BGPT: Create Graphs: Plot epitope conservancy WT BA.1 JN.1

Explore by Goal

Long Response Copied

Epitope conservancy (Epitope conservation at 100%)

Plotting the epitope conservancy counts reported for WT, Omicron BA.1, and Omicron JN.1. Graph inputs are the reported 100% conservancy totals plus the breakdown into linear and discontinuous components. Source:

Figure 1 — 100% conservancy total epitope counts (WT vs BA.1 vs JN.1)

Interpretation (skeptical, evidence-bound)

The reported 100% conservancy total drops from WT = 465 to BA.1 = 49 and JN.1 = 41 in the studied analysis.
These conservancy counts come from an immunoinformatics conservancy analysis workflow (as described in the study summary metadata provided here), not from direct binding/neutralization measurements for each conserved epitope.
The “breakdown” plot intentionally shows different reported bins (e.g., linear 100% vs discontinuous 90–99% bin) because only those exact component-bin counts were present in the provided extracted dataset.

Scientific blind spots / limitations to keep in mind

Small, single-city pediatric cohort and cross-sectional design can limit generalizability; additionally, conservancy counts do not prove functional immunodominance or causality.
Epitope “conservancy” is dependent on the epitope definitions and thresholds used by the conservancy tool; different epitope selection sets or conservation cutoffs could change counts.

Feedback:

Updated: March 21, 2026

Top Data Sources Export MCP

1. This study reviews the advancements in epitope-focused vaccine design against influenza A and B viruses, highlighting the identification of conserved epitopes and the development of both stem-based universal and receptor-binding site (RBS)-based subtype-specific vaccines. [2016]

8QualityResults Limitations Context Blindspots Methods Sample Conflict

↗ Paper Review ↗ Full Paper

2. This study presents the development of a novel epitope conservancy analysis tool designed to assess the variability of epitopes within protein sequences, facilitating the design of epitope-based diagnostics and vaccines. [2007]

8QualityResults Limitations Context Blindspots Methods Sample Conflict

↗ Paper Review ↗ Full Paper

3. The study introduces MutClust, a density-aware clustering method that integrates mutation probability and mutation diversity (H-score) to identify SARS-CoV-2 mutation hotspots from 224,318 genomes, links these hotspots to disease severity using a KDCA multi-omics patient cohort, and reveals immunological associations—particularly NK cell–related pathways and HLA-epitope affinity changes—with severe COVID-19 outcomes. [2025]

8QualityResults Limitations Context Blindspots Methods Sample Conflict Data

↗ Paper Review ↗ Full Paper

4. An observational MOSAIC cohort study of 107 vaccinated healthcare workers showing that durable protection against symptomatic Omicron infection requires balanced immunity to conserved and non-conserved Spike epitopes, with RBD-directed antibodies and conserved T cell responses driving protection rather than booster antibody titers alone. [2025]

8QualityResults Limitations Context Blindspots Methods Sample Data

↗ Paper Review ↗ Full Paper

5. This study provides a comprehensive analysis of 1,560 SARS-CoV-2 Spike protein structures, identifying 14 distinct epitopes and predicting immune escape potential through interaction-energy informed geometric clustering and longitudinal genomic data analysis. [2024]

8QualityResults Limitations Context Blindspots Methods Sample

↗ Paper Review ↗ Full Paper

Keep Exploring

Which exact epitope definition/set and conservancy thresholds were used to produce the WT/BA.1/JN.1 counts, and how would the counts change under alternative thresholds?

How do conservancy reductions relate quantitatively to neutralization changes (WT vs BA.1 vs JN.1) in the same cohort?

Can we map the conserved-epitope loss to specific Spike regions (RBD vs non-RBD) based on the study’s epitope annotations?

Analysis Wizard

It calculates variant-to-WT fold decreases from the provided 100% conservancy totals and outputs summary metrics and arrays used for Plotly bar charts for WT, BA.1, and JN.1.

Science Art

Science Movie

Make a narrated HD Science movie for this answer ($32 per minute)

Discussion

BGPT Bias

I prioritize exact, explicitly provided numerical data over plausible but unprovided conservation breakdowns, which can underuse otherwise relevant context.

Stay current without chasing every paper.

Know what changed, what holds up, and what remains uncertain. Every Friday. No ads.

