Complete genomic sequence analyses of Apple stem pitting virus isolates from China

The complete genomic sequences of a Chinese ASPV isolates KL1 and KL9 were determined from ten overlapping cDNA clones. The genomes of both isolates were 9265 nucleotides excluding the poly (A) tail and contained five open reading frames (ORFs). The identities between two complete genomes were 92.5% at nt level. Multiple alignment of the amino acid sequences showed that 110 aa variations between two genomic sequences and the variable domains mainly distributed in 5′-terminal of ORF1, ORF3, and ORF5, respectively. Two complete genomic sequences shared 71.4–77.3% identities with other ASPV isolates at nt level. Phylogenetic relationship analysis of the coat protein genes revealed that ASPV isolates had high variables and formed three groups. All ASPV isolates from apples were clustered to group I, whereas pear were clustered to groups II (except NC_003462) and both KL1 and KL9 were clustered to group III. Nucleotide sequences diversity analysis showed that the between-population d _NS /d _S ratio 0.092 was similar to these for within-group (0.092–0.095); there was no geographic differentiation between ASPV isolates.     

Sequence diversity and potential recombination events in the coat protein gene of Apple stem pitting virus

The variability of the Apple stem pitting virus (ASPV) coat protein (CP) gene was investigated. The CP gene of ten virus isolates from apple and pear trees was sequenced. Comparison of all sequenced virus isolates revealed high diversity of the CP gene (70.7-93.5% at the nucleotide level and 77.8-98.7% at the amino acid level). Additionally, one or two deletions in the N-terminal part of the coat protein gene of the studied virus isolates were identified. The ratio of nonsynonymous to synonymous polymorphic sites indicated that purifying selection has acted to eliminate deleterious mutations in coding sites. Moreover, the evidences for recombination in analyzed sequences were provided. It is likely that recombination, along with selection, enhances the speed of elimination of deleterious mutations in ASPV, following the mutational deterministic hypothesis of Kondrashov.     

The S7 gene and VP7 protein are highly conserved among temporally and geographically distinct American isolates of epizootic hemorrhagic disease virus

Complete sequences of genome segment 7 (S7) from six isolates of epizootic hemorrhagic disease virus serotype 1 (EHDV-1) and 37 isolates of serotype 2 (EHDV-2) were determined. These isolates were made between 1978 and 2001 from the southeast, mid-Atlantic, Midwest and intermountain United States. Analysis of the S7 sequence similarities showed 98.1% identity among the EHDV-1 isolates and 91.0% identity among the EHDV-2 isolates. Comparison of the deduced amino acid similarities showed an even greater degree of similarity among the isolates (100% among the EHDV-1 isolates and 98.9% identity among the EHDV-2 isolates). There was only 75.8% identity between the EHDV-1 and EHDV-2 isolates at the nucleic acid level; however, there was 93.7% identity between the two groups at the amino acid level. The ratio of non-synonymous to synonymous nucleotide indicates a strong selection for silent substitutions. There was no evidence for reassortment between EHDV-1 and EHDV-2 isolates. The high degree of conservation of S7 gene codons and the VP7 protein, suggests that little variation is allowed in preserving the function of this protein. The high degree of conservation also validates the use of diagnostic tests for EHDV based on S7 and VP7.     

Comparison of the coat protein genes of Lettuce big-vein associated virus isolates from Australia with those of isolates from other continents

The complete coat protein (CP) nucleotide sequences of seven Lettuce big-vein associated virus (LBVaV) isolates from Australia were compared to those of 22 other LBVaV and five tobacco stunt virus (TStV) isolates. On phylogenetic analysis, clade I contained only LBVaV isolates from Europe, sub-clade IIa only Australian LBVaV isolates, IIb only Japanese LBVaV isolates, and IIc only TStV isolates from Japan. In the amino acid sequences deduced, the central region of the gene was most divergent. Mean Dn/Ds ratios were 0.283 and 0.124 for clades I and II, respectively. The suggestion that TStV is a strain of LBVaV was supported.     

