Comparison of the evolutionary phylodynamic of Delta and Omicron variants of SARS-CoV-2

Abstract

Due to the inconsistency of the information regarding the evolution of the last two waves caused by the Delta and Omicron variants, we are attempting to provide a phylodynamic analysis. We used the nucleotide sequences of the Delta (n = 89) and Omicron (n = 74) variants recorded in the GISAID database to perform an analysis based on the contemporary model of the birth-death horizon. An average rate of evolution of 3.677 × 10− 4 subs /site/year (range,1.311× 10− 4−6.144×10− 4 ) for the DELTA variant, this gives an estimated mean of tMRCA corresponding to the root of the tree dated at 43.5 days. While for OMICRON a mean evolutionary rate of 3.898×10 − 3 subs/site/year (range,2.686×10− 3 − 5.102×10− 3) gave an estimated mean of tMRCA corresponding to the root of the tree dated at 26.4 days. The median of Re for the Indian DELTA = 1.81 (range, 0.196–3.94), and increased to 3.837 ≈ 4 on March 30, 2021. While for the South African OMICRON Re = 0.97 (range,0.41–1.54), and rose to 9.59 ≈ 9 on December 14, 2021. The average doubling times of the two waves are estimated respectively at 9 days for the DELTA variant and at 3 days for the OMICRON variant. The spread of the OMICRON pandemic is almost three times faster than that of the DELTA. The mean doubling times of the two waves are 9 days for the DELTA variant and 3 days for the OMICRON variant, respectively. As a result, the OMICRON pandemic is spreading nearly three times faster than the DELTA.

Spatiotemporal Evolution of SARS-CoV-2 Alpha and Delta Variants during a Large Nationwide Outbreak in Vietnam, 2021

“…The role of vaccination in shaping the evolution of SARS-CoV-2 merits further research. Finally, our estimated evolutionary rate of AY.57 lineage was within the range of previously estimated values for the Delta variant [36,40].…”

“…Our estimated dN/dS ratio for entire coding region suggested that the evolution of AY.57 lineage was driven by a weak purifying selection, although this varied across the virus genome, with ORF1b, ORF3a, E gene and ORF7a exhibiting a positive selection. Of note, a recent report showed that the vaccines had played a role in selective adaptation of SARS-CoV-2 Delta variant [39]. As a consequence, different mutation profiles were recorded between vaccine breakthrough infection and non-breakthrough infection groups [39].…”

“…Of note, a recent report showed that the vaccines had played a role in selective adaptation of SARS-CoV-2 Delta variant [39]. As a consequence, different mutation profiles were recorded between vaccine breakthrough infection and non-breakthrough infection groups [39]. The role of vaccination in shaping the evolution of SARS-CoV-2 merits further research.…”

Sequence analysis of the Spike, nsp12 (RNA-dependent RNA polymerase), nsp3 (PLpro), and nsp5 (3CLpro) genes reveals a distinct evolutionary pattern of SARS-CoV-2 variants circulating in Yogyakarta and Central Java provinces, Indonesia

“…3.898 x 10 -3 subs/site/year (range: 2.686 x 10 -3 to 5.102 x 10 -3 ) and 3.677 × 10 -4 subs/site/year (range: 1.311 x 10 -4 to 6.144 x 10 -4 ) for the Omicron and Delta variants, respectively. 61 Alterations in amino acids that decrease viral fitness are often eliminated by negative selection, while changes that improve viral fitness are retained by positive selection. On the other hand, amino-acid alterations are regarded as "neutral" when they have no effects on viral fitness.…”