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
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 antibodi...
Saved in:
Published in | Viruses Vol. 14; no. 12; p. 2764 |
---|---|
Main Authors | , , , , , , , |
Format | Journal Article |
Language | English |
Published |
Switzerland
MDPI AG
01.12.2022
MDPI |
Subjects | |
Online Access | Get full text |
Cover
Loading…
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
(95% HPD = 1.021 × 10
- 1.869 × 10
) substitution/site/year, respectively, whereas 3 November 2021 (95% highest posterior density (HPD) 26 September-28 November 2021) and 1.074 × 10
(95% HPD = 6.444 × 10
- 1.586 × 10
) 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. |
---|---|
AbstractList | 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. 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. 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.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. 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 (95% HPD = 1.021 × 10 - 1.869 × 10 ) substitution/site/year, respectively, whereas 3 November 2021 (95% highest posterior density (HPD) 26 September-28 November 2021) and 1.074 × 10 (95% HPD = 6.444 × 10 - 1.586 × 10 ) 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. 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[sup.−3] (95% HPD = 1.021 × 10[sup.−3] − 1.869 × 10[sup.−3] ) substitution/site/year, respectively, whereas 3 November 2021 (95% highest posterior density (HPD) 26 September–28 November 2021) and 1.074 × 10[sup.−3] (95% HPD = 6.444 × 10[sup.−4] − 1.586 × 10[sup.−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. |
Audience | Academic |
Author | Sahu, Upasana Singh, Ashutosh Sanyal, Aniket Kaushik, Rahul Bhatia, Sandeep Kumar, Naveen Zhang, Kam Y J Uversky, Vladimir N |
AuthorAffiliation | 1 Diagnostics & Vaccines Group, ICAR-National Institute of High Security Animal Diseases, Bhopal 462022, India 3 Center for Biosystems Dynamics Research, Laboratory for Structural Bioinformatics, Yokohama 230-0045, Japan 4 Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, FL 33612, USA 2 Biotechnology Research Center, Technology Innovation Institute, Abu Dhabi P.O. Box 3692, United Arab Emirates 5 Federal Research Center ‘Pushchino, Scientific Center for Biological Research of the Russian Academy of Sciences’, Institute for Biological Instrumentation of the Russian Academy of Sciences, 142290 Pushchino, Russia |
AuthorAffiliation_xml | – name: 1 Diagnostics & Vaccines Group, ICAR-National Institute of High Security Animal Diseases, Bhopal 462022, India – name: 5 Federal Research Center ‘Pushchino, Scientific Center for Biological Research of the Russian Academy of Sciences’, Institute for Biological Instrumentation of the Russian Academy of Sciences, 142290 Pushchino, Russia – name: 4 Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, FL 33612, USA – name: 2 Biotechnology Research Center, Technology Innovation Institute, Abu Dhabi P.O. Box 3692, United Arab Emirates – name: 3 Center for Biosystems Dynamics Research, Laboratory for Structural Bioinformatics, Yokohama 230-0045, Japan |
Author_xml | – sequence: 1 givenname: Naveen orcidid: 0000-0002-3326-5465 surname: Kumar fullname: Kumar, Naveen organization: Diagnostics & Vaccines Group, ICAR-National Institute of High Security Animal Diseases, Bhopal 462022, India – sequence: 2 givenname: Rahul orcidid: 0000-0002-6489-6913 surname: Kaushik fullname: Kaushik, Rahul organization: Center for Biosystems Dynamics Research, Laboratory for Structural Bioinformatics, Yokohama 230-0045, Japan – sequence: 3 givenname: Ashutosh surname: Singh fullname: Singh, Ashutosh organization: Diagnostics & Vaccines Group, ICAR-National Institute of High Security Animal Diseases, Bhopal 462022, India – sequence: 4 givenname: Vladimir N orcidid: 0000-0002-4037-5857 surname: Uversky fullname: Uversky, Vladimir N organization: Federal Research Center 'Pushchino, Scientific Center for Biological Research of the Russian Academy of Sciences', Institute for Biological Instrumentation of the Russian Academy of Sciences, 142290 Pushchino, Russia – sequence: 5 givenname: Kam Y J orcidid: 0000-0002-9282-8045 surname: Zhang fullname: Zhang, Kam Y J organization: Center for Biosystems Dynamics Research, Laboratory for Structural Bioinformatics, Yokohama 230-0045, Japan – sequence: 6 givenname: Upasana surname: Sahu fullname: Sahu, Upasana organization: Diagnostics & Vaccines Group, ICAR-National Institute of High Security Animal Diseases, Bhopal 462022, India – sequence: 7 givenname: Sandeep surname: Bhatia fullname: Bhatia, Sandeep organization: Diagnostics & Vaccines Group, ICAR-National Institute of High Security Animal Diseases, Bhopal 462022, India – sequence: 8 givenname: Aniket surname: Sanyal fullname: Sanyal, Aniket organization: Diagnostics & Vaccines Group, ICAR-National Institute of High Security Animal Diseases, Bhopal 462022, India |
BackLink | https://www.ncbi.nlm.nih.gov/pubmed/36560768$$D View this record in MEDLINE/PubMed |
BookMark | eNptks2O0zAQxyO0iP2AAy-ALHGBQ4q_YscXpG5ZoFJXRRS4Wo7tZF2ldtdJivo6PCluu5QtQpZsa-Y_v7Fn5jI788HbLHuJ4IgQAd9tEEUYc0afZBdICJFTgYqzR_fz7LLrlhAyJiB_lp0TVjDIWXmR_bpWW9s55cFtaK0eWhXBB9U734CxV-22sx2YhFXlvDXgp-vvwO3QJ39ITvAlhtq1O-1iaBrb9SBxpt7YtU2b78E8usb5ZDXgZhPaYRcHQg0W46-LfBJ-5BjMV07HZL0ej9BemC448ap8lnKqRH2ePa1V29kXD-dV9v3jzbfJ53w2_zSdjGe5Lgjr84oQSAWDBdRFoXnFCqsgKamAglNNmFE1Q5XSBlGslGW6wLxglhONTWU4I1fZ9MA1QS3lOrqVilsZlJN7Q4iNVLF3urVSEIpLwqAptaWU4wrRujSa1URVDCORWO8PrPVQrazRqRhRtSfQU493d7IJGyl4WVK4A7x5AMRwP6TSypXrtG1b5W0YOpneXiJY8H2u1_9Il2GIqT97FSsRZgj_VTUqfcD5OqS8egeVY04ZR5xCnlSj_6jSMjb1KU1d6rc9DXh7CEhN7Lpo6-MfEZS74ZTH4UzaV4-LclT-mUbyG0kJ3lQ |
