Omicron SARS-CoV-2 Variants in an In Silico Genomic Comparison Study with the Original Wuhan Strain and WHO-Recognized Variants of Concern
, , e | 21 dic 2022
INFORMAZIONI SU QUESTO ARTICOLO
Article Category: Original Paper
Pubblicato online: 21 dic 2022
Pagine: 577 - 587
Ricevuto: 19 set 2022
Accettato: 12 nov 2022
DOI: https://doi.org/10.33073/pjm-2022-053
Parole chiave
© 2022 Elmutuz H. Elssaig et al., published by Sciendo
This work is licensed under the Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International License.
Fig. 1
Fig. 2
The unique non-common mutations among Omicron variants.
| Nucleotide mutation | Protein mutation | Type of mutation | Gene | Comment |
|---|---|---|---|---|
| C24503T | L981F | Nonsynonymous | S gene | Not detected in (EPI-ISL-6640916) variant |
| ΔΔGTTTGTCTG 11283–1129 | Δ3674–3676 ΔLSG | Frameshift (deletion) | ORF1a/b | Not detected in variant (EPI_ISL_6647956) |
| C27807T | Synonymous | ORF7b | Not detected in (EPI_ISL_8182845) variant | |
| T13195C | synonymous | ORF1a/b | Not detected in one (EPI_ISL_8182845) variant | |
| Ins22194T T22195G | Δ211N | Frameshift (deletion) | S gene | |
| T22197G A22198C | L212I | Nonsynonymous | S gene | |
| INS22202–22203 AG |
INS214–216 EPE | Frameshift (insertion) | S gene | |
| T22673C C22674T | S371L | Nonsynonymous | S gene | |
| T22882G | N440K | Nonsynonymous | S gene | |
| G22898A | G446S | Nonsynonymous | S gene | |
| T22679C | S373P | Nonsynonymous | S gene | |
| G22813T | K417N | Nonsynonymous | S gene | Not detected in one (EPI_ISL_8182845) variant |
| Δ6513–6515 ΔGTT | Δ2083 S L2084I | Frameshift (deletion) | ORF1a/b | Not and detected EPI_ISL_in 6647956two variants ) (EPI-ISL-6640916 |
| A27259C | Synonymous | M gen | Not detected in two variants (EPI_ISL_6647956 and (EPI_ISL_8182845) | |
| G22992A | S477N | Nonsynonymous | S gene | Not detected in three variants |
| A23013C | E484A | Nonsynonymous | S gene | |
| A23040G | Q493R | Nonsynonymous | S gene | |
| G23048A | G496S | Nonsynonymous | S gene | |
| A23055G | Q498R | Nonsynonymous | S gene |
Distribution and type of mutations among variants of concern of SARS-CoV-2.
| of mutation Type | 3’UTR | ORF10 | N gene | ORF8 | ORF7b | ORF7a | ORF6 | M gene | E gene | ORF3 | S gene | ORFa/b1 | 5’UTR | Total |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Non-coding | 2 | – | – | – | – | – | – | – | – | – | – | – | 3 | 5 |
| Non- synonymous | – | – | 11 | 6 | 1 | 3 | – | 4 | 2 | 5 | 52 | 43 | – | 127 |
| Synonymous | – | – | 5 | 1 | 1 | – | 1 | – | 1 | 2 | 4 | 36 | – | 51 |
| Frame shift/insertion | – | – | 1 | – | – | – | – | – | – | – | 3 | – | – | 4 |
| Frame shift/deletion | – | – | 4 | – | – | – | – | – | – | – | 15 | 3 | – | 22 |
| Nonsense | – | – | – | 1 | – | – | – | – | – | – | – | – | – | 1 |
| 2 | 21 | 8 | 2 | 3 | 1 | 4 | 3 | 7 | 74 | 82 | 3 | 210 |
Mutations shared between Omicron and other VOCs.
