- Volume 75, Issue 7, 1994
Volume 75, Issue 7, 1994
- Animal
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Hepatitis C virus particle detected by immunoelectron microscopic study
To clarify the morphology of hepatitis C virus (HCV), an indirect immunogold electron microscopic study was carried out on two plasma samples with high HCV RNA titres using polyclonal and monoclonal antibodies specific to the putative HCV envelope protein. Spherical virus-like particles, 55 to 65 nm in diameter with spikelike projections, were found in 114 to 116 g/ml fractions after sucrose density gradient centrifugation. These particles were found only in HCV-infected blood donors and had morphological features similar to those of flaviviruses. Moreover, these particles specifically reacted with the polyclonal and monoclonal antibodies to the putative HCV envelope protein. This is the first known report in which the morphology of the HCV particle is clearly shown.
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Entire nucleotide sequence and characterization of a hepatitis C virus of genotype V/3a
The entire nucleotide sequence of a hepatitis C virus (HCV) genome (NZL1) of genotype V/3a was determined from overlapping cDNA clones obtained from a human carrier in New Zealand. It comprised 9425 nucleotides (nt) including a 5-untranslated region of 339 nt, a single large open reading frame encoding a polyprotein of 3021 amino acids, a 3′-untranslated region of 23 nt, and 3 -terminal poly(U) stretches of variable lengths. The NZL1 genome was compared with 15 HCV isolates of other genotypes for which the full- length sequence has been determined. It differed from them by 31·1 to 34·3% in nucleotide sequence identity and by 24·5 to 29·1% in amino acid sequence identity, confirming the distinction of genotype V/3a from the other isolates.
The nucleotide sequence data reported in this paper are deposited in the DDBJ/GenBank/EMBL Data Libraries under the accession no. D17763.
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Sialoglycoproteins that bind influenza A virus and resist viral neuraminidase in different animal sera
Sialoglycoproteins that are resistant to degradation by viral neuraminidase can effectively neutralize influenza A viruses, because they bind irreversibly to the viruses. To detect such proteins in animal sera, we developed an immunochemical assay based on Western blotting techniques. We assessed the binding activity of sialoglycoproteins in sera from nine different animals toward the A/Aichi/2/68 (H3N2) and A/PR/8/34 (H1N1) strains of influenza virus, with or without viral and bacterial neuraminidase treatment. Using this assay, we found that animal sera contain a spectrum of sialoglycoproteins defined by differing abilities to bind influenza A viruses and to resist the viral neuraminidase. Structural analysis of these inhibitors would provide useful information for the development of anti-influenza virus compounds.
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Comparative analysis of VP8* sequences from rotaviruses possessing M37-like VP4 recovered from children with and without diarrhoea
Rotavirus strains belonging to G types 1 to 4 and having a P3 genotype (M3 7-like VP4) were recovered from children with symptomatic and asymptomatic infections. Partial sequences of their VP4 genes were determined in an attempt to characterize these strains further. The genomic regions encoding VP8*, the connecting and putative fusion peptides and three other regions in VP5* were sequenced. The deduced amino acid sequences were compared with rotavirus strains belonging to different P genotypes that had been previously reported. High degrees of identity were found between the VP8* fragment of all human P3 strains (92·7 to 99·7%) suggesting that they belong to the same genotype, regardless of differences in their virulence. Furthermore, based on comparative sequence analysis, we did not identify any amino acid(s) that differ appreciably between symptomatic and asymptomatic strains and could therefore be associated with virulence. The results suggest that the P3 genotype, although frequently associated with asymptomatic infections, may not be the single determining factor in attenuation of symptoms.
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A comparison of the VP7 gene sequences of human and bovine rotaviruses
The sequences of the gene encoding VP7 (the major outer capsid protein) from one bovine and three human rotavirus strains were determined because of their unusual VP7 specificities. Two of the human strains (PA 169 and PA 151) had VP7 serotype 6 specificity whereas the two other strains, recovered from a child (HAL 1166) and a calf (678) belonged to VP7 serotype 8. The serotype 8 strains exhibited a high degree of sequence conservation when compared with each other and with other serotype 8 strains previously sequenced. The serotype 6 human strains shared a greater degree of sequence similarity with previously reported serotype 6 bovine strains than with other rotavirus serotypes; however the degree of sequence similarity among PA 169, PA 151 and the bovine strains was lower than had been previously reported for strains belonging to the same serotype. The demonstration of rotavirus serotypes that are shared between human and animal species supports the concept that interspecies transmission occurs and may play a role in rotavirus evolution.