CitedBy_id | crossref_primary_10_1038_s41598_024_55599_0 crossref_primary_10_1016_j_jviromet_2024_114995 |
Cites_doi | 10.1098/rstb.1994.0079 10.1093/sysbio/syq085 10.1016/j.xcrm.2021.100255 10.1002/gch2.1018 10.1016/S0140-6736(21)02844-0 10.1093/molbev/mss075 10.1038/s41586-022-04411-y 10.3201/eid2710.211538 10.1016/j.chom.2022.01.006 10.1101/2022.02.11.480177 10.1038/s41586-021-04385-3 10.1038/s41586-021-04388-0 10.2307/2533156 10.1002/jmv.27780 10.1080/01621459.1995.10476572 10.1038/d41586-022-00215-2 10.1111/all.15065 10.1093/molbev/msv035 10.1093/jac/dkaa444 10.1002/cbic.202200059 10.1016/j.virusres.2020.198098 10.1038/s41586-021-04266-9 10.1016/j.jgg.2021.12.003 10.1093/molbev/msv022 10.1016/j.ijsu.2022.106698 10.1101/2021.04.30.441434 10.3389/fmicb.2022.978259 10.1101/2021.12.13.21267748 10.1007/s00239-001-0034-9 10.1214/ss/1028905934 10.1001/jama.2022.2274 10.1126/science.abj9932 10.1038/s41591-022-01911-2 10.1038/nmeth.4285 10.1080/10635150500433722 10.1093/ve/veaa087 10.1093/ve/vew007 10.1093/molbev/msi105 10.1101/2021.02.24.432576 10.1038/s41586-021-03944-y 10.1002/jmv.25701 10.1016/j.envres.2022.113303 10.1128/mBio.02707-20 10.1111/cbdd.14035 10.1016/j.chom.2021.11.005 10.1093/ve/veac078 10.1126/science.abn4947 10.1016/j.meegid.2021.105005 10.1126/science.abh2644 10.1038/s41564-020-0770-5 10.1016/j.ijsu.2022.106835 10.1093/sysbio/syy032 10.1016/j.ebiom.2021.103381 10.1073/pnas.1918304117 10.1016/0304-4149(82)90011-4 10.1093/molbev/mst030 10.2807/1560-7917.ES.2017.22.13.30494 10.1038/s41586-021-04387-1 10.1093/molbev/msl051 10.1016/j.heliyon.2021.e06564 10.1002/jmv.25731 10.1016/j.jaut.2021.102779 10.1371/journal.pcbi.1006650 10.1038/s41467-021-26401-w 10.1093/molbev/msi103 10.1038/s41586-021-03402-9 10.1016/j.cell.2021.05.031 10.1016/j.jinf.2020.03.058 10.1016/j.cell.2020.08.012 10.1002/jmv.27561 10.1093/molbev/msu300 10.1093/molbev/mst010 10.1186/1471-2148-8-289 10.1126/science.acx9738 10.1371/journal.pbio.0040088 10.1093/bib/bbab145 10.1093/genetics/161.3.1307 10.1093/molbev/msr125 10.1038/s41586-021-04389-z |
ContentType | Journal Article |
Copyright | COPYRIGHT 2022 MDPI AG 2022 by the authors. Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (https://creativecommons.org/licenses/by/4.0/). Notwithstanding the ProQuest Terms and Conditions, you may use this content in accordance with the terms of the License. 2022 by the authors. 2022 |
Copyright_xml | – notice: COPYRIGHT 2022 MDPI AG – notice: 2022 by the authors. Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (https://creativecommons.org/licenses/by/4.0/). Notwithstanding the ProQuest Terms and Conditions, you may use this content in accordance with the terms of the License. – notice: 2022 by the authors. 2022 |
DBID | CGR CUY CVF ECM EIF NPM AAYXX CITATION 3V. 7U9 7X7 7XB 88E 8FE 8FH 8FI 8FJ 8FK ABUWG AFKRA AZQEC BBNVY BENPR BHPHI CCPQU COVID DWQXO FYUFA GHDGH GNUQQ H94 HCIFZ K9. LK8 M0S M1P M7P PIMPY PQEST PQQKQ PQUKI PRINS 7X8 5PM DOA |
DOI | 10.3390/v14122764 |
DatabaseName | Medline MEDLINE MEDLINE (Ovid) MEDLINE MEDLINE PubMed CrossRef ProQuest Central (Corporate) Virology and AIDS Abstracts Health & Medical Collection (Proquest) ProQuest Central (purchase pre-March 2016) Medical Database (Alumni Edition) ProQuest SciTech Collection ProQuest Natural Science Collection Hospital Premium Collection Hospital Premium Collection (Alumni Edition) ProQuest Central (Alumni) (purchase pre-March 2016) ProQuest Central (Alumni) ProQuest Central UK/Ireland ProQuest Central Essentials Biological Science Collection AUTh Library subscriptions: ProQuest Central ProQuest Natural Science Collection ProQuest One Community College Coronavirus Research Database ProQuest Central Health Research Premium Collection Health Research Premium Collection (Alumni) ProQuest Central Student AIDS and Cancer Research Abstracts SciTech Premium Collection (Proquest) (PQ_SDU_P3) ProQuest Health & Medical Complete (Alumni) Biological Sciences Health & Medical Collection (Alumni Edition) PML(ProQuest Medical Library) Biological Science Database Access via ProQuest (Open Access) ProQuest One Academic Eastern Edition (DO NOT USE) ProQuest One Academic ProQuest One Academic UKI Edition ProQuest Central China MEDLINE - Academic PubMed Central (Full Participant titles) Directory of Open Access Journals |
DatabaseTitle | MEDLINE Medline Complete MEDLINE with Full Text PubMed MEDLINE (Ovid) CrossRef Publicly Available Content Database ProQuest Central Student ProQuest Central Essentials ProQuest Health & Medical Complete (Alumni) ProQuest Central (Alumni Edition) SciTech Premium Collection ProQuest One Community College ProQuest Natural Science Collection ProQuest Central China ProQuest Central Health Research Premium Collection Health and Medicine Complete (Alumni Edition) Natural Science Collection ProQuest Central Korea Biological Science Collection AIDS and Cancer Research Abstracts ProQuest Medical Library (Alumni) Virology and AIDS Abstracts ProQuest Biological Science Collection ProQuest One Academic Eastern Edition Coronavirus Research Database ProQuest Hospital Collection Health Research Premium Collection (Alumni) Biological Science Database ProQuest SciTech Collection ProQuest Hospital Collection (Alumni) ProQuest Health & Medical Complete ProQuest Medical Library ProQuest One Academic UKI Edition ProQuest One Academic ProQuest Central (Alumni) MEDLINE - Academic |
