pinecone/core-2020-05-10-deduplication huggingface dataset:
Antigenic Variants of Yellow Fever Virus with an Altered Neurovirulence Phenotype in Mice

AbstractThe live-attenuated yellow fever (YF) vaccine virus, strain 17D-204, has long been known to consist of a heterologous population of virions. Gouldet al.(J. Gen. Virol.70, 1889–1894 (1989)) previously demonstrated that variant viruses exhibiting a YF wild-type-specific envelope (E) protein epitope are present at low frequency in the vaccine pool and were able to isolate representative virus variants with and without this epitope, designated 17D(+wt) and 17D(−wt), respectively. These variants were employed here in an investigation of YF virus pathogenesis in the mouse model. Both the 17D-204 parent and the 17D(+wt) variant viruses were lethal for adult outbred mice by the intracerebral route of inoculation. However, the 17D(−wt) variant was significantly attenuated (18% mortality rate) and replicated to much lower titer in the brains of infected mice. A single amino acid substitution in the envelope (E) protein at E-240 (Ala → Val) was identified as responsible for the restricted replication of the 17D(−wt) variantin vivo.The 17D(+wt) variant has an additional second-site mutation, believed to encode a reversion to the neurovirulence phenotype of the 17D-204 parent virus. The amino acid substitution in the E protein at E-173 (Thr → Ile) of the 17D(+wt) variant which results in the appearance of the wild-type-specific epitope or nucleotide changes in the 5′ and 3′ noncoding regions of the virus are proposed as a candidates
The Virion Host Shutoff Function of Herpes Simplex Virus Type 1 Plays a Role in Corneal Invasion and Functions Independently of the Cell Cycle

AbstractA significant restriction was demonstrated in the ability of herpes simplex virus type 1 virion host shutoff (vhs) mutant viruses to invade the corneal epithelium. Viral replication and invasion was confined to the areas of the cornea which were scarified prior to infection. Differences between wild-type andvhsmutant replication in corneasin vivowere 100- to 1000-fold at all timepoints postinfection. Smaller but still significant growth restrictions were observed in cultured corneal cells. This difference betweenin vitroandin vivois not likely to be due to differences in cell cycle status sincevhs-induced RNA degradation can occur in both cycling and noncycling cellsin vitro.The vhs function is therefore important for invasion of the cornea and secondarily the nervous system and is thereby required for efficient establishment of latency
Microvesicles Are a Source of Contaminating Cellular Proteins Found in Purified HIV-1 Preparations

AbstractIdentification and quantitation of cellular proteins associated with HIV-1 particles are complicated by the presence of nonvirion-associated cellular proteins that copurify with virions. Many cellular proteins are associated with nonviral particles that bud from the surface of cells called microvesicles. Microvesicles band in sucrose gradients in a range of densities that includes the same density as retroviruses. To characterize these microvesicles, HIV-1-infected and uninfected human T-cell lines were propagated and virus and microvesicles were purified from clarified cell culture supernatants by sucrose density gradient centrifugation or centrifugation through 20% sucrose pads. Microvesicles were found to contain various proteins, including HLA DR and β2-M, and a substantial amount of RNA and DNA. The concentrations of HIV-1 p24CA, HLA DR, and β2-microglobulin (β2-M) were determined by radioimmunoassay. The ratios of HIV-1 p24CAto HLA DR and β2-M were found to vary with respect to the HIV-1 isolate, host cell, and other factors. Electron microscopic analysis of microvesicles revealed that they consisted of particles of various sizes and morphologies. Although HIV-1 particles are known to contain some cellular proteins, microvesicles from HIV-1 infected H9 cells appeared to contain little or no HIV-1 gp120SU
Construction of Infectious cDNA Clones for Dengue 2 Virus: Strain 16681 and Its Attenuated Vaccine Derivative, Strain PDK-53