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The complete sequence of a human astrovirus
More LessWe have determined the complete genomic sequence of human astrovirus serotype 1 isolated in Newcastle upon Tyne. The genome is 6813 nucleotides long and contains three sequential open reading frames (ORFs). The two closest to the 5′ end are linked by a ribosomal frameshifting motif and contain sequence motifs indicative of non-structural virus proteins: serine protease and RNA-dependent RNA polymerase. A nuclear addressing sequence is also located here. The 3′ ORF encodes the virion structural polypeptides as a polyprotein precursor. This genomic organization resembles that of the plant virus family Luteoviridae.
Nucleotide sequence data described in this paper appear in the EMBL database under accession no. Z25771.
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Nucleotide sequence and expression of the spike (S) gene of canine coronavirus and comparison with the S proteins of feline and porcine coronaviruses
More LessWe have cloned, sequenced and expressed the spike (S) gene of canine coronavirus (CCV; strain K378). Its deduced amino acid sequence has revealed features in common with other coronavirus S proteins: a stretch of hydrophobic amino acids at the amino terminus (the putative signal sequence), another hydrophobic region at the carboxy terminus (the membrane anchor), heptad repeats preceding the anchor, and a cysteine-rich region located just downstream from it. Like other representatives of the same antigenic cluster (CCV-Insavc-1 strain, feline infectious peritonitis and enteric corona- viruses, porcine transmissible gastroenteritis and respiratory coronaviruses, and the human coronavirus HCV 229E), the CCV S polypeptide lacks a proteolytic cleavage site present in many other coronavirus S proteins. Pairwise comparisons of the S amino acid sequences within the antigenic cluster demonstrated that the two CCV strains (K378 and Insavc-1) are 93·3% identical, about as similar to each other as they are to the two feline coronaviruses. The porcine sequences are clearly more divergent mainly due to the large differences in the amino-terminal (residues 1 to 300) domains of the proteins; when only the carboxy-terminal parts (residues 301 and on) are considered the homologies between the canine, feline and porcine S polypeptides are generally quite high, with identities ranging from 90·8 % to 96·8 %. The human coronavirus is less related to the other members of the antigenic group. A phylogenetic tree constructed on the basis of the S sequences showed that the two CCVs are evolutionarily more related to the feline than to the porcine viruses. Expression of the CCV S gene using the vaccinia virus T7 RNA polymerase system yielded a protein of the expected M r (approximately 200K) which could be immunoprecipitated with an anti-feline infectious peritonitis virus polyclonal serum and which was indistinguishable from the S protein synthesized in CCV-infected cells.
The nucleotide sequence data presented in this paper have been submitted to the EMBL database and assigned the accession number X77047.
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Molecular cloning and nucleotide sequencing of the 3′-terminal genomic RNA of the porcine reproductive and respiratory syndrome virus
More LessThe genomic RNA of a porcine reproductive and respiratory syndrome virus (PRRSV) isolate from the U.S.A., VR 2385 (ATCC), was copied into cDNA after priming with oligo(dT) and cloned into phage lambda. The cDNA clones representing the 3′-terminal genomic RNA of the virus were isolated and sequenced. The genome is a positive-stranded, polyadenylated RNA with an estimated size of 15 kb. Analysis of the resulting sequence identified three complete open reading frames (ORFs) with the potential to encode polypeptides with predicted M rs of 22·2K (ORF 5), 19·1K (ORF 6) and 13·6K (ORF 7). ORF 7, which is closest to the 3′ end, is predicted to encode a highly basic nucleocapsid protein displaying 58 % amino acid identity to the corresponding protein of the Lelystad virus (LV), a European PRRSV isolate. ORFs 6 and 5, preceding ORF 7, are each predicted to encode proteins containing several hydrophobic domains that are thought to be membrane- associated. The VR 2385 ORF 6 protein is the most conserved structural protein. It has 78% amino acid identity to the equivalent LV protein, and ORF 5 shares only 54% of its amino acid sequence. Northern blot analysis revealed a 3′-coterminal nested set of six subgenomic RNAs in VR 2385 virus-infected CRL 11171 cells. Our results indicate that VR 2385, like LV, is a member of the newly proposed arterivirus group. However, the striking genetic variation and the difference in pathogenicity between LV and VR 2385 suggest that the viruses causing PRRS in the U.S.A. and Europe are highly variable and they may represent different genotypes.
The nucleotide sequence data reported in this paper have been deposited with the GenBank database and assigned the accession number U03040.
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Apoptosis induced by infectious bursal disease virus
More LessChicken peripheral blood lymphocytes (PBLs) show morphological and biochemical features of apoptosis (programmed cell death) when infected in vitro with infectious bursal disease virus (IBDV). DNA extracted from IBDV-infected lymphocytes displayed an intense laddering pattern when visualized after agarose gel electrophoresis. IBDV-infected PBLs had significantly higher apoptotic and necrotic indices measured by acridine orange-ethidium bromide staining than did control lymphocytes. Electron micrographs of the IBDV-infected PBLs revealed features typical of apoptosis such as peripheral condensation of chromatin, blebbing of the plasma membrane and fragmentation of the nucleus and of the cell leading to the formation of apoptotic bodies. These findings indicate that IBDV, in addition to causing necrosis, can also induce apoptosis in avian lymphocytes in vitro.
