- Volume 73, Issue 10, 1992
Volume 73, Issue 10, 1992
- Review Article
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- Articles
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- Animal
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Idiotypic Expression of Anti-gp120 Antibodies in Unrelated Human Immunodeficiency Virus-infected Individuals
Although it is recognized that human immunodeficiency virus (HIV) env genes exhibit a high degree of variability, little is known about the molecular heterogeneity of gp120-specific antibodies in infected individuals. As a first step to approach this issue, we investigated the idiotypic relatedness of anti-gp120 antibodies present in the serum of HIV-infected individuals. Idiotypic determinants (idiotopes) are fingerprints of the variable region of the antibody molecule and, as such, they represent unique probes with which to explore the diversity of the immune response. We isolated IgG anti-gp120 antibodies from the serum of a seropositive asymptomatic individual by affinity chromatography. The purified antibodies were shown to bind gp120 and gp160 by ELISA, Western blotting and radio-immunoprecipitation. They also recognized HIV-infected human T cells as detected by immunofluorescence. Anti-idiotypic reagents were generated against this gp120 idiotype, and one of them was used to study anti-gp120 idiotypic diversity in a panel of 65 sera drawn from AIDS and AIDS-related complex patients, and from HIV seropositive asymptomatic individuals. Sixty normal human sera were used as negative controls. We found no evidence for common idiotopes on anti-gp120 antibodies of unrelated individuals. In contrast, we also noticed that the idiotypic profile expressed sequentially at two different intervals in a persistently infected individual showed little variation. Finally, when the diversity of murine anti-gp120 antibodies with a monoclonal anti-idiotype was analysed, no evidence of cross-reactive idiotopes in the murine system was found.
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Stimulation of Specific Immune Responses to Simian Immunodeficiency Virus Using Chimeric Hepatitis B Core Antigen Particles
More LessSubunit approaches to vaccines against viral diseases have resulted in the development of a number of methods for presentation of defined epitopes to the immune system. We have exploited a highly immunogenic presentation system based on hepatitis B core antigen (HBcAg) particles to produce a number of candidate vaccines against simian immunodeficiency virus (SIV). Recombinant particles have been produced in bacteria which carry multiple copies of defined or predicted neutralizing epitopes of SIV at a number of different sites within the particle. In parallel, a number of synthetic peptide-based SIV vaccines have been produced based on homology to reported neutralizing epitopes in human immunodeficiency virus. Although potent immune responses were elicited against both particulate and peptide forms of the antigen, neutralizing antibodies were not induced as judged by available assays.
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Interactions Between Bluetongue Virus Core and Capsid Proteins Translated in Vitro
More LessTo determine whether the two major core proteins (VP3 and VP7) of bluetongue virus can interact in vitro to form morphological structures, linearized VP3 and VP7 cDNA clones were transcribed using SP6 polymerase and the resultant transcripts were co-translated using rabbit reticulocyte lysates. The structures derived were isolated by sedimentation through a sucrose gradient and found to resemble VP3–VP7 core-like particles (CLPs) expressed in vivo. Reacting CLPs synthesized in vivo with outer capsid proteins translated in vitro (VP2 or VP5) indicated that each outer capsid protein has the capacity to bind to a preformed CLP. This was confirmed by in vivo expression of the appropriate genes using baculovirus vectors. The interaction of VP2 or VP5 with the CLP was analysed by electron microscopy and by using immunogoldlabelled monoclonal antibody.
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Comparison of the Major Structural Core Proteins of Tick-borne and Culicoides-borne Orbiviruses
More LessComparison of sequence data for Broadhaven (BRD) virus, a tick-borne orbivirus, and bluetongue virus (BTV), the type species of the genus, indicated that RNA segments 2 and 7 of BRD virus encode the two structural core proteins, VP2 and VP7, respectively. Segment 2 is 2792 nucleotides in length with a coding capacity for a protein (VP2) of 908 amino acids and a net charge of +8.5 at neutral pH. Segment 7 is 1174 nucleotides in length with a coding capacity for a protein (VP7) of 356 amino acids and a net charge of +11.5 at neutral pH. Comparison of the two sequences with BTV serotype 10 revealed amino acid identity of 35% between the product of segment 2 and BTV VP3, and 21% between the product of segment 7 and BTV VP7. The core proteins therefore show evidence of significant evolutionary divergence compared with that shown between different insect-borne orbiviruses. In particular, the amino terminus of BRD virus VP7 differed markedly from the equivalent region in VP7 of BTV and African horse sickness virus. This region is thought to interact with the outer capsid layer of insect-borne orbiviruses.
