SARS-CoV-2 Variant Recombinant Proteins

Assay Genie offers a large range of industry-leading recombinant proteins for SARS-CoV-2 (COVID-19) research. Due to the emergence of different variants, Assay Genie has launched Spike proteins for the Alpha, Beta & Gamma variants to help in the fight against COVID-19. Also included in this new range are other variants identified such as E484K, V367F, K458R, F342, V483A, A435S, N354D, D614G, G476S and W436R.

SARS-CoV-2 Structure

SARS-CoV-2 Variants

SARS-CoV-2 Variant Proteins

SARS-CoV-2 Mutations

Rapid Tests

SARS-CoV-2 Structure

Coronaviruses are a family of viruses named for their crown-like appearance when imaged (corona being the Latin for crown). The large, type I transmembrane spike glycoprotein accounts for this notable feature. It is a heavily-glycosylated, cell-surface protein which is thought to mediate viral entry into susceptible cells. This spike glycoprotein, called ‘S’, is trimeric in structure. In addition to the S protein, there are three other structural base proteins: the envelope, membrane, and nucleocapsid. The S protein has two distinct functional domains, termed S1 and S2, both of which are necessary for a coronavirus to successfully enter a cell.

SARS-CoV-2 Uptake

ACE2 is a receptor of human coronaviruses, such as SARS and HCoV-NL63. It has been determined to be a functional receptor which facilitates the uptake of SARS-CoV-2 into host cells [1-4]. ACE2 is expressed in multiple locations and cell types, notably including alveolar epithelial cells, surface enterocytes within the small intestine, and vascular endothelial cells of the lung, kidneys and heart [5].

SARS-CoV-2 entry into susceptible cells is mediated by the S1 subunit of the coronavirus transmembrane 'spike' glycoprotein. S1 contains a receptor binding domain (RBD) at residues 318–510, which recognises and binds to the LYS341 residue of ACE2 with high affinity [6,7].

The RBD is therefore the critical determinant of virus-receptor interaction and is responsible for infectivity of SARS-CoV-2 viral molecules.

SARS-CoV-2 Variants

SARS-CoV-2 variants arise from adaptive mutations in the genome of the virus which can affect it’s pathogenic potential. The major proteins which have site-specific mutations are the S (Spike glycoprotein) and N (Nucleoprotein). There are variants of interest (VOI) and variants of concern (VOC). Usually if a variant spreads rapidly such as the Alpha, Beta, Gamma & Delta variants, it becomes a VOC. The vast majority of SARS-CoV-2 variants are deemed more transmissible and they often cause an increased severity of disease when they infect people.

COVID-19 is an ongoing public healthcare emergency. To overcome the pandemic and find balance within society, it has been said that identifying changes in viral infectivity is crucial. This may allow regions affected by low infectivity strains to refine quarantine policies so that the process of repairing the economy can begin. Conversely, in regions affected by highly infective strains, more stringent quarantine policies may be implemented to reduce incident cases, hospital admissions, and deaths. In this way, the monitoring of SARS-CoV-2 mutations therefore may be the best approach to curbing the spread of disease. Not only this, but with more research on the variant strains of SARS-CoV-2 will come improved therapies for the treatment of COVID-19.

Alpha (B.1.1.7 lineage)	Beta (B.1.351 lineage)	Gamma (P.1 lineage)	Delta (B.1.617.2 lineage)
Kappa (B.1.617.1 lineage)	Lambda (C.37 lineage)	Mu (B.1.621 lineage)	Omicron (B.1.1.529 lineage)

List of common SARS-CoV-2 Variants

Alpha (B.1.1.7 lineage)

The Alpha variant was found in the United Kingdom (UK) in September 2020. The Alpha variant has 17 mutations in the genome of the virus. 8 of these mutations are found in the S protein and they are Δ69-70 deletion, Δ144 deletion, N501Y, A570D, P681H, T716I, S982A, D1118H. In particular, N501Y has been shown to enhance viral attachment and entry into host cells because it causes the S protein to have an increased affinity for ACE 2 receptors.

