Sequence analysis of human rhinoviruses in the RNA-dependent RNA polymerase coding region reveals large within-species variation

Human rhinoviruses (HRVs; family Picornaviridae), the most frequent causative agents of respiratory infections, comprise more than 100 distinct serotypes. According to previous phylogenetic analysis of the VP4/VP2-coding sequences, all but one of the HRV prototype strains distribute between the two established species, Human rhinovirus A (HRV-A) and Human rhinovirus B (HRV-B). Here, partial sequences of the RNA-dependent RNA polymerase (3D polymerase)-coding gene of 48 HRV prototype strains and 12 field isolates were analysed. The designated division of the HRV strains into the species HRV-A and HRV-B was also seen in the 3D-coding region. Phylogenetically, HRV-B clustered closer to human enterovirus (HEV) species HEV-B, HEV-C and poliovirus than to HRV-A. Intraspecies variation within both HRV-A and HRV-B was greater in the 3D-coding region than in the VP4/VP2-coding region, with the difference maxima reaching 48 % at the nucleotide level and 36 % at the amino acid level in HRV-A and 53 and 35 %, respectively, in HRV-B. Within both species, a few strains formed a separate cluster differing from the majority of strains as much as HEV-B from HEV-C. Furthermore, the tree topology within HRV-A differed from that for VP4/VP2, suggesting possible recombination events in the evolutionary history of the strains. However, all 12 field isolates clustered similarly, as in the capsid region. These results showed that the within-species variation in the 3D region is greater in HRV than in HEV. Furthermore, HRV variation in the 3D region exceeds that in the capsid-coding region.

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Genetic clustering of all 102 human rhinovirus prototype strains: serotype 87 is close to human enterovirus 70

Journal of General Virology ◽

10.1099/0022-1317-83-2-333 ◽

2002 ◽

Vol 83 (2) ◽

pp. 333-340 ◽

Cited By ~ 153

Author(s):

Carita Savolainen ◽

Soile Blomqvist ◽

Mick N. Mulders ◽

Tapani Hovi

Keyword(s):

Respiratory Infections ◽

Genetic Relationships ◽

Amino Acid Level ◽

Genetic Group ◽

Genetic Identification ◽

Human Enterovirus ◽

Field Isolates ◽

Group A ◽

Enterovirus 70 ◽

Group B

Human rhinoviruses (HRV), common agents of respiratory infections, comprise 102 designated serotypes. The genetic relationships of HRV prototype strains and the possibility of using genetic identification of a given HRV field strain were studied. Genomic sequences in the VP4/VP2 region were obtained from all 102 prototype strains. Phylogenetic analysis included 61 recently isolated Finnish field strains. Seventy-six out of the 102 prototype strains clustered in the HRV genetic group A and 25 in group B. Serotype 87 clustered separately and together with human enterovirus 70. The ‘percentage’ interserotypic differences were generally similar to those between different enterovirus serotypes, but for six pairs of HRV serotypes they were less than 10%. The maximum variation in genetic group A was 41% at the nucleotide level and 28% at the amino acid level, and in genetic group B 34% and 20%, respectively. Judging from the observed interserotypic differences, the 61 Finnish field isolates might represent as many as 19 different serotypes. One cluster of the field strains did not directly associate with any of the prototype strains and might represent a new serotype. However, larger numbers of field isolates of known serotype need to be characterized, possibly also in the VP1 region, to evaluate the feasibility of genetic typing of HRV strains.

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Dominant CD4-dependent RNA-dependent RNA polymerase-specific T-cell responses in children acutely infected with human enterovirus 71 and healthy adult controls

Immunology ◽

10.1111/imm.12235 ◽

2014 ◽

Vol 142 (1) ◽

pp. 89-100 ◽

Cited By ~ 5

Author(s):

Shuangsuo Dang ◽

Ning Gao ◽

Yaping Li ◽

Mei Li ◽

Xiufang Wang ◽

...

Keyword(s):

T Cell ◽

Rna Polymerase ◽

Healthy Adult ◽

Enterovirus 71 ◽

T Cell Responses ◽

Human Enterovirus ◽

Rna Dependent Rna Polymerase ◽

Human Enterovirus 71 ◽

Cell Responses

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Inhibition of coxsackievirus B3 and related enteroviruses by antiviral short interfering RNA pools produced using φ6 RNA-dependent RNA polymerase

Journal of General Virology ◽

10.1099/vir.0.011338-0 ◽

2009 ◽

Vol 90 (10) ◽

pp. 2468-2473 ◽

Cited By ~ 10

Author(s):

Michaela Nygårdas ◽

Tytti Vuorinen ◽

Antti P. Aalto ◽

Dennis H. Bamford ◽

Veijo Hukkanen

Keyword(s):

