Human rhinoviruses (HRVs) are responsible for many of the characteristic symptoms of common cold, such as a sore throat, runny nose, nasal congestion, sneezing, and coughing. However, despite the high detection rate in children, most HRV infections are asymptomatic. Therefore, these viruses are gene...
Human rhinoviruses (HRVs) are responsible for many of the characteristic symptoms of common cold, such as a sore throat, runny nose, nasal congestion, sneezing, and coughing. However, despite the high detection rate in children, most HRV infections are asymptomatic. Therefore, these viruses are generally ignored, even though a close association between HRV infections in early life and subsequent induction of asthma has been reported. Therefore, it is necessary to conduct further research on HRV diagnostics, treatments, epidemiology, and vaccines.
This report describes recent studies on HRVs, including their surveillance systems, taxonomy, immune responses as well as vaccines. In addition, recombination events in HRVs were confirmed using the sequences of reference HRVs and isolated HRVs from Korea, and the RNA secondary structure of the internal ribosomal entry site (IRES) of the 5′ NCR region was predicted. Building on these studies, it was interesting to confirm the occurrence of an inter-species recombination event which was not mentioned in previous reports. In addition, the secondary structure of the IRES region of RNA, which plays an important role in the transcription and translation of the virus, has been confirm to be maintained despite a difference in the nucleotide sequence. This result suggest that recombination event lead the genetic diversity of HRVs, but the despite genetic diversity, the secondary structure of HRV IRES was preserved, by such like compensatory substitution, to maintain an evolutionarily advantageous manner.Human rhinoviruses (HRVs), in the Enterovirus genus within the family Picornaviridae, are a highly prevalent cause of acute respiratory infection (ARI). Enteroviruses are genetically highly variable, and recombination between serotypes is known to be a major contribution to their diversity. Recently it was reported that recombination events in HRVs cause the diversity of HRV-C. This study analyzed parts of the viral genes spanning the 5′ non- coding region (NCR) through to the viral protein (VP) encoding sequences of 105 HRV field isolates from 51 outpatient cases of Acute Respiratory Infectious Network (ARINET) and 54 inpatient cases of severe lower respiratory infection (SLRI) surveillance, in order to identify recombination in field samples. When analyzing parts of the 5′ NCR and VP4/VP2 encoding sequences, the intra- and interspecies recombinants in field strains of HRV-A and –C were found. Nineteen cases of recombination events (18.1%) were found among 105 field strains. For HRV-A, there were five cases (4.8%) of intra species recombination events and three cases (2.8%) of interspecies recombination events. For HRV-C, there were four cases (3.8%) of intra species recombination events and seven cases (6.7%) of interspecies recombination events. Recombination events were significantly more frequently observed in the ARINET samples (18 cases) than in the SLRI samples (1 case; P< 0.0001). The recombination breakpoints were located in nucleotides (nt) 472–554, which comprise stem-loop 5 in the internal ribosomal entry site (IRES), based on the HRV-B 35 sequence (accession no. FJ445187). The findings in this study regarding genomic recombination in circulating HRV-A and -C strains suggest that recombination might play a role in HRV fitness and could be a possible determinant of disease severity caused by various HRV infections in patients with ARI.Objectives: This study was designed to investigate the genetic diversity in the stem loop (SL)-IV sub-domain of the human rhinovirus (HRV) internal ribosomal entry site (IRES), which plays key roles in the initiation of viral translation by host protein interaction.
Methods: To investigate, the primary SL-IV sequences of 194 HRVs, consisting of 97 reference strains and 97 clinical isolates, including the IRES sub-domains SL-IVa, SL-IVb, SL-IVc, and SL-IVd were analyzed by Lasergene, MEGA 4, and WebLogo. Additionally, secondary structures of SL-IV were predicted and classified by RNAfold and CentroidHomfold-LAST.
Results: The predicted secondary structures of SL-IV showed variations in the position of bulbs, size of loop, and length of stems. SL-IVc had the most highly conserved nucleotide sequence, with structures classified into two groups by the location of poly(C) loop. Of the SL-IVc sequences analyzed, 74 (79.56%) were classified in the major group and 19 (20.44%) in the minor group. Thirteen compensatory substitution pairs of SL-IVc contributed to maintaining the stem structure.
Conclusion: This study showed that the IRES secondary structures of a large number of reference and clinical HRVs were highly conserved with several compensatory substitutions. It is suggested that these results will facilitate investigations of HRV function based on IRES secondary structures.
