce virus-resistant plants is now almost a standard technique. A variety of sequences from a large number of viruses have been used but the mechanisms remain largely unknown. There are probably at least two distinct types of mechanisms operating: one requiring the expression of the viral protein(s) and the other dependent only on the presence of transgene-derived RNA. In this review, we will discuss this RNA-mediated resistance and its similarities with cosuppression, a recently described phenomenon leading to suppression of transgene expression and homologous sequences. We present a critical view of the current models available to explain this type of resistance.

Autoimmunity in hepatitis C and D virus infection.

A large number of viruses are capable of inducing acute or chronic hepatitis. The syndrome of chronic hepatitis encompasses not only viral but also autoimmune liver diseases. The hepatitis C virus, and recently also the hepatitis D virus have been found to be associated with an array of autoimmune syndromes, diseases and markers of autoimmunity. The relationship of hepatotropic virus infection and the immune system leading to virus-associated autoimmunity, and its distinction from genuine autoimmune disease represents a fascinating field of research. Clinically, the differentiation between autoimmune liver diseases, virus infection and virus-associated autoimmunity is difficult and epidemiological evaluations have not come up with universally applicable and valid classification criteria. However, both autoimmune liver diseases and viral hepatitis can readily be diagnosed and distinguished through precise and molecularly determined immunological testing systems. The overlap of both, virus-associated autoimmunity, is still at the centre of research activities aimed at establishing diagnostic and risk-assessment criteria. Studies of molecular autoantigens and autoepitopes have begun to define the differences of the B-cell response in autoimmune disease and virus-associated autoimmunity. This provides data that may contribute to the safe application of therapeutic strategies as different as immunosuppression and interferon-alpha (IFN-alpha). The present review focuses on the clinical, epidemiological and molecular aspects of these disease entities.

Evolution of mutation rate and virulence among human retroviruses.

High mutation rates are generally considered to be detrimental to the fitness of multicellular organisms because mutations untune finely tuned biological machinery. However, high mutation rates may be favoured by a need to evade an immune system that has been strongly stimulated to recognize those variants that reproduced earlier during the infection. HIV infections conform to this situation because they are characterized by large numbers of viruses that are continually breaking latency and large numbers that are actively replicating throughout a long period of infection. To be transmitted, HIVs are thus generally exposed to an immune system that has been activated to destroy them in response to prior viral replication in the individual. Increases in sexual contact should contribute to this predicament by favouring evolution toward relatively high rates of replication early during infection. Because rapid replication and high mutation rate probably contribute to rapid progression of infections to AIDS, the interplay of sexual activity, replication rate, and mutation rate helps explain why HIV-1 has only recently caused a lethal pandemic, even though molecular data suggest that it may have been present in humans for more than a century. This interplay also offers an explanation for geographic differences in progression to cancer found among infections due to the other major group of human retroviruses, human T-cell lymphotropic viruses (HTLV). Finally, it suggests ways in which we can use natural selection as a tool to control the AIDS pandemic and prevent similar pandemics from arising in the future.

Antiviral enantiomeric preference for 5'-noraristeromycin.

In order to determine if the potent antiviral properties of (+/-)-5'-noraristeromycin reside in one of its enantiomers, an analysis of each enantiomer has been carried out. A five-step route to the (+)-stereoisomer is described from (+)-(1R,4S)-4-hydroxy-2-cyclopenten-1-yl acetate, whereas the synthesis of the (-)-enantiomer had been reported previously from the same starting material. The (-)-2 and (+)-2 enantiomers were evaluated for antiviral activity against a large number of viruses and found to display an antiviral activity spectrum characteristic of (S)-adenosyl-L-homocysteine hydrolase inhibitors. The (-)-enantiomer retained the significant anticytomegalovirus properties previously reported for the racemic 2 and was, on the average, 10-fold more potent than (+)-2 in inhibiting virus replication, tumor cell growth, and (S)-adenosyl-L-homocysteine hydrolase activity.

Effect of concentrating the virus‐rich 2‐2nm size fraction of seawater on the formation of algal flocs (marine snow)

Particle aggregates >0.5 mm in diameter (marine snow) are an important component of marine environments. Viruses are now recognized as active members of the marine microbial food web, infecting both planktonic primary producers and bacteria. The effect of adding material from the 2–200‐nm size fraction, concentrated from seawater with ultrafiltration, on the development of phytoplankton biomass and formation of algal flocs was examined. At higher concentrations of material in this size fraction (2.3 times enrichment with virus‐like particles), the buildup of phytoplankton biomass was initially delayed. After 8 d, these enrichments resulted in the formation and persistence of up to 5 times higher numbers of larger aggregates (≥ 1‐mm equivalent spherical diameter) concomitant with even higher phytoplankton biomass. Both the size distribution of algal aggregates and primary production can be affected by material in the size range of 2–200 nm containing large numbers of viruses.

Synthesis and antiviral properties of (+/-)-5'-noraristeromycin and related purine carbocyclic nucleosides. A new lead for anti-human cytomegalovirus agent design.

(+/-)-5'-Noraristeromycin (3) has been prepared in three steps beginning with the 2,3-O-isopropylidene derivative of (+/-)-(1 alpha, 2 beta, 3 beta, 4 alpha)-4-amino-1,2,3-cyclopentanetriol (7). Also prepared from the same starting material were the related hypoxanthine (4), guanine (5), and 2,6-diaminopurine (6) analogues. Compounds 3-6 were evaluated for antiviral activity against a large number of viruses with marked activity being observed for 3 towards vaccinia virus, human cytomegalovirus, vesicular stomatitis virus, parainfluenza (type 3) virus, measles virus, respiratory syncytial virus, reovirus (type 1), and the arenaviruses Junin and Tacaribe. None of the compounds showed cytotoxicity to the host cell monolayers used in the antiviral studies. Both 3 and 6 have been found to be inhibitors of S-adenosyl-L-homocysteine hydrolase (AdoHcy hydrolase), which likely accounts for their antiviral activity. Inhibition of AdoHcy hydrolase represents a new approach to human cytomegalovirus drug design that should be pursued. Also, the activity of 3 should be further scrutinized for the treatment of pox-, rhabdo-, paramyxo-, reo-, and arenavirus infections.