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Updated: Sep 19, 2025
Quantification and Whole Genome Characterization of SARS-CoV-2 RNA in Wastewater and Air Samples
Published on: June 30, 2023
Post-pandemic surveillance of seven key respiratory pathogens using targeted next-generation sequencing (tNGS): A
Jue Wang1, Shiliang Cheng1, Yufei Zhang2
1Department of Clinical Laboratory, Shandong Provincial Third Hospital, Shandong University, Jinan 250031, Shandong, China.
Background:
Respiratory tract infections (RTIs) represent a substantial public health concern, particularly as the circulation patterns of pathogens undergo changes. This research utilized targeted next-generation sequencing (tNGS) to examine the epidemiological distribution of seven key RTI-associated pathogens, among patients hospitalized with RTI-indicative symptoms from February 2023 to February 2024.
Methods:
The clinical and demographic information of 5,556 RTI-affected individuals was subjected to retrospective analysis. Pharyngeal swab samples were gathered, and tNGS was implemented to concurrently identify multiple pathogens. The positivity rates were contrasted based on age, sex, and season, and variations in infection patterns across different demographic categories and seasonal periods.
Results:
Among the analyzed samples, 55.74 % were found to be positive for at least one pathogen. Flu-A had the highest prevalence rate of 16.45 %, succeeded by HRV at 13.48 % and SARS-CoV-2 at 10.89 %. Mixed infections were detected in 7.9 % of instances, with the combination of Flu-A and HRV being the most frequently observed dual-pathogen scenario. An age-stratified examination showed a higher overall positivity rate among children in the 4-18-year-old age group and a considerably greater RSV positivity rate among children aged 0-3 years. Season based analysis demonstrated peak infection rates in the winter season (61.09 %). Female patients were found to have a significantly higher positivity rate for influenza B compared to male patients.
Conclusions:
tNGS is a valuable tool for comprehensive pathogen detection, supporting more effective and timely public health responses and clinical management strategies tailored to age and seasonal infection trends in the post-pandemic period.
