pinecone/core-2020-05-10-deduplication huggingface dataset:
Effect of Mutations in the Small Envelope Protein of Hepatitis B Virus on Assembly and Secretion of Hepatitis Delta Virus

AbstractThe gene coding for the small (S) envelope protein of hepatitis B virus was mutated to identify sequences important for the envelopment of the nucleocapsid during morphogenesis of hepatitis delta virus (HDV) virions. This study was focused on a domain of the S protein that is exposed in the cytoplasm during synthesis and thereby represented a good candidate for interaction with the viral nucleocapsid during virion assembly. The mutations consisted of deletion/insertions spanning the entire cytosolic domain of S between amino acid residues 24 and 80. Although the expression of mutants clustered between residues 59 and 80 could not be obtained, we demonstrated that a large part of the cytosolic loop, from residues 29–47 and 49–59, does not contain motifs essential for production of hepatitis B virus subviral particles or HDV virions. However, deletion of residues 24–28 led to the synthesis of S protein mutant, which was competent for secretion of subviral particles but deficient for production of HDV. We concluded that the sequence between Arg-24 and Ile-28 located at the carboxyl boundary of the transmembrane signal I for S contains residue or residues important for HDV particle assembly
The Effect of Low-Profile Serine Substitutions in the V3 Loop of HIV-1 gp120 IIIB/LAI on the Immunogenicity of the Envelope Protein

AbstractMany microbial antigens contain powerful hypervariable epitopes that fail to induce broadly protective immunity because they dominate the immune response at the expense of more conserved but weaker epitopes. If the undesired B cell epitopes are eliminated, the immune system could be focused on the conserved epitopes and produce a stronger antibody response to conserved parts of the protein and thus become a more efficacious immunogen for a vaccine. We examined this possibility using the human immunodeficiency virus envelope glycoprotein (gp)120 IIIB/LAI and selectively replaced the amino acids from the V3 region and analyzed the overall immunogenicity of the mutant proteins after nucleic acid immunization in mice. The most variable residues of the human immunodeficiency virus type 1 gp120 V3 loop sequence were replaced with serine, which has a small uncharged hydrophilic side chain and therefore is likely to be less immunogenic than amino acids found in wildtype V3 sequences. The serine substitutions did not affect the ability of soluble CD4 to bind the mutant molecules compared with wildtype gp120 and monoclonal antibodies against both linear and discontinuous epitopes located in the V1/V2, C1, and C4 regions of the molecule. These data suggest that the V3 loop substitutions did not grossly affect the overall conformation of the envelope molecule. Immunization of CBA × BALB/c F1 mice with DNA expression plasmids for the wild-type gp120 sequence induced a predominantly IgGIantibody response with end point titers of 104–5 × 104. The antibodies reacted only with conformationally intact gp120. Serine replacements targeted to both sides of the V3 loop had a major impact on gp120 immunogenicity, with a markedly reduced response in the majority of animals tested. Analysis of the epitope specificity of the responses suggests that N-terminal amino acids in the V3 loop contribute to the major immunodominant epitope and provides no evidence that their removal enhances immunogenicity of the conserved regions
Murine Antibodies against E2 and Hypervariable Region 1 Cross-Reactively Capture Hepatitis C Virus

AbstractThe absence of readily available animal and cell culture models for hepatitis C virus (HCV) replication has bottlenecked research on protective immunity to HCV infection. Antibodies reactive with HCV virionsin vitroare assumed to be candidates for neutralizing or inhibitory antibodies against HCV. To find potentially neutralizing or inhibitory antibody candidates, anti-C, anti-E1, anti-E2, and anti-HVR1 antisera acquired from mice immunized with corresponding recombinant proteins or synthetic peptides were used to capture HCV viral particlesin vitrobased on antibody–virus interaction assays. Both anti-E2 and anti-HVR1 antibodies effectively captured HCVin vitro. Furthermore, it was found that anti-E2 and anti-HVR1 antibodies could immunoprecipitate an isolate of HCV unrelated to the original antigenic HCV isolate. ELISA confirmed that anti-HVR1 antibodies cross-reactively bind to these unrelated HVR1 peptides. These findings suggest that anti-E2 and anti-HVR1 antibodies induced in mice have the ability to bind with HCV particles in an isolate cross-reactive manner and highlight the possible application of combining several sequences of HVR1 to generate broadly reactive anti-HVR1 antibodies
Competitionin Vivobetween a Cytopathic Variant and a Wild-Type Duck Hepatitis B Virus

