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  • Rachel C Williams
    School of Environmental and Natural Sciences, Bangor University
  • Kata Farkas
    School of Environmental and Natural Sciences, Bangor University
  • Alvaro Garcia-Delgado
    School of Environmental and Natural Sciences, Bangor University
  • Latifah Adwan
    School of Environmental and Natural Sciences, Bangor University
  • Jessica L Kevill
    School of Environmental and Natural Sciences, Bangor University
  • Gareth Cross
    Science Evidence Advice Division
  • Andrew J Weightman
    Cardiff University
  • Davey L Jones
    School of Environmental and Natural Sciences, Bangor University

Genomic surveillance of SARS-CoV-2 has given insight into the evolution and epidemiology of the virus and its variant lineages during the COVID-19 pandemic. Expanding this approach to include a range of respiratory pathogens can better inform public health preparedness for potential outbreaks and epidemics. Here, we simultaneously sequenced 38 pathogens including influenza viruses, coronaviruses and bocaviruses, to examine the abundance and seasonality of respiratory pathogens in urban wastewater. We deployed a targeted bait capture method and short-read sequencing (Illumina Respiratory Virus Oligos Panel; RVOP) on composite wastewater samples from 8 wastewater treatment plants (WWTPs) and one associated hospital site. By combining seasonal sampling with whole genome sequencing, we were able to concurrently detect and characterise a range of common respiratory pathogens, including SARS-CoV-2, adenovirus and parainfluenza virus. We demonstrated that 38 respiratory pathogens can be detected at low abundances year-round, that hospital pathogen diversity is higher in winter vs. summer sampling events, and that significantly more viruses are detected in raw influent compared to treated effluent samples. Finally, we compared detection sensitivity of RT-qPCR vs. next generation sequencing for SARS-CoV-2, enteroviruses, influenza A/B, and respiratory syncytial viruses. We conclude that both should be used in combination; RT-qPCR allowed accurate quantification, whilst genomic sequencing detected pathogens at lower abundance. We demonstrate the valuable role of wastewater genomic surveillance and its contribution to the field of wastewater-based epidemiology, gaining rapid understanding of the seasonal presence and persistence for common respiratory pathogens. By simultaneously monitoring seasonal trends and early warning signs of many viruses circulating in communities, public health agencies can implement targeted prevention and rapid response plans.

Original languageEnglish
Article number121612
JournalWater research
Volume256
Early online date13 Apr 2024
DOIs
Publication statusPublished - 1 Jun 2024
Externally publishedYes

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