pinecone/core-2020-05-10-deduplication huggingface dataset:
The M2 Gene Segment Is Involved in the Capacity of Reovirus Type 3 Abney to Induce the Oily Fur Syndrome in Neonatal Mice, a S1 Gene Segment-Associated Phenotype

AbstractOral inoculation of reovirus type 3 Abney (T3A) into neonatal mice induces hepatitis and the biliary atresia-associated oily fur syndrome (OFS), a phenotype previously linked to the S1 gene. We found that following oral inoculation, none of three T3A mutants, JH2, JH3, and JH4, containing different single amino acid substitutions in the M2 gene, induced the OFS or extensive liver necrosis. Similarly, reassortant viruses containing both a JH4-S1 and a JH4-M2 gene segment did not induce the OFS, whereas another reassortant containing a JH4-S1 gene and a M2 gene from reovirus type 3 Dearing fully recovered this capacity. Together, these results constitute the first evidence for the involvement of the M2 gene in the S1 gene-associated capacity of T3A to induce hepatobiliary disease in neonatal mice
Identification of Infectious Bursal Disease Virus Quasispecies in Commercial Vaccines and Field Isolates of This Double-Stranded RNA Virus

AbstractQuasispecies of infectious bursal disease virus (IBDV) vaccine and wild-type strains were identified using real-time RT-PCR at a region of the viral genome known for sequence variability. The LightCycler (Idaho Technology, Inc.) and hybridization probe system (Roche, Molecular Biochemicals) were used. An anchor probe labeled with LightCycler Red 640 and mutation probe labeled with fluorescein were designed using the Del-E IBDV sequence. The sequence of the mutation probe included nucleotides in the hydrophilic B region of VP2 that are important to a viral neutralizing epitope. This Del-E mutation probe was allowed to hybridize to the RT-PCR products following amplification and its temperature of dissociation (Tm) from each viral template was determined using the LightCycler melting peak analysis. The observed Tm for the Del-E mutation probe with its homologous virus, Del-E, was usually 65.5°C but ranged from 65 to 66.4°C. Peak melting temperatures for the test viruses were inversely proportional to the number of mutations observed between the Del-E mutation probe and target virus sequence. All the IBDV vaccine strains tested and all but two of the wild-type strains exhibited more than one melting peak, indicating that genetic subpopulations or quasispecies of the viruses were present in the samples. Since the mutation probe was located at a site which encodes a neutralizing epitope of the virus, it is possible that the genetic differences observed are translated into antigenic changes in this VP2 epitope and contribute to antigenic diversity in the quasispecies cloud
Identification and Characterization of a Baboon Reovirus-Specific Nonstructural Protein Encoded by the Bicistronic S4 Genome Segment

AbstractAll characterized orthoreoviruses encode a characteristic spike-like protein on their polycistronic S1 genome segments that mediates virus cell attachment. In the case of baboon reovirus (BRV), the polycistronic S-class genome segment corresponds to the smallest S4 segment. We recently determined that the 5′-proximal open reading frame (ORF) of the bicistronic S4 segment encodes a nonstructural protein responsible for virus-induced syncytium formation. Current analysis indicates that the p16 protein encoded by the 3′-proximal ORF of the BRV S4 genome segment shows no sequence similarity to any other protein encoded by the orthoreoviruses, including the well-characterized σ1/σC reovirus cell attachment protein. Results indicate that p16 is a BRV-specific nonstructural protein that is not required for virus infection in cell culture and is not involved in viral cell attachment. In conjunction with previous studies of the BRV S1, S2, and S3 genome segments, the current results indicate that, unlike all other orthoreoviruses, BRV does not encode a cell attachment protein in its S-class genome segments. Furthermore, cell binding and infectivity studies suggested BRV may not utilize a functional homolog of the prototypical reovirus σ1/σC cell receptor-binding protein to mediate endocytic uptake by cells
Intraepithelial DNA Immunisation with a Plasmid Encoding a Codon Optimised COPV E1 Gene Sequence, But Not the Wild-Type Gene Sequence Completely Protects against Mucosal Challenge with Infectious COPV in Beagles

