pinecone/core-2020-05-10-deduplication huggingface dataset:
Recombinant Respiratory Syncytial Viruses with Deletions in the NS1, NS2, SH, and M2-2 Genes Are Attenuated in Vitro and in Vivo

AbstractRespiratory syncytial virus (RSV) encodes several proteins that lack well-defined functions; these include NS1, NS2, SH, and M2-2. Previous work has demonstrated that NS2, SH, and M2-2 can each be deleted from RSV genome and thus are considered as accessory proteins. To determine whether RSV can replicate efficiently when two or more transcriptional units are deleted, we removed NS1, NS2, SH, and M2-2 genes individually and in different combinations from an infectious cDNA clone derived from human RSV A2 strain. The following six mutants with two or more genes deleted were obtained: ΔNS1NS2, ΔM2-2SH, ΔM2-2NS2, ΔSHNS1, ΔSHNS2, and ΔSHNS1NS2. Deletion of M2-2 together with NS1 was detrimental to RSV replication. It was not possible to obtain a recombinant RSV when all four genes were deleted. All of the double and triple deletion mutants exhibited reduced replication and small plaque morphology in vitro. Replication of these deletion mutants was more reduced in HEp-2 cells than in Vero cells. Among the 10 single and multiple gene deletion mutants obtained, ΔM2-2NS2 was most attenuated. ΔM2-2NS2 formed barely visible plaques in HEp-2 cells and had a reduction of titer of 3 log10 compared with the wild-type recombinant RSV in infected HEp-2 cells. When inoculated intranasally into cotton rats, all of the deletion mutants were attenuated in the respiratory tract. Our data indicated that the NS1, NS2, SH, and M2-2 proteins, although dispensable for virus replication in vitro, provide auxiliary functions for efficient RSV replication
Lentiviral Vectors Pseudotyped with Envelope Glycoproteins Derived from Gibbon Ape Leukemia Virus and Murine Leukemia Virus 10A1

AbstractLentiviral vectors pseudotyped with the envelope glycoproteins (Env) of amphotropic murine leukemia virus (MLV) and the G protein of vesicular stomatitis virus (VSV-G) have been successfully used in recent preclinical gene therapy studies. We report here the generation of infectious HIV-1-derived vector particles pseudotyped with the Env of the molecular clone 10A1 of MLV and with chimeric envelope glycoprotein variants derived from gibbon ape leukemia virus (GaLV) and MLV. Formation of infectious HIV-1 (GaLV) pseudotype vectors was only possible with the substitution of the cytoplasmic tail of GaLV Env with that of MLV. The lentiviral vectors exhibited a host cell range identical with that of MLV(GaLV) and MLV(10A1) vectors, which are known to enter cells either via the GaLV-receptor Glvr-1 (Pit-1) or via the amphotropic receptor Ram-1 (Pit-2) in addition to Glvr-1, respectively. Thus, HIV-1(GaLV) and HIV-1(10A1) pseudotype vectors may be useful for efficient gene transfer into a variety of human tissues like primary human hematopoietic cells
Protective Immunity against Feline Immunodeficiency Virus Induced by Inoculation with vif-Deleted Proviral DNA

AbstractTo determine whether live-attenuated feline immunodeficiency virus (FIV) proviral DNA will induce protective immunity, a plasmid clone constructed with a FIV provirus containing a deletion in the viral accessory gene vif (FIV-pPPR-Δvif) was inoculated as proviral DNA into four cats by the intramuscular route. After 43 weeks, these cats were boosted with the same proviral plasmid. Analysis of peripheral blood mononuclear cells at several time points after the primary and booster inoculations revealed no detectable virus or proviral DNA. At 6 weeks after the booster, immunized cats and additional naive control cats were challenged with a cell-free preparation of the infectious biological isolate FIV-PPR by the intraperitoneal route. Virus was detected after challenge in unvaccinated control cats but not in any of the FIV-pPPR-Δvif-immunized cats. Both FIV Gag- and Env-specific cytotoxic T lymphocyte (CTL) activities were detected in peripheral blood cells of control cats after challenge infection, whereas only one of four cats immunized with FIV-pPPR-Δvif DNA exhibited a measurable CTL response to Env following challenge. Although anti-Gag antibodies were not detected after both proviral DNA inoculation and challenge, anti-Env antibodies were found in FIV-pPPR-Δvif-immunized cats after vaccination as well as after challenge. These findings indicate that inoculation with FIV-pPPR-Δvif proviral DNA induced resistance to challenge with infectious FIV and that a vif deletion mutant may provide a relatively safe attenuated lentiviral vaccine
Inhibition of the RNA-Dependent Transactivation and Replication of Human Immunodeficiency Virus Type 1 by a Fluoroquinoline Derivative K-37

