Spike Protein Mutation Signatures in Circulating SARS-CoV-2 Variants Highlighting Immune Escape Markers and Lineage-Specific Deletion Patterns in Q1 2025

This dataset presents an analysis of Spike protein amino acid mutations in SARS-CoV-2 sequences collected between January to April 2025, with a focus on identifying mutation signatures linked to immune escape, lineage-specific deletions, and emerging variant patterns .The dataset includes:A binary mutation matrix of Spike AA mutations across sequencesA list of lineage-specific mutationsIdentified co-occurring mutation pairsA summary of hypotheses derived from mutation patternsBased on alignment and lineage assignment via Nextclade, this work highlights several mutations of interest:Key Hypotheses Investigated:Hypothesis 1 : S:T20N emerges as a novel mutation in the HF.1.1 lineage Located in the N-terminal domain (NTD), this mutation may affect antigenicity or conformational stability. Hypothesis 2 : S:L452W appears in emerging recombinant variants such as KP.2 and LB.1Linked to increased ACE2 binding and reduced neutralization, suggesting fitness advantage. Hypothesis 3 : S:K356T is a potential marker for immune escape. Found in multiple XBB and JN.1 sequences; located in a known NTD supersite targeted by monoclonal antibodies. Hypothesis 4 : Deletions like S:H69-V70del are limited to specific clusters. These deletions may help viruses evade detection or enhance replication efficiency. This dataset supports ongoing surveillance efforts and provides insight into the molecular evolution of SARS-CoV-2 during early 2025.All scripts used in data processing are included to ensure full FAIR compliance and promote transparency and reproducibility.