Simultaneous detection and characterization of common respiratory pathogens in wastewater through genomic sequencing

Williams, Rachel C., Farkas, Kata, Garcia-Delgado, Alvaro, Adwan, Latifah, Kevill, Jessica L., Cross, Gareth, Weightman, Andrew J. ORCID: https://orcid.org/0000-0002-6671-2209 and Jones, Davey L. 2024. Simultaneous detection and characterization of common respiratory pathogens in wastewater through genomic sequencing. Water Research 256 , 121612. 10.1016/j.watres.2024.121612

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Abstract

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.

Item Type:	Article
Date Type:	Publication
Status:	Published
Schools:	Biosciences Water Research Institute (WATER)
Publisher:	Elsevier
ISSN:	0043-1354
Date of First Compliant Deposit:	10 June 2024
Date of Acceptance:	12 April 2024
Last Modified:	10 Jun 2024 10:17
URI:	https://orca.cardiff.ac.uk/id/eprint/169653

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