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Omicron variants exhibit rapid evolution with numerous spike glycoprotein mutations. Phylogenetic analysis reveals potential intermediate variants and evolutionary links between Delta and Omicron lineages, including the Centaurus variant.

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Area of Science:

  • Virology
  • Molecular Biology
  • Genetics

Background:

  • The emergence of SARS-CoV-2 variants, particularly Omicron, has raised concerns due to rapid mutation accumulation.
  • Previous variants like Delta showed a slower mutation rate compared to the Omicron lineage.

Purpose of the Study:

  • To investigate the temporal and phylogenetic relationships among SARS-CoV-2 variants, focusing on Delta and Omicron lineages.
  • To understand the evolutionary pathways and potential intermediate strains in Omicron's development.

Main Methods:

  • Structural and phylogenetic analysis of the spike glycoprotein.
  • Comparative mutation analysis between Delta and various Omicron sublineages (BA.1, BA.2, BA.2.12.1, BA.4, BA.5, and Centaurus/BA.2.75).

Main Results:

  • Omicron variants possess significantly more mutations (~30) than Delta (7) in the spike glycoprotein.
  • Phylogenetic analysis suggests common mutations link Delta and Omicron.
  • Evidence points to the existence of Omicron BA.1 and BA.2 prior to their isolation and identifies at least three potential intermediate variants.
  • Evolutionary pathways identified for BA.2.12.1, BA.4, BA.5 from BA.2, and Centaurus from BA.2.12.1.

Conclusions:

  • The study establishes a phylogenetic correlation between Delta and Omicron variants.
  • The rapid succession of Omicron subvariants suggests accelerated evolution, potentially involving multiple intermediate strains.
  • Understanding these evolutionary dynamics is crucial for tracking and responding to emerging SARS-CoV-2 variants.