Comparative Efficacy of Multiplex PCR vs. Next-Generation Sequencing (NGS) in the Early Detection of Emerging Respiratory Viral Pathogens in Tertiary Care Settings.

Original Research | 2026 | Volume-3 | Issue-1 | Page 15-22

Comparative Efficacy of Multiplex PCR vs. Next-Generation Sequencing (NGS) in the Early De

Download NEXT-GENERATION SEQUENCING (NGS) IN THE EARLY DE • 694KB

1. Mr. Ansul Kumar. Department of Microbiology, Narayan Para Medical College, Sasaram

2. Mr. Himanshu Soni, Department of Biochemistry, Santosh Deemed to be University, Ghaziabad, India

3. Mrs. Rani Kumari, Department of Biochemistry, Krishna Mohan Medical College and Hospital, Mathura.

Corresponding Author:-

Mr. Ansul Kumar

Department of Microbiology

Narayan Para Medical College

Sasaram

Abstract

Background: The rapid identification of emerging respiratory viral pathogens is critical in tertiary care settings to guide clinical management and infection control. This study compares the diagnostic efficacy of Multiplex Polymerase Chain Reaction (mPCR) and Next-Generation Sequencing (NGS) in the early detection of viral respiratory infections.

Methods: A prospective comparative analysis was conducted using respiratory samples from patients presenting with acute respiratory distress at three tertiary care centers. Samples were processed using a standard syndromic mPCR panel and mDNS (metagenomic NGS). Efficacy was measured based on diagnostic yield, turnaround time (TAT), sensitivity, and the ability to detect novel or mutated viral strains.

Results: Multiplex PCR demonstrated a superior TAT, providing results within 4–6 hours, making it highly effective for immediate clinical triage. However, NGS exhibited a significantly higher diagnostic yield, identifying pathogens in 18% of samples that tested negative via mPCR. While mPCR was restricted to a predefined panel, NGS successfully identified emerging variants and co-infections with high genomic resolution. The sensitivity of mPCR remained high for common seasonal viruses, but NGS proved indispensable for identifying rare or "off-target" emerging pathogens.

Conclusion: Both modalities play complementary roles in tertiary diagnostics. mPCR is the preferred first-line tool for rapid, cost-effective screening of known pathogens. Conversely, NGS serves as a powerful secondary surveillance tool, offering unmatched depth for detecting emerging pathogens and characterizing viral evolution. A tiered diagnostic approach is recommended to optimize patient outcomes and pandemic preparedness in high-acuity clinical environments.

Keywords: Multiplex PCR, Next-Generation Sequencing, Respiratory Pathogens, Tertiary Care