DatabaseTitleList | MEDLINE - Academic CrossRef MEDLINE Publicly Available Content Database |
Database_xml | – sequence: 1 dbid: DOA name: DOAJ Directory of Open Access Journals url: https://www.doaj.org/ sourceTypes: Open Website – sequence: 2 dbid: NPM name: PubMed url: https://proxy.k.utb.cz/login?url=http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed sourceTypes: Index Database – sequence: 3 dbid: EIF name: MEDLINE url: https://proxy.k.utb.cz/login?url=https://www.webofscience.com/wos/medline/basic-search sourceTypes: Index Database – sequence: 4 dbid: BENPR name: AUTh Library subscriptions: ProQuest Central url: https://www.proquest.com/central sourceTypes: Aggregation Database |
DeliveryMethod | fulltext_linktorsrc |
Discipline | Biology Public Health |
EISSN | 1999-4915 |
ExternalDocumentID | oai_doaj_org_article_93428360d8ce4472b14f8dc6f3ab6219 A746717407 10_3390_v14122764 36560768 |
Genre | Research Support, Non-U.S. Gov't Journal Article |
GeographicLocations | India South Africa |
GeographicLocations_xml | – name: India – name: South Africa |
GrantInformation_xml | – fundername: Indian Council of Agricultural Research (ICAR)—National Agricultural Science Fund grantid: NASF/ABA-8028/2020–21 |
GroupedDBID | --- 2WC 3V. 53G 5VS 7X7 88E 8FE 8FH 8FI 8FJ A8Z AADQD AAFWJ AAHBH ABDBF ABUWG AFKRA AFPKN AFZYC ALIPV ALMA_UNASSIGNED_HOLDINGS BBNVY BENPR BHPHI BPHCQ BVXVI CCPQU CGR CUY CVF DIK E3Z EBD ECM EIF ESTFP ESX FYUFA GROUPED_DOAJ GX1 HCIFZ HMCUK HYE IAO IHR ISR ITC KQ8 LK8 M1P M48 M7P MODMG M~E NPM O5R O5S OK1 PGMZT PIMPY PQQKQ PROAC PSQYO RIG RPM TR2 TUS UKHRP AAYXX CITATION 7U9 7XB 8FK AZQEC COVID DWQXO GNUQQ H94 K9. PQEST PQUKI PRINS 7X8 5PM |
ID | FETCH-LOGICAL-c536t-b330496050c55c7b65ea038490974c36daf61bacd142aae6c52756e73c2dbd763 |
IEDL.DBID | RPM |
ISSN | 1999-4915 |
IngestDate | Tue Oct 22 15:11:50 EDT 2024 Tue Sep 17 21:32:19 EDT 2024 Mon Sep 09 17:30:46 EDT 2024 Sat Oct 19 00:54:33 EDT 2024 Thu May 09 20:52:35 EDT 2024 Tue May 07 05:00:32 EDT 2024 Wed Aug 14 12:28:12 EDT 2024 Wed Oct 23 10:04:35 EDT 2024 |
IsDoiOpenAccess | true |
IsOpenAccess | true |
IsPeerReviewed | true |
IsScholarly | true |
Issue | 12 |
Keywords | COVID-19 SARS-CoV-2 Omicron tMRCA mutational profiling selection pressure evolutionary rate |
Language | English |
License | Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (https://creativecommons.org/licenses/by/4.0/). |
LinkModel | DirectLink |
MergedId | FETCHMERGED-LOGICAL-c536t-b330496050c55c7b65ea038490974c36daf61bacd142aae6c52756e73c2dbd763 |
Notes | ObjectType-Article-1 SourceType-Scholarly Journals-1 ObjectType-Feature-2 content type line 23 These authors contributed equally to this work. |
ORCID | 0000-0002-3326-5465 0000-0002-4037-5857 0000-0002-9282-8045 0000-0002-6489-6913 |
OpenAccessLink | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9788409/ |
PMID | 36560768 |
PQID | 2756812612 |
PQPubID | 2032319 |
ParticipantIDs | doaj_primary_oai_doaj_org_article_93428360d8ce4472b14f8dc6f3ab6219 pubmedcentral_primary_oai_pubmedcentral_nih_gov_9788409 proquest_miscellaneous_2758105719 proquest_journals_2756812612 gale_infotracmisc_A746717407 gale_infotracacademiconefile_A746717407 crossref_primary_10_3390_v14122764 pubmed_primary_36560768 |
PublicationCentury | 2000 |
PublicationDate | 2022-12-01 |
PublicationDateYYYYMMDD | 2022-12-01 |
PublicationDate_xml | – month: 12 year: 2022 text: 2022-12-01 day: 01 |
PublicationDecade | 2020 |
PublicationPlace | Switzerland |
PublicationPlace_xml | – name: Switzerland – name: Basel |
PublicationTitle | Viruses |
PublicationTitleAlternate | Viruses |
PublicationYear | 2022 |
Publisher | MDPI AG MDPI |
Publisher_xml | – name: MDPI AG – name: MDPI |
References | Focosi (ref_59) 2021; 27 Smyth (ref_84) 2022; 13 Mohapatra (ref_11) 2022; 104 Mohapatra (ref_16) 2021; 94 Dejnirattisai (ref_23) 2021; 399 Posada (ref_49) 2006; 23 Gelman (ref_45) 1998; 13 Drummond (ref_47) 2012; 29 Li (ref_82) 2022; 8 Tegally (ref_7) 2021; 592 Tegally (ref_26) 2022; 28 Benvenuto (ref_74) 2020; 81 Huang (ref_65) 2021; 67 ref_10 Nguyen (ref_32) 2015; 32 Xie (ref_44) 2010; 60 Saito (ref_73) 2021; 602 Elbe (ref_27) 2017; 1 Drummond (ref_38) 2005; 22 ref_19 Griffiths (ref_37) 1994; 344 Salpini (ref_75) 2020; 76 Wu (ref_76) 2021; 29 Kass (ref_42) 1995; 90 ref_61 Dhar (ref_8) 2021; 374 Mohapatra (ref_13) 2022; 94 Sood (ref_50) 2021; 94 ref_25 ref_69 ref_24 ref_63 Kingman (ref_36) 1982; 13 Murrell (ref_51) 2013; 30 Nie (ref_81) 2020; 287 Kumar (ref_87) 2021; 22 Liu (ref_60) 2021; 602 Posada (ref_78) 2002; 54 ref_71 Katoh (ref_28) 2013; 30 Alai (ref_5) 2021; 7 Cele (ref_22) 2021; 602 Shu (ref_67) 2017; 22 Li (ref_80) 2020; 92 Wei (ref_85) 2021; 48 Han (ref_21) 2021; 12 Drummond (ref_34) 2002; 161 Liu (ref_66) 2021; 184 Rambaut (ref_33) 2016; 2 ref_35 Stolz (ref_77) 2020; 117 Murrell (ref_54) 2015; 32 Kumar (ref_88) 2022; 13 Starr (ref_62) 2021; 2 Lyngse (ref_70) 2022; 13 Kannan (ref_17) 2021; 126 Sinsheimer (ref_41) 1996; 52 Frost (ref_48) 2005; 22 Smith (ref_53) 2015; 32 Rambaut (ref_2) 2020; 5 Heled (ref_39) 2008; 8 Planas (ref_64) 2021; 602 Walls (ref_56) 2020; 182 Mlcochova (ref_72) 2021; 599 Mohapatra (ref_15) 2022; 99 Lartillot (ref_43) 2006; 55 Hall (ref_29) 1999; 41 Mohapatra (ref_12) 2022; 103 Martin (ref_30) 2020; 7 Kupferschmidt (ref_86) 2021; 374 Ulloa (ref_18) 2022; 327 Mohapatra (ref_14) 2022; 23 ref_40 Cao (ref_57) 2021; 602 ref_1 ref_3 Li (ref_79) 2020; 92 Pond (ref_52) 2011; 28 Faria (ref_6) 2021; 372 Rambaut (ref_46) 2018; 67 Augusto (ref_20) 2021; 77 Mallapaty (ref_83) 2022; 602 Kalyaanamoorthy (ref_31) 2017; 14 Kaushik (ref_55) 2022; 212 ref_4 Viana (ref_9) 2022; 603 Engelhart (ref_58) 2022; 5 Escalera (ref_68) 2022; 30 |
