In the ongoing effort to monitor and respond to evolving SARS-CoV-2 variants, the U.S. Centers for Disease Control and Prevention (CDC) has introduced a powerful new tool: Aquascope, an open-source bioinformatics pipeline developed specifically for wastewater genomic surveillance. This system enables public health authorities to track the emergence and spread of viral lineages using data gathered from sewage—an increasingly vital resource in understanding community-level transmission dynamics. A recent study published in Emerging Infectious Diseases presents the first large-scale application of Aquascope, focusing on the JN.1 variant that rose to prominence across the United States from late 2023 to mid-2024.
Conducted by researchers at the CDC and partner organizations, this retrospective analysis used wastewater samples collected from over 130 locations in 32 U.S. jurisdictions to estimate variant prevalence from November 2023 to July 2024. The study underscores how Aquascope improves upon previous systems by enabling faster, more scalable, and more reproducible analysis of viral sequences.
The research underscores wastewater surveillance as a cost-effective complement to clinical testing, capable of capturing infections that otherwise go unrecorded, especially among asymptomatic or untested individuals.
Wastewater Surveillance Comes of Age
Wastewater surveillance has matured into a critical pillar of pandemic response. Since its inception in 2020, the CDC’s National Wastewater Surveillance System (NWSS) has evolved to detect viral RNA from SARS-CoV-2 across thousands of U.S. communities. Aquascope now marks a significant upgrade in the genomic arm of NWSS, replacing the older C-WAP system with a more robust and user-friendly solution.
Key Features of Aquascope
- Built in Nextflow, enabling high-performance and cloud computing integration
- Employs containerized, open-source tools for quality control, variant detection, and lineage abundance estimation
- Offers reproducibility, scalability, and integration with existing CDC data platforms
Tracking JN.1—From Emergence to Decline
Using 3,377 wastewater samples collected across 130 sites in 32 U.S. jurisdictions, the team applied Aquascope to sequence data processed under consistent laboratory protocols. The result: a clear timeline showing how JN.1 was first detected in mid-November 2023, surged to dominance by early December, peaked in March 2024, and then steadily declined into late July.
Notable Trends Identified
The wastewater surveillance trends closely aligned with clinical sequencing data, reinforcing both the reliability of Aquascope and the broader National Wastewater Surveillance System (NWSS) framework. Following its initial detection, the JN.1 variant rapidly became the predominant lineage within a matter of weeks. Subsequently, sublineages such as JN.1.7 and JN.1.11.1 emerged and maintained a consistent presence throughout the monitoring period. In parallel, other lineages like KP.2 and KP.3 also appeared and exhibited varying levels of prevalence, highlighting the dynamic nature of SARS-CoV-2 variant circulation as captured through wastewater analysis.
Broader Applications and Future Directions
While Aquascope was designed for SARS-CoV-2, its architecture supports the integration of other pathogen barcoding libraries, enabling broader public health applications. Using Freyja’s deconvolution algorithm, Aquascope could one day quantify pathogens like influenza, RSV, or novel zoonotic viruses from mixed wastewater samples.
Challenges and Future Enhancements
Despite its advantages, Aquascope faces several implementation challenges. The pipeline’s computational intensity necessitates high-performance computing resources, which may pose a barrier for smaller laboratories with limited infrastructure. To address this, the CDC is working to integrate Aquascope into a more scalable platform that will be accessible to public health partners nationwide. Additionally, while the current system depends on pre-characterized SARS-CoV-2 lineage barcodes, future updates aim to enhance its capacity to detect previously uncharacterized or novel variants, broadening its utility for emerging pathogen surveillance.
Implications for Public Health Professionals
For epidemiologists and global health professionals, these findings reinforce the value of investing in genomic wastewater surveillance. As global pathogens evolve with increasing speed and stealth, systems like NWSS—now supercharged by Aquascope—provide early warning signals for variant emergence. This capability is crucial for shaping timely public health responses, informing vaccination strategies, and allocating healthcare resources effectively. By harnessing wastewater as a window into population health, public health agencies gain a powerful, noninvasive tool for detecting outbreaks before they hit clinical radar.
READ MORE:
Feistel DJ, Welsh R, Mercante J, et al. Detection and Tracking of SARS-CoV-2 Lineages through National Wastewater Surveillance System Pathogen Genomics. Emerging Infectious Diseases, 2 May 2025.