Table 1.

Characteristics of different SARS-CoV-2 variants and efficacy of COVID-19 vaccines

Mutant strains of SARS-CoV-2	Pango lineage	First identified	GISAID clade	Site of mutation	Key mutation	Additional amino acid changes observed	Alteration of vaccine effectiveness	Antibody response	Reference
Alpha variant	B.1.1.7	UK, September 2020	GRY	Spike protein	N501Y mutation: enhanced the viral binding potency with ACE2 receptor. H69del/V70del mutation: responsible for S gene targeting failure. P681H mutation: effectively increase the viral cell entry	+ S:484 K  + S:452R	The efficacy of the AstraZeneca vaccine’s 70% and of the Pfizer vaccine is roughly 90%	High	[162, 163]
Beta variant	B.1.351	South Africa, May 2020	GH/501Y.V2	Spike protein	There are 23 mutations with 17 amino acid changes, but the notable mutations in this variant are K417N, E484K, and N501Y on the spike protein. These mutations are able to increase their binding efficacy to the ACE2 receptor	+ S:L18F	The Pfizer vaccine was 75% effective against any infection caused by the Beta variant after two doses. Novavax clinical trials in the UK revealed 89% efficacy, compared to merely 60% in South Africa, where the Beta strain was prevalent. Similarly, trials of the Johnson & Johnson vaccine in South Africa found lower levels of protection against moderate-to-severe COVID-19 than in the USA	Reduced	[163, 164]
Gamma variant	P.1	Brazil, November 2020	GR/501Y.V3	Spike protein	17 numbers of novel amino acid changes were observed, where 10 numbers of mutation in its S protein. The three main alarming mutations are N501Y, E484K, and K417T	+ S:681H	After vaccination with Moderna or Pfizer, the variant has been demonstrated to be relatively resistant to neutralisation by convalescent plasma and vaccinee sera. The severity of the loss, however, was minor (3.8 to 4.8-fold)	High	[165]
Delta variant	B.1.617.2	India, October 2020	G/478 K.V1	Spike protein	L452R and P681R mutations were observed in spike protein. Some extra mutations were observed such as Y145H, A222V, etc., in the Delta Plus variant	+ S:417 N + S:484 K	mRNA-1273 Vaccine effectiveness against infection with the Delta variant declined from 94.1% (90.5 to 96.3%) 14–60 days after vaccination to 80.0% (70.2 to 86.6%) 151–180 days after vaccination	High	[166, 167]
Epsilon variant	B.1.429B.1.427	Cedars-Sinai Medical Center, California July 2020	CAL.20C	Spike protein	I4205V in ORF1a; D1183Y in ORF1b; L452R; W152C and L452R; these mutations were identified in spike protein	+ S:13I	Neutralizing antibody titers against the B.1.427/B.1.429 variations are reduced (3 to sixfold) as compared to wild-type pseudoviruses, according to an analysis of neutralising antibody responses following spontaneous infection or mRNA vaccination	High	[168, 169]
Lambda variant	C.37	Peru, December2020	GR/452Q.V1	Spike protein	G75V,T76I, L452Q, F490S, D614G, and T859N amino acid mutations were observed in S protein	–	Lambda variant of interest confers increased infectivity and immune escape from neutralizing antibodies elicited by CoronaVac	High	[170, 171]
Mu variant	B.1.621	Colombia, January 2021	GH	Spike protein	T95I, Y144S, Y145N, R346K, E484K, or the escape mutation, N501Y, D614G, P681H, and D950N were observed	–	Mu variant shows a pronounced resistance to antibodies elicited by natural SARS-CoV-2 infection and by the BNT162b2 mRNA vaccine	High	[172, 173]
Omicron variant	B.1.1.529	Multiple countries, November 2021	GRA	Spike protein	A67V, Δ69-70, T95I, G142D, Δ143-145, Δ211, L212I, ins214EPE, G339D, S371L, S373P, S375F, K417N, N440K, G446S, S477N, T478K, E484A, Q493R, G496S, Q498R, N501Y, Y505H, T547K, D614G, H655Y, N679K, P681H, N764K, D796Y, N856K, Q954H, N969K, L981F; these mutations were observed in spike protein. Many other mutations were located in RBD 319 to 541	+ R346K	Three doses of the Pfizer BioNTech Vaccine potently minimize the Omicron variant. After two significant doses of this vaccine, reduction of titer neutralization was noted	High	[174, 175]