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[Molecular characterization of aphthous fever virus isolated during the years 1993-1994 in Argentina].

Nucleotide sequence and phylogenetic analysis of the VP1 structural protein have been used extensively as diagnostic and epidemiological tools for foot and mouth disease virus (FMDV). In this report we have applied this methodology to the analysis of the VP1 coding sequence from FMDV strains isolated in Argentina during 1993-1994. The results demonstrated that the field isolates were related to the vaccine strains used at that time. However the involvement of the vaccine virus appeared to be different for outbreaks caused by FMD viruses type O or C. These data provide a database essential for determining the origin of new epizootics.

Animals↗

PubMed2005

Enteroviruses 76, 89, 90 and 91 represent a novel group within the species Human enterovirus A.

Molecular methods have enabled the rapid identification of new enterovirus (EV) serotypes that would have been untypable using existing neutralizing antisera. Nineteen strains of four new EV types termed EV76 (11 isolates), EV89 (two isolates), EV90 (four isolates) and EV91 (two isolates), isolated from clinical specimens from patients in France (one isolate) and Bangladesh (18 isolates), are described. Nucleotide sequences encoding the VP1 capsid protein (882-888 nt) are less than 65 % identical to the homologous sequences of the recognized human EV serotypes, but within each group the sequences are more than 78 % identical. The deduced amino acid sequences of the complete capsid (P1) region are more than 94 % identical within type but less than 76 % identical to those of the recognized serotypes. For both VP1 and P1, the 19 isolates are monophyletic by type with respect to all other EV serotypes. Using the proposed molecular typing scheme, these data support their identification as four new types within the species Human enterovirus A (HEV-A). In almost all cases, the VP1 sequences were more similar to those of some simian EVs than to the human EVs. Partial 3D sequences of all 19 isolates also clustered within HEV-A; they were monophyletic as a group, but not by type, suggesting that recombination has occurred among viruses of these four types. Partial 3D sequences were more closely related to those of simian EVs than to human viruses in HEV-A. These results suggest that the four new types may represent a new subgroup within HEV-A, in addition to the existing human and simian subgroups.

Bangladesh↗

PubMed2001

The genome segment B encoding the RNA-dependent RNA polymerase protein VP1 of very virulent infectious bursal disease virus (IBDV) is phylogenetically distinct from that of all other IBDV strains.

A full-length cDNA clone of the segment B of the very virulent infectious bursal disease virus (IBDV) strain BD 3/99 was constructed and the full-length nucleotide sequence was established. The nucleotide sequence encoding VP1, an RNA-dependent RNA polymerase, of BD 3/99 was aligned with that of 17 other IBDV strains including six very virulent, three classical virulent, five classical attenuated, one antigenic variant and two serotype 2 strains. The VP1 genes of all very virulent strains were 97.5% to 99.8% identical. With the exception of an atypical Australian strain, 002-73, all of the classical virulent or attenuated and antigenic variant strains were also 97.5% to 100% identical. Serotype 2 strains showed only 4-6% divergence from serotype 1 classical virulent or attenuated strains; in contrast, however, the very virulent strains were 10.5% to 12.5% divergent from the classical virulent or attenuated strains as well as serotype 2 strains. Analysis of the deduced amino acid sequence of VP1 revealed 17 common, including 8 unique amino acid substitutions in the very virulent strains. In the phylogenetic tree the very virulent strains formed a distinct cluster and all other strains including classical virulent, attenuated and antigenic variant strains and even serotype 2 strains were grouped together. It is suggested that the VP1 of very virulent IBDV is phylogenetically distinct from that of all other IBDV strains and probably originated from a hitherto unidentified source.

Amino Acid Sequence↗

PubMed1998

Characterizing sequence variation in the VP1 capsid proteins of foot and mouth disease virus (serotype 0) with respect to virion structure.

