pinecone/core-2020-05-10-deduplication huggingface dataset:
Replication of African Swine Fever Virus DNA in Infected Cells

AbstractWe have examined the ultrastructural localization of African swine fever virus DNA in thin-sections of infected cells byin situhybridization and autoradiography. Virus-specific DNA sequences were found in the nucleus of infected Vero cells at early times in the synthesis of the viral DNA, forming dense foci localized in proximity to the nuclear membrane. At later times, the viral DNA was found exclusively in the cytoplasm. Electron microscopic autoradiography of African swine fever virus-infected macrophages showed that the nucleus is also a site of viral DNA replication at early times. These results provide further evidence of the existence of nuclear and cytoplasmic stages in the synthesis of African swine fever virus DNA. On the other hand, alkaline sucrose sedimentation analysis of the replicative intermediates synthesized in the nucleus and cytoplasm of infected macrophages showed that small DNA fragments (∼6–12S) were synthesized in the nucleus at an early time, whereas at later times, larger fragments of ∼37–49S were labeled in the cytoplasm. Pulse–chase experiments demonstrated that these fragments are precursors of the mature cross-linked viral DNA. The formation of dimeric concatemers, which are predominantly head-to-head linked, was observed by pulsed-field electrophoresis and restriction enzyme analysis at intermediate and late times in the replication of African swine fever virus DNA. Our findings suggest that the replication of African swine fever virus DNA proceeds by ade novostart mechanism with the synthesis of small DNA fragments, which are then converted into larger size molecules. Ligation or further elongation of these molecules would originate a two-unit concatemer with dimeric ends that could be resolved to generate the genomic DNA by site-specific nicking, rearrangement, and ligation as has been proposed in thede novostart model of Baroudyet al.(B. M. Baroudy, S. Venkatesam, and B. Moss, 1982,Cold Spring Harbor Symp. Quant. Biol.47, 723–729) for the replication of vaccinia virus DNA
Vaccinia Virus DNA Polymerase Promotes DNA Pairing and Strand-Transfer Reactions

AbstractVaccinia virus infection results in the synthesis of a protein that promotes joint molecule formation and strand-transfer reactionsin vitro. We show here that this activity is also expressed by vaccinia DNA polymerase (gpE9L). Recombinant vaccinia polymerase was produced using a hybrid vaccinia/T7 expression system and purified to homogeneity. This protein catalyzed joint molecule formation and strand transferin vitroin reactions containing single-stranded circular and linear duplex DNAs. The reaction required homologous substrates and magnesium ions and was stimulated by DNA aggregating agents such as spermidine HCl andEscherichia colisingle-strand DNA binding protein. There was no requirement for a nucleoside triphosphate cofactor. The reaction ceased when ∼20% of the double-stranded substrate had been incorporated into joint molecules and required stoichiometric quantities of DNA polymerase (0.5–1 molecules of polymerase per double-stranded DNA end). Electron microscopy showed that the joint molecules formed during these reactions contained displaced strands and thus represented the products of a strand-exchange reaction. We also reexamined the link between replication and recombination using a luciferase-based transfection assay and cells infected with DNA polymeraseCts42mutant viruses. These data substantiate the claim that there exists an inextricable link between replication and recombination in poxvirus-infected cells. Together, these biochemical and genetic data suggest a way of linking poxviral DNA replication with genetic recombination
Cell-Cycle Perturbation in Sf9 Cells Infected withAutographa californicaNucleopolyhedrovirus

AbstractFlow cytometry analysis of the cell-cycle progression was performed in Sf9 cells infected withAutographa californicanucleopolyhedrovirus (AcNPV) in the cultures partially synchronized by aphidicolin exposure and deprivation. Cells infected with AcNPV during the G1 phase progressed and were arrested in the S phase in the 4 h following the infection, whereas cells infected during the S phase did not progress past the S phase. Cells infected during the G2/M phase remained in the G2/M phase without mitosis during a period of 10 h. Such cell-cycle arrest was also observed in the cells infected with ts8, a temperature-sensitive mutant of AcNPV that is defective in both genomic DNA synthesis and late gene expression. Cells with >4 N DNA content accumulated in the cultures infected with wild-type AcNPV, whereas no such cells appeared in the cultures infected with ts8, suggesting that viral origin of the DNA overaccumulated in the cells with >4 N DNA content. This was confirmed by the slot blot hybridization experiments, which showed that viral DNA, but not cellular DNA, increased strikingly in Sf9 cells during the infection with AcNPV. These results indicate that AcNPV targets at least two different checkpoints to prevent normal cell-cycle progression of Sf9 cells and that neither viral DNA replication nor expression of viral late genes is a necessary prerequisite for such AcNPV-induced cell-cycle arrest. It is suggested that the cell-cycle arrest in AcNPV-infected Sf9 cells is an event triggered early in infection by specific interaction of viral gene products with cellular components that regulate cell-cycle progression
Mammalian Reovirus L3 Gene Sequences and Evidence for a Distinct Amino-Terminal Region of the λ1 Protein

