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Complete coding sequence characterization and comparative analysis of the putative novel human rhinovirus (HRV) species C and B.

Linsuwanon P, Payungporn S, Suwannakarn K, Chieochansin T, Theamboonlers A, Poovorawan Y - Virol. J. (2011)

Bottom Line: Human Rhinoviruses (HRVs) are well recognized viral pathogens associated with acute respiratory tract illnesses (RTIs) abundant worldwide.These findings indicated that the elementary units shaping the genetic diversity of HRV-C could be found in the nonstructural 2A and 3D genes.This study provides information for understanding HRV genetic diversity and insight into the role of selection pressure and recombination mechanisms influencing HRV evolution.

View Article: PubMed Central - HTML - PubMed

Affiliation: Center of Excellence in Clinical Virology, Department of Pediatrics, Faculty of Medicine, Chulalongkorn University and Hospital, Bangkok, Thailand.

ABSTRACT

Background: Human Rhinoviruses (HRVs) are well recognized viral pathogens associated with acute respiratory tract illnesses (RTIs) abundant worldwide. Although recent studies have phylogenetically identified the new HRV species (HRV-C), data on molecular epidemiology, genetic diversity, and clinical manifestation have been limited.

Result: To gain new insight into HRV genetic diversity, we determined the complete coding sequences of putative new members of HRV species C (HRV-CU072 with 1% prevalence) and HRV-B (HRV-CU211) identified from clinical specimens collected from pediatric patients diagnosed with a symptom of acute lower RTI. Complete coding sequence and phylogenetic analysis revealed that the HRV-CU072 strain shared a recent common ancestor with most closely related Chinese strain (N4). Comparative analysis at the protein level showed that HRV-CU072 might accumulate substitutional mutations in structural proteins, as well as nonstructural proteins 3C and 3 D. Comparative analysis of all available HRVs and HEVs indicated that HRV-C contains a relatively high G+C content and is more closely related to HEV-D. This might be correlated to their replication and capability to adapt to the high temperature environment of the human lower respiratory tract. We herein report an infrequently occurring intra-species recombination event in HRV-B species (HRV-CU211) with a crossing over having taken place at the boundary of VP2 and VP3 genes. Moreover, we observed phylogenetic compatibility in all HRV species and suggest that dynamic mechanisms for HRV evolution seem to be related to recombination events. These findings indicated that the elementary units shaping the genetic diversity of HRV-C could be found in the nonstructural 2A and 3D genes.

Conclusion: This study provides information for understanding HRV genetic diversity and insight into the role of selection pressure and recombination mechanisms influencing HRV evolution.

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Average G+C composition percentage along the ORF of HRVs and HEV. Each viral gene was depicted in relation to ORF arrangement. Average values were computed from multiple sequence alignments of representative serotypes or strains with each species by using 500 bp sliding window and 10 bp increment size. Standard deviation (SD) value of each species' representative data was represented by the shaded area.
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Figure 6: Average G+C composition percentage along the ORF of HRVs and HEV. Each viral gene was depicted in relation to ORF arrangement. Average values were computed from multiple sequence alignments of representative serotypes or strains with each species by using 500 bp sliding window and 10 bp increment size. Standard deviation (SD) value of each species' representative data was represented by the shaded area.

Mentions: Compared with the closest relative, all HRV species exhibited a lower percentage of average G+C composition than other enterovirus members (Figure 6). HRV-A and HRV-B showed a relatively low average G+C content (38% and 39%, respectively) whereas HRV-Cs displayed the highest average value at 43%. HRV-C's 2A cysteine-type protease encoding region showed a unique G+C content more similar to enterovirus composition than other HRV species. In comparison the other enterovirus species, HEV-A and HEV-B, showed similar GC content (48%), polioviruses displayed 46%, HEV-C 45%, and HEV-D exhibited the lowest G+C content at 42%, closely related to HRV-C.


