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At least 19 recordsLinked to original sources
PubMed2003

Genomic evidence that simian virus 2 and six other simian picornaviruses represent a new genus in Picornaviridae.

Analysis of the VP1 capsid protein coding region of simian virus (SV) 2, SV16, SV18, SV42, SV44, SV45, and SV49 demonstrates that they are clearly distinct from members of the Enterovirus genus and from members of other existing picornavirus genera. To further characterize this group of viruses and to clarify their classification within the Picornaviridae, we have determined the complete genomic sequence of SV2 (8126 nucleotides). The genome was typical of members of Picornaviridae, encoding a single open reading frame. The putative polyprotein contained typical picornavirus protease cleavage sites, yielding mature proteins homologous to each of the known picornavirus proteins. SV2 contained an amino-terminal extension of the reading frame, which was analogous to the leader protein of members of the Aphthovirus, Cardiovirus, Erbovirus, Kobuvirus, and Teschovirus genera, but there was no significant amino acid homology with any of these known leader proteins. The 2A protein also aligned poorly with the 2A proteins of other picornaviruses. The deduced amino acid sequences of the SV2 structural and nonstructural proteins were related to but phylogenetically distinct from those of enteroviruses and human rhinoviruses. The major distinguishing features of SV2 were the presence of a type 2 internal ribosome entry site in the 5'-NTR, a putative leader protein encoded upstream of the structural proteins, and an unusually large 2A protein. On the basis of the molecular analysis, we propose that SV2, SV16, SV18, SV42, SV44, SV45, SV49, and porcine enterovirus 8 be classified as members of a new genus in Picornaviridae and that SV2 (strain 2383) be designated as the type strain.

5' Untranslated Regions↗
PubMed2002

Phylogenetic analysis of Ljungan virus and A-2 plaque virus, new members of the Picornaviridae.

In addition to the viruses belonging to the nine proposed genera of the Picornaviridae, Enterovirus, Rhinovirus, Cardiovirus, Aphtovirus, Hepatovirus, Parechovirus, Kobuvirus, Erbovirus and Teschovirus, two new members of this family have recently been discovered. Three strains of Ljungan virus (LV) were isolated from bank voles (Clethrionomys glareolus) and A-2 plaque virus (A-2) was isolated from human sera. To study the genetic relationship between these recently discovered viruses and the members of the family Picornaviridae, an evolutionary analysis has been carried out using the amino acid sequences of the two nonstructural proteins 2C and 3D. Phylogenetic analysis using prime members of the nine genera support the division of picornaviruses into the proposed genera. The study also supports a previous suggestion based on analysis of partial sequences of the structural proteins that LV is more related to the genus of Parechovirus than to other picornaviruses, but also shows that the three LV strains used in the comparison constitute a distinct monophyletic group, clearly separated from the parechoviruses. The analyses using the 2C and 3D sequences clearly showed that A-2 was related to the genera of Rhinovirus and Enterovirus, but it was not possible to group the A-2 with high confidence into one of the genera. Comparison using the VP1 protein sequences of Enterovirus and Rhinovirus showed that although the A-2 virus is positioned between the two genera, the virus is more related to the genus of Enterovirus than to Rhinovirus. Our analysis of the three LV strains based on the phylogenetic analysis of the 2C and 3D proteins suggests that the strains used in this study constitute a monophyletic group clearly related to Parechovirus of Picornaviridae. The taxonomic position of the A-2 virus is presently uncertain but available data indicate that this virus may be classified as a member of the genus of Enterovirus.

Animals↗
PubMed2000

Sequencing and characterization of A-2 plaque virus: A new member of the Picornaviridae family.

