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Open Access Research article

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

Caroline Tapparel1*, Thomas Junier2, Daniel Gerlach2, Samuel Cordey1, Sandra Van Belle1, Luc Perrin1, Evgeny M Zdobnov234 and Laurent Kaiser1

Author Affiliations

1 Central Laboratory of Virology, Division of Infectious Diseases, University of Geneva Hospitals, 24 Rue Micheli-du-Crest, 1211 Geneva 14, Switzerland

2 Department of Genetic Medicine and Development, University of Geneva Medical School, 1 Rue Michel-Servet, 1211 Geneva 14, Switzerland

3 Swiss Institute of Bioinformatics, 1 Rue Michel-Servet, 1211 Geneva 14, Switzerland

4 Imperial College London, South Kensington Campus, SW7 2AZ London, UK

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BMC Genomics 2007, 8:224  doi:10.1186/1471-2164-8-224

Published: 10 July 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.