Immunocapture Polymerase Chain Reaction for the Detection and Characterization of Cacao Swollen Shoot Virus 1 A Isolates

Oligonucleotides derived from the flanking regions of the putative coat protein gene of the cacao swollen shoot badnavirus isolate I A (CSSV-1 A) were able to prime the synthesis of specific products directly from extracts from CSSV-IA-infected leaves by immunocapture polymerase chain reaction (IC-PCR), following trapping of virions with polyclonal antibodies to CSSV-1 A. CSSV isolates serologically distinct from CSSV-I A were not detected by IC-PCR when the CSSV-I A-derived primers were used following trapping with homologous antisera. IC-PCR was at least 100-fold more sensitive than double antibody sandwich (DAS)-ELISA in comparative tests on samples from greenhouse-grown cacao plants. The superior sensitivity of IC-PCR over DAS-ELISA was confirmed in attempts to detect and identify CSSV-I A isolates in field samples and permitted detection of CSSV-I A isolates even in symptomless leaves from plants showing stem swelling only. The IC-PCR products obtained from four randomly selected field samples were sequenced and shown to contain a region of the CSSV-I A genome where ORF X overlaps ORF 3. Analysis of the partial amino acid sequences deduced from ORF 3 and ORF X of the four field isolates revealed a considerable variation in these CSSV-I A gene products.     

Cell-to-cell movement and assembly of a plant closterovirus: roles for the capsid proteins and Hsp70 homolog.

Diverse animal and plant viruses are able to translocate their virions between neighboring cells via intercellular connections. In this work, we analyze the virion assembly and cell-to-cell movement of a plant closterovirus and reveal a strong correlation between these two processes. The filamentous virions of a closterovirus possess a long body formed by the major capsid protein (CP) and a short tail formed by the minor capsid protein (CPm). Genetic and biochemical analyses show that the functions of these virion components are distinct. A virion body is required primarily for genome protection, whereas a tail represents a specialized device for cell-to-cell movement. Furthermore, tail assembly is mediated by the viral Hsp70 homolog (Hsp70h) that becomes an integral part of the virion. Inactivation of the ATPase domain of Hsp70h results in assembly of tailless virions that are incapable of translocation. A dual role for the viral molecular chaperone Hsp70h in virion assembly and transport, combined with the previous finding of this protein in intercellular channels, allowed us to propose a model of closteroviral movement from cell to cell.     

A 165 kd protein of the herpes simplex virion shares a common epitope with the regulatory protein, ICP4

We have investigated the possibility that immediate-early (IE) protein ICP4 could be a part of herpes simplex virus type 1 (HSV-1) virion particle. Immunodetection with a monoclonal antibody against ICP4 reveals that a component of the virion, migrating at 165 kd, shares a common epitope with this immediate-early protein. Immunolocalization studies on purified virions indicate that the antigen can be detected only in virions without membranes, and is located outside the capsid, most probably in the tegument. Ultrastructural localizations on HSV-1 infected BHK cells extracted with a nonionic detergent confirm that the protein immunoreacting with anti-ICP4 is present in virions.     

The herpes simplex virus type 1 DNA packaging protein UL17 is a virion protein that is present in both the capsid and the tegument compartments

The UL17 protein of herpes simplex virus type 1 is essential for packaging the viral genome into the procapsid, a spherical assembly intermediate, and is present in the mature virus particle. We have examined the distribution of UL17 in various assembly products and virions to determine which component of the virus particle UL17 is associated with and at what stage in capsid assembly UL17 is required. UL17 was present in the procapsid, in the DNA-containing angularized C capsid, and in two other angularized capsid forms, A and B, that lack DNA and are thought to be dead-end products. The results suggest that UL17 is a minor capsid protein which is incorporated into the procapsid during assembly of the particle. UL17 was also found in virions and in noninfectious structures known as light (L) particles, which possess a tegument and envelope but lack a capsid. The level of UL17 in these particles was much greater than the amount that could be attributed to capsid contamination of the purified L-particle preparation, suggesting that UL17 is also a tegument protein. The finding that virions contain approximately twofold more UL17 than do C capsids provided further support for the idea that UL17 is present in two different structural components within the mature virion. The UL25 packaging protein, which is also present in virions, was not found in significant amounts in L particles, indicating that it is associated only with the capsid. UL6, the third virion-associated packaging protein, was present in slightly increased levels in L particles.     

Structural components of the arenavirus Pichinde.

