Mutational cascade of SARS-CoV-2 leading to evolution and emergence of omicron variant
Copyright © 2022 Elsevier B.V. All rights reserved..
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.
| Medienart: |
E-Artikel |
|---|
| Erscheinungsjahr: |
2022 |
|---|---|
| Erschienen: |
2022 |
| Enthalten in: |
Zur Gesamtaufnahme - volume:315 |
|---|---|
| Enthalten in: |
Virus research - 315(2022) vom: 02. Juli, Seite 198765 |
| Sprache: |
Englisch |
|---|
| Beteiligte Personen: |
Bansal, Kanika [VerfasserIn] |
|---|
| Links: |
|---|
| Anmerkungen: |
Date Completed 17.05.2022 Date Revised 17.12.2022 published: Print-Electronic Citation Status MEDLINE |
|---|
| doi: |
10.1016/j.virusres.2022.198765 |
|---|
| funding: |
|
|---|---|
| Förderinstitution / Projekttitel: |
|
| PPN (Katalog-ID): |
NLM338971726 |
|---|
| LEADER | 01000naa a22002652 4500 | ||
|---|---|---|---|
| 001 | NLM338971726 | ||
| 003 | DE-627 | ||
| 005 | 20231226001852.0 | ||
| 007 | cr uuu---uuuuu | ||
| 008 | 231226s2022 xx |||||o 00| ||eng c | ||
| 024 | 7 | |a 10.1016/j.virusres.2022.198765 |2 doi | |
| 028 | 5 | 2 | |a pubmed24n1129.xml |
| 035 | |a (DE-627)NLM338971726 | ||
| 035 | |a (NLM)35367284 | ||
| 035 | |a (PII)S0168-1702(22)00093-4 | ||
| 040 | |a DE-627 |b ger |c DE-627 |e rakwb | ||
| 041 | |a eng | ||
| 100 | 1 | |a Bansal, Kanika |e verfasserin |4 aut | |
| 245 | 1 | 0 | |a Mutational cascade of SARS-CoV-2 leading to evolution and emergence of omicron variant |
| 264 | 1 | |c 2022 | |
| 336 | |a Text |b txt |2 rdacontent | ||
| 337 | |a ƒaComputermedien |b c |2 rdamedia | ||
| 338 | |a ƒa Online-Ressource |b cr |2 rdacarrier | ||
| 500 | |a Date Completed 17.05.2022 | ||
| 500 | |a Date Revised 17.12.2022 | ||
| 500 | |a published: Print-Electronic | ||
| 500 | |a Citation Status MEDLINE | ||
| 520 | |a Copyright © 2022 Elsevier B.V. All rights reserved. | ||
| 520 | |a 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 | ||
| 520 | |a 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 | ||
| 520 | |a 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) | ||
| 520 | |a 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 | ||
| 650 | 4 | |a Journal Article | |
| 650 | 4 | |a NSP, non-structural protein | |
| 650 | 4 | |a SARS-CoV-2, COVID-19, genome-wide, evolution, variants, VOC, VOI, VUM, SNP, mutation, non-synonymous, silent mutation, spike, RNA dependent RNA polymerase, NSP, UTR: Abbreviations: VOC, variant of concern | |
| 650 | 4 | |a UTR, untranslated region | |
| 650 | 4 | |a VOI, variant of interest | |
| 650 | 4 | |a VUM, variant under monitoring | |
| 650 | 4 | |a rdrp, RNA dependent RNA polymerase | |
| 650 | 7 | |a Spike Glycoprotein, Coronavirus |2 NLM | |
| 650 | 7 | |a spike protein, SARS-CoV-2 |2 NLM | |
| 700 | 1 | |a Kumar, Sanjeet |e verfasserin |4 aut | |
| 773 | 0 | 8 | |i Enthalten in |t Virus research |d 1984 |g 315(2022) vom: 02. Juli, Seite 198765 |w (DE-627)NLM01292136X |x 1872-7492 |7 nnns |
| 773 | 1 | 8 | |g volume:315 |g year:2022 |g day:02 |g month:07 |g pages:198765 |
| 856 | 4 | 0 | |u http://dx.doi.org/10.1016/j.virusres.2022.198765 |3 Volltext |
| 912 | |a GBV_USEFLAG_A | ||
| 912 | |a GBV_NLM | ||
| 951 | |a AR | ||
| 952 | |d 315 |j 2022 |b 02 |c 07 |h 198765 | ||