Traceable Claims in Bioinformatics

See what computational analyses actually reported, with provenance for every claim.Know what the science actually supports before you trust the answer.

Explore by Goal

Long Response Copied

Top Data Sources Export MCP

1. This study reviews the advancements in epitope-focused vaccine design against influenza A and B viruses, highlighting the identification of conserved epitopes and the development of both stem-based universal and receptor-binding site (RBS)-based subtype-specific vaccines. [2016]

2. This study presents the development of a novel epitope conservancy analysis tool designed to assess the variability of epitopes within protein sequences, facilitating the design of epitope-based diagnostics and vaccines. [2007]

5. This study provides a comprehensive analysis of 1,560 SARS-CoV-2 Spike protein structures, identifying 14 distinct epitopes and predicting immune escape potential through interaction-energy informed geometric clustering and longitudinal genomic data analysis. [2024]

9. This study evaluates the conservation of 14 anti-tick vaccine targets in Rhipicephalus (Boophilus) microplus across diverse populations, revealing significant variability in protein conservation and implications for vaccine development. [2025]

10. This study investigates the conservation of SARS-CoV-2 epitopes in the newly identified HKU5-CoV-2 virus and explores potential vaccine candidates based on structural protein analysis. [2025]

Ask a Follow-Up

Keep Exploring

Which exact epitope definition/set and conservancy thresholds were used to produce the WT/BA.1/JN.1 counts, and how would the counts change under alternative thresholds?

How do conservancy reductions relate quantitatively to neutralization changes (WT vs BA.1 vs JN.1) in the same cohort?

Can we map the conserved-epitope loss to specific Spike regions (RBD vs non-RBD) based on the study’s epitope annotations?

Analysis Wizard

It calculates variant-to-WT fold decreases from the provided 100% conservancy totals and outputs summary metrics and arrays used for Plotly bar charts for WT, BA.1, and JN.1.

Science Art

Science Movie

Make a narrated HD Science movie for this answer ($32 per minute)

Discussion

BGPT Bias

I prioritize exact, explicitly provided numerical data over plausible but unprovided conservation breakdowns, which can underuse otherwise relevant context.

Stay current without chasing every paper.

My BGPT

Trending

Traceable Claims in Bioinformatics

See what computational analyses actually reported, with provenance for every claim.Know what the science actually supports before you trust the answer.

Explore by Goal

Long Response Copied

Top Data Sources ExportMCP

1. This study reviews the advancements in epitope-focused vaccine design against influenza A and B viruses, highlighting the identification of conserved epitopes and the development of both stem-based universal and receptor-binding site (RBS)-based subtype-specific vaccines. [2016]

2. This study presents the development of a novel epitope conservancy analysis tool designed to assess the variability of epitopes within protein sequences, facilitating the design of epitope-based diagnostics and vaccines. [2007]

5. This study provides a comprehensive analysis of 1,560 SARS-CoV-2 Spike protein structures, identifying 14 distinct epitopes and predicting immune escape potential through interaction-energy informed geometric clustering and longitudinal genomic data analysis. [2024]

9. This study evaluates the conservation of 14 anti-tick vaccine targets in Rhipicephalus (Boophilus) microplus across diverse populations, revealing significant variability in protein conservation and implications for vaccine development. [2025]

10. This study investigates the conservation of SARS-CoV-2 epitopes in the newly identified HKU5-CoV-2 virus and explores potential vaccine candidates based on structural protein analysis. [2025]

Ask a Follow-Up

Keep Exploring

Which exact epitope definition/set and conservancy thresholds were used to produce the WT/BA.1/JN.1 counts, and how would the counts change under alternative thresholds?

How do conservancy reductions relate quantitatively to neutralization changes (WT vs BA.1 vs JN.1) in the same cohort?

Can we map the conserved-epitope loss to specific Spike regions (RBD vs non-RBD) based on the study’s epitope annotations?

Analysis Wizard

It calculates variant-to-WT fold decreases from the provided 100% conservancy totals and outputs summary metrics and arrays used for Plotly bar charts for WT, BA.1, and JN.1.

Science Art

Science Movie

Make a narrated HD Science movie for this answer ($32 per minute)

Discussion

BGPT Bias

I prioritize exact, explicitly provided numerical data over plausible but unprovided conservation breakdowns, which can underuse otherwise relevant context.

Stay current without chasing every paper.

My BGPT

Trending

Top Data Sources Export MCP