Purified Pichinde virions grown in monolayers of BHK-21 cells were found to contain three major species of virion proteins as described previously (Ramos et al., J. Virol. 10:661-667, 1972). Two of the proteins were glycosylated (G1, molecular weight = 64,000; G2, molecular weight = 38,000) and were present in similar proportions on the outer surface of the virions. A third protein (N, molecular weight = 66,000) was not glycosylated and, in association with the viral RNA species, was the major protein component of the viral nucleocapsids. An estimate of the approximate number of molecules of these three major proteins per virion was made. Minor amounts of other proteins were also routinely observed in Pichinde virus preparations. None of the three major protein species were phosphorylated to any significant exten, nor did they contain sulfated components. Two virion RNA species (L and S), but no 18S rRNA species, were detected in Pichinde virus preparations obtained from infected BHK-21 cells.     

Stochastic kinetics of reproduction of virions inside a cell

We analyze intracellular viral kinetics in the framework of the model incorporating viral genome replication, mRNA synthesis and degradation, protein synthesis and degradation, capsid assembly, and virion release from a cell. Due to the existence of the critical concentration of viral capsid proteins and other features of reproduction of virions inside a cell, the kinetics is demonstrated to exhibit three distinct initial stages. Specifically, (i) the exponential growth of the viral genome, mRNA and protein concentrations is followed by (ii) the transient stage to (iii) the steady-state regime. The formation of mature virions starts during the transient stage. Comparison of the kinetics, obtained by using the mass-action law and Monte Carlo (MC) technique, indicates that they are nearly identical during the initial exponential growth of the viral intermediates and also during the steady-state stage. The transition from the initial stage to the steady-state regime occurs however somewhat faster in the determenistic case even if the steady-state populations of virions and genomes are appreciable (e.g., about 250 and 500, respectively).     

Highly Divergent Strains of Porcine Reproductive and Respiratory Syndrome Virus Incorporate Multiple Isoforms of Nonstructural Protein 2 into Virions

Viral structural proteins form the critical intermediary between viral infection cycles within and between hosts, function to initiate entry, participate in immediate early viral replication steps, and are major targets for the host adaptive immune response. We report the identification of nonstructural protein 2 (nsp2) as a novel structural component of the porcine reproductive and respiratory syndrome virus (PRRSV) particle. A set of custom α-nsp2 antibodies targeting conserved epitopes within four distinct regions of nsp2 (the PLP2 protease domain [OTU], the hypervariable domain [HV], the putative transmembrane domain [TM], and the C-terminal region [C]) were obtained commercially and validated in PRRSV-infected cells. Highly purified cell-free virions of several PRRSV strains were isolated through multiple rounds of differential density gradient centrifugation and analyzed by immunoelectron microscopy (IEM) and Western blot assays using the α-nsp2 antibodies. Purified viral preparations were found to contain pleomorphic, predominantly spherical virions of uniform size (57.9 nm ± 8.1 nm diameter; n = 50), consistent with the expected size of PRRSV particles. Analysis by IEM indicated the presence of nsp2 associated with the viral particle of diverse strains of PRRSV. Western blot analysis confirmed the presence of nsp2 in purified viral samples and revealed that multiple nsp2 isoforms were associated with the virion. Finally, a recombinant PRRSV genome containing a myc-tagged nsp2 was used to generate purified virus, and these particles were also shown to harbor myc-tagged nsp2 isoforms. Together, these data identify nsp2 as a virion-associated structural PRRSV protein and reveal that nsp2 exists in or on viral particles as multiple isoforms.     

Identification of proteins in human cytomegalovirus (HCMV) particles: the HCMV proteome

Human cytomegalovirus (HCMV), a member of the herpesvirus family, is a large complex enveloped virus composed of both viral and cellular gene products. While the sequence of the HCMV genome has been known for over a decade, the full set of viral and cellular proteins that compose the HCMV virion are unknown. To approach this problem we have utilized gel-free two-dimensional capillary liquid chromatography-tandem mass spectrometry (MS/MS) and Fourier transform ion cyclotron resonance MS to identify and determine the relative abundances of viral and cellular proteins in purified HCMV AD169 virions and dense bodies. Analysis of the proteins from purified HCMV virion preparations has indicated that the particle contains significantly more viral proteins than previously known. In this study, we identified 71 HCMV-encoded proteins that included 12 proteins encoded by known viral open reading frames (ORFs) previously not associated with virions and 12 proteins from novel viral ORFs. Analysis of the relative abundance of HCMV proteins indicated that the predominant virion protein was the pp65 tegument protein and that gM rather than gB was the most abundant glycoprotein. We have also identified over 70 host cellular proteins in HCMV virions, which include cellular structural proteins, enzymes, and chaperones. In addition, analysis of HCMV dense bodies indicated that these viral particles are composed of 29 viral proteins with a reduced quantity of cellular proteins in comparison to HCMV virions. This study provides the first comprehensive quantitative analysis of the viral and cellular proteins that compose infectious particles of a large complex virus.     