AbstractHuman immunodeficiency virus type 1 (HIV-1) is unique in that it encodes its own transcriptional activator Tat, which specifically binds to the viral mRNA sequence TAR (transactivation response) element and activates viral transcription at the step of elongation as well as initiation. We recently reported that fluoroquinoline derivatives inhibited HIV-1 replication most likely by blocking viral transcription. In this report, we investigated the mechanism of action of one such compound 7-(3,4-dehydro-4-phenyl-1-piperidinyl)-1,4-dihydro-6-fluoro-1-methyl-8-trifluoromethyl-4-oxoquinoline-3-carboxylic acid (K-37). We demonstrated that K-37 inhibited not only Tat but also other RNA-dependent transactivators. No effect was observed with DNA-dependent transactivators such as p65 (NF-κB) and Gal4VP16. Moreover, K-37 did not inhibit carboxyl-terminal domain (CTD)-kinase activities of CDK-activating kinase (CAK) and positive transcription elongation factor b (P-TEFb), which are known to be involved in Tat-mediated transactivation at the step of transcriptional elongation. It is suggested that RNA-mediated transactivation may involve a common unknown factor to which K-37 directly interacts. Since K-37 did not appear to block DNA-mediated transactivation and thus did not show strong nonspecific cytotoxicity as reported previously, K-37 and its derivative compounds are considered to be feasible candidates for a novel AIDS therapy
Mutational Analysis of the Putative Receptor-Binding Domain of Moloney Murine Leukemia Virus Glycoprotein gp70

AbstractThe entry of Moloney murine leukemia virus (MoMuLV) to murine cells is mediated by the binding of its envelope glycoprotein gp70 to its receptor, the cationic amino acid transporter MCAT-1. The binding property of the envelope protein lies mainly in the N-terminal half of the protein. To identify essential residues involved in the binding of gp70 to its receptor, we have mutated amino acids within the putative receptor-binding domain of MoMuLV gp70. Changes in the residues P94 and W100 resulted in lower viral titers in comparison to the wild-type virions. Single, double, or triple point mutations involving the residue W100 make the envelope protein severely defective in binding to its receptor. Binding studies and cell fusion experiments with murine XC cells suggested that the residue W100 might play an important role in the process of infection by making contact between gp70 and its receptor
Characterization of a Monoclonal Antibody Directed to the Surface of MA104 Cells That Blocks the Infectivity of Rotaviruses

AbstractRhesus rotavirus (RRV) binds to sialic acid residues on the surface of target cells, and treatment of these cells with neuraminidase greatly reduces virus binding with the consequent reduction of infectivity. Variants that can efficiently infect neuraminidase-treated cells have been isolated, indicating that attachment to sialic acid is not an essential step for animal rotaviruses to infect cells. To identify and characterize the neuraminidase-resistant receptor for rotaviruses, we have isolated a hybridoma that secrets a monoclonal antibody (MAb) (2D9) that specifically blocks the infectivity of wild-type (wt) RRV and of its sialic acid-independent variant nar3, in untreated as well as in neuraminidase-treated cells. The infectivity of a human rotavirus was also inhibited, although to a lesser extent. MAb 2D9 blocks the binding of the variant to MA104 cells, while not affecting the binding of wt RRV; in addition, this MAb blocked the attachment of a recombinant glutathione S-transferase (GST)–VP5 fusion protein, but did not affect the binding of GST–VP8. Altogether these results suggest that MAb 2D9 is directed to the neuraminidase-resistant receptor. This receptor seems to mediate the direct attachment of the variant to the cell, through VP5, while the receptor is used by wt RRV for a secondary interaction, after its initial binding to sialic acid, through VP8. MAb 2D9 interacts specifically with the cell surface by indirect immunofluorescence, immunoelectron microscopy, and FACS. By a solid-phase immunoisolation technique, MAb 2D9 was found to react with three proteins of ca. 47, 55, and 220 kDa, which might form a complex
Defining CTL-Induced Pathology: Implications for HIV

