pinecone/core-2020-05-10-deduplication huggingface dataset:
Genetic Relatedness of Sindbis Virus Strains from Europe, Middle East, and Africa

AbstractThe relatedness of 40 strains of Sindbis virus (SIN) from Europe, the Middle East, and Africa was investigated by limited sequencing within the gene encoding the E2 glycoprotein corresponding to amino acid residues 117 to 229 and encompassing one of the major neutralization epitopes. Phylogenetic analyses using distance matrix and parsimonious methods identified two major genetic clusters of western SIN strains, although the variability was less than that of the corresponding region for Venezuelan equine encephalomyelitis virus with a maximum divergence of 12.4% versus 28.5%, respectively. One cluster comprising 19 strains included the HR derivate of the Egypt SIN prototype, AR339, and strains from Israel, Saudi-Arabia, Italy, Slovak Republic, Azerbaijan, as well as three Swedish strains. Another cluster of 17 strains included the Ockelbo virus (OCK) prototype, Edsbyn 5/82, and the majority of SIN strains from northern Europe including strains from Sweden, Norway, and Karelia, as well as two strains from South Africa. A third cluster, supported by the Neighbor Joining method, was made up of four strains from South Africa, Uganda, and Cameroon. Residue 212, either Ser or Thr, previously appointed important for the differences in neutralization assays between SIN and Edsbyn 5/82, respectively, correlated with the two major genetic clusters, but was a Thr for two of the three Swedish strains in the SIN prototype cluster, and a Ser in one Swedish and one Karelian strain in the OCK cluster. The finding of strains similar to prototype SIN in Middle Sweden and of strains in South Africa relating to the northern cluster of SIN strains supports the notion of the dispersal of SIN by migrating birds as previously suggested for New World alphaviruses
Virus RNA Persists within the Retina in Coronavirus-Induced Retinopathy

AbstractThe murine coronavirus, mouse hepatitis virus (MHV), JHM strain, induces a biphasic retinal disease in adult BALB/c mice. In the early phase, Day 1 to Day 7, a retinal vasculitis is noted which is associated with the presence of viral proteins and infectious virus. In the late phase, Day 10 to Day 140, a retinal degeneration is associated with the absence of viral proteins, infectious virus, and inflammatory cells. The purpose of this study was to determine if viral RNA persists within the retina during the retinal degenerative phase of the disease. BALB/c mice were inoculated by the intravitreal route with 104.0TCID50/5 μl of virus. The presence of viral RNA was detected byin situhybridization with a viral cDNA probe and viral proteins were identified by immunocytochemical staining. During the acute phase of the infection, viral RNA was found in the retina, RPE, ciliary body epithelium, and the iris epithelium. During the late phase of the infection, viral RNA was almost exclusively found within the retina and RPE and not in the anterior segment of the eye. Within the retina, viral RNA was detected in the ganglion cell layer, the inner retina, the outer retina, and the RPE cell. Immunocytochemical staining identified viral protein within the retina only from Day 1 to Day 8. This ocular disease was also associated with a persistent systemic infection. Both viral RNA and viral proteins were identified within the liver during the first 8 days. However, only viral RNA was detected in the liver from Day 8 to Day 60. These studies demonstrate that MHV established an acute infection (Day 1–8) where infectious virus and viral proteins were identified. This was followed by a persistent infection within the retina and liver where only viral RNA were detected byin situhybridization
Endogenous D-Type (HERV-K) Related Sequences Are Packaged into Retroviral Particles in the Placenta and Possess Open Reading Frames for Reverse Transcriptase

AbstractAll primates studied to date produce retroviral-like particles in their placentae. We have purified these particles from two primate species, one Old World (human) and one New World (marmoset), and have identified the retroviral sequences which are packaged into these particles. Three families of sequences have been detected in these particles in human, all of which have the highest homology to B- and D-type retroviruses and to the human endogenous retrovirus HERV-K10. Previous studies have reported that the New World monkeys do not possess sequences with homology to HERV-K10. We have identified a new family of low-copy-number sequences which are present in New World monkeys and which possess 70% homology to the HERV-K family. Particles from both species possess reverse transcriptase activity and we have found that some of these retroviral particles package sequences which encode long open reading frames inpol,as revealed by expression cloning inEscherichia coli.These open reading frames could encode the reverse transcriptase enzyme activity found in the particles
Rev/RRE-Independent Mason–Pfizer Monkey Virus Constitutive Transport Element-Dependent Propagation of SIVmac239 Vectors Using a Single Round of Replication Assay

