Viruses have to exploit host transcription and translation mechanisms to replicate in a hostile host cellular environment, and therefore, it is likely that the infected host may impose pressure on viral evolution. In this study, we investigated differences in codon usage preferences among the highly mutable single strain RNA viruses which infect vertebrate or invertebrate hosts, respectively. We incorporate principal component analysis (PCA) and k-mean methods to clustering viruses infected with different type of hosts. The relative synonymous codon usage (RSCU) indices of all genes in 32 RNA viruses were calculated, and the correlation of the RSCU indices among different viruses was analyzed by the PCA. Our results show a positive correlation in codon usage preferences among viruses that target the same host category. Results of k-means clustering analysis further confirmed the statistical significance of this study, demonstrating that viruses infecting vertebrate hosts have different codon usage preferences to those of invertebrate viruses. Based on the analysis of the effective number of codons (ENC) in relation to the GC-content at the synonymous third codon position (GC3s), we further identified that mutational pressure was the dominant evolution driving force in making the different codon usage preferences. This study suggests a new and effective way to characterize host-dependent RNA viruses based on the codon usage pattern.

This study proposes a new and effective way to gain a better understanding of the features of the S-OIV genome and evolutionary processes based on the codon usage pattern. It is useful to trace influenza viral origins and cross-species virus transmission.

In view of the rising prevalence of dengue virus and mixing of host and vector populations, complete full-length sequence determination of dengue strains isolated from different epidemic areas is important for the study of virus evolution, pathogenicity, vaccine efficiency and diagnosis. Based on the genomic analysis of 51 complete dengue virus sequences, all of which cocirculated in Thailand between 1974 and 2001, we report here the occurrence of homologous recombination in the NS5 nonstructural gene region of dengue virus type 2 (DENV-2) strains. In order to analyze those 51 virus sequences at one time, we chose to use a highly sensitive recombination detection program called RDP. When RDP detects a possible recombination event, further bootscanning and phylogenetic tree analyses are applied to these candidate sequences to identify this recombination event. We found that within the DENV-2 subfamily, the strain ThNH63/93 is the evolutionary product of a recombination event between ThNH62/93 and ThD2_0284_90 strains. The strain ThNH62/93 was identified as the major parent, while the strain ThD2_0284_90 was the minor parent. The recombination site was determined to localize between positions 7967 (±36 nt) and 8283 (±36 nt) with a significance level of p < 0.001. Our results showed, for the first time, that an intraserotype recombination event occurred between DENV-2 strains in the nonstructural gene region; by contrast, an interserotype recombination between different serotypes of dengue strains was not identified. This study thus supports the theory that homologous recombination plays a key role in dengue virus evolution.