An evolutionary insight into Severe Acute Respiratory Syndrome Coronavirus 2 Omicron variant of concern.

•A comprehensive phylogenetic analysis of SARS-CoV-2 Omicron variants was performed.•Codon usage in variants of concern (VOCs) Spike genes is linked to strain genotype.•Omicron belongs to a complete different genetic lineage from previous variants.•Omicron strains evolved from ancestors that existed around May 15th, 2020.•A rate of evolution of 5.61 × 10−4 substitutions/site/year was found for Omicron VOC.•Spike genes have suitable genetic information for VOCs assignment specific genotypes.