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Synthesis and Processing of the Haemagglutinin—esterase Glycoprotein of Bovine Coronavirus Encoded in the E3 Region of Adenovirus
The haemagglutinin—esterase gene (HE) of bovine coronavirus (BCV) encodes a major viral membrane glycoprotein that elicits BCV-neutralizing antibodies. The BCV HE gene was cloned into a human adenovirus serotype 5 (Ad5) transfer vector in place of early transcription region 3, and a helper-independent recombinant virus was constructed by rescue of the transcription unit by homologous in vivo recombination between the vector and Ad5 genomic DNA. The BCV HE polypeptide expressed by this recombinant Ad was characterized in vivo and in vitro. A 65K polypeptide was identified using an anti-BCV antibody in both human (293) and bovine (MDBK) cells infected with the recombinant Ad. In the absence of a reducing agent, migration of the 65K polypeptide was shifted to 130K, indicating that the recombinant HE polypeptide existed in a dimeric form. The HE polypeptide was glycosylated, as demonstrated by labelling with [3H]glucosamine, and was immunoreactive with three distinct groups of conformation-specific anti-HE monoclonal antibodies (MAbs). Cells infected with recombinant Ad expressing BCV HE exhibited both haemadsorption activity and acetylesterase activity. In addition, the anti-HE group A MAbs HC10-5 and KD9-40 inhibited both the haemadsorption activity and esterase activity of the recombinant HE polypeptide, suggesting that the antigenic domain responsible for BCV neutralization may overlap (or is closely associated with) the domain(s) responsible for haemagglutination and/or acetylesterase activities. When mice were inoculated intraperitoneally with live recombinant Ad, a significant level of BCV-neutralizing HE-specific antibody was induced. These results indicate that the recombinant Ad replicates and directs the synthesis of the BCV HE polypeptide in vivo.
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Heterotypic Lymphoproliferative Response in Pigs Vaccinated With Foot-and-mouth Disease Virus. Involvement of isolated Capsid Proteins
More LessThe in vitro viral lymphoproliferative response of pigs vaccinated against foot-and-mouth disease virus (FMDV) has been characterized. Peripheral blood mononuclear cells from immunized animals up to 1 year post-immunization (p.i.) showed a time-dependent FMDV-specific response, as assayed by virus-specific cellular blastogenesis. The optimum viral concentration decreased with time (around 20 weeks p.i.), and the response was faster and weaker. Lymphoproliferation appeared to be mainly due to CD4+ T cells. The response was heterotypic, being induced by all FMDV serotypes tested (C, A and O) after only two vaccinations with FMDV of serotype C (C-S8). Each individual structural protein assessed (VP1, VP2 and VP3) induced proliferation, with VP3 and VP1 being more effective stimulators. In vitro serum neutralization activity and FMDV-specific IgG production were found to be active even at 1 year p.i.
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Nucleotide Sequence of the Tick-borne Orthomyxo-like Dhori/India/1313/61 Virus Membrane Protein Gene
More LessThe complete nucleotide sequence of the sixth largest segment of ssRNA (RNA-6) of the tick-borne orthomyxo-like Dhori/India/1313/61 virus was determined by using cloned cDNA derived from infected cell mRNA and dideoxynucleotide sequencing of viral RNA. RNA-6 contains 962 nucleotides and is predicted to encode a protein of 270 amino acids with an M r of 30498 in its first open reading frame (ORF). This protein is likely to represent the viral membrane (M1) protein, based on its predicted M r of 29000 (estimated by PAGE), its relatively high abundance in infected cells and amino acid composition analysis. In addition, a second ORF was found which overlaps the M1 protein gene sequence by 327 nucleotides. This additional reading frame, in the +3 frame, potentially can encode a protein of 141 amino acids. However, S1 nuclease analysis of RNA-6 mRNA from infected cells indicated that there was only a single abundant RNA species corresponding in size to the full-length genomic RNA (0.96 kb). Further studies are needed to determine whether expression of the second ORF occurs and how that expression might arise.
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A Monoclonal Antibody Recognizes a Human Cell Surface Glycoprotein Involved In Measles Virus Binding
More LessMeasles virus (MV) has a very limited host range, humans being the only natural reservoir of the virus. This restriction may be due to the absence of an MV receptor on the surface of non-primate cells. We have studied the MV-binding ability of several cell lines and attempted to characterize the receptor by studying the binding of 35S-labelled MV and by a rosette formation technique. We confirmed that all the human cell lines examined (HeLa, Raji and Jurkat) bound MV and that the murine cell lines (BW and L) did not. The glycoprotein nature of the receptor activity was demonstrated by the fact that it could be removed from the cell membrane using proteolytic enzymes and by its failure to be re-expressed in the presence of a protein synthesis inhibitor or an N-glycosylation inhibitor. A monoclonal antibody isolated after immunization of mice with Raji cells specifically inhibited MV binding and infection of human cells, and recognized human and simian but not murine cells. Depending on the cell line (HeLa, Raji, Jurkat or Vero), this antibody immunoprecipitated one or two glycoproteins with apparent M rs of 57K and/or 67K from human and simian cells, but not from murine cells.
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Location of the Epitope Recognized by Monoclonal Antibody 63G on the Primary Structure of Human Respiratory Syncytial Virus G Glycoprotein and the Ability of Synthetic Peptides Containing this Epitope to Induce Neutralizing Antibodies
More LessThe location of the epitope recognized by monoclonal antibody (MAb) 63G on the primary structure of the human respiratory syncytial virus G glycoprotein was determined by testing the reactivity of synthetic peptides with the MAb. The role of individual amino acids in this epitope was determined by using a set of 13-mer peptides containing sigle residue deletions. Residues 204 to 209 were found to be essential for antibody binding. These results are in full agreement with previous sequence data for escape mutants selected with MAb 63G. Several peptides, free or bound to keyhole limpet haemocyanin (KLH), were used to raise antisera in rabbits. The antipeptide antibodies reacted with the G protein in Western blots. However, only peptide G1-KLH (residues 187 to 200 bound to KLH) induced antibodies that reacted with the intact G protein and inhibited infectivity. These findings are discussed in terms of the antigenic structure of the G glycoprotein and the molecular engineering of peptide antigens.
