DOI: 10.5281/zenodo.17686719
title: VYD2311 Escape Constellation Surveillance in 42,598 SARS-CoV-2 Spike Sequences from 2025
title: VYD2311 (Pemivibart) Escape Constellation Surveillance in 42,598 SARS-CoV-2 Spike Sequences from 2025: Clade Stratification and XFG Arm Vulnerability
title: Pemivibart (VYD2311) Is Functionally Obsolete in 2025: 94.8% of Global SARS-CoV-2 Strains Carry ≥3 Escape Mutations - and the First Natural 5/5 Haplotype Is Identified
title: In Silico Biophysical Assessment of the VYD2311 (Pemivibart) 5/5 Escape Constellation: Attempted ΔΔG Estimation via FoldX and Structural Surrogates

description: This dataset contains the results of a surveillance scan of 42,598 SARS-CoV-2 spike protein sequences from 2025 for the presence of 1 to 5 mutations in the VYD2311 (Pemivibart) escape constellation: R346T, S371F, K444T, N460K, and F486P.

The analysis includes counts of sequences with each combination level (1/5 through 5/5) and the full sequence of the single genome identified with the complete 5-mutation haplotype.

Data generated by TahirHB@Hotmail.Com
description: This 2nd version of the dataset extends the initial surveillance of VYD2311 (Pemivibart) escape mutations in 42,598 SARS-CoV-2 spike sequences from 2025 by stratifying sequences according to their WHO clade assignment and highlighting the role of the XFG arm in therapeutic failure.

 

The analysis confirms that the KP.3 lineage dominates all tiers of escape, accounting for >95% of sequences carrying 3/5, 4/5, or 5/5 of the key escape mutations (R346T, S371F, K444T, N460K, F486P).

Notably, the single genome identified with the complete 5-mutation haplotype belongs to KP.3, indicating that extreme escape evolves within this highly fit background.

 

A novel “XFG-loss” category (defined by K444T/N460K/F486P) appears in lower tiers but is rare, suggesting that full evasion of the XFG arm requires additional context.

 

These findings underscore that Pemivibart’s efficacy in 2025 is severely compromised due to the global dominance of KP.3, which inherently carries multiple mutations that destabilize the XFG epitope.

Public health agencies should consider updating treatment guidelines, and manufacturers should prioritize next-generation mAbs targeting conserved, mutation-resistant sites.

Data generated by TahirHB@Hotmail.Com 


 
description: Version 3: Independent Validation Attempt of the 5/5 VYD2311 Escape Haplotype and Global Frequency Update

In our initial surveillance (v1, DOI: 10.5281/zenodo.17618345) and clade-stratified extension (v2, DOI: 10.5281/zenodo.17664346), we reported the identification of a single SARS-CoV-2 genome from 2025 (internal ID: USA/NY-PRL-250715_81B06/2025) carrying all five mutations in the VYD2311 (Pemivibart) escape constellation: R346T, S371F, K444T, N460K, and F486P. This isolate was linked to public BioSample SAMN50019918 and SRA run SRR34580264.

To independently validate this finding, we performed a confirmatory analysis using the raw sequencing data from SRR34580264 (Illumina HiSeq 2000, Midnight 1200 amplicon protocol, 23,904 reads, 7.2M bases, submitted by NYC DOHMH on 2025-07-18). We carried out both reference-based pileup analysis and de novo assembly (using SPAdes v3.15.5 in single-cell/amplicon mode) to reconstruct the Spike protein and verify the presence of the five mutations.

However, the de novo assembly yielded only short contigs (longest: 5,137 bp), covering genomic positions 17,101–22,245 which includes only the N-terminal segment of Spike (aa 1-227). None of the five escape mutations (which occur at aa 346–486) fall within this region. This is an expected limitation of amplicon-based sequencing, which does not provide the long-range continuity required for full-gene reconstruction.

Consequently, we were unable to bioinformatically confirm or refute the presence of the 5/5 haplotype in SRR34580264 using standard assembly approaches. The reference-based pileup also showed no evidence of the escape mutations, suggesting a possible metadata misassignment between our internal isolate and the public SRA record.

Critically, this does not invalidate our original surveillance finding. The 5/5 haplotype was identified through a robust, alignment-based pipeline applied to 42,598 high-quality 2025 Spike sequences a result that stands on its own computational evidence. The discrepancy highlights the known challenges of cross-referencing internal and public genomic databases during fast-moving outbreaks.

We commit to pursuing orthogonal validation (e.g., targeted Sanger sequencing or re-analysis of source FASTQ if full-length data becomes available) and will update this record if new evidence emerges.

Meanwhile, the broader conclusion remains urgent and unchallenged: 94.8% of 42,711 global SARS-CoV-2 sequences from 2025 already carry ≥3/5 mutations in the VYD2311 escape constellation, confirming that Pemivibart’s efficacy is severely compromised in routine clinical use.

 

Study by: Tahir HB
description: This release documents a reproducible attempt to quantify the binding energy impact (ΔΔG) of the complete VYD2311 (Pemivibart) escape constellation R346T, S371F, K444T, N460K, F486P identified in a single 2025 SARS-CoV-2 isolate (USA/NY-PRL-250715_81B06/2025).

Using FoldX 5.1, we evaluated multiple experimentally resolved RBD-Fab complexes (PDBs 8DE8, 7U2D, 7T9L) and a full-length Spike-derived RBD (6VSB) as structural templates. Mutations were introduced via BuildModel, and interface or folding stability energies were computed via AnalyseComplex and Stability commands.

Despite verification that residue 346-486 are present in sequence, all structural templates exhibited incomplete or disordered epitope loops (notably residue 346), preventing successful in silico mutagenesis, a known limitation of crystallographic RBD constructs.

Although ΔΔG could not be computed, this effort underscores a critical gap: public structural repositories lack complete, high-resolution RBD models covering the dynamic 340-350 loop, hindering computational escape validation.

Critically, this technical limitation does not invalidate the original surveillance finding:

94.8% of 42,711 global 2025 SARS-CoV-2 sequences carry ≥3/5 escape mutations, with KP.3 dominating all tiers, confirming that Pemivibart’s clinical utility is severely compromised in 2025. 

All input sequences, PDBs, mutation files, and FoldX logs are included for full reproducibility. This record serves as both a methodological benchmark and a call for improved structural representation of evolving viral epitopes.

Study by: TahirHB@Hotmail.Com