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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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Related in: MedlinePlus

Complete coding sequence similarity plot illustrating pairwise sequence identity between HRV-CU072 compared with the most closely related Chinese strain (N4; green line) and other HRV members (HRV-C024; yellow line, HRV-76; blue line, HRV-35; gray line). Constructed using SimPlot v3.2 with Jukes-Cantor parameter, window size of 400 bp and a step size of 20 bp, and 1,000 bootstrap replicates.
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Figure 2: Complete coding sequence similarity plot illustrating pairwise sequence identity between HRV-CU072 compared with the most closely related Chinese strain (N4; green line) and other HRV members (HRV-C024; yellow line, HRV-76; blue line, HRV-35; gray line). Constructed using SimPlot v3.2 with Jukes-Cantor parameter, window size of 400 bp and a step size of 20 bp, and 1,000 bootstrap replicates.

Mentions: The entire coding sequences of the 6 additional HRV strains elucidated in this study have been submitted to the GenBank database and assigned accession numbers HQ123440-HQ123445. Nucleotide and deduced amino acid sequence analysis revealed considerably different phylogenetic clustering features of the strains HRV-CU072 (HQ123440) and HRV-CU211 (HQ123444) as showed in Figure 1. The strain HRV-CU072 displayed relatively low pairwise sequence identity compared with other HRV-Cs (66%) (Figure 2). Furthermore, scanning bootstrap analysis supported our finding that the strain HRV-CU211 is a putative new HRV strain derived from intra-species recombination of HRV-B (Figure 3).


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)

Complete coding sequence similarity plot illustrating pairwise sequence identity between HRV-CU072 compared with the most closely related Chinese strain (N4; green line) and other HRV members (HRV-C024; yellow line, HRV-76; blue line, HRV-35; gray line). Constructed using SimPlot v3.2 with Jukes-Cantor parameter, window size of 400 bp and a step size of 20 bp, and 1,000 bootstrap replicates.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

Figure 2: Complete coding sequence similarity plot illustrating pairwise sequence identity between HRV-CU072 compared with the most closely related Chinese strain (N4; green line) and other HRV members (HRV-C024; yellow line, HRV-76; blue line, HRV-35; gray line). Constructed using SimPlot v3.2 with Jukes-Cantor parameter, window size of 400 bp and a step size of 20 bp, and 1,000 bootstrap replicates.
Mentions: The entire coding sequences of the 6 additional HRV strains elucidated in this study have been submitted to the GenBank database and assigned accession numbers HQ123440-HQ123445. Nucleotide and deduced amino acid sequence analysis revealed considerably different phylogenetic clustering features of the strains HRV-CU072 (HQ123440) and HRV-CU211 (HQ123444) as showed in Figure 1. The strain HRV-CU072 displayed relatively low pairwise sequence identity compared with other HRV-Cs (66%) (Figure 2). Furthermore, scanning bootstrap analysis supported our finding that the strain HRV-CU211 is a putative new HRV strain derived from intra-species recombination of HRV-B (Figure 3).

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