Delta D - a sublineage of Delta variant dominating the world now

The early phase of the COVID-19 pandemic showed the evolution of SARS-CoV-2 dominated mostly by neutral substitutions. In contrast, the second year of the pandemic was punctuated by the emergence of several variants that bore evidence of dramatic evolution.

Delta vs other variants:

Most variants are characterized by long branches leading to their emergence, with an excess of non-synonymous substitutions occurring particularly in the Spike and Nucleocapsid proteins.

In contrast, the Delta variant that is now becoming globally dominant
- lacks the signature long branch, and
- is characterized by a step-wise evolutionary process that is ongoing.

Other variants display star-like topologies, whereas Delta is displaying several distinct clades within Delta that are denoted as clades A-E. Sequences from the 'Delta D' clade are dramatically increasing in frequency across different regions of the globe.

Delta D is characterized by an excess of non-synonymous mutations, mostly occurring in ORF1a/b, and also T140I in ORF7b, and G215C in Nucleocapsid. Delta surge these days is composed almost exclusively of Delta D.

In all countries, Delta D clade has gained dominance over other Delta clades (A, B, C, E) over time.

In India, initially, all Delta clades co-occurred. First sequences of Delta D lineage mutations were detected in Feb- Mar 2021. Later, Delta D clade gained dominance only in May 2021.

This study "The unique evolutionary dynamics of the SARS-CoV-2 Delta variant" can be read here

Concluding remarks:

The evolution of Delta into five clades - A, B, C, D, E - and then the subsequent dominance of Delta D clade from February - March 2021 onwards should be studied in detail to understand how different geographic regions in the world are responding to the virus. Also, it will give us a better idea about the different pictures emerging across the world among the vaccinated vs unvaccinated. It should also answer the most important question - "is the virus becoming less pathogenic?"

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