AbstractDNA plasmids encoding the open reading frames of canine oral papillomavirus (COPV) nonstructural early genes E1, E2, or E7 protein were delivered into both oral mucosal and cutaneous epithelial sites in beagle dogs using particle-mediated immunotherapeutic delivery (PMID) technology. Control dogs were vaccinated with plasmid encoding either hepatitis B virus surface antigen (HBVs) or COPV L1. Using a prophylactic immunisation protocol, a priming dose of plasmid DNA was followed by a booster dose 6 weeks later. Four weeks after boost, all dogs were challenged with infectious COPV particles. Following viral challenge, as shown previously (M. A. Stanley et al., 2001, Vaccine 19, 2783–2792), mucosal papillomas developed in the negative-control HBVs vaccinated dogs, but all animals in the COPV L1 group were fully protected from disease development. In the early gene-vaccinated groups five of six in the E1-vaccinated dogs, two of six in E2-vaccinated dogs, and three of six in the E7-vaccinated beagles developed oral papillomas. Compared to the HBVs negative-control group the oral papillomas that did develop in the early-gene vaccinated beagles were significantly smaller, shorter in duration, and fewer in number. Taken together the disease burden was markedly reduced and this was statistically significant. In a second experiment one group of animals was vaccinated with plasmid encoding the wild-type COPV E1 gene, and a separate group was vaccinated with plasmid encoding a synthetic codon-optimised COPV E1 gene sequence. None of the codon-optimised E1-vaccinated animals developed papillomas at any challenge site. However, all animals vaccinated with wild-type E1 had papillomas. These data suggest that immunisation by PMID with papillomavirus early genes can significantly impact upon subsequent disease development and that full protection can be achieved using improved vectors encoding codon-optimised gene sequences perhaps emphasizing the importance of antigen load in the generation of protective responses to papillomavirus proteins
Immunogenicity and Ability of Variable Loop-Deleted Human Immunodeficiency Virus Type 1 Envelope Glycoproteins to Elicit Neutralizing Antibodies

AbstractIt has been extremely difficult to elicit broadly cross-reactive neutralizing antibodies (Nabs) against human immunodeficiency virus type 1 (HIV-1). In this study, we compared the immunogenic properties of the wild-type and variable loop-deleted HIV-1 envelope glycoproteins. Mice were immunized with recombinant vaccinia viruses expressing either the wild-type or the variable loop-deleted (V1–2, V3, V4, and V1–3) HIV-1DH12 gp160s. The animals were subsequently boosted with respective recombinant gp120s. All envelope constructs elicited similar levels of gp120-binding antibodies when analyzed by enzyme-linked immunosorbent assay (ELISA). However, the highest neutralizing activity was observed in sera from animals immunized with the wild-type envelope protein, followed by those immunized with ΔV4 and ΔV1–2. No neutralizing activity was detected in sera from animals immunized with ΔV3 or ΔV1–3. To identify immunogenic epitopes, ELISA was performed with overlapping 15-mer peptides that cover the entire length of gp120. For the wild-type gp120, the immunogenic epitopes mapped primarily to the variable loops V1–2 and to the conserved regions C1 and C5. When they were plotted onto known coordinates of gp120 core crystal structure, the epitopes in the conserved regions mapped predominantly to the inner domain of the protein. By immunizing with variable loop-deleted envelopes, the immune responses could be redirected to other regions of the protein. However, the newly targeted epitopes were neither on the exposed surface of the protein nor on the receptor binding regions. Interestingly, the removal of the V3 loop resulted in loss of immunoreactivity for both V3 and V1/V2 loops, suggesting structural interaction between the two regions. Our results suggest that obtaining broadly reactive Nabs may not be achieved simply by deleting the variable loops of gp120. However, the observation that the immune responses could be redirected by altering the protein composition might allow us to explore alternative strategies for modifying the antigenic properties of HIV-1 envelope glycoprotein
Infected Cell Protein No. 22 Is Subject to Proteolytic Cleavage by Caspases Activated by a Mutant That Induces Apoptosis

