key: cord-0682879-liiclkdd authors: Bansal, Kanika; Kumar, Sanjeet title: Mutational cascade of SARS-CoV-2 leading to evolution and emergence of omicron variant date: 2021-12-07 journal: bioRxiv DOI: 10.1101/2021.12.06.471389 sha: 2a58df0774a67a2aeb83d554205a22bf0e8dedc1 doc_id: 682879 cord_uid: liiclkdd Background Emergence of new variant of SARS-CoV-2, namely omicron, has posed a global concern because of its high rate of transmissibility and mutations in its genome. Researchers worldwide are trying to understand the evolution and emergence of such variants to understand the mutational cascade events. Methods We have considered all omicron genomes (n = 302 genomes) available till 2nd December 2021 in the public repository of GISAID along with representatives of variants of concern (VOC), i.e., alpha, beta, gamma, delta, and omicron; variant of interest (VOI) mu and lambda; and variant under monitoring (VUM). Whole genome-based phylogeny and mutational analysis were performed to understand the evolution of SARS CoV-2 leading to emergence of omicron variant. Results Whole genome-based phylogeny depicted two phylogroups (PG-I and PG-II) forming variant specific clades except for gamma and VUM GH. Mutational analysis detected 18,261 mutations in the omicron variant, majority of which were non-synonymous mutations in spike (A67, T547K, D614G, H655Y, N679K, P681H, D796Y, N856K, Q954H), followed by RNA dependent RNA polymerase (rdrp) (A1892T, I189V, P314L, K38R, T492I, V57V), ORF6 (M19M) and nucleocapsid protein (RG203KR). Conclusion Delta and omicron have evolutionary diverged into distinct phylogroups and do not share a common ancestry. While, omicron shares common ancestry with VOI lambda and its evolution is mainly derived by the non-synonymous mutations. (https://www.ncbi.nlm.nih.gov/nuccore/NC_045512.2) and omicron 156 (OL677199.1) (https://www.ncbi.nlm.nih.gov/nuccore/OL677199) separately. Omicron hCoV-19/Botswana/R42B5_BHP_AAC25114/2021 VOC_Omicron_hCoV-19/Botswana/R42B5_BHP_AAC25114/2021 betacoronavirus EPI_ISL_6752026 11-11-2021 Africa Botswana Lobatse Africa Botswana Lobatse genome 29693 Human 43 Male B.1.1.529 GR Omicron hCoV-19/Botswana/R42B90_BHP_000842207/2021 VOC_Omicron_hCoV-19/Botswana/R42B90_BHP_000842207/2021 betacoronavirus EPI_ISL_6752027 21-11-2021 Africa Botswana Gaborone Africa Botswana Gaborone genome 29684 Human 58 Male B.1.1.529 GR Omicron hCoV-19/Botswana/R43B69_BHP_2421009581/2021 VOC_Omicron_hCoV-19/Botswana/R43B69_BHP_2421009581/2021 betacoronavirus EPI_ISL_6774081 23-11-2021 Africa Botswana Gaborone Africa Botswana Gaborone genome 29714 Human 38 Male B.1.1.529 GR 21-11-2021 Africa Botswana Palapye Africa Botswana Palapye genome 29714 Human 44 Male B.1.1.529 GR Palapye Primary Hospital Laboratory Botswana Harvard HIV Reference Laboratory Sikhulile Moyo, Wonderful T. Choga, Dorcas Maruapula Omicron hCoV-19/Botswana/R43B68_BHP_121142361/2021 VOC_Omicron_hCoV-19/Botswana/R43B68_BHP_121142361/2021 betacoronavirus EPI_ISL_6774083 23-11-2021 Africa Botswana Gaborone Africa Botswana Gaborone genome 29714 Human 41 Female B.1.1.529 GR Omicron hCoV-19/Botswana/R43B34_BHP_AAC25685/2021 VOC_Omicron_hCoV-19/Botswana/R43B34_BHP_AAC25685/2021 betacoronavirus EPI_ISL_6774084 22-11-2021 Africa Botswana Gaborone Africa Botswana Gaborone genome 29714 Human 32 Female B.1.1.529 GR Omicron hCoV-19/Botswana/R43B71_BHP_121142518/2021 VOC_Omicron_hCoV-19/Botswana/R43B71_BHP_121142518/2021 betacoronavirus EPI_ISL_6774085 23-11-2021 Africa Botswana Gaborone Africa Botswana Gaborone genome 29714 Human 48 Male B.1.1.529 GR 21-11-2021 Africa Botswana Palapye Africa Botswana Palapye genome 29714 Human 39 Male B.1.1.529 GR Palapye Primary Hospital Laboratory Botswana Harvard HIV Reference Laboratory Sikhulile Moyo, Wonderful T. Choga, Dorcas Maruapula Omicron hCoV-19/Botswana/R43B67_BHP_2021010142/2021 VOC_Omicron_hCoV-19/Botswana/R43B67_BHP_2021010142/2021 betacoronavirus EPI_ISL_6774087 