Analysis of Genetic Diversity and Sites of Recombination in Human Rhinovirus Species C

被引:77
作者
McIntyre, Chloe L. [1 ]
Leitch, E. Carol McWilliam [1 ]
Savolainen-Kopra, Carita [2 ]
Hovi, Tapani [2 ]
Simmonds, Peter [1 ]
机构
[1] Univ Edinburgh, Ctr Infect Dis, Edinburgh EH9 1QH, Midlothian, Scotland
[2] Natl Inst Hlth & Welf, FIN-00300 Helsinki, Finland
基金
英国医学研究理事会;
关键词
RESPIRATORY-TRACT INFECTIONS; 5' NONCODING REGION; HUMAN-ENTEROVIRUS-B; HUMAN PARECHOVIRUSES; CLINICAL-FEATURES; SEQUENCE-ANALYSIS; HRV-C; EVOLUTION; CHILDREN; GENOME;
D O I
10.1128/JVI.00962-10
中图分类号
Q93 [微生物学];
学科分类号
071005 ; 100705 ;
摘要
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.
引用
收藏
页码:10297 / 10310
页数:14
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