pinecone/core-2020-05-10-deduplication huggingface dataset:
Natural Populations of Woodchuck Hepatitis Virus Contain Variant Precore and Core Sequences Including a Premature Stop Codon in the Epsilon Motif

AbstractWe have determined a consensus sequence and the type and the frequency of spontaneous sequence variations in the woodchuck hepatitis virus (WHV) precore gene and the 5′ region of the core gene in 101 serum samples from 53 naturally WHV-infected woodchucks by polymerase chain reaction sequencing. Twenty of the 53 woodchucks were found to have variant sequences. Ten patterns of variant sequences were identified in these 20 animals. WHV sequences from 4 woodchucks had 1 nucleotide change, 3 had 2 nucleotide changes and 3 had 3 nucleotide changes. The nucleotide changes were not randomly distributed, but were limited to only 8 sites. Four sites were in the epsilon motif of the precore gene and four were in the 5′ region of the core gene. Sixteen of the 53 (30%) woodchucks had precore sequence variants. All altered sites were analogous to previously described mutations in hepatitis B virus. There was a nucleotide change at nucleotide 2016 in codon 29 of the precore region that produced a stop codon in 4 animals. This site is analogous to a common hepatitis B virus e antigen mutation. The sequence from the initial blood samples from 3 of 4 animals with this stop codon producing variant appeared to be the consensus sequence; however, in later samples the variant occurred as a mixed infection with the consensus sequence. The mixed infections were chronic and the proportion of the variant sequence was maintained or increased in the course of infection. In the fourth animal only the variant was found and it persisted for over 14 months of infection. WHV appears to be a valuable model for the study of the structure and function of the hepadnavirus precore region
A Feldmannia Algal Virus Has Two Genome Size-Classes

AbstractPersistent viruses occur intracellularly in brown algae, specifically the Ectocarpales, and as reported here in the genusFeldmannia. Feldmanniaspecies are small (1 mm–several cm), filamentous forms with single-celled meiotic sporangia that normally produce haploid zoospores. In the isolate reported here, spores were not observed in the sporangia but rather numerous (∼106per cell) polyhedral viruses are formed in their place. Two dsDNA genome classes of 158 and 178 kbp, with two restriction site variants of each, are described. The individual abundance of each genome in viral preparations is affected by culture temperature. A cosmid library was used to generate circular restriction enzyme (BamHI,NotI, andPstI) site maps
Inhibition of Feline Immunodeficiency Virus Infectionin Vitroby Envelope Glycoprotein Synthetic Peptides

AbstractSixty-six 20- to 23-amino-acid synthetic peptides, partially overlapping by 10–12 amino acids, spanning the entire sequence of the envelope SU and TM glycoproteins of the Petaluma isolate of FIV, have been used to investigate the Env domains involved in viral infection. Peptides 5 to 7, spanning amino acids225E–P264located in a conserved region of the SU protein, and peptides 58 to 61, spanning amino acids757N–P806and encompassing hypervariable region 8 of TM protein, exhibited a remarkable and specific antiviral effect against the homologous and one heterologous isolate, as judged by inhibition of FIV-induced syncytium formation and p25 production in CrFK cells. Peptides 5 and 7, but not peptides 58 and 59, also inhibited viral replication of a fresh FIV isolate on nontransformed lymphoid cells. By flow cytometry, peptides 5, 7, 58, and 59 were shown to bind the surface of FIV permissive cells. The antiviral activity of peptides 5 and 7, however, was time-dependent, as inhibition of FIV replication was seen when the peptides were administered before or within 3 hr after virus inoculation; in contrast, TM peptides 58 and 59 exerted a potent inhibitory effect when added up to 24 hr after virus inoculation. Circular dychroism analysis showed that peptide 5 folds to a helical conformation in the presence of a hydrophobic environment. Although the basis for the antiviral action of the peptides is not understood, our data suggest that the inhibitory peptides may act by interacting with cell-surface molecules involved in viral infection
Succession of Mutations in the Sabin Strain of Type 3 Poliovirus Replicating in the Central Nervous System of Monkeys

