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Analysis of genetic diversity and sites of recombination in human rhinovirus species C.
J Virol. 2010 Oct; 84(19):10297-310.JV

Abstract

Human rhinoviruses (HRVs) are a highly prevalent and diverse group of respiratory viruses. Although HRV-A and HRV-B are traditionally detected by virus isolation, a series of unculturable HRV variants have recently been described and assigned as a new species (HRV-C) within the picornavirus Enterovirus genus. To investigate their genetic diversity and occurrence of recombination, we have performed comprehensive phylogenetic analysis of sequences from the 5' untranslated region (5' UTR), VP4/VP2, VP1, and 3Dpol regions amplified from 89 HRV-C-positive respiratory samples and available published sequences. Branching orders of VP4/VP2, VP1, and 3Dpol trees were identical, consistent with the absence of intraspecies recombination in the coding regions. However, numerous tree topology changes were apparent in the 5' UTR, where >60% of analyzed HRV-C variants showed recombination with species A sequences. Two recombination hot spots in stem-loop 5 and the polypyrimidine tract in the 5' UTR were mapped using the program GroupingScan. Available HRV-C sequences showed evidence for additional interspecies recombination with HRV-A in the 2A gene, with breakpoints mapping precisely to the boundaries of the C-terminal domain of the encoded proteinase. Pairwise distances between HRV-C variants in VP1 and VP4/VP2 regions fell into two separate distributions, resembling inter- and intraserotype distances of species A and B. These observations suggest that, without serological cross-neutralization data, HRV-C genetic groups may be equivalently classified into types using divergence thresholds derived from distance distributions. The extensive sequence data from multiple genome regions of HRV-C and analyses of recombination in the current study will assist future formulation of consensus criteria for HRV-C type assignment and identification.

Authors+Show Affiliations

Centre for Infectious Diseases, University of Edinburgh, Summerhall, Edinburgh EH9 1QH, UK.No affiliation info availableNo affiliation info availableNo affiliation info availableNo affiliation info available

Pub Type(s)

Journal Article
Research Support, Non-U.S. Gov't

Language

eng

PubMed ID

20668080

Citation

McIntyre, Chloe L., et al. "Analysis of Genetic Diversity and Sites of Recombination in Human Rhinovirus Species C." Journal of Virology, vol. 84, no. 19, 2010, pp. 10297-310.
McIntyre CL, McWilliam Leitch EC, Savolainen-Kopra C, et al. Analysis of genetic diversity and sites of recombination in human rhinovirus species C. J Virol. 2010;84(19):10297-310.
McIntyre, C. L., McWilliam Leitch, E. C., Savolainen-Kopra, C., Hovi, T., & Simmonds, P. (2010). Analysis of genetic diversity and sites of recombination in human rhinovirus species C. Journal of Virology, 84(19), 10297-310. https://doi.org/10.1128/JVI.00962-10
McIntyre CL, et al. Analysis of Genetic Diversity and Sites of Recombination in Human Rhinovirus Species C. J Virol. 2010;84(19):10297-310. PubMed PMID: 20668080.
* Article titles in AMA citation format should be in sentence-case
TY - JOUR T1 - Analysis of genetic diversity and sites of recombination in human rhinovirus species C. AU - McIntyre,Chloe L, AU - McWilliam Leitch,E Carol, AU - Savolainen-Kopra,Carita, AU - Hovi,Tapani, AU - Simmonds,Peter, Y1 - 2010/07/28/ PY - 2010/7/30/entrez PY - 2010/7/30/pubmed PY - 2010/9/30/medline SP - 10297 EP - 310 JF - Journal of virology JO - J Virol VL - 84 IS - 19 N2 - Human rhinoviruses (HRVs) are a highly prevalent and diverse group of respiratory viruses. Although HRV-A and HRV-B are traditionally detected by virus isolation, a series of unculturable HRV variants have recently been described and assigned as a new species (HRV-C) within the picornavirus Enterovirus genus. To investigate their genetic diversity and occurrence of recombination, we have performed comprehensive phylogenetic analysis of sequences from the 5' untranslated region (5' UTR), VP4/VP2, VP1, and 3Dpol regions amplified from 89 HRV-C-positive respiratory samples and available published sequences. Branching orders of VP4/VP2, VP1, and 3Dpol trees were identical, consistent with the absence of intraspecies recombination in the coding regions. However, numerous tree topology changes were apparent in the 5' UTR, where >60% of analyzed HRV-C variants showed recombination with species A sequences. Two recombination hot spots in stem-loop 5 and the polypyrimidine tract in the 5' UTR were mapped using the program GroupingScan. Available HRV-C sequences showed evidence for additional interspecies recombination with HRV-A in the 2A gene, with breakpoints mapping precisely to the boundaries of the C-terminal domain of the encoded proteinase. Pairwise distances between HRV-C variants in VP1 and VP4/VP2 regions fell into two separate distributions, resembling inter- and intraserotype distances of species A and B. These observations suggest that, without serological cross-neutralization data, HRV-C genetic groups may be equivalently classified into types using divergence thresholds derived from distance distributions. The extensive sequence data from multiple genome regions of HRV-C and analyses of recombination in the current study will assist future formulation of consensus criteria for HRV-C type assignment and identification. SN - 1098-5514 UR - https://www.unboundmedicine.com/medline/citation/20668080/Analysis_of_genetic_diversity_and_sites_of_recombination_in_human_rhinovirus_species_C_ L2 - https://journals.asm.org/doi/10.1128/JVI.00962-10?url_ver=Z39.88-2003&rfr_id=ori:rid:crossref.org&rfr_dat=cr_pub=pubmed DB - PRIME DP - Unbound Medicine ER -