References_xml | – volume: 344 start-page: 403 year: 1994 ident: ref_37 article-title: Sampling theory for neutral alleles in a varying environment publication-title: Philos. Trans. R. Soc. B Biol. Sci. doi: 10.1098/rstb.1994.0079 contributor: fullname: Griffiths – volume: 60 start-page: 150 year: 2010 ident: ref_44 article-title: Improving Marginal Likelihood Estimation for Bayesian Phylogenetic Model Selection publication-title: Syst. Biol. doi: 10.1093/sysbio/syq085 contributor: fullname: Xie – volume: 2 start-page: 100255 year: 2021 ident: ref_62 article-title: Complete map of SARS-CoV-2 RBD mutations that escape the monoclonal antibody LY-CoV555 and its cocktail with LY-CoV016 publication-title: Cell Rep. Med. doi: 10.1016/j.xcrm.2021.100255 contributor: fullname: Starr – volume: 1 start-page: 33 year: 2017 ident: ref_27 article-title: Data, disease and diplomacy: GISAID’s innovative contribution to global health publication-title: Glob. Chall. doi: 10.1002/gch2.1018 contributor: fullname: Elbe – volume: 399 start-page: 234 year: 2021 ident: ref_23 article-title: Reduced neutralisation of SARS-CoV-2 omicron B.1.1.529 variant by post-immunisation serum publication-title: Lancet doi: 10.1016/S0140-6736(21)02844-0 contributor: fullname: Dejnirattisai – volume: 29 start-page: 1969 year: 2012 ident: ref_47 article-title: Bayesian Phylogenetics with BEAUti and the BEAST 1.7 publication-title: Mol. Biol. Evol. doi: 10.1093/molbev/mss075 contributor: fullname: Drummond – volume: 603 start-page: 679 year: 2022 ident: ref_9 article-title: Rapid epidemic expansion of the SARS-CoV-2 Omicron variant in southern Africa publication-title: Nature doi: 10.1038/s41586-022-04411-y contributor: fullname: Viana – volume: 27 start-page: 2728 year: 2021 ident: ref_59 article-title: Emergence of SARS-CoV-2 Spike Protein Escape Mutation Q493R after Treatment for COVID-19 publication-title: Emerg. Infect. Dis. doi: 10.3201/eid2710.211538 contributor: fullname: Focosi – volume: 30 start-page: 373 year: 2022 ident: ref_68 article-title: Mutations in SARS-CoV-2 variants of concern link to increased spike cleavage and virus transmission publication-title: Cell Host Microbe doi: 10.1016/j.chom.2022.01.006 contributor: fullname: Escalera – ident: ref_25 doi: 10.1101/2022.02.11.480177 – volume: 602 start-page: 657 year: 2021 ident: ref_57 article-title: Omicron escapes the majority of existing SARS-CoV-2 neutralizing antibodies publication-title: Nature doi: 10.1038/s41586-021-04385-3 contributor: fullname: Cao – volume: 602 start-page: 676 year: 2021 ident: ref_60 article-title: Striking antibody evasion manifested by the Omicron variant of SARS-CoV-2 publication-title: Nature doi: 10.1038/s41586-021-04388-0 contributor: fullname: Liu – volume: 52 start-page: 193 year: 1996 ident: ref_41 article-title: Bayesian Hypothesis Testing of Four-Taxon Topologies Using Molecular Sequence Data publication-title: Biometrics doi: 10.2307/2533156 contributor: fullname: Sinsheimer – volume: 94 start-page: 3506 year: 2022 ident: ref_13 article-title: The recombinant variants of SARS-CoV-2: Concerns continues amid COVID-19 pandemic publication-title: J. Med Virol. doi: 10.1002/jmv.27780 contributor: fullname: Mohapatra – volume: 90 start-page: 773 year: 1995 ident: ref_42 article-title: Bayes Factors publication-title: J. Am. Stat. Assoc. doi: 10.1080/01621459.1995.10476572 contributor: fullname: Kass – volume: 602 start-page: 26 year: 2022 ident: ref_83 article-title: Where did Omicron come from? Three key theories publication-title: Nature doi: 10.1038/d41586-022-00215-2 contributor: fullname: Mallapaty – ident: ref_1 – volume: 77 start-page: 111 year: 2021 ident: ref_20 article-title: In vitro data suggest that Indian delta variant B.1.617 of SARS-CoV-2 escapes neutralization by both receptor affinity and immune evasion publication-title: Allergy doi: 10.1111/all.15065 contributor: fullname: Augusto – volume: 41 start-page: 95 year: 1999 ident: ref_29 article-title: BioEdit: A User-Friendly Biological Sequence Alignment Editor and Analysis Program for Windows 95/98/NT publication-title: Nucleic Acids Symp. Ser. contributor: fullname: Hall – volume: 13 start-page: 1 year: 2022 ident: ref_70 article-title: Household transmission of SARS-CoV-2 Omicron variant of concern subvariants BA.1 and BA.2 in Denmark publication-title: Nat. Commun. contributor: fullname: Lyngse – ident: ref_4 – volume: 32 start-page: 1365 year: 2015 ident: ref_54 article-title: Gene-Wide Identification of Episodic Selection publication-title: Mol. Biol. Evol. doi: 10.1093/molbev/msv035 contributor: fullname: Murrell – volume: 76 start-page: 396 year: 2020 ident: ref_75 article-title: Key genetic elements, single and in clusters, underlying geographically dependent SARS-CoV-2 genetic adaptation and their impact on binding affinity for drugs and immune control publication-title: J. Antimicrob. Chemother. doi: 