AbstractTo complement evidence for nucleoside triphosphate phosphohydrolase (NTPase), RNA helicase, RNA 5′ triphosphate phosphohydrolase, and nucleic acid-binding activities by the core shell protein λ1 of mammalian orthoreoviruses (reoviruses), we determined nucleotide sequences of the λ1-encoding L3 gene segments from three isolates: type 1 Lang (T1L), type 2 Jones (T2J), and type 3 Dearing (T3D). The T1L and T3D L3 gene sequences and deduced λ1 protein sequences shared high levels of identity (97.7% and 99.3%, respectively). The λ1 sequences differed at only 9 of 1275 amino acids. Two single-nucleotide insertions relative to a previously published sequence for T3D L3 extended the λ1 open reading frame to within 60 nucleotides of the plus-strand 3′ end for T3D and the other isolates sequenced, in keeping with the short 3′ nontranslated regions of the other nine gene segments. Seven of the nine amino acid differences between T1L and T3D λ1 were located within the amino-terminal 500 residues of λ1, a region with putative sequence similarities to NTPases and RNA helicases. The T2J L3 and λ1 sequences were found to be more divergent, especially within the amino-terminal 180 residues of λ1, preceding the putative CCHH zinc finger motif. The T2J L3 sequence, along with partial sequences for L3 genes from three other reovirus isolates, suggested that one or more of the polymorphisms at amino acids 71, 215, 500, 1011, and/or 1100 in λ1 contribute to the L3-determined differences in ATPase activities by T1L and T3D cores. The findings contribute to our ongoing efforts to elucidate sequence-structure–function relationships for the λ1 core protein
Alterations in RANTES Gene Expression and T-Cell Prevalence in Intestinal Mucosa during Pathogenic or Nonpathogenic Simian Immunodeficiency Virus Infection

AbstractRANTES, a β-chemokine, can suppress human immunodeficiency virus (HIV) as well as simian immunodeficiency virus (SIV) infections in T-lymphocyte cultures in vitro. However, the association of RANTES levels in peripheral blood with viral loads and disease outcome in HIV infection has been inconclusive. SIV-infected rhesus macaques were evaluated to determine whether RANTES gene expression correlated with suppression of viral infection in intestinal lymphoid tissues. Intestinal tissues were obtained from rhesus macaques infected with either pathogenic or nonpathogenic SIVmac variants at various stages of infection (primary acute, asymptomatic, and terminal). We examined the level of SIV infection (in situ hybridization), RANTES expression (quantitative competitive RT-PCR), and T-cell counts (immunohistochemistry). The most pronounced increase in RANTES gene expression in intestinal tissues was observed in primary SIV infection, which correlated with the pathogenicity of the infecting virus and not the tissue viral loads. Our results demonstrated that in contrast to the occurrence of viral suppression by RANTES in vitro, there was no direct correlation between high RANTES gene expression and suppression of viral loads in intestinal lymphoid tissues. Thus RANTES expression in the gut lymphoid tissue may not be a correlate for viral suppression. However, RANTES gene expression in primary SIV infection may be part of early host immune response to viral infection
Specific and Nonspecific Immune Stimulation of MHC-II-Deficient Mice Results in Chronic HSV-1 Infection of the Trigeminal Ganglia Following Ocular Challenge