Complete coding sequence characterization and comparative analysis of the putative novel human rhinovirus (HRV) species C and B.

Linsuwanon P, Payungporn S, Suwannakarn K, Chieochansin T, Theamboonlers A, Poovorawan Y - Virol. J. (2011)

Average G+C composition percentage along the ORF of HRVs and HEV. Each viral gene was depicted in relation to ORF arrangement. Average values were computed from multiple sequence alignments of representative serotypes or strains with each species by using 500 bp sliding window and 10 bp increment size. Standard deviation (SD) value of each species' representative data was represented by the shaded area.
© Copyright Policy - open-access
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC3025962&req=5

Figure 6: Average G+C composition percentage along the ORF of HRVs and HEV. Each viral gene was depicted in relation to ORF arrangement. Average values were computed from multiple sequence alignments of representative serotypes or strains with each species by using 500 bp sliding window and 10 bp increment size. Standard deviation (SD) value of each species' representative data was represented by the shaded area.
Mentions: Compared with the closest relative, all HRV species exhibited a lower percentage of average G+C composition than other enterovirus members (Figure 6). HRV-A and HRV-B showed a relatively low average G+C content (38% and 39%, respectively) whereas HRV-Cs displayed the highest average value at 43%. HRV-C's 2A cysteine-type protease encoding region showed a unique G+C content more similar to enterovirus composition than other HRV species. In comparison the other enterovirus species, HEV-A and HEV-B, showed similar GC content (48%), polioviruses displayed 46%, HEV-C 45%, and HEV-D exhibited the lowest G+C content at 42%, closely related to HRV-C.

Bottom Line: Human Rhinoviruses (HRVs) are well recognized viral pathogens associated with acute respiratory tract illnesses (RTIs) abundant worldwide.These findings indicated that the elementary units shaping the genetic diversity of HRV-C could be found in the nonstructural 2A and 3D genes.This study provides information for understanding HRV genetic diversity and insight into the role of selection pressure and recombination mechanisms influencing HRV evolution.

View Article: PubMed Central - HTML - PubMed

Affiliation: Center of Excellence in Clinical Virology, Department of Pediatrics, Faculty of Medicine, Chulalongkorn University and Hospital, Bangkok, Thailand.

ABSTRACT

Background: Human Rhinoviruses (HRVs) are well recognized viral pathogens associated with acute respiratory tract illnesses (RTIs) abundant worldwide. Although recent studies have phylogenetically identified the new HRV species (HRV-C), data on molecular epidemiology, genetic diversity, and clinical manifestation have been limited.

Result: To gain new insight into HRV genetic diversity, we determined the complete coding sequences of putative new members of HRV species C (HRV-CU072 with 1% prevalence) and HRV-B (HRV-CU211) identified from clinical specimens collected from pediatric patients diagnosed with a symptom of acute lower RTI. Complete coding sequence and phylogenetic analysis revealed that the HRV-CU072 strain shared a recent common ancestor with most closely related Chinese strain (N4). Comparative analysis at the protein level showed that HRV-CU072 might accumulate substitutional mutations in structural proteins, as well as nonstructural proteins 3C and 3 D. Comparative analysis of all available HRVs and HEVs indicated that HRV-C contains a relatively high G+C content and is more closely related to HEV-D. This might be correlated to their replication and capability to adapt to the high temperature environment of the human lower respiratory tract. We herein report an infrequently occurring intra-species recombination event in HRV-B species (HRV-CU211) with a crossing over having taken place at the boundary of VP2 and VP3 genes. Moreover, we observed phylogenetic compatibility in all HRV species and suggest that dynamic mechanisms for HRV evolution seem to be related to recombination events. These findings indicated that the elementary units shaping the genetic diversity of HRV-C could be found in the nonstructural 2A and 3D genes.

Conclusion: This study provides information for understanding HRV genetic diversity and insight into the role of selection pressure and recombination mechanisms influencing HRV evolution.

Show MeSH
Related in: MedlinePlus