10.1093/jac/dkaa444 contributor: fullname: Salpini – ident: ref_69 – ident: ref_10 – volume: 23 start-page: e202200059 year: 2022 ident: ref_14 article-title: Challenges of the Omicron (B.1.1.529) Variant and Its Lineages: A Global Perspective publication-title: Chembiochem doi: 10.1002/cbic.202200059 contributor: fullname: Mohapatra – volume: 287 start-page: 198098 year: 2020 ident: ref_81 article-title: Phylogenetic and phylodynamic analyses of SARS-CoV-2 publication-title: Virus Res. doi: 10.1016/j.virusres.2020.198098 contributor: fullname: Nie – volume: 602 start-page: 300 year: 2021 ident: ref_73 article-title: Enhanced fusogenicity and pathogenicity of SARS-CoV-2 Delta P681R mutation publication-title: Nature doi: 10.1038/s41586-021-04266-9 contributor: fullname: Saito – volume: 48 start-page: 1111 year: 2021 ident: ref_85 article-title: Evidence for a mouse origin of the SARS-CoV-2 Omicron variant publication-title: J. Genet. Genom. doi: 10.1016/j.jgg.2021.12.003 contributor: fullname: Wei – volume: 32 start-page: 1342 year: 2015 ident: ref_53 article-title: Less Is More: An Adaptive Branch-Site Random Effects Model for Efficient Detection of Episodic Diversifying Selection publication-title: Mol. Biol. Evol. doi: 10.1093/molbev/msv022 contributor: fullname: Smith – volume: 5 start-page: 130 year: 2022 ident: ref_58 article-title: Massively multiplexed affinity characterization of therapeutic antibodies against SARS-CoV-2 variants publication-title: Antib. Ther. contributor: fullname: Engelhart – volume: 103 start-page: 106698 year: 2022 ident: ref_12 article-title: The recently emerged BA.4 and BA.5 lineages of Omicron and their global health concerns amid the ongoing wave of COVID-19 pandemic –Correspondence publication-title: Int. J. Surg. doi: 10.1016/j.ijsu.2022.106698 contributor: fullname: Mohapatra – ident: ref_63 doi: 10.1101/2021.04.30.441434 – volume: 13 start-page: 978259 year: 2022 ident: ref_88 article-title: Editorial: Emerging and re-emerging viral zoonoses publication-title: Front. Microbiol. doi: 10.3389/fmicb.2022.978259 contributor: fullname: Kumar – ident: ref_24 doi: 10.1101/2021.12.13.21267748 – volume: 54 start-page: 396 year: 2002 ident: ref_78 article-title: The Effect of Recombination on the Accuracy of Phylogeny Estimation publication-title: J. Mol. Evol. doi: 10.1007/s00239-001-0034-9 contributor: fullname: Posada – volume: 13 start-page: 163 year: 1998 ident: ref_45 article-title: Simulating normalizing constants: From importance sampling to bridge sampling to path sampling publication-title: Stat. Sci. doi: 10.1214/ss/1028905934 contributor: fullname: Gelman – volume: 327 start-page: 1286 year: 2022 ident: ref_18 article-title: Estimates of SARS-CoV-2 Omicron Variant Severity in Ontario, Canada publication-title: JAMA doi: 10.1001/jama.2022.2274 contributor: fullname: Ulloa – volume: 374 start-page: 995 year: 2021 ident: ref_8 article-title: Genomic characterization and epidemiology of an emerging SARS-CoV-2 variant in Delhi, India publication-title: Science doi: 10.1126/science.abj9932 contributor: fullname: Dhar – volume: 28 start-page: 1785 year: 2022 ident: ref_26 article-title: Emergence of SARS-CoV-2 Omicron lineages BA.4 and BA.5 in South Africa publication-title: Nat. Med. doi: 10.1038/s41591-022-01911-2 contributor: fullname: Tegally – volume: 14 start-page: 587 year: 2017 ident: ref_31 article-title: ModelFinder: Fast model selection for accurate phylogenetic estimates publication-title: Nat. Methods doi: 10.1038/nmeth.4285 contributor: fullname: Kalyaanamoorthy – volume: 55 start-page: 195 year: 2006 ident: ref_43 article-title: Computing Bayes Factors Using Thermodynamic Integration publication-title: Syst. Biol. doi: 10.1080/10635150500433722 contributor: fullname: Lartillot – volume: 7 start-page: veaa087 year: 2020 ident: ref_30 article-title: RDP5: A computer program for analyzing recombination in, and removing signals of recombination from, nucleotide sequence datasets publication-title: Virus Evol. doi: 10.1093/ve/veaa087 contributor: fullname: Martin – volume: 2 start-page: vew007 year: 2016 ident: ref_33 article-title: Exploring the temporal structure of heterochronous sequences using TempEst (formerly Path-O-Gen) publication-title: Virus Evol. doi: 10.1093/ve/vew007 contributor: fullname: Rambaut – volume: 22 start-page: 1208 year: 2005 ident: ref_48 article-title: Not So Different After All: A Comparison of Methods for Detecting Amino Acid Sites Under Selection publication-title: Mol. Biol. Evol. doi: 10.1093/molbev/msi105 contributor: fullname: Frost – ident: ref_71 doi: 10.1101/2021.02.24.432576 – volume: 599 start-page: 114 year: 2021 ident: ref_72 article-title: SARS-CoV-2 B.1.617.2 Delta variant replication and immune evasion publication-title: Nature doi: 10.1038/s41586-021-03944-y contributor: fullname: Mlcochova – volume: 92 start-page: 501 year: 2020 ident: ref_79 article-title: Transmission dynamics and evolutionary history of 2019-nCoV publication-title: J. Med Virol. doi: 10.1002/jmv.25701 contributor: fullname: Li – ident: ref_3 – volume: 212 start-page: 113303 year: 2022 ident: ref_55 article-title: A novel structure-based approach for identification of vertebrate susceptibility to SARS-CoV-2: Implications for future surveillance programmes publication-title: Environ. Res. doi: 10.1016/j.envres.2022.113303 contributor: fullname: Kaushik – ident: ref_61 