AbstractSeveral examples of human hepatitis B virus strains with enhanced replicationin vitrohave been described. To understand whether this characteristic could be a cause of liver disease, we have studied a variant of the closely related duck hepatitis B virus (DHBV) that had enhanced levels of cccDNA accumulation, previously shown to be cytopathicin vitro,as a model for the pathogenesis of analogous viruses in humans.In vivoliver damage caused by this variant (G133E) occurred only during the first 2 weeks p.i., after which time cccDNA levels and liver histology returned to near normal despite continued virus replication. To determine whether recovery was due to the emergence of noncytopathic revertant, we tested whether wild-type virus would have a selective advantage in competition with the cytopathic mutant in a fully infected liver. In a mixed infection of ducklings with G133E and a small amount of wild-type virus, the wild-type virus was detected as the predominant genotype after recovery of normal liver histology. Two candidate revertant viral genomes were cloned directly from the serum virus of G133E-infected birds after recovery and tested for (i) control of cccDNA levels in primary hepatocyte cultures and (ii) their ability to compete with wild-type virus in a mixed infection. At least one noncytopathic revertant was identified by these two criteria. The results support the conclusion that the recovery from liver damage in G133E-infected ducklings was due to the emergence of spontaneous noncytopathic revertants rather than to host suppression of virus cytotoxicity. The results indicate that acute liver injury may result from infection with a cytopathic hepadnavirus but that such viruses may be rapidly replaced by noncytopathic variants during persistent infection
Rubella Virus Induces Apoptosis in Culture Cells

AbstractThe replication of rubella virus (RUB) in Vero cells, an adherent cell line, results in apoptotic death of infected cells as detected by chromatin fragmentation assays. In infected cultures, virtually all of the cells that had become detached (a hallmark feature of RUB-induced cytopathology) were apoptotic; they were predominantly dead as shown by propidium iodide and trypan blue exclusion tests. In contrast, the majority of the cells in the infected monolayers that remained adherent were alive and contained intact chromatin. Thus simple counting of detached cells in the medium is a convenient way of measuring the extent of RUB-induced apoptosis. RUB-induced cytopathology was inhibited by z-VAD-fmk, an inhibitor of caspases that are involved in the execution stages of apoptosis, confirming the induction of apoptosis by RUB. The lack of apoptotic adherent cells (maximally 1% at any time point through 6 days postinfection) indicates that the induction of apoptosis is asynchronous since cells become uniformly virus antigen-positive by day 2 postinfection. To elucidate whether this asynchronicity and the ability of RUB to persistently infect Vero cells were due to a suppression of apoptosis, we examined whether RUB can suppress chemically induced apoptosis. Staurosporine (ST) was found to be an efficient inducer of apoptosis in Vero cells. ST treatment of RUB-infected and RUB persistently infected cells resulted in a much higher proportion of detached cells, higher even than in Vero cells treated with ST alone. This indicates that RUB does not suppress ST-induced apoptosis and, rather, that ST and RUB acted cumulatively in inducing apoptosis, possibly indicating that they use different induction pathways
Rescue of the Epstein–Barr Virus BZLF1 Mutant, Z(S186A), Early Gene Activation Defect by the BRLF1 Gene Product

AbstractExpression of the Epstein–Barr virus (EBV) immediate-early protein, BZLF1 (Z), is sufficient to disrupt viral latency. Z transcriptionally activates the EBV early genes by binding to upstream Z-responsive elements (ZREs). Recently, a serine-to-alanine mutation of Z residue 186 (within the basic DNA binding domain) was shown to inhibit the ability of Z to induce lytic infection in latently infected cells, although the Z(S186A) mutant could still bind several known ZREs and activated an early EBV promoter (BMRF1) in transient reporter gene assays (Francis, A. L., Gradoville, L., and Miller, G. (1997).J. Virol.71, 3054–3061). We now show that a specific deficiency in the ability to bind to ZRE elements in the immediate-early BRLF1 promoter may account for the inability of Z(S186A) to activate BRLF1 expression. Furthermore, we demonstrate that the ability of Z(S186A) to induce early BMRF1 and BHRF1 gene expression is rescued by cotransfection with a BRLF1 expression vector. However, the Z(S186A)/BRLF1 (R) combination cannot induce full lytic replication, suggesting that Z(S186A) may also be deficient in a replication-specific function. These results suggest that in the context of the intact viral genome, both Z and R expression are required for activation of early gene transcription in latently infected cells
Marker Rescue of the Host Range Restriction Defects of Modified Vaccinia Virus Ankara

