pinecone/core-2020-05-10-deduplication huggingface dataset:
Analysis of RNA Packaging in Wild-Type and Mosaic Protein Capsids of Flock House Virus Using Recombinant Baculovirus Vectors

AbstractFlock house virus (FHV) is a small icosahedral insect virus of the family Nodaviridae. Its genome consists of two positive-sense RNA molecules, RNA1 (replicase gene) and RNA2 (coat protein gene), which are encapsidated into a single virion. Expression of coat protein in Sf21 cells using a baculovirus vector results in formation of virus-like particles (VLPs) whose capsids are structurally indistinguishable from native virions. However, RNA packaging is not specific for RNA2, the coat protein message. Using ribonuclease protection assays, we showed that the fraction of RNA2 in VLPs is 19% relative to the amount present in a population of native virions. To investigate possible reasons for the reduced level of RNA2, we generated two new baculovirus vectors, AcR1δ and AcR2δ, expressing the replicase gene and the coat protein gene, respectively. The inserted genes carried the self-cleaving hepatitis delta ribozyme sequence at the 3′ end to allow for synthesis of RNA1 and RNA2 transcripts with authentic 3′ ends. Infection of Sf21 cells with AcR2δ yielded VLPs that contained 66% RNA2 relative to native virions. Coinfection of Sf21 cells with AcR1δ and AcR2δ launched self-directed FHV replication and resulted in formation of particles most of which contained RNA1 and RNA2. However, a small fraction of particles containing cellular RNA was detected as well. The latter particles could be eliminated by infecting Sf21 cells with AcR1δ followed by transfection with in vitro synthesized transcripts of RNA2. We have further utilized this system to show that two coat protein deletion mutants with distinct RNA packaging defects form mosaic virus capsids but do not complement each other to rescue specific packaging of FHV RNAs
Clonotype Tracking of TCR Repertoires during Chronic Virus Infections

AbstractHuman viral infections such as HIV and EBV typically evoke a strong and diverse CD8+ T cell response. Relatively little is known about the extent to which TCR repertoire evolution occurs during viral infection or how repertoire evolution affects the efficacy of the CD8+ T cell response. In this study we describe a general approach for tracking TCR repertoire evolution during viral infection. IFNγ surface capture and MHC class I tetramer staining were independently used to isolate EBV-specific CD8+ T cells from peripheral blood. Anchored RT-PCR and clonotype TCR repertoire analysis were performed immediately after isolating the cells. We find that the TCR repertoires of the IFNγ-secreting and MHC class I tetramer staining populations were similar. In one subject a detailed analysis of the TCR repertoire during the first year of EBV infection was performed and over 600 TCR sequences targeting an EBV-immunodominant epitope were analyzed. Although some repertoire evolution occurred during the year, in general, the degree of repertoire drift was small. TCR repertoire analysis for an HIV-immunodominant epitope revealed a highly conserved amino acid motif in the Dβ region of TCR that recognizes the epitope and suggested that T cell precursor frequency influences which epitopes are targeted early in HIV infection. This methodology, which allows one to sort antigen-specific T cells based on different functional assays and to obtain a snapshot of their TCR repertoire with relative ease, should lead to a richer understanding of the rules underlying antigen recognition and T cell evolution during viral infection
Complementation Analysis of the Dales Collection of Vaccinia Virus Temperature-Sensitive Mutants

AbstractA collection of randomly generated temperature-sensitive (ts) vaccinia virus (strain IHD-W) mutants were reported by S. Dales et al., (1978, Virology, 84, 403–428) in 1978 and characterized by electron microscopy. We have performed further genetic analysis on the Dales collection of mutants to make the mutants more useful to the scientific community. We obtained the entire Dales collection, 97 mutants, from the American Type Culture Center (ATCC). All 97 mutants were grown and reassessed for temperature sensitivity. Of these, 16 mutants were either very leaky or showed unacceptably high reversion indices even after plaque purification and therefore were not used for further analysis. The remaining 81 ts mutants were used to perform a complete complementation analysis with each other and the existing Condit collection of ts vaccinia virus (strain WR) mutants. Twenty-two of these 81 Dales mutants were dropped during complementation analysis due to erratic or weak behavior in the complementation test. Of the 59 mutants that were fit for further investigation, 30 fall into 13 of Condit's existing complementation groups, 5 comprise 3 previously identified complementation groups independent of the Condit collection, and 24 comprise 18 new complementation groups. The 59 mutants which were successfully characterized by complementation will be accessioned by and made available to the scientific community through the ATCC
Isolation and Characterisation of the Rabies Virus N°-P Complex Produced in Insect Cells