AbstractWe identified nine nucleotide differences between the genomes of dengue-2 (DEN-2) 16681 virus and its vaccine derivative, strain PDK-53. These included a C-to-T (16681-to-PDK-53) mutation at nucleotide position 57 of the 5′-untranslated region, three silent mutations, and substitutions prM-29 Asp to Val, NS1-53 Gly to Asp, NS2A-181 Leu to Phe, NS3-250 Glu to Val, and NS4A-75 Gly to Ala. Unpassaged PDK-53 vaccine contained two genetic variants as a result of partial mutation at NS3-250. We constructed infectious cDNA clones for 16681 virus and each of the two PDK-53 variants. DEN-2 16681 clone-derived viruses were identical to the 16681 virus in plaque size and replication in LLC-MK2cells, replication in C6/36 cells, E and prM epitopes, and neurovirulence for suckling mice. PDK-53 virus and both clone-derived PDK-53 variants were attenuated in mice. However, the variant containing NS3-250-Glu was less temperature sensitive and replicated better in C6/36 cells than did PDK-53 virus. The variant containing NS3-250-Val had smaller, more diffuse plaques, decreased replication, and increased temperature sensitivity in LLC-MK2cells relative to PDK-53 virus. Both PDK-53 virus and the NS3-250-Val variant replicated poorly in C6/36 cells relative to 16681 virus. Unpassaged PDK-53 vaccine virus and the virus passaged once in LLC-MK2cells had genomes of identical sequence, including the mixed NS3-250-Glu/Val locus. Although the NS3-250-Val mutation clearly affected virus replicationin vitro,it was not a major determinant of attenuation for PDK-53 virus in suckling mice
Upstream Stimulatory Factor Family Binds to the Herpes Simplex Virus Type 1 Latency-Associated Transcript Promoter

AbstractThe herpes simplex virus type 1 (HSV-1) latency-associated transcript (LAT) promoter 1 (LP1) is the only viral promoter that exhibits detectable transcriptional activity during a latent HSV infection. The LAT promoter-binding factor (LPBF) regulatory sequence (nucleotides −65 to −72 relative to the transcriptional start site of the 8.3-kb primary transcript) closely resembles the core recognition sequence required for binding members of the upstream stimulatory factor (USF)/major late transcription factor (MLTF) family. In this analysis, we demonstrate that oligonucleotides containing either the LPBF recognition sequence or the USF/MLTF recognition sequences from previously described promoters bind cellular factors which exhibit very similar mobilities in electrophoretic mobility shift (EMS) analyses. We also observe a high degree of similarity in competition profiles obtained in competition EMS analyses utilizing oligonucleotides containing recognition sequences for either LPBF or USF/MLTF. Furthermore, antibody supershift EMS analyses have demonstrated that the factors binding the LPBF or USF/MLTF recognition sites in these oligonucleotides are antigenically related, if not identical, and that greater than 90% of the LPBF-binding activity is antigenically related to USF. In addition, we demonstrate that both forms ofin vitro-translated USF proteins (43 and 44 kDa) bind to the LPBF recognition sequence within HSV-1 LP1. Taken together, these data indicate that USF is capable of binding to the HSV-1 LPBF recognition sequence and that USF is a major LPBF-binding activity in cells of neuronal and nonneuronal lineage. These data further support the hypothesis that USF may indeed play a significant role in the transcriptional activity of HSV-1 LP1
Control of Equine Infectious Anemia Virus Is Not Dependent on ADCC Mediating Antibodies

AbstractHorses infected with equine infectious anemia virus (EIAV) have recurrent episodes of viremia which are eventually controlled, but the immune mechanisms have not been identified. Antibodies were detected to the surface of EIAV-infected cells within 1 month postinfection and remained for at least 3.5 years postinfection. These antibodies recognized cell surface-exposed envelope (Env) glycoproteins, but could not mediate antibody dependent cellular cytotoxicity (ADCC) using EIAV-WSU5-infected equine kidney (EK) cells as targets and peripheral blood mononuclear cells (PBMC) or polymorphonuclear cells (PMN) as effector cells. Furthermore, purified IgG antibodies from horses infected with either EIAV-WSU5 or EIAV-Wyo did not mediate ADCC of infected target cells. Armed effector cells could not be detected in infected horse blood nor could effector cells be prearmed by incubation with serum antibodies to cell surface antigens. The use of EIAV-WSU5-infected equine macrophages as target cells did not result in ADCC. In contrast, serum antibody from EHV-1 vaccinated horses and PBMC or PMN as effector cells caused ADCC of EHV-1-infected EK cells. These results indicate that ADCC is not involved in the control of EIAV in carrier horses
Efficient Autoproteolytic Processing of the MHV-A59 3C-like Proteinase from the Flanking Hydrophobic Domains Requires Membranes