A-2 plaque virus (A2 virus) was originally isolated from the icteric-phase sera of US servicemen with viral hepatitis in the 1960s, but apart from a preliminary characterization little is known about the agent. We have now successfully cloned and sequenced the complete viral genome. A2 viral RNA consists of 7312 nucleotides, excluding the 62 nucleotide poly(A) tract at the 3' end, with one large open reading frame. Although clearly a member of the Picornaviridae, there is low homology to the available sequences, suggesting it is only loosely related to the classic rhino/enterovirus genus. In addition, there was no reactivity with group specific monoclonal antibody blends against polioviruses, enteroviruses 70 and 71, coxsackievirus B, and echoviruses. Two tamarins were inoculated with A2 virus to study viral pathogenesis. Both animals that received A2 virus became transiently viremic 1 week after the infection, as determined by RT-PCR, and they developed an antibody response to A2 virus. However, no physical signs or biochemical abnormalities, including elevated liver transaminases, were observed. In addition, no liver samples from patients with fulminant hepatitis (n = 7) or controls (n = 7) were positive for A2 viral RNA nor was anti-A2 neutralizing antibody detected in sera from hepatitis patients (n = 14), healthy laboratory donors (n = 14), or US blood donors (n = 33); however, most sera contained antibodies reactive with A2 virus proteins. These results suggest that A2 virus is a new member of the Picornaviridae but that its pathogenicity in nonhuman primates and association with human disease still need to be determined.

Anemia, Aplastic↗
PubMed2001

Conserved RNA secondary structures in Picornaviridae genomes.

The family Picornaviridae contains important pathogens including, for example, hepatitis A virus and foot-and-mouth disease virus. The genome of these viruses is a single messenger-active (+)-RNA of 7200-8500 nt. Besides coding for the viral proteins, it also contains functionally important RNA secondary structures, among them an internal ribosomal entry site (IRES) region towards the 5'-end. This contribution provides a comprehensive computational survey of the complete genomic RNAs and a detailed comparative analysis of the conserved structural elements in seven of the currently nine genera in the family PICORNAVIRIDAE: Compared with previous studies we find: (i) that only smaller sections of the IRES region than previously reported are conserved at single base-pair resolution and (ii) that there is a number of significant structural elements in the coding region. Furthermore, we identify potential cis-acting replication elements in four genera where this feature has not been reported so far.

5' Untranslated Regions↗
PubMed1981

Chromatographic purification from Streptococcus faecium extract of a factor active on Picornaviridae.

"In vitro" antiviral activity against Picornaviridae and the trials for purification from Str. faecium extract of a factor responsible of these effects are reported. Fractionation on Bio-Gel P-150 and on DEAE-cellulose column and analytical methods for protein and aminosugars were used. Present results demonstrate an antiviral activity of Str. faecium extract against Picornaviridae. Virus inhibiting activity is not correlated with the majority of the Folin reacting proteins, which are present in the bacterial extract. No reliable relationship could be detected for aminosugars containing components, since the amount of aminosugar in fraction from Bio-Gel is extremely low and widely distributed.

Antiviral Agents↗
PubMed2001

Construction of an infectious cDNA clone of Aichi virus (a new member of the family Picornaviridae) and mutational analysis of a stem-loop structure at the 5' end of the genome.

Aichi virus is the type species of a new genus, Kobuvirus, of the family Picornaviridae. In this study, we constructed a full-length cDNA clone of Aichi virus whose in vitro transcripts were infectious to Vero cells. During construction of the infectious cDNA clone, a novel sequence of 32 nucleotides was identified at the 5' end of the genome. Computer-assisted prediction of the secondary structure of the 5' end of the genome, including the novel sequence, suggested the formation of a stable stem-loop structure consisting of 42 nucleotides. The function of this stem-loop in virus replication was investigated using various site-directed mutants derived from the infectious cDNA clone. Our data indicated that correct folding of the stem-loop at the 5' end of the positive strand, but not at the 3' end of the negative strand, is critical for viral RNA replication. The primary sequence in the lower part of the stem was also suggested to be crucial for RNA replication. In contrast, nucleotide changes in the loop segment did not so severely reduce the efficiency of virus replication. A double mutant, in which both nucleotide stretches of the middle part of the stem were replaced by their complementary nucleotides, had efficient RNA replication and translation abilities but was unable to produce viruses. These results indicate that the stem-loop at the 5' end of the Aichi virus genome is an element involved in both viral RNA replication and production of infectious virus particles.

Amino Acid Sequence↗
PubMed2004

Inhibitors of 3C cysteine proteinases from Picornaviridae.