Beta (B.1.351 lineage)

The Beta variant was discovered in South Africa in October 2020. The Beta variant includes 9 mutations in the S protein, L18F, D80A, D215G, R246I, K417N, E484K, N501Y, D614G, and A701V. Out of these 9 mutations, 3 of them (K417N, E484K, and N501Y) are included in the receptor-binding domain (RBD). The remaining mutations are located in the envelope (E) (P71L), N ( T205I) and the Open Reading Frame (ORF1a) (K1655N).

Gamma (P.1 lineage)

The Gamma variant was reported in Brazil in January 2021. This variant has 10 mutations in the S protein, L18F, T20N, P26S, D138Y, R190S, H655Y, T1027I V1176, K417T, E484K, and N501Y. Similar to the B.1.351 lineage, there are 3 mutations which are located in the RBD and they are L18F, K417N, E484K.

Delta (B.1.617.2 lineage)

The Delta variant was first discovered in India in October 2020. The Delta variant has 15 mutations in the S protein, T19R, (V70F*), T95I, G142D, R158G, (A222V*), (W258L*), (K417N*), L452R, T478K, D614G, P681R, D950N, 156 deletion and 157deletion.

Kappa (B.1.617.1 lineage)

The Kappa variant was first discovered in India in 2020. The kappa variant has 8 different mutations in total, T95I, G142D, E154K, L452R, E484Q, D614G, P681R, Q1071H. The mutations of the S protein are L452R, E484Q, D614G, P681R.

Lambda (C.37 lineage)

The Lambda variant was first detected in Peru in December 2020. The lambda variant has 7 mutations in the S proteins, G75V, T76I, Δ247/253 deletion, L452Q, F490S, D614G, and T859N.

Mu (B.1.621 Lineage)

The Mu Variant was first detected in Colombia in January 2021. The Mu variant has R346K, E484K and N501Y mutations in the RBD and D614G, P681H and D950N mutations in other regions of the S protein.

Omicron (B.1.1.529 lineage)

The Omicron variant is one of the newest SARS-CoV-2 variants to arise and it has been designated a VOC by the World Health Organisation (WHO). The Omicron variant was first reported in South Africa in November 2021. Researchers are still investigating the full extent of the infection caused by Omicron and it’s pathogenesis. Preliminary results illustrate an increased risk of reinfection with this variant in comparison to other SARS-CoV-2 variants. There are over 35 changes to the S protein.

SARS-CoV-2 Variant Mutations

SARS-CoV-2 Variant	Mutation
Alpha (B.1.1.7 lineage)	Mutations of the S protein: N501Y, A570D, D614G, P681H, T7161, S982A, D1118H, H69-V70 deletion, Y144 deletion
Beta (B1.351 lineage)	Mutations of the S protein: L18F, D80A, D215G, R2461, K417N, E484K, N501Y, D1614G, A701V, LAL 242-244 deletions
Gamma (P.1 lineage)	Mutations of the S protein: L18F, T20 N, P26S, D138Y, R190S, K417T, E484K, N501Y, D614G, H655Y, T1027I, V1176F
Delta (B.1.617.2 lineage)	Mutations of the S protein: T19R, (V70F), T95I, G142D, R158G, (A222V), (W258L), (K417N), L452R, T478K, D614G, P681R, D950N, 156 deletion, 157deletion
Kappa (B.1.617.1 lineage)	Mutations of the S protein: L452R, E484Q, D614G, P681R
Lambda (C.37 lineage)	Mutations of the S protein: G75V, T76I, L452Q, F490S, D614G, T859N, 247/253 deletions
Mu (B.1.621 Lineage)	Mutations of the S protein: R346K, E484K, N501Y, D614G, P681H, D950N
Omicron (B.1.1.529 lineage)	Mutations of the S protein: A67V, ΔH69-V70, T95I, G142D, V143-Y145, N211I, ΔL212I, 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

SARS-CoV-2 Common Mutations

There are several different strains of SARS-CoV-2. The amino acid sequence of the RBD of such strains are largely conserved. In spite of this, over the past number of months, mutations in the RBD have appeared globally that may be the cause of the spread of strains with enhanced infectivity.

In total there are numerous SARS-CoV-2 strains that contain a mutation within the RBD domain of the SARS-CoV-2 molecule [4]. These can be clustered into 9 main types, which are described below.