AbstractThe replicase gene of the coronavirus MHV-A59 encodes a serine-like proteinase similar to the 3C proteinases of picornaviruses. This proteinase domain is flanked on both sides by hydrophobic, potentially membrane-spanning, regions. Cell-free expression of a plasmid encoding only the 3C-like proteinase (3CLpro) resulted in the synthesis of a 29-kDa protein that was specifically recognized by an antibody directed against the carboxy-terminal region of the proteinase. A protein of identical mobility was detected in MHV-A59-infected cell lysates.In vitroexpression of a plasmid encoding the 3CLpro and portions of the two flanking hydrophobic regions resulted in inefficient processing of the 29-kDa protein. However, the efficiency of this processing event was enhanced by the addition of canine pancreatic microsomes to the translation reaction, or removal of one of the flanking hydrophobic domains. Proteolysis was inhibited in the presence ofN-ethylmaleimide (NEM) or by mutagenesis of the catalytic cysteine residue of the proteinase, indicating that the 3CLpro is responsible for its autoproteolytic cleavage from the flanking domains. Microsomal membranes were unable to enhance thetransprocessing of a precursor containing the inactive proteinase domain and both hydrophobic regions by a recombinant 3CLpro expressed fromEscherichia coli.Membrane association assays demonstrated that the 29-kDa 3CLpro was present in the soluble fraction of the reticulocyte lysates, while polypeptides containing the hydrophobic domains associated with the membrane pellets. With the help of a viral epitope tag, we identified a 22-kDa membrane-associated polypeptide as the proteolytic product containing the amino-terminal hydrophobic domain
Origins of Dengue Type 2 Viruses Associated with Increased Pathogenicity in the Americas

AbstractThe recent emergence and spread of dengue hemorrhagic fever in the Americas have been a major source of concern. Efforts to control this disease are dependent on understanding the pathogenicity of dengue viruses and their transmission dynamics. Pathogenicity studies have been hampered by the lack ofin vitroorin vivomodels of severe dengue disease. Alternatively, molecular epidemiologic studies which associate certain dengue virus genetic types with severe dengue outbreaks may point to strains with increased pathogenicity. The comparison of nucleotide sequences (240 bp) from the E/NS1 gene region of the dengue virus genome has been shown to reflect evolutionary relationships and geographic origins of dengue virus strains. This approach was used to demonstrate an association between the introduction of two distinct genotypes of dengue type 2 virus and the appearance of dengue hemorrhagic fever in the Americas. Phylogenetic analyses suggest that these genotypes originated in Southeast Asia and that they displaced the native, American genotype in at least four countries. Vaccination and other control efforts should therefore be directed at decreasing the transmission of these “virulent” genotypes
Role of the Amino-Terminal Extracellular Domain of CXCR-4 in Human Immunodeficiency Virus Type 1 Entry

AbstractWe have studied the role of the N-terminal extracellular domain of the human immunodeficiency virus type 1 (HIV-1) coreceptor, CXCR-4, in the entry and fusion of syncytium-inducing strains of HIV-1. Progressive deletions were introduced in the N-terminal extracellular domain of CXCR-4 and the effect on infection by different isolates was tested. Infection of cells expressing the different CXCR-4 deletion mutants by HIV-1 LAI and 89.6 was reduced only about twofold. In contrast, the HIV-1 GUN-1 and RF isolates were substantially more impaired in their ability to mediate cell-free infection and cell–cell fusion. Since LAI and RF are T-cell line-tropic viruses while 89.6 and GUN-1 are dual tropic, no clear correlation between tropism and requirements for CXCR-4 N-terminal sequences emerged. We also introduced point mutations at the two N-linked glycosylation sites. The isolates tested (LAI, RF, GUN-1, and 89.6) were not affected by the removal of predicted N-linked glycosylation sites in CXCR-4. We conclude that distinct virus strains interact differently with the CXCR-4 coreceptor and that the N-terminal extracellular domain is not the sole functional domain important for HIV-1 entry
Differential Immune Recognition of LCMV Nucleoprotein and Glycoprotein in Transgenic Mice Expressing LCMV cDNA Genes