Differentiation of citrus tristeza virus isolates by serological analysis of p25 coat protein peptide maps

A procedure was developed to purify rapidly and easily a sufficient quantity of native p25 coat protein (CP) to allow comparison of five isolates of citrus tristeza virus (CTV) by serological analysis of peptide maps, using monoclonal and polyclonal antibodies. CTV particles were concentrated by centrifugation and purified by agarose gel electrophoresis. The CP was extracted from gel slices riched in virions and protein yields were about three times greater than those obtained previously and of comparable purity. The purified CP was partially digested with either V8 or papain endo-protease, and the peptides generated were separated and electroblotted to a membrane. Protein blots were tested with four monoclonal antibodies and one source of polyclonal antibodies. The serological maps generated by papain allowed differentiation of all the isolates examined, and those generated by V8 endoprotease allowed discrimination of four of the five isolates tested. Some of these isolates had been indistinguishable based on their reactivity in DASI-ELISA, dsRNA pattern and biological characterization. Serological analysis of peptide maps, as described below, allowed accurate comparison of CTV isolates with minimum amounts of p25 CP and proved superior to other techniques for discriminating CTV isolates.     

Encapsidation of genomic but not subgenomic Turnip yellow mosaic virus RNA by coat protein provided in trans

We have studied the encapsidation requirements of Turnip yellow mosaic virus (TYMV) genomic and subgenomic RNA using an "agroinfiltration" procedure involving transient expression of RNAs and coat protein (CP) in Nicotiana benthamiana leaves. Although N. benthamiana is a nonhost, expression of TYMV RNA in its leaves by agroinfiltration resulted in efficient local infection and production of the expected virions containing genomic and subgenomic RNAs together with empty capsids. A nonreplicating genomic RNA with a mutation in the polymerase domain was efficiently encapsidated by CP provided in trans, even though RNA levels were a thousand-fold lower than in normal infections. In contrast, encapsidation of CP mRNA was not observed under these conditions, even when the CP mRNA had authentic 5'- and 3'-termini. Deletion of the 3'-tRNA-like structure from the genomic RNA did not alter the encapsidation behavior, suggesting that this feature does not play a role in the encapsidation of TYMV RNA. Our results indicate differences in the encapsidation process between genomic and subgenomic RNAs, and suggest an interaction between RNA replication and the packaging of subgenomic RNA.     

Tobacco mosaic virus coat protein and the large subunit of the host protein ribulose-1,5-biphosphate carboxylase share a common antigenic determinant

An immunological relationship was detected between the coat protein of the common (U1) strain of tobacco mosaic virus (TMV) and the large subunit of the ubiquitous CO2-fixing host enzyme, ribulose-1,5-biphosphate carboxylase (RuBisCo). When assayed by Western immunoblotting or indirect ELISA, polyclonal antisera to TMV coat protein and to RuBisCo reacted with both antigens. In addition, a monoclonal antibody specific for the C-terminal antigenic determinant of TMV coat protein reacted with RuBisCo. Conversely, several monoclonal antibodies generated to the large subunit of RuBisCo reacted with TMV coat protein. This cross-reactivity was verified by an examination of the amino acid sequences of both proteins. A region of homology was found between the carboxy proximal portion of coat protein and the sequence 60-73 residues from the amino terminus of RuBisCo large subunit. This homology was not mirrored at the nucleic acid level because of different codon usages for the two proteins.     

Monoclonal antibody identifies a highly conserved and immunodominant epitope of the human immunodeficiency virus transmembrane protein

A murine monoclonal antibody (MAb), 10E9, has been generated which identifies a conserved and immunodominant epitope of the human immunodeficiency virus (HIV) transmembrane protein, gp41. The MAb reacts with the protein backbone of the mature env gene product and also with polyprotein precursor, gp160. Human sera were tested for their ability to competitively inhibit the immunoreactivity of MAb 10E9. Of 100 serum samples obtained from patients with acquired immune deficiency syndrome (AIDS) or AIDS-related complex (ARC), all showed strong inhibition to the reaction. In contrast, sera obtained from normal donors or those with other viral infections failed to perturb the binding activity of MAb 10E9. The geographic diversity of the AIDS/ARC patients studied provides evidence that the 10E9 epitope of gp41 is highly conserved.     

