Tajima D test accurately forecasts Omicron / COVID-19 outbreak

On 26 November 2021, the World Health Organization designated the SARS-CoV-2 variant B.1.1.529, Omicron, a variant of concern. However, the phylogenetic and evolutionary dynamics of this variant remain unclear. An analysis of the 131 Omicron variant sequences from November 9 to November 28, 2021 reveals that variants have diverged into at least 6 major subgroups. 86.3% of the cases have an insertion at amino acid 214 (INS214EPE) of the spike protein. Neutrality analysis of DH (−2.814, p <0.001) and Zeng’s E (0.0583, p =1.0) tests suggested that directional selection was the major driving force of Omicron variant evolution. The synonymous ( D _syn ) and nonsynonymous ( D _nonsyn ) polymorphisms of the Omicron variant spike gene were estimated with Tajima’s D statistic to eliminate homogenous effects. Both D ratio ( D _nonsyn / D _syn , 1.57) and Δ D ( D _syn - D _nonsyn , 0.63) indicate that purifying selection operates at present. The low nucleotide diversity (0.00008) and Tajima D value (−2.709, p <0.001) also confirms that Omicron variants had already spread in human population for more than the 6 weeks than has been reported. These results, along with our previous analysis of Delta and Lambda variants, also supports the validity of the Tajima’s D test score, with a threshold value as −2.50, as an accurate predictor of new COVID-19 outbreaks.