Human rhinoviruses (HRVs) are responsible for many of the characteristic symptoms of common cold, such as a sore throat, runny nose, nasal congestion, sneezing, and coughing. However, despite the high detection rate in children, most HRV infections are asymptomatic. Therefore, these viruses are generally ignored, even though a close association between HRV infections in early life and subsequent induction of asthma has been reported. Therefore, it is necessary to conduct further research on HRV diagnostics, treatments, epidemiology, and vaccines.
This report describes recent studies on HRVs, including their surveillance systems, taxonomy, immune responses as well as vaccines. In addition, recombination events in HRVs were confirmed using the sequences of reference HRVs and isolated HRVs from Korea, and the RNA secondary structure of the internal ribosomal entry site (IRES) of the 5′ NCR region was predicted. Building on these studies, it was interesting to confirm the occurrence of an inter-species recombination event which was not mentioned in previous reports. In addition, the secondary structure of the IRES region of RNA, which plays an important role in the transcription and translation of the virus, has been confirm to be maintained despite a difference in the nucleotide sequence. This result suggest that recombination event lead the genetic diversity of HRVs, but the despite genetic diversity, the secondary structure of HRV IRES was preserved, by such like compensatory substitution, to maintain an evolutionarily advantageous manner.Human rhinoviruses (HRVs), in the Enterovirus genus within the family Picornaviridae, are a highly prevalent cause of acute respiratory infection (ARI). Enteroviruses are genetically highly variable, and recombination between serotypes is known to be a major contribution to their diversity. Recently it was reported that recombination events in HRVs cause the diversity of HRV-C. This study analyzed parts of the viral genes spanning the 5′ non- coding region (NCR) through to the viral protein (VP) encoding sequences of 105 HRV field isolates from 51 outpatient cases of Acute Respiratory Infectious Network (ARINET) and 54 inpatient cases of severe lower respiratory infection (SLRI) surveillance, in order to identify recombination in field samples. When analyzing parts of the 5′ NCR and VP4/VP2 encoding sequences, the intra- and interspecies recombinants in field strains of HRV-A and –C were found. Nineteen cases of recombination events (18.1%) were found among 105 field strains. For HRV-A, there were five cases (4.8%) of intra species recombination events and three cases (2.8%) of interspecies recombination events. For HRV-C, there were four cases (3.8%) of intra species recombination events and seven cases (6.7%) of interspecies recombination events. Recombination events were significantly more frequently observed in the ARINET samples (18 cases) than in the SLRI samples (1 case; P< 0.0001). The recombination breakpoints were located in nucleotides (nt) 472–554, which comprise stem-loop 5 in the internal ribosomal entry site (IRES), based on the HRV-B 35 sequence (accession no. FJ445187). The findings in this study regarding genomic recombination in circulating HRV-A and -C strains suggest that recombination might play a role in HRV fitness and could be a possible determinant of disease severity caused by various HRV infections in patients with ARI.Objectives: This study was designed to investigate the genetic diversity in the stem loop (SL)-IV sub-domain of the human rhinovirus (HRV) internal ribosomal entry site (IRES), which plays key roles in the initiation of viral translation by host protein interaction.
Methods: To investigate, the primary SL-IV sequences of 194 HRVs, consisting of 97 reference strains and 97 clinical isolates, including the IRES sub-domains SL-IVa, SL-IVb, SL-IVc, and SL-IVd were analyzed by Lasergene, MEGA 4, and WebLogo. Additionally, secondary structures of SL-IV were predicted and classified by RNAfold and CentroidHomfold-LAST.
Results: The predicted secondary structures of SL-IV showed variations in the position of bulbs, size of loop, and length of stems. SL-IVc had the most highly conserved nucleotide sequence, with structures classified into two groups by the location of poly(C) loop. Of the SL-IVc sequences analyzed, 74 (79.56%) were classified in the major group and 19 (20.44%) in the minor group. Thirteen compensatory substitution pairs of SL-IVc contributed to maintaining the stem structure.
Conclusion: This study showed that the IRES secondary structures of a large number of reference and clinical HRVs were highly conserved with several compensatory substitutions. It is suggested that these results will facilitate investigations of HRV function based on IRES secondary structures.
주제어
#Human rhinovirus IRES Evolution Recombination Compensatory substitution 생명공학
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