AbstractIn a step toward creating live-attenuated or DNA subunit vaccines for AIDS, the replication of simian immunodeficiency virus (SIV) was studied independently of the Rev and RRE (Rev-responsive element) regulatory system, over a single round. To accomplish this, theenvgene of an SIV vector was made defective by the insertion of a SV40 promoter/enhancerhygromycin B phosphotransferasegene cassette. Using this vector as the backbone, molecular clones of SIV were generated that contained a mutated Rev, Rev(−), a deleted RRE, RRE(−), or both, Rev(−)RRE(−). It has been shown recently that human immunodeficiency virus type 1 (HIV-1) Rev and RRE functions can be replacedin vitroby acis-acting sequence, constitutive transport element (CTE), from simian type D retroviruses. To determine whether such acis-acting element from Mason–Pfizer monkey virus (MPMV) would substitute for SIV Rev and RRE functions, the MPMV CTE was inserted either into the Nef ORF or at the junction ofvpxandvprof our Rev(−), RRE(−), and Rev(−)RRE(−) SIV molecular clones. Cell-free viral stocks harvested from Cos cells following transfections of these molecular clones revealed that these stocks were infectious over a single round of replication; however, their replication was attenuated 16-fold compared to that of wild-type virus. In addition, our experiments revealed that CTE functions in a position-dependent manner such that its insertion at the junction ofvpxandvprattenuated SIV replication 8- to 12-fold compared to the attenuation observed when it was inserted in thenefregion. Our results demonstrate that MPMV CTE is capable of substituting for SIV Rev and RRE functions, resulting in an attenuated ability to produce infectious virus
Complete Nucleotide Sequence and Full-Length cDNA Clone of S.A.AR86, a South African Alphavirus Related to Sindbis

AbstractS.A.AR86 and Girdwood S.A., two South African Sindbis-like arboviruses, are closely related antigenically to the Swedish isolate, Ockelbo82 [Lundström, J. O., Vene, S., Saluzzo, J. F., and Niklasson, B. (1993)Am. J. Trop. Med. Hyg.49(5), 531–537]. Each of these viruses is associated with human disease, and Girdwood S.A. was isolated from a human case. In addition, S.A.AR86 is unique among Sindbis-like viruses in that adult mice remain sensitive to lethal infection with S.A.AR86. The complete genomic sequences of S.A.AR86 and Girdwood S.A. were determined. The S.A.AR86 RNA genome contained 11,663 nucleotides, excluding the 5′ CAP structure and 3′ poly(A) tail. In comparison to the consensus sequence of the prototype Egyptian Sindbis strain AR339, S.A.AR86 differed at 5.57% of the nucleotides, including a 54-nucleotide deletion, two insertions of 6 nucleotides each, and a 3-nucleotide insertion in the 3′ terminal one-third of the S.A.AR86 nsP3 gene. S.A.AR86 is one of only three alphaviruses sequenced to date that does not have an opal termination codon between the nsP3 and the nsP4 genes. These genes are separated by a cysteine codon in the S.A.AR86 genome. The genome of Girdwood S.A. was 11,717 nucleotides in length, excluding the 5′ CAP and 3′ poly(A) tail. Girdwood S.A. contained an opal termination codon between nsP3 and nsP4 and did not have the large 54-nucleotide deletion in nsP3, although Girdwood S.A. did contain the remaining insertions and deletions characteristic of S.A.AR86. S.A.AR86 was more closely related to Girdwood S.A. than to the Egyptian isolate, and the South African isolates as a group were more closely related to the Swedish isolate. Comparison of the S.A.AR86 sequence to that of Ockelbo82, Girdwood S.A., and Sindbis virus AR339 revealed several codons where S.A.AR86 differed from the conserved amino acid encoded by the other three viruses. These changes may be related to the ability of S.A.AR86 to initiate a lethal central nervous system infection in adult mice. To fulfill a prerequisite for testing this hypothesis, a full-length cDNA clone of S.A.AR86 was constructed from which infectious genomic RNA replicas could be derived. The sequence of this clone differed from the S.A.AR86 genomic RNA sequence at four translationally silent positions, and virus derived from the clone reproduced the adult mouse neurovirulence phenotype of its biological progenitor
Genomic Organization and Sequence Conservation in Type ITrichomonas vaginalisViruses

