Emerging Infectious Diseases (May 2025)

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

  • Dorian J. Feistel,
  • Rory Welsh,
  • Jeffrey Mercante,
  • Miguella Mark-Carew,
  • Jason Caravas,
  • Arun Boddapati,
  • Samantha Sevilla,
  • Matthew H. Seabolt,
  • Dhwani Batra,
  • Suchitra Chavan,
  • Shatavia Morrison,
  • Jesse Yoder,
  • Hannah Long,
  • Satvik Mishra,
  • Benjamin Lorentz,
  • Andi Dhroso,
  • Iryna V. Goraichuk,
  • Seonghye Jeon,
  • Daniel M. Cornforth

DOI
https://doi.org/10.3201/eid3113.241411
Journal volume & issue
Vol. 31, no. 13
pp. 57 – 60

Abstract

Read online

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