The VP1 capsid protein of foot and mouth disease virus (FMDV) is highly polymorphic and contains several of the major immunogenic sites important to effective antibody neutralization and subsequent viral clearance by the immune system. Whether this high level of polymorphism is of adaptive value to the virus remains unknown. In this study we examined sequence data from a set of 55 isolates in order to establish the nature of selective pressures acting on this gene. Using the known molecular structure of VP1, the rates and ratios of different types of nonsynonymous and synonymous changes were compared between different parts of the protein. All parts of the protein are subject to purifying selection, but this is greatest amongst those amino acid residues within beta-strands and is significantly reduced at residues exposed on the capsid surface, which include those residues demonstrated by previous mutational analyses to permit the virus to escape from monoclonal antibody binding. The ratios of nonsynonymous substitution resulting in various forms of physicochemically radical and conserved amino acid change were shown to be largely equal throughout these different parts of the protein. There was a consistently higher level of nonsynonymous and charge radical sites in those regions of the gene coding for residues exposed on the outer surface of the capsid and a marked difference in the use of amino acids between surface and nonsurface regions of the protein. However, the analysis is consistent with the hypothesis that the observed sequence variation arises where it is least likely to be disruptive to the higher-order structure of the protein and is not necessarily due to positive Darwinian selection.

Amino Acid Sequence↗

PubMed1976

Location of the sequences coding for capsid proteins VP1 and VP2 on polyoma virus DNA.

The 19S and 16S polyoma virus late mRNAs have been separated on sucrose-formamide density gradients and translated in vitro. The 16S RNA codes only for polyoma capsid protein VP1, while the 19S RNA codes in addition for capsid protein VP2. Since the 19S and 16S species have been previously mapped on the viral genome, these results allow us to deduce the location of the sequences coding for VP1 and VP2. Comparison of the chain lengths of the capsid proteins with the size of the viral mRNAs coding for them suggests that VP1 and VP2 are entirely virus-coded. Purified polyoma 19S RNA directs the synthesis of very little VP1 in vitro, although it contains all the sequences required to code for the protein. The initiation site for VP1 synthesis which is located at an internal position on the messenger is probably inactive either because it is inaccessible or because it lacks an adjacent "capped" 5' terminus. Similar inactive internal initiation sites have been reported for other eucarotic viral mRNAs (for example, Semliki forest virus, Brome mosaic virus, and tobacco mosaic virus), suggesting that while eucaryotic mRNAs may have more than one initiation site for protein synthesis, only those sites nearer the 5' terminus of the mRNA are active.

Base Sequence↗

PubMed2001

Foot-and-mouth disease type O viruses exhibit genetically and geographically distinct evolutionary lineages (topotypes).

Serotype O is the most prevalent of the seven serotypes of foot-and-mouth disease (FMD) virus and occurs in many parts of the world. The UPGMA method was used to construct a phylogenetic tree based on nucleotide sequences at the 3' end of the VP1 gene from 105 FMD type O viruses obtained from samples submitted to the OIE/FAO World Reference Laboratory for FMD. This analysis identified eight major genotypes when a value of 15% nucleotide difference was used as a cut-off. The validity of these groupings was tested on the complete VP1 gene sequences of 23 of these viruses by bootstrap resampling and construction of a neighbour-joining tree. These eight genetic lineages fell within geographical boundaries and we have used the term topotype to describe them. Using a large sequence database, the distribution of viruses belonging to each of the eight topotypes has been determined. These phylogenetically based epidemiological studies have also been used to identify viruses that have transgressed their normal ecological niches. Despite the high rate of mutation during replication of the FMD virus genome, the topotypes appear to represent evolutionary cul-de-sacs.

Africa, Eastern↗

PubMed1980

Polyoma virus DNA: Sequence from the late region that specifies the leader sequence for late mRNA and codes for VP2, VP3, and the N-terminus of VP1.

The DNA sequence of part of the late region of the polyoma virus genome is presented. This sequence of 1,348 nucleotide pairs encompasses the leader region for late mRNA and the coding sequence for the two minor capsid proteins VP2 and VP3. The coding sequence for the N-terminus of the major capsid protein overlaps the C-terminus of VP2/VP3 by 32 nucleotide pairs. From the DNA sequence the sizes and sequences of VP2 and VP3 could be predicted. Potential splicing signals for the processing of late mRNA's could be identified. Comparisons are made between the sequence of polyoma virus DNA and corresponding regions of simian virus 40 DNA.