23-11-2021 Africa Botswana Gaborone Africa Botswana Gaborone genome 29714 Human 47 Male B.1.1.529 GR Omicron hCoV-19/Botswana/R43B70_BHP_4021000195/2021 VOC_Omicron_hCoV-19/Botswana/R43B70_BHP_4021000195/2021 betacoronavirus EPI_ISL_6774088 23-11-2021 Africa Botswana Gaborone Africa Botswana Gaborone genome 29714 Human 38 Male B.1.1.529 GR Omicron hCoV-19/Botswana/R43B33_BHP_AAC25682/2021 VOC_Omicron_hCoV-19/Botswana/R43B33_BHP_AAC25682/2021 betacoronavirus EPI_ISL_6774089 22-11-2021 Africa Botswana Gaborone Africa Botswana Gaborone genome 29707 Human 5 Male B.1.1.529 GR Omicron hCoV-19/Botswana/R43B65_BHP_2021010151/2021 VOC_Omicron_hCoV-19/Botswana/R43B65_BHP_2021010151/2021 betacoronavirus EPI_ISL_6774090 23-11-2021 Africa Botswana Gaborone Africa Botswana Gaborone genome 29714 Human 52 Male B.1.1.529 GR Omicron hCoV-19/Botswana/R43B66_BHP_521004487/2021 VOC_Omicron_hCoV-19/Botswana/R43B66_BHP_521004487/2021 betacoronavirus EPI_ISL_6774091 23-11-2021 Africa Botswana Gaborone Africa Botswana Gaborone genome 29714 Human 47 Male B.1.1.529 GR Africa Botswana Palapye Africa Botswana Palapye genome 29714 Human 45 Male B.1.1.529 GR Palapye Primary Hospital Laboratory Botswana Harvard HIV Reference Laboratory Sikhulile Moyo, Wonderful T. Choga, Dorcas Maruapula 23-11-2021 Africa Botswana Gaborone Africa Botswana Gaborone genome 29714 Human 35 Male B.1.1.529 GK Botswana Harvard HIV Reference Laboratory Botswana Harvard HIV Reference Laboratory Sikhulile Moyo, Wonderful T. Choga, Dorcas Maruapula genome 29827 Human 28 Female B.1.621.1 GH Cerballiance Charentes Angouleme CERBA HealthCare Bénédicte Roquebert Mu hCoV-19/Colombia/VAC-UTP-VG-024/2021 VOI_Mu_hCoV-19/Colombia/VAC South America Colombia Valle del Cauca South America Colombia Valle del Cauca genome 29781 Human unknown Male B.1.621 GH SYNLAB ÁNGEL DIAGNÓSTICA -Valle del Cauca Laboratorio de Biología Molecular y Biotecnología -Universidad Tecnológica de Pe Fredy A. Tabares-Villa Mu hCoV-19/Colombia/VAC-UTP-VG-026/2021 VOI_Mu_hCoV-19/Colombia/VAC South America Colombia Valle del Cauca South America Colombia Valle del Cauca genome 29781 Human unknown Female B.1.621 GH SYNLAB ÁNGEL DIAGNÓSTICA -Valle del Cauca Laboratorio de Biología Molecular y Biotecnología -Universidad Tecnológica de Pe Fredy A. Tabares-Villa Mu hCoV-19/Colombia/VAC-UTP-VG-027/2021 VOI_Mu_hCoV-19/Colombia/VAC South America Colombia Valle del Cauca South America Colombia Valle del Cauca genome 29781 Human unknown Female B.1.621 GH SYNLAB ÁNGEL DIAGNÓSTICA -Valle del Cauca Laboratorio de Biología Molecular y Biotecnología -Universidad Tecnológica de Pe Fredy A. Tabares-Villa Mu hCoV-19/Colombia/VAC-UTP-VG-029/2021 VOI_Mu_hCoV-19/Colombia/VAC South America Colombia Valle del Cauca South America Colombia Valle del Cauca genome 29775 Human unknown Female B.1.621 GH SYNLAB ÁNGEL DIAGNÓSTICA -Valle del Cauca Laboratorio de Biología Molecular y Biotecnología -Universidad Tecnológica de Pe Fredy A. Tabares-Villa Mu hCoV-19/Colombia/VAC-UTP-VG-025/2021 VOI_Mu_hCoV-19/Colombia/VAC South America Colombia Valle del Cauca South America Colombia Valle del Cauca genome 29778 Human unknown Male B.1.621 GH SYNLAB ÁNGEL DIAGNÓSTICA -Valle del Cauca Laboratorio de Biología Molecular y Biotecnología -Universidad Tecnológica de Pe Fredy A. Tabares-Villa Mu hCoV-19/Colombia/VAC-UTP-VG-228/2021 VOI_Mu_hCoV-19/Colombia/VAC-UTP-VG-228/2021 betacoronavirus EPI_ISL_5603360 South America Colombia Valle del Cauca South America Colombia Valle del Cauca genome 29781 Human unknown Female B.1.621 GH SYNLAB ÁNGEL DIAGNÓSTICA -Valle del Cauca Laboratorio de Biología Molecular y Biotecnología -Universidad Tecnológica de Pe Fredy A. Tabares-Villa Mu hCoV-19/USA/IN-LH000111869/2021 VOI_Mu_hCoV-19/USA/IN-LH000111869/2021 betacoronavirus EPI_ISL_5736581 2021 North America USA Indiana North America USA Indiana genome 29799 Human 38 Female B.1.621 GH PPHC-Purdue Unversity Animal Disease Diagnostic Laboratory