AbstractSabin strains of oral poliovirus vaccine (OPV) undergo limited genetic changes during replication in cell cultures, the gastrointestinal tract of vaccinees, and the central nervous system of monkeys. Some of these changes are associated with loss of attenuation markers. Here we report the dynamics of mutant accumulation in the Sabin strain of poliovirus type 3 inoculated intraspinally into monkeys. Thr → Ile reversion in amino acid 6 of VP1 (2493 C → U) occurred within the first few days postinoculation (p.i.), but decreased on later days and completely disappeared by Day 17 p.i. 472 U → C reversion in the 5′-untranslated region appeared to accumulate slower and by Day 17 completely substituted for the vaccine-type nucleotide at this site. These results indicate that experimental infection of the central nervous system of monkeys consists of early and late phases in which a different genetic constitution of the virus is favored. In several isolates one additional neurovirulent revertant was found: a Phe → Ser at amino acid 91 of VP3 (2034 U → C). Since this mutation was never detected in vaccine lots and is strongly selected against in cell cultures at temperatures below 38.5°, it does not threaten the safety of OPV
Mutations within the Primer Binding Site of the Human Immunodeficiency Virus Type 1 Define Sequence Requirements Essential for Reverse Transcription

AbstractThe primer binding site (PBS) is involved in two stages during the reverse transcription of the retroviral RNA genome. In the early stage, the PBS provides complementary sequences through which tRNALys,3binds the viral RNA genome to initiate minus-strand DNA synthesis; in the later stages, complementarity between the plus- and minus-strand copies of the PBS is required to facilitate the second template transfer needed to complete reverse transcription. We previously constructed a mutant HIV-1 proviral genome, designated as pHXB2PBS(pheC + 5) (now referred to as pheC + 5), which was used to identify regions of the PBS involved in the initiation and second template transfer steps of reverse transcription. To further define the sequence requirements of the PBS for the initiation of reverse transcription, we have made single nucleotide substitutions within the first six nucleotides of the pheC + 5 PBS. Our results demonstrate that mutations within the first five nucleotides of the PBS which disrupt base paring with tRNALys,3-PBS results in an noninfectious virus; a G-U base pair at position six of the tRNALys,3-PBS complex was tolerated. In contrast to the requirements for initiation, we found that complementary binding between only three base pairs of the plus- and minus-strand PBSs was required for the extension of plus-strand DNA during the second template transfer. Furthermore, regions of the minus-strand DNA of up to 24 nucleotides could be looped-out to facilitate the complementarity required for the completion of plus-strand DNA synthesis. Taken together, the results of our studies demonstrate that different features of the PBS with respect to RNA:RNA and DNA:DNA interactions are required for initiation of reverse transcription and the completion of plus-strand DNA synthesis, respectively
Glycoproteins gI and gE of Feline Herpesvirus-1 Are Virulence Genes: Safety and Efficacy of a gI–gE−Deletion Mutant in the Natural Host

AbstractFeline rhinotracheitis virus (FRV) is an important upper respiratory tract pathogen of cats. FRV is a member of the subfamily Alphaherpesvirinae and is designated feline herpesvirus-1 (FHV-1). Besides upper respiratory clinical signs, FHV-1 may cause generalized infections in neonates or abortions in pregnant queens. Recently we described a recombinant FHV-1 strain with a deletion in the genes for glycoproteins gI and gE (FHVβ-galgIgEΔ) and reported that cats vaccinated subcutaneously with high doses of the recombinant FHV-1 strain responded with only mild clinical signs and developed strong immunity against subsequent virulent virus challenge. Here we compare the intranasal and subcutaneous routes of administration of this strain and assess its ability to induce protective immunity and prevent virus shedding after challenge. Cats vaccinated subcutaneously or intranasally with high doses of the recombinant FHV-1 strain responded with only mild clinical signs and developed strong immunity against subsequent virulent virus challenge. This was especially evident when the mutant vaccine was administered oronasally. In contrast, intranasal administration of two other FHV-1 isolates induced severe clinical signs in cats. We conclude from testing this FHV-1 mutant in the natural host that deletion of gE and a portion of gI genes strongly reduces viral virulence but that immunogenicity is maintained
CD40/CD40L Interactions and Cytokines Regulate HIV Replication in B Cellsin Vitro