The Picornaviridae are among the smallest icosahedral positive-sense single stranded RNA containing viruses known, and comprise one of the largest and most important families of human and animal pathogens. The hepatitis A virus (HAV) and human rhinovirus (HRV) are important pathogens that belong to the picornavirus family. All picornaviruses have a 3C proteinase that processes an initially biosynthesized precursor protein and is crucial for viral maturation and replication. Although it is a cysteine proteinase, this 3C enzyme has a topology similar to those of the chymotrypsin-like serine proteinases. A series of inhibitors of HAV and HRV 3C proteinases were synthesized and tested as potential lead compounds for the design of therapeutic agents for human picornaviral pathogens. This research shows that thiol-reactive groups or "warheads" such as iodoacetamides, beta-lactones, Michael acceptors, ketones and pseudoxazolones can be used as effective tools to inhibit the HAV and HRV 3C proteinase enzymes. In addition, studies based on enzyme-inhibitor kinetics, mass spectrometry and NMR spectroscopy were effectively used to gain knowledge concerning enzyme-inhibitor mechanism of action and enzyme-inhibitor regiospecific reactivity.

Animals↗
PubMed2001

A biochemical approach reveals cell-surface molecules utilised by Picornaviridae: Human Parechovirus 1 and Echovirus 1.

Although receptor virus interactions of several Picornaviridae have been studied in the past, it is becoming apparent that these interactions might be more complex than previously thought. In this study, we have chosen to identify the cell-surface molecules involved in the infectious cycle of two common human pathogens and members of the Piconaviridae family, Echovirus 1 (Echo1) and Human Parechovirus 1 (HPEV1) also known as Echovirus 22. In order to identify the specific cell-surface protein molecules involved in Echo1 and HPEV1 infectious cycles, we have deviced a method, by which free virions were used as an affinity surface, allowing either Echo1 or HPEV1 to bind to solubilised proteins from cells susceptible to the virus infection. The virus-cell-surface protein complexes were then analysed by SDS-PAGE and two-dimensional electrophoresis. Echo1 was shown to bind to two integrin-like proteins of 150 and 120 kDa. While HPEV1 attached to two integrin-like proteins of 120 and 100 kDa. The identity of these proteins was identified via Western blotting. Thus, overall we can conclusively report that Echo1 utilises integrin alpha2beta1, whereas HPEV1 utilises integrin alphavbeta3 on the cell surface.

Blotting, Western↗
PubMed1988

Queensland fruit fly virus, a probable member of the Picornaviridae.

A picornavirus was isolated from various life stages of the Queensland fruit fly, Dacus tryoni. This virus, Queensland fruit fly virus (QFFV) has virions with a diameter of 30 nm and a sedimentation coefficient of 178 S. One third of the particles in preparations were empty capsids or natural top component (NTC) with a sedimentation coefficient of 95 S. The buoyant density (rho) of virions and NTC in CsCl was 1.34 and 1.30 g/ml respectively; small amounts of a dense component (rho = 1.45 g/ml) were also detected. The capsid contained three major protein species of molecular weight (mol.wt.) 41,700, 36,500, and 31,300, in approximately equimolar proportions. NTC contained three major species of mol. wt. 44,700, 41,700, and 31,300. The nucleic acid present only in the bottom component virions was RNA and comprised about 30% of the particle weight and had a mol. wt of 2.88 kd, contained a poly(A) tract, and had a base ratio: G = 20; A = 32; C = 15; U = 33. The mol. wt. of the virion was estimated to be approximately equal to 9.5 kd. When virions were heated at 56 degrees C and above, they converted into artificial top component (ATC), which had the same protein composition as the virion when analysed by SDS-PAGE. In immunodiffusion tests the virions and NTC were indistinguishable, but a minor difference in antigenicity was detected between the virions and ATC. Virions were stable between pH 3 and 9 inclusive, and between 5 and 7 in the presence of 0.14 M NaCl. Immunodiffusion tests showed that QFFV was serologically unrelated to a range of picornaviruses as well as an unclassified virus isolated from the Mediterranean fruit fly, Ceratitis capitata. The data show that QFFV is probably a member of the Picornaviridae, genus Enterovirus.

Animals↗
PubMed2004

Phylogeny of the Picornaviridae and differential evolutionary divergence of picornavirus proteins.