genome 29714 Human 32 Female B.1.640 GH Fondation Congolaise pour la recherche medicale (FCRM), Francine Ntoumi Fondation Congolaise pour la Recherche Médicale Mfoutou Mapanguy Claujens Chastel; Batchi-Bouyou Armel Landry South America Ecuador Guayas South America Ecuador Guayas genome 29783 Human unknown unknown C.37 GR Omics Sciences Laboratory Omics Sciences Laboratory Derly Andrade Molina, Rubén Armas González genome 29769 Human 38 Male C.37 GR Laboratorio de Referencia Nacional de Virus Respiratorios Lambda hCoV-19/Argentina/INEI096534/2020 VOI_Lambda_hCoV-19/Argentina/INEI096534/2020 betacoronavirus EPI_ISL_21586938-11-2020 South America Argentina Ciudad Autonoma de Buenos Aires South America Argentina Ciudad Autonoma de Buenos Aires genome 29792 Human 27 Female C.37 GR Servicio Virosis Respiratorias-Departamento Virología-INEI Instituto Nacional Enfermedades Infecciosas C South America Peru Lima South America Peru Lima genome 29496 Human 34 Female C.37 GR Laboratorio de Referencia Nacional de Virus Respiratorio. Instituto Nacional de Salud Perú Laboratorio de Referencia Nacional de Biotecnología y Biología Molecular. Institut Carlos Padilla Rojas betacoronavirus EPI_ISL_1629764 1-1-2021 South America Peru Lima South America Peru Lima genome 29744 Human unknown unknown C.37 GR Instituto de Medicina Tropical Alexander Von Humboldt, Universidad Peruana Cayetano Here Laboratorio de Genómica Microbiana genome 29791 Human 22 Male C.37 GR Laboratorio de Referencia Nacional de Virus Respiratorios genome 29786 Human 25 Male C.37 GR Laboratorio de Referencia Nacional de Virus Respiratorios genome 29783 Human 40 Female C.37 GR Laboratorio de Referencia Nacional de Virus Respiratorios genome 29496 Human 47 Female C.37 GR Laboratorio de Referencia Nacional de Virus Respiratorio. Instituto Nacional de Salud Perú Laboratorio de Referencia Nacional de Biotecnología y Biología Molecular. Institut Carlos Padilla Rojas genome 29496 Human 38 Female C.37 GR Laboratorio de Referencia Nacional de Virus Respiratorio. Instituto Nacional de Salud Perú Laboratorio de Referencia Nacional de Biotecnología y Biología Molecular. Institut Carlos Padilla Rojas genome 29496 Human 74 Female C.37 GR Laboratorio de Referencia Nacional de Virus Respiratorio. Instituto Nacional de Salud Perú Laboratorio de Referencia Nacional de Biotecnología y Biología Molecular. Institut Carlos Padilla Rojas South America Peru Callao South America Peru Callao genome 29901 Human unknown unknown C.37 GR Laboratorio de Referencia Nacional de Virus Respiratorio genome 29890 Human unknown unknown C.37 GR Laboratorio de Referencia Nacional de Virus Respiratorio genome 29901 Human unknown unknown C.37 GR Laboratorio de Referencia Nacional de Virus Respiratorio genome 29898 Human unknown unknown C.37 GR Laboratorio de Referencia Nacional de Virus Respiratorio genome 29895 Human unknown unknown C.37 GR Laboratorio de Referencia Nacional de Virus Respiratorio genome 29899 Human unknown unknown C.37 GR Laboratorio de Referencia Nacional de Virus Respiratorio genome 29863 Human unknown unknown C.37 GR Laboratorio de Referencia Nacional de Virus Respiratorio South America Peru Lima South America Peru Lima genome 29895 Human unknown unknown C.37 GR Laboratorio de Referencia Nacional de Virus Respiratorio genome 29901 Human unknown unknown C.37 GR Laboratorio de Referencia Nacional de Virus Respiratorio genome 29887 Human unknown unknown C.37 GR Laboratorio de Referencia Nacional de Virus Respiratorio genome 29901 Human unknown unknown C.37 GR Laboratorio de Referencia Nacional de Virus Respiratorio genome 29874 Human unknown unknown C.37 GR Laboratorio de Referencia Nacional de Virus Respiratorio genome 29901 Human unknown unknown C.37 GR Laboratorio de Referencia Nacional de Virus Respiratorio South America Peru Callao South America Peru Callao genome 29888 Human unknown unknown C.37 GR Laboratorio de Referencia Nacional de Virus Respiratorio