AbstractThe severely attenuated and host range (HR) restricted modified vaccinia virus Ankara (MVA) was derived by >500 passages in chick embryo fibroblasts, during which multiple deletions and mutations occurred. To determine the basis of the HR defect, we prepared cosmids from the parental vaccinia virus Ankara genome and transfected them into nonpermissive monkey BS-C-1 cells that had been infected with MVA. Recombinant viruses that formed macroscopic plaques were detected after transfections with DNA segments that mapped near the left end of the viral genome. Plaque-forming viruses, generated by transfections with four individual cosmids and one pair of minimally overlapping cosmids, were purified, and their HRs were evaluated in BS-C-1 cells, rabbit RK-13 cells, and human HeLa, MRC-5, and A549 cells. The acquisition of the K1L and SPI-1 HR genes and the repair of large deletions were determined by polymerase chain reaction or pulse-field gel electrophoresis ofNotIrestriction enzyme digests of genomic DNA. The following results indicated the presence of previously unrecognized vaccinia virus HR genes: (1) the major mutations that restrict HR are within the left end of the MVA genome because the phenotypes of some recombinants approached that of the parental virus, (2) acquisition of the K1L gene correlated with the ability of recombinant viruses to propagate in RK-13 cells but did not enhance replication in human or monkey cell lines, (3) acquisition of the SPI-1 gene correlated with virus propagation in A549 cells but not with the extent of virus spread in monkey or other human cell lines, (4) there are at least two impaired HR genes because rescue occurred with nonoverlapping or minimally overlapping cosmids and recombinant viruses with intermediate HRs were isolated, and (5) at least one of the new HR genes did not map within any of the major deletions because the size of the left terminalNotIfragment was not appreciably altered in some recombinant viruses
HIV-1 Gag Proteins: Diverse Functions in the Virus Life Cycle

AbstractThe Gag proteins of HIV-1, like those of other retroviruses, are necessary and sufficient for the assembly of virus-like particles. The roles played by HIV-1 Gag proteins during the life cycle are numerous and complex, involving not only assembly but also virion maturation after particle release and early postentry steps in virus replication. As the individual Gag domains carry out their diverse functions, they must engage in interactions with themselves, other Gag proteins, other viral proteins, lipid, nucleic acid (DNA and RNA), and host cell proteins. This review briefly summarizes our current understanding of how HIV-1 Gag proteins function in the virus life cycle
Intracellular Trafficking and Interactions of the HIV-1 Tat Protein

AbstractFusions of the human immunodeficiency virus type 1 (HIV-1) transactivator protein Tat to the green fluorescent protein (GFP) were used to study the intracellular localization, trafficking, and interactions of Tat in human cells. Tagging Tat with GFP did not change its nuclear localization or ability to act as a transactivator. Tat-GFP expressed at low levels was found in the nucleus, whereas overexpression resulted in nucleolar accumulation. A Tat-GFP hybrid protein containing in addition the HIV-1 Rev nuclear export signal (NES) localized predominantly to the cytoplasm. This shuttle protein, Tat-GFP-NES, transactivated the HIV-1 long terminal repeat. Thus a Tat molecule being only transiently present in the nucleus is active and nucleolar accumulation of Tat is not prerequisite for function. A coexpression assay previously used to define protein interaction domains in the HIV-1 Rev protein [R. H. Stauber, E. Afonina, S. Gulnik, J. Erickson, and G. N. Pavlakis (1998a).Virology251, 38–48.] indicated that Tat exists predominantly as a monomer and does not form stable multimers with B23 in living cells. Using a heterokaryon fusion assay, we found that Tat-GFP was able to shuttle between the nucleus and the cytoplasm. Tat therefore has the potential to perform functions in the nucleus as well as in the cytoplasm
Inefficient Recognition of Autologous Viral Sequences by Intrahepatic Hepatitis C Virus-Specific Cytotoxic T Lymphocytes in Chronically Infected Subjects

