Molecular and biological characteristics of echovirus 22, a representative of a new picornavirus group

Stanway, Glyn; Kalkkinen, Nisse; Roivainen, Merja; Ghazi, Farideh; Khan, Mahboob; Smyth, Michael; Meurman, Olli; Hyypiä, Timo

doi:10.1128/jvi.68.12.8232-8238.1994

Cited by 191 publications

(101 citation statements)

References 27 publications

(40 reference statements)

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“…This location for myristylation most resembles that of HPeV at position 13, while DHV has a canonical sequence at position 31 and LV has one at position 3. The non-near-terminal position of the putative myristylation site of SePV-1 indicates that, as proposed for DHV and as shown for HPeV, myristylation may not occur and that alternative modifications at the amino terminus of the polyprotein may direct it to a lipid environment (14,17,36).…”

Section: Sequencing Of New Virusmentioning

confidence: 68%

A Highly Divergent Picornavirus in a Marine Mammal

Kapoor

Victoria

Simmonds

et al. 2008

J Virol

124

115

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Nucleic acids from an unidentified virus from ringed seals (Phoca hispida) were amplified using sequenceindependent PCR, subcloned, and then sequenced. The full genome of a novel RNA virus was derived, identifying the first sequence-confirmed picornavirus in a marine mammal. The phylogenetic position of the tentatively named seal picornavirus 1 (SePV-1) as an outlier to the grouping of parechoviruses was found consistently in alignable regions of the genome. A mean protein sequence identity of only 19.3 to 30.0% was found between the 3D polymerase gene sequence of SePV-1 and those of other picornaviruses. The predicted secondary structure of the short 506-base 5-untranslated region showed some attributes of a type IVB internal ribosome entry site, and the polyprotein lacked an apparent L peptide, both properties associated with the A recent analysis of lungs, lymph nodes, and nasal swabs from ringed seals hunted in 2000 to 2002 from Ulukhaktok (formerly known as Holman) on the shore of the Beaufort Sea demonstrated the presence of a virus causing strong cytopathic effects (CPE) in Vero cells. The causative agent of CPE passed through a 0.45-m filter was resistant to detergent inactivation and was therefore thought to be a nonenveloped virus. Here, we analyzed this virus using sequence-independent PCR amplification and sequence similarity searches. We report the full genome sequence of a novel picornavirus with a deep root on the Picornaviridae family phylogenetic tree. Consistent with the nomenclature for other picornaviruses, we suggest the name seal picornavirus 1 (SePV-1) for this new virus and propose that it represent the prototype of a new picornavirus genus. MATERIALS AND METHODS Extraction of viral nucleic acids.A nasal swab from a seal hunted in 2002 was used to inoculate Vero cells, which developed CPE. CPE was transferable to a fresh cell culture. The supernatant from this cell culture was used as the input to nonspecifically amplify viral nucleic acids. For enrichment of viral particles from the supernatant of infected cells, 2 ml of culture supernatant was clarified (5,000 ϫ g for 10 min) and filtered through a 0.45-m-pore-size sterile filter (Millipore HV Durapole) to remove large particles. To concentrate virus particles, 1.5 ml of filtrate was then centrifuged at 35,000 ϫ g for 3 h at 10°C, and the resulting pellet was resuspended in 100 l of water containing 1ϫ Turbo DNase buffer. To remove non-viral-particle-protected DNA from the cultured cells, 20 U of TurboDNase (Ambion) was added, followed by incubation at 37°C for 90 min. Particle-protected nucleic acids were then extracted using a viral RNA extraction kit (Qiagen).Random amplification, subcloning, and sequencing. Viral RNA was mixed with 50 pmol of primer RA01 (GCCGGAGCTCTGCAGATATCNNNNNNN NNN), denatured at 75°C for 5 min, and chilled on ice. A reaction mix of 9 l containing 4 l of 5ϫ first-strand buffer (Invitrogen), 1 l of 100 mM dithiothreitol (DTT), 1 l solution containing each deoxynucleoside triphosphate (dNTP) at 10 mM, 8 units of ...