Mutations in the highly conserved SLQYLA motif of Vif in a simian-human immunodeficiency virus result in a less pathogenic virus and are associated with G-to-A mutations in the viral genome

The simian-human immunodeficiency virus (SHIV)/macaque model for human immunodeficiency virus type 1 has become a useful tool to assess the role of accessory genes in lentiviral pathogenesis. In this study, we introduced two amino acid changes in the highly conserved SLQYLA domain (to AAQYLA) of the SIV Vif protein. The resulting virus, SHIV_VifAAQYLA, was used to infect three macaques, which were followed for over six months. Plasma viral loads and circulating CD4⁺ T cell levels were assessed during the course of infection. The three macaques inoculated with SHIV_VifAAQYLA did not develop significant CD4⁺ T cell loss over the course of their infection, had plasma viral RNA loads that were over 100-fold lower than macaques inoculated with parental SHIV_KU-1bMC33, and developed no histological lesions in lymphoid tissues. DNA and RT-PCR analysis revealed that only a select number of tissues were infected with this virus. Sequence analysis indicates that the site-directed changes were stable during the first three weeks after inoculation but thereafter the S147A amino acid substitution changed to a threonine in two of three macaques. The L148A substitution remained stable in the vif amplified from the PBMC of all three macaques. Sequence analysis of vif, vpu, env and nef genes revealed G-to-A mutations in the genes amplified from macaques inoculated with SHIV_VifAAQYLA, which were higher than in a macaque inoculated with parental SHIV_KU-1bMC33. We found that the majority (> 85%) of the G-to-A mutations were in the context of 5′-TC (minus strand) and not 5′-CC, suggestive that one or more of the rhesus APOBEC3 proteins may be responsible for the observed mutational patterns. The data also suggest that rhesus APOBEC3G probably accounted for a minority of the mutations since its GG-to-AG mutational pattern was infrequently detected. Finally, macaques inoculated with SHIV_VifAAQYLA developed immunoprecipitating antibody responses against the virus. The results from this study provide the first in vivo evidence of the importance of the SLQYLA domain in viral pathogenesis and show that targeted mutations in vif can lead to a persistent infection with G-to-A changes accumulating in the viral genome.     

The complete nucleotide sequence of a severe stem pitting isolate of Citrus tristeza virus from Spain: comparison with isolates from different origins

Summary. The genomic RNA of the severe stem pitting Citrus tristeza virus (CTV) isolate T318A from Spain (19252 nt) was completely sequenced. It showed strong sequence similarities with the severe isolates SY568 from California and NUagA from Japan, and distant relationships with mild non-stem pitting isolates T385 from Spain and T30 from Florida. Contrasting with other severe CTV isolates, T318A had a predominant sequence variant even in the highly variable 5′-terminal untranslated region, in which a unique sequence variant (type II) previously associated with severe stem pitting isolates was detected. The high homogeneity of the T318A population suggests that the sequence obtained is probably responsible for the symptoms induced and makes it a useful tool to delimit pathogenicity determinants.     

The transforming protein of avian reticuloendotheliosis virus is a soluble cytoplasmic protein which is associated with a protein kinase activity

