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Journal of Biomedicine and Biotechnology
Volume 2012 (2012), Article ID 460837, 7 pages
http://dx.doi.org/10.1155/2012/460837
Research Article

Patterns of Synonymous Codon Usage on Human Metapneumovirus and Its Influencing Factors

Department of Laboratory Medicine, Suzhou Municipal Hospital Affiliated Nanjing Medical University, 26 Daoqian Street, Jiangsu, Suzhou 215002, China

Received 18 July 2012; Revised 26 September 2012; Accepted 30 September 2012

Academic Editor: Sanford I. Bernstein

Copyright © 2012 Qiao Zhong et al. This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

Abstract

Human metapneumovirus (HMPV) is an important agent of acute respiratory tract infection in children, while its pathogenicity and molecular evolution are lacking. Herein, we firstly report the synonymous codon usage patterns of HMPV genome. The relative synonymous codon usage (RSCU) values, effective number of codon (ENC) values, nucleotide contents, and correlation analysis were performed among 17 available whole genome of HMPV, including different genotypes. All preferred codons in HMPV are ended with A/U nucleotide and exhibited a great association with its high proportion of these two nucleotides in their genomes. Mutation pressure rather than natural selection is the main influence factor that determines the bias of synonymous codon usage in HMPV. The complementary pattern of codon usage bias between HMPV and human cell was observed, and this phenomenon suggests that host cells might be also act as an important factor to affect the codon usage bias. Moreover, the codon usage biases in each HMPV genotypes are separated into different clades, which suggest that phylogenetic distance might involve in codon usage bias formation as well. These analyses of synonymous codon usage bias in HMPV provide more information for better understanding its evolution and pathogenicity.