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Section: Sequencing Of New Virusmentioning

confidence: 68%

A Highly Divergent Picornavirus in a Marine Mammal

Kapoor

Victoria

Simmonds

et al. 2008

J Virol

124

115

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“…HPeV-6 strain 2005-823 contains a cis-acting replication element that is located in VP0, as described recently (2). Furthermore, HPeV-6 strain 2005-823 has a 28-amino-acid extension in the N terminus of VP3 and conserved motifs in the 2A protein that share homology with the H-rev-107 family of cellular proteins (5,15). An imperfect repeat in the 3ЈUTR region is present, as described previously (2), which contains some nucleotide changes.…”

mentioning

confidence: 85%

“…Infections can cause relatively mild symptoms such as diarrhea but also life-threatening diseases such as encephalitis (14). HPeVs were formerly known as echovirus 22 (HPeV-1) and echovirus 23 (HPeV-2; two strains) but were reclassified by phylogenetic analysis as a new genus (6,8,10,13,15). Additional genotypes have been identified recently (1-3, 7, 17), and one of the two strains of HPeV-2 (strain CT86-6760) was reclassified as HPeV-5 (2).…”

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confidence: 99%

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Human Parechovirus Type 1, 3, 4, 5, and 6 Detection in Picornavirus Cultures

et al. 2008

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Picornavirus cultures that could not be typed in neutralization assays were analyzed by VP1 reverse transcription-PCR (RT-PCR) and a virus discovery tool (VIDISCA). Human parechoviruses (HPeVs) were frequently identified, among which were the uncommon isolates HPeV-4, HPeV-5, and HPeV-6. The HPeV-5 isolate could be amplified only by VIDISCA and not by VP1 RT-PCR.Enteroviruses and human parechoviruses (HPeVs) belong to the family Picornaviridae. Infections can cause relatively mild symptoms such as diarrhea but also life-threatening diseases such as encephalitis (14). HPeVs were formerly known as echovirus 22 (HPeV-1) and echovirus 23 (HPeV-2; two strains) but were reclassified by phylogenetic analysis as a new genus (6,8,10,13,15). Additional genotypes have been identified recently (1-3, 7, 17), and one of the two strains of HPeV-2 (strain CT86-6760) was reclassified as HPeV-5 (2). The VP1 protein of enteroviruses and HPeV is the most variable and immunogenic protein. Serotyping is performed with specific antisera directed to the different enteroviruses and HPeV types. Nowadays, genotyping is used as an alternative method for typing. In genotyping, a clinical isolate with a VP1 nucleotide identity to known genotypes of higher then 75% or with an amino acid identity to known genotypes of 85% or higher is considered the same enterovirus type (11,12).In the study presented here, we analyzed 25 virus isolates that showed an enterovirus-like cytopathic effect (CPE) in cell culture. We used a universal enterovirus VP1 reverse transcription-PCR (RT-PCR) and a universal HPeV VP1 RT-PCR that should theoretically amplify all enteroviruses and all HPeVs (3, 9). Furthermore, we employed the VIDISCA method.

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“…Due to its unique pathogenicity and genetic distance when compared to other picornaviruses, hepatitis A virus (HAV), previously designated as enterovirus 72, was reclassified in hepatovirus genus (Minor, 1991). More recently, two echoviruses (serotypes 22 and 23) with exceptional molecular properties have been assigned to a new genus, parechovirus Stanway et al, 1994;Mayo and Pringle, 1998). Examples of clinical diseases associated with picornavirus infections are shown in Table 1.…”

Section: Introductionmentioning

confidence: 99%

Molecular detection and typing of human picornaviruses

1999

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Picornaviruses include several important clinical pathogens which cause diseases varying from common cold to poliomyelitis and hepatitis. Introduction of RT-PCR methods for the detection of these viruses has significantly facilitated the diagnosis of picornavirus infections and elucidated their etiological role in clinical illnesses. Partial sequence analysis of the genomes has been used for typing of the viruses and in studies of molecular epidemiology of picornaviruses. These molecular approaches are likely to become the most predominant techniques for the diagnosis and epidemiological analysis, particularly in the enterovirus infections.

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Molecular and biological characteristics of echovirus 22, a representative of a new picornavirus group

Abstract: Recent sequence analysis revealed that the human pathogen echovirus 22 (EV22) is genetically distant from all the other picornaviruses studied to date (T.

Cited by 191 publications

References 27 publications

A Highly Divergent Picornavirus in a Marine Mammal

A Highly Divergent Picornavirus in a Marine Mammal

Human Parechovirus Type 1, 3, 4, 5, and 6 Detection in Picornavirus Cultures

Molecular detection and typing of human picornaviruses

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