Complementary RNA Species Isolated from Vesicular Stomatitis (HR Strain) Defective Virions

The wild-type strain of vesicular stomatitis virus (VSV) contains in its complete virion (VSV-1, B particles) a minus strand RNA. The principle defective particle of the wild-type strain (VSV-111, T particles) contains a shorter minus strand, homologous to part of the VSV-1 genome. Neither virion contains any detectable complementary (plus) strand RNA. In contrast, a preparation of a heat-resistant (HR) strain of VSV containing defective virions was found to contain both plus (21%) and minus strand RNA, present in several distinct size classes. It was found that the RNA in the HR virion preparation was at least 94% single-stranded and principally (96%) in ribonucleoprotein complexes. On extraction the plus and minus strand RNA species partially annealed to give a population of double- and multistranded RNA species. A small amount of RNA polymerase activity was associated with the HR defective virus preparation.     

Intracellular viral kinetics limited by the supply of amino acids for synthesis of viral proteins

A minimal model proposed by the author [Zhdanov, V.P., 2004. Stochastic kinetics of reproduction of virions inside a cell. Biosystems 77, 143–150] to describe intracellular viral kinetics includes genome replication, mRNA and protein synthesis and degradation, capsid assembly, and virion release from a cell. Here, this model is complemented by the terms describing the balance of the amino acid determining the rate of the synthesis of viral capsid protein. If the effect of virions on this balance is negligible, the model predicts either a steady state or unlimited growth of the virion population. In the latter case, the cell eventually reaches the situation when the amino-acid concentration is reduced due to the synthesis of viral protein. For this stage, the viral-genome replication is asymptotically predicted to be unlimited while the virion population is limited. The unlimited viral-genome replication practically means that the cell will either die or the kinetics will be limited by additional feedbacks which were not taken into account in the model. All these findings, illustrating the use of the methods of integrative biology of biosystems, help to understand the role of the amino-acid supply in intracellular viral kinetics.     

A型流感病毒的基因组包装

A型流行性感冒病毒的负链RNA基因组由编码病毒中12个蛋白质的八个节段组成。在病毒组装的最后阶段，病毒体从细胞顶端胞浆膜突出时将这些基因组的病毒体（v）RNAs吸收进其中。基因组分段赋予了流感病毒进化的优势，但也提出了问题，在病毒体组装时需要八个节段每一个的至少一个复制本以产生完全有传染性的病毒颗粒。历史上一直存在争论：一方赞同确保足额的基因组合并的特异性包装机制；另一方赞同基因组节段被随机选择而不是以充足数量被包装以确保能自行产生合理比例病毒体的替代模式。近年来人们对该问题已达成一致意见：大多数病毒体仅包含八个节段，特异性机制为选择每个vRNA的某一复制本的确发挥了作用。本综述总结了得出这一结论所做的工作，叙述了在识别特异性包装信号方面最新的进展，讨论了这些RNA元素运转的可能机制。     

Isolation of human immunodeficiency virus type 1 cores: retention of Vpr in the absence of p6(gag)

Mature human immunodeficiency virus type 1 (HIV-1) virions contain a typically cone-shaped core that encases the viral genome. In this study, we established conditions which allowed the efficient isolation of morphologically intact HIV-1 cores from virions. The isolated cores consisted mostly of cones which appeared uniformly capped at both ends but were heterogeneous with respect to the shape of the broad cap as well as the dimensions and angle of the cone. Vpr, a nonstructural virion component implicated in the nuclear import of the viral genome, was recovered in core preparations of HIV-1 and simian immunodeficiency viruses from African green monkeys. Unexpectedly, p6(gag), a structural protein required for the incorporation of Vpr, was absent from HIV-1 core preparations. Taken together, our results indicate that the incorporation of Vpr into the virion core is a conserved feature of primate lentiviruses and that the interactions required for the uptake of Vpr into assembling particles differ from those which confine Vpr within the core.     

Production of Uninfectious Human Immunodeficiency Virus Type 1 Containing Viral Protein R Fused to a Single-Chain Antibody against Viral Integrase

A single-chain antibody (scAb) against human immunodeficiency virus type 1 (HIV-1) integrase was expressed as a fusion protein of scAb and HIV-1 viral protein R (Vpr), together with the HIV-1 genome, in human 293T cells. The expression did not affect virion production much but markedly reduced the infectivity of progeny virions. The fusion protein was found to be incorporated into the virions. The incorporation appears to account for the reduced infectivity.     