AbstractUsing ourin vitromodel of normal B cell infection, we investigated whether cellular interactions and/or cytokines directing the B cell response also regulate HIV replication. Phorbol esters and CD40 Ab plus IL4, added prior to infection, substantially increased subsequent viral replication. Postinfection, IL2 with or without IL4 and, to a lesser extent, CD40/CD40L interactions enhanced viral replication. In contrast, IL10 down-regulated HIV replication induced by cytokines, without affecting spontaneous or CD40 Ab-induced replication. Both enhancing and inhibitory effects of cytokines on viral replication were independent of their ability to modulate B cell proliferation. Thus, these two phenomena seem to be independently regulated in human B cells
The Effect of Simian Immunodeficiency Virus Infectionin Vitroandin Vivoon the Cytokine Production of Isolated Microglia and Peripheral Macrophages from Rhesus Monkey

AbstractMicroglia are the major target for human immunodeficiency virus (HIV) infection within the central nervous system. Because only a few cells are productively infected, it has been suggested that an aberrant cytokine production by this cell population may be an indirect mechanism leading to the development of neurological disorders in HIV-infected patients. Therefore we decided to study the secretion pattern of several interleukins (IL) by microglial cells and peripheral blood macrophages isolated from uninfected and simian immunodeficiency virus (SIV)-infected Rhesus monkeys. We found that uninfected, unstimulated primate microglia produce more IL-6 and less TNFα than peripheral blood macrophages, but generate comparable levels of IL-1β and IL-8. After infection with SIVin vitro,synthesis of all cytokines tested is increased compared to uninfected cultures and to peripheral blood macrophages. Microglia isolated from infected animals produce more IL-8 and TNFα than the uninfected cultures and display a strongly increased capacity to secrete TNFα upon stimulation with lipopolysaccharide. In addition, production of IL-6 byin vivo-infected microglia increases with time in culture to very high levels despite the fact that only a few cells contained replicating virus. These findings clearly show that the cytokine production of microglia is impaired after SIV infection bothin vitroandin vivoand that a low level of viral replication is sufficient for these alterations to occur. In conclusion, the results of this study further support a possible role of cytokines in the pathogenesis of neuro-AIDS
Inhibition of Human Parainfluenza Virus-3 Replication by Interferon and Human MxA

AbstractWe have investigated the IFN-mediated inhibition of human parainfluenza virus-3 (HPIV-3) replication in cultured human A549 cells. IFN-α inhibited the virus yield significantly with concomitant reduction of viral RNA accumulation by more than 90%. Further studies indicated that the inhibitory action of IFN was at the level of primary transcription of HPIV3 replication. Since the IFN-inducible protein, MxA, has been shown to inhibit virus replication in several RNA viruses, we examined the role of MxA in HPIV-3 replication using a stably transfected human glioblastoma cell line expressing MxA. In these cells HPIV-3 replication was decreased by more than 100-fold depending on the virus dosage used with concomitant inhibition of viral RNA synthesis by about 80%. However, the viral primary transcription was not affected in this MxA-producing cell line. In contrast, in the parental cell line IFN-mediated inhibition occurred at the primary transcription step of HPIV-3 replication. These data suggest that, in addition to MxA, other IFN-inducible proteins are involved in the anti-HPIV-3 effect of IFN in both the cell lines used
Structural Limitations of the Ad5 E1A 12S Nuclear Localization Signal