AbstractOcular herpes simplex virus type 1 (HSV-1) infection of MHC-II-deficient mice (AO/Oβ mice) or their parental C57BL/6J wild-type mice resulted in the establishment of typical HSV-1 latent infections in the trigeminal ganglia (TG) of the surviving mice by day 28 postinfection. Latency was characterized by the complete absence of infectious virus in TG extracts, the ability to recover latent virus only following prolonged tissue culture cultivation of explanted TG, and the presence of HSV-1 DNA in TG extracts. When mice were vaccinated prior to ocular HSV-1 challenge, latency appeared unaltered in the C57BL/6J wild-type mice. However, in AO/Oβ mice, clearance of virus from the TG appeared to be seriously impaired, resulting in a chronic productive infection, rather than a latent infection. Infectious virus was readily detected in TG extracts of vaccinated AO/Oβ mice until at least 63 days postinfection. Glycoprotein B mRNA was also readily detected, confirming continued viral transcription. These chronic infections occurred regardless of whether the AO/Oβ mice were vaccinated with HSV-1-specific antigens (i.e., live HSV-1 strain KOS, recombinantly expressed HSV-1 glycoprotein D plus Freund's adjuvant, or a mixture of seven recombinantly expressed HSV-1 glycoproteins plus adjuvant) or non-HSV-1-specific antigens (i.e., tissue culture medium plus 5% fetal bovine serum, the expression vector plus adjuvant, or adjuvant alone). Passive transfer of HSV-1 neutralizing antibody to vaccinated AO/Oβ mice between days 0 and 28 post-ocular challenge did not clear infectious virus from the TG. Passive transfer of anti-HSV-1 antibody or purified naive mouse serum to unvaccinated AO/Oβ mice on days 3 or 6 post-HSV-1 ocular challenge also resulted in chronic, rather than latent, infection of the TG. Passive transfer of naive sera from B-cell-deficient mice or injection of keyhole limpet hemocyanin or purified IgG, but not PBS or dextran, 3 days after HSV-1 challenge also resulted in chronic infection of the TG
Use of Site-Specific Mutagenesis and Monoclonal Antibodies to Map Regions of CD46 That Interact with Measles Virus H Protein

AbstractResearchers at our laboratory have been dissecting the binding domains of the receptor for the Edmonston laboratory strain of measles virus (CD46) through site-specific mutagenesis. We initially substituted most of the hydrophilic amino acids in the two external short consensus regions (SCRI and SCRII) of CD46 with the amino acid alanine [Hsu et al. (1997) J. Virol. 71:6144–6154] and found that the glutamic-arginine residues at positions 58 and 59 were particularly sensitive to change. Here we consider the roles of hydrophobic amino acids in the binding between measles virus H protein and CD46. Hydrophobic amino acids in the SCRI and SCRII domains of CD46 were systematically replaced with serine. The effects of these changes were monitored through the interaction of Sf9 insect cells expressing the H protein and mouse OST-7 cells synthesizing the mutant CD46 molecules. Binding was quantified through a colorimetric assay for β-galactosidase that was also produced by the insect cells. Our results indicate that E45, Y54, 58E/R59, Y68, F69, Y101, I102, R103, D104, and Y117 seem to be critical residues for the binding of CD46 to measles virus H protein. The hydrophilic amino acid R59 in SCR1 and hydrophobic residues Y101, I102, and Y117 in SCR2 seem to be especially important for interaction between H protein and CD46. In addition, we mapped the antigenic epitopes of five monoclonal antibodies that are known to inhibit the binding between H protein and CD46. Three of these antibodies recognized regions in SCR1, and two reacted with amino acids in SCR2. For the most part, the determinants recognized by the monoclonal antibody corresponded to the amino acids that were most sensitive to change in the binding process. The SCR1 and SCR2 domains of CD46 were modeled from an analogous region in another complement regulatory protein, factor H, whose three-dimensional structure has been previously reported. Amino acids implicated in binding seem to lie on one planar face of the SCR1 and SCR2 domains. These studies serve as a prelude to understanding the structural interactions that occur between CD46 and the measles virus H protein
Novel Expression of Mouse Adenovirus Type 1 Early Region 3 gp11K at Late Times after Infection

