Abstract
Human rhinovirus species C (HRV-C) was recently discovered, and this virus has been associated with various acute respiratory illnesses (ARI). However, the molecular evolution of the major antigens of this virus, including VP1, VP2, and VP3, is unknown. Thus, we performed complete VP1, VP2, and VP3 gene analyses of 139 clinical HRV-C strains using RT-PCR with newly designed primer sets and next-generation sequencing. We assessed the time-scale evolution and evolutionary rate of these genes using the Bayesian Markov chain Monte Carlo method. In addition, we calculated the pairwise distance and confirmed the positive/negative selection sites in these genes. The phylogenetic trees showed that the HRV-C strains analyzed using these genes could be dated back approximately 400 to 900 years, and these strains exhibited high evolutionary rates (1.35 to 3.74 × 10−3 substitutions/site/year). Many genotypes (>40) were confirmed in the phylogenetic trees. Furthermore, no positively selected site was found in the VP1, VP2, and VP3 protein. Molecular modeling analysis combined with variation analysis suggested that the exterior surfaces of the VP1, VP2 and VP3 proteins are rich in loops and are highly variable. These results suggested that HRV-C may have an old history and unique antigenicity as an agent of various ARI.
Highlights
Human rhinovirus species C (HRV-C) was recently discovered, and this virus has been associated with various acute respiratory illnesses (ARI)
The availability of the degenerate primer HRV-C_6410R was evaluated with 8 randomly selected clinical specimens; a 5.8-kb RT-PCR product was observed for all 8 tested samples, suggesting that the primer could efficiently amplify the long range of the HRV-C genome
We studied the molecular evolution of the full length VP1, VP2, and VP3 genes in HRV-C detected from ARI
Summary
Human rhinovirus species C (HRV-C) was recently discovered, and this virus has been associated with various acute respiratory illnesses (ARI). The positive pressure of the host may lead to changes in the selection site, leading to changes in antigenicity faster than if spontaneous mutations had occurred[7] Such factors should be considered when we refer to the evolution of viral genes[7]. Recent phylogenetic technologies, including the Bayesian Markov chain Monte Carlo (MCMC) method, enable us to perform cluster analysis and time scale evolution of the various viral genes[8]. We calculated the structure of the VP1, VP2 and VP3 proteins in silico Using these advanced methods, we studied the molecular evolution of the VP1, VP2, and VP3 genes in HRV-C (139 strains) detected in various ARI patients
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