AbstractTo reveal the genetic conservation of type ITrichomonas vaginalisviruses (TVV) we cloned and sequenced the 4.6-kb ds RNA of a TVV-T5 isolate for comparison with the cDNA sequence of a related TVV-T1 ds RNA. Analogous to TVV-T1, the TVV-T5 ds RNA also contains an upstream capsid protein gene overlapped with a downstream RNA-dependent RNA polymerase (RDRP) gene by a +1 reading frame shift. A conserved ribosomal slippage heptamer (C CUU UUU) was found within the consensus 14-nt overlap, and the context of the sequence surrounding the heptamer suggests a potential ribosomal frameshifting in the biosynthesis of RDRP from the initiation of capsid protein either through two consecutive −1 shifts or a +1 shift
Analysis of FeLV-FAIDS Provirus Burden and Productive Infection in Lymphocyte Subsetsin Vivo

AbstractTo help elucidate the immunopathogenesis of feline leukemia virus (FeLV)-induced immunodeficiency we studied the tropism of viruses derived from the FeLV-FAIDS isolate for lymphocyte subpopulations in cats. FeLV-FAIDS is composed of a replication-competent virus typical of subgroup A FeLV (prototype, clone 61E) and a family of replication-defective but immunopathogenic variant viruses (prototype, clone 61C). We sorted CD4+, CD8+, and IgG+ lymphocytes to ≥97% purity and analyzed viral load in each cell population via genome-specific semiquantitative PCR. Both the 61E and 61C viruses were tropic for CD4+ and CD8+ T cells as well as IgG+ B lymphocytes in blood and lymph node. High provirus burden were established for both virus genomes—ranging from 0.3 to >2 copies/cell. To identify the fraction of circulating cells which expressed viral antigenin vivo,we developed a flow cytometric method to simultaneously label blood leukocytes for surface immunophenotype and intracytoplasmic FeLV CA (p27 Gag). These experiments established that 20 to 60% of CD4+, CD8+, and IgG+ lymphocytes and >85% of monocytes and granulocytes expressed FeLV p27 intracellularly. Thus thein vivotarget cells for FeLV-FAIDS infection are manifold and include CD4+ and CD8+ T cells, B cells, and myeloid cells
Long-Term, Large-Population Passage of Aphthovirus Can Generate and Amplify Defective Noninterfering Particles Deleted in the Leader Protease Gene

AbstractDuring serial undiluted passage of a clonal population of foot-and-mouth disease virus (FMDV C-S8c1) in BHK-21 cells, two species of defective RNA were generated and selected. Sequence analysis revealed that they included deletions within the L-coding region, and retained the correct reading frame for viral protein synthesis. These deleted RNAs directed the synthesis of capsid protein VP1, were packaged in particles sedimenting with standard virus, required homologous infectious helper virus in order to produce viral particles, but did not interfere with the replication of helper virus. While detection of defective particles in FMDV required more than 100 serial passages, once produced, these defective RNAs could be stably maintained upon further passages in the FMDV C-S8c1 quasispecies. Furthermore, a high fitness, monoclonal-antibody-resistant virus was able to replace the standard virus and support the amplification of the deleted particles. This is the first description of naturally occurring, defective particles of FMDV
Replication and Pathogenicity after Intranasal and Intracranial Inoculation of Swine with a Recombinant Pseudorabies Virus Containing a Deletion at the UL/IR Junction