We have identified the product (p57v-rel) of the transforming gene, v-rel, of avian reticuloendotheliosis virus (REV-T) using antisera generated against nonoverlapping sequences representing the middle and carboxy-terminal regions of the v-rel protein expressed in Escherichia coli (N.K. Herzog and H.R. Bose, Jr., 1986, Proc. Natl. Acad. Sci. USA 83, 812-816). The amino-terminal region of the v-rel protein was also expressed in E. coli and used to generate antisera. The immunoglobulin-enriched fractions of these antisera were used to determine the subcellular location of p57v-rel in REV-T transformed lymphoid cells. Cells were fractionated into nuclear, mitochondrial, microsomal, and cytoplasmic fractions. The majority of p57v-rel was found in the cytoplasm. Examination of REV-T transformed lymphoid cells labeled with 32Pi revealed that the majority of the phosphorylated form of the v-rel protein was also found in the cytoplasm. Indirect immunofluorescence of REV-T transformed cells gave a diffuse cytoplasmic pattern indicating that p57v-rel was not associated with any discrete cellular organelle. The distribution of p57v-rel was similar in REV-T transformed lymphoid cells labeled with [35S]methionine for short and long periods of time, suggesting that p57v-rel is a soluble cytoplasmic protein throughout its lifetime. The v-rel protein was phosphorylated when immune complexes precipitated from transformed cells with the immunoglobulin fractions obtained from antisera against the amino-terminal, middle, and carboxy-terminal regions of v-rel were incubated with [gamma-32P]ATP and Mn2+. The phosphorylation of p57v-rel in the in vitro immune complex kinase assay was inhibited when the immunoglobulin-enriched fraction of these antisera was preincubated with the homologous v-rel fusion proteins. Preincubation with heterologous proteins did not block the phosphorylation of p57v-rel. These observations suggest that p57v-rel is associated with a protein kinase activity. Most of the kinase activity was found in the soluble cytoplasmic fraction of transformed cells. The transforming protein encoded by v-rel is a relatively stable protein with a half-life of approximately 7 to 8 hr in transformed lymphoid cells.     

The partial sequencing of the genomic RNA of a UK isolate of Pepino mosaic virus and the comparison of the coat protein sequence with other isolates from Europe and Peru

Summary.  A 3599 nucleotide portion of the genomic RNA of a UK isolate of Pepino mosaic virus (PepMV), isolated from tomato, has been sequenced (Accession No. AF340024). The region sequenced includes the 3′-end of the RNA polymerase, the triple gene block (TGB), the coat protein (CP) and 3′ untranslated region (UTR). In addition, the CP sequences of another 15 PepMV isolates, including 14 European tomato isolates and a Peruvian pepino isolate, have been determined and compared. This analysis shows that all the tomato isolates share over 99% identity, but only between 96–97% identity with the Peruvian pepino isolate. Received June 1, 2001 Accepted July 17, 2001     

Old and New World arenaviruses share a highly conserved epitope in the fusion domain of the glycoprotein 2, which is recognized by Lassa virus-specific human CD4+ T-cell clones

Data from human studies and animal experiments indicate a dominant role of T-cells over antibodies in controlling acute Lassa virus infection and providing immunity to reinfection. Knowledge of the epitopes recognized by T-cells may therefore be crucial to the development of a recombinant Lassa virus vaccine. In order to study human T-cell reactivity to the most conserved structural protein of Lassa virus, the glycoprotein 2 (GP2), seven GP2-specific CD4+ T-cell clones (TCCs) were generated from the lymphocytes of a Lassa antibody positive individual. All TCC displayed high specific proliferation, showed DR-restriction, and produced IFN-gamma upon stimulation with recombinant GP2. The epitope of four of the clones was localized to a short stretch of 13 amino acids located in the N-terminal part of GP2 (aa 289-301, numbering according to sequence of GPC). This epitope is conserved in all strains of Lassa virus and lymphocytic choriomeningitis virus (LCMV), shows >90% similarity in all New World arenaviruses of clade B, and overlaps with the proposed fusion domain of GP2. Peptides with conservative aa exchanges, as they naturally occur in the epitope 289-301 of the Old World arenavirus Mopeia and some New World arenaviruses, continued to effectively stimulate the Lassa-GP2-specific T-cell clones tested. The finding of a human T-helper cell epitope, which is highly conserved between Old and New World arenaviruses, is of importance for the design of arenavirus vaccines.     

Four genotypic variants of a Spodoptera exigua Nucleopolyhedrovirus (Se-SP2) are distinguishable by a hypervariable genomic region