AbstractWhen the nucleoprotein (N) of nonsegmented negative-strand RNA viruses is expressed in insect cells, it binds to cellular RNA and forms N-RNA complexes just like viral nucleocapsids. However, in virus-infected cells, N is prevented from binding to cellular RNA because a soluble complex is formed between N and the viral phosphoprotein (P), the N°-P complex. N is only released from this complex for binding to newly made viral or complementary RNA. We coexpressed rabies virus N and P proteins in insect cells and purified the N°-P complex. Characterisation by gel filtration, polyacrylamide gel electrophoresis, analytical ultracentrifugation, native mass spectroscopy, and electron microscopy showed that the complex consists of one N protein plus two P proteins, i.e., an N°-P2 complex
Pseudocowpox virus Encodes a Homolog of Vascular Endothelial Growth Factor

AbstractWe have identified a gene encoding a homolog of vascular endothelial growth factor (VEGF) in the Pseudocowpox virus (PCPV) genome. The predicted protein shows 27% amino acid identity to human VEGF-A. It also shows 41 and 61% amino acid identity to VEGFs encoded by orf virus (ORFV) strains NZ2 and NZ7, respectively. Assays of the expressed VEGF-like protein of PCPV (PCPVVR634VEGF) demonstrated that PCPVVR634VEGF is mitogenic for endothelial cells and is capable of inducing vascular permeability. PCPVVR634VEGF bound VEGF receptor-2 (VEGFR-2) but did not bind VEGFR-1 or VEGFR-3. These results indicate that PCPVVR634VEGF is a biologically active member of the VEGF family which shares with the ORFV-encoded VEGFs a receptor binding profile that differs from those of all cellular members of the VEGF family. It seems likely that the biological activities of PCPVVR634VEGF contribute to the proliferative and highly vascularized nature of PCPV lesions
Binding Characteristics Determine the Neutralizing Potential of Antibody Fragments Specific for Antigenic Domain 2 on Glycoprotein B of Human Cytomegalovirus

AbstractSite I of antigenic domain 2 (AD-2) on human cytomegalovirus glycoprotein B (gB) is poorly immunogenic in both man and mouse and knowledge about antibody repertoires reactive with this epitope is thus limited. Here we have characterized a phage display-derived repertoire of antibody fragments specific for this epitope in terms of antigen recognition, fine-specificity, and virus-neutralizing capacity. Our results show that the functional properties within a closely related repertoire may differ widely and that the effectiveness of the members of the repertoire to neutralize the virus is determined by the fine-specificity and kinetics of the interaction with the antigen. The half-life of the interaction between monomeric antibody fragments and gB seems to be particularly critical for the neutralizing capacity. We also demonstrate that sequence variation within gB allows virus variants to escape at least a part of the AD-2-specific neutralizing antibody repertoire, apparently without preventing antibody binding to the epitope
Emergence of Cytotoxic T Lymphocyte Escape Mutants following Antiretroviral Treatment Suspension in Rhesus Macaques Infected with SIVmac251

AbstractStructured treatment interruption (STI) of antiretroviral drugs has been proposed as an alternative approach for managing patients infected with HIV-1. While STI is thought to spare drug-related side effects and enhance the HIV-1-specific immune response, the long-lasting clinical benefit of this approach remains uncertain, particularly in patients with long-standing HIV-1 infection. Here, we investigated the basis of unabated virological replication following different STI regimens in rhesus macaques that expressed the MHC class I Mamu-A*01 molecule treated during acute and long-standing infection with SIVmac251. An amino acid change at the anchor residue within the immunodominant Mamu-A*01-restricted Gag181–189 CM9 epitope (T → A) in one of six macaques with acute SIVmac251 infection and in three of four macaques with long-standing SIVmac251 infection (T → A; T → S; S → C) was found in the majority of plasma virus. These amino acid changes have been shown to severely decrease binding of the corresponding peptides to the Mamu-A*01 molecule and, in the case of the T → A change, escape from CTL. In one macaque with long-standing SIVmac251 infection, a mutation emerged that conferred resistance to one of the antiretroviral drugs (PMPA) as well. These results provide insights into the mechanism underlying the limited capacity of repeated interruption of antiretroviral therapy as an approach to restrain viral replication. In addition, these data also suggest that interruption of therapy may be less effective in chronic infection because of preexisting immune escape and that immune escape is a risk of interruption of therapy
Control of Lymphocytic Choriomeningitis Virus Infection in Granzyme B Deficient Mice