AbstractWe have generated doubly transgenic (DT) mice that independently express cDNA genes for the nucleocapsid protein (NP) and the surface glycoproteins (GP) of lymphocytic choriomeningitis virus (LCMV). By RT-PCR, transcription of both transgenes was detected at low levels in brain and kidney but was not observed in the thymus. Additionally, transcription of the GP transgene was observed in the spleen. Following challenge with exogenous LCMV, an anti-NP CTL response was induced in LCMV-infected DT mice, suggesting that nonresponsiveness to NP had not been established. In contrast, LCMV-infected DT mice were nonresponsive to GP and failed to mount any CTL response against GP, either at Day 7 or Day 30 postinfection or following expansion of splenocyte populationsin vitro.A significant number (33%) of adult DT mice survived intracerebral infection with LCMV, suggesting that virus-induced immunopathology in the central nervous system can be diminished by combined expression of the transgenes whereas no protective effect was conferred on singly transgenic mice, expressing NP or GP alone. The DT mice therefore create a novel host genetic background for comparative studies of the anti-LCMV immune responses relative to parental C57Bl/6 mice
CD4-Independent Infection by HIV-2 (ROD/B): Use of the 7-Transmembrane Receptors CXCR-4, CCR-3, and V28 for Entry

AbstractWe have assayed a variety of 7tm chemokine receptors (CCR-2b, CCR-3, CCR-4, CCR-5, CXCR-1, CXCR-4) and two orphan 7tm receptors (V28 and EBI.1) for their ability to allow infection of CD4-negative feline kidney CCC cells by the HIV-2 strains ROD/A and ROD/B. We found that ROD/B was able to use CXCR-4 transiently expressed in CCC cells, and infection by ROD/A was enhanced 15-fold in the presence of sCD4. Feline CCC cells also became permissive to ROD/B and ROD/A entry when transiently transfected with the chemokine receptor CCR-3 or the orphan 7tm receptor V28, when cultured in the presence of sCD4. Entry of ROD/A into CCC cells expressing CCR-3 could be blocked by 800 ng/ml eotaxin, the natural ligand for CCR-3
Repression of Bax Gene Expression by the HTLV-I Tax Protein: Implications for Suppression of Apoptosis in Virally Infected Cells

AbstractThe human T-cell leukemia virus-encoded oncoprotein Tax is a potent deregulator of cellular gene expression. Here we report that Tax represses transcription of the humanbaxgene, a gene whose protein product accelerates apoptosis. This repression is mediated through a 27-bp sequence in thebaxpromoter that contains a putative basic helix–loop–helix binding site. Deletion of this sequence abolishes Tax-mediated repression ofbax.Repression of thebaxgene may be biologically significant, as we also show that HTLV-I-infected cell lines are resistant to a variety of physical, chemical, and biological stimuli which induce apoptosis in uninfected T-cells. The repression of genes involved in promoting apoptosis, including thebaxgene, may contribute to retroviral survival, and initiate a pathway toward malignant transformation
Sequence Analysis of HIV-1 Group O from Norwegian Patients Infected in the 1960s1

AbstractThree Norwegians, a couple and their daughter, died from AIDS in 1976 after up to 10 years of clinical manifestations of HIV infection (Lindboeet al.,1986,Acta Pathol. Microbiol. Immunol. Scand.94, 117–123; Frølandet al.,1988,Lanceti, 1344–1345). We here demonstrate the presence of HIV DNA in autopsy materials from the father and the daughter. In phylogenetic analysis, the obtained sequences of the HIVpolandvifgenes clustered with the HIV-1 group O clade. The genotyping was confirmed by detection of antibodies against HIV-1 group O in blood samples from the father and the mother. That these and other early isolates of HIV-1 are very similar to the presently circulating viruses and not intermediates between the present subtypes, verifies that the latest common ancestor of HIV-1 existed long before the emergence of the present epidemic. The presence of HIV-1 group O 30 years ago suggests that the limited spread of these viruses, compared to HIV-1 group M viruses, is not due to a later emergence of the group O viruses
ThetaxGene Sequences Form Two Divergent Monophyletic Lineages Corresponding to Types I and II of Simian and Human T-Cell Leukemia/Lymphotropic Viruses

