Unsupervised detection of novel SARS-CoV-2 mutations and lineages in wastewater samples using long-read sequencing.

ABSTRACT: The COVID-19 pandemic has underscored the importance of virus surveillance in public health and wastewater-based epidemiology (WBE) has emerged as a non-invasive, cost-effective method for monitoring SARS-CoV-2 and its variants at the community level. Unfortunately, current variant surveillance methods depend heavily on updated genomic databases with data derived from clinical samples, which can become less sensitive and representative as clinical testing and sequencing efforts decline.In this paper, we introduce HERCULES (High-throughput Epidemiological Reconstruction and Clustering for Uncovering Lineages from Environmental SARS-CoV-2), an unsupervised method that uses long-read sequencing of a single 1 Kb fragment of the Spike gene. HERCULES identifies and quantifies mutations and linea

SUBMITTER: Garcia I 

PROVIDER: S-EPMC11780762 | biostudies-literature | 2025 Jan

REPOSITORIES: biostudies-literature