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Mutation and codon bias analysis of the spike protein of Omicron, the recent variant of SARS-CoV-2.
Lu, Yunbiao; Wang, Weixiu; Liu, Hao; Li, Yue; Yan, Ge; Franzo, Giovanni; Dai, Jianjun; He, Wan-Ting.
Afiliación
  • Lu Y; School of Pharmacy, China Pharmaceutical University, 639 Longmian Avenue, Nanjing 211198, People's Republic of China.
  • Wang W; School of Pharmacy, China Pharmaceutical University, 639 Longmian Avenue, Nanjing 211198, People's Republic of China.
  • Liu H; School of Pharmacy, China Pharmaceutical University, 639 Longmian Avenue, Nanjing 211198, People's Republic of China.
  • Li Y; School of Pharmacy, China Pharmaceutical University, 639 Longmian Avenue, Nanjing 211198, People's Republic of China.
  • Yan G; School of Pharmacy, China Pharmaceutical University, 639 Longmian Avenue, Nanjing 211198, People's Republic of China.
  • Franzo G; Department of Animal Medicine, Production and Health (MAPS), University of Padua, Viale dell'Università 16, Legnaro 35020, PD, Italy.
  • Dai J; School of Pharmacy, China Pharmaceutical University, 639 Longmian Avenue, Nanjing 211198, People's Republic of China. Electronic address: jjdai@cpu.edu.cn.
  • He WT; School of Pharmacy, China Pharmaceutical University, 639 Longmian Avenue, Nanjing 211198, People's Republic of China. Electronic address: hewt@cpu.edu.cn.
Int J Biol Macromol ; 250: 126080, 2023 Oct 01.
Article en En | MEDLINE | ID: mdl-37536405
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) Omicron variant is a heavily mutated virus and designated as a variant of concern. To investigate the codon usage pattern of this new variant, we performed mutation and codon bias analysis for Omicron as well as for its sub-lineages BA.1 and BA.2 and compared them with the original SARS-CoV-2 and the Delta variant sequences obtained in this study. Our results indicate that the sub-lineage BA.1 and BA.2 have up to 23 sites of difference on the spike protein, which have minimal impact on function. The Omicron variant and its sub-lineages have similar codon usage patterns and A/U ending codons appear to be preferred over G/C ending codons. The Omicron has a lower degree of codon usage bias in spite of evidence that natural selection, mutation pressure and dinucleotide abundance shape the codon usage bias of Omicron, with natural selection being more significant on BA.2 than the other sub-lineages of Omicron. The codon usage pattern of Omicron variant that we explored provides valid information for a clearer understanding of Omicron and its sub-lineages, which could find application in vaccine development and optimization.
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Texto completo: 1 Colección: 01-internacional Base de datos: MEDLINE Asunto principal: Uso de Codones / COVID-19 Límite: Humans Idioma: En Revista: Int J Biol Macromol Año: 2023 Tipo del documento: Article Pais de publicación: Países Bajos

Texto completo: 1 Colección: 01-internacional Base de datos: MEDLINE Asunto principal: Uso de Codones / COVID-19 Límite: Humans Idioma: En Revista: Int J Biol Macromol Año: 2023 Tipo del documento: Article Pais de publicación: Países Bajos