Rna Polymerase ◽

Genomic Sequence ◽

Coxsackievirus B3 ◽

Human Enterovirus ◽

Rna Dependent Rna Polymerase ◽

Coxsackievirus B4 ◽

Novel Approach ◽

Experimental Therapies ◽

Coxsackievirus A9 ◽

Interfering Rna

Coxsackievirus B3 (CBV3) is a member of the human enterovirus B species and a common human pathogen. Even though much is known about the enteroviral life cycle, no specific drugs are available to treat enterovirus infections. RNA interference (RNAi) has evolved to be an important tool for antiviral experimental therapies and gene function studies. We describe here a novel approach for RNAi against CBVs by using a short interfering (siRNA) pool covering 3.5 kb of CBV3 genomic sequence. The RNA-dependent RNA polymerase (RdRP) of bacteriophage φ6 was used to synthesize long double-stranded RNA (dsRNA) from a cloned region (nt 3837–7399) of the CBV3 genome. The dsRNA was cleaved using Dicer, purified and introduced to cells by transfection. The siRNA pool synthesized using the φ6 RdRP (φ6–siRNAs) was considerably more effective than single-site siRNAs. The φ6–siRNA pool also inhibited replication of other enterovirus B species, such as coxsackievirus B4 and coxsackievirus A9.

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VP1 of infectious bursal disease virus is an RNA-dependent RNA polymerase

Journal of General Virology ◽

10.1099/vir.0.19772-0 ◽

2004 ◽

Vol 85 (8) ◽

pp. 2221-2229 ◽

Cited By ~ 110

Author(s):

Ursula I. von Einem ◽

Alexander E. Gorbalenya ◽

Horst Schirrmeier ◽

Sven-Erik Behrens ◽

Tobias Letzel ◽

...

Keyword(s):

Enzyme Activity ◽

Rna Polymerase ◽

Disease Virus ◽

Infectious Bursal Disease Virus ◽

Infectious Bursal Disease ◽

Coding Region ◽

Rdrp Activity ◽

Rna Dependent Rna Polymerase ◽

Double Stranded Rna ◽

Bursal Disease

Segment B of the bisegmented, double-stranded RNA genome of infectious bursal disease virus (IBDV) encodes the viral protein VP1. This has been presumed to represent the RNA-dependent RNA polymerase (RdRp) as it contains motifs that are typical for the RdRp of plus-strand RNA viruses. Here it is demonstrated that baculovirus-expressed wild-type but not motif A mutated VP1 acts as an RdRp on IBDV-specific RNA templates. Thus, on a plus-strand IBDV segment A cRNA template, minus-strand synthesis occurred in such a way that a covalently linked double-stranded RNA product was generated (by a ‘copy-back’ mechanism). Importantly, enzyme activity was observed only with templates that comprised the 3′ non-coding region of plus-strand RNAs transcribed from IBDV segments A and B, indicating template specificity. RdRp activity was shown to have a temperature optimum of 37 °C and required magnesium ions for enzyme activity. Thus, it has been demonstrated unequivocally that VP1 represents the RdRp of IBDV.

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Expression of Enzymatically Active Rabbit Hemorrhagic Disease Virus RNA-Dependent RNA Polymerase in Escherichia coli

Journal of Virology ◽

10.1128/jvi.72.4.2999-3004.1998 ◽

1998 ◽

Vol 72 (4) ◽

pp. 2999-3004 ◽

Cited By ~ 31

Author(s):

Ana López Vázquez ◽

José M. Martín Alonso ◽

Rosa Casais ◽

José A. Boga ◽

Francisco Parra

Keyword(s):

Escherichia Coli ◽

Rna Polymerase ◽

Disease Virus ◽

Rabbit Hemorrhagic Disease Virus ◽

Hemorrhagic Disease ◽

Coding Region ◽

Recombinant Polypeptide ◽

Rna Dependent Rna Polymerase ◽

Rabbit Hemorrhagic Disease

ABSTRACT The rabbit hemorrhagic disease virus (RHDV) (isolate AST/89) RNA-dependent RNA-polymerase (3Dpol) coding region was expressed in Escherichia coli by using a glutathioneS-transferase-based vector, which allowed milligram purification of a homogeneous enzyme with an expected molecular mass of about 58 kDa. The recombinant polypeptide exhibited rifampin- and actinomycin D-resistant, poly(A)-dependent poly(U) polymerase. The enzyme also showed RNA polymerase activity in in vitro reactions with synthetic RHDV subgenomic RNA in the presence or absence of an oligo(U) primer. Template-size products were synthesized in the oligo(U)-primed reactions, whereas in the absence of added primer, RNA products up to twice the length of the template were made. The double-length RNA products were double stranded and hybridized to both positive- and negative-sense probes.

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The human astrovirus RNA-dependent RNA polymerase coding region is expressed by ribosomal frameshifting.

Journal of Virology ◽

10.1128/jvi.68.9.5588-5595.1994 ◽

1994 ◽

Vol 68 (9) ◽

pp. 5588-5595 ◽

Cited By ~ 66

Author(s):

B Marczinke ◽

A J Bloys ◽

T D Brown ◽

M M Willcocks ◽

M J Carter ◽

...

