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Efficacy on Delta Variant : SARS-CoV-2 Delta variant Mutation Report

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  • Efficacy on Delta Variant : SARS-CoV-2 Delta variant Mutation Report

SARS-CoV-2 Delta variant Mutation:

SARS-CoV-2 Delta variant, also known as lineage B.1.617.2, is a variant of lineage B.1.617 of SARS-CoV-2, the virus that causes COVID-19. It was first detected in India in late 2020. The World Health Organization (WHO) named it the Delta variant on 31 May 2021.

It has mutations in the gene encoding the SARS-CoV-2 spike protein causing the substitutions T478K, P681R and L452R, which are known to affect transmissibility of the virus as well as whether it can be neutralised by antibodies for previously circulating variants of the COVID-19 virus. Public Health England (PHE) in May 2021 observed secondary attack rates to be 51–67% higher than the alpha variant. In a July technical briefing in England, the Delta variant has case fatality rate of 0.2% (0.13% if unvaccinated), while the Alpha variant has 1.9%.

“Delta plus” variant:

Variants of SARS-CoV-2 Delta (lineage B.1.617.2). Delta with K417N corresponds to lineages AY.1 and AY.2 and has been nicknamed “Delta plus” or “Nepal variant”. It has the K417N mutation which is also present in the Beta variant. The exchange at position 417 is a lysine-to-asparagine substitution. As of 15 July 2021, the AY.3 variant accounted for approximately 21% of cases in the United States.


The Delta/ B.1.617.2 genome has 13 mutations (15 or 17 according to some sources, depending on whether more common mutations are included) which produce alterations in the amino-acid sequences of the proteins it encodes. Four of them, all of which are in the virus’s spike protein code, are of particular concern:

D614G. The substitution at position 614, an aspartic acid-to-glycine substitution, is shared with other highly transmissible variants like Alpha, Beta and Gamma.

T478K. The exchange at position 478 is a threonine-to-lysine substitution.

L452R. The substitution at position 452, a leucine-to-arginine substitution, confers stronger affinity of the spike protein for the ACE2 receptor and decreased recognition capability of the immune system. These mutations, when taken individually, are not unique to the variant; rather, their simultaneous occurrence is.

P681R. The substitution at position 681, a proline-to-arginine substitution, which, according to William A. Haseltine, may boost cell-level infectivity of the variant “by facilitating cleavage of the S precursor protein to the active S1/S2 configuration”.

The E484Q mutation is present in the B.1.617.2 genome.


The Delta variant has mutations in the gene encoding the SARS-CoV-2 spike protein causing the substitutions T478K, L452R, E484Q, D950N, E156G, G142D, P681R, T19R, 156DEL, 157DEL, K417N and R158G.


The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is a new coronavirus associated with severe acute respiratory syndrome. We used a molecular docking protocol to anticipate possible sites for nine ligands from the Protein Data Bank’s twelve SARS-CoV-2 Delta variant Mutation proteins. The current analysis reveals that 12 mutated SARS-CoV-2 Delta variant Mutation protein interacted with nine ligands and showed the best interaction with T478K, L452R, E484Q, D950N, E156G, G142D, P681R, T19R, 156DEL, 157DEL, K417N, and R158G with binding energy greater than -5.00 (kcal/mol).
All nine ligand compounds had the best interaction with all SARS-CoV-2 Delta variant Mutation proteins, whereas Spike Glycoprotein (7KDJ-Mutant) had the best interaction with all nine ligand compounds, with binding energies ranging from -5.01 to -6.99 kcal/mol, as indicated by the single asterisk (*). The encouraging result and very good binding energy of all nine ligands with the eight SARS-CoV-2 Delta variant Mutation protein were good, ranging from -7.01 to -8.99 and marked by a double asterisk (**).
The manner of binding and interacting active site amino acids between SARS-CoV-2 proteins ligand were effectively confirmed by molecular docking studies, as well as the hydrogen bond interaction of ligand SARS-CoV-2 Delta variant mutation protein. The ligand compounds one, two, three, six, seven, eight, and nine have the highest binding energy of all the proteins.