AbstractMutations were introduced into mouse adenovirus type 1 (MAV-1) early region 3 (E3) initiator codons by homologous recombination between viral DNA and a plasmid containing a mutagenized E3 region. The resulting mutant virus, pmE312, contained ATG → TTA mutations at codon positions 1 and 4 and was expected to be null for the expression of the E3 proteins. However, gp11K, an MAV-1 E3 glycoprotein of 14K molecular weight, was detected in mutant-infected cell lysates at levels about 10–12% of that of wild-type (wt) virus at late times in infection. The gp11K polypeptide produced by pmE312 at late times was immunoprecipitated with two E3-specific antisera prepared against different regions of the protein. Like gp11K produced by wt virus infections, it was sensitive to endoglycosidase H (endo H) and thus resident in the endoplasmic reticulum (ER). In pmE312-infected cells treated with cytosine arabinoside (araC), an inhibitor of DNA replication, the gp11K protein was not detected by immunoprecipitation. This indicates that gp11K expression in pmE312-infected cells at late times was dependent on DNA replication and that it was thus translated from a late transcript. In vitro translation of poly(A)+ RNA from mock-, wild-type-, and pmE312-infected cells showed that gp11K was translated from late mRNA as an ∼28K fusion between a late protein and gp11K. Our data are consistent with a model in which gp11K is expressed at late times as a late protein–gp11K chimera in both wt- and mutant-infected cells. This chimera is then processed: removal of a large N-terminal sequence results in the observed 14K ER-localized gp11K
Nucleotides 1506–1625 of Bovine Papillomavirus Type 1 Genome Can Enhance DNA Packaging by L1/L2 Capsids

AbstractWe have previously described a DNA-packaging assay using bovine papillomavirus type 1 (BPV-1) virus-like particles (VLPs) and have identified a region of the BPV genome that assists in packaging. In this study, we identify a specific BPV sequence involved in DNA packaging by BPV-1 VLPs. In the initial screening of BPV-1 genomic sequences essential for DNA packaging, we observed that a plasmid with deletions between nucleotides (nt) 948 and 2113 failed to be packaged into BPV-1 VLPs. However, plasmids containing nt 948 to 2113 were efficiently packaged, suggesting that this 1.2-kb fragment contains a packaging enhancement sequence (PES). Further mapping of the BPV-1 genome showed that this packaging sequence lies between nt 1506 and 1625. Furthermore, this packaging sequence is also recognized by HPV6b VLPs, suggesting that a common packaging mechanism may be used by the two papillomavirus types. Given the phylogenetic difference between these two viral types, it is likely that other papillomavirus types may also use the same packaging mechanism. Identification of the PES has allowed a minimal viral genome sequence to be used in the packaging assay, improving the usefulness of the assay in studying the process of papillomavirus DNA encapsidation
Nuclear Localization of the Protein from the Open Reading Frame x1 of the Borna Disease Virus Was through Interactions with the Viral Nucleoprotein

AbstractPrevious studies have predicted the presence of a small open reading frame (ORFx1) located between ORF-1 and ORF-2 of the Borna disease viral (BDV) genome. The ORFx1 is expressed as a p10 protein that is localized in the nucleus and cytoplasm of BDV-infected cells. In this study, we cloned the nucleotide sequence of ORFx1 into expression vectors and showed that it is expressed as p10. An anti-p10 serum gave nuclear and cytoplasmic staining of cells persistently infected with BDV. Immunoprecipitation of p10 from BDV-infected cells coprecipitated the p40 nucleoprotein N and the 24-kDa viral phosphoprotein P. Transient transfection of noninfected cells showed that p10 and p40 can be coprecipitated and revealed that p10 localized in the cytoplasm was imported into the nucleus in the presence of the BDV p40 N.In vitroprotein–protein interaction studies on solid phase showed the direct interaction of the p10 with the BDV N protein. The subcellular distribution of p10 and its interaction with p40 suggest that this protein may play a role in the nuclear replication and/or transcription of BDV
Recombinant Viruses Expressing the Foot-and-Mouth Disease Virus Capsid Precursor Polypeptide (P1) Induce Cellular but Not Humoral Antiviral Immunity and Partial Protection in Pigs