AbstractEvolutionary associations of human and simian T-cell leukemia/lymphotropic viruses I and II (HTLV-I/II and STLV-I/II) are inferred from phylogenetic analysis oftaxgene sequences. Samples studied consisted of a geographically diverse assemblage of viral strains obtained from 10 human subjects and 20 individuals representing 12 species of nonhuman primates. Sequence analyses identified distinct substitutions, which distinguished between viral types I and II, irrespective of host species. Phylogenetic reconstruction of nucleotide sequences strongly supported two major evolutionary groups corresponding to viral types I and II. With the type I lineage, clusters were composed of strains from multiple host species. A genetically diverse, monophyletic lineage consisting of eight new viral strains from several species of Asian macaques was identified. The second lineage consisted of a monophyletic assemblage of HTLV-II/STLV-II strains from Africa and the New World, including an isolate from a pygmy chimp (Pan paniscus) as an early divergence within the lineage. High levels of genetic variation among strains from Asian STLV-I macaque suggest the virus arose in Asia. Evidence of the origin of the type II virus is less clear, but diversity among HTLV-II variants from a single isolated population of Mbati villagers is suggestive but not proof of an African origin
Immunosenescence in HIV Pathogenesis

AbstractTelomeres are complex protein–DNA structures located at the ends of eukaryotic chromosomes. In a normal cell, telomere DNA shortens with cell divisions. Such a telomere loss may act as a mitotic clock to eventually signal cell cycling exit and cellular senescence. In a transversal study, we found a marked decrease in telomere length of peripheral blood mononuclear cells in HIV-infected patients with advanced immunodeficiency. This telomere reduction concerns T4, T8, and B lymphocytes, providing evidence of high turnover of these cells in the course of HIV infection. These data suggest that replicative senescence could be involved in the final immunosuppression and may have important therapeutical implications
In VitroSelection for Different Mutational Patterns in the HIV-1 Reverse Transcriptase Using High and Low Selective Pressure of the Nonnucleoside Reverse Transcriptase Inhibitor HBY 097

AbstractIn vitroresistance of HIV-1 against high levels of HBY 097 ((S)-4-isopropoxycarbonyl-6-methoxy-3-(methylthiomethyl)-3,4-dihydro-quinoxaline-2(1H)-thione) and other quinoxaline nonnucleoside reverse transcriptase inhibitors (NNRTIs) is characterized by a specific amino acid substitution in the reverse transcriptase (RT), Gly190Glu. This change results in decreased RT polymerase activity and in reduced growth properties of the corresponding viral variant. Here we show that the appearance of the crippling mutation at codon 190 can be prevented by lowering the selective pressure exerted by HBY 097. Under low selective pressure an accumulation of other NNRTI-specific mutations is observed. Up to five NNRTI-specific substitutions were detected in some of these virus lineages. In addition, we report novel RT amino acid changes which were not observed previously, including Val106Ile, Val106Leu, and Gly190Thr. HBY 097 selects for different mutational patterns under high and low selective pressure conditions, respectively. Thus, the type of mutations which appear in HIV-infected patients undergoing therapy may be determined by the levels of the selecting drug
Continued Evolution of H1N1 and H3N2 Influenza Viruses in Pigs in Italy

AbstractSwine influenza viruses possessing avian genes were first detected in Europe in 1979 (Scholtisseket al.,1983,Virology,129, 521–523) and continue to circulate in pigs in that region of the world. To characterize the molecular epidemiology of swine influenza viruses currently circulating in Europe, we used dot-blot hybridization and sequence analysis to determine the origin of the genes encoding the nonsurface proteins (“internal” genes) of 10 H1N1 and 11 H3N2 swine influenza viruses isolated in Italy between 1992 and 1995. All of the 126 genes examined were of avian origin; thus the currently circulating H3N2 strains which possess A/Port Chalmers/1/73-like surface glycoproteins appear to be descendants of the reassortant human–avian viruses that emerged between 1983 and 1985 in Italy. Sequence analysis of matrix (M), nonstructural, and nucleoprotein genes, as well as phylogenetic analysis of M gene showed that the H1N1 and H3N2 viruses from the pigs were closely related to recent isolates of the avian-like swine H1N1 influenza strain currently circulating in northern Europe and were distinguishable from the genes of viruses isolated from European swine in 1979. To evaluate the frequency of transmission of swine H1N1 and H3N2 viruses to man, we tested 123 human sera for hemagglutination-inhibiting antibodies against avian and mammalian H1N1 and H3N2 virus strains. Our findings indicate that swine influenza viruses possessing A/Port Chalmers/1/73-like hemagglutinin may have transmitted to approximately 20% of young persons under 20 years of age who had contact with pigs. Thus, H3N2 swine viruses, possibly possessing avian-derived internal genes, may be entering humans more often than was previously thought. We strongly recommend that pigs be regularly monitored as a potential early warning system for detection of future pandemic strains