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Mapping codon usage of the translation initiation region in porcine reproductive and respiratory syndrome virus genome

Jun-hong Su1, Xiao-xia Ma2, Ya-li He3, Ji-dong Li14, Xu-sheng Ma1, Yong-xi Dou1, Xue-nong Luo1 and Xue-peng Cai1*

Author Affiliations

1 State Key Laboratory of Veterinary Etiological Biology, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, 730046, PR China

2 College of Life Science and Engineering, Northwest University for Nationalities, Lanzhou, 730030, PR China

3 The School of Public Health, Lanzhou University, Lanzhou, 730000, RP China

4 School of Agriculture, Ningxia University, Yinchuan, 750021, RP China

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Virology Journal 2011, 8:476  doi:10.1186/1743-422X-8-476

Published: 21 October 2011



Porcine reproductive and respitatory syndrome virus (PRRSV) is a recently emerged pathogen and severely affects swine populations worldwide. The replication of PRRSV is tightly controlled by viral gene expression and the codon usage of translation initiation region within each gene could potentially regulate the translation rate. Therefore, a better understanding of the codon usage pattern of the initiation translation region would shed light on the regulation of PRRSV gene expression.


In this study, the codon usage in the translation initiation region and in the whole coding sequence was compared in PRRSV ORF1a and ORFs2-7. To investigate the potential role of codon usage in affecting the translation initiation rate, we established a codon usage model for PRRSV translation initiation region. We observed that some non-preferential codons are preferentially used in the translation initiation region in particular ORFs. Although some positions vary with codons, they intend to use codons with negative CUB. Furthermore, our model of codon usage showed that the conserved pattern of CUB is not directly consensus with the conserved sequence, but shaped under the translation selection.


The non-variation pattern with negative CUB in the PRRSV translation initiation region scanned by ribosomes is considered the rate-limiting step in the translation process.

PRRSV; codon usage bias; translation initiation region; translation efficiency; translation selection