AbstractPseudorabies virus (PRV) is a neurotropic herpesvirus of swine. Previously, we described construction of a recombinant strain of PRV (LLTβΔ2) which contains a 3.0-kb deletion spanning the junction of the unique long and internal repeat sequences. Compared to the parental strain, Indiana-Funkhauser, and a virus rescued for the deleted sequences (LLTβres), LLTβΔ2 replicated efficiently at the site of inoculation, yet exhibited significantly reduced virulence when inoculated intranasally in pigs. In this report, we investigated the effect of the deletion on PRV replication and virulence after intracranial inoculation of swine, in comparison to replication and virulence after intranasal inoculation, in order to more precisely locate the defect in LLTβΔ2. Four-day-old pigs were infected intranasally with LLTβΔ2 or LLTβres and necropsied at various times postinfection. Compared to LLTβres-infected pigs, tissue distribution of virus, PRV antigen, and lesions of LLTβΔ2-infected pigs were comparable in all peripheral tissues examined, including trigeminal ganglia, but were reduced in tissues from the central nervous system (CNS). LLTβΔ2 was able to replicate in the CNS after intracranial inoculation into the cerebral cortex of 2-day-old piglets and to spread from CNS to peripheral tissues. Neurovirulence of LLTβΔ2 was somewhat reduced, as demonstrated by delayed onset of neurological signs and death in intracranially inoculated pigs. These results indicate that decreased neurovirulence after intranasal inoculation is not due to inability of LLTβΔ2 to replicate in CNS tissues. The difference in the amount of antigen detected in CNS tissues after intracranial inoculation compared to intranasal inoculation suggests that one defect in LLTβΔ2 is reduced ability to spread from peripheral neurons to the CNS after intranasal inoculation
Cytostatic Effect of Epstein–Barr Virus Latent Membrane Protein-1 Analyzed Using Tetracycline-Regulated Expression in B Cell Lines

AbstractTetracycline-regulated vectors were used to obtain inducible expression in stable transfected B cell lines of two Epstein–Barr virus (EBV) latent genes, LMP1 and EBNA2. The transfected genes were tightly repressed by low, nontoxic concentrations of tetracycline (≤1 μg/ml) and, following removal of tetracycline, were induced to levels comparable to or up to 3× that of EBV-transformed normal lymphoblastoid cell lines. In transfected DG75 cells, induced expression of LMP1, but not of EBNA2, led to the expected upregulation of various cell surface markers, including: CD40, CD54, CD58, and HLA class I. A novel observation was that both LMP1 and EBNA2 independently caused the downregulation of surface IgM, an effect mirrored in EBV-positive Burkitt lymphoma lines undergoing phenotypic drift during the transition from latency I to latency III in which both LMP1 and EBNA2 are upregulated. Most remarkably, induced LMP1 expression almost completely inhibited cell growth for 4 to 5 days, after which the cells recovered a limited proliferative capacity. The cytostatic effect of LMP1 was observed in all three B cell lines studied: DG75, BJAB, and Akata. Further analysis showed that induction of LMP1 coincided with a reduction in the levels of c-myc, and that the cytostatic effect was due to an accumulation of cells at the G2/M phase of the cell cycle. These data suggest a novel function for the LMP1 oncogene in controlling the proliferation of EBV-infected cells by regulating progress through G2/M phase
The RNA-Binding and Effector Domains of the Viral NS1 Protein Are Conserved to Different Extents among Influenza A and B Viruses

AbstractThe NS1 protein of the influenza A/Udorn/72 virus possesses two important functional domains: an RNA-binding domain near the amino-terminal end and an effector domain in the carboxyl half of the molecule. Though the NS1 proteins of influenza A and B viruses share little sequence homology, an RNA-binding domain with the same activities is preserved in the NS1 protein of influenza B/Lee/40 virus. The RNA-binding domains of the NS1 proteins of these influenza A and B viruses share the following properties: (i) they specifically bind to the same three RNA targets, poly(A), U6 snRNA, and double-stranded (ds) RNA; (ii) a polypeptide containing an amino-terminal sequence of the protein possesses all the RNA-binding activity of the full-length protein and exists in the form of a dimer; (iii) the binding to U6 snRNA causes an inhibition of pre-mRNA splicingin vitro;and (iv) the binding to dsRNA blocks the activation of the PKR kinasein vitro.The conservation of the RNA-binding domain of the NS1 protein among influenza A and B viruses strongly suggests that this domain is required for the replication of all these influenza viruses. In contrast, the NS1 protein of influenza B virus (NS1B protein) lacks an effector domain that functions like that of the NS1 protein of influenza A virus (NS1A protein). The effector domain of the NS1A protein is required for two of itsin vivoactivities: the inhibition of the nuclear export of poly(A)-containing mRNA and the inhibition of pre-mRNA splicing. The NS1B protein lacks these twoin vivoactivities. In addition, a naturally occuring, truncated NS1A protein lacks such an effector domain. Consequently, an effector domain that functions like that of full-length NS1A proteins is not absolutely required for the replication of influenza A and B viruses. We discuss the implications of these results for the roles of the RNA-binding and effector domains of the NS1 protein during infection by influenza A and B viruses
Intracellular Oligomerization of Influenza Virus Nucleoprotein