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Differential Effect of DNA Supercoiling on Transcription of Adenovirus Genes in vitro
More LessWe examined the effect of DNA template topology on the transcription of immediate early (E1a), early (E1b) and late (pIX) adenovirus genes in vitro. Transcription in whole cell extracts was measured by quantitative hybridization to end-labelled DNA and protection of hybrids from S1 nuclease digestion. Two- to fourfold more E1a RNA was synthesized from supercoiled, compared to linear, DNA templates. Similarly, transcription of the E1b gene was stimulated three- to sevenfold when the template was supercoiled. In contrast, RNA synthesis from the late pIX gene was found to be independent of DNA topology. These results show that DNA topology affects transcription in a promoter-specific manner.
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Evidence That the Transcriptional Trans-activating function of the Bovine Papillomavirus Type 1 E2 Gene is not Required for Viral DNA Amplification in Division-arrested cells
More LessAmplification of bovine papillomavirus type 1 (BPV-1) DNA in growth-arrested mouse cell cultures appears to mimic the process of induction of vegetative BPV-1 DNA synthesis in cells of the stratum spinosum in productively infected bovine warts. In both cases, cells permissive for viral DNA amplification express large amounts of viral E2 protein which accumulates within the cell nucleus. Whereas in latently infected virus-transformed cells truncated transcriptional repressor forms of E2 predominate, our previous studies have demonstrated that the full-length E2 transcriptional trans-activator protein is preferentially expressed during the period of maximal BPV-1 DNA amplification in growth-arrested cell cultures. To investigate the role of the full-length E2 gene in the induction of viral DNA amplification in this experimental viral replication system we have used a mutant BPV-1 genome (BPVE2-ts1) containing an E2 gene which is temperature-sensitive (ts) for transcriptional trans-activation. This mutant genome has also been shown to be ts for stable viral plasmid DNA replication and for the induction of cell transformation. We show here that viral DNA amplification was not severely impaired when BPVE2-ts1-transformed cells were tested at the restrictive temperature, indicating that the transcriptional trans-activating function of E2 was not essential for viral DNA amplification in division-arrested cells and, moreover, that the trans-activation and replication functions of E2 were separable. Consistent with this hypothesis, amplification of the BPVE2-ts1 genome at the restrictive temperature was still associated with the accumulation of large amounts of nuclear E2 antigen, showing that the mutation did not disrupt nuclear transport or render the E2 protein highly unstable. Furthermore, C127 cells harbouring ts E2 and full-length E1 expression constructs supported transient plasmid replication of a BPV origin vector at the restrictive temperature. These observations imply that E2 functions primarily as a viral replication factor in the vegetative phase of BPV-1 DNA replication, and suggest a fundamental difference in the genetic regulation of stable BPV-1 plasmid DNA replication in mitotic cells and viral DNA amplification in postmitotic cells.
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Phylogenetic Classification of Human Papillomaviruses: Correlation With Clinical Manifestations
More LessHuman papillomaviruses (HPVs) are a heterogeneous group of small dsDNA viruses which cause a variety of proliferative epithelial lesions at specific anatomical sites. Although more than 65 different virus types have been cloned and characterized, no uniform classification system exists. In order to classify HPV DNA types, phylogenetic trees were constructed based on nucleotide sequence alignments using parsimony and distance matrix algorithms. The resulting phylogenetic trees provide a classification of the HPVs into specific groups encompassing the known tissue tropism and oncogenic potential of each HPV type. The implications of a phylogenetic taxonomy on the diagnostic detection of HPVs and the concept of different HPV species are discussed.
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Comparison of the Locations of Homologous Fowlpox and Vaccinia Virus Genes Reveals Major Genome Reorganization
More LessWe have derived a restriction enzyme map for the fowlpox virus FP9 strain. Sites for BamHI, PvuII, PstI and NcoI have been mapped mainly by Southern blotting. The size of the genome derived from the restriction maps (254 kb) corresponds to the figure of 260 ± 8 kb determined from analysis of genomic DNA by pulsed-field electrophoresis. The map can be compared with a previously published map for a different strain of fowlpox virus using the PstI digest which is common to both studies. Some 65 kb of fowlpox virus sequence, in 11 blocks, as well as individual M13 clones have been aligned with the map. Where those blocks correspond with blocks of homologous genes in vaccinia virus, it is possible to compare the genomic locations for those genes in the two viruses. This comparison reveals that, whereas there are blocks of sequence within which genes exist in the same relative position in the two viruses, the genomic location of those sequence blocks differs widely between the two viruses.