V367F

V367F is one of the most common mutations of the SAR-CoV-2 viral molecule. It has been found in a total of 6 strains globally, and has been causative of the highly infective strains of SARS-CoV-2 found in Hong Kong and France [4]. As the RBD is conserved in SARS-CoV-2, the coincidence of six strains with the same mutation across large geographic distances indicates that this mutant is more robust and that these strains originated as a novel sub-lineage, given the close isolation dates (January 22 and 23 (2020), respectively) [4]. An alternate view is that asymptomatic individuals with the same mutation were “super-infecting” travellers.

By experimental comparison to the prototype spike protein, the spike protein containing the V367F mutation experiences significantly enhanced binding affinity to target receptor, ACE2, thus suggesting enhanced infectivity [4]. This is presumably due to the structural stabilization of the RBD beta-sheet scaffold caused by the V367F mutation [4].

D614G

The D614G mutation differs slightly from other SARS-CoV-2 mutations. The D614G mutation is located in the S1 region and is outside of the RBD of the SARS-CoV-2 S protein. It has been confirmed that the D614G change increases virus infectivity by elevating it's sensitivity to protease and that this mutation has spread widely [8]. This mutation has been observed alongside several of the dominant mutations in the RBD domain, such as V367F, S477N, V483A, K458R ,G485R, A520S, P384L, A522V, and P330S [8]. As explained previously, the V367F mutants were initially discovered in January, 2020 in Hong Kong. Following this, the highly infective D614G+V367F dual mutant was discovered in the Netherlands in March, 2020. This dual mutant spread rapidly and has since been detected mostly in Europe in countries such as United Kingdom, the Netherlands, Spain, Northern Ireland, Switzerland, and Iceland, as well as in the USA, Australia, and Taiwan [4].

K458R

This mutation, although one of the most common mutations observed of the SARS-CoV-2 viral molecule, has been witnessed only in co-existence with the D614G mutation [9]. Experimentation has been carried out establish if both K458R and D614G mutations increase infectivity of SAR-CoV-2 in a synergistic manner [9]. When assessed, the D614G+K458R strain showed increased infectivity in comparison to the reference spike protein. However, when compared with single D614G variant of SARS-CoV-2, there was no difference in affinity or infectivity. This therefore suggests that although the K458R co-exists with the D614G mutation, it has no effect on infectivity.

F342L

The F342L strain of SARS-CoV-2 was found originally in England [4]. Experimental analysis has indicated that the F342L mutant strain demonstrates similar binding affinity to target ACE2 receptors when compared with a prototype SARS-CoV-2 molecule [4]. This suggests that the F342L mutation does not effect infectivity of SAR-CoV-2.

A435S

The A435S mutation was originally detected in Finland. Similar to F342L and G475S, the A435S strain has been shown to experience similar affinity to ACE2 as SARS-CoV-2 molecules with non-mutated RBDs [4].

N354D

N354D is one of the 'higher affinity' mutants. This strain was first detected in Shenzhen, China [4]. It is most commonly observed as a dual mutant strain alongside D364Y. Experimental analysis has shown D364Y to be the main contributor to the enhanced infectivity of this dual mutant strain [4]. Both mutations have since not been be detected in China or globally. It is speculated this may be due to the strict quarantine regimen implemented in China at the beginning of the pandemic [4].

V483A

V483A has been predominantly observed in the U.S.A. It is considered to have similar infectivity than the non-mutated form of SARS-CoV-2. Thirteen sub-lineages of V483A has been detected in the U.S.A. It has often been observed alongside the S1 D614G mutant [8].

G476S

Similar to the V483A strain, the G476S strain has been widely detected in the U.S.A. There have been seven sub-lineages of G476S detected. This strain is said to experience similar affinity to ACE2, thus meaning it is similarly infective as SARS-CoV-2 with no mutations in it's RBD [8].

W436R

This was one of the original mutant variants detected of SARS-CoV-2. The W436R strain was first detected in Wuhan. It is considered one of the most infective strains of the virus, alongside V367F, N354D/D364Y, and D614G [4]. The W436R mutation within the RBD of SARS-CoV-2 has been shown to increase binding affinity between it and ACE2 due to the stabilization of the beta structure scaffold of the RBD, as caused by the mutation.