pinecone/core-2020-05-10-deduplication huggingface dataset:
Productive Infection of Human Primary Cells and Cell Lines with Porcine Endogenous Retroviruses

AbstractPorcine endogenous retroviruses (PERVs) infect human cells in vitro and therefore represent a risk for xenotransplantation. However, first clinical transplantations of pig cells into humans or ex vivo perfusions did not result in transmission of PERVs. On the other hand, recent experiments with SCID mice demonstrated infections with PERV in vivo. In order to define and characterize human target cells, we studied numerous primary human cells and cell lines. Infection with PERVs was shown for human peripheral blood mononuclear cells, primary endothelial cells, and primary aortic smooth muscle cells as well as lymphocytic, monocytic, and epithelial cell lines
Intron Conservation in the DNA Polymerase Gene Encoded by Chlorella Viruses

AbstractPreviously we reported that 19 of 42 viruses that infect Chlorella strain NC64A (NC64A viruses) contain a short, nuclear-located, spliceosomal-processed intron in a pyrimidine dimer-specific glycosylase/apyrimidine lyase (pdg) gene. Surprisingly, the nucleotide sequence of the intron region is more conserved than the exon regions of the gene (L. Sun et al., 2000, J. Mol. Evol. 50, 82–92). For comparative purposes, we determined the nucleotide sequence of a similar intron type and its flanking coding regions in the DNA polymerase (dnapol) gene from the same 42 NC64A viruses and also 5 viruses that infect Chlorella strain Pbi. Thirty-eight of the 42 NC64A viruses contained a 101-nucleotide intron and the remaining 4 had an 86-nucleotide intron located in the same position in dnapol. The 4 viruses with the smaller intron in dnapol also have a smaller intron in their pdg gene. There was no intron in the dnapol gene of the 5 Pbi viruses. Phylogenetic analyses indicate that the dnapol genes containing the 86-nucleotide intron represent the ancestral condition among the NC64A viruses. The intron in the dnapol gene is phase 0 (keeps codons intact), which differs from the phase 1 intron in the pdg gene. The intron in the dnapol gene, unlike the pdg intron, was conserved (83 to 100% identical) to about the same extent as the coding regions of the gene (78 to 100% identical)
Molecular and Genetic Evidence for a Virus-Encoded Glycosyltransferase Involved in Protein Glycosylation

AbstractThe major capsid protein, Vp54, of chlorella virus PBCV-1 is a glycoprotein that contains either one glycan of ∼30 sugar residues or two similar glycans of ∼15 residues. Previous analysis of PBCV-1 antigenic mutants that contained altered Vp54 glycans led to the conclusion that unlike other glycoprotein-containing viruses, most, if not all, of the enzymes involved in the synthesis of the Vp54 glycan are probably encoded by PBCV-1 (I.-N. Wang et al., 1993, Proc. Natl. Acad. Sci. USA 90, 3840–3844). In this report we used molecular and genetic approaches to begin to identify these virus genes. Comparing the deduced amino acid sequences of the putative 375 PBCV-1 protein-encoding genes to databases identified seven potential glycosyltransferases. One gene, designated a64r, encodes a 638-amino-acid protein that has four motifs conserved in “Fringe type” glycosyltransferases. Analysis of 13 PBCV-1 antigenic mutants revealed mutations in a64r that correlated with a specific antigenic variation. Dual-infection experiments with different antigenic mutants indicated that viruses that contained wild-type a64r could complement and recombine with viruses that contained mutant a64r to form wild-type virus. Therefore, we conclude that a64r encodes a glycosyltransferase involved in synthesizing the Vp54 glycan. This is the first report of a virus-encoded glycosyltransferase involved in protein glycosylation
A Plasmid of Phytoplasma Encodes a Unique Replication Protein Having Both Plasmid- and Virus-like Domains: Clue to Viral Ancestry or Result of Virus/Plasmid Recombination?