AbstractThe Ad5 E1A 12S gene encodes an oncoprotein with the ability to immortalize and cooperate with other viral or cellular oncoproteins to transform primary epithelial cells. The immortalizing function is dependent on the protein's efficient localization to the nucleus. A five amino acid nuclear localization signal (NLS), Lys-Arg-Pro-Arg-Pro, has been identified at the extreme COOH-terminus. This signal is necessary but not sufficient for efficient nuclear localization. A mutational analysis has been undertaken to further characterize the 12S NLS. The individual amino acids of the signal appear to have varying functional relevance. The lysine residue (a.a. 239) and the first arginine residue (a.a. 240) are the most critical. Changing the second arginine (a.a. 242) to threonine or either proline (a.a. 241 or 243) to alanine marginally diminishes signal function. Replacing the 12S NLS with the SV40 large T antigen (LT) NLS does not measurably affect the protein's nuclear localization. Sequences directly upstream of the NLS have a significant role in the proper localization of the 12S protein as illustrated by inefficiently localized mutants that have deletions of these sequences. Analyses of these mutants using a monoclonal antibody that recognizes the COOH-terminal four amino acids of the NLS have revealed that their signals are probably masked. To further investigate the importance of protein context in signal function, several NLS insertion mutants were constructed. Two regions in the first exon with predicted high surface probabilities and no known functions were chosen as sites for NLS insertions. Neither a wild-type 12S- nor a SV40 LT-NLS was functional in any of the new locations, indicating that for 12S, positioning of the NLS in the protein is critical
Influenza B Virus NB Glycoprotein Is a Component of the Virion

AbstractThe influenza B virus NB glycoprotein is abundantly expressed at the surface of virus-infected cells. NB spans the membrane once and has an 18 amino acid ectodomain, a 22 amino acid transmembrane domain, and a 60 amino acid cytoplasmic tail. The NB N-terminal ectodomain contains two asparagine residues that are modified by the addition of N-linked carbohydrate chains, which become further modified by the addition of polylactosaminoglycan. We have now shown that NB is also modified by addition of palmitic acid. To determine if NB is incorporated into virions, metabolic labeling, immunoblotting, and immunogold electron microscopy techniques were used. NB was identified in virions grown in MDCK cells or in embryonated chicken eggs in two forms: (a) NB modified by addition of polylactosaminoglycan (NBpl), and (b) a cleaved species (NBc) that has a smaller molecular weight than unglycosylated NB (NB12). Proteinase K digestion of purified virions converted NBplto NBc. Examination of virions purified by isopycnic centrifugation by electronmicroscopy and immunogold staining, using an affinity-purified antibody raised to a peptide derived from the NB cytoplasmic tail, showed staining for NB in influenza B virions. Quantification of the amount of NB in purified virions using two unrelated biochemical methods indicated there are on average approximately 15–100 molecules of NB per virion. Although the number of NB molecules incorporated on average into an influenza B virus particle is small, this finding is reminiscent of the number of molecules (14–68 monomers) found on average of the M2integral membrane protein of influenza A virus
Activation oforiLyt,the Lytic Origin of DNA Replication of Epstein–Barr Virus, by BZLF1

AbstractoriLyt,thecis-acting element of the lytic origin of DNA replication of Epstein–Barr virus, is activated by the viral transactivator BZLF1 which belongs to the extended bZIP class of transcription factors. Seven binding sites for BZLF1, so-called ZRE sites, are located withinoriLyt.By mutational analysis of individual ZRE sites, we found that lytic DNA replication is dependent on only four of these sites which colocate with the promoter of the BHLF1 gene. The remaining three ZRE sites distal to the BHLF1 promoter were dispensable for DNA replication and did not contribute to long-range transcriptional activation of this promoter by BZLF1. This finding indicated that a similar set of ZRE sites is involved in DNA replication and transcriptional activation. To determine the function of BZLF1 in DNA replication, BZLF1 mutants with successive deletions in the transactivation domain were analyzed in replication assays. Unexpectedly, most BZLF1 mutants which failed to support DNA replication were found to be equally defective in transcriptional activation. Therefore, similartrans-acting domains of BZLF1 are involved both in replication and in transcription
Long-Term Protection against HIV-1 Infection Conferred by tat or rev Antisense RNA Was Affected by the Design of the Retroviral Vector