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Two Major Types of JC Virus Defined in Progressive Multifocal Leukoencephalopathy Brain by Early and Late Coding Region DNA Sequences
More LessA 610-bp region of the JC virus (JCV) genome sequenced from brains of 11 progressive multifocal leukoencephalopathy (PML) patients contains 20 sites of point mutations that allow reliable classification of JCV isolates into two types. These type-determining sites were located in the region extending from position 2131 in the VP1 gene, through the intergenic region, to position 2740 in the T antigen gene. At these 20 sites the presence of different nucleotides creates two distinct patterns of substitution, with six isolates having the Type 1 pattern and five having the Type 2 pattern. Only four of the 11 isolates had ‘crossovers’ to the opposite type consensus DNA sequence at a small number of sites, indicating a very high type specificity. Additionally, three type-determining sites occur in the non-coding region to the left of the origin of replication. Other mutations occurred at random sites, making each strain unique, although one strain, 105, is identical to the Type 1 consensus. The JCV prototype strain Mad-1 was found to be Type 1 and differs from the consensus sequence at five sites. The other previously sequenced JCV strain, GS/B, is Type 2. At three sites out of five in the T antigen C terminus there is a type-specific amino acid substitution; however, none of the type-determining mutations in the VP1 gene cause an amino acid substitution. Comparison of each type’s consensus DNA sequence to that of BK virus suggests that Type 2 represents the ancestral JCV sequence from which Type 1 diverged during human evolution.
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Inhibition of Human Cytomegalovirus Maturation by Brefeldin A
More LessBrefeldin A (BFA) was found to interfere with specific events of human cytomegalovirus (HCMV) maturation in human fibroblasts. Ultrastructural as well as biochemical studies suggested that short-term exposure of infected cultures to BFA during the late infectious cycle primarily prevented Golgi-dependent processes, e.g. envelopment of naked cytoplasmic nucleocapsids in the trans-Golgi network (TGN) and normal processing of glycoprotein B. In contrast, the nuclear phase of viral morphogenesis, e.g. transport budding at the nuclear envelope, was not impaired. These observations were compatible with the interpretation that HCMV morphogenesis may involve sequential budding events at the nuclear envelope and at cisternae of the TGN. BFA treatment during the early infectious cycle efficiently inhibited HCMV-DNA synthesis and thus late viral functions, preventing production of viral progeny. Cytotoxicity was excluded as a cause for these findings.
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Glycoprotein H of Human Cytomegalovirus (HCMV) Forms a Stable Complex With The HCMV UL115 Gene Product
More LessThe human cytomegalovirus (HCMV) UL75 gene product is the homologue of herpes simplex virus type 1 (HSV-1) glycoprotein H (gH), a virion glycoprotein that is essential for infectivity and which is conserved among members of the alpha-, beta- and gamma-herpesviruses. It has previously been shown that HSV-1 gH forms a stable complex with HSV-1 gL, the product of the UL1 gene, and the formation of this complex facilitates the cell surface expression of gH. None of the open reading frames within the HCMV genome encode a product with discernible sequence homology with HSV-1 gL, but an examination of the arrangement of conserved genes in HCMV suggested that the UL115 gene is a ‘positional homologue’ of HSV-1 UL1 which, like UL1, encodes a small secreted glycoprotein. Co-expression of HCMV gH (the UL75 gene product) and the UL115 gene product revealed that these proteins form a disulphide-linked complex and that the formation of this complex results in cell surface expression of gH. This complex is analogous to the gH:gL complex of HSV-1 and the HCMV UL115 gene product is therefore the functional homologue of HSV-1 gL.
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Monoclonal Antibody E-13 (M-810) to Human Cytomegalovirus Recognizes an Epitope Encoded by Exon 2 of the Major Immediate Early Gene
More LessMonoclonal antibody (MAb) E-13 to human cytomegalovirus is used widely for diagnostic and fundamental studies, and has been shown to be directed against an immediate early (IE) protein(s). To determine which viral antigen is detected by MAb E-13, four subfragments from the open reading frame encoded by exons 2, 3 or 4 of IE-1 were cloned in the bacterial expression vector pROS. The resulting fusion proteins contained amino acids 77 to 491 encoded by mainly exon 4, amino acids 25 to 78 encoded by exon 3, amino acids 1 to 85 encoded by exons 2 and 3, and amino acids 1 to 24 encoded by exon 2. The reactivity of MAb E-13 with the fusion proteins was assayed by Western blotting. MAb E-13 was shown to react exclusively with proteins encoded by exon 2 and therefore recognizes IE proteins which contain the N-terminal amino acid sequence encoded by exon 2, namely the major 72K IE protein, the 82K to 86K IE-2 protein and the 52K to 55K IE-2 protein. MAb E-13 can be used to detect both IE-1- and IE-2-encoded proteins, which share the polypeptide encoded by exon 2.
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Neutralizing Mechanisms of Two Human Monoclonal Antibodies Against Human Cytomegalovirus Glycoprotein 130/55
More LessThe neutralization of human cytomegalovirus (HCMV) after adsorption to the cell surface at 4 °C was studied using two neutralizing monoclonal antibodies (C-23 and C-41) recognizing glycoprotein 130/55. HCMV adsorbed to cells was neutralized by C-23 (complement-independent), but not by C-41 (complement-dependent). Furthermore, the virus remained sensitive to C-23 for 120 min after shifting up from 4 °C to 37 °C, suggesting that C-23 might block an early stage of virus penetration into cells, and also that transition from virus attachment to virus penetration might be quite slow. The cell-to-cell infection of HCMV was also blocked only by C-23, and not by C-41. On the basis of the results presented here, we suggest that C-41 blocks the attachment of virus to the cell surface whereas C-23 prevents the penetration of virus into the cell.