Four genotypes named SP2A, SP2B, SP2C and SP2D were obtained in vivo by infecting S. exigua larvae with limiting dilutions of the Spanish field isolate Spodoptera exigua Nucleopolyhedrovirus (Se-SP2) of SeMNPV. The cloning of variants SP2A, SP2B and SP2C took 1, 6, and 3 passages, respectively, before the DNA profiles showed all bands in equimolar concentrations, and they remained constant for at least six further passages indicating the stability of their genotypes. The SP2D variant isolation took over ten passages and it was genetically less stable. Physical maps of their genomes were constructed for the restriction enzymes BamHI, BglII, PstI, and XbaI. The region between 8-10 m.u. was highly variable and characteristic of each cloned genotype and, hence, can be used as RFLP markers for all four genotypic variants. This region, included in the PstI-MB fragment, was cloned and sequenced showing that all the Se-SP2 variants contained a homologous region (hr) with a variable number of 98 bp sequences tandemly repeated, which were used to distinguish genotypic variants from each other. The biological activity of the genotypic variants SP2A, SP2B, and SP2C when compared in terms of LD50 and LT50, were not significantly different. However, the SP2D genotypic variant was found to be significantly less infective (higher LD50). The emergence of new genotypes in the Se-SP2 field populations is discussed.     

Humoral immune response elicited by highly attenuated variants of vaccinia virus and by an attenuated recombinant expressing HIV-1 envelope protein

Attenuated variants of vaccinia virus have excellent potential for the construction of safe recombinant live vaccines. In this investigation, highly attenuated variants of vaccinia virus with several genetic markers and a variant recombinant were tested in Balb/c mice for their ability to induce humoral immune response. Mice primed with variants that had an 8-MDa deletion at the left end of the viral genome induced similar levels of circulating anti-vaccinia antibodies as the wild-type virus. However, mice primed with variants that had several genetic lesions (deletions and point mutations) induced lower levels of circulating anti-vaccinia antibodies. Mice primed and boosted with a recombinant variant with several genetic lesions, and containing the complete envelope gene of the human immunodeficiency virus (HIV) and the bacterial beta-galactosidase (beta-gal) gene, induced significant antibody response to gp 160 and beta-gal. The antibody response to gp 160 was markedly increased by successive inoculations with the recombinant variant. Our findings provide evidence that the extent of activation of the immune system by vaccinia variants can be modulated by the nature of the virus genetic lesion. In addition, when these variants are used as recombinant vaccines, it is possible to induce low levels of circulating anti-vaccinia antibodies after priming and yet achieve significant antibody response to virus-expressed foreign antigens, even after repeated boosters. Such variants could be useful in the design of live recombinant viruses as safe vaccines.     

Comparisons of coat protein gene sequences show that East African isolates of Sweet potato feathery mottle virus form a genetically distinct group

Summary.  Sweet potato feathery mottle virus (SPFMV, genus Potyvirus) infects sweet potatoes (Ipomoea batatas) worldwide, but no sequence data on isolates from Africa are available. Coat protein (CP) gene sequences from eight East African isolates from Madagascar and different districts of Uganda (the second biggest sweet potato producer in the world) and two West African isolates from Nigeria and Niger were determined. They were compared by phylogenetic analysis with the previously reported sequences of ten SPFMV isolates from other continents. The East African SPFMV isolates formed a distinct cluster, whereas the other isolates were not clustered according to geographic origin. These data indicate that East African isolates of SPFMV form a genetically unique group. Accepted September 27, 1999     

A potently neutralizing SARS-CoV-2 antibody inhibits variants of concern by utilizing unique binding residues in a highly conserved epitope

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Analysis of a three-dimensional structure of Potato leafroll virus coat protein obtained by homology modeling.

Viruses of the family Luteoviridae are ssRNA plant viruses that have particles that exhibit icosahedral symmetry. To identify the residues that might be exposed on the surface of the Potato leafroll virus (PLRV; genus Polerovirus, family Luteoviridae) capsid, and therefore involved in biological interactions, we performed a structural analysis of the PLRV coat protein (CP) on the basis of comparisons with protein sequences and known crystal structures of CPs of other viruses. The CP of PLRV displays 33% sequence similarity with that of Rice yellow mottle virus (genus Sobemovirus) when the sequences were aligned by using the hidden Markov model method. A structure model for PLRV CP was designed by protein homology modeling, using the crystal structure of RYMV as a template. The resulting model is consistent with immunological and site-directed mutagenesis data previously reported. On the basis of this model it is possible to predict some surface properties of the PLRV CP and also speculate about the structural evolution of small icosahedral viruses.