Pan-Structural Co-evolution of Pemivibart (VYD222/VYD2311) Escape Mutations in SARS-CoV-2: Genomic Surveillance of R346, K444, F456, and F486 Across 3.8 Million USA Genomes Span 2020 to 2025

This dataset presents a comprehensive analysis of co-evolutionary signals between four high-impact pemivibart (VYD222/VYD2311) escape residues in the SARS-CoV-2 spike protein R346, K444, F456, and F486 and mutations in the Envelope (E), Membrane (M), and Nucleocapsid (N) structural proteins. Based on 3,786,747 USA SARS-CoV-2 genomes from public metadata (Jan 2020 - Dec 2025), we provide: Residue-level amino acid frequencies at each spike positionStructured co-occurrence counts between spike escape and non-spike variantsMutual Information (MI) scores quantifying non-random associations across the virionGeographically annotated USA state-level summaries This resource reveals pervasive, genome-wide linkage between therapeutic escape and structural protein evolution, offering critical insight for monoclonal antibody durability assessment and next-generation antiviral design. List of Files Included Primary Residue Data346.csv, 444.csv, 456.csv, 486.csv→ Amino acid calls at each spike position per genome, with location and frequency metrics Co-occurrence & Mutual Information 346_vs_E_mi.csv.zst, 346_vs_M_mi.csv.zst, 346_vs_N_mi.csv.zst444_vs_E_mi.csv.zst, 444_vs_M_mi.csv.zst, 444_vs_N_mi.csv.zst456_vs_E_mi.csv.zst, 456_vs_M_mi.csv.zst, 456_vs_N_mi.csv.zst486_vs_E_mi.csv.zst, 486_vs_M_mi.csv.zst, 486_vs_N_mi.csv.zst → Joint counts and MI (bits) for all significant spike-structural protein pairs Summary Reports346_summary.txt, 444_summary.txt, 456_summary.txt, 486_summary.txt→ Per-residue USA-wide frequency and variant breakdownspemivibart_structural_mi_global_summary.txt→ Integrated interpretation of top co-evolving signals(All files are provided in open, machine-readable formats; CSVs are Zstandard-compressed for efficiency.) Study by: Tahir Bhatti