🧬 PRRSV ORF5 Evolutionary Intelligence System (EII Platform)

🚀 Live System

• 🌐 Dashboard: https://prrsv-orf5.aiconceptlimited.com.ng/
• ⚙️ Automated pipeline: NCBI → QC → Alignment → EII
• 📊 Real-time evolutionary intelligence monitoring

📊 Live Dashboard

👉 https://prrsv-orf5.aiconceptlimited.com.ng/

🔍 Overview

This platform is designed for research, surveillance, and exploratory evolutionary analysis of PRRSV. The PRRSV ORF5 Evolutionary Intelligence System is an automated genomic surveillance platform designed to monitor the evolutionary dynamics of PRRSV (Porcine Reproductive and Respiratory Syndrome Virus) using ORF5 gene sequences.

The system integrates multiple biologically meaningful signals into a unified metric called the Evolutionary Intelligence Index (EII), enabling real-time tracking of viral evolution.

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🚀 Key Features

• 🔄 Automated sequence retrieval from NCBI

• 🧪 Quality control and filtering of sequences

• 🧬 Multiple sequence alignment using MAFFT

• 🔗 Codon-aware sequence alignment

• 📊 Multi-signal evolutionary analysis:

  • Epitope Drift (Shannon entropy)
  • Selection Pressure (codon variability)
  • Glycosylation Dynamics (N-X-S/T motif detection)
  • Phylogenetic Instability (pairwise sequence divergence)
  • Distance Outliers (anomaly detection)

• 🗄️ MySQL database integration

• 📈 Real-time dashboard (Dash + Plotly)

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🧠 Evolutionary Intelligence Index (EII)

The EII is computed as:

EII = mean(all normalized evolutionary signals) × 100

This produces a single score (0–100) representing the evolutionary activity of PRRSV.

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⚙️ System Architecture

Pipeline workflow:

1. Fetch sequences from NCBI
2. Perform quality control
3. Align sequences (MAFFT)
4. Perform codon alignment
5. Compute evolutionary signals
6. Store results in database
7. Visualize via dashboard

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📁 Project Structure

prrsv_eii/
│
├── pipeline/              # Core processing pipeline
├── dashboard/             # Visualization dashboard
├── data/                  # Generated data (ignored in Git)
├── logs/                  # Pipeline logs
├── docs/                  # Screenshots / assets
├── requirements.txt
├── README.md
├── .gitignore
└── LICENSE

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🔧 Installation & Setup

1. Clone the repository

git clone https://github.com/agarba360-beep/prrsv-eii.git
cd prrsv-eii

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2. Create virtual environment

python3 -m venv venv
source venv/bin/activate

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3. Install dependencies

pip install -r requirements.txt

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4. Configure database

Create a .env file:

DB_HOST=localhost
DB_USER=prrsv_admin
DB_PASSWORD=your_password
DB_NAME=prrsv_genomics

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▶️ Running the System

Run full pipeline

python pipeline/run_pipeline_full.py

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Launch dashboard

python dashboard/dashboard_readonly.py

Open in browser:

https://prrsv-orf5.aiconceptlimited.com.ng/

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🔍 System Inspection (VERY IMPORTANT)

Check raw sequences

SELECT COUNT(*) FROM sequences_raw;
SELECT accession, LENGTH(sequence) FROM sequences_raw LIMIT 5;

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Check QC results

SELECT COUNT(*) FROM qc_sequences;
SELECT * FROM qc_sequences LIMIT 5;

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Check EII history

SELECT * FROM eii_index ORDER BY created_at DESC LIMIT 10;

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Check evolutionary signals

SELECT * FROM eii_signals;

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Check latest snapshot

SELECT * FROM eii_latest;

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Inspect alignment files

head data/alignments/orf5_aligned.fasta
head data/alignments/orf5_codon_aligned.fasta

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📊 Dashboard Features

• Real-time EII monitoring
• Signal composition visualization
• Evolutionary trend analysis
• Risk and impact classification

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🧪 Scientific Notes

• Epitope Drift → Shannon entropy across alignment positions
• Selection Pressure → codon-level variation proxy
• Glycosylation Dynamics → N-X-S/T motif detection
• Phylogenetic Instability → mean pairwise Hamming distance
• Distance Outliers → extreme divergence detection

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🤝 Contributions

Contributions are welcome:

• Improve biological accuracy (e.g., dN/dS models)
• Add phylogenetic tree inference
• Optimize performance
• Enhance dashboard features

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📌 Future Improvements

• Integration with HyPhy / PAML for true selection analysis
• Phylogenetic tree visualization
• Geographic and temporal analysis
• API development
• Cloud deployment

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👨‍💻 Author

Developed by AI Concepts Limited, Nigeria For advanced virology research and genomic intelligence.

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⚠️ Disclaimer

This system is intended for research purposes only. Not for clinical or diagnostic use.

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📜 License

MIT License