AbstractCytotoxic T lymphocytes (CTL) capable of recognizing prototype hepatitis C virus (HCV) sequences have been shown to localize to the liver in chronically infected individuals, where they are thought to influence hepatic inflammation and viral replication. We isolated three intrahepatic CD8+CTL clones from two individuals with chronic HCV infection and compared the recognition of prototype and autologous HCV sequences. These CTL recognized epitopes within the NS2 (amino acids 957–964) or NS3 (amino acids 1402–1410 and 1406–1415) proteins in the context of HLA B37, B8, or A2.1, respectively. The corresponding predominant autologous HCV sequences (SDWAANGL, ELAAKLVGL, and ALRGMGVNAV, respectively) differed from the HCV-1 sequences used for screening (RDWAHNGL, ELAAKLVAL, and KLVALGINAV, respectively) at one to five residues. For each CTL clone, recognition of the autologous HCV sequence required significantly higher peptide concentrations than did recognition of the HCV-1 sequence; for two of the clones, recognition was minimal or absent at peptide concentrations as high as 25 μM. These data show that intrahepatic HCV-specific CD8+CTL clones can be relatively inefficient at recognizing autologous viral epitopes. Inefficient recognition of autologous HCV sequences should influence the interpretation of data generated using prototype HCV sequences and might have implicationsin vivo
Phylogeographic Patterns of Feline Immunodeficiency Virus Genetic Diversity in the Domestic Cat

AbstractFeline immunodeficiency virus (FIV) has a worldwide distribution among feral and domesticated cats and in many cases induces immunodeficiency disease analogous to that of human acquired immune deficiency syndrome. FIV is genetically homologous to human immunodeficiency virus (HIV) in both genome organization and gene sequence and, like HIV, exhibits enormous sequence variation throughout the range of host species. We sampled 91 feral cats from six disparate locales and studied the phylogenetic relationships of viral DNA from infected cats using bothpolandenvgenes (520 and 684 bp, respectively). The patterns from the two genes recapitulated previously described major FIV clades and showed concordance between phylogenetic patterns of thepolandenvgenes. Evidence for recombination between thepolandenvgenes was not found among a sampling of nine isolates, although evidence for intragenic exchange within theenvgene was observed in two isolates. A small local population of cats from a rural farm in the United Kingdom had a remarkably high FIV antibody prevalence (47%), but displayed 8-fold less overall diversity of FIV genomic variation compared with FIV from different parts of the world. We interpret this low variation as a consequence of a recent monophyletic introduction of FIV into the population
Rotavirus Disease, but Not Infection and Development of Intestinal Histopathological Lesions, Is Age Restricted in Rabbits

AbstractThe rabbit model of rotavirus infection has proved to be useful for assessing active immunity and protection after infection or vaccination with virus or virus-like particles. One limitation of the rabbit model is that after experimental infection of rabbits, clinical diarrhea is not routinely induced. Lack of diarrhea in the rabbit model has been proposed to be due to the fluid absorptive capability of the cecum or attenuation of virus strains through tissue culture adaptation. To test whether a wild-type lapine rotavirus strain BAP (BAPwt) isolated from diarrheic rabbits would cause disease on passage in rabbits, 1-, 2-, 10-, and 16-week-old rabbits were orally inoculated with BAPwt, its tissue culture-adapted counterpart strain (BAP-2), tissue culture-adapted lapine strain ALA, or PBS. Lapine rotavirus infection in 1-week-old, but not ≥2-week-old, rabbits resulted in the development of disease characterized by soft, wet, yellow-to-brownish-green partially formed-to-liquid stools observed only at the time of virus antigen shedding. The level and duration of virus shedding after infection were prolonged in 1-week-old rabbits compared with rabbits ≥2 weeks of age. Although diarrhea was not observed beyond the first 2 weeks of life, histopathological changes, including villus shortening and fusion, increased vacuolation of epithelial cells, and mononuclear infiltration of the lamina propria, were observed throughout the small intestine between 12 and 120 h after ALA infection in 1-week-old, 1- to 2-month-old, and 11-month-old rabbits. In 11-month-old rabbits, onset of intestinal damage appeared to be slightly delayed, was less severe, and was not observed in the duodenum. There were no differences in the immune responses to rotavirus infection in rabbits of different age groups (1 week to 5 years of age). All lapine rotavirus-inoculated rabbits seroconverted and were protected from virus challenge at 28 days postinoculation. Like in mice, rotavirus disease is age restricted in rabbits
Virological Importance of the Protease-Cleavage Site in Human Immunodeficiency Virus Type 1 Nef Is Independent of both Intravirion Processing and CD4 Down-regulation

