Genome‐wide analysis of synonymous codon usage in Huaiyangshan virus and other bunyaviruses

Abstract

Huaiyangshan virus (HYSV) is a newly discovered bunyavirus, which is transmitted by ticks and causes hemorrhagic fever-like illness in human. The interplay of codon usage among viruses and their hosts is expected to affect viral survival, evasion from host's immune system and evolution. However, little is known about the codon usage in HYSV genome. In the present study, we analyzed synonymous codon usage in 120 available full-length HYSV sequences and performed a comparative analysis of synonymous codon usage patterns in HYSV and 42 other bunyaviruses. The relative synonymous codon usage (RSCU) analysis showed that the preferred synonymous codons were G/C-ended. A comparative analysis of RSCU between HYSV and its hosts reflected that codon usage patterns of HYSV were mostly coincident with that of its hosts. Our data suggested that although mutational bias dominated codon usage, patterns of codon usage in HYSV were also under the influence of nature selection. Phylogenetic analysis based on RSCU values across different HYSV strains and 42 other bunyaviruses suggested that codon usage pattern in HYSV was the most similar with that of Uukuniemi virus among these bunyaviruses and that viruses belonged to Phlebovirus showed a diversity of codon usage patterns.

Effects of Arbovirus Multi-Host Life Cycles on Dinucleotide and Codon Usage Patterns

“…However, as described earlier in this review, tRNA expression differs during immune responses, based on nutrition, and between species [59,68,71,80]. Therefore, for many RNA viruses, and arboviruses in particular, codon bias does not correlate strongly with host codon use, this is true in Flaviviruses [9,76,77,81], Huaiyangshan (Bunyavirus) [82], and VSV (Rhabdovirus) [83]. For viruses infecting arthropods, the mosquito underabundant tRNA genes TGG, CCT, and TGT, all correspond with normal, or even elevated, representation of CCU, AGG, and ACA codons in insect infecting flaviviruses [9,60] (Figure 2A).…”

Synonymous codon usage of genes in polymerase complex of Newcastle disease virus

“…Factors like natural selection, mutational pressure, translational efficiency, and compositional constraints mostly influence the synonymous codon usage bias within an organism . Codon usage bias has been explored in order to understand the evolutionary biology of different viruses . In NDV variation of synonymous codon usage pattern is gene function and geography specific but not host specific .…”