Transmission dynamics and mutational prevalence of the novel Severe acute respiratory syndrome coronavirus‐2 Omicron Variant of Concern. Issue 5 (4th February 2022)

• Record Type: Journal Article
• Authors: Saxena, Shailendra K.; Kumar, Swatantra; Ansari, Saniya; Paweska, Janusz T.; Maurya, Vimal K.; Tripathi, Anil K.; Abdel‐Moneim, Ahmed S.
• Other Names: Luo Guangxiang (George) guestEditor.; Ly Hinh guestEditor.; Gao Shou‐Jiang guestEditor.
• Is Part Of: Journal of medical virology. Volume 94:Issue 5(2022)
• Page Start: 2160
• Page End: 2166
• Publication Date: 2022-02-04
• Subjects: COVID‐19 -- Delta -- Omicron -- B.1.1.529 -- receptor‐binding domain -- SARS‐CoV‐2 -- Variants of Concern; Virology -- Periodicals; 616
• DOI: 10.1002/jmv.27611
• Languages: English
• ISSNs: 0146-6615

Abstract

Abstract: The novel Severe acute respiratory syndrome coronavirus‐2 (SARS‐CoV‐2) variant, Omicron (PANGO lineage B.1.1.529) is being reported from all around the world. The WHO has categorized Omicron as a Variant of Concern (VOC) considering its higher transmissibility and infectivity, vaccine breakthrough cases. As of January 6, 2022, Omicron has been reported in at least 149 countries. Therefore, this study was planned to investigate the transmission dynamics and mutational prevalence of the novel SARS‐CoV‐2 Omicron variant. The transmission dynamics and Omicron SARS‐CoV‐2 divergence was studied using GISAID and Nextstrain which provides information about the genetic sequences, epidemiological, geographical, and species‐specific data of human, avian, and animal viruses. Further, the mutation prevalence in spike glycoprotein of Omicron was studied, and the frequency of the crucial mutations was compared with the other prevalent VOCs. The transmission dynamics suggest that the Omicron was first identified in South Africa and then it was reported in the United Kingdom followed by the United States and Australia. Further, our phylogenetic analysis suggests that Omicron (BA.1) was clustered distinctly from the other VOCs. In the Spike glycoprotein, the Omicron (B.1.1.529) demonstrates critical 32 amino acid changes. This study may help us to understand mutational hotspots, transmission dynamics, phylogenetic divergence, effect on testing and immunity, which shall promote the progress of the clinical application and basic research. Highlights: First report showing the transmissibility of the novel sSevere acute respiratory syndrome coronavirus‐2 (SARS‐CoV‐2) Omicron (B.1.1.529) Variant of Concern. Transmission dynamics analysis suggests that Omicron is more transmissible than other Variant of Concerns (VOCs). Omicron (BA.1) is clustered distinctly from the other VOCs in a monophyletic clade. The K417N, N440K, and G446S are the less prevalent mutations identified in the RBD of the Omicron SARS‐CoV‐2.