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

Emerg Infect Dis. 2025 May;31(13):57-60. doi: 10.3201/eid3113.241411.

Abstract

We conducted retrospective analysis of the emergence of the SARS-CoV-2 JN.1 variant in US wastewater during November 2023-July 2024 using Aquascope, a bioinformatics pipeline for the National Wastewater Surveillance System. This study highlights the value of open-source bioinformatics tools in tracking pathogen variants for public health monitoring.

Keywords: COVID-19; SARS-CoV-2; bioinformatics; computational biology; public health surveillance; respiratory infections; severe acute respiratory syndrome coronavirus 2; viruses; wastewater surveillance; wastewater-based epidemiological monitoring; zoonoses.

MeSH terms

  • COVID-19* / epidemiology
  • COVID-19* / virology
  • Computational Biology / methods
  • Genome, Viral
  • Genomics / methods
  • Humans
  • Phylogeny
  • Retrospective Studies
  • SARS-CoV-2* / classification
  • SARS-CoV-2* / genetics
  • SARS-CoV-2* / isolation & purification
  • United States / epidemiology
  • Wastewater* / virology
  • Wastewater-Based Epidemiological Monitoring*

Substances

  • Wastewater