Codon Usage Bias Analysis of Bluetongue Virus Causing Livestock Infection

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.

Keywords: Culicoides; Reoviridae; bluetongue virus; codon usage bias; evolution; nucleotide composition.

FIGURE 1

Nucleotide content distribution and composition. (A) The mean frequency for A, U, G, and C composition in 50 different BTV sequences are shown. (B) The mean frequency for AU and GC composition indicates AU richness. (C) The mean values of the nucleotide content frequency at the third codon position. (D) Analysis for AU and GC composition at the third codon position suggests higher AU content than GC at the third codon position. Standard deviation was marked in the plot.

FIGURE 2

ENC–GC3 plots of 50 BTV strains: different BTV strains are shown in various color schemes. The solid line indicates the expected ENC vs. GC3 plot under the null model. We explored codon usage for all BTV strains. The plots concentrated between the 53.62 and 55.63 range suggest that codon usage bias is caused by mutational pressure.

FIGURE 3

Variation analysis in BTV genomes: based on the RSCU values, all the strains are plotted in variance plane. The first and second principal axes represent different geographical origin. Each point represents a strain and shows in different colors.

FIGURE 4

CAI of BTV to its hosts. In the plot, the x-axis represents the vector (Culicoides) and the host species (B. taurus and O. aries). The y-axis represents the CAI value. Different colors represent various species: red—B. taurus, blue—O. aries, and orange—Culicoides. To avoid the CAI value between the BTV and each host overlapping, we performed a 50% disturbance in the horizontal direction (width = 0.5, height = 0).

FIGURE 5

Correlation analysis among different indices of BTVs. The dark blue indicates a negative correlation, and the dark red indicates a positive correlation; the higher value indicates a more significant correlation.