AbstractThe genomes of most prokaryotic and eukaryotic single-stranded (ss) DNA viruses, and some prokaryotic plasmids such as pLS1, commonly replicate via a rolling circle replication (RCR) strategy, and thus the viruses are hypothesized to have evolved from the plasmids, although evidence for this view is sparse. We have sequenced a circular plasmid of 3933 nt, pOYW, obtained from onion yellows phytoplasma (OY-W), a cell-wall-less, unculturable prokaryote that inhabits the cytoplasm of both plant and insect cells. pOYW contains five open reading frames (ORFs) on the same strand and apparently replicates by an RCR mechanism. Its rep gene (ORF5) encodes a unique protein, pOYW-Rep, with an unprecedented structure. The N-terminal region of pOYW-Rep has similarities to the RCR initiator protein (Rep) of pLS1 family plasmids but, unlike the Rep of other plasmids, its C-terminal region was unexpectedly similar to the helicase domain of the replication-associated proteins (Rap) of eukaryotic viruses, especially circoviruses (ssDNA viruses of vertebrates). The pOYW-Rep was specifically detected in OY-W-infected plant phloem cells, suggesting that it is a functional protein. We suggest that an ancestral phytoplasma plasmid pOYW may have acquired a helicase domain from host phytoplasmal DNA, entered the surrounding eukaryotic cytoplasm, and subsequently evolved into an ancestral eukaryotic ssDNA virus. Alternatively, a pOYW ancestor could have obtained the helicase domain by recombination with a virus: this would be the first example of recombination between plasmids and viruses
Mutations in the GDD Motif of Rubella Virus Putative RNA-Dependent RNA Polymerase Affect Virus Replication

AbstractRubella virus (RV) nonstructural proteins are translated as a p200 polyprotein that undergoes proteolytic cleavage into p150 and p90. From conserved amino acid sequence motifs in polypeptides, p90 has been proposed to be the RV RNA-dependent RNA polymerase (RdRp). To test whether the conserved GDD motif is involved in RdRp catalytic activity, three different alanine substitutions were introduced into it. Substitution of glycine by alanine (G1966A) resulted in impaired virus infectivity. Alteration of either aspartate residue completely abolished virus replication. A fully infectious variant was isolated from the G1966A mutant. Sequencing analysis showed that the alanine residue substituted in G1966A mutant had reverted to glycine in this variant. Complementation experiments were carried out to rescue the replication-defective RNA carrying G1966A, D1967A, or D1968A mutations. The defective RNA with G1966A mutation in p90 replicated efficiently when the helper genome that supplied a wild-type p90 was provided in trans. However, the replication-defective RNA with D1967A or D1968A was not rescued by supplementation of p90 in trans. Our studies support the idea that the GDD motif is critical for RV replication and p90 function as RV RdRp
Analysis of Cellular Factors Influencing the Replication of Human Immunodeficiency Virus Type I in Human Macrophages Derived from Blood of Different Healthy Donors

AbstractWe analyzed parameters influencing HIV-1 infectibility of cells of the monocyte/macrophage lineage (MO/MAC) isolated from different healthy donors. The proportion of in vitro-infected cells and replication kinetics in different donor MAC ranged from 0.03 to 99% p24 antigen-positive MAC and from undetectable RT activity up to 5 × 106 cpm/ml/90 min, respectively. As a quantitative measurement for HIV-1 susceptibility of donor MO/MAC, we determined TCID50 values of defined virus stocks which varied up to 3000-fold depending on the donor MAC used for titration. As host factors which may influence the viral infection we determined the expression of virus receptors CD4, CCR5, CXCR4, and CCR3 as well as the secretion of the natural ligands of CCR5, which altogether showed no correlation with HIV-1 infectibility of the cells. Moreover, other MO-derived secretory factors which might affect viral infection of these cells could be excluded. Furthermore, expression of maturation-related antigens CD14, CD16, HLA-DR, and MAX.1/CPM was determined. Analysis of the reverse transcription process revealed that restricted HIV-1 infection was reflected by highly reduced or even undetectable full-length HIV-1 DNA formation, although early and intermediate transcripts appeared, suggesting that viral replication is blocked after entry at the level of early reverse transcription
Herpes Simplex Virus Type 1 Suppresses the Interferon Signaling Pathway by Inhibiting Phosphorylation of STATs and Janus Kinases during an Early Infection Stage