AbstractIt has previously been shown that the purified influenza virus nucleoprotein (NP) forms the oligomersin vitroin NP preparations obtained from virions (Wileyet al.,1977,Virology,79, 446–448; Ruigrok and Baudin, 1995,J. Gen. Virol.,76, 1009–1014) and infected cells (Becht and Weiss, 1991, Behring Inst. Mitt., Justus-Liebig Universitat, Giessen, 89, 1–11). We have shown in this report that boiling-sensitive NP oligomers (di- and trimers) are formedin vivoin the course of intracellular influenza virus replication. They are detected by PAGE about 10 min after monomeric 56-kDa NP molecules are synthesized. NP oligomers are formed by different strains of influenza virus in different cell lines. Some influenza virus strains are characterized by complete conversion of NP monomers into oligomers and others by only partial conversion. In the Triton X-114 phase partitioning system NP oligomers show more hydrophobicity than NP monomers. NP oligomers are detected in the sedimentable and soluble fractions of both cell lysate and extracellular medium. The possibility is discussed that oligomeric NP is a native and functionally significant form of influenza virus NP
A Rho-Dependent Transcription Termination Site Regulated by Bacteriophage P4 RNA Immunity Factor

AbstractThe genes required for replication of the temperate bacteriophage P4, which are coded by the phage left operon, are expressed from a constitutive promoter (PLE). In the lysogenic state, repression of the P4 replication genes is achieved by premature transcription termination. The leader region of the left operon encodes all the genetic determinants required for prophage immunity, namely: (i) the P4 immunity factor, a short, stable RNA (CI RNA) that is generated by processing of the leader transcript; (ii) two specific target sequences that exhibit complementarity with the CI RNA. RNA–RNA interactions between the CI RNA and the target sites on the mRNA leader region are essential for transcription termination. To understand how transcription termination is elicited by the P4 immunity mechanism, it is relevant to identify the transcription termination site. This, however, could not be directly inferred from the 3′-end of the transcription products because of the extensive and complex processing and degradation of the leader RNA. In this work, by making use of a tRNA gene as a reporter, we identify the termination site of the immunity transcripts (timm). This is a Rho-dependent terminator located within the first translated gene of the left operon and is regulated by P4 immunity. Analysis of the P4 transcription pattern inEscherichia coli rhomutants suggests that termination attimmmay also be important for the efficient processing of the CI RNA
Spike Glycoprotein-Mediated Fusion in Biliary Glycoprotein-Independent Cell-Associated Spread of Mouse Hepatitis Virus Infection

AbstractThe mouse hepatitis virus (MHV) spike glycoprotein mediates attachment of the virus to the MHV receptor, the murine biliary glycoprotein (BGP) carcinoembryonic antigen. Monoclonal antibody CC1 directed against BGP specifically inhibited infection of DBT, Sac-, GT1-7, and OBL21 cells by wild-type MHV-4 and the neuron-adapted variant OBLV60. Binding to this receptor was necessary to establish infection by cell-free MHV; however, the presence of BGP was not required for infection by cell-associated virus. Cell-associated infection induced syncytium formation on Vero and BHK cells, which lack murine BGP; this activity was not inhibited by monoclonal antibody CC1. Antibody CC1 also did not prevent syncytium formation on DBT cells, which bear BGP. In infectious center assays, the MHV-4 variant OBLV60, which exhibits acid-dependent fusion, spread to cells lacking BGP only when exposed to acidic media. Therefore, spike-mediated fusion was required for BGP-independent spread of MHV infection. Furthermore, BGP-independent, cell-associated spread of MHV-4 was prevented by monoclonal antibodies 5A13.5 and 5B19.2 directed against the spike glycoprotein, but not by other neutralizing and nonneutralizing anti-spike antibodies. Expression of spike glycoprotein by recombinant vaccinia virus resulted in fusion of BGP-negative cells; monoclonal antibodies 5A13.5 and 5B19.2 strongly inhibited spike-mediated fusion in this assay