Characterization of codon usage pattern in SARS-CoV-2
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Characterization of codon usage pattern in SARS-CoV-2 Wei Hou
Abstract 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 SARSCoV-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. Keywords: COVID-19, Coronaviruses, SARS-CoV-2, Codon usage pattern
Introduction Coronaviruses (CoVs) belong to the family Coronavirdiae comprises large, single, positive-sense singlestranded RNA viruses including four genera of CoVs, namely, Alphacoronavirus, Betacoronavirus, Deltacoronavirus, and Gammacoronavirus [1]. Several coronavirus species were extensively known to cause human disease [1–3], including two alphacoronaviruses (HCoV-229E, HCoV-NL63) and four betacoronaviruses (HCoV-OC43, HCoV-HKU, sereve acute respiratory syndrome coronavirus SARS-CoV and Middle East respiratory syndrome coronavirus MERS-CoV). Very recently, the outbreak of coronavirus disease 2019 (COVID-19) due to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) Correspondence: [email protected] Tianjin Second People’s Hospital and Tianjin Institute of Hepatology, 7 Sudi South Road, Nankai District, Tianjin 300192, China
has posed significant threats to international health [4– 9]. However, the genetic traits as well as evolutionary processes in this newly emerging coronavirus are not fully characterized, and their roles in viral pathogenesis are yet largely unknown. To further explore the codon usage pattern of SARS-CoV-2 to get a better picture of the codon architecture of this novel coronavirus, genomic sequences of the SARS-CoV-2 and other representative coronaviruses were analyzed via bioinformatic approaches.
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