Amino Acid Sequence↗

PubMed1995

The proposed gene for VP1 of HAV encodes for a larger protein than that observed in HAV-infected cells and virions.

The termini of hepatitis A virus (HAV) mature proteins have been assigned mainly by their homology to other picornaviruses and their apparent electrophoretic mobility; the proposed coding sequence for VP1 is supposed to encompass 900 nucleotides from position 2208 to 3107 of the HAV genome. In order to further characterize this protein, we analyzed the in vitro-and in vivo-synthesized translation products of the putative VP1 gene. cDNA coding for full-length VP1 was cloned under the control of a T7 promoter in pTF7-5; the resulting plasmid (pTF7-5/VP1) was used for both synthesis of RNA to program rabbit reticulocyte lysates and construction of a recombinant vaccinia virus (rvv/T7-VP1). Immunoblot analysis and immunoprecipitation using antisera raised against a synthetic peptide corresponding to amino acids 13 of 33 of VP1 (13-33/VP1) led to identification of a 37-kDa protein in lysates of in vitro translated VP1 and rvv/T7-VP1-infected HFS cells, whereas a 33-kDa protein was detected with purified virions and in lysates of HAV-infected HFS cells. Because the antiserum used was directed against an amino-terminal part of VP1 and the amino terminus of VP1 is identified by sequence analysis, these results show that VP1 present in the HAV virions and infected cells is shorter than previously proposed and suggest that the real carboxy terminus of VP1 is approximately 40 amino acids upstream. In order to limit the possible carboxy-terminal sites in the predicted region, we investigated in vitro synthesized translation products of a set of constructs with C-termini ending at potential cleavage sites for viral proteases 3C. The construct containing the nucleotides from position 2208 to 3026 codes for a protein (1-273/VP1) which exhibits the same electrophoretic mobility as VP1 synthesized by HAV in vivo.

Amino Acids↗

PubMed2002

Genetic diversity of echovirus 30 during a meningitis outbreak, demonstrated by direct molecular typing from cerebrospinal fluid.

Echovirus 30 is one of the enterovirus serotypes isolated most frequently in meningitis cases. The genetic diversity of echovirus 30 was investigated in patients hospitalised during an outbreak in 2000 in Clermont-Ferrand, France. A nested reverse transcription-PCR (RT-PCR) assay was developed for qualitative analysis of the echovirus 30 VP1 encoding sequence directly from cerebrospinal fluid. The viral sequences obtained for 22 patients were compared with those of virus isolates obtained from nine patients with echovirus 30 meningitis admitted to hospital in 1996-1997 and with echovirus 30 sequences from international databases. In 2000, meningitis cases were caused by two virus variants (C3 and C4) distinct genetically from the other two variants (C1 and C2) identified during the period 1996-1997. A detailed phylogenetic analysis established that the C1, C2, and C3 variants had close relatives among viruses previously identified in other geographical areas. The C4 variant had not been described earlier. The genomic differences observed between the four echovirus 30 variants arose at synonymous sites indicating that the viruses shared similar antigenic sites in the VP1 encoding sequence. Overall, these observations suggest wide circulation of different echovirus 30 variants and periodic importation of new viruses. The apparent displacement observed between virus variants did not result from a selective advantage caused by antigenic variation.

Adolescent↗

PubMed2000

High affinity interactions of Coxsackievirus A9 with integrin alphavbeta3 (CD51/61) require the CYDMKTTC sequence of beta3, but do not require the RGD sequence of the CAV-9 VP1 protein.