AbstractThe importance of the induction of virus neutralizing antibodies to provide protection against foot-and-mouth disease virus (FMDV) infection is well established. However, recent studies with recombinant adenovirus expressing the precursor polypeptide of the viral capsid (P1) indicate that cattle inoculated with this recombinant vector developed partial protection against FMDV infection, in the absence of a detectable specific humoral response. Other viral vectors have been widely used to induce protective immunity against many pathogens, and it has been reported that the use of different vectors for priming and boosting injections can provide a synergistic effect on this response. In this work, we determined the immunogenicity of two recombinant viruses (adenovirus and vaccinia) expressing P1-FMDV, administered either individually or sequentially, and the protection that they induced against FMDV challenge in pigs. A double immunization with the adeno-P1 virus was the most effective strategy at inducing protective immunity. In contrast to previous reports, the use of two different vectors for priming and boosting did not show a synergistic effect on the protection induced against FMD. Interestingly, immunized pigs developed FMDV-specific T cell responses but not detectable antibodies. Thus, the protection observed was likely to be mediated by a cellular immune response
Mutations in Sabin 2 Strain of Poliovirus and Stability of Attenuation Phenotype

AbstractIn this study, we attempted to identify the molecular determinants in the genome of the attenuated Sabin 2 vaccine strain of poliovirus that may change during vaccine production and result in an increase in monkey neurovirulence. An extensive search for suitable vaccine lots identified six batches that had failed the monkey neurovirulence test (MNVT). On repeated tests, these batches were found to have acceptable levels of monkey neurovirulence. One of the batches was additionally passaged six times under conditions used in vaccine production, and the resulting high-passage sample was screened for the presence of mutations and tested in monkeys. In addition to the previously described A → G reversion at nucleotide 481, high-passage stock also contained a mutation in the VP1-coding region (3364 = G → A) that consistently accumulated in the course of passaging. However, despite the presence of substantial amounts of these mutations, high-passage stock passed the MNVT. Replication of Sabin 2 poliovirus in the central nervous system of transgenic mice susceptible to poliovirus or in cultures of mouse cells, resulted in another mutation (3363 = A → G). Even though its presence correlated with paralysis in mice, the introduction of 3363-G into the Sabin 2 genome did not increase neurovirulence of the virus. Previous studies identified the 481-G mutation as an important determinant of monkey neurovirulence. We prepared virus samples with varying amounts of genetically defined single mutants at this nucleotide and tested them in monkeys. The results demonstrated that even a 100% substitution at this site introduced into Sabin 2 strain did not increase monkey neurovirulence. The determination of the nucleotide sequence of an alternative strain used for the production of type 2 OPV (Chung 2) showed that it contained 100% of the wild-type 481-G but possessed an extremely low level of neurovirulence. These results demonstrate the remarkable stability of the attenuated phenotype of the Sabin 2 strain and show that (1) no batch of OPV 2 has ever repeatedly failed the MNVT, (2) growing the virus beyond the passage level allowed in vaccine production did not result in increased neurovirulence in monkeys, (3) a test for neurovirulence in transgenic mice may be more sensitive than the MNVT, and (4) determination of the mutational profile of vaccine batches detects inconsistencies in vaccine manufacturing processing that would not be detected by the MNVT
High-Yield Reassortant Influenza Vaccine Production Virus Has a Mutation at an HLA-A 2.1-Restricted CD8+ CTL Epitope on the NS1 Protein

AbstractCurrent influenza virus vaccines are prepared using high-yield reassortant virus strains obtained from a mixed infection of the new virus strain and a prototype high-yielding virus strain. The high-titered reassortant virus strain used as vaccine seed virus possesses the recent virus HA and NA and contains the internal genes from the high-growing prototype parent. We established a human CD8+ cytotoxic T cell (CTL) line, 10-2C2, which recognizes an HLA-A2.1-restricted influenza A virus H1, H2, H3 cross-reactive T cell epitope on amino acids 122–130 of the NS1 protein, and unexpectedly we observed that there was decreased lysis of target cells infected with the A/Texas/36/91 (H1N1) vaccine virus strain compared to the lysis of target cells infected with the prototype A/PR/8/34 (H1N1) virus. RT-PCR results showed that the A/Texas vaccine virus strain contained a quasispecies. Approximately 50% of viral RNA of the NS1 gene had a nucleotide substitution that resulted in the N → K amino acid change at the sixth position of the nonamer peptide. Current influenza vaccines are inactivated and do not contain the NS1 protein; however, future influenza vaccines may include live attenuated vaccines and with this mutation a live virus would fail to induce a CD8+ CTL response to this epitope in individuals with HLA-A2.1, a very common allele, and potentially have reduced efficacy