Genome-wide diversity and selective pressure in the human rhinovirus

Kistler, Amy; Webster, Dale R.; Rouskin, Silvi; Magrini, Vincent; Credle, Joel J.; Schnurr, David P.; Boushey, Homer A.; Mardis, Elaine R.; Li, Hao; DeRisi, Joseph L.

doi:10.1186/1743-422x-4-40

Cited by 81 publications

(85 citation statements)

References 95 publications

(96 reference statements)

Supporting

Mentioning

Contrasting

Unclassified

Order By: Relevance

“…Recombination has been considered to play a significant role in genetic diversification of HEV, but its importance in HRV strain diversification is currently unclear because of the limited amount of HRV sequences available (Kistler et al, 2007b;Simmonds & Welch, 2006). By analysing four distinct genomic regions from the set of 28 HRV field strains in this study, we noticed the inconsistent clustering of some HRV field and prototype strains in the 59 NCR and 3D polymerase coding region as compared to the capsid region.…”

Section: Discussionmentioning

confidence: 75%

Molecular characterization of human rhinovirus field strains isolated during surveillance of enteroviruses

Blomqvist

Savolainen-Kopra

Paananen

et al. 2009

Journal of General Virology

View full text Add to dashboard Cite

Human rhinoviruses (HRVs), which are the most frequent causative agents of acute upper respiratory tract infections, are abundant worldwide. We have identified HRV strains in environmental specimens collected in Finland, Latvia and Slovakia during the surveillance of polioand other enteroviruses. These acid-sensitive HRV strains were isolated under conditions optimized for growth of most of the enteroviruses, i.e. in stationary human rhabdomyosarcoma cells incubated at 36 6C. Phylogenetic analysis of the sequences derived from the partial 59 noncoding region and the capsid region coding for proteins VP4/VP2 and VP1 showed that the HRV field strains clustered together with prototype strains of the HRV minor receptor group. Partial sequences of the 3D polymerase coding region generally followed this pattern, with the exception of a set of three HRV field strains that formed a subcluster not close to any of the established HRV-A types, suggesting that recombination may have occurred during evolution of these HRV strains. Phylogenetic analysis of the VP4/VP2 capsid protein coding region showed that the 'environmental' HRV field strains were practically identical to HRV strains recently sequenced by others in Australia, the United States and Japan. Analysis of amino acids corresponding to the intercellular adhesion molecule-1 receptor footprint in major receptor group HRVs and also in the low-density lipoprotein receptor footprint of minor receptor group HRVs showed conservation of the 'minor receptor group-like' amino acids, indicating that the field strains may have maintained their minor receptor group specificity. INTRODUCTIONHuman rhinoviruses (HRVs) belong to the family Picornaviridae and together with human enteroviruses (HEV) and a number of non-human enterovirus strains comprise the largest genus (Enterovirus) in the family (Knowles, 2008). Clinical illnesses caused by HRV are typically mild and self-limiting upper respiratory tract infections or common colds, but HRVs have also been increasingly associated with other clinical consequences of respiratory tract infection such as acute otitis media (NoksoKoivisto et al., 2004;Pitkaranta et al., 1998;Vesa et al., 2001), acute community-acquired sinusitis (Pitkaranta et al., 1997(Pitkaranta et al., , 2001), bronchiolitis (Hayden, 2004), pneumonia (Papadopoulos, 2004 and exacerbations of existing respiratory disorders such as asthma (Gern, 2002) and chronic obstructive pulmonary disease (Greenberg, 2002).HRV encompasses 100 designated serotypes, including two antigenically distinct subtypes of serotype HRV1 (HRV1A and HRV1B) (Hamparian et al., 1987;Kapikian et al., 1967Kapikian et al., , 1971. The current taxonomy is based on genetic relationships of HRV. Genetic analysis of VP4/VP2 (Savolainen et al., 2002a) and VP1 (Laine et al., 2005; Ledford et al., 2004) capsid protein coding regions showed that the 100 serotypes cluster into two genetically distinct species, HRV-A and HRV-B. One HRV strain originally assigned as HRV87 belongs to the enterovirus species H...

