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 <b>Spike protein amino acid mutations </b>in <b>SARS-CoV-2 sequences collected between January to April 2025</b>, with a focus on identifying <b>mutation signatures linked to immune escape</b>, <b>lineage-specific deletions</b>, and <b>emerging variant patterns </b>.The dataset includes:A <b>binary mutation matrix </b>of Spike AA mutations across sequencesA list of <b>lineage-specific mutations</b>Identified <b>co-occurring mutation pairs</b>A summary of hypotheses derived from mutation patternsBased on alignment and lineage assignment via <b>Nextclade</b>, this work highlights several mutations of interest:Key Hypotheses Investigated:<b>Hypothesis 1 </b>: <code>S:T20N</code> emerges as a novel mutation in the <b>HF.1.1 </b>lineage Located in the N-terminal domain (NTD), this mutation may affect antigenicity or conformational stability. <b>Hypothesis 2 </b>: <code>S:L452W</code> appears in emerging recombinant variants such as <b>KP.2 </b>and <b>LB.1</b>Linked to increased ACE2 binding and reduced neutralization, suggesting fitness advantage. <b>Hypothesis 3 </b>: <code>S:K356T</code> 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. <b>Hypothesis 4 </b>: Deletions like <code>S:H69-V70del</code> 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 <b>FAIR compliance</b> and promote transparency and reproducibility.<br>