AbstractWe have investigated whether granzyme B (GzmB) is required for effective cytotoxic T lymphocyte (CTL) mediated control of lymphocytic choriomeningitis virus (LCMV) infection. Clearance of LCMV from tissues of GzmB-deficient (GzmB−) mice following intraperitoneal infection with LCMV was impaired compared with control mice; however, the virus was ultimately eliminated. The impaired clearance of LCMV in GzmB− mice was not due to a deficiency in the generation of LCMV-specific T cells. In addition, CTL from LCMV-infected GzmB− mice efficiently lysed virus-infected cells in vitro, but were deficient in their ability to induce rapid DNA fragmentation in target cells. We examined whether the development of protective immunity against intracranial (i.c.) rechallenge with LCMV was compromised in GzmB− mice. We found that clearance of LCMV from the brain following secondary i.c. infection also was slower in the absence of GzmB; however, the virus was ultimately eliminated and the mice survived. Our data indicate that clearance of LCMV is delayed in the absence of GzmB expression, but that other CTL effector molecules can compensate for the absence of this granule constituent in vivo
Ability of Small Animal Cells to Support the Postintegration Phase of Human Immunodeficiency Virus Type-1 Replication

AbstractWe examine the potential for a broad range of small animal cells, including rodent, mink, and avian cells, from multiple tissues to support postintegration steps of HIV-1 replication. These cells were engineered so as to support a stable expression of human cyclin T1 and were further transduced with HIV-1 gag and pol genes. Viral gene expression was activated by the presence of human cyclin T1, but, with the exception of mink cells, was not at the level seen in human cells. Furthermore, there were considerable defects in p24 CA release, in particular in the case of rodent cells. Fractionation of Gag proteins by sucrose floatation revealed that the Gag in human cells trafficked to membrane fractions and was processed to p24 CA and p17 MA efficiently. Confocal imaging demonstrated that Gag was localized in a punctate pattern at the plasma membrane as well as intracellular membrane trans-Golgi cisternae in these cells. In contrast, the majority of Gag in rodent cells was largely present in cytosolic complexes and remained unprocessed. Labeling with [9,10(n)-3H]myristic acid showed a similar degree of N-myristoylated Pr55gag in rodent and human cells, indicating that while N-myristoylation of Gag was essential for membrane binding, it was not sufficient to confer membrane targeting specificity. Remarkably, despite the reduced level of intracellular Gag processing, mink Mv.1.Lu cells did not appear to differ significantly from human cells in support of virion assembly and release. Analysis of reciprocal heterokaryons suggested that the cellular factor(s) required for efficient assembly and release of infectious virions is lacking in murine cells but appears to be functionally present in mink as well as human cells. Our findings confirm and extend previous reports of multiple blocks to HIV replication in nonhuman cells that are most profound in murine cells. They also raise the possibility that other small animals, such as mink, could serve as novel model systems for studying HIV-1 infection and disease
The Importance of Alfalfa Mosaic Virus Coat Protein Dimers in the Initiation of Replication

AbstractDeletion and substitution mutations affecting the oligomerization of alfalfa mosaic virus (AMV) coat protein (CP) were studied in protoplasts to determine their effect on genome activation, an early step in AMV replication. The CP mutants that formed dimers, CPΔC9 and CPC-ARF, were highly active in initiating replication with 63–84% of wild-type (wt) CP activity. However, all mutants that did not form dimers, CPΔC18, CPΔC19, CPC-WFP, and CPC-W, were much less active with 19–33% of wt CP activity. The accumulation and solubility of mutant CPs expressed from a virus-based vector in Nicotiana benthamiana were similar to that of wt CP. Analysis of CP–RNA interactions indicated that CP dimers and CP monomers interacted very differently with AMV RNA 3′ ends. These results suggest that CP dimers are more efficient for replication than CP monomers because of differences in RNA binding rather than differences in expression and accumulation of the mutant CPs in infected cells
The N-linked Glycan g15 within the V3 Loop of the HIV-1 External Glycoprotein gp120 Affects Coreceptor Usage, Cellular Tropism, and Neutralization