| Nucleotide mutation | mutation Protein | Type of mutation | Gene | Comment |
|---|---|---|---|---|
| Δ21767-21769 ΔCAT | Δ69H | Frameshift (deletion) | S gene | Shared with Alpha variant (EPI_ISL_6756515) |
| Δ21770 ΔG | Δ70V | Frameshift (deletion) | S gene | |
| C23525T | H655Y | Nonsynonymous | S gene | Shared with Gamma variant (EPI_ISL_6228367) |
| C10029T | T3255I | Nonsynonymous | ORF1a/b | Shared with Delta (EPI_ISL_6832166) |
| C21846T | T95I | Nonsynonymous | S gene | and Mu (EPI_ISL_4470504) variants |
| C23604A | P681H | Nonsynonymous | S gene | Shared and Mu with (EPI_Alpha ISL_(4470504EPI_ISL_) 6756515variants ) |
| G28881T | R203K | Nonsynonymous | N gene | Shared with Alpha (EPI_ISL_6756515) |
| G28882A | Synonymous | N gene | and Gamma (EPI_ISL_6228367) variants | |
| G28883C | G204R | Nonsynonymous | N gene | |
| C22995A | T478K | Nonsynonymous | S gene | Shared with Delta (EPI_ISL_6832166) variant |
| A23063T | N501Y | Nonsynonymous | S gene | Shared with Alpha (EPI_ISL_6756515), Beta (EPI_ISL_5416540), Gamma (EPI_ISL_6228367), Mu (EPI_ISL_4470504), variants |
The unique common mutations among Omicron variants.
| Nucleotide Mutation | Protein mutation | Type of mutation | Gene |
|---|---|---|---|
| A2832G | K856R | Nonsynonymous | ORF1a/b |
| 3T5386G | – | Synonymous | ORF1a/b |
| G8393A | A2710T | Nonsynonymous | ORF1a/b |
| C10449A | – | Synonymous | ORF1a/b |
| A11537G | I3758V | Nonsynonymous | ORF1a/b |
| C15240T | – | Synonymous | ORF1a/b |
| A18163G | I5968V | Nonsynonymous | ORF1a/b |
| ΔΔ21762 21764 ΔC ΔA | A67V | Frameshift (deletion) | S gene |
| Δ21767–21769 ΔCAT | Δ69H | Frameshift (deletion) | S gene |
| Δ21770 ΔG | Δ70V | Frameshift (deletion) | S gene |
| Δ21987–21988 ΔGT | G142D | Frameshift (deletion) | S gene |
| Δ21989–21991 ΔGTT | Δ143V | Frameshift (deletion) | S gene |
| Δ21992–21994 ΔTAT | Δ144Y | Frameshift (deletion) | S gene |
| Δ21995 ΔG | Δ145Y | Frameshift (deletion) | S gene |
| G22578A | G339D | Nonsynonymous | S gene |
| C23202A | T547K | Nonsynonymous | S gene |
| C23525T | H655Y | Nonsynonymous | S gene |
| T23599G | N679K | Nonsynonymous | S gene |
| C23854A | N764K | Nonsynonymous | S gene |
| G23948T | D796Y | Nonsynonymous | S gene |
| C24130A | N856K | Nonsynonymous | S gene |
| A24424T | Q954H | Nonsynonymous | S gene |
| T24469A | N969K | Nonsynonymous | S gene |
| C25000T | – | Synonymous | S gene |
| C25584T | – | Synonymous | ORF3a |
| C26270T | T9I | Nonsynonymous | E gene |
| A26530G | D3G | Nonsynonymous | M gene |
| G26709A | A63T | Nonsynonymous | M gene |
| C28311T | P13L | Nonsynonymous | N gene |
| Δ28363–28364 ΔGA | – | Frameshift (deletion) | N gene |
| Δ28365–28367 ΔGAA | Δ31E | Frameshift (deletion) | N gene |
| Δ28368–28370 ΔCGC | Δ32R | Frameshift (deletion) | N gene |
| Δ28371 ΔA | Δ33S | Frameshift (deletion) | N gene |