AbstractEarlier reports have shown that the d120 mutant of herpes simplex virus 1 lacking both copies of the gene encoding the infected cells protein No. 4 (ICP4) induces apoptosis in a variety of cell lines. The programmed cell death induced by this mutant is blocked by overexpression of Bcl-2 or by transduction of infected cells with the gene encoding the viral US3 protein kinase. HEp-2 cells infected with the d120 mutant express predominantly α proteins. Studies on these proteins revealed the accumulation of a Mr 37,500 protein that reacted with antibody directed against the carboxyl-terminal domain of ICP22. We report that the Mr 37,500 protein is a product of the proteolytic cleavage of ICP22 by a caspase activated by the d120 mutant. Thus the accumulation of the Mr 37,500 protein was blocked in cells transduced with the US3 protein kinase, in cells overexpressing Bcl-2, or in infected cells treated with the general caspase inhibitor zVAD-fmk. Exposure of ICP22 made in wild-type virus-infected cells to caspase 3 yielded two polypeptides, of which one could not be differentiated from the Mr 37,500 protein with respect to electrophoretic mobility. We conclude that the cellular apoptotic response targets at least one viral protein for destruction
DC-SIGN and DC-SIGNR Bind Ebola Glycoproteins and Enhance Infection of Macrophages and Endothelial Cells

AbstractEbola virus exhibits a broad cellular tropism in vitro. In humans and animal models, virus is found in most tissues and organs during the latter stages of infection. In contrast, a more restricted cell and tissue tropism is exhibited early in infection where macrophages, liver, lymph node, and spleen are major initial targets. This indicates that cellular factors other than the broadly expressed virus receptor(s) modulate Ebola virus tropism. Here we demonstrate that the C-type lectins DC-SIGN and DC-SIGNR avidly bind Ebola glycoproteins and greatly enhance transduction of primary cells by Ebola virus pseudotypes and infection by replication-competent Ebola virus. DC-SIGN and DC-SIGNR are expressed in several early targets for Ebola virus infection, including dendritic cells, alveolar macrophages, and sinusoidal endothelial cells in the liver and lymph node. While DC-SIGN and DC-SIGNR do not directly mediate Ebola virus entry, their pattern of expression in vivo and their ability to efficiently capture virus and to enhance infection indicate that these attachment factors can play an important role in Ebola transmission, tissue tropism, and pathogenesis
Influenza A Virus Hemagglutinin Containing Basolateral Localization Signal Does Not Alter the Apical Budding of a Recombinant Influenza A Virus in Polarized MDCK Cells

AbstractMorphogenesis of influenza virus is a complex multistep process involving transport of all viral components as either individual or subviral components to the specified assembly site and interaction among the viral components in an ordered fashion to initiate the budding process. Envelope glycoprotein(s) is believed to be the major determinant in selecting the viral budding site since the majority of the viral glycoproteins are directed to the budding site independent of other viral components. Influenza viruses bud from the apical surface of polarized epithelial cells and all three envelope proteins, hemagglutinin (HA), neuraminidase (NA), and M2, are also targeted independently to the apical surface. Since HA is the major viral envelope protein, we decided to test whether basolaterally expressed HA can make the virus bud from the basolateral surface. Accordingly, we introduced the tyrosine-based basolateral-sorting signal to the cytoplasmic tail of HA by changing Cys561 → Tyr561 and generated a transfectant virus by reverse genetics. Compared to the parent WSN virus, the mutant virus (HAtyr virus) contained less HA on its envelope. While the wild-type (wt) HA was >95% apical, the mutated HA (HAtyr) was approximately 60% basolateral in both transfected and virus-infected polarized MDCK cells. Also, HAtyr protein exhibited a much higher rate of endocytosis than the wt HA, in both apical and basolateral surface of transfected as well as virus-infected cells. However, the HAtyr virus, similar to wt WSN virus, was seen to bud almost exclusively (>99%) from the apical side of polarized MDCK cells. This finding was confirmed by using neuraminidase to facilitate virus release, by treating the collected virus particles with trypsin to cleave HA0 → HA1 and HA2, by protein analysis of released virus particles, and finally, by electron microscopy. Therefore HA, the major glycoprotein alone, does not determine the budding site, and other factor(s), possibly both viral and host, is responsible for selecting the budding site of influenza virus
Transcriptional Analysis of Porcine Circovirus Type 2