AbstractWe have studied infectivity and neutralization of X4, R5, and R5X4 tropic HIV-1 mutants, which are lacking N-linked glycosylation sites for glycans g13, g14, g15, and g17 in the V3 loop region of gp120. X4-tropic NL4-3 mutants lacking combinations of g14/15 or g15/17 showed markedly higher infectivity in CXCR4-specific infection. The role of g15 in CCR5-specific infection was investigated using viruses with high (NL-918, R5-monotropic), medium (NL-991, R5-monotropic), and low (NL-952, R5X4-dualtropic) CCR5-specific infectivity. For NL-991, a reduction of infectivity on GHOST-CCR5 cells was observed for a mutant lacking g15. For NL-952 mutants all lacking g15, a complete loss of CCR5-specificity was observed and NL-952 was shifted from R5X4 to X4 tropism. For all mutants of NL4-3, NL-991, and NL-952, where the lack of g15 markedly influenced infectivity or coreceptor usage, neutralization was enhanced. In contrast, NL-918 mutants with or without g15 showed no difference in neutralization and no difference in GHOST-CCR5 infection rates. Thus, for viruses with a low or medium CCR5-specificity the role of g15 for changing CCR5-usage and sensitivity to neutralization was more significant than for viruses with high infection rates on GHOST-CCR5 cells. Our data demonstrate that V3 glycans play an important role in the usage of CXCR4 and CCR5. The lack of g15 was relevant for a more efficient use of CXCR4, whereas interaction with CCR5 was facilitated in the presence of g15. This study also demonstrates that glycan g15 is involved in blocking of neutralizing antibodies and shifting HIV tropism from R5X4 to X4
Replication, Immunogenicity, and Protective Properties of Live-Attenuated Simian Immunodeficiency Viruses Expressing Interleukin-4 or Interferon-γ

AbstractNef deletion mutants of SIV-expressing interleukin-4 (SIV-IL4) or interferon-γ (SIV-IFN) were constructed to study the effect of interferon-γ (IFN-γ) and interleukin-4 (IL-4) on viral load, immunogenicity, and protective properties. Four rhesus monkeys were infected with SIV-IL4 and four were infected with SIV-IFN. During the acute phase of infection, the cell-associated viral load, but not the plasma viral RNA load, was approximately 10-fold lower in SIV-IFN-infected macaques than in SIV-IL4-infected rhesus monkeys. The viral load declined to hardly detectable levels 4 months postinfection in all animals. SIV antibody titers and the affinity of these antibodies were higher in SIV-IL4-infected macaques than in SIV-IFN-infected animals, consistent with a stimulation of T helper cell type 2 immune responses by IL-4. At peak viremia, there was a trend to higher interleukin-12 and perforin mRNA levels of the lymph nodes in the SIV-IFN-infected macaques than in the SIV-IL4-infected monkeys. Deletion of the viral IFN gene, but not the viral IL-4 gene, after the development of antiviral immune responses suggests a repressive effect of IFN, but not IL-4, on virus spread in vivo. A trend to higher set point viral RNA levels in SIV-IL4-infected monkeys in comparison to monkeys infected with the parental nef deletion mutant and similar viral RNA levels during the acute phase of infection suggest that IL-4 expression leads to a slight reduction in the control of virus replication by host immune responses. However, SIV-IL4 and SIV-IFN induced protection against a homologous challenge virus. Subsequent challenge with an SIV-HIV-1 hybrid virus (SHIV) also revealed protection in the absence of neutralizing antibodies
Cell-Surface-Expressed HIV-1 Envelope Induces the Death of CD4 T Cells during GP41-Mediated Hemifusion-like Events

AbstractCells expressing the HIV-1 envelope glycoprotein complex (gp120/gp41, Env) induce the death of target cells either after cell-to-cell fusion or after cell-to-cell contact in a fusion-independent fashion. Here, we demonstrate that Env-induced death of single cells (including primary CD4 T cells) required gp120 and gp41 function. The gp41 peptide C34, which blocked syncytium formation, completely inhibited the death of single target cells by specifically acting on gp41 function. Moreover, Env-induced single cell death was exclusively observed in CD4 cells and was associated with specific gp41-mediated transfer of lipids from the membrane of Env-expressing cells to the target cell but not with detectable cytoplasm mixing (complete fusion). We conclude that after gp120 function, gp41 mediates close cell-to-cell contacts, thereby triggering cell death in single uninfected cells in the absence of detectable cell-to-cell fusion
Antibody Fragments Selected by Phage Display against the Nuclear Localization Signal of the HIV-1 Vpr Protein Inhibit Nuclear Import in Permeabilized and Intact Cultured Cells