AbstractWe examined the influence on the interferon (IFN) signaling pathway of infection with herpes simplex virus type 1 (HSV-1) strain VR3. Data from reporter gene assays showed that expression of both type I and type II IFN-inducible genes was dramatically suppressed during the early stage of HSV-1 infection (2 to 3 h postinfection). During these periods, phosphorylation levels of janus kinases (JAKs) and STATs did not increase after treatment of HSV-1-infected FL cells with IFN-α or IFN-γ, although cellular protein levels of the JAKs and the STATs were not significantly changed. In contrast, the inhibitory effect of HSV-1 on phosphorylation of STAT1 was not observed in U937 cells, which show resistance to steady-state accumulation of RNA for HSV-1 immediate-early genes. The phosphorylation of STAT1 in FL cells was not inhibited by infection with a UV-inactivated virus. These results indicate that viral gene expression or viral protein production is necessary for the inhibition of phosphorylation by HSV-1
The Poliovirus Receptor CD155 Mediates Cell-to-Matrix Contacts by Specifically Binding to Vitronectin

AbstractThe human receptor for poliovirus (CD155) is an immunoglobulin-like molecule with unknown normal function(s). Here we provide evidence that CD155 binds specifically to vitronectin with a dissociation constant (Kd) of 72 nM as determined by surface plasmon resonance. Based on sequence homology to the CD155 gene, three poliovirus receptor-related genes (PRR1, PRR2, and PRR3) were cloned recently. PRR proteins were reported by others to mediate homophilic cell adhesion. Neither PRR1 nor PRR2 binds poliovirus and it is assumed that their physiological functions differ from that of CD155. Indeed, mPRR2 was found to bind to vitronectin only weakly, while its self-adhesion activity is characterized by a Kd of 310 nM. Moreover, there is no evidence for CD155 self-adhesion. Both CD155 and vitronectin colocalize to follicular dendritic cells and B cells inside the germinal centers of secondary lymphoid tissue (tonsils)—an observation suggesting that the CD155/vitronectin interaction is required for the establishment of a proper immune response in this particular context
Analysis of Dominant-Negative Effects of Mutant Env Proteins of Human Immunodeficiency Virus Type 1

AbstractThe Env protein of human immunodeficiency virus type 1 is assembled into a stable trimer, and oligomerization is required for maintenance of viral infectivity. This property of Env suggests that Env mutants may have a dominant-negative effect on virus infectivity. To investigate this possibility, we established a packaging cell line in which both wild-type and mutant Env proteins could be expressed simultaneously in a single cell. We analyzed the effects of two types of Env mutants: cytoplasmic tail-truncated TM mutants and a mutant defective in gp120/gp41 cleavage. The cytoplasmic tail-truncated proteins were found to be incorporated into virions by forming an oligomer with wild-type TM, but could not inhibit the wild-type function. In contrast, phenotypic mixing of cleavage-defective Env with the wild-type protein caused dramatic inhibition of infectivity, indicating that this mutant has a strong dominant-negative phenotype
Induction of Adult-like Antibody, Th1, and CTL Responses to Measles Hemagglutinin by Early Life Murine Immunization with An Attenuated Vaccinia-Derived NYVAC(K1L) Viral Vector

AbstractAlthough initially developed in adult animals, novel viral vectors expressing recombinant measles antigens must eventually prove their success in the early life setting, where the efficacy of the currently used live-attenuated measles virus vaccine is limited. The immunological requirements for vaccine candidates include the generation of protective antibody responses as well as the induction of Th1 and cytotoxic T lymphocytes (CTL) responses, which is challenging in the neonatal setting. Here, we report that young BALB/c mice immunized with a single dose of a vaccinia-based NYVAC(K1L) vector generate adult-like antihemagglutinin (HA) antibody responses as well as adult-like Th1 and CTL responses. Despite this strong immunogenicity in early life, antibody responses (but not T-cell responses) to a single dose of NYVAC(K1L)-HA remained susceptible to inhibition by preexisting measles antibodies, calling for use of prime-boost strategies. NYVAC(K1L)-HA is the first attenuated live viral vector demonstrated as capable of inducing adult-like antibody, Th1, and CTL responses against measles in an early life murine immunization model, a capacity previously only reported for measles DNA vaccines
TATA Box Occupancy in the SV40 Transcription Elongation Complex