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Sequence and expression of a baculovirus protein with antigenic similarity to telokin
More LessA protein from baculovirus-infected cells reacted with an antibody against the smooth muscle protein telokin. Because of this unusual similarity, the protein, termed telokin-like protein-20 (TLP20), was isolated and characterized. Its M r on denaturing polyacrylamide gels was 28K and the protein contained a high proportion of β structure. A cDNA for TLP20 was isolated and sequenced. The 3′ non-coding sequence contained a region of high identity with the 5′ end of two other baculovirus genes. The 5′ non-coding region contains several baculovirus regulatory elements. Surprisingly, the derived amino acid sequence showed no homologies to telokin. The cDNA was cloned into a bacterial expression vector and the subsequently expressed protein had a slightly lower M r than the native protein, but cross-reacted with telokin antibody. This paper reports the characterization of a new baculovirus protein that shares some antigenic similarities to the smooth muscle protein telokin.
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Identification of the gp67 gene of a baculovirus pathogenic to the spruce budworm, Choristoneura fumiferana multinucleocapsid nuclear polyhedrosis virus
More LessThe baculovirus gp67 gene encodes a pH-dependent membrane fusion protein and has been identified in both Autographa califomica multinucleocapsid nuclear polyhedrosis virus (AcMNPV) and Orygia pseudotsugata MNPV (OpMNPV). We have identified a homologous gene in the spruce budworm virus, Choristoneura fumiferana MNPV (CfMNPV). The CfMNPV gp67 gene is 79% identical to AcMNPV gp67 at the level of nucleotide sequence and 82% identical at the level of predicted amino acid sequence. As with OpMNPV and AcMNPV gp67, the CfMNPV gp67 protein is found exclusively in the budded virus phenotype of the baculovirus.
The nucleotide sequence data reported in this paper have been submitted to the GenBank database and given the accession number L124120.
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Genome organization of the DNA-binding protein gene region of Cryptophlebia leucotreta granulosis virus is closely related to that of nuclear polyhedrosis viruses
More LessThe nucleotide sequence and genomic organization of a conserved genome region within the EcoRI G fragment of Cryptophlebia leucotreta granulosis virus (C1GV) is presented. Five open reading frames (ORFs) were identified which were homologous to those of Auto- grapha califomica nuclear polyhedrosis virus (AcMNPV), located upstream of the helicase gene (pl43) at 63·6 to 65·6 map units. The ORFs of C1GV and AcMNPV share nucleotide sequence homologies of about 47 to 53 % and are very similarly arranged. One of the C1GV ORFs potentially encodes a basic DNA- binding protein with an M r of about 7·3K. Its predicted amino acid sequence mainly consists of multiple arginine and serine residues and shows a 52 to 55 % identity to the DNA-binding proteins of AcMNPV and other nuclear polyhedrosis viruses. Its amino acid composition conforms to that of the DNA-binding proteins of Plodia interpunctella granulosis virus and Spodoptera litura granulosis virus.
The nucleotide sequence reported here will appear in the EMBL, GenBank and DDBJ nucleotide sequence databases under the accession number X77048.
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- Plant
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Nucleotide sequence, genomic organization and synthesis of infectious transcripts from a full-length clone of artichoke mottle crinkle virus
More LessThe complete nucleotide sequence of the genome of artichoke mottle crinkle virus (AMCV), a member of the tombusvirus group, has been determined. The genome is 4790 nucleotides (nt) in length. A full-length cDNA of the AMCV genome has been cloned in pUC9 downstream of the T7 RNA polymerase promoter. Transcripts were infective when inoculated onto Nicotiana clevelandii and N. benthamiana plants. The AMCV genome contains five open reading frames (ORFs). The first ORF from the 5′ terminus (ORF1) encodes a protein with a predicted M rof 33K. ORF2 extends through the amber termination codon of ORF1 to yield a polypeptide of predicted M r92K and which is the putative RNA- dependent RNA polymerase. ORF3 codes for the coat protein (41K). Two nested ORFs in different reading frames (ORFs 4 and 5) code for a 22K and a 19K polypeptide respectively. Sequence homologies suggest that the 22K protein could be involved in eell-to-cell movement of virus. ORFs 3, 4 and 5 are translated from two 3′ coterminal subgenomic (sg) RNAs, the 5′ termini of which have been mapped. The two sg RNAs are 2155 (sgl) and 934 (sg2) nt in length. ORF3 is expressed from sgl RNA whereas ORFs 4 and 5 are potentially expressed from sg2 RNA. Time course experiments with Cynara scolymus protoplasts indicate that during AMCV infection both positive and negative strands of genomic and sg RNAs are produced and that sg2 RNA is produced before and at a higher level than sgl RNA.
