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Tang MHE, Bennedbaek M, Gunalan V, Qvesel AG, Thorsen TH, Larsen NB, Rasmussen LD, Krogsgaard LW, Rasmussen M, Stegger M, Alexandersen S. Variations in the persistence of 5'-end genomic and subgenomic SARS-CoV-2 RNAs in wastewater from aircraft, airports and wastewater treatment plants. Heliyon 2024; 10:e29703. [PMID: 38694057 PMCID: PMC11061675 DOI: 10.1016/j.heliyon.2024.e29703] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2023] [Revised: 04/08/2024] [Accepted: 04/14/2024] [Indexed: 05/03/2024] Open
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.
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Affiliation(s)
- Man-Hung Eric Tang
- Department of Bacteria, Parasites and Fungi, Statens Serum Institut, Copenhagen, Denmark
| | - Marc Bennedbaek
- Department of Virus and Microbiological Special Diagnostics, Statens Serum Institut, Copenhagen, Denmark
| | - Vithiagaran Gunalan
- Department of Virus and Microbiological Special Diagnostics, Statens Serum Institut, Copenhagen, Denmark
| | - Amanda Gammelby Qvesel
- Department of Virus and Microbiological Special Diagnostics, Statens Serum Institut, Copenhagen, Denmark
| | - Theis Hass Thorsen
- Department of Bacteria, Parasites and Fungi, Statens Serum Institut, Copenhagen, Denmark
| | | | - Lasse Dam Rasmussen
- Department of Virus and Microbiological Special Diagnostics, Statens Serum Institut, Copenhagen, Denmark
| | - Lene Wulff Krogsgaard
- Department of Infectious Disease Epidemiology and Prevention, Statens Serum Institut, Copenhagen, Denmark
| | - Morten Rasmussen
- Department of Virus and Microbiological Special Diagnostics, Statens Serum Institut, Copenhagen, Denmark
| | - Marc Stegger
- 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
| | - Soren Alexandersen
- 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
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Krogsgaard LW, Benedetti G, Gudde A, Richter SR, Rasmussen LD, Midgley SE, Qvesel AG, Nauta M, Bahrenscheer NS, von Kappelgaard L, McManus O, Hansen NC, Pedersen JB, Haimes D, Gamst J, Nørgaard LS, Jørgensen ACU, Ejegod DM, Møller SS, Clauson-Kaas J, Knudsen IM, Franck KT, Ethelberg S. Results from the SARS-CoV-2 wastewater-based surveillance system in Denmark, July 2021 to June 2022. Water Res 2024; 252:121223. [PMID: 38310802 DOI: 10.1016/j.watres.2024.121223] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/19/2023] [Revised: 11/01/2023] [Accepted: 01/28/2024] [Indexed: 02/06/2024]
Abstract
The microbiological analysis of wastewater samples is increasingly used for the surveillance of SARS-CoV-2 globally. We described the setup process of the national SARS-CoV-2 wastewater-based surveillance system in Denmark, presented its main results during the first year of activities, from July 2021 to June 2022, and discussed their operational significance. The Danish SARS-CoV-2 wastewater-based surveillance system was designed to cover 85 % of the population in Denmark and it entailed taking three weekly samples from 230 sites. Samples were RT-qPCR tested for SARS-CoV-2 RNA, targeting the genetic markers N1, N2 and RdRp, and for two faecal indicators, Pepper Mild Mottle Virus and crAssphage. We calculated the weekly SARS-CoV-2 RNA concentration in the wastewater from each sampling site and monitored it in view of the results from individual testing, at the national and regional levels. We attempted to use wastewater results to identify potential local outbreaks, and we sequenced positive wastewater samples using Nanopore sequencing to monitor the circulation of viral variants in Denmark. The system reached its full implementation by October 2021 and covered up to 86.4 % of the Danish population. The system allowed for monitoring of the national and regional trends of SARS-CoV-2 infections in Denmark. However, the system contribution to the identification of potential local outbreaks was limited by the extensive information available from clinical testing. The sequencing of wastewater samples identified relevant variants of concern, in line with results from sequencing of human samples. Amidst the COVID-19 pandemic, Denmark implemented a nationwide SARS-CoV-2 wastewater-based surveillance system that integrated routine surveillance from individual testing. Today, while testing for COVID-19 at the community level has been discontinued, the system is on the frontline to monitor the occurrence and spread of SARS-CoV-2 in Denmark.