doi: 10.1128/mBio.02707-20 – volume: 99 start-page: 769 year: 2022 ident: ref_15 article-title: SARS-CoV-2 and its variants of concern including Omicron: A never ending pandemic publication-title: Chem. Biol. Drug Des. doi: 10.1111/cbdd.14035 contributor: fullname: Mohapatra – volume: 29 start-page: 1788 year: 2021 ident: ref_76 article-title: Nucleocapsid mutations R203K/G204R increase the infectivity, fitness, and virulence of SARS-CoV-2 publication-title: Cell Host Microbe doi: 10.1016/j.chom.2021.11.005 contributor: fullname: Wu – volume: 8 start-page: veac078 year: 2022 ident: ref_82 article-title: Lineage BA.2 Dominated the Omicron SARS-CoV-2 Epidemic Wave in the Philippines publication-title: Virus Evol. doi: 10.1093/ve/veac078 contributor: fullname: Li – ident: ref_19 doi: 10.1126/science.abn4947 – volume: 94 start-page: 105005 year: 2021 ident: ref_50 article-title: Identification and molecular characterization of H9N2 viruses carrying multiple mammalian adaptation markers in resident birds in central-western wetlands in India publication-title: Infect. Genet. Evol. doi: 10.1016/j.meegid.2021.105005 contributor: fullname: Sood – volume: 372 start-page: 815 year: 2021 ident: ref_6 article-title: Genomics and epidemiology of the P.1 SARS-CoV-2 lineage in Manaus, Brazil publication-title: Science doi: 10.1126/science.abh2644 contributor: fullname: Faria – volume: 5 start-page: 1403 year: 2020 ident: ref_2 article-title: A dynamic nomenclature proposal for SARS-CoV-2 lineages to assist genomic epidemiology publication-title: Nat. Microbiol. doi: 10.1038/s41564-020-0770-5 contributor: fullname: Rambaut – volume: 104 start-page: 106835 year: 2022 ident: ref_11 article-title: Emerging novel sub-lineage BA.2.75: The next dominant omicron variant? publication-title: Int. J. Surg. doi: 10.1016/j.ijsu.2022.106835 contributor: fullname: Mohapatra – volume: 67 start-page: 901 year: 2018 ident: ref_46 article-title: Posterior Summarization in Bayesian Phylogenetics Using Tracer 1.7 publication-title: Syst. Biol. doi: 10.1093/sysbio/syy032 contributor: fullname: Rambaut – volume: 67 start-page: 103381 year: 2021 ident: ref_65 article-title: Q493K and Q498H substitutions in Spike promote adaptation of SARS-CoV-2 in mice publication-title: eBioMedicine doi: 10.1016/j.ebiom.2021.103381 contributor: fullname: Huang – volume: 117 start-page: 17104 year: 2020 ident: ref_77 article-title: Bayesian inference of reassortment networks reveals fitness benefits of reassortment in human influenza viruses publication-title: Proc. Natl. Acad. Sci. USA doi: 10.1073/pnas.1918304117 contributor: fullname: Stolz – volume: 13 start-page: 235 year: 1982 ident: ref_36 article-title: The coalescent publication-title: Stoch. Process. Appl. doi: 10.1016/0304-4149(82)90011-4 contributor: fullname: Kingman – volume: 30 start-page: 1196 year: 2013 ident: ref_51 article-title: FUBAR: A Fast, Unconstrained Bayesian AppRoximation for Inferring Selection publication-title: Mol. Biol. Evol. doi: 10.1093/molbev/mst030 contributor: fullname: Murrell – volume: 22 start-page: 30494 year: 2017 ident: ref_67 article-title: GISAID: Global initiative on sharing all influenza data—From vision to reality publication-title: Eurosurveillance doi: 10.2807/1560-7917.ES.2017.22.13.30494 contributor: fullname: Shu – volume: 602 start-page: 654 year: 2021 ident: ref_22 article-title: Omicron extensively but incompletely escapes Pfizer BNT162b2 neutralization publication-title: Nature doi: 10.1038/s41586-021-04387-1 contributor: fullname: Cele – volume: 23 start-page: 1891 year: 2006 ident: ref_49 article-title: Automated Phylogenetic Detection of Recombination Using a Genetic Algorithm publication-title: Mol. Biol. Evol. doi: 10.1093/molbev/msl051 contributor: fullname: Posada – volume: 7 start-page: e06564 year: 2021 ident: ref_5 article-title: Pan-India novel coronavirus SARS-CoV-2 genomics and global diversity analysis in spike protein publication-title: Heliyon doi: 10.1016/j.heliyon.2021.e06564 contributor: fullname: Alai – volume: 92 start-page: 602 year: 2020 ident: ref_80 article-title: Evolutionary history, potential intermediate animal host, and cross-species analyses of SARS-CoV-2 publication-title: J. Med. Virol. doi: 10.1002/jmv.25731 contributor: fullname: Li – volume: 126 start-page: 102779 year: 2021 ident: ref_17 article-title: Omicron SARS-CoV-2 variant: Unique features and their impact on pre-existing antibodies publication-title: J. Autoimmun. doi: 10.1016/j.jaut.2021.102779 contributor: fullname: Kannan – volume: 13 start-page: 1 year: 2022 ident: ref_84 article-title: Tracking cryptic SARS-CoV-2 lineages detected in NYC wastewater publication-title: Nat. Commun. contributor: fullname: Smyth – ident: ref_35 doi: 10.1371/journal.pcbi.1006650 – volume: 12 start-page: 1 year: 2021 ident: ref_21 article-title: Molecular insights into receptor binding of recent emerging SARS-CoV-2 variants publication-title: Nat. Commun. doi: 10.1038/s41467-021-26401-w contributor: fullname: Han – volume: 22 start-page: 1185 year: 2005 ident: ref_38 article-title: Bayesian Coalescent Inference of Past Population Dynamics from Molecular Sequences publication-title: Mol. Biol. Evol. doi: 10.1093/molbev/msi103 contributor: fullname: Drummond – volume: 592 start-page: 438 year: 2021 ident: ref_7 article-title: Detection of a SARS-CoV-2 variant of concern in South Africa publication-title: Nature