Analysis of Synonymous Codon Usage Bias in Flaviviridae Virus

Abstract

Background. Flaviviridae viruses are single-stranded, positive-sense RNA viruses, which threat human constantly mediated by mosquitoes, ticks, and sandflies. Considering the recent increase in the prevalence of the family virus and its risk potential, we investigated the codon usage pattern to understand its evolutionary processes and provide some useful data to develop the medications for most of Flaviviridae viruses. Results. The overall extent of codon usage bias in 65 Flaviviridae viruses is low with the average value of GC contents being 50.5% and the highest value being 55.9%; the lowest value is 40.2%. ENC values of Flaviviridae virus genes vary from 48.75 to 57.83 with a mean value of 55.56. U- and A-ended codons are preferred in the Flaviviridae virus. Correlation analysis shows that the positive correlation between ENC value and GC content at the third nucleotide positions was significant in this family virus. The result of analysis of ENC, neutrality plot analysis, and correlation analysis revealed that codon usage bias of all the viruses was affected mainly by natural selection. Meanwhile, according to correspondence analysis (CoA) based on RSCU and phylogenetic analysis, the Flaviviridae viruses mainly are made up of two groups, Group I (Yellow fever virus, Apoi virus, Tembusu virus, Dengue virus 1, and others) and Group II (West Nile virus lineage 2, Japanese encephalitis virus, Usutu virus, Kedougou virus, and others). Conclusions. All in, the bias of codon usage pattern is affected not only by compositional constraints but also by natural selection. Phylogenetic analysis also illustrates that codon usage bias of virus can serve as an effective means of evolutionary classification in Flaviviridae virus.

Evolution of codon usage in 2019-new coronavirus causing human infection

“…That makes it clear that possible SARS-Cov-2 transmission in humans is based on its vector (bat). Models of the infection of animals have indicated the substantial constraints on the evolution of arbovirus [43][44][45][46]. Consistent with the earlier reports, our results have clearly showed the correlation of overall SARS-Cov-2 codon usage patterns with bat and not with human.…”

Genome codon bias analysis of dengue virus type 1

“…The content of A/U is higher than G/C; the RSCU analysis indicates that DENV-1 prefers A/U-ended codons, especially A-ended codons (Roy et al, 2019). This is similar to studies on codon preference of Flaviviridae viruses (Yao et al, 2019). And It is also similar to studies on codon preference of other RNA viruses such as Ebola virus (Cristina et al, 2015;Kustin and Stern, 2020).…”

“…Analysis of the ENC-GC3s plots indicated that the genomic genes of DENV-1 were more affected by natural selection, which is consistent with the codon preference of Flaviviridae viruses (Yao et al, 2019). Results of the neutrality analysis validated the results derived from ENC-GC3 plots and further suggested that natural selection pressures had a greater influence on the spread and mutation of DENV-1.…”

Deciphering the co-adaptation of codon usage between respiratory coronaviruses and their human host uncovers candidate therapeutics for COVID-19

“…Preliminary comparative genomics studies suggested the divergence between SARS-CoV-2 and other CoVs, namely SARS-CoV and MERS-CoV ( Wu et al, 2020 ). Codon usage bias, the differential use of codons encoding a given amino acid, is vital for examining the expressivity and the adaptation of exogenous viral genes to the hosts ( Deb et al, 2020 ; Oldfield et al, 2020 ; Yao et al, 2019 ). Codon usage can play a significant role in modulating the expression of viral genes via codon optimization ( Morgunov and Babu, 2014 ; Victor et al, 2019 ; Zalucki et al, 2009 ).…”