Covid-19 genomic analysis reveals clusters of emerging sublineages within the delta variant

The emerging SARS-CoV-2 variants may potentially have enhanced transmissibility and virulence of the virus, and impacts on performance of diagnostic tools and efficacy of vaccines. Genomic surveillance provides an opportunity to detect and characterize new mutations early enough for effective deployment of control strategies. Here, genomic data from Germany and United Kingdom were examined for genetic diversity by assessing gene mutations and inferring phylogeny, and simplifying genomic data workflow for faster visualization and interpretation. Delta variant sublineages were grouped into seven distinct clusters of spike mutations located in N-terminal domain of S1 region (T95I, D138H, *D142G, Y145H and A222V) and S2 region (T719I and *N950D). The most predominant cluster was T95I mutation, with the highest frequencies (71.1% - 83.9%) in Wales, England and Scotland, and the least frequencies (8.9% - 12.1%) in Germany. Two mutations, *D142G and *N950D here described as *reverse mutations and T719I mutation, were largely unique to Germany. In a month, frequencies of D142G had increased from 55.6% to 67.8 % in Germany. Additionally, a cluster of D142G+T719I/T mutation went up from 27.7% to 34.1%, while a T95I+ D142G+N950D/N cluster rose from 19.2% to 26.2%. Although, two distinct clusters of T95I+D138H (2.6% - 3.8%) and T95I+Y145H+A222V (2.5% - 8.5%) mutations were present in all the countries, they were most predominant in Wales and Scotland respectively. Results suggest divergent evolutionary trajectories between the clusters of T95I mutation and those of D142G mutation. These findings provide insights into underlying dynamics of evolution of the delta variant. Future studies may evaluate the epidemiological and biological implications of these sublineages.