doi: 10.1038/s41586-021-03402-9 contributor: fullname: Tegally – volume: 184 start-page: 3438 year: 2021 ident: ref_66 article-title: Binding and molecular basis of the bat coronavirus RaTG13 virus to ACE2 in humans and other species publication-title: Cell doi: 10.1016/j.cell.2021.05.031 contributor: fullname: Liu – volume: 81 start-page: e24 year: 2020 ident: ref_74 article-title: Evolutionary analysis of SARS-CoV-2: How mutation of Non-Structural Protein 6 (NSP6) could affect viral autophagy publication-title: J. Infect. doi: 10.1016/j.jinf.2020.03.058 contributor: fullname: Benvenuto – volume: 182 start-page: 1295 year: 2020 ident: ref_56 article-title: Deep mutational scanning of SARS-CoV-2 receptor binding domain reveals constraints on folding and ACE2 binding publication-title: Cell doi: 10.1016/j.cell.2020.08.012 contributor: fullname: Walls – volume: 94 start-page: 1780 year: 2021 ident: ref_16 article-title: Omicron (B.1.1.529 variant of SARS-CoV-2); An emerging threat: Current global scenario publication-title: J. Med Virol. doi: 10.1002/jmv.27561 contributor: fullname: Mohapatra – volume: 32 start-page: 268 year: 2015 ident: ref_32 article-title: IQ-TREE: A Fast and Effective Stochastic Algorithm for Estimating Maximum-Likelihood Phylogenies publication-title: Mol. Biol. Evol. doi: 10.1093/molbev/msu300 contributor: fullname: Nguyen – volume: 30 start-page: 772 year: 2013 ident: ref_28 article-title: MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability publication-title: Mol. Biol. Evol. doi: 10.1093/molbev/mst010 contributor: fullname: Katoh – volume: 8 start-page: 289 year: 2008 ident: ref_39 article-title: Bayesian inference of population size history from multiple loci publication-title: BMC Evol. Biol. doi: 10.1186/1471-2148-8-289 contributor: fullname: Heled – volume: 374 start-page: 1179 year: 2021 ident: ref_86 article-title: Where did ‘weird’ Omicron come from? publication-title: Science doi: 10.1126/science.acx9738 contributor: fullname: Kupferschmidt – ident: ref_40 doi: 10.1371/journal.pbio.0040088 – volume: 22 start-page: bbab145 year: 2021 ident: ref_87 article-title: Insights into the evolutionary forces that shape the codon usage in the viral genome segments encoding intrinsically disordered protein regions publication-title: Briefings Bioinform. doi: 10.1093/bib/bbab145 contributor: fullname: Kumar – volume: 161 start-page: 1307 year: 2002 ident: ref_34 article-title: Estimating Mutation Parameters, Population History and Genealogy Simultaneously from Temporally Spaced Sequence Data publication-title: Genetics doi: 10.1093/genetics/161.3.1307 contributor: fullname: Drummond – volume: 28 start-page: 3033 year: 2011 ident: ref_52 article-title: A Random Effects Branch-Site Model for Detecting Episodic Diversifying Selection publication-title: Mol. Biol. Evol. doi: 10.1093/molbev/msr125 contributor: fullname: Pond – volume: 602 start-page: 671 year: 2021 ident: ref_64 article-title: Considerable escape of SARS-CoV-2 Omicron to antibody neutralization publication-title: Nature doi: 10.1038/s41586-021-04389-z contributor: fullname: Planas |
SSID | ssj0066907 |
Score | 2.3884013 |
Snippet | 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... |
SourceID | doaj pubmedcentral proquest gale crossref pubmed |
SourceType | Open Website Open Access Repository Aggregation Database Index Database |
StartPage | 2764 |
SubjectTerms | Algorithms Bayes Theorem Bayesian analysis Coronaviruses COVID-19 Datasets Dating Disease transmission Divergence Epidemiology Evolution Evolution & development evolutionary rate Genomes Humans Mutation mutational profiling Pandemics Phylogenetics Phylogeny Public health Regression analysis SARS-CoV-2 - genetics SARS-CoV-2 Omicron selection pressure Severe acute respiratory syndrome coronavirus 2 Spike Glycoprotein, Coronavirus Spike protein tMRCA |
SummonAdditionalLinks | – databaseName: Directory of Open Access Journals dbid: DOA link: http://utb.summon.serialssolutions.com/2.0.0/link/0/eLvHCXMwrV1Lb9QwELZQpUpcEJRXoFQGIXEKTezYTo67faggLUUsRb1ZfgU4kEVstlL_Dr-UGTsbbcSBC7codiLHM2PP58x8Q8hrz2QIokI-bQYApZE-bwrnc_AFnHBWtYxjvvPig7y4qt5fi-udUl8YE5bogdPEHTccKcFk4WsXqkoxW1Zt7Z1subGSlSl1rxRbMJXWYImYL_EIcQD1xzdlVTKmZDXZfSJJ_99L8c5eNI2T3Nl4zu-Te4PHSGdppA_IndAdkP1UQ_L2Ifk9N7cBMyHpYlvplp4aDGamiXAkrCkYPQDg4CmeutLFph9OAOnHWLEb-y43X_FPE4X3vBsr4_b0MtbNgruent0MWkpXLV3OPi3zk9WXnNHLHxjT19H57G0ZO8IFg_fZHHBugOVq_YhcnZ99PrnIh8ILuRNc9rnFQw6ANqJwQjhlpQim4HXVFIA-HJfetLK0xvmyYsYE6QSSyAfFHfPWw4r1mOx1qy48JZSz2rnWWSNBcKAYdahF03hw0prgVCgy8morEP0z8WtowCUoNT1KLSNzFNXYASmx4w1QFD0oiv6XomTkDQpao-GCNJ0Z8g9gnEiBpWdYeAXwWaEycjjpCQbnps1bVdGDwa81TgD4SuAvZuTl2IxPYhBbF1ab2KfGsso4lidJs8ZP4kiCBNAvI2qic5NvnrZ0379FOvBG1YjSn_2PSXpO7jLM74jxOodkr_-1CS_A6-rtUTSwPznZKYo priority: 102 providerName: Directory of Open Access Journals – databaseName: Coronavirus Research Database dbid: COVID link: http://utb.summon.serialssolutions.com/2.0.0/link/0/eLvHCXMwnV3fa9RAEB70iiCIP6rVaJVVBJ_SJrvJJnmSu2tLK5wnni19C9kfqSImtZcr1D_Hv9SZZHM2Cj74FrJ7ye7x7cx-k9lvAF4bLq2NI9LT5khQMmn8LNDGx72AjrVKSi7ovPPsvTw8jt6dxqcu4LZ0aZW9TWwNtak1xch3SaYcnRE65Lfn332qGkVfV10JjZuwIVJkOiPYmM5PjvZ6WyyJ-3V6QgLJ_e5lGIWcJzIaeKFWrP9vk3zNJw3zJa85oIN7kPdD7_JOvu6sGrWjf_yh6vj_c7sPd93elI07MD2AG7bahFtdtcqrTbjThfhYd3LpIfycFFeWzmCyWV9jl-0VlEbNOqkTu2RobpB6W8Mo3stmq8bFHtmHtlY49V2szugbF8PnHK1r8jZs3lbswruG7V-69cHqki3GHxf-tD7xOZt_o2zCik3GO2HbES84Pk_5yLAtGsrlIzg-2P80PfRdyQdfx0I2vqLwCpKqONBxrBMlY1sEIo2yAHmPFtIUpQxVoU0Y8aKwUsf039lEaG6UQVu5BaOqruwTYIKnWpdaFVKFEUIytWmcZQa3h5nViQ08eNVDID_vlD1yZESEk3yNEw8mBI51BxLjbm_UF2e5W9t5Jki1TgYm1TaKEo7vK1OjZSkKJdEjePCGoJWTyUD86MKdfMBxkvhWPqaSL8gMg8SD7UFPXOp62NzjJ3emZpn_Bo8HL9fN9EtKn6tsvWr7pFTQmcbyuMPyekqC5JeQdHqQDFA-mPOwpfryuRUiz5KU4gNP_z2sZ3Cb05mRNgdoG0bNxco-x51co1645foLq5tK6A