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Identification of Genes Encoding Two Capsid Proteins (VP24 and VP26) of Herpes Simplex Virus Type 1
More LessThe capsid of herpes simplex virus type 1 is composed of seven proteins. VP5, VP19C, VP22a and VP23 have been shown previously to be the products of genes UL19, UL38, UL26.5 and UL18, respectively. The genes encoding VP21, VP24 and VP26 have not been identified to date. We have determined amino acid sequences of fragments of isolated capsid proteins generated by partial cleavage with CNBr. The results confirm the gene assignments for VP5, VP19C and VP23. They also show that VP26 is the product of gene UL35 and that VP24 contains the protease domain present in the N-terminal portion of the UL26-encoded protein. VP21 was not investigated, but we suggest that it is the C-terminal portion of the UL26-encoded protein remaining after release of VP24 and that it thus corresponds to a form of VP22a extended at the N terminus.
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Alternative Splicing Determines The Carboxy Terminus of the Epstein—Barr Virus Nuclear Antigen 5 Species Expressed in the Burkitt's Lymphoma Cell Line Daudi
More LessThe Daudi strain of Epstein—Barr virus (EBV) possesses a genomic deletion, relative to the B95-8 EBV prototype, that removes the entire Epstein—Barr virus nuclear antigen 2 (EBNA2) open reading frame (ORF) and the sequences encoding the carboxy terminus of EBNA5. Immunoblot analysis carried out in this study indicates that two species of EBNA5 (31K and 37K) are expressed in Daudi cells. Nucleotide sequence analysis of Daudi cDNA clones has confirmed that, as a consequence of the genomic deletion, exons usually appearing further downstream in EBNA messages (exons U or HF) are spliced directly onto the truncated EBNA5 ORF. Furthermore, the use of alternative splicing suggests that the two EBNA5 species expressed in Daudi cells possess different carboxy termini.
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Identification of a Gag Protein Epitope Conserved Among All Four Groups of Primate Immunodeficiency Viruses by Using Monoclonal Antibodies
Five monoclonal antibodies (MAbs) were raised against the gag proteins of simian immunodeficiency virus (SIV) from African green monkey (SIVagmTYO-7). Two MAbs reacted with the matrix protein p17 and the other three with the core protein p24. Studies on the cross-reactivity of the MAbs revealed that the anti-p24 MAbs detected an epitope shared by the viruses belonging to the human immunodeficiency virus type 2 (HIV-2)/SIVmac group and SIVagmTYO-7 and SIVagmTYO-5. The anti-p17 MAbs recognized an epitope present on all these viruses and on SIVagmTYO-1, HIV-1 and SIVmnd. This finding demonstrates for the first time that the matrix protein, p17 or p18, respectively, of all nine HIV and SIV isolates tested in this study expresses at least one conserved immunogenic epitope recognized serologically. By using synthetic peptides, this epitope was identified at the N terminus of p17. Furthermore, this epitope was analysed by multiple sequence alignments of the peptide with homologous sequences of HIV and SIV p17.
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Genomic Characterization and Mutation Rate of Hepatitis C Virus Isolated From a Patient Who Contracted Hepatitis During an Epidemic of non-A, non-B Hepatitis in Japan
More LessTo investigate the genomic characterization of hepatitis C virus (HCV) isolated from a patient who contracted hepatitis during an epidemic of non-A, non-B (NANB) hepatitis in Shimizu city, Japan, we have cloned the nucleotide sequence of the viral genome (HCV-KF) spanning the structural domain. When compared to other previously reported HCV isolates, HCV-KF showed an overall identity at the amino acid level of 90.0 to 92.1% with Japanese isolates and 80.9 to 82.1% with American-like isolates. The HCV-KF genome displays an insertion of three nucleotides in-frame (corresponding to one amino acid) found at the junction between the E1 and E2/NS1 region. The mutation rate of the HCV-KF genome was assessed by comparing the nucleotide and deduced amino acid sequences of the viral RNA obtained from the serum of the original patient with viral sequences derived from the serum of a chimpanzee inoculated with the same serum 9 years previously. The substitution rate of the viral genome was estimated at 0.9 × 10−13 nucleotides per site per year for the HCV structural region. The highest mutation rate was found in the hypervariable region within the E2/NS1 domain. It is suggested that the outbreak in Shimizu city was caused by a strain of HCV closely related to the Japanese-like subgroup of isolates.