show abstract

Section: Discussionmentioning

confidence: 75%

Molecular characterization of human rhinovirus field strains isolated during surveillance of enteroviruses

Blomqvist

Savolainen-Kopra

Paananen

et al. 2009

Journal of General Virology

View full text Add to dashboard Cite

show abstract

“…The use of sequence-independent amplification of viral nucleic acids (2,19,35,38) for viral metagenomics avoids the potential limitations of traditional methods, including the failure of virus to replicate in cell cultures, unsuccessful PCR amplification or microarray hybridization due to high-level genetic divergence from known viruses, and the failure of antibodies to known viruses to cross-react. The application of viral metagenomics may also be useful for the study of diseases with unexplained etiologies possibly involving uncharacterized viruses or combinatorial viral infections (13,21).…”

mentioning

confidence: 99%

Metagenomic Analyses of Viruses in Stool Samples from Children with Acute Flaccid Paralysis

Victoria

Kapoor

et al. 2009

J Virol

343

345

View full text Add to dashboard Cite

We analyzed viral nucleic acids in stool samples collected from 35 South Asian children with nonpolio acute flaccid paralysis (AFP). Sequence-independent reverse transcription and PCR amplification of capsid-protected, nuclease-resistant viral nucleic acids were followed by DNA sequencing and sequence similarity searches. Limited Sanger sequencing (35 to 240 subclones per sample) identified an average of 1.4 distinct eukaryotic viruses per sample, while pyrosequencing yielded 2.6 viruses per sample. In addition to bacteriophage and plant viruses, we detected known enteric viruses, including rotavirus, adenovirus, picobirnavirus, and human enterovirus species A (HEV-A) to HEV-C, as well as numerous other members of the Picornaviridae family, including parechovirus, Aichi virus, rhinovirus, and human cardiovirus. The viruses with the most divergent sequences relative to those of previously reported viruses included members of a novel Picornaviridae genus and four new viral species (members of the Dicistroviridae, Nodaviridae, and Circoviridae families and the Bocavirus genus). Samples from six healthy contacts of AFP patients were similarly analyzed and also contained numerous viruses, particularly HEV-C, including a potentially novel Enterovirus genotype. Determining the prevalences and pathogenicities of the novel genotypes, species, genera, and potential new viral families identified in this study in different demographic groups will require further studies with different demographic and patient groups, now facilitated by knowledge of these viral genomes.

show abstract

“…HRV is a member of the Picornaviridae family and is composed of a nonenveloped particle with a positive-sense single-stranded RNA genome. The genome consists of 11 genes that are translated as a single polyprotein, which is divided into three regions (P1, P2 and P3) that are subsequently cleaved into four mature structural (VP4, VP2, VP3 and VP1) and seven non-structural proteins (2A, 2B, 2C, 3A, 3B, 3C PRO and 3D POL ) (Kirchberger et al 2007, Kistler et al 2007, Mackay 2008. Three HRV species have been described: A, B and C (Lau et al 2007, Palmenberg et al 2009).…”

mentioning

confidence: 99%

Human rhinovirus in the lower respiratory tract infections of young children and the possible involvement of a secondary respiratory viral agent

Paula

Carneiro

Yokosawa

et al. 2011

Mem. Inst. Oswaldo Cruz

View full text Add to dashboard Cite

show abstract

Genome-wide diversity and selective pressure in the human rhinovirus

Cited by 81 publications

References 95 publications

Molecular characterization of human rhinovirus field strains isolated during surveillance of enteroviruses

Molecular characterization of human rhinovirus field strains isolated during surveillance of enteroviruses

Metagenomic Analyses of Viruses in Stool Samples from Children with Acute Flaccid Paralysis

Human rhinovirus in the lower respiratory tract infections of young children and the possible involvement of a secondary respiratory viral agent

Contact Info

Product

Resources

About