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Affiliation(s)
- Lene Wulff Krogsgaard
- Department of Infectious Disease Epidemiology and Prevention, Statens Serum Institut, Artillerivej 5, 2300 Copenhagen, Denmark
| | - Guido Benedetti
- Department of Infectious Disease Epidemiology and Prevention, Statens Serum Institut, Artillerivej 5, 2300 Copenhagen, Denmark.
| | - Aina Gudde
- Department of Infectious Disease Epidemiology and Prevention, Statens Serum Institut, Artillerivej 5, 2300 Copenhagen, Denmark
| | - Stine Raith Richter
- Department of Virus and Microbiological Special Diagnostics, Statens Serum Institut, Artillerivej 5, 2300 Copenhagen, Denmark
| | - Lasse Dam Rasmussen
- Department of Virus and Microbiological Special Diagnostics, Statens Serum Institut, Artillerivej 5, 2300 Copenhagen, Denmark
| | - Sofie Elisabeth Midgley
- Department of Virus and Microbiological Special Diagnostics, Statens Serum Institut, Artillerivej 5, 2300 Copenhagen, Denmark
| | - Amanda Gammelby Qvesel
- Department of Virus and Microbiological Special Diagnostics, Statens Serum Institut, Artillerivej 5, 2300 Copenhagen, Denmark
| | - Maarten Nauta
- Department of Infectious Disease Epidemiology and Prevention, Statens Serum Institut, Artillerivej 5, 2300 Copenhagen, Denmark
| | - Naja Stolberg Bahrenscheer
- Department of Infectious Disease Epidemiology and Prevention, Statens Serum Institut, Artillerivej 5, 2300 Copenhagen, Denmark
| | - Lene von Kappelgaard
- Department of Infectious Disease Epidemiology and Prevention, Statens Serum Institut, Artillerivej 5, 2300 Copenhagen, Denmark
| | - Oliver McManus
- Department of Infectious Disease Epidemiology and Prevention, Statens Serum Institut, Artillerivej 5, 2300 Copenhagen, Denmark; European Programme for Intervention Epidemiology Training (EPIET), European Centre for Disease Prevention and Control, Gustav III: s Boulevard 40, 16973 Solna, Sweden
| | - Nicco Claudio Hansen
- Test Centre Denmark, Statens Serum Institut, Artillerivej 5, 2300 Copenhagen, Denmark
| | - Jan Bryla Pedersen
- Department of Finance, Statens Serum Institut, Artillerivej 5, 2300 Copenhagen, Denmark
| | - Danny Haimes
- Danish Patient Safety Authority, Islands Brygge 67, 2300 Copenhagen, Denmark
| | - Jesper Gamst
- Eurofins Environment, Ladelundvej 85, 6600 Vejen, Denmark
| | | | | | | | | | - Jes Clauson-Kaas
- HOFOR - Greater Copenhagen Utility, Ørestads Boulevard 35, 2300 Copenhagen, Denmark
| | - Ida Marie Knudsen
- HOFOR - Greater Copenhagen Utility, Ørestads Boulevard 35, 2300 Copenhagen, Denmark
| | - Kristina Træholt Franck
- Department of Virus and Microbiological Special Diagnostics, Statens Serum Institut, Artillerivej 5, 2300 Copenhagen, Denmark
| | - Steen Ethelberg
- Department of Infectious Disease Epidemiology and Prevention, Statens Serum Institut, Artillerivej 5, 2300 Copenhagen, Denmark; Department of Public Health, Global Health Section, University of Copenhagen, Øster Farimagsgade 5, 1014 Copenhagen, Denmark
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Qvesel AG, Bennedbæk M, Larsen NB, Gunalan V, Krogsgaard LW, Rasmussen M, Rasmussen LD. SARS-CoV-2 Variants BQ.1 and XBB.1.5 in Wastewater of Aircraft Flying from China to Denmark, 2023. Emerg Infect Dis 2023; 29:2559-2561. [PMID: 37885051 PMCID: PMC10683830 DOI: 10.3201/eid2912.230717] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2023] Open
Abstract
We analyzed wastewater samples from 14 aircraft arriving in Denmark directly from China during January 9-February 12, 2023. Wastewater from 11 aircraft was SARS-CoV-2-positive by PCR; 6 predominantly contained BQ.1 and XBB.1 subvariants. Wastewater-based surveillance can contribute to public health monitoring of SARS-CoV-2 and other emerging infectious agents.