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Sequence analysis of the membrane protein gene of human coronavirus OC43 and evidence for O-glycosylation
More LessThe gene encoding the membrane (M) protein of the OC43 strain of human coronavirus (HCV-OC43) was amplified by a reverse transcription-polymerase chain reaction of viral RNA with HCV-OC43- and bovine coronavirus (BCV)-specific primers. The nucleotide sequence of the cloned 1.5 kb fragment revealed an open reading frame (ORF) of 690 nucleotides which was identified as the M protein gene from its homology to BCV. This ORF encodes a protein of 230 amino acids with an M r of 26416. The gene is preceded by the motif UCCAAAC, analogous to the consensus coronavirus transcription initiation sequence. The M protein of HCV-OC43 shows features typical of all coronavirus M proteins studied: a hydrophilic, presumably external N terminus including about 10% of the protein, and a potential N-glycosylation site followed by three major hydrophobic transmembrane domains. The amino acid sequence of the M protein of HCV-OC43 has 94% identity with that of the Mebus strain of BCV, and also contains six potential O-glycosylation sites in the exposed N-terminal domain. Indeed, the glycosylation of the M protein was not inhibited in the presence of tunicamycin, which is indicative of O-glycosylation, as previously reported for BCV and murine hepatitis virus. Virions released from tunicamycin-treated cells contained the M glycoprotein but were devoid of both peplomer (S) and haemagglutinin-esterase (HE) proteins. Thus, inhibition of the N-glycosylation of the S and HE structural proteins prevented their incorporation into progeny virions, an indication that they are dispensable for virion morphogenesis, unlike the M protein.
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Antigenic and Genetic Characterization of the Haemagglutinins of Recent Cocirculating Strains of Influenza B Virus
More LessThe antigenic and genetic characteristics of the haemagglutinins of influenza type B viruses isolated since 1988 during periods of both widespread activity (1990/1991) and sporadic activity (1989/1990) were examined using microneutralization tests and direct RNA sequencing. During 1989/1990, influenza B viruses representative of two distinct lineages antigenically and genetically related to either B/Victoria/2/87 or B/Yamagata/16/88 were isolated, and a minor drift variant of B/Yamagata/16/88, B/Hong Kong/22/89, was identified. In 1990/1991, B/Hong Kong/22/89- or B/Yamagata/16/88-like viruses accounted for the majority of the influenza virus isolates in most countries. Sequence analysis of the HA1 domains of representative viruses confirmed the containued existence of two main lineages among recent strains of influenza B virus and identified unique amino acid changes that could account for the altered antigenic reactivity of some variants. Sequence analysis of the HA2 domains of some of the recent influenza B viruses allowed for a comparison of the evolutionary rates and patterns between the HA1 and HA2 domains.
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Nucleotide Sequence Analysis of the Simian Virus 41 Gene Encoding the Large (L) Protein and Construction of a Phylogenetic Tree for the L Proteins of Paramyxoviruses
The complete nucleotide sequence of the simian virus 41 (SV41) large (L) protein gene was determined. The L gene spanned 6883 nucleotides including a putative trailer RNA, and the L mRNA contained a single large open reading frame encoding a polypeptide of 2269 amino acids. Dot-matrix comparisons under stringent conditions identified domains highly conserved among paramyxoviruses. Domain 3 is the most highly conserved, and has been hypothesized to be the RNA polymerase active site. A phylogenetic tree was constructed from the sequences of the L proteins of seven paramyxoviruses. SV41 was most closely related to human parainfluenza virus type 2 (HPIV-2), and SV41, HPIV-2 and SV5 form a subgroup. The intergenic sequences at the nucleocapsid protein-phosphoprotein and haemagglutinin—neuraminidase-L protein gene junctions, and the 5′ trailer sequence of SV41 were also determined, and it was shown that the first 13 nucleotides of the 5′ trailer sequence are complementary to those of the 3′ leader sequence. The intergenic, and gene-start and -end sequences of SV41, HPIV-2 and SV5 are shown.
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Are Sinc and the PrP gene congruent? Evidence from PrP gene analysis in Sinc congenic mice
More LessCongenic mouse strains VM/Dk and VM-Sinc s7/Dk differ at the Sinc gene, which controls the incubation period of scrapie in mice; VM/Dk mice are Sinc p7p7 and VM-Sinc s7/Dk mice are Sinc s7s7. Restriction fragment length polymorphism and DNA sequencing analysis demonstrated that the PrP genes also differ in these strains, confirming the close genetic linkage of Sinc and PrP. Using the restriction enzyme HhaI, we have shown that at least 100 kb of DNA flanking the PrP gene differs between the two strains, and therefore the congruence of the Sinc and PrP genes is still not certain.
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Molecular cloning of a mink prion protein gene
More LessTransmissible mink encephalopathy (TME) is a rare disease which is presumably transmitted to ranchraised mink from scrapie-infected sheep offal or bovine spongiform encephalopathy-infected cattle products. Although the infectious agent of TME has not been isolated, there is circumstantial evidence that TME is caused by prions. The experimental host range of TME includes sheep, cattle, monkeys and hamsters. However, TME has never been transmitted to mice. Since experiments in transgenic animals have shown that the prion protein (PrP) gene modulates the susceptibility, incubation time and neuropathology of prion-induced disease, we have started to analyse the mink PrP gene. PrP, as deduced from a genomic DNA sequence, consists of 257 amino acids and overall shows similarity of 84 to 90% with the sequences of the PrPs of other mammalian species. It remains to be determined whether these differences in the primary structure of PrP will explain the peculiar host range of TME.
