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Scientific article
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English

New complete genome sequences of human rhinoviruses shed light on their phylogeny and genomic features

Contributors

Tapparel, Caroline; Junier, Thomas; Gerlach, Daniel; Cordey, Samuel; Van Belle, Sandra; Perrin, Luc; Zdobnov, Evgeny; Kaiser, Laurent

Published in

BMC genomics, vol. 8, 224

Publication date

2007

Abstract

BACKGROUND: Human rhinoviruses (HRV), the most frequent cause of respiratory infections, include 99 different serotypes segregating into two species, A and B. Rhinoviruses share extensive genomic sequence similarity with enteroviruses and both are part of the picornavirus family. Nevertheless they differ significantly at the phenotypic level. The lack of HRV full-length genome sequences and the absence of analysis comparing picornaviruses at the whole genome level limit our knowledge of the genomic features supporting these differences. RESULTS: Here we report complete genome sequences of 12 HRV-A and HRV-B serotypes, more than doubling the current number of available HRV sequences. The whole-genome maximum-likelihood phylogenetic analysis suggests that HRV-B and human enteroviruses (HEV) diverged from the last common ancestor after their separation from HRV-A. On the other hand, compared to HEV, HRV-B are more related to HRV-A in the capsid and 3B-C regions. We also identified the presence of a 2C cis-acting replication element (cre) in HRV-B that is not present in HRV-A, and that had been previously characterized only in HEV. In contrast to HEV viruses, HRV-A and HRV-B share also markedly lower GC content along the whole genome length. CONCLUSION: Our findings provide basis to speculate about both the biological similarities and the differences (e.g. tissue tropism, temperature adaptation or acid lability) of these three groups of viruses.

Keywords

  • Base Composition
  • Base Sequence
  • Chromosome Mapping
  • Genome, Viral
  • Humans
  • Molecular Sequence Data
  • Nucleic Acid Conformation
  • Phylogeny
  • Regulatory Elements, Transcriptional
  • Rhinovirus/ genetics
  • Sequence Analysis, DNA
  • Sequence Analysis, RNA
  • Sequence Homology, Amino Acid
  • Sequence Homology, Nucleic Acid
  • Serotyping
  • Untranslated Regions/genetics

UNIGE affiliation entities

UNIGE research groups

Citation (ISO format)

TAPPAREL, Caroline et al. New complete genome sequences of human rhinoviruses shed light on their phylogeny and genomic features. In: BMC genomics, 2007, vol. 8, p. 224. doi: 10.1186/1471-2164-8-224

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Additional URL for this publication

http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1949831/pdf/1471-2164-8-224.pdf

Journal ISSN

1471-2164
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1170downloads

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