AbstractIn order to gain insight into requirements for template activation and commitment in mammalian transcription, TATA site occupancy was measured in native SV40 viral transcription complexes that were in the process of transcription elongation at the time of cell lysis. This was accomplished by quantifying resistance to restriction enzyme digestion of transcription complexes in nuclear lysate. The rate of cleavage at the TATA site of the late gene in the native complex was slower than that of a bare DNA control, both for wild-type virus and for a virus containing a TATA consensus sequence. These results suggest that the TATA site in the transcription elongation complex in vivo is occupied with transcription factor TBP/TFIID. When considered in light of previous work, these findings support a model in which transcription activation involves reinitiation from a promoter that contains both activator and TFIID bound in a stable complex
Induction of Apoptosis in Vitro by the 17-kDa Nonstructural Protein of Infectious Bursal Disease Virus: Possible Role in Viral Pathogenesis

AbstractInfectious bursal disease virus (IBDV) causes severe immunodeficiency in young chickens by destroying the precursors of antibody-producing B cells in the bursa of Fabricius. It has been shown that IBDV infection induces apoptosis in chicken embryo and tissue culture cells. We previously reported that an IBDV mutant lacking the expression of 17-kDa nonstructural (NS) protein exhibited decreased apoptotic effects in cell culture as compared to the parental IBDV, suggesting that the NS protein may be involved in induction of apoptosis. Here, we report that the NS protein of IBDV alone is capable of inducing apoptosis in cell culture. Transfection of chicken B-lymphocyte cell line (RP9) and chicken embryo fibroblast cells with a plasmid DNA, containing the NS protein gene under the control of the immediate-early promoter-enhancer region of human cytomegalovirus, induced programmed cell death in both cell lines. Apoptosis changes, such as chromatin condensation, DNA fragmentation, and the appearance of apoptotic nuclear bodies, were observed in cell cultures 48-h posttransfection. As reported earlier, the mutant IBDV grew to lower titers with slower replication kinetics and lower cytopathogenicity when compared to that of the parental virus. Here, we demonstrate that the mutant virus is closely associated with cells and its yield from the supernatant was approximately 30-fold lower than the wild-type due to increased cell association, indicating a deficiency in lysis of virus-infected cells. Taken together, our results indicate that the NS protein of IBDV is highly cytotoxic, which brings about the release of the viral progeny from cells, and thus play an important role in viral pathogenesis
A Novel Mechanism to Ensure Terminal Initiation by Hepatitis C Virus NS5B Polymerase

AbstractHepatitis C virus (HCV) nonstructural protein 5B (NS5B) RNA-dependent RNA polymerase (RdRp) has acquired a unique β-hairpin in the thumb subdomain which protrudes toward the active site. We report here that this β-hairpin plays an important role in positioning the 3′ terminus of the viral RNA genome for correct initiation of replication. The presence of this β-hairpin interferes with polymerase binding to preannealed double-stranded RNA (dsRNA) molecules and allows only the single-stranded 3′ terminus of an RNA template to bind productively to the active site. We propose that this β-hairpin may serve as a “gate” which prevents the 3′ terminus of the template RNA from slipping through the active site and ensures initiation of replication from the terminus of the genome. This hypothesis is supported by the ability of a β-hairpin deletion mutant that utilizes dsRNA substrates and initiates RNA synthesis internally. The proposed terminal initiation mechanism may represent a novel replication strategy adopted by HCV and related viruses
Identification of DNA Components Required for Induction of Cotton Leaf Curl Disease

AbstractCotton leaf curl disease (CLCuD) is a major constraint to cotton production in Pakistan. Infectious clones of the monopartite begomovirus cotton leaf curl virus (CLCuV), associated with diseased cotton, are unable to induce typical symptoms in host plants. We have identified and isolated a single-stranded DNA molecule approximately 1350 nucleotides in length which, when coinoculated with the begomovirus to cotton, induces symptoms typical of CLCuD, including vein swelling, vein darkening, leaf curling, and enations. This molecule (termed DNA β) requires the begomovirus for replication and encapsidation. The CLCuV/DNA 1/DNA β complex, together with a similar complex previously identified in Ageratum conyzoides, represent members of an entirely new type of infectious, disease-causing agents. The implications of this finding to our understanding of the evolution of new disease-causing agents are discussed
Plants Expressing Tomato Golden Mosaic Virus AL2 or Beet Curly Top Virus L2 Transgenes Show Enhanced Susceptibility to Infection by DNA and RNA Viruses

