Key result
SARS-CoV-2 shows low codon usage bias favoring A/U endings, driven by mutation pressure and natural selection.
Why the study?
Genetic traits and evolutionary processes in SARS-CoV-2 are not fully characterized, and their roles in viral pathogenesis are largely unknown.
Bioinformatic analysis reveals that SARS-CoV-2 has a relatively low codon usage bias similar to related non-human betacoronaviruses, which may provide insights into its evolution and inform vaccine development.
Hypothesis-generating for betacoronavirus evolution; leaves open codon optimization for future vaccines.
The outbreak of coronavirus disease 2019 (COVID-19) due to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has posed significant threats to international health. The genetic traits as well as evolutionary processes in this novel coronavirus are not fully characterized, and their roles in viral pathogenesis are yet largely unknown. To get a better picture of the codon architecture of this newly emerging coronavirus, in this study we perform bioinformatic analysis, based on publicly available nucleotide sequences of SARS-CoV-2 along with those of other members of human coronaviruses as well as non-human coronaviruses in different hosts, to take a snapshot of the genome-wide codon usage pattern of SARS-CoV-2 and uncover that all over-represented codons end with A/U and this newly emerging coronavirus has a relatively low codon usage bias, which is shaped by both mutation pressure and natural selection. Additionally, there is slight variation in the codon usage pattern among the SARS-CoV-2 isolates from different geo-locations. Furthermore, the overall codon usage pattern of SARS-CoV-2 is generally similar to that of its phylogenetic relatives among non-human betacoronaviruses such as RaTG13. Taken together, we comprehensively analyze the characteristics of codon usage pattern in SARS-CoV-2 via bioinformatic approaches. The information from this research may not only be helpful to get new insights into the evolution of SARS-CoV-2, but also have potential value for developing coronavirus vaccines.
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Wei Hou (2020) studied SARS-CoV-2 (n=100). SARS-CoV-2 genome sequences vs. Other human and non-human coronaviruses was evaluated on Codon usage bias parameters (ICDI, CBI, ENC). SARS-CoV-2 exhibits a relatively low codon usage bias, with all over-represented codons ending in A/U, shaped by both mutation pressure and natural selection.
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