COVID-19 mutations: An overview

Table 1 Showing characteristic features of various variants of concerns

VOCs	Transmissibility	Severity	Effect on neutralization by mABs		SGTF	Present status	Vaccine efficacy
Alpha	Increased transmissibility (50%-100%) with R0 1.75-fold higher compared to original lineage[32]	Increased severity. Hazard of death of 55% (95%CI: 39%–72%) higher than in cases without SGTF after adjustment[33]	No impact on neutralization by mABs, and minimal impact by convalescent and/or post-vaccination sera[18]. E484K and/or various NTD mutations cause a significant fall in neutralization efficacy[39]		Presence	De-escalated	The ChAdOx1 nCoV-19 vaccine showed an efficacy of 70.4%[40]. The first and second dose of BNT162b2 vaccine (Pfizer–BioNTech) reported 48.7% and 93.7% effectiveness, respectively[41]. The reported efficacy of 2-doses of mRNA-1273 vaccine 98.4%[42]
Beta	Increased transmissibility	Increased risk of hospitalization, ICU admission, and mortality in comparison to Alpha and Gamma variants, but less severe disease compared to Delta[44]	45-fold decreased susceptibility to Bamlanivimab-etesevimab therapy. Casirivimab-imdevimab and sotrovimab retained susceptibility[38-40]. Moderate reduction in neutralization by convalescent and post-vaccination sera[45]		Absent	De-escalated	Full vaccination efficacy 73.0% (95%CI: 64.3%–79.5%)[46]
Gamma	1.7 to 2.4-fold higher transmissible than previous (non-P.1) infection[48]. Increased risk of reinfection	1.2 to 1.9 times more likely to result in mortality compared with previous lineages[48]	> 511 fold decreased susceptibility to Bamlanivimab-etesevimab but no change in susceptibility with Casirivimab-imdevimab and Sotrovimab[38-40]. Reduced neutralization to convalescent and post-vaccination sera		Absent	De-escalated	Full vaccination efficacy against Gamma variants 63.0% (95%CI: 47.9%–73.7%)[46]
Delta	40%-60% more transmissible than Alpha variant[49]	Increased severity of the disease[51,52] and increased risk of hospitalization[52,53].A shorter time interval between disease onset to hospitalization in comparison to the wild-type variant[44]	Neutralization is affected minimally		Absent	De-escalated	Moderate reduction in vaccine efficacy against symptomatic infection but retained efficacy against severe disease and hospitalization[45]. The 2-dose mRNA-1273 vaccine: 86.7% (95%CI: 84.3%-88.7%) efficacy against infection and 97.5% (92.7%-99.2%) efficacy against hospital admission. The 2-doses of BNT162b2 and ChAdOx1 nCoV-19 vaccine 88.0% (95%CI: 85.3%-90.1%) and 67.0% (95%CI: 61.3%-71.8%), respectively[41]
Omicron	Increased risk of transmissibility, reinfection/breakthrough infection	Severity less compared to Delta variant	Reduced or absent neutralization efficacy by vaccines and mABs[56]		SGTF except BA.2 lineage[64]	Few sublineages de-escalated (BA.1, BA.2, BA.3, BA.4, BA.5 etc.)	Booster doses are needed to mount a more appropriate immune response against symptomatic or non-symptomatic infections, transmission, and serious manifestations[44]

VOCs: Variants of concerns; SGTF: “S” gene target failure; ICU: Intensive care unit; mAbs: Monoclonal antibodies; NTD: N-terminal domain.

Table 2 Showing the five variants of concerns and their mutations

WHO label	Pango lineage	GISAID clade	Nextstrain clade	Spike protein substitutions	First detected	WHO date of designation
Alpha	B.1.1.7	GRY	201(V1)	Deletion 69-70, Deletion 144, N501Y, A570D, D614G, P681H, T716I, S982A, D1118H	United Kingdom	18th December 2020
Beta	B.1.351	GH/501Y.V2	20H(V2)	D80A, D215G, DeletionL242, DeletionA243, DeletionL244, K417N, E484K, N501Y, D614G, A701V	South Africa	18th December 2020
Delta	B.1.617.2	G/478K.V1	21A	T19R, T95I, G142D, Deletion156, Deletion157, R158G, L452R, T478K, D614G, P681R and D950N	India	VOI: 4th April, 2021 VOC: 11th May, 2021
Gamma	P.1	GR/501Y.V3	20J(V3)	L18F, T20N, P26S, D138Y, R190S, K417T, E484K, N501Y, D614G, H655Y, T1027I	Brazil	11th January 2021
Omicron	B.1.1.529 lineage	GR/484A	21K	A76V, T95I, Y145del, G339D, N440K, G446S, S477N, T478K, E484A, Q493R, G496S, Q498R, N501Y, Y505H, T547K, D614G, H655Y, N679K, P681H, N764K, D796Y, N856K, Q954H, N969K, L981F, L212I, S371L, S373P, S375F, K417N. ORF1a: K856R, ORF1a: L2084I, ORF1a: A2710T, ORF1a: T3255I, ORF1a: P3395H, ORF1a: I3758V, ORF1b: P314L, ORF1b: I1566V, and ORF9b: P10S	Botswana and South Africa	26th November 2021

WHO: World health organization; GISAID: Global initiative on sharing all influenza data; VOI: Variants of interest; VOC: Variants of concern.