SARS-CoV-2 (COVID-19) Spike Variant Recombinant Proteins

There are multiple SARS-CoV-2 variants currently spreading across the planet, with four of them being designated “Variants of Concern” (VOC) by the World Health Organization (WHO). Several nomenclature systems for these variants exist, and the Greek alphabet designation introduced by WHO is the latest (Table 1). All four of these viruses have mutations (~seventeen to twenty-three) at different points in their genomes, with eight to eleven of these alterations occurring in their respective spike proteins (all have D614G, Figure 1). At this point, most experts think the present vaccines will have efficacy against these variants though there is some unease among scientists and physicians about increased transmissibility and virulence, particularly in regions with low vaccination rates. As the greatest interest has focused on the spike mutations, we offer the following images to illustrate their location in these genomes.

Table 1. VOC Nomenclature

Figure 1. Identified Mutations in VOC Spike Proteins

Table 2. Key VOC Spike Protein Mutations

B.1.1.7 (SARS-CoV-2 Alpha)

In late 2020, the United Kingdom reported the B.1.1.7 variant (aka Alpha) that appears to be significantly more transmissible and perhaps more virulent. Eight of its twenty-three mutations are in the spike protein, with N501Y in the receptor binding domain (RBD) being of most concern as it may be involved in increased ACE2 affinity.

B.1.351 (SARS-CoV-2 Beta)

In January of 2021, the B.1.351 variant (aka Beta) was found in South Africa. It has twenty-one mutations, with eight being in the spike protein. As with the other two variants, it includes the N501Y mutation but also has two additional RBD mutations (E484K, K417N). It appears to be more transmissible, and the E484K mutation is worrisome as it was shown to reduce antibody recognition.

P.1 (SARS-CoV-2 Gamma)

Near the end of January 2021, Japanese authorities reported a new SARS-CoV-2 virus variant obtained from four Brazilian travelers. This variant is designated P.1 (aka Gamma) and has seventeen mutations, with eleven in spike. Some evidence suggests that this virus may also be more transmissible and have some immune escape capability. It has mutations at the same three RBD residues that are altered in the Beta genome.

B.1.617.2 (SARS-CoV-2 Delta)

B.1.617 was first detected in Maharashtra, India in December 2020. There are three sublineages categorized, with B.1.617.2/Delta being designated a VOC due to reports that it is now dominant in many countries, including India and the UK. The B.1.617.2 variant carries ten mutations in spike protein and may be more resistant to neutralization by vaccines and certain monoclonal antibody therapies.

B.1.1.529 / BA.1 (SARS-CoV-2 Omicron)

On 26 November 2021, B.1.1.529 was designated by WHO as a VOC named Omicron. This variant has more than thirty mutations, with three small deletions and one insertion in the spike S1 region, and fifteen point mutations in the RBD. Infection of Omicron variant increased steeply, raising the concerns whether the combination of these mutations may lead to increased transmissibility and immune escape properties.

BA.2 (SARS-CoV-2 Omicron)

The SARS-CoV-2 BA.2 lineage is one of several subvariants of the Variant of Concern (VOC) Omicron and is presently supplanting the fading Omicron BA.1 lineage across the planet. BA.2 and BA.1 share as many as 32 mutations distributed throughout their respective genomes, though BA.2 has upwards of 28 unique alterations. BA.1 and BA.2 are both more transmissible and display enhanced immune evasion capabilities compared to Delta. At this point, clinical disease caused by BA.2 does not appear to be more severe, and there is some optimism that BA.2 will not result in a major surge in hospitalizations and deaths.

BA.2.12.1, BA.4, and BA.5 (SARS-CoV-2 Omicron)

Omicron BA.2.12.1, BA.4, and BA.5 are three recently emerged subvariants with higher transmissibility than BA.2 that are rapidly becoming dominant in many countries. These three variants contain similar RBD sequences to BA.2 with the addition of mutations at L452 and F486, namely L452Q (BA.2.12.1) and L452R with F486V (BA.4 and BA.5). BA.4 and BA.5 share the same spike protein sequence.

BA.2.12.1, BA.4, and BA.5 display immune escape properties that are superior to BA.2 in three-dose vaccination and even post-vaccination, post-BA.1 infection plasma scenarios, suggesting that BA.1-component vaccine boosters will not be entirely protective. At this point, immune evasion capability seems to increase with each subsequent Omicron subvariant. Fortunately, some data suggest that the increased transmissibility is not translating to large increases in hospitalizations and deaths seen with previous variants, though the impact of BA.4 and BA.5 appears to vary from country to country.

BQ.1 and BF.7 (SARS-CoV-2 Omicron, BA.4/5 subvariants)

     BA.4/5 lineage subvariants account for about 77.1% of all Omicron-related lineages. BQ.1 and BF.7 are two of several BA.4/5 subvariants that are of particular concern, due primarily to their increased immune evasion and monoclonal antibody resistance capabilities. BF.7 acquired the R346T, and BQ.1 both the K444T and N460K, spike mutations. Recent work indicates that the N460K mutation plays a significant role in the enhanced neutralization resistance of BQ.1 ⁹. In addition, variant splintering, where distinct subvariants rise to dominance in different world regions, undermines unified vaccine design and treatment regimen plans.

GeneTex is now developing reagents to support research into these SARS-CoV-2 variants, beginning with recombinant spike/RBD proteins that include many of these key mutations.

Wild-type and Single Mutation Spike Proteins

XBB (Omicron) Spike Protein

BQ.1 (Omicron) Spike Protein

BF.7 (Omicron) Spike Protein

BA.2.75 (Omicron) Spike Protein

BA.4 / BA.5 (Omicron) Spike Protein

BA.2.12.1 (Omicron) Spike Protein

BA.2 (Omicron) Spike Protein

B.1.1.529 / BA.1 (Omicron) Spike Protein

B.1.1.7 (Alpha) Spike Proteins

B.1.351 (Beta) Spike Proteins

P.1 (Gamma) Spike Proteins

B.1.617.2 (Delta) Spike Proteins

B.1.617.1 (Kappa) Spike Protein

C.37 (Lamda) Spike Protein

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