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Pear Blister Canker Viroid is a Member of the Apple Scar Skin Subgroup (apscaviroids) and also has Sequence Homology with Viroids from other Subgroups
More LessThe sequence of pear blister canker viroid (PBCVd), the putative causal agent of pear blister canker (PBC) disease, has been determined. PBCVd consists of a single-stranded circular RNA of 315 nucleotide residues which assumes a branched conformation when it is folded in the model of lowest free energy. PBCVd has highest sequence similarity with grapevine 1B viroid (52.4%), but also contains sequences related to regions present in viroids that belong to different subgroups, suggesting that PBCVd could have developed from RNA recombination between viroids replicating in a common host plant. PBCVd contains almost the entire central sequence which is conserved in the members of the apple scar skin subgroup (apscaviroids) as well as a conserved sequence located in the left-terminal region of apscaviroids and pospiviroids (whose type member is potato spindle tuber viroid). A consensus phylogenetic tree has been obtained in which PBCVd and other viroids previously classified as apscaviroids appear closely related, allowing consideration of PBCVd as a new member of this subgroup.
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Defective Interfering L RNA Segments of Tomato Spotted Wilt Virus Retain Both Virus Genome Termini and have Extensive Internal Deletions
Defective interfering (DI) RNA molecules derived from the genomic L RNA segment of tomato spotted wilt virus (TSWV) were generated during sequential passage of the virus at high multiplicity. Characterization of DI RNAs from four distinct isolates by Northern blot analysis and sequence determination revealed that both the 5′ and 3′ genomic termini were retained in these molecules. Each DI RNA contained a single internal deletion of approximately 60% to 80% of the L RNA segment. All DI RNAs studied maintain an open reading frame (ORF) which suggests that these defective molecules should be translatable by ribosomes. Detection of only defective molecules with ORFs indicates either that association with ribosomes or translation is a prerequisite for the selection and maintenance of replicating DI RNAs, or that the truncated proteins produced play a role in their selection or replication. Analysis of the junction sites in the DI RNAs showed that short nucleotide sequences are repeated, one at the release and another at the reinitiation point on the L RNA. One of these is lost during the generation of the DI molecules. The presence of repeated sequences at the junction sites seems to be unique for tospovirus DI L RNAs; they have not been described for other DI systems of either positive- or negative-strand RNA viruses. A model for TSWV DI RNA generation is proposed in which the viral polymerase can ‘jump’ across the internal sequences from one secondary structure to another containing the repeated sequences, during the replication of the viral complementary L RNA segment.
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Replication of Grapevine Fanleaf Virus Satellite RNA Transcripts in Chenopodium quinoa Protoplasts
More LessA set of full-length cDNA clones of the satellite RNA of grapevine fanleaf nepovirus isolate F13 (GFLV-F13) was constructed with a variable number of additional, non-viral nucleotides at the 5′ and 3′ ends. The biological activity of the RNAs transcribed from these constructs was tested in Chenopodium quinoa protoplasts using a helper virus. When inoculated with arabis mosaic virus S (ArMV-S) RNA as helper, transcripts with 33 non-viral nucleotides at the 5′ end (tr45p4) did not replicate, whereas transcripts with only one non-viral nucleotide at the 5′ end (tr3S and tr3M) did replicate. Capping of the transcripts enhanced their replication. On the other hand, the presence of extra nucleotides at the 3′ end had little influence on the biological activity of the in vitro transcripts. In contrast with ArMV-S, GFLV isolate 24 was not a helper for tr3M transcripts, indicating a specific interaction between the helper strain and the satellite RNA.
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Cross-reacting and Heterospecific Monoclonal Antibodies Produced Against Arabis Mosaic Nepovirus
More LessMonoclonal antibodies (MAbs) were produced against arabis mosaic nepovirus (AMV). A hybridoma screening procedure was applied which involved the testing of culture supernatants, before the hybridomas were cloned to single cell lines, for their reaction with eight nepoviruses [AMV, cherry leafroll virus (CLRV), grapevine fanleaf virus (GFLV), peach rosette mosaic virus, raspberry ringspot virus (RRSV), tobacco ringspot virus, tomato black ring virus (TBRV) and tomato ringspot virus]. In addition to AMV-specific MAbs, this screening technique has allowed the selection of two cross-reacting MAbs: one reacting with AMV and GFLV, and one reacting with AMV and RRSV. This is the first report of MAbs cross-reacting with these nepoviruses. In addition, five heterospecific MAbs (HS-MAbs) could be selected: two reacting with RRSV, two with CLRV and one with TBRV. The usefulness of the screening technique that was applied for the selection of cross-reacting MAbs and HS-MAbs, and the potential use of such antibodies are discussed.
