Position-wise mutation analysis and temporal changes in SARS CoV-2 Envelope (E) protein variants

SARS CoV-2 is a positive-sense, single-stranded RNA virus. The genome of the virus undergoes numerous mutations, making the development of universally effective drugs challenging. Among its structural proteins, the Envelope (E) protein acts as an ion transporter and virulence factor, making it a potential therapeutic target. Based on the literature available to date, we have identified several functionally important sites in the E protein. These include residues involved in lysosomal deacidification; those of the FYXY motif, involved in amyloid formation in the host; and the PDZ-binding DLLV motif. We focus our analysis on the significance of these residues while also searching for other interesting mutational patterns. In this study, we conducted a comprehensive mutational analysis of the SARS CoV-2 E protein utilizing bioinformatics, statistics, and structural modeling tools. Over 1.4 million sequences were retrieved from the NCBI virus database, filtered, clustered, and aligned chronologically. By employing a combination of web-based tools and in-house Python scripts, we analyzed per-residue Shannon entropy, mutation types, evolutionary pressure, and predicted structural impact (via ∆∆G). We observed a significant number of residues under diversifying selection. This suggests that new amino acids are being sampled at various positions in the protein, providing functional or structural benefits to the virus. A cyclical pattern of mutation and reversion was observed at position 9, stabilizing at a particular mutation. Similar trends appeared at position 11. These mutations may be functionally relevant, which need to be explored in future. However, the key regions have remained conserved over time.