B.1.617.2+ (delta+)

As of August 2021, Delta variants have been subdivided in the Pango lineage designation system into variants from AY.1 to AY.28.

Delta with K417N originally corresponded to lineages AY.1 and AY.2 subsequently also lineage AY.3, and has been nicknamed "Delta plus" or "Nepal variant".  It has the K417N mutation, which is also present in the Beta variant. The mutation at position 417 is a lysine-to-asparagine substitution.

The lineage B.1.617+ was first identified in Maharashtra (western part of India) when an analysis was performed on samples collected from this region. It has shown that an increase of ∼60–70% of samples with E484Q and L452R mutations increases the transmission capacity of this variant resulting into more infection

As of mid-October 2021, the AY.3 variant accounted for a cumulative prevalence of approximately 5% in the United States, and 2% worldwide. In mid-October the AY.4.2 Delta sublineage was expanding in England, and being monitored and assessed. It contains mutations A222V and Y145H in its spike protein, not considered of particular concern. It has been suggested that AY.4.2 might be 10-15% more transmissible than the original Delta variant. Mid-October 2021, AY.4.2 accounted for an estimated 10% of cases, and has led to an additional growth rate rising to about 1% (10% of 10%) per generational time of five days or so. This additional growth rate would grow with increasing prevalence. Without AY.4.2 and no other changes, the number of cases in the UK would have been about 10% lower. In the UK it was reclassified as a "variant under investigation" (but not "of concern") in late October 2021.

B.1.617.2 lineage

Lineage B.1.617.2, also known as Delta variant (WHO) is from lineage B.1.617, which was first detected in the state of Maharashtra, India in late 2020 and has been associated with the second wave of COVID-19 infections in the country. It has now spread to 62 countries, including the UK, where it is currently the dominant variant, replacing the lineage B.1.1.7 (Alpha variant) . This variant carries 10 mutations in the S glycoprotein, four of them are of particular concern: L452R, T478K, D614G and P681R, which may associate with high viral transmissibility and increase in neutralisation escape. Unlike its parent B.1.617 variant, the E484Q mutation is not present in the B.1.617.2 genome. The L452R mutation, which also presents in the lineage B.1.427/B.1.429 (Epsilon variant) has been shown to be associated with increased transmissibility and resistance to some nAbs.

Below PDB:77v7f-->mutated to > AY.4.2 Delta sublineage.(Note: A chain only) using Swiss-Pdb-- no further minimization or molecular dynamics simulations performed.

614G, 478K, 452R, 681R, 484E, A222V, Y145H, K417N
-------------->spin on -------->- spin off
->zoom in to V222 (Val) -------->- zoom out


What We Know About the 'Delta Plus' AY.4.2 COVID Mutations Y145H and A222V. Oct. 2021

Former FDA Chief Scott Gottlieb, MD, Calls for Research into UK Surge of New Delta Plus Variant, AY.4.2 Oct. 2021

Evolutionary analysis of the Delta and Delta Plus variants of the SARS-CoV-2 viruses Nov. 2021

SARS-CoV-2 Variant Classifications and Definitions Oct. 2021

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