Variations in the persistence of 5'-end genomic and subgenomic SARS-CoV-2 RNAs in wastewater from aircraft, airports and wastewater treatment plants.

Autor:	Tang ME; Department of Bacteria, Parasites and Fungi, Statens Serum Institut, Copenhagen, Denmark., Bennedbaek M; Department of Virus and Microbiological Special Diagnostics, Statens Serum Institut, Copenhagen, Denmark., Gunalan V; Department of Virus and Microbiological Special Diagnostics, Statens Serum Institut, Copenhagen, Denmark., Qvesel AG; Department of Virus and Microbiological Special Diagnostics, Statens Serum Institut, Copenhagen, Denmark., Thorsen TH; Department of Bacteria, Parasites and Fungi, Statens Serum Institut, Copenhagen, Denmark., Larsen NB; TestCenter Denmark, Statens Serum Institut, Copenhagen, Denmark., Rasmussen LD; Department of Virus and Microbiological Special Diagnostics, Statens Serum Institut, Copenhagen, Denmark., Krogsgaard LW; Department of Infectious Disease Epidemiology and Prevention, Statens Serum Institut, Copenhagen, Denmark., Rasmussen M; Department of Virus and Microbiological Special Diagnostics, Statens Serum Institut, Copenhagen, Denmark., Stegger M; Department of Bacteria, Parasites and Fungi, Statens Serum Institut, Copenhagen, Denmark.; Antimicrobial Resistance and Infectious Diseases Laboratory, Harry Butler Institute, Murdoch University, Perth, Western Australia, Australia., Alexandersen S; Division of Diagnostic Preparedness, Statens Serum Institut, Copenhagen, Denmark.; Department of Animal and Veterinary Sciences, Aarhus University, Tjele, Denmark.; Deakin University, School of Medicine, Waurn Ponds, Geelong, Australia.
Jazyk:	angličtina
Zdroj:	Heliyon [Heliyon] 2024 Apr 16; Vol. 10 (9), pp. e29703. Date of Electronic Publication: 2024 Apr 16 (Print Publication: 2024).
DOI:	10.1016/j.heliyon.2024.e29703
Abstrakt:	Wastewater sequencing has become a powerful supplement to clinical testing in monitoring SARS-CoV-2 infections in the post-COVID-19 pandemic era. While its applications in measuring the viral burden and main circulating lineages in the community have proved their efficacy, the variations in sequencing quality and coverage across the different regions of the SARS-CoV-2 genome are not well understood. Furthermore, it is unclear how different sample origins, viral extraction and concentration methods and environmental factors impact the reads sequenced from wastewater. Using high-coverage, amplicon-based, paired-end read sequencing of viral RNA extracted from wastewater collected directly from aircraft, pooled from different aircraft and airport buildings or from regular wastewater plants, we assessed the genome coverage across the sample groups with a focus on the 5'-end region covering the leader sequence and investigated whether it was possible to detect subgenomic RNA from viral material recovered from wastewater. We identified distinct patterns in the persistence of the different genomic regions across the different types of wastewaters and the existence of chimeric reads mapping to non-amplified regions. Our findings suggest that preservation of the 5'-end of the genome and the ability to detect subgenomic RNA reads, though highly susceptible to environment and sample processing conditions, may be indicative of the quality and amount of the viral RNA present in wastewater. Competing Interests: The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper. (© 2024 Published by Elsevier Ltd.)
Databáze:	MEDLINE
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