AbstractPorcine circovirus type 2 (PCV2) is the causative agent of an emerging swine disease, postweaning multisystemic wasting syndrome. In this work, the RNAs of PCV2 synthesized during productive infection in porcine kidney cells were characterized. A total of nine RNAs were detected. They include the viral capsid protein RNA (CR), a cluster of five Rep-associated RNAs (designated Rep, Rep′, Rep3a, Rep3b, and Rep3c), and three NS-associated RNA (designated NS515, NS672, and NS0). Members of the Rep-associated RNA cluster all share common 5′ and 3′ nucleotide sequences and they also share 200 common 3′ nucleotides with the NS-associated RNAs. Rep, capable of coding for the replication-associated-protein (RepP), appears to be the primary transcript that gives rise to Rep′, Rep3a, Rep3b, and Rep3c by alternate splicing. Protein sequence alignment showed that RepP and the Rep′ protein of PCV2 are equivalent to those described for PCV type 1 (PCV1) (a nonpathogenic virus), which had been shown to be essential for viral DNA replication. The results also suggest that NS515, NS672, and NS0 are transcribed from three different promoters inside ORF1 downstream of the Rep promoter. To date, only three RNAs (CR, Rep, and Rep′) have been reported for PCV1-infected porcine kidney cells. Therefore, it is important to apply similar strategies from this study to reexamine the transcription pattern of PCV1
Identification of a Unique Family of F-Box Proteins in Atadenoviruses

AbstractOvine adenovirus isolate 287 (OAdV-7) is the prototype of the atadenoviruses, a genus whose strategy for infection and replication is still being elucidated. A transcription unit at the right end of the genome contains four related genes (ORFs RH1, 2, 4, and 6), at least three of which are nonessential for replication in vitro. Related genes are also present in the genomes of bovine and avian atadenoviruses. To investigate how these apparently redundant genes are decoded, a more detailed transcription map of the right end of the OAdV-7 genome has been deduced. Eight transcripts that were derived from a promoter in the terminal repeat sequence were identified. Five were potentially bicistronic. The transcripts could encode all the potential proteins of the region subject to efficient reinitiation of translation. However, the most interesting and surprising finding in this work was that the related RH proteins carry an F-box motif. This was first identified in OAdV-7 RH1 and subsequently found in RH2, 4, and 6 proteins and the related reading frames from the bovine and avian atadenoviruses. Although very rare among viral proteins, several hundred cellular proteins contain F-box motifs. F-box proteins facilitate the degradation of a variety of important regulatory proteins via SCF ubiquitin ligase complexes. Thus, it appears that atadenoviruses have adopted a strategy to regulate a key cellular pathway(s) that distinguishes them from the other adenovirus genera and from most viruses in general
Low-Neurovirulence Theiler's Viruses Use Sialic Acid Moieties on N-linked Oligosaccharide Structures for Attachment

AbstractLow-neurovirulence BeAn and DA Theiler's murine encephalomyelitis viruses (TMEV) cause persistent infection in the central nervous system (CNS) of susceptible mouse strains, leading to an inflammatory demyelinating process. A role for a specific virus–cell receptor interaction has been posited to explain why only low- and not high-neurovirulence TMEV cause persistent CNS infections. Low- but not high-neurovirulence TMEV use sialic acid for attachment to mammalian cells, which may contribute to neurovirulence attenuation and viral persistence. Analysis of BeAn virus binding and infection in cells with altered (mutated) cell-surface expression of sialic acid containing glyconjugates indicated that both binding and infection are mediated entirely by N-linked glycoproteins. By contrast, GDVII virus binding and infection appears to be dependent only in part on N-linked glycoproteins and not on O-linked glycoproteins or glycolipids. These results indicate that low-neurovirulence BeAn virus uses a sialic acid moiety expressed on an N-linked carbohydrate of a glycoprotein that serves as the protein entry receptor
Characterization of the Poliovirus 147S Particle: New Insights into Poliovirus Uncoating