A rooted phylogenetic analysis of the viral family Picornaviridae identified several major clusters within this viral family. The genus Parechovirus, including Ljungan virus, was found to be basal to the family. Within the family, there were two major subgroups: (1) a cluster including viruses assigned to the genera Enterovirus and Rhinovirus; and (2) a cluster including Teschovirus, Cardiovirus, Erbovirus, Aphthovirus, and probably Kobuvirus. Within the former cluster, the genera Enterovirus and Rhinovirus were found not to be monophyletic. Principal components analysis was used to identify different patterns with regard to the relative sequence divergence of the 11 polyproteins encoded by the picornavirus genome. In comparisons of closely related pairs of viruses, the nonstructural proteins were generally more conserved than the capsid proteins 1B, 1C, and 1D. This pattern is most likely explained by the predominance of host antibody-driven selection on the differentiation of closely related viral genomes. However, the same pattern was not seen in more distantly related pairs of viruses, which showed a number of distinct patterns with regard to the relative conservation of the 11 proteins.

Biological Evolution↗
PubMed2006

Hepatitis C virus-related internal ribosome entry sites are found in multiple genera of the family Picornaviridae.

The internal ribosome entry site (IRES) elements from porcine enterovirus 8 and simian virus 2, two members of a proposed new genus within the family Picornaviridae, were characterized. These IRES elements, in common with the porcine teschovirus 1 IRES, were found to be related functionally and structurally to the IRES element from Hepatitis C virus, a member of the family Flaviviridae. Partial secondary structure predictions were derived and functional assays demonstrated that these IRES elements continued to be active when eIF4G was cleaved and when the activity of eIF4A was blocked.

5' Untranslated Regions↗
PubMed1998

Complete nucleotide sequence and genetic organization of Aichi virus, a distinct member of the Picornaviridae associated with acute gastroenteritis in humans.

The complete nucleotide sequence of a novel enteric virus, Aichi virus, associated with nonbacterial acute gastroenteritis in humans was determined. The Aichi virus genome proved to be a single-stranded positive-sense RNA molecule with 8,251 bases excluding a poly(A) tail; it contains a large open reading frame with 7,302 nucleotides that encodes a potential polyprotein precursor of 2,433 amino acids. The genome contains a 5' nontranslated region (NTR) with 712 bases and a 3' NTR with 240 bases followed by a poly(A) tail. The structure of the genome, VPg-5' NTR-leader protein-structural proteins-nonstructural proteins-3' NTR-poly(A), was found to be typical of a picornavirus. The VP0-VP3 and VP3-VP1 cleavage sites were determined to be Q-H and Q-T, respectively, by N-terminal amino acid sequence analyses using purified virion proteins. Possible cleavage sites, Q-G, Q-A, and Q-S, which cleave P2 and P3 polyproteins were found to be similar to those of picornaviruses. A dendrogram based on 3Dpol proteins indicated that Aichi virus is genetically distinct from the known six genera of picornaviruses including entero-, rhino-, cardio-, aphtho-, and hepatovirus and echovirus 22. Considering this together with other properties of the virus (T. Yamashita, S. Kobayashi, K. Sakae, S. Nakata, S. Chiba, Y. Ishihara, and S. Isomura, J. Infect. Dis. 164:954-957, 1991), we propose that Aichi virus be regarded as a new genus of the family Picornaviridae.

Acute Disease↗
PubMed1978

Sikhote-Alin virus, a new member of the cardiovirus group (Picornaviridae) isolated from Ixodes persulcatus ticks in Primorie Region.

A virus, designated Sikhote-Alin, was isolated in 1970 from Ixodes persulcatus ticks collected from a wild boar in the Primorie region (U.S.S.R.) Sikhote-Alin virus showed no haemagglutinating activity and no antigenic relationships with arboviruses of 12 antigenic groups, 17 ungrouped tick-borne arboviruses, porcine enteroviruses and coxsackie A (types 1-18) viruses. An one-way antigenic relationship was demonstrated by complement fixation with cardioviruses (Mengo and Columbia-SK strains). The virus contains RNA, is resistant to lipid solvents, highly thermostable in the presence of 1 M MgCl2 and its size is over 20 nm but less than 25 nm. All these properties make it possible to consider it as a new member of the cardiovirus group (genus Enterovirus; Picornaviridae).

