Analysis of preferred codon usage in the coronavirus N genes and their implications for genome evolution and vaccine design

Abstract

The nucleocapsid (N) protein of a coronavirus plays a crucial role in virus assembly and in its RNA transcription. It is important to characterize a virus at the nucleotide level to discover the virus's genomic sequence variations and similarities relative to other viruses that could have an impact on the functions of its genes and proteins. This entails a comprehensive and comparative analysis of the viral genomes of interest for preferred nucleotides, codon bias, nucleotide changes at the 3 rd position (NT3s), synonymous codon usage and relative synonymous codon usage. In this study, the variations in the N proteins among 13 different coronaviruses (CoVs) were analysed at the nucleotide and amino acid levels in an attempt to reveal how these viruses adapt to their hosts relative to their preferred codon usage in the N genes. The results revealed that, overall, eighteen amino acids had different preferred codons and eight of these were over-biased. The N genes had a higher AT% over GC% and the values of their effective number of codons ranged from 40.43 to 53.85, indicating a slight codon bias. Neutrality plots and correlation analyses showed a very high level of GC3s/GC correlation in porcine epidemic diarrhea CoV (pedCoV), followed by Middle East respiratory syndrome-CoV (MERS CoV), porcine delta CoV (dCoV), bat CoV (bCoV) and feline CoV (fCoV) with r values 0.81, 0.68, -0.47, 0.98 and 0.58, respectively. These data implied a high rate of evolution of the CoV genomes and a strong influence of mutation on evolutionary selection in the CoV N genes. This type of genetic analysis would be useful for evaluating a virus's host adaptation, evolution and is thus of value to vaccine design strategies.

Codon Usage and Phenotypic Divergences of SARS-CoV-2 Genes

“…We calculated the nucleotide compositions of the coronavirus genomes under study (see Table 1). Previous results showed that the gene N, which follows the trend A > U > G > C [12] and the coronavirus RNA genomes are biased towards high AU content and low GC content [31]. In line with that, our results show that the nucleotide A is the most frequent base and the nucleotide composition follows the trend A > U > G > C (see Table 2).…”

“…The corresponding gene products are involved in essential viral functions. Briefly, S protein regulates viral attachment to the receptor of the target host cell [39]; E protein functions to assemble the virions and acts as an ion channel [40] M protein plays a role in viral assembly and is involved in the biosynthesis of new virus particles [41]; N protein forms the ribonucleoprotein complex with the viral RNA [12]; RdRP catalyzes viral RNA synthesis. For these five proteins the RSCU vectors in each virus of the dataset are shown in Figures 4 and A5.…”

Codon usage and evolutionary rates of the 2019-nCoV genes

“…The nucleotide content of 30 coronaviruses coding sequences are calculated. The results reveal that the nucleotide A is the most frequent base and the nucleotide frequencies are in order A >T>G>C [19]. For nCoV we note a different trend T>A>G>C, but in totally AT% is more used than GC% (See Table 3).…”

“…So, only five virall genes are classified according to their viral location and studied for each virus because the short length and insufficient codon usage diversity of the other genes might have biased the results. The corresponding gene products including S protein regulates virus attachment to the receptor of the target host cell [2]; the E protein functions to assemble the virions and acts as an ion channel [18], the M protein plays a role in virus assembly and is involved in biosynthesis of new virus particles [17] the N protein forms the ribonucleoprotein complex with the virus RNA [19]. Finally, RdRP catalyzes viral RNA syntesis.…”

Comparative genomic analysis revealed specific mutation pattern between human coronavirus SARS-CoV-2 and Bat-SARSr-CoV RaTG13

“…Different organisms, even different protein coding genes of the same species, have different frequency of codon usage (16). The RSCU bias will reveal the difference of the host source.…”