Detection and Tracking of SARS-CoV-2 Lineages through National Wastewater Surveillance System Pathogen Genomics

Area of Science:

• Environmental microbiology
• Virology
• Bioinformatics

Background:

• Wastewater surveillance is a critical tool for monitoring pathogen circulation.
• Emergence and spread of novel SARS-CoV-2 variants pose public health challenges.
• The JN.1 variant became a significant lineage globally.

Purpose of the Study:

• To analyze the emergence and prevalence of the SARS-CoV-2 JN.1 variant in US wastewater.
• To evaluate the utility of the Aquascope bioinformatics pipeline for variant tracking.
• To demonstrate the importance of open-source tools in public health surveillance.

Main Methods:

• Retrospective analysis of wastewater data from November 2023 to July 2024.
• Utilized Aquascope, an open-source bioinformatics pipeline.
• Data sourced from the National Wastewater Surveillance System (NWSS).

Main Results:

• Documented the emergence and temporal trends of the SARS-CoV-2 JN.1 variant in US wastewater.
• Demonstrated the successful application of Aquascope in identifying and tracking the JN.1 variant.
• Highlighted the effectiveness of wastewater surveillance for real-time public health insights.

Conclusions:

• The study confirms the value of wastewater-based epidemiology for monitoring SARS-CoV-2 variant dynamics.
• Open-source bioinformatics tools like Aquascope are essential for efficient and scalable public health surveillance.
• Continued investment in wastewater surveillance infrastructure is crucial for future pandemic preparedness.