Animal Population Groups↗
PubMed2006

Molecular analysis of duck hepatitis virus type 1 reveals a novel lineage close to the genus Parechovirus in the family Picornaviridae.

Duck hepatitis virus type 1 (DHV-1) was previously classified as an enterovirus, based primarily on observed morphology and physicochemical properties of the virion. The complete nucleotide sequences of two strains (DRL-62 and R85952) of DHV-1 have been determined. Excluding the poly(A) tail, the genomes are 7691 and 7690 nt, respectively, and contain a single, large open reading frame encoding a polyprotein of 2249 aa. The genome of DHV-1 is organized as are those of members of the family Picornaviridae: 5' untranslated region (UTR)-VP0-VP3-VP1-2A1-2A2-2B-2C-3A-3B-3C-3D-3' UTR. Analysis of the genomic and predicted polyprotein sequences revealed several unusual features, including the absence of a predicted maturation cleavage of VP0, the presence of two unrelated 2A protein motifs and a 3' UTR extended markedly compared with that of any other picornavirus. The 2A1 protein motif is related to the 2A protein type of the genus Aphthovirus and the adjacent 2A2 protein is related to the 2A protein type present in the genus Parechovirus. Phylogenetic analysis using the 3D protein sequence shows that the two DHV-1 strains are related more closely to members of the genus Parechovirus than to other picornaviruses. However, the two DHV-1 strains form a monophyletic group, clearly distinct from members of the genus Parechovirus.

3' Untranslated Regions↗
PubMed1987

The complete nucleotide sequence of coxsackievirus B4 and its comparison to other members of the Picornaviridae.

The genome of the prototype stain of coxsackievirus B4 (J.V.B. Benschoten) has been cloned in Escherichia coli and its complete nucleotide sequence determined. Excluding the poly(A) tract, the RNA genome is 7395 nucleotides in length and appears to encode a single polyprotein of 2183 amino acids. The predicted amino acid sequence of the polyprotein shows close homology (88%) to that of the previously sequenced coxsackievirus B3 and to certain regions of the polyproteins of the polioviruses and human rhinovirus 14. This allows identification of putative polyprotein cleavage signals, antigenic domains and other structural features likely to be important to the biological integrity of the virus.

Amino Acid Sequence↗
PubMed2002

Molecular analysis of three Ljungan virus isolates reveals a new, close-to-root lineage of the Picornaviridae with a cluster of two unrelated 2A proteins.

Ljungan virus (LV) is a suspected human pathogen recently isolated from bank voles (Clethrionomys glareolus). In the present study, it is revealed through comparative sequence analysis that three newly determined Swedish LV genomes are closely related and possess a deviant picornavirus-like organization: 5' untranslated region-VP0-VP3-VP1-2A1-2A2-2B-2C-3A-3B-3C-3D-3' untranslated region. The LV genomes and the polyproteins encoded by them exhibit several exceptional features, such as the absence of a predicted maturation cleavage of VP0, a conserved sequence determinant in VP0 that is typically found in VP1 of other picornaviruses, and a cluster of two unrelated 2A proteins. The 2A1 protein is related to the 2A protein of cardio-, erbo-, tescho-, and aphthoviruses, and the 2A2 protein is related to the 2A protein of parechoviruses, kobuviruses, and avian encephalomyelitis virus. The unprecedented association of two structurally different 2A proteins is a feature never previously observed among picornaviruses and implies that their functions are not mutually exclusive. Secondary polyprotein processing of the LV polyprotein is mediated by proteinase 3C (3C(pro)) possessing canonical affinity to Glu and Gln at the P1 position and small amino acid residues at the P1' position. In addition, LV 3C(pro) appears to have unique substrate specificity to Asn, Gln, and Asp and to bulky hydrophobic residues at the P2 and P4 positions, respectively. Phylogenetic analysis suggests that LVs form a separate division, which, together with the Parechovirus genus, has branched off the picornavirus tree most closely to its root. The presence of two 2A proteins indicates that some contemporary picornaviruses with a single 2A may have evolved from the ancestral multi-2A picornavirus.

3' Untranslated Regions↗