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:
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.