Integrins are transmembrane molecules involved in numerous cell matrix, cell-cell adhesion phenomena and also utilised as viral receptors. These interactions with integrins are mediated by brief oligopeptide recognition sequences. The Arg-Gly-Asp sequence (RGD), is recognized by many integrins, including integrin alphavbeta3 (CD51/61). Coxsackievirus A9 (CAV-9), a human pathogen that has an Arg-Gly-Asp sequence in the VP1 capsid protein, has been known to be one of the many viruses that utilise integrin alphavbeta3 as a receptor. In order to determine important binding sites of CAV-9 on integrin alphavbeta3, we performed binding studies of CAV-9 on CHO-alphavbeta3, CHO-alphavbeta1 and CHO-alphavbeta1-3-1 mutant cell line, in the presence of function blocking mAb specific for integrin alphavbeta3 and natural ligand vitronectin. Our experiments show that the CYDMKTTC sequence (187-193 residue) of integrin beta3, which has been shown to be involved in ligand specificity, is an important binding site for CAV-9. We also report that an RGD-less Coxsackievirus A9 mutant can bind efficiently on the ligand binding site of integrin alphavbeta3. Thus documenting the capability of this RNA virus to interact with integrin alphavbeta3, without the presence of an Arg-Gly-Asp sequence.

Amino Acid Sequence↗

PubMed1986

Characterization of hepatitis A virus structural proteins.

HAV particles isolated from infected cells banded at buoyant densities of 1.42, 1.32, and 1.20 g/ml, and distinctive protein patterns were established by gel electrophoresis and reverse phase high performance liquid chromatography. The relatively higher amounts of p30 in particles with lower buoyant densities suggest that this protein is VP0 and is part of the immature picornavirion. The protein elution profiles obtained by HPLC were virtually identical for all the HAV strains examined but differed from those of other picornaviruses. The N-terminal amino acid sequence of VP1 and VP2 was determined and aligned to the nucleotide sequence. Sequencing VP0 and VP3 was not possible, probably because the amino termini are blocked. VP1, VP3, and VP0 induced specific antibodies in rabbits.

Antibodies, Viral↗

PubMed1983

Localization of a poliovirus type 1 neutralization epitope in viral capsid polypeptide VP1.

Poliovirus type 1 cDNA sequences coding for viral capsid polypeptide VP1 were inserted into the beta-lactamase sequence of Escherichia coli plasmid pBR322. Resulting recombinant plasmid pSW119 expressed in Escherichia coli a VP1-beta-lactamase fusion protein that reacted with antibodies raised against poliovirus capsid polypeptide VP1 and with a monoclonal poliovirus type 1 neutralizing antibody, C3. Deletions of various lengths were generated within the VP1 sequence. The hybrid proteins expressed by the deleted plasmids did not react any more with C3 when the region of VP1 amino acids 95-110 (poliovirus nucleotides 2,754-2,806) was deleted. Therefore, the C3 epitope responsible for virus neutralization is most probably located in this region of the capsid polypeptide.

Amino Acid Sequence↗

PubMed1994

Direct PCR detection of foot-and-mouth disease virus.

A PCR assay for the detection and characterization of foot-and-mouth disease virus was developed. The procedure allows RT-PCR amplification following direct adsorption of viral suspensions to microtiter plates, avoiding previous steps of phenol-extraction or heating. Using this procedure, FMDV-specific (based on 3D gene sequences), as well as serotype-specific (based on VP1 gene sequences) amplification were achieved for viral samples of serotypes A, O and C, either from cell culture supernatants or from lesions of infected animals. The assay allowed detection of around 15 PFU, being 500-fold more sensitive than a conventional indirect ELISA. This new method constitutes a simple, rapid and efficient alternative for the diagnosis and characterization of FMDV by PCR.

Animals↗

PubMed1983

The molecular basis of the antigenic variation of foot-and-mouth disease virus.

We have cloned and sequenced the viral protein (VP1)-coding regions of two foot-and-mouth disease virus (FMDV) serotypes (C1 and A5). Comparison of the derived amino acid sequences with the known VP1 sequence of FMDV O1K and the two FMDV A subtypes A10 and A12 shows two highly variable regions in the protein, at positions 40-60 and 130-160, as possible antigenic sites. In both variable regions, several sites could be detected where all three sequences of the A subtypes are identical but the three types A, C and O differ from each other. The second variable region overlaps with a major immunogenic determinant of the virus.

