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Progress Development Report: Evolutionary-Aware Target Discovery

Author

UGM Pandemic Preparedness Team

Published

June 29, 2026

Welcome to the Pandemic Preparedness Progress Report. This portal serves as the official documentation for the development of our Evolutionary-Aware Target Discovery Pipeline, designed to identify robust and mutation-resistant diagnostic targets for emerging pathogens.

Executive Summary

Pathogens with epidemic potential, particularly those causing Acute Respiratory Infections (ARI) such as Influenza A and Coronaviruses, exhibit high mutation rates. Conventional molecular diagnostics (e.g., RT-PCR and Recombinase Polymerase Amplification - RAA) frequently suffer from diagnostic escape due to primer mismatch at target sites.

To address this challenge, our pipeline integrates global genomic surveillance data with phylogenetic and evolutionary selection pressure analyses. By mapping codon-by-codon evolutionary dynamics, the pipeline identifies target regions under strong purifying selection (negative selection) and high ancestral conservation. Targeting these genetically constrained regions ensures the longevity and diagnostic sensitivity of designed assays, mitigating the risk of diagnostic escape.

Technical Pipeline Workflow

The target discovery pipeline is structured into four main phases spanning ten core modules (M01 to M10):

Phase Core Modules Objective & Key Activities
Phase 1: Genomic & Phylodynamics M01 – M04 Acquisition, quality control, multiple sequence alignment, and phylogenetic tree reconstruction.
Phase 2: Selection & Conservation M05 – M07 Mapping of codon-by-codon evolutionary selection pressure (HyPhy) and ancestral sequence conservation scoring.
Phase 3: Design & Specificity M08 – M09 Design of RAA primers/probes (using PrimerLab) and BLAST-based specificity filtering.
Phase 4: Simulated Evaluation M10 Simulated multi-metric in-silico validation of candidates across global databases.

Document Navigation Structure

The documentation portal is organized into distinct functional sections:

  • Genomic Surveillance: Details the data acquisition logic (including socio-demographic tourist traffic justification from BPS data) and sequence statistics of target pathogen datasets.
  • Technical Architecture: A step-by-step walkthrough of Modules M01 through M10, documenting execution commands, underlying methodologies, and troubleshooting protocols.
  • Results & Biological Insights: Evaluates candidate primers/probes and presents in-silico PCR/RAA evaluation heatmaps across global database strains.

Consortium & Funding

This development initiative is part of the national project “Peningkatan Kapasitas Laboratorium untuk Deteksi Patogen Berpotensi Pandemik bagi Human Dalam Persiapan Menghadapi Pandemi” (FY 2026), supported and funded by the Badan Riset dan Inovasi Nasional (BRIN).

The project is carried out through a multi-institutional research consortium:

  • Pusat Riset Biomedis, Organisasi Riset Kesehatan, BRIN
  • Universitas Gadjah Mada (UGM)
  • Universitas Indonesia (UI)
  • Universitas Telkom
  • University of Bern, Switzerland (International Collaborator)
  • Tokyo University of Agriculture and Technology, Japan (International Collaborator)