Development and characterization of novel empty adenovirus capsids and their impact on cellular gene expression

Adenovirus (Ad) has been extensively studied as a eukaryotic viral vector. As these vectors have evolved from first-generation vectors to vectors that contain either very few or no viral genes ("gutless" Ad), significant reductions in the host innate immune response upon infection have been observed. Regardless of these vector improvements an unknown amount of toxicity has been associated with the virion structural proteins. Here we demonstrate the ability to generate high particle numbers (10(11) to 10(12)) of Ad empty virions based on a modification of Cre/lox gutless Ad vectors. Using a battery of analyses (electron microscopy, atomic force microscopy, confocal images, and competition assays) we characterized this reagent and determined that it (i) makes intact virion particles, (ii) competes for receptor binding with wild-type Ad, and (iii) enters the cell proficiently, demonstrating an ability to carry out essential steps of viral entry. To further study the biological impact of these Ad empty virions on infected cells, we carried out DNA microarray analysis. Compared to that for recombinant Ad, the number of mRNAs modulated upon infection was significantly reduced but the expression signatures were similar. This reagent provides a valuable tool for studies of Ad in that researchers can examine the effect of infection in the presence of the virion capsid alone.     

Molecular mechanisms of virus spread and virion components as tools of virulence. A review

Despite of differences in replication strategy among virus families, some basic principles have remained similar. Analogous mechanisms govern virus entry into cells and the use of enzymes which direct the replication of the virus genome. The function of many cell surface receptors (such as glycosoaminoglycans, glycoproteins, proteins) which interact with viral capsid proteins or envelope glycoproteins has recently been elucidated. The list of cellular receptors (Table I) is still far from being final. The capsid components, similarly as the envelope glycoproteins, may form specific pocket like sites, which interact with the cell surface receptors. Neutralizing antibodies usually react with antigenic domains adjacent to the receptor binding site(s) and hamper the close contact inevitable for virion attachment. In the case of more complex viruses, such as herpes simplex virus, different viral glycoproteins interact with several cellular receptors. At progressed phase of adsorption the virions are engulfed into endocytic vesicles and the virion fusion domain(s) become(s) activated. The outer capsid components of reoviruses which participate in adsorption and fusion may get activated already in the lumen of digestive tract, i.e. before their engulfment by resorptive epithelium cells. Activation of the hydrophobic fusion domain(s) is a further important step allowing to pass through the lipid bilayer when penetrating the cell membrane in order to reach the cytosol. Activation of the virion fusion domain is accomplished by a conformation change, which occurs at acid pH (influenza virus hemagglutinin, sigma 1 protein of the reovirus particle) and/or after protease treatment. The herpes simplex virus fusion factors (gD and gH) undergo conformation changes by a pH-independent mechanism triggered due to interaction with the cell surface receptor(s) and mediated by mutual interactions with the viral envelope glycoproteins. The virion capsid or envelope components participating in the entry and membrane fusion are not the only tools of virulence. The correct function of virus coded proteins, which participate in replication of the viral genome, and/or in the supply of necessary nucleotides, may be very essential. In the case of enteroviruses, which RNA interacts with ribosomes directly, the correct configuration of the non-coding viral RNA sequence is crucial for initiation of translation occurring in the absence of the classical "cap" structure.     

Differences in the subpopulations of the structural proteins of polyoma virions and capsids: biological functions of the multiple VP1 species.

The structural proteins of polyoma virions and capsids were analyzed by isoelectric focusing and sodium dodecyl sulfate-polyacrylamide gel electrophoresis. Polyoma virion VP1 was found to be composed of six distinct species which had pI's between pH 6.75 and 5.75. Polyoma capsid VP1 was found to contain four species with pI's between pH 6.60 and 5.75. The different forms of virion and capsid VP1 appeared to be generated by modifications (phosphorylation and acetylation) of the initial translation product. The most basic of the virion VP1 species (pI, pH 6.75) was absent in capsids and was found to be exclusively associated with the viral nucleoprotein complex. Three of the virion VP1 species and three of the capsid VP1 species were found in capsomere preparations enriched for hexon subunits. Two VP1 species were specifically immune precipitated from virions with hemagglutination-inhibiting antibodies. These two VP1 species were common to both virions and capsids. Polyoma virions, but not capsids, possessed a single VP1 species which was immune precipitated with neutralizing antibodies. Both virion and capsid VP2 were found to have pI's of approximately pH 5.50. Virion VP3 had a pI of approximately pH 7.00, whereas capsid VP3 had a pI of approximately pH 6.50.