Prevalence of SARS-CoV-2 variants in Prague wastewater determined by nanopore-based sequencing

Chemosphere. 2024 Mar:351:141162. doi: 10.1016/j.chemosphere.2024.141162. Epub 2024 Jan 11.


The early detection of upcoming disease outbreaks is essential to avoid both health and economic damage. The last four years of COVID-19 pandemic have proven wastewater-based epidemiology is a reliable system for monitoring the spread of SARS-CoV-2, a causative agent of COVID-19, in an urban population. As this monitoring enables the identification of the prevalence of spreading variants of SARS-CoV-2, it could provide a critical tool in the fight against this viral disease. In this study, we evaluated the presence of variants and subvariants of SARS-CoV-2 in Prague wastewater using nanopore-based sequencing. During August 2021, the data clearly showed that the number of identified SARS-CoV-2 RNA copies increased in the wastewater earlier than in clinical samples indicating the upcoming wave of the Delta variant. New SARS-CoV-2 variants consistently prevailed in wastewater samples around a month after they already prevailed in clinical samples. We also analyzed wastewater samples from smaller sub-sewersheds of Prague and detected significant differences in SARS-CoV-2 lineage progression dynamics among individual localities studied, e.g., suggesting faster prevalence of new variants among the sites with highest population density and mobility.

Keywords: Epidemiology; Nanopore-based sequencing; Prague; SARS-CoV-2; Variants; Wastewater.

MeSH terms

  • COVID-19* / epidemiology
  • Humans
  • Nanopores*
  • Pandemics
  • Prevalence
  • RNA, Viral
  • SARS-CoV-2 / genetics
  • Wastewater


  • Wastewater
  • RNA, Viral

Supplementary concepts

  • SARS-CoV-2 variants