AbstractThe AL2 gene of the geminivirus tomato golden mosaic virus (TGMV) encodes a transcriptional activator protein (TrAP) that is required for efficient expression of the viral coat protein (CP) and BR1 gene promoters. In contrast, L2, the positional homolog of AL2 in the related beet curly top virus (BCTV), is not required for CP expression, raising questions about the functional relationship between the AL2 and L2 gene products. In this study, transgenic Nicotiana benthamiana and N. tabacum var. Samsun plants expressing a truncated AL2 gene (AL21–100, lacking the activation domain) or full-length L2 were prepared. These transgenic plants showed a novel enhanced susceptibility (ES) phenotype following inoculation with TGMV, BCTV, or tobacco mosaic virus (TMV), an unrelated RNA virus. ES is characterized by a reduction in the mean latent period (from 1 to 9 days) and by a decrease in the inoculum concentration required to infect transgenic plants (ID50 reduced 6- to 60-fold). However, ES does not result in an enhancement of disease symptoms, and viral nucleic acids do not accumulate to substantially greater levels in infected transgenic plants. That both viral transgenes condition ES suggests that their products share the ability to suppress a host stress or defense response that acts against DNA and RNA viruses. The data further indicate that the transcriptional activation activity of AL2 protein is not required for suppression. The nature of the response targeted by the AL2 and L2 gene products is discussed
Extreme Genetic Diversity among Pirital Virus (Arenaviridae) Isolates from Western Venezuela

AbstractPirital-like virus isolates from rodents collected in a variety of habitats within a six-state area of central Venezuela were analyzed genetically by amplifying a portion of the nucleocapsid protein gene using RT-PCR. Comparisons of the sequences from 30 selected Pirital-like virus isolates demonstrated up to 26% divergence in nucleotide sequences and up to 16% divergence in deduced amino acid sequences. Within the Pirital monophyletic group, 14 distinct lineages or genotypes, differing by at least 6% in nucleotide sequences, were identified. Although sample sizes were small for some lineages, many of the different genotypes were sampled in only one region or locality, suggesting allopatric divergence. Complement fixation tests with representatives of the most divergent Pirital virus lineages failed to delineate multiple species or subtypes within the Pirital clade. These results indicate that the previously proposed 12% nucleocapsid protein amino acid sequence divergence cutoff value for delineating arenavirus species is not appropriate for the entire family. When individual clones were examined from PCR amplicons, a mean of 0.17% sequence diversity vs the consensus sequences was detected, suggesting diverse quasispecies populations within infected rodent hosts. Possible explanations for the extreme genetic diversity within and among Pirital virus populations in infected rodents are discussed
No Evidence of HIV and SIV Sequences in Two Separate Lots of Polio Vaccines Used in the First U.S. Polio Vaccine Campaign

AbstractWe obtained sealed vials of two different polio vaccine lots, expiration date 1955, which were used in the first U.S. polio vaccine campaign. These early lots were pulled from the market because they contained live infectious poliovirus which caused polio in some of the vaccines. Theoretically, these vaccines could have contained other infectious retroviruses, including HIV. No viral sequences were detected using RT-PCR analyses with primers capable of amplifying chimpanzee SIV and HIV-1-related viruses nor with primers for macaque SIV, sooty mangabey SIV, and HIV-2-related viruses. Poliovirus sequences were readily amplified by RT-PCR, suggesting that the technique used would have detected SIV or HIV sequences, if present
The Transcription/Replication Activity of the Polymerase of Influenza A Viruses Is Not Correlated with the Level of Proteolysis Induced by the PA Subunit

AbstractThe PA subunit of the influenza virus polymerase has been shown to induce degradation of coexpressed proteins, but its role in the replication activity of the polymerase is not fully understood. Here, PA proteins derived from several influenza A viruses were examined at 37 and 33°C for both the level of proteolysis they induced and the efficiency with which they ensured transcription/replication of a viral-like RNA within a polymerase complex reconstituted in vivo from cloned cDNAs. Two mutants of A/Victoria/3/75 PA showed a decreased ability to induce proteolysis as compared to the wild-type PA, but still appeared to be as active as the wild-type protein with respect to the polymerase activity. Furthermore, we observed that the ability of PR8-PA to induce proteolysis was severely impaired at 33°C as compared to 37°C, while the efficiency with which the PR8-derived polymerase complex ensured transcription/replication of the viral-like RNA was similar at both temperatures. Taken together, our observations suggest that the transcription/replication activity of the polymerase of influenza A viruses is not correlated with the level of proteolysis induced by the PA subunit