COMPARATIVE EFFECTIVENESS OF ELISA, PCR, AND NGS FOR EMERGING INFECTIOUS DISEASES

Background: Emerging infectious diseases require rapid and accurate diagnostic tools to guide clinical decision-making and public health interventions. Traditional and molecular diagnostic methods such as ELISA, PCR, and Next-Generation Sequencing (NGS) are commonly used, yet direct comparative data on their effectiveness remain limited. Objective: To assess and compare the diagnostic accuracy and reliability of ELISA, PCR, and NGS for rapid detection of infectious diseases in a tertiary care setting. Methods: This diagnostic accuracy study was conducted over eight months (March–October 2024) across three tertiary care hospitals in Punjab, Pakistan. A total of 384 adult patients with clinical suspicion of infectious diseases were enrolled based on inclusion/exclusion criteria. Biological samples were analyzed using ELISA, PCR, and NGS in parallel. Sensitivity, specificity, predictive values, and diagnostic accuracy were calculated for each method using a composite reference standard. Inter-rater agreement was assessed with Cohen’s kappa. Statistical analysis was performed using SPSS version 26. Results: PCR demonstrated the highest sensitivity (94.8%) and specificity (97.5%), followed by NGS (91.1%, 95.6%) and ELISA (79.2%, 87.8%). PCR also showed the highest diagnostic accuracy (96.1%) and inter-rater reliability (κ = 0.91). NGS identified a higher rate of mixed infections (17.4%) and offered broader pathogen detection. ELISA was fastest in turnaround time (4.8 ± 1.3 hours) but less reliable in early-stage diagnosis. Conclusion: PCR remains the most effective diagnostic tool for rapid and accurate infectious disease detection. NGS adds value in complex or atypical infections, while ELISA provides quick preliminary results in resource-limited settings. A tiered diagnostic strategy integrating these tools can optimize disease management.