AbstractThe relationship between virus and host cells is multifactorial and nonlinear. This indicates that the effect of an immune response on infection can lead to several different outcomes. These include severe immunopathology. We seek to define properties of CTL-induced pathology in viral infections and examine the implications for HIV disease progression. We find that CTL-induced pathology is observed if the rate of viral replication is fast relative to the CTL responsiveness of the host. Theoretical predictions are consistent with empirical data on LCMV infection. These conditions are also sufficient to induce pathology in HIV infection. However, the absence of HIV-specific CTL can result in an equivalent depletion of the CD4 T cell pool as a consequence of the short life span of activated T cells. A mathematical model describing the evolution of HIV coreceptor usage in the context of lytic and nonlytic CD8 cell responses might account for the relatively long time span required to result in disease. Viral evolution toward parameter ranges allowing CTL-induced pathology is difficult to achieve. It requires the emergence of fast viral replication together with escape from nonlytic CTL responses. However, according to the model, fast viral replication can result in the evolution of virus strains that are susceptible to chemokine-mediated inhibition of viral replication
Genetic Diversity of Primary HIV-1 Isolates and Their Sensitivity to Antibody-Mediated Neutralization

AbstractWide differences exist among primary isolates of HIV-1 in their sensitivity to antibody-mediated neutralization. While it is well documented that even short-term tissue culture amplification of HIV-1 leads to a reduction in the genetic diversity of the viral quasispecies seen in vivo, viral isolates, while relatively homogeneous, are generally not clonal. We investigated whether the extent of genetic diversity within primary viral isolates correlates with their general susceptibility to neutralization. We compared the number of V1V2 and V3-V5 envelope variants detectable within 16 primary isolates selected to represent the extremes of the neutralization sensitive and resistant phenotypes. Using DNA heteroduplex tracking assays to estimate the extent of genetic diversity in these two regions of the envelope locus, we found that these primary isolates were made up of one to five distinguishable V1V2 and V3-V5 sequence variants. We found that higher levels of env genetic diversity did not correlate with increased resistance to antibody neutralization
Neutralization and Enhancement of HIV-1 Infection by Sera from HIV-1 Infected Individuals Who Progress to Disease at Different Rates

AbstractWe examined the neutralizing/enhancing activity in sera collected at an early and a later time point postinfection from 13 HIV-positive nonprogressors, 13 moderate progressors, and 13 rapid progressors to determine the relationship between neutralizing/enhancing activity and disease progression. Early sera from each group reduced virus replication at low dilutions (10−1 to 10−2) when compared with negative sera. The reduction was statistically significant for moderate and rapid progressors at 10−1 dilution (P = 0.02 and P = 0.02 respectively) but not for nonprogressors (P = 0.16). Late sera from nonprogressors and moderate progressors reduced virus replication at low dilution but late sera from rapid progressors lost neutralizing activity. These data suggest that an association exists between neutralizing activity in sera and nonprogression or slower progression to disease and that loss of neutralizing activity is associated with disease progression. At higher dilutions (10−3 to 10−6), both early and late sera from each group increased virus replication over negative sera. The levels and frequency of enhancement were higher for sera from a subgroup of nonprogressors than a subgroup of rapid progressors who exhibited enhancement. This suggests that enhancement is not associated with disease progression. The neutralizing/enhancing activity observed in sera of these three groups of subjects suggest that enhancement levels may reflect the overall level of antibody response to HIV. The replication patterns observed for early and late sera from individuals in the different groups reflect changes in antibody activity that appear to be associated with protection or disease progression
Molecular and Biological Interactions between Two HIV-1 Strains from a Coinfected Patient Reveal the First Evidence in Favor of Viral Synergism

AbstractAn intravenous drug user was found to be dually infected with two genetically and phylogenetically distinct human immunodeficiency virus type 1 (HIV-1) subtype B strains (designated groups I and II). Viral isolation revealed a simultaneous copassaging of two strains in PBMC. The culture of viral strains on monocytes and monocyte-derived macrophages preferentially segregated the two viral strains. The group I strain utilized CXCR4 and group II used CCR5 coreceptor for entry. Sequencing of >100 clones from uncultured PBMC consistently showed the predominance of group II virus in vivo. Importantly, the group II virus alone could not productively infect PBMC, but when used together with group I virus for infection, the group II virus regained its high replication potential and predominance in cultured PBMC. These data are the first to provide direct evidence in favor of molecular and biological interaction between two infecting strains in a coinfected patient and show their differential pathogenic effects, tropism, and modes of entry. In addition, our data provide the first evidence for synergism between these two strains. Cumulatively, these data emphasize that in order to clearly interpret coreceptor usage, biological segregation of viral strains from primary isolates in vitro may be imperative
Induction of Hepatitis C Virus-Specific Cytotoxic T Lymphocytes in Mice by an Intrahepatic Inoculation with an Expression Plasmid

