Employing Metagenomic Next-Generation Sequencing for Enhanced Surveillance of Respiratory Viruses in Fever Clinics: A Comparative Analysis in the Context of the COVID-19 Pandemic in a General Hospital

Background: Clinical surveillance in hospitals, especially in fever clinic, plays a critical role in detecting and managing emerging infectious diseases, serving as an initial alert system for public health epidemics. However, current clinical surveillance networks lack effective methods for comprehensive viral monitoring. Aim and Methods: This study aimed to establish a pathogen monitoring method using metagenomic next-generation sequencing (mNGS) for pooled specimens in fever clinics, enhancing the capacity for broad-spectrum viral surveillance. We randomly selected oropharyngeal swab specimens from patients at the Fever Clinic who underwent SARS-CoV-2 nucleic acid testing between June 2022 and June 2023. These specimens were pooled, nucleic acids were extracted following standardized protocols, and pathogens were identified through the mNGS technique. Results: Our results indicated that mNGS for pooled samples exhibited RNA viral detection efficiency equivalent to that of targeted next-generation sequencing (tNGS) for individual samples. Data obtained from mNGS demonstrated a strong correlation with influenza surveillance data from the Guangzhou CDC. Our surveillance method adeptly tracked the progression of the H3N2 epidemic through June 2023 and pinpointed the spread of COVID-19 by late November 2023. Additionally, our analysis exposed notable variations in the respiratory viral spectrum among patients before and after the COVID-19 outbreak. Conclusion: Utilizing mNGS for mixed-sample detection in fever clinics proved effective and feasible for pathogen surveillance. The approach enhanced understanding of respiratory virus epidemiology, supporting reduced circulation of non-SARS-CoV-2 respiratory viruses during and after the COVID-19 pandemic. This innovative method strengthens public health surveillance by enabling timely detection and response to respiratory virus outbreaks.