Document Type
Article
Publication Date
2022
Keywords
COVID-19, Sars-cov-2 Omicron, Tmrca (Time to The Most Recent Common Ancestor), Evolutionary Rate, Mutational Profiling, Selection Pressure
Digital Object Identifier (DOI)
https://doi.org/10.3390/v14122764
Abstract
The ongoing evolution of severe acute respiratory syndrome-coronavirus-2 (SARS-CoV-2) has resulted in the recent emergence of a highly divergent variant of concern (VOC) defined as Omicron or B.1.1.529. This VOC is of particular concern because it has the potential to evade most therapeutic antibodies and has undergone a sustained genetic evolution, resulting in the emergence of five distinct sub-lineages. However, the evolutionary dynamics of the initially identified Omicron BA.1 and BA.2 sub-lineages remain poorly understood. Herein, we combined Bayesian phylogenetic analysis, mutational profiling, and selection pressure analysis to track the virus’s genetic changes that drive the early evolutionary dynamics of the Omicron. Based on the Omicron dataset chosen for the improved temporal signals and sampled globally between November 2021 and January 2022, the most recent common ancestor (tMRCA) and substitution rates for BA.1 were estimated to be that of 18 September 2021 (95% highest posterior density (HPD), 4 August–22 October 2021) and 1.435 × 10−3 (95% HPD = 1.021 × 10−3 − 1.869 × 10−3) substitution/site/year, respectively, whereas 3 November 2021 (95% highest posterior density (HPD) 26 September–28 November 2021) and 1.074 × 10−3 (95% HPD = 6.444 × 10−4 − 1.586 × 10−3) substitution/site/year were estimated for the BA.2 sub-lineage. The findings of this study suggest that the Omicron BA.1 and BA.2 sub-lineages originated independently and evolved over time. Furthermore, we identified multiple sites in the spike protein undergoing continued diversifying selection that may alter the neutralization profile of BA.1. This study sheds light on the ongoing global genomic surveillance and Bayesian molecular dating analyses to better understand the evolutionary dynamics of the virus and, as a result, mitigate the impact of emerging variants on public health.
Rights Information
This work is licensed under a Creative Commons Attribution 4.0 License.
Was this content written or created while at USF?
Yes
Citation / Publisher Attribution
Viruses, v. 14, issue 12, art. 2764
Scholar Commons Citation
Kumar, Naveen; Kaushik, Rahul; Singh, Ashutosh; Uversky, Vladimir N.; Zhang, Kam Y. J.; Sahu, Upasana; Bhatia, Sandeep; and Sanyal, Aniket, "Bayesian Molecular Dating Analyses Combined with Mutational Profiling Suggest an Independent Origin and Evolution of SARS-CoV-2 Omicron BA.1 and BA.2 Sub-Lineages" (2022). Molecular Medicine Faculty Publications. 1030.
https://digitalcommons.usf.edu/mme_facpub/1030
