FluReScan

FluReScan is a bioinformatics pipeline for influenza antiviral resistance analysis using amino acid sequences and WHO resistance interpretation rules.

The pipeline supports inhibitor resistance analysis for:

• Neuraminidase inhibitors:

  • Oseltamivir

  • Zanamivir

  • Peramivir

  • Laninamivir

• M2 ion channel inhibitors:

  • Amantadine

  • Rimantadine

• Polymerase inhibitors:

  • Baloxavir

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Features

• Reference-guided amino acid alignment using MAFFT
• Protein-specific reference selection
• Quality control using amino acid identity thresholds
• Detection of:
  • Amino acid substitutions
  • Amino acid deletions
  • Unknown residues (X)
• WHO antiviral resistance interpretation
• Literature-supported mutation annotation
• Classification of non-relevant mutations
• Batch processing of multifasta files
• Automatic HTML and TSV report generation

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Supported proteins

• NA_1 (Influenza A H1N1 neuraminidase)
• NA_2 (Influenza A H3N2 neuraminidase)
• NA_B (Influenza B neuraminidase)
• M2
• PA_A
• PA_B

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Installation

Clone repository:

bash git clone https://github.com/criscruz43/FluReScan.git cd FluReScan

Create environment:

mamba env create -f environment.yml mamba activate flurescan_env

Run FluReScan:

python FluReScan.py

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Project structure

FluReScan/ ├── AA-SEQ/ ├── AA-SEQ-REF/ ├── DATABASE/ │ ├── FluRescan_database.tsv │ └── Literature_database.tsv ├── ANTIVIRAL-RESULTS/ ├── FluReScan.py ├── environment.yml ├── LICENSE ├── CITATION.cff └── README.md

Input

Place amino acid multifasta files in:

AA-SEQ/

Example:

RUN01_NA_1.fasta RUN01_M2.fasta RUN01_PA_A.fasta

Filename naming convention determines:

• Protein assignment
• Influenza subtype
• Reference selection

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Output

FluReScan automatically generates:

ANTIVIRAL-RESULTS/

Output files:

• results.tsv → antiviral interpretation results
• metrics.tsv → mutation statistics
• frequency.tsv → mutation frequencies
• report.html → interactive report

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Example run

Copy example files:

cp examples/example_H1N1_NA_1.fasta AA-SEQ/

Run FluReScan:

python FluReScan.py

Expected output:

ANTIVIRAL-RESULTS/

└── RUN01/

├── results.tsv

├── metrics.tsv

├── frequency.tsv

└── report.html

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Dependencies

Required software:

• Python ≥ 3.9
• MAFFT
• pandas
• Biopython

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Citation

If you use FluReScan in your research please cite:

Cruz C. FluReScan: Influenza antiviral resistance analysis pipeline. GitHub repository: https://github.com/criscruz43/FluReScan

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License

MIT License