Keyword(s):

Rna Polymerase ◽

Coding Region ◽

Rna Dependent Rna Polymerase ◽

Ribosomal Frameshifting ◽

Human Astrovirus

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Phylogenetic analysis of human rhinovirus capsid protein VP1 and 2A protease coding sequences confirms shared genus-like relationships with human enteroviruses

Journal of General Virology ◽

10.1099/vir.0.80445-0 ◽

2005 ◽

Vol 86 (3) ◽

pp. 697-706 ◽

Cited By ~ 50

Author(s):

Pia Laine ◽

Carita Savolainen ◽

Soile Blomqvist ◽

Tapani Hovi

Keyword(s):

Phylogenetic Analysis ◽

Amino Acid ◽

Capsid Protein ◽

Phylogenetic Trees ◽

Amino Acid Sequences ◽

Human Rhinovirus ◽

Human Enterovirus ◽

Coding Region ◽

Coding Sequences ◽

Capsid Protein Vp1

Phylogenetic analysis of the capsid protein VP1 coding sequences of all 101 human rhinovirus (HRV) prototype strains revealed two major genetic clusters, similar to that of the previously reported VP4/VP2 coding sequences, representing the established two species, Human rhinovirus A (HRV-A) and Human rhinovirus B (HRV-B). Pairwise nucleotide identities varied from 61 to 98 % within and from 46 to 55 % between the two HRV species. Interserotypic sequence identities in both HRV species were more variable than those within any Human enterovirus (HEV) species in the same family. This means that unequivocal serotype identification by VP1 sequence analysis used for HEV strains may not always be possible for HRV isolates. On the other hand, a comprehensive insight into the relationships between VP1 and partial 2A sequences of HRV and HEV revealed a genus-like situation. Distribution of pairwise nucleotide identity values between these genera varied from 41 to 54 % in the VP1 coding region, similar to those between heterologous members of the two HRV species. Alignment of the deduced amino acid sequences revealed more fully conserved amino acid residues between HRV-B and polioviruses than between the two HRV species. In phylogenetic trees, where all HRVs and representatives from all HEV species were included, the two HRV species did not cluster together but behaved like members of the same genus as the HEVs. In conclusion, from a phylogenetic point of view, there are no good reasons to keep these two human picornavirus genera taxonomically separated.

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Putative recombination signature and significance of insertion/deletion events in the RNA-dependent RNA polymerase coding region of sugarcane yellow leaf virus

Biochimie ◽

10.1016/j.biochi.2012.04.007 ◽

2012 ◽

Vol 94 (8) ◽

pp. 1764-1772 ◽

Cited By ~ 11

Author(s):

Abdelaleim Ismail ElSayed ◽

Moncef Boulila ◽

Ewald Komor ◽

Yun J. Zhu

Keyword(s):

Rna Polymerase ◽

Yellow Leaf ◽

Coding Region ◽

Rna Dependent Rna Polymerase ◽

Sugarcane Yellow Leaf Virus ◽

Leaf Virus

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Identification of a Conserved RNA-dependent RNA Polymerase (RdRp)-RNA Interface Required for Flaviviral Replication

Journal of Biological Chemistry ◽

10.1074/jbc.m116.724013 ◽

2016 ◽

Vol 291 (33) ◽

pp. 17437-17449 ◽

Cited By ~ 19

Author(s):

Kenneth Hodge ◽

Chairat Tunghirun ◽

Maliwan Kamkaew ◽

Thawornchai Limjindaporn ◽

Pa-thai Yenchitsomanus ◽

...

Keyword(s):

Dengue Virus ◽

Rna Polymerase ◽

Viral Protein ◽

Rna Virus ◽

Coding Region ◽

Rna Dependent Rna Polymerase ◽

Protein Coding ◽

The World ◽

Positive Sense ◽

Rna Motif

Dengue virus, an ∼10.7-kb positive-sense RNA virus, is the most common arthropod-communicated pathogen in the world. Despite dengue's clear epidemiological importance, mechanisms for its replication remain elusive. Here, we probed the entire dengue genome for interactions with viral RNA-dependent RNA polymerase (RdRp), and we identified the dominant interaction as a loop-forming ACAG motif in the 3′ positive-stranded terminus, complicating the prevailing model of replication. A subset of interactions coincides with known flaviviral recombination sites inside the viral protein-coding region. Specific recognition of the RNA element occurs via an arginine patch in the C-terminal thumb domain of RdRp. We also show that the highly conserved nature of the consensus RNA motif may relate to its tolerance to various mutations in the interacting region of RdRp. Disruption of the interaction resulted in loss of viral replication ability in cells. This unique RdRp-RNA interface is found throughout flaviviruses, implying possibilities for broad disease interventions.

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