Wastewater genomic surveillance of SARS-CoV-2 by nanopore sequencing uncovers JN.1 prevalence and novel spike mutational hotspots in Athens during winter 2024-2025.

doi:10.1016/j.scitotenv.2026.181972

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Article

Wastewater genomic surveillance of SARS-CoV-2 by nanopore sequencing uncovers JN.1 prevalence and novel spike mutational hotspots in Athens during winter 2024-2025.

The Science of the total environment - 25 Aug 2026

Diamantopoulos Marios A, Adamopoulos Panagiotis G, Athanasopoulou Konstantina, Zafeiriadou Anastasia, Markou Athina, Thomaidis Nikolaos S, Scorilas Andreas

Abstract excerpt

Wastewater-based epidemiology (WBE) provides an efficient, population-wide tool for monitoring SARS-CoV-2 transmission and evolution, overcoming limitations of clinical testing. Here, we designed and applied an upgraded Spike-Seq workflow integrating third-generation nanopore sequencing on the PromethION platform to achieve complete spike gene coverage from wastewater samples collected in Athens (December...

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PMID: 42335736
DOI: 10.1016/j.scitotenv.2026.181972

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