AbstractThe HIV-1 Nef protein is present within the virion and is processed there by the viral protease. Mutational analysis indicated that residues 54–60 in HIV-1 Nef were required for intravirion cleavage. When viruses were produced using T cell lines or primary lymphoblasts, these residues were also required for optimal viral infectivity. However, substitution of native Nef residues with those of a functional Gag cleavage site demonstrated that intravirion cleavage was insufficient for the virological function of this domain. Furthermore, the importance of certain cleavage site residues to infectivity was conditional on the producer cell type. In particular, a mutant containing a deletion of residues 54–57 was phenotypicallynefdefective when produced using T cells (CEM, A2.01, or primary lymphoblasts) but was minimally impaired when produced from 293 or HeLa cells. This mutant was cleavage resistant, indicating that proteolytic processing of Nef was dispensable for infectivity enhancement when virions were assembled in certain non-T cells. Residues 54–61 of the cleavage site, including 54–57, were also required for Nef-mediated down-regulation of CD4. However, the surface expression of CD4 on HeLa cells in amounts comparable to that on the surface of primary T lymphoblasts did not create a producer cell environment in which residues 54–57 acquired greater virological importance. Furthermore, these residues were required for optimal infectivity even during virion assembly in T cells (A2.01) that expressed a CD4 molecule that is unable to respond to Nef. These data suggested that in producer T cells, certain cleavage site residues (54–57) contribute to a Nef-mediated virological effect that is unlikely to be linked causally to CD4 down-regulation. Conversely, in the context of 293 cells as viral producers, the Δ54–57 mutant separated genetically down-regulation of CD4 (for which it was defective) from enhancement of infectivity (for which it was functional). Together, these data indicate that the virological function of the cleavage site domain is both independent of intravirion proteolytic processing of Nef and independent of CD4 down-regulation
A Novel Kinase Activity Associated with Nef Derived from Neurovirulent Simian Immunodeficiency Virus

AbstractThe Nef proteins of Simian immunodeficiency virus (SIV) and human immunodeficiency virus (HIV) have been shown to associate with several cellular kinases. Further, the ability of SIVmac239 Nef to associate with a p21-activated kinase (PAK)-related kinase has been correlated with pathogenic progression to AIDS in rhesus macaques. Because the ability of Nef to associate with the PAK-related kinase is viral isolate dependent, we reasoned that viral isolates derived from distinct physiological locations may encode Nef proteins that exhibit distinct kinase association profiles. In this study, we compared kinase activities associated with Nef proteins derived from the prototypic lymphocyte-tropic SIVmac239 and a macrophage-tropic, neurovirulent clone, SIV/17E-Fr. Our findings not only support previous studies that have documented the association of SIVmac239 Nef with a PAK-related kinase and a Nef-associated kinase complex (NAKC) but describe a novel serine kinase activity detectable only in conjunction with the Nef protein derived from the neurovirulent clone, SIV/17E-Fr. The latter Nef protein does not associate with PAK, and unlike PAK or NAKC, this novel kinase activity is enhanced in association with nonmyristoylated forms of Nef and can utilize both ATP and GTP as phosphodonors. We also show that at least one substrate for the kinase is Nef itself and demonstrate that the SIV/17E-Fr Nef protein is phosphorylated in SIV-infected cells. These results suggest that the ability to associate with cellular kinases in general may be a conserved feature of Nef, but particular kinase/Nef associations may evolve with changes in the host environment concomitant with viral spread
The Truncated Form of the Epstein–Barr Virus LMP-1 Is Dispensable or Complimentable by the Full-Length Form in Virus Infection and Replication

AbstractThe Epstein–Barr virus (EBV) latent membrane protein-1 (LMP-1) gene of the Akata virus strain was cloned, and its nucleotide sequence was determined. Compared with the B95–8 strain, the translation initiation codon for the truncated LMP-1 gene, which is expressed in the lytic cycle, was lost. Immunoblotting showed that Akata EBV produces no truncated LMP-1 protein in any state and that the full-length LMP-1 protein is expressed at a significant level during lytic infection. The results suggest that the truncated LMP-1 protein is dispensable for EBV infection and replication or that the full-length form can “functionally” complement the truncated form if the truncated form has a function