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Complete Nucleotide Sequence and Genetic Organization of Papaya Ringspot Virus RNA
The complete nucleotide sequence of the RNA genome of papaya ringspot virus (PRSV) was determined from four overlapping cDNA clones and by direct sequencing of viral RNA. The genomic RNA is 10326 nucleotides in length, excluding the poly(A) tract, and contains one large open reading frame that starts at nucleotide positions 86 to 88 and ends at positions 10118 to 10120, encoding a polyprotein of 3344 amino acids. The highly conserved sequence AAAUAAAANANCUCAACACAACAUA at the 5′ end of the RNA of PRSV and those of the other five reported potyviruses shows 80% similarity, suggesting that this region may play a common important role for potyvirus replication. Two cleavage sites of the polyprotein were determined by amino acid sequencing of the N termini of helper component (HC-Pro, amorphous inclusion) and cylindrical inclusion (CI) proteins. Other cleavage sites were predicted by analogy with the other potyviruses. The genetic organization of PRSV is similar to that of the other potyviruses except that the first protein processed from the N terminus of the polyprotein (NT protein) has an M r of 63K, 18K to 34K larger than those of the other potyviruses. The cleavage site for liberating the N terminus of the HC-Pro protein was found at the same location downstream from the consensus sequence FI(V)VRG as that reported for tobacco vein mottling virus. The NT protein of potyviruses is the most variable and may be considered important for identification of individual potyviruses. The most conserved protein of potyviruses appears to be the NIb protein, the putative polymerase for the replication of the potyviral RNA. The genetic organization of PRSV RNA is tentatively proposed to be VPg-5′ leader-63K NT-52K HC-Pro-46K-72K CI-6K-48K NIa-59K NIb-35K coat protein-3′ noncoding region-poly(A) tract.
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Nucleotide Sequence Responsible for the Synthesis of a Truncated Coat Protein of Brome Mosaic Virus Strain ATCC66
More LessThe ATCC66 strain of brome mosaic virus (BMV) (propagated at Kyoto University) contained two types of coat protein in its virion whereas the Russian strain of BMV has been known to contain a single coat protein; both strains have two initiation codons for coat protein in the same reading frame at the 5′-proximal end of the gene in RNA 4. Comparative studies on the nucleotide sequences of the ATCC66 and Russian strains of BMV demonstrated that in the ATCC66 strain, two adjacent adenine residues were absent from RNA 3 in the leader sequences of the coat protein gene just a few nucleotides 5′ to the first initiation codon of the coat protein gene. Using biologically active cDNA clones of BMV RNA of the ATCC66 strain, we inserted two adjacent adenine residues into the cDNA of RNA 3 to obtain an RNA 3 transcript which has the same nucleotide sequence as the Russian strain in the non-coding leader sequence of the coat protein gene. Barley protoplasts inoculated with this RNA 3 transcript together with RNA 1 and 2 produced a single coat protein. To obtain further insight into the mechanism of translation of the BMV coat protein, we constructed several types of RNA 4 by changing the sequence surrounding the first AUG codon in the coat protein gene and analysed the in vitro translation products of the mutant RNA 4. The results confirmed that the absence of the two adjacent adenine residues was responsible for the production of two types of coat protein in the ATCC66 strain. The deletion of the two adjacent adenine residues in ATCC66 resulted in a base substitution of A with U three nucleotides 5′ to the first AUG in the coat protein gene. The base substitution reduced translational activity from the first AUG codon and concomitantly increased translational activity from the second AUG codon from which a truncated coat protein was translated.
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Nucleotide Sequence of Shallot Virus X RNA Reveals a 5′-proximal Cistron Closely Related to Those of Potexviruses and a Unique Arrangement of the 3′-proximal Cistrons
More LessThe 8890 nucleotide RNA sequence of shallot virus X (ShVX), a new virus isolated from shallot, has been determined. The sequence contains six open reading frames (ORFs) which encode putative proteins (in the 5′ to 3′ direction) of M r 194528 (ORF1), 26333 (ORF2), 11245 (ORF3), 42209 (ORF4), 28486 (ORF5) and 14741 (ORF6). The ORF1 protein was found to be highly homologous to the putative potexvirus RNA replicases; ORF2, -3, -5 and -6 proteins also have analogues among the potex- and/or carlavirus-encoded proteins. ORF3 is followed by an AUG-lacking frame coding for an amino acid sequence homologous to that of the 7K to 8K proteins of the triple gene block of the above-mentioned viruses. The putative ORF4 protein has no reliable homology with proteins in the database. The results obtained testify that, except for the unique 42K protein gene, the ShVX genome combines a number of elements typical of both carla- and potexviruses.
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Geminivirus replication proteins are related to prokaryotic plasmid rolling circle DNA replication initiator proteins
More LessIt is demonstrated, by means of computer-assisted analysis, that C1 protein involved in the replication of geminivirus DNA is related to the rolling circle replication initiator proteins of eubacterial plasmids, particularly the plasmids of the pMV158 family. Three sequence motifs conserved in the geminivirus and plasmid replication proteins were delineated, one of them encompassing the Tyr residue that presumably forms a covalent linkage to DNA. These findings are compatible with the results of recent analyses of geminivirus replicative intermediates suggesting a rolling circle mechanism for geminivirus DNA replication. It is hypothesized that C1 protein initiates the rolling circle replication of geminivirus DNA by nicking a specific site in the virus-sense DNA and covalently linking to the 5′ side of the nick. The putative rolling circle replication initiator domain comprises the N-terminal portion of C1, whereas its C-terminal part is a putative helicase domain. By analogy with prokaryotic systems, it is speculated that the replication initiator domain and the helicase domain function coordinately. The possibility of the origin of geminiviruses from prokaryotic circular ssDNA replicons is discussed.
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Volumes and issues
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Volume 105 (2024)
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