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Partial characterization of the lettuce infectious yellows virus genomic RNAs, identification of the coat protein gene and comparison of its amino acid sequence with those of other filamentous RNA plant viruses
More LessPurified virions of lettuce infectious yellows virus (LIYV), a tentative member of the closterovirus group, contained two RNAs of approximately 8500 and 7300 nucleotides (RNAs 1 and 2 respectively) and a single coat protein species with M r of approximately 28000. LIYV-infected plants contained multiple dsRNAs. The two largest were the correct size for the replicative forms of LIYV virion RNAs 1 and 2. To assess the relationships between LIYV RNAs 1 and 2, cDNAs corresponding to the virion RNAs were cloned. Northern blot hybridization analysis showed no detectable sequence homology between these RNAs. A partial amino acid sequence obtained from purified LIYV coat protein was found to align in the most upstream of four complete open reading frames (ORFs) identified in a LIYV RNA 2 cDNA clone. The identity of this ORF was confirmed as the LIYV coat protein gene by immunological analysis of the gene product expressed in vitro and in Escherichia coli. Computer analysis of the LIYV coat protein amino acid sequence indicated that it belongs to a large family of proteins forming filamentous capsids of RNA plant viruses. The LIYV coat protein appears to be most closely related to the coat proteins of two clostero-viruses, beet yellows virus and citrus tristeza virus.
The nucleotide sequence reported in this paper has been submitted to the GenBank database and assigned the accession number U05242.
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Nucleotide sequences of apple stem pitting virus and of the coat protein gene of a similar virus from pear associated with vein yellows disease and their relationship with potex- and carlaviruses
More LessThe nucleotide sequence (9306 nucleotides) of cDNA clones of apple stem pitting virus (ASPV) obtained from a double-stranded RNA template, extracted from diseased plant tissue, was determined. The genome is composed of five open reading frames (ORFs) encoding putative proteins with M rs of 247083, 25147, 12832, 7429 and 43712, and has a poly(A) tail. Using two oligonucleotides designed from the ASPV sequence information a 1598 bp fragment from near the 3′ terminus of the viral RNA, containing the coat protein of M r 43 766, was amplified from vein yellows (VY)-infected pear plants by PCR. The sequence determined showed eight nucleotide changes resulting in five amino acid substitutions compared with the sequence of ASPV. When compared to potex-, carla-, clostero- and capillo- viruses, the ASPV genome organization appeared to be most closely related to that of potexviruses, but with a larger coat protein of M r 44K (ORF5). The predicted coat protein size was confirmed by immunoblot analysis. The results show that ASPV does not fall into subgroup A of the closteroviruses but that it probably belongs in an as yet undefined group of viruses. They also suggest that the virus associated with VY is a strain of ASPV.
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Avocado sunblotch disease: a persistent viroid infection in which variants are associated with differential symptoms
More LessVariants of avocado sunblotch viroid (ASBVd) of between 247 and 250 nucleotides in length have been recovered from diseased avocado tissues. The sunblotch syndrome covers a complex pattern of disease symptoms which are associated with infection by variants of ASBVd. The viroid species are designated ASBVd-B, ASBVd-V and ASBVd-Sc from their association with bleached, variegated or symptomless carrier tissues respectively. Host-viroid interactions and structural relationships among the variants suggest a transition in sunblotch disease from a severe acute to a persistent mild form of infection.
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Nucleotide sequence of the coat protein genes of strawberry latent ringspot virus: lack of homology to the nepoviruses and comoviruses
More LessThe sequence of the 3′-terminal 2424 nucleotides of RNA-2 of the flowering cherry strain of strawberry latent ringspot virus (SLRV) was determined from cDNA clones. The sequence contains a reading frame in the virus-sense strand of 2070 nucleotides, a 3′ untranslated region of 552 nucleotides and a 3′-terminal poly(A) tract. The positions of the two coat proteins of SLRV within the reading frame were determined from sequence data obtained by N-terminal sequencing using Edman degradation. The larger coat protein with an M r of 43K is located 5′ of the smaller coat protein of 27K, and the two proteins are apparently cleaved at a Ser-Gly bond. Although there are numerous similarities between SLRV and the nepoviruses and comoviruses, there is no significant homology between the SLRV coat proteins and the coat proteins of either group. Furthermore, the hydropathy profiles of the SLRV coat proteins are unlike those of either group. No comparisons could be made with the fabaviruses owing to lack of sequencing information. This lack of homology suggests that SLRV is more distantly related to the nepoviruses and comoviruses than has been considered previously.
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