AbstractWe have constructed a series of retroviral vectors in which the expression of antisense RNA targeted at the full length coding sequence of HIV-1 tat or rev was driven by three different promoters and in the context of double-copy or single-copy vectors. Jurkat cells transduced by these vectors were shown to express the expected tat or rev antisense RNA without alteration in cell proliferation or surface CD4 expression. After challenge with HIV, four patterns of protection were identified, with the degree of protection being determined primarily by the design of the expression system. In those patterns showing long-term complete protection, we could detect no HIV p24 in the culture supernatants or in the cells, and no HIV RNA or HIV proviral DNA (by PCR), during a 23-week follow-up. Experiments designed to rescue any live virus still formed in the culture after 20 weeks’ challenge demonstrated that, with some constructs, infectious virus could no longer be isolated, while with other constructs, only a low level of infectious virus was still being formed and providing a continuing virus challenge, although all other markers of infection remained undetectable. Our results demonstrated that antisense RNA expression driven by tRNA promoter in the context of a double-copy vector conferred better long-term protection against HIV infection compared to that driven by HIV LTR or MLV LTR promoters, and that the optimized vectors may be useful in developing a gene therapy against HIV-1 infection and AIDS
Conservation of DNA Sequence in the Predicted Major Late Promoter Regions of Selected Mastadenoviruses

AbstractThe major late promoter (MLP) of the subgroup C human adenoviruses is a preeminent model for the study of the mechanisms of basal and activated transcription, bothin vivoandin vitro.However, while the structure and function of the human virus MLP has been the subject of extensive investigation, the conservation of the various promoter elements among the adenoviruses from different species has not been examined. Conservation of specific elements would strongly suggest the importance and universality of their function. To address this issue, sequences were obtained from cloned DNAs of several representative Mastadenoviridae, mouse adenovirus type 1 (MAV-1), Tupaia adenovirus type 1 (TAV-1), and two bovine adenoviruses of two distinct subgroups, BAV-3 and BAV-7. The results of the sequencing studies showed that the TATA box and an upstream inverted CAAT box are conserved in all species and that the binding site for transcription factor USF is present in all except MAV-1, in which a sequence similar to an Sp1-binding site is present at a similar position. The initiator element (INR) sequence is not well conserved, and only one or other of the two downstream activating elements, DE1 and DE2, is predicted to be present in the nonprimate virus MLP regions. Ribonuclease protection assays on RNA isolated from MAV-1-infected cells late in infection indicated that the predicted MLP is functional, and transcription initiation and splice donor sites were identified. The human virus MLP is embedded in the essential DNA polymerase sequence on the opposite DNA strand. The primary amino acid sequences of the C-terminal regions of the predicted DNA polymerases show strong conservation of sequence motifs observed in replicative polymerases ranging from prokaryotes to mammals, and additional regions of strong conservation among the adenovirus polymerases. Pairwise comparisons between the newly sequenced regions of the polymerases and previously published sequences show that BAV-7 is most dissimilar to all others, while TAV-1 has a greater similarity to the primate sequences than to the others. The sequence data from both strands were also used to construct phylogenetic trees, based on BAV-7 as the outgroup. The trees constructed from the two sets of sequences are broadly similar, showing close relationships between primate viruses, but differing in the order of divergence of TAV-1 and MAV-1 branches
Mechanisms of Immunization with a Replication-Defective Mutant of Herpes Simplex Virus 1

AbstractWe have investigated the mechanisms by which subcutaneous immunization of mice with a replication-defective mutant of herpes simplex virus 1 protects against infection of the eye and latent infection of the trigeminal ganglion following corneal challenge. First, we have shown that immunization reduces the number of trigeminal ganglion neurons in challenged animals that express the latency-associated transcript. This indicates that the reduction in the incidence of latent infection by challenge virus is likely due to immune mechanisms and not saturation of the potential sites of latent infection by the immunizing mutant virus itself. Second, the duration of protective immunity against acute infection, keratitis, and latent infection was similar in mice immunized with replication-defective or -competent virus; thus, the replication-defective mutant virus is able to induce durable immunity apparently without spread in the host. Third, although the mutant virus showed no evidence of replicationin vivo,it was present in footpad tissue in an infectious form for several days. This surprising observation raises the possibility that continued infection events by input virus over an extended period of time may have a boosting effect on the developing immune response which could explain, at least in part, the capacity of these replication-defective mutant viruses to elicit a robust and durable immunity despite their inability to spread within the host