Omicron variant genome evolution and phylogenetics

Journal of Medical Virology - Tập 94 Số 4 - Trang 1627-1632 - 2022
Mahmoud Kandeel1,2, Maged E. Mohamed3,4, Hany M. Abd El‐Lateef5,6, Katharigatta N. Venugopala7,3, Hossam S. El‐Beltagi8,9
1Department of Biomedical Sciences, College of Veterinary Medicine, King Faisal University, Al-Hofuf, Saudi Arabia
2Department of Pharmacology, Faculty of Veterinary Medicine, Kafrelshikh University, Kafrelshikh, Egypt
3Department of Pharmaceutical Sciences, College of Clinical Pharmacy, King Faisal University, Al-Ahsa, Saudi Arabia
4Department of Pharmacognosy, College of Pharmacy, Zagazig University, Zagazig, Egypt
5Department of Chemistry, College of Science, King Faisal University, Al-Ahsa, Saudi Arabia
6Department of Chemistry, Faculty of Science, Sohag University, Sohag, Egypt
7Department of Biotechnology and Food Science, Faculty of Applied Sciences, Durban University of Technology, Durban, South Africa
8Agricultural Biotechnology Department, College of Agriculture and Food Sciences, King Faisal University, Al-Ahsa, Saudi Arabia
9Biochemistry Department, Faculty of Agriculture, Cairo University, Giza, Egypt

Tóm tắt

AbstractFollowing the discovery of the SARS‐CoV‐2 Omicron variant (B.1.1.529), the global COVID‐19 outbreak has resurfaced after appearing to be relentlessly spreading over the past 2 years. This new variant showed marked degree of mutation, compared with the previous SARS‐CoV‐2 variants. This study investigates the evolutionary links between Omicron variant and recently emerged SARS‐CoV‐2 variants. The entire genome sequences of SARS‐CoV‐2 variants were obtained, aligned using Clustal Omega, pairwise comparison was computed, differences, identity percent, gaps, and mutations were noted, and the identity matrix was generated. The phylogenetics of Omicron variants were determined using a variety of evolutionary substitution models. The ultrametric and metric clustering methods, such as UPGMA and neighbor‐joining (NJ), using nucleotide substitution models that allowed the inclusion of nucleotide transitions and transversions as Kimura 80 models, revealed that the Omicron variant forms a new monophyletic clade that is distant from other SARS‐CoV‐2 variants. In contrast, the NJ method using a basic nucleotide substitution model such as Jukes–Cantor revealed a close relationship between the Omicron variant and the recently evolved Alpha variant. Based on the percentage of sequence identity, the closest variants were in the following order: Omicron, Alpha, Gamma, Delta, Beta, Mu, and then the SARS‐CoV‐2 USA isolate. A genome alignment with other variants indicated the greatest number of gaps in the Omicron variant's genome ranging from 43 to 63 gaps. It is possible, given their close relationship to the Alpha variety, that Omicron has been around for much longer than predicted, even though they created a separate monophyletic group. Sequencing initiatives in a systematic and comprehensive manner is highly recommended to study the evolution and mutations of the virus.

Từ khóa


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Thông tin xuất bản

Journal of Medical Virology

Tập 94 Số 4

1627-1632

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