AbstractA Sabin 1 strain poliovirus (PV) mutant, S1(2Y-1I), carrying a Tyr at amino acid position VP2142 and an Ile at position VP1160, can establish persistent infections in HEp-2c cells. This mutant forms atypical 147S particles upon interaction at 0°C with either cells expressing PV receptor (PVR) CD155, or PVR-IgG2a, a chimeric molecule consisting of an extracellular moiety of PVR and the hinge and Fc portion of a mouse IgG2a. Upon interaction with PVR at 37°C, S1(2Y-1I), similar to the parental strain, forms both 135S A particles and 80S empty capsids. At 0°C, surprisingly, at a concentration equal to or greater than 5 nM, PVR-IgG2a induced both the extrusion of VP4 from the capsid of S1(2Y-1I) and the formation of 80S particles. The same transitions were observed at 0°C with the parental strain Sabin 1 at 40 nM PVR-IgG2a. Thus, the formation of 80S particles and VP4 extrusion, considered as one of the steps of PV uncoating, can be temperature-independent at high PVR concentration. This implies that structural changes of the PV capsid occurred following adsorption at low temperature
The V Proteins of Simian Virus 5 and Other Paramyxoviruses Inhibit Induction of Interferon-β

AbstractIn this article we show that the paramyxovirus SV5 is a poor inducer of interferon-β (IFN-β). This inefficient induction is a consequence of the expression of an intact viral V protein. In the absence of the viral V protein cysteine-rich C-terminal domain, IFN-β mRNA is strongly induced and the transcription factors NF-κB and IRF-3 are activated significantly. The V protein can work in isolation from SV5 to block intracellular dsRNA signaling. The mechanism of block to dsRNA signaling is distinct from that previously observed for blocking IFN signaling in that proteolysis of candidate factors cannot be detected, and furthermore, the respective blocks require distinct protein domains. Blocking of the induction of IFN-β by dsRNA requires the C-terminal cysteine-rich domain, a feature that is highly conserved among paramyxoviruses. We demonstrate that the V proteins from other paramyxoviruses have equivalent functions and speculate that limiting the yield of IFN-β during infection may be a general property of paramyxoviruses
Recovery of Paramyxovirus Simian Virus 5 with a V Protein Lacking the Conserved Cysteine-rich Domain: The Multifunctional V Protein Blocks both Interferon-β Induction and Interferon Signaling

AbstractThe V protein of the Paramyxovirus simian virus 5 (SV5) is a multifunctional protein containing an N-terminal 164 residue domain that is shared with the P protein and a distinct C-terminal domain that is cysteine-rich and which is highly conserved among Paramyxoviruses. We report the recovery from Vero cells [interferon (IFN) nonproducing cells] of a recombinant SV5 (rSV5) that lacks the V protein C-terminal specific domain (rSV5VΔC). In Vero cells rSV5VΔC forms large plaques and grows at a rate and titer similar to those of rSV5. In BHK or CV-1 cells rSV5VΔC forms small plaques and grows poorly. However, even when grown in Vero cells rSV5VΔC reverts to pseudo-wild-type virus in four to five passages, indicating the importance of the V protein for successful replication of SV5. Whereas rSV5 grows in many cell types with minimal cytopathic effect (CPE), rSV5VΔC causes extensive CPE in the same cell types. To overcome the antiviral state induced by IFN, many viruses have evolved mechanisms to counteract the effects of IFN by blocking the production of IFN and abrogating IFN signaling. Whereas rSV5 blocks IFN signaling by mediating the degradation of STAT1, rSV5VΔC does not cause the degradation of STAT1 and IFN signaling occurs through formation of the ISGF3 transcription complex. Furthermore, we find that rSV5 infection of cells prevents production of IFN-β. The transcription factor IRF-3 which is required for transcription of the IFN-β gene is not translocated from the cytoplasm to the nucleus in rSV5-infected cells. In contrast, in rSV5VΔC-infected cells IRF-3 is localized predominantly in the nucleus and IFN-β is produced. By using ectopic expression of IRF-3, it was shown that after dsRNA treatment and expression of the V protein IRF-3 remained in the cytoplasm, whereas after dsRNA treatment and expression of the P protein (which lacks the C-terminal cysteine-rich domain) IRF-3 was localized predominantly in the nucleus. Thus, SV5 blocks two distinct pathways of the innate immune response, both of which require the presence of the C-terminal specific cysteine-rich domain of the multifunctional SV5 V protein