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Rasmussen M, Møller FT, Gunalan V, Baig S, Bennedbæk M, Christiansen LE, Cohen AS, Ellegaard K, Fomsgaard A, Franck KT, Larsen NB, Larsen TG, Lassaunière R, Polacek C, Qvesel AG, Sieber RN, Rasmussen LD, Stegger M, Spiess K, Tang MHE, Vestergaard LS, Andersen TE, Hoegh SV, Pedersen RM, Skov MN, Steinke K, Sydenham TV, Hoppe M, Nielsen L, Krause TG, Ullum H, Jokelainen P. First cases of SARS-CoV-2 BA.2.86 in Denmark, 2023. Euro Surveill 2023; 28:2300460. [PMID: 37676147 PMCID: PMC10486197 DOI: 10.2807/1560-7917.es.2023.28.36.2300460] [Citation(s) in RCA: 15] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2023] [Accepted: 09/07/2023] [Indexed: 09/08/2023] Open
Abstract
We describe 10 cases of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variant BA.2.86 detected in Denmark, including molecular characteristics and results from wastewater surveillance that indicate that the variant is circulating in the country at a low level. This new variant with many spike gene mutations was classified as a variant under monitoring by the World Health Organization on 17 August 2023. Further global monitoring of COVID-19, BA.2.86 and other SARS-CoV-2 variants is highly warranted.
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Affiliation(s)
- Morten Rasmussen
- Virus Research and Development Laboratory, Virus & Microbiological Special Diagnostics, Statens Serum Institut, Copenhagen, Denmark
- These authors contributed equally to this work and share first authorship
| | - Frederik Trier Møller
- These authors contributed equally to this work and share first authorship
- Infectious Disease Epidemiology and Prevention, Statens Serum Institut, Copenhagen, Denmark
| | - Vithiagaran Gunalan
- Virus Research and Development Laboratory, Virus & Microbiological Special Diagnostics, Statens Serum Institut, Copenhagen, Denmark
| | - Sharmin Baig
- Sequencing and Bioinformatics, Bacteria, Parasites & Fungi, Statens Serum Institut, Copenhagen, Denmark
| | - Marc Bennedbæk
- Virus Research and Development Laboratory, Virus & Microbiological Special Diagnostics, Statens Serum Institut, Copenhagen, Denmark
| | | | | | - Kirsten Ellegaard
- Sequencing and Bioinformatics, Bacteria, Parasites & Fungi, Statens Serum Institut, Copenhagen, Denmark
| | - Anders Fomsgaard
- Virus Research and Development Laboratory, Virus & Microbiological Special Diagnostics, Statens Serum Institut, Copenhagen, Denmark
| | - Kristina Træholt Franck
- Virus Surveillance and Research Laboratory, Virus & Microbiological Special Diagnostics, Statens Serum Institut, Copenhagen, Denmark
| | | | - Tine Graakjær Larsen
- Infectious Disease Epidemiology and Prevention, Statens Serum Institut, Copenhagen, Denmark
| | - Ria Lassaunière
- Virus Research and Development Laboratory, Virus & Microbiological Special Diagnostics, Statens Serum Institut, Copenhagen, Denmark
| | - Charlotta Polacek
- Virus Research and Development Laboratory, Virus & Microbiological Special Diagnostics, Statens Serum Institut, Copenhagen, Denmark
| | - Amanda Gammelby Qvesel
- Virus Surveillance and Research Laboratory, Virus & Microbiological Special Diagnostics, Statens Serum Institut, Copenhagen, Denmark
| | - Raphael Niklaus Sieber
- Sequencing and Bioinformatics, Bacteria, Parasites & Fungi, Statens Serum Institut, Copenhagen, Denmark
| | - Lasse Dam Rasmussen
- Virus Surveillance and Research Laboratory, Virus & Microbiological Special Diagnostics, Statens Serum Institut, Copenhagen, Denmark
| | - Marc Stegger
- Sequencing and Bioinformatics, Bacteria, Parasites & Fungi, Statens Serum Institut, Copenhagen, Denmark
- Antimicrobial Resistance and Infectious