Abstract
Bluetongue virus (BTV) is a double-stranded RNA virus with multiple segments and belongs to the genus Orbivirus within the family Reoviridae. BTV is spread to livestock through its dominant vector, biting midges of genus Culicoides. Although great progress has been made in genomic analyses, it is not fully understood how BTVs adapt to their hosts and evade the host’s immune systems. In this study, we retrieved BTV genome sequences from the National Center for Biotechnology Information (NCBI) database and performed a comprehensive research to explore the codon usage patterns in 50 BTV strains. We used bioinformatic approaches to calculate the relative synonymous codon usage (RSCU), codon adaptation index (CAI), effective number of codons (ENC), and other indices. The results indicated that most of the overpreferred codons had A-endings, which revealed that mutational pressure was the major force shaping codon usage patterns in BTV. However, the influence of natural selection and geographical factors cannot be ignored on viral codon usage bias. Based on the RSCU values, we performed a comparative analysis between BTVs and their hosts, suggesting that BTVs were inclined to evolve their codon usage patterns that were comparable to those of their hosts. Such findings will be conducive to understanding the elements that contribute to viral evolution and adaptation to hosts.
Highlights
Bluetongue virus (BTV) causes a vector-borne viral disease [bluetongue (BT)], is an economically important virus of ruminants that belongs to the genus Orbivirus of the Reoviridae family, and has a genome that consists of multiple segments of double-stranded RNA
The nucleotide contents of the BTV complete coding sequences were measured to evaluate the impact of nucleotide composition on the codon usage pattern
To further explore the nucleotide composition analysis of BTVs, mean values were considered for each codon at the third position of synonymous codons (A3, U3, G3, and C3)
Summary
Bluetongue virus (BTV) causes a vector-borne viral disease [bluetongue (BT)], is an economically important virus of ruminants that belongs to the genus Orbivirus of the Reoviridae family, and has a genome that consists of multiple segments of double-stranded RNA. BTV is widely distributed and has caused serious losses to countries worldwide. It was first reported in South Africa and later named by Huntcheon (Mehlhorn et al, 2007). Through analysis and comparison of capsid and outer coat protein nucleotide sequences, it is possible to explore the phylogenetic relationship of BTV serotypes using VP2 genes as a determinant (Gould and Pritchard, 1990). In 1999, sequence and phylogenetic analyses of the VP2 gene of BTV strains from China, Australia, South Africa, and the United States indicated that these viruses were grouped on the basis of serotype (Bonneau et al, 1999). Multiple BTV vaccines could limit the severity of viral infection, they could not completely prevent the disease
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