AbstractWe assessed the possibility of intrahepatic inoculation with a plasmid encoding hepatitis C virus (HCV) proteins to elicit HCV-specific cytotoxic T lymphocytes (CTL) in mice as a conventional animal model of HCV infection. BALB/c mice were intrahepatically or intramuscularly inoculated with an expression plasmid DNA encoding HCV structural proteins under the control of the elongation factor 1-α promoter. Expressions of HCV-core protein and envelope proteins (E1 and E2) in hepatocytes were detected immunohistochemically 6 days after inoculation. CTL responses were examined using target cells either pulsed with a specific peptide or infected with a recombinant vaccinia virus expressing HCV structural protein. Both intrahepatically and intramuscularly DNA-inoculated mice developed CD8+, MHC class I-restricted CTL responses that recognized the peptide pulsed as well as HCV proteins expressing target cells. These studies demonstrated the usefulness of a murine model of HCV infection induced by direct intrahepatic DNA inoculation for understanding the immunopathogenic mechanisms in HCV infection
Direct Measurement of CD8+ T Cell Responses in Macaques Infected with Simian Immunodeficiency Virus

AbstractThe simian immunodeficiency virus (SIV) macaque model system has been used extensively to study AIDS pathogenesis and to test candidate vaccines for their ability to protect against homologous or heterologous challenge with pathogenic SIV or SHIV. Recent studies suggest that stimulation of HIV-1-specific CTL responses is important for effective vaccination against HIV-1. While quantitative measurements of SIV-specific cytotoxic T lymphocyte (CTL) responses have been facilitated by the use of tetrameric peptide complexes, this technique is currently limited to the study of Mamu-A*01-positive rhesus macaques. Furthermore, very few SIV-specific CTL epitopes have been identified, and there is limited identification of other MHC alleles in macaques. In this study, cytokine flow cytometry (CFC) was used to quantify SIV-specific CD8+ antigen-reactive T cells in macaques infected with SIV. We found a strong correlation (r = 0.96, P < 0.001) between CD8+ antigen-reactive T cells stained with the Mamu-A*01 p11C, C-M tetramer and production of intracellular TNF-α in the CFC assay. Furthermore, the CFC assay was used to identify a novel SIV-specific CTL epitope in Envelope (SIV Env, a.a. 486–494, sequence AEVAELYRL). The use of the CFC assay facilitates the study of antigen-reactive T cell responses in SIV infection and vaccination
Poliovirus Induces Apoptosis in the Human U937 Promonocytic Cell Line

AbstractThe human promonocytic U937 cell line, which is moderately susceptible to poliovirus infection, has been used to investigate the induction of apoptosis by this virus. Infection of U937 cells with poliovirus induces morphological changes typical of apoptosis. Poliovirus-resistant U937 cells (PRU) have been isolated that are resistant to apoptosis induced by poliovirus, but that undergo apoptosis after treatment with TNF plus cycloheximide. Despite the fact that poliovirus triggers nitric oxide production in U937 cells, the inhibitor of inducible nitric oxide (NO) synthase, Nω-monomethyl-l-arginine, did not hinder apoptosis after infection, suggesting that NO does not play a direct role in this process. Finally, poliovirus infection of U937 cells led to the cleavage of pro-caspase-3 and poly(ADP-ribose)polymerase, indicating the activation of the CPP32 ICE-like cysteine protease in the induction of apoptosis. Our findings suggest that cellular death takes place in U937 cells productively infected by poliovirus as a result of apoptosis and involves caspase activation
Impaired Entry of Soluble Receptor-Resistant Mutants of Mouse Hepatitis Virus into Cells Expressing MHVR2 Receptor

