{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,5,8]],"date-time":"2026-05-08T16:12:34Z","timestamp":1778256754058,"version":"3.51.4"},"reference-count":88,"publisher":"MDPI AG","issue":"12","license":[{"start":{"date-parts":[[2022,12,12]],"date-time":"2022-12-12T00:00:00Z","timestamp":1670803200000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"Indian Council of Agricultural Research (ICAR)\u2014National Agricultural Science Fund","award":["NASF\/ABA-8028\/2020\u201321"],"award-info":[{"award-number":["NASF\/ABA-8028\/2020\u201321"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Viruses"],"abstract":"<jats:p>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\u2019s 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\u201322 October 2021) and 1.435 \u00d7 10\u22123 (95% HPD\u2009 = \u20091.021 \u00d7 10\u22123 \u2212 1.869 \u00d7 10\u22123) substitution\/site\/year, respectively, whereas 3 November 2021 (95% highest posterior density (HPD) 26 September\u201328 November 2021) and 1.074 \u00d7 10\u22123 (95% HPD\u2009 = \u20096.444 \u00d7 10\u22124 \u2212 1.586 \u00d7 10\u22123) 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.<\/jats:p>","DOI":"10.3390\/v14122764","type":"journal-article","created":{"date-parts":[[2022,12,12]],"date-time":"2022-12-12T03:36:09Z","timestamp":1670816169000},"page":"2764","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":9,"title":["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"],"prefix":"10.3390","volume":"14","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-3326-5465","authenticated-orcid":false,"given":"Naveen","family":"Kumar","sequence":"first","affiliation":[{"name":"Diagnostics & Vaccines Group, ICAR-National Institute of High Security Animal Diseases, Bhopal 462022, India"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-6489-6913","authenticated-orcid":false,"given":"Rahul","family":"Kaushik","sequence":"additional","affiliation":[{"name":"Biotechnology Research Center, Technology Innovation Institute, Abu Dhabi P.O. Box 3692, United Arab Emirates"},{"name":"Center for Biosystems Dynamics Research, Laboratory for Structural Bioinformatics, Yokohama 230-0045, Japan"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Ashutosh","family":"Singh","sequence":"additional","affiliation":[{"name":"Diagnostics & Vaccines Group, ICAR-National Institute of High Security Animal Diseases, Bhopal 462022, India"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-4037-5857","authenticated-orcid":false,"given":"Vladimir N.","family":"Uversky","sequence":"additional","affiliation":[{"name":"Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, FL 33612, USA"},{"name":"Federal Research Center \u2018Pushchino, Scientific Center for Biological Research of the Russian Academy of Sciences\u2019, Institute for Biological Instrumentation of the Russian Academy of Sciences, 142290 Pushchino, Russia"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-9282-8045","authenticated-orcid":false,"given":"Kam Y. J.","family":"Zhang","sequence":"additional","affiliation":[{"name":"Center for Biosystems Dynamics Research, Laboratory for Structural Bioinformatics, Yokohama 230-0045, Japan"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Upasana","family":"Sahu","sequence":"additional","affiliation":[{"name":"Diagnostics & Vaccines Group, ICAR-National Institute of High Security Animal Diseases, Bhopal 462022, India"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Sandeep","family":"Bhatia","sequence":"additional","affiliation":[{"name":"Diagnostics & Vaccines Group, ICAR-National Institute of High Security Animal Diseases, Bhopal 462022, India"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Aniket","family":"Sanyal","sequence":"additional","affiliation":[{"name":"Diagnostics & Vaccines Group, ICAR-National Institute of High Security Animal Diseases, Bhopal 462022, India"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"1968","published-online":{"date-parts":[[2022,12,12]]},"reference":[{"key":"ref_1","unstructured":"GISIAD (2022, October 21). 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