Amino Acid Sequence↗

PubMed1993

Molecular epidemiology of foot-and-mouth disease virus type O.

A phylogenetic tree based on the VPI sequences of type O foot-and-mouth disease virus (FMDV) has been derived. Direct sequencing of PCR products has been used to obtain the VP1 gene sequences of new isolates. The tree exhibits four main lineages that largely correlate with the geographical origin of isolates. The analysis supports a close relationship between European O1 field isolates and vaccine strains, with the exception of O Thalheim Aus/81 and O Wuppertal Ger/82 which were probably of non-European origin. Analysis of nucleotide substitutions indicates that synonymous mutations play a major role in FMDV evolution.

Amino Acid Sequence↗

PubMed2001

Molecular typing of echovirus serotype 4 isolates.

We report on clinical samples Stuttgart/97, Berlin/99 and Jasi/99 associated with aseptic meningitis. All three samples contained echovirus 4 (E4) but Stuttgart/97 was simultaneous infected with echovirus 30 (E30). The genetic relationship of the E4 strains was assessed using RT-PCR and direct sequencing of amplicons derived from the genomic region encoding the capsid protein VP1. The sequences have been compared with each other and with sequences of further E4 strains obtained from GenBank. The analysis confirms that sequences of recent isolates have drifted away from elderly strains over a longer period of time. Several amino acid changes in assumed antigenic sites of the VP1 gene may be sufficient to cause changes in antigenic specificity and therefore they may be a reason for failure of serological typing of some new antigenic E4 variants.

Amino Acid Sequence↗

PubMed1983

Comparison of nonphosphorylated and phosphorylated species of polyomavirus major capsid protein VP1 and identification of the major phosphorylation region.

The major virion protein of polyomavirus, VP1, consists of about six isoelectric species designated A through F. The minor species D, E, and F are phosphorylated and are thought to serve as viral receptors. We first wanted to distinguish whether all VP1 species are derived by post-translational modification from a common amino acid sequence or whether one or more of the species contain a region(s) of altered amino acid sequence resulting from alternate mRNA processing. We compared the VP1 species by detailed peptide mapping with several combinations of specific protease and radioisotopic labels. This approach enabled us to examine more than 80% of the predicted VP1 sequence, including the amino-and carboxy-termini. We found no evidence of sequence differences among any of the VP1 species. The specific incorporation of 32Pi was found to be the same for all of the phosphorylated species. Comparison of the phosphorylation sites of in vivo 32Pi-labeled D, E, and F by peptide mapping showed them to be identical. Each phosphorylated species contained a single major phosphopeptide and several minor phosphopeptides. The major phosphoamino acid, identified by acid hydrolysis, was phosphothreonine, with phosphoserine also present. By using chemical cleavage methods, we localized the major phosphorylation region to a central portion of the VP1 sequence. We discuss some features of this region and relate this information to functional implications of phosphorylation.

Amino Acid Sequence↗

PubMed1991

[Synthesis, cloning, and expression of artificial genes, coding antigenic determinants of the foot-and-mouth virus substrain A22].

Chemical-enzymatic synthesis and cloning in Escherichia coli of double-stranded DNAs, coding for simple and complex antigenic determinants of foot-and-mouth disease virus (FMDV) strain A22, have been carried out. The simple antigenic determinants are a part of the viral coat protein VP1 (amino acid sequence 131-152 or 131-160) whereas the complex antigenic determinants comprise additionally the amino acid sequence 200-213 of VP1 linked to N-terminus of simple antigenic determinants through a tetrapeptide spacer Pro-Pro-Ser-Pro. Recombinant DNAs containing genes for antigenic determinants of FMDV fused with C-terminus of gene for human tumor necrosis factor (hrTNF) have been constructed. Expression of the hybrid genes and properties of the proteins coded were studied. All recombinant proteins were shown to interact specifically with polyclonal antibodies both against hrTNF and FMDV strain A22. The recombinant proteins produced by bacteria are perspective for study as a vaccine against FMDV.

Amino Acid Sequence↗