AbstractMouse hepatitis virus (MHV) JHMV and its soluble receptor-resistant (srr) mutants, srr7, srr11, and srr18, grew and induced syncytia equally well in BHK-R1 cells expressing the MHVR1 receptor derived from MHV-susceptible BALB/c mice. In contrast, srr growth and syncytia formations were drastically reduced relative to wild-type (wt) virus in BHK-R2 cells expressing the MHVR2 receptor from MHV-resistant SJL mice. Infections by these srr mutants in BHK-R2 cells were 0.7 to 1.5 log10 less efficient than those of wt virus. BHK cells expressing both MHVR1 and MHVR2 supported srr replication to the same extent as did BHK-R1 cells, suggesting that inefficient infection by srr mutants in BHK-R2 cells resulted from the absence of the effective receptor MHVR1. Virus-receptor binding tests failed to demonstrate a difference between the abilities of wt and srr18 to bind MHVR2. The binding of srr7 and srr11 to both MHVR1 and MHVR2 was revealed lower by two- to fourfold relative to the wt binding. The fusion activity of srr S proteins as examined by the expression with recombinant vaccinia virus was apparently lower than that of the wt S protein in BHK-R2 cells, while there was not such a remarkable difference in BHK-R1 cells. This suggests that the most likely reason for inefficient infection by mutants in BHK-R2 is impaired virus entry into cells. These observations suggest that inefficient infections in BHK-R2 cells by srr mutants occur in the absence of a functional receptor MHVR1, which plays an important role in srr entry into cells
Selective Inhibition of Nuclear Steroid Receptor Function by a Protein from a Human Tumorigenic Poxvirus

AbstractThe poxvirus molluscum contagiosum (MC) has a worldwide distribution and its prevalence is on the rise. Here we report that the MCV MC013L protein inhibits glucocorticoid and vitamin D, but not retinoid or estrogen, nuclear receptor transactivation. A direct interaction of MC013L with glucocorticoid and vitamin D receptor is supported by yeast two-hybrid, GST pull-down, and far Western blot analyses. Glucocorticoids act as potent inhibitors of keratinocyte proliferation, while vitamin D and retinoids promote and block terminal differentiation, respectively. Therefore, MC013L may promote efficient virus replication by blocking the differentiation of infected keratinocytes. MC013L may be the first member of a new class of poxvirus proteins that directly modulate nuclear receptor-mediated transcription
Enveloped Virus Is the Major Virus Form Produced during Productive Infection with the Modified Vaccinia Virus Ankara Strain

AbstractModified vaccinia virus Ankara (MVA) is a highly attenuated virus strain that may be useful as a vaccine vector. Ultrastructural examination of purified MVA showed that most of the viral particles are enveloped in contrast to the Copenhagen strain (COP). In CsCl gradients, the majority of the MVA particles displayed a light buoyant density characteristic of the enveloped form. Consistent with these results, MVA particles were poorly labeled with antibodies against the surface of intracellular mature virus but strongly labeled with antibodies against an envelope antigen. Furthermore, MVA was more resistant than the COP strain to neutralization by mouse anti-COP antibodies. These results suggest that the MVA strain may be particularly suitable for the engineering of envelope proteins and that MVA may be able to resist the humoral immunity displayed by previously vaccinated individuals
Relationship of Oligomerization to DNA Binding of Wheat Dwarf Virus RepA and Rep Proteins

AbstractMembers of the genus Mastrevirus (family Geminiviridae) produce a complementary-sense (c-sense) transcription unit with the potential to encode two proteins, RepA and Rep. In the present work, we have studied the DNA–protein complexes formed by the Wheat dwarf virus (WDV) RepA protein within the WDV large intergenic region. WDV RepA forms large nucleoprotein complexes near the TATA boxes of the viral complementary-sense and virion-sense (v-sense) promoters (the RepA C- and V-complexes, respectively), a location similar to those of WDV Rep–DNA complexes but with distinct DNase I footprints. We have also studied the relationship of oligomerization of WDV RepA and Rep proteins to DNA–protein complex formation. Using chemical cross-linking, we have determined that both WDV proteins can form oligomers in solution. Interestingly, the pH is critical for the monomer–oligomer equilibrium and small changes produce a displacement in such a way that at pH ≤ 7.0, the predominant species is an octamer while at pH ≥ 7.4 it is a monomer. Complex formation is also strongly affected by pH and occurs more efficiently at pH 7.0–7.4. We found that preformed oligomers interact very poorly with DNA. Thus, our data are consistent with a stepwise model for protein–DNA complex assembly in which monomers interact with DNA and then with other monomers to assemble an oligomeric structure on the DNA. These results may be relevant for studies on the DNA binding, replication, and transcription properties of geminivirus proteins