AbstractThe HIV-1 Vpr protein harbors a nuclear localization signal in its N-terminal domain. A peptide bearing this domain and which is designated VprN has been used as a target to screen a phage display single chain Fv (scFv) library. Here we report the isolation of anti-VprN scFv fragments from this library. The purified scFv fragments were able to bind the VprN peptide in an ELISA-based system and to inhibit VprN-mediated nuclear import in permeabilized as well as in intact microinjected cells. Furthermore, the anti-VprN scFv fragments recognized the full-length recombinant Vpr protein and inhibited its nuclear import. The same scFv fragments did not inhibit nuclear import mediated by the nuclear localization signal of the SV40 large T-antigen demonstrating a specific effect. The use of the described inhibitory anti-VprN scFv fragments to study nuclear import of viral karyophilic proteins and their therapeutic potential is discussed
The Intracellular Association of the Nucleocapsid Protein (NP) of Hantaan Virus (HTNV) with Small Ubiquitin-like Modifier-1 (SUMO-1) Conjugating Enzyme 9 (Ubc9)

AbstractSmall ubiquitin-like modifier-1 (SUMO-1) conjugating enzyme 9 (Ubc9) conjugates SUMO-1 to target proteins and modulates cellular processes such as signal transduction, transcription regulation, and cell growth regulation. We demonstrated here that the nucleocapsid protein (NP) of Hantaan virus (HTNV) was associated with Ubc9 and SUMO-1 in vivo. Analysis of the interaction between the truncated NPs and Ubc9 revealed that the amino acid residues at the positions between 101 and 238 in the NP were responsible for the interaction. Furthermore, a consensus binding motif of Ubc9 and SUMO-1, MKAE, within this region, especially the second amino acid of the motif, K residue, was crucial for the interaction, and the interaction was essential for the NP to be localized in the perinuclear region. These results indicate that the assembly of the HTNV-NP is regulated by the interaction between the NP and Ubc9. This is the first report to demonstrate the interaction of Ubc9 with a structural protein of negative-strand RNA viruses
Bhendi Yellow Vein Mosaic Disease in India Is Caused by Association of a DNA β Satellite with a Begomovirus

AbstractYellow vein mosaic disease is the major limitation in the production of bhendi or okra (Abelmoschus esculentus), an important vegetable crop of India. This disease is caused by a complex consisting of the monopartite begomovirus Bhendi yellow vein mosaic virus (BYVMV, family: Geminiviridae) and a small satellite DNA β component. BYVMV can systemically infect bhendi upon agroinoculation but produces only mild leaf curling in this host. DNA β induces typical symptoms of bhendi yellow vein mosaic disease (BYVMD) when co-agroinoculated with the begomovirus to bhendi. The DNA β component associated with BYVMD has a number of features in common with those reported for ageratum yellow vein disease and cotton leaf curl disease. BYVMV represents a new member of the emerging group of monopartite begomoviruses requiring a satellite component for symptom induction
Recovery of Infectivity from cDNA Clones of Nodamura Virus and Identification of Small Nonstructural Proteins

AbstractNodamura virus (NoV) was the first isolated member of the Nodaviridae, and is the type species of the alphanodavirus genus. The alphanodaviruses infect insects; NoV is unique in that it can also lethally infect mammals. Nodaviruses have bipartite positive-sense RNA genomes in which RNA1 encodes the RNA-dependent RNA polymerase and the smaller genome segment, RNA2, encodes the capsid protein precursor. To facilitate the study of NoV, we generated infectious cDNA clones of its two genomic RNAs. Transcription of these NoV1 and NoV2 cDNAs in mammalian cells led to viral RNA replication, protein synthesis, and production of infectious virus. Subgenomic RNA3 was produced during RNA replication and encodes nonstructural proteins B1 and B2 in overlapping ORFs. Site-directed mutagenesis of these ORFs, followed by SDS–PAGE and MALDI–TOF mass spectrometry analyses, showed synthesis of B1 and two forms of B2 (B2-134 and B2-137) during viral replication. We also characterized a point mutation in RNA1 far upstream of the RNA3 region that resulted in decreased RNA3 synthesis and RNA2 replication, and a reduced yield of infectious particles. The ability to reproduce the entire life cycle of this unusual nodavirus from cDNA clones will facilitate further analysis of NoV RNA replication and pathogenesis