priority: 102 providerName: ProQuest – databaseName: Scholars Portal Journals: Open Access dbid: M48 link: http://utb.summon.serialssolutions.com/2.0.0/link/0/eLvHCXMwdV1Zb9QwELZKEagviJtAQQYh8ZSSOD6SB4R2S6uCtBSxLOpb5CsFqU1gN1uxf4dfykwubQS8RfHEOWY8ns8Zf0PIS8ek94IjnzYDgJJJF2aRdSHEAlZYowqW4H7n2Ud5suAfzsTZDulrbHYfcPVPaIf1pBbLi4NfPzdvYcC_QcQJkP31VcxjxpTk18h1xhOOhj7jw88EiQCwJRUai--RmwlyzyjkWd2alRry_r9d9NYcNc6f3JqQjm-TW10kSSet6u-QHV_eJTfa2pKbe-T3VG887pCks74CLn2nMcmZtkQkfkXBGQAw9o7iaiydretuZZB-aip5o-x8fY5_oCj0836omFvT06aeFpx19Oiqs15aFXQ--TwPD6uvIaOnl5jrV9Lp5CBuBOGAQX8mBPzrwY2t7pPF8dGXw5OwK8gQWpHIOjS4-AGQR0RWCKuMFF5HScqzCFCJTaTThYyNti7mTGsvrUByea8Sy5xx4MkekN2yKv0jQhOWWltYo6WJORhM6lORZQ6Ct8xb5aOAvOgVkv9oeTdywCuowHxQYECmqKpBAKmymxPV8jzvRl6eJcgpJyOXWs-5YnC_InVWFok2Evx1QF6honM0MdCm1d2-BHhOpMbKJ1iQBXBbpAKyP5KEgWjHzb2p5L0d5_gBIIaCODIgz4dmvBKT20pfrRuZFMst47M8bC1reKXeQAOiRjY3eudxS_n9W0MTnqkU0fvj__b5hOwx3MzRJOfsk916ufZPIcSqzbNmAP0BneIi_A priority: 102 providerName: Scholars Portal |
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 |
URI | https://www.ncbi.nlm.nih.gov/pubmed/36560768 https://www.proquest.com/docview/2756812612 https://www.proquest.com/docview/2758105719/abstract/ https://pubmed.ncbi.nlm.nih.gov/PMC9788409 https://doaj.org/article/93428360d8ce4472b14f8dc6f3ab6219 |
Volume | 14 |
hasFullText | 1 |
inHoldings | 1 |
isFullTextHit | |
isPrint | |
link | http://utb.summon.serialssolutions.com/2.0.0/link/0/eLvHCXMwnV1bb5swFLbaTpP2Mu0-ti7ypkl7IgEb2_CYpOnaSWmiZq3yhsA2XaUFqiap1L-zX7pzDERBe9sLibABk3Px-Zzj7xDy1TBprYiQT5sBQEmk8ZNAGx9iAS10rgrGcb_z9EKeXUU_lmJ5QES7F8Yl7ev8tl_-XvXL218ut_JupQdtnthgPh0D8kFcMjgkh4rzFqLX7lci3KsphDjg-cFDGIWMKYkFeDgyzShkVd2bgxxV_78OeW9G6mZL7k0_py_I8yZupMN6fC_JgS1fkad1JcnH1-TPKHu0uB-STtt6t_Qkw5RmWtOO2DUF0wcYbA3FtVc63W6adUA6d3W7se9ie4P_N1G4z_muPu6Gzlz1LDhr6OSh0VVaFXQxvFz44-raZ3S2wsy-ko6G_dB1hC8M7pf7gHYtOK31G3J1Ovk5PvOb8gu-Flxu_ByXOgDgiEALoVUuhc0CHkdJABhEc2myQoZ5pk0YsSyzUgukkreKa2ZyA37rLTkqq9K-J5SzWOtC55nMwwjUI7axSBIDoVpitbKBR760AknvapaNFNAJCjDdCdAjIxTVrgMSY7sT1f1N2qhHmnBkkJOBibWNIsXgeUVstCx4lkvwzh75hoJO0XxBmjprdiHAOJEIKx1i-RVAaYHyyHGnJ5id7ja3qpI2Zr9O8QeAiAmiRo983jXjlZjKVtpq6_rEWFwZx_Ku1qzdK7UK6hHV0bnOO3dbwEYcKXhjEx_--8qP5BnDrR0uVeeYHG3ut_YTBFybvAdmtlQ98mQ0uZhfwud4dn1-0nPLF3D8vgzhOI3injPEvzE6MZk |
link.rule.ids | 230,315,733,786,790,870,891,2115,2236,12083,21416,24346,27955,27956,31752,31753,33777,33778,38549,43343,43838,43928,53825,53827,74100,74657,74767 |
linkProvider | National Library of Medicine |
linkToHtml | http://utb.summon.serialssolutions.com/2.0.0/link/0/eLvHCXMwnV1Lb9NAEF5BKgQS4lFehgILQuLk1F7ba_uEkrRVAk2DSFv1tvI-XBDCLo1dqfwcfikz9jrUIHHgZnkn9m707czOeOYbQt5oxo2JQuTTZuCgpFy7qae0C2cBFSkZ5yzAeuf5AZ8ehe9PohMbcFvZtMpOJzaKWpcKY-TbSFMOxggM8ruz7y52jcKvq7aFxnWyAYaVJQOyMVkcz3Y6XczR92v5hAJw7rcv_NBnLOZhzwo1ZP1_q-QrNqmfL3nFAO3dJaKbept38nVYV3KofvzB6vj_a7tH7tizKR21YLpPrplik9xou1VebpLbbYiPtpVLD8jPcXZpsAaTzrseu3QnwzRq2lKdmBUFdQOut9EU4710Xlc29kg_Nr3CUXZZn-I3LgrPma178lZ00XTsgrua7l7Y_UHLnC5Hn5bupDx2GV18w2zCgo5HQ78RhAsGz5MueNgGFOXqITna2z2cTF3b8sFVUcArV2J4BZyqyFNRpGLJI5N5QRKmHvg9KuA6y7kvM6X9kGWZ4SrC_87EgWJaatCVj8igKAvzhNCAJUrlSmZc-iFAMjFJlKYajoepUbHxHPK6g4A4a5k9BHhEiBOxxolDxgiOtQCScTc3yvNTYfe2SANkreOeTpQJw5jB-_JEK54HmeRgERzyFqElUGUAflRmKx9gnki-JUbY8gU8Qy92yFZPEra66g93-BFW1azEb_A45NV6GH-J6XOFKetGJsGGzjiXxy2W10sKkH4JnE6HxD2U99bcHym-fG6IyNM4wfjA039P6yW5OT2c74v92cGHZ-QWw_qRJh9oiwyq89o8h1NdJV_YrfsLQxBNzw |
linkToPdf | http://utb.summon.serialssolutions.com/2.0.0/link/0/eLvHCXMwfV1Nb9QwEB1BEQgJIShfgQIGIXEKmziJk5zQbttVC2xbsbTaW-SvtD2QlG62Uv8Ov5SZxBsaIXFbxU7W0Yxn_JzxewAfDBfWJjHxaXMEKLkwfh5o4-NaQCdapSWP6Lzz7EDsHcdfFsnC1T8tXVnlOia2gdrUmvbIR0RTjskIE_KodGURRzvTzxe_fFKQoi-tTk7jNtzBLBmQjEO66MGXIBTYMQtFCPNHV2Eccp6KeJCPWtr-f4Pzjew0rJy8kYqmj-ChW0OycWf0x3DLVptwt1OVvN6EB91WHOtOGD2B3xN5bemsJJuttXDZjqRyZ9ZRktglw7CAENkaRvuybLZq3B4hO2o1vanvfHVK36IYPme_185t2GGrrIVXDdu9cn7M6pLNx9_n_nZ94nN2-JOq_io2GX8K2474g-PzlI9I2GJAWz6F4-nuj-0930kz-DqJROMr2gZB8JMEOkl0qkRiZRBlcR4gPtGRMLIUoZLahDGX0gqdkP1sGmlulMGY9gw2qrqyL4BFPNO61EoKFcboOpnNkjw3uIzLrU5t4MH7tYGKi46Bo0DkQlYseit6MCHT9R2INLu9UF-eFm4OFnlE7HIiMJm2cZxy_L8yM1qUkVQCI7cHH8nwBU1ttK6W7oQCjpNIsooxSbMgggtSD7YGPXFK6mHz2nUKFxKWxV8H9uBd30x3UplbZetV2ycj4WUay_PO0_pXiogmCcGhB-nABwfvPGypzs9awvA8zQjHv_z_sN7CPZxRxbf9g6-v4D6nYx5t2c4WbDSXK_saF1-NetPOqj_k6C2s |
openUrl | ctx_ver=Z39.88-2004&ctx_enc=info%3Aofi%2Fenc%3AUTF-8&rfr_id=info%3Asid%2Fsummon.serialssolutions.com&rft_val_fmt=info%3Aofi%2Ffmt%3Akev%3Amtx%3Ajournal&rft.genre=article&rft.atitle=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&rft.jtitle=Viruses&rft.au=Kumar%2C+Naveen&rft.au=Kaushik%2C+Rahul&rft.au=Singh%2C+Ashutosh&rft.au=Uversky%2C+Vladimir+N&rft.date=2022-12-01&rft.eissn=1999-4915&rft.volume=14&rft.issue=12&rft_id=info:doi/10.3390%2Fv14122764&rft_id=info%3Apmid%2F36560768&rft.externalDocID=36560768 |
thumbnail_l | http://covers-cdn.summon.serialssolutions.com/index.aspx?isbn=/lc.gif&issn=1999-4915&client=summon |
thumbnail_m | http://covers-cdn.summon.serialssolutions.com/index.aspx?isbn=/mc.gif&issn=1999-4915&client=summon |
thumbnail_s | http://covers-cdn.summon.serialssolutions.com/index.aspx?isbn=/sc.gif&issn=1999-4915&client=summon |