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CC BY-NC-ND V4.0, Open Access
Journal article
Variations in the persistence of 5’-end genomic and subgenomic SARS-CoV-2 RNAs in wastewater from aircraft, airports and wastewater treatment plants
Heliyon, Vol.10(9), e29703
2024
Abstract
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.
Details
- Title
- Variations in the persistence of 5’-end genomic and subgenomic SARS-CoV-2 RNAs in wastewater from aircraft, airports and wastewater treatment plants
- Authors/Creators
- Man-Hung Eric Tang - Department of Bacteria, Parasites and Fungi, Statens Serum Institut, Copenhagen, DenmarkMarc Bennedbaek - Statens Serum InstitutVithiagaran Gunalan - Statens Serum InstitutAmanda Gammelby Qvesel - Department of Virus and Microbiological Special Diagnostics, Statens Serum Institut, Copenhagen, DenmarkTheis Hass Thorsen - Statens Serum InstitutNicolai Balle Larsen - TestCenter Denmark, Statens Serum Institut, Copenhagen, DenmarkLasse Dam Rasmussen - Department of Virus and Microbiological Special Diagnostics, Statens Serum Institut, Copenhagen, DenmarkLene Wulff Krogsgaard - Statens Serum InstitutMorten Rasmussen - Statens Serum InstitutMarc Stegger - Statens Serum InstitutSoren Alexandersen - Statens Serum Institut
- Publication Details
- Heliyon, Vol.10(9), e29703
- Publisher
- Elsevier Ltd
- Identifiers
- 991005659469107891
- Copyright
- © 2024 Published by Elsevier Ltd
- Murdoch Affiliation
- Harry Butler Institute
- Language
- English
- Resource Type
- Journal article
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