DOI: 10.5281/zenodo.18145428
title: 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

description: 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

 
description: This analysis demonstrates that pemivibart escape is not confined to the spike receptor-binding domain but is systemically reinforced by coordinated mutations across the viral structural proteome. 

The strong mutual information between spike escape residues and variants in E, M, and N, particularly recurrent signals like M:D3N, E:T9I, and N:R203K suggests that single-epitope monoclonal antibodies face inherent evolutionary vulnerability in the context of a highly optimized, pan-structural adaptive landscape. 

These data support a strategic shift toward multi-epitope or non-spike therapeutic platforms for durable pandemic preparedness.
description: This dataset directly supports the findings in:  Print: "Global Genomic Surveillance Reveals Pre-EUA Fixation of Pemivibart (VYD2311) Escape Constellations inSARS-CoV-2". https://doi.org/10.20944/preprints202512.2013.v1

 
description: In this study, we reference the antibody engineering platform disclosed in U.S. Patent US 11,866,514 B2 and several other US Patents, used as a structural and developmental context for pemivibart (VYD222) and its successor VYD2311. The patent describes a modular Fc-engineering approach incorporating mutations such as F405L and K409R in the CH3 domain, a stabilized CPPC hinge, and optional modifications at sites like N297 (to modulate effector function) or H435 (to tune FcRn-mediated half-life) designed to improve heterodimer formation, serum persistence, and manufacturability. 

Critically, this platform leaves the variable domains, and thus the antigen-binding specificity, unchanged. Both pemivibart and VYD2311 therefore target the identical RBD epitope, engaging the same four contact residues: R346, K444, F456, and F486 (SARS-CoV-2 Wuhan-Hu-1 numbering).

Our genomic surveillance spanning global, U.S. EU. lineages explicitly tracks these shared residues, as their mutational status determines susceptibility to both molecules, irrespective of Fc-level enhancements
description: The Pharmacokinetic Backbone and the Vanishing Epitope: An Open Inquiry into Fc Engineering in the Context of Pre-Eroded Therapeutic Targets

Monoclonal antibodies (mAbs) against SARS‑CoV‑2 have been engineered with increasing sophistication, particularly through Fc domain modifications designed to extend serum half-life such as via FcRn-binding mutations such as YTE or LS, silence pro-inflammatory effector functions such as LALA or N297A/Q, or stabilize heterodimeric architectures such as F405L/K409R. These strategies treat the Fc as a modular, pharmacokinetic “backbone” which is a delivery chassis that can be optimized independently of antigen recognition, which is encoded in the Fab.

In the case of pemivibart (VYD222) and its successor VYD2311, both molecules share an identical Fab, engaging the same four RBD residues that are R346, K444, F456, and F486 which is a structural footprint confirmed by X‑ray crystallography (Cα RMSD = 0.45 Å relative to adintrevimab). Our global genomic surveillance across ~10 million SARS‑CoV‑2 spike sequences (2020 to Q4 2025) now reveals that 94.8% of 2025 isolates carry ≥3 of the 5 core escape mutations (R346T, S371F, K444T, N460K, F486P), with high-order constellations already circulating in late 2023 predating both the EUA for pemivibart (March 2024) and the IND clearance for VYD2311 (October 2025).

This raises a foundational question: What is the therapeutic relevance of Fc optimization when the Fab no longer binds its target in the overwhelming majority of circulating strains??

Fc engineering operates in a virologically silent domain: SARS‑CoV‑2 does not interact with FcRn or FcγRs, and thus cannot evolve in response to Fc modifications. Yet, prolonged serum persistence of a non-binding mAb may amplify selective pressure in immunocompromised hosts, such as the individuals who form the intended user base for these agents, potentially accelerating the emergence of higher-order escape haplotypes.

The Invivyd ECCMID 2025 poster describes VYD2311 as having undergone “half-life optimization” following affinity maturation but provides no empirical data on:

A- Specific Fc mutations such as LS, YTE, LALA, N297A, F405L/K409R?

B- FcRn binding affinity such as at pH 6.0 vs. 7.4?

C- FcγR engagement or silencing status?

D- Thermal or conformational stability of the Fc domain?

E- Pharmacokinetic or effector function assays of ADCC, ADCP?

The claim of optimization appears to rest on platform-level assumptions possibly derived from prior art such as US Patent 11,866,514 B2 or may be any other closely relevant patent rather than molecule-specific biophysical validation. This is not uncommon in early-stage development, but it becomes consequential when deployed against a target that is already functionally erased from the global virome.

Notably, the parental antibody adintrevimab was explicitly engineered with LALA (L234A/L235A) mutations to mitigate FcγR-mediated inflammation in the lungs and understandably this is a standard safety measure for respiratory mAbs, as seen in Evusheld and RSV therapeutics. Yet, no such disclosure is made for pemivibart or VYD2311, despite both being IgG1λ antibodies administered intravenously for pre-exposure prophylaxis in high-risk populations.

This omission invites several questions that we like to raise:

Q.1- Was FcγR silencing retained, modified, or omitted in VYD2311??

Q.2- If omitted, does the molecule retain wild-type FcγR binding potential and if so, could this pose a risk of sterile inflammation or immune complex-mediated pathology in the absence of neutralization?

Q.3- Did the pursuit of half-life extension such as via LS/YTE necessitate trade-offs with effector function silencing, given known biophysical interactions between the hinge and FcRn interface?

Q4. In the absence of public Fc characterization, how do regulators, clinicians, or public health agencies assess the safety-risk profile of a therapeutically inert molecule with extended serum persistence?

The datasets presented here spanning co-evolutionary networks, regional escape signatures, and high-resolution haplotype tracking confirm that epitope erosion is not a post-deployment phenomenon but a pre-existing, deterministic trajectory. In such a context, Fc enhancements may not rescue efficacy but instead extend exposure to a non-functional agent.

Thus, while the Fc domain remains structurally robust and virologically invisible, its strategic deployment against a vanishing epitope opens a suite of unresolved scientific and clinical questions. These concern not only pharmacokinetic claims, but also safety in vulnerable populations, evolutionary consequences of prolonged sub-neutralizing antibody pressure, and the transparency of engineering disclosures in the public health record.

The answers to these questions are not yet in the literature. But the data now demand that they be asked.

Study Conducted by: Tahir HB
description: List of Abbrevations used in this study:

1. mAb : monoclonal antibody  2. Fc : crystallizable fragment  3. Fab : antigen-binding fragment  4. FcRn : neonatal Fc receptor  5. FcγR : Fc gamma receptor  6. RBD : receptor-binding domain  7. EUA : Emergency Use Authorization  8. IND : Investigational New Drug  9. BLA : Biologics License Application  10. IC₅₀ : half-maximal inhibitory concentration  11. IgG1λ : immunoglobulin G1 lambda isotype  12. LS : M428L/N434S (Fc half-life extension mutation)  13. YTE : M252Y/S254T/T256E (Fc half-life extension mutation)  14. LALA : L234A/L235A (Fc effector-silencing mutation)  15. ADCC : antibody-dependent cellular cytotoxicity  16. ADCP : antibody-dependent cellular phagocytosis  17. CDC : complement-dependent cytotoxicity  18. ADE : antibody-dependent enhancement  19. PK : pharmacokinetics  20. PD : pharmacodynamics  21. VLP : virus-like particle  22. sVNA : serum virus-neutralizing antibody  23. EC₅₀ : half-maximal effective concentration  24. RMSD : root mean square deviation 25. CH3 : constant heavy chain domain 3  26. CH2 : constant heavy chain domain 2  27. PDB : Protein Data Bank  28. MI : mutual information  29. CPPC : Cys-Pro-Pro-Cys (hinge motif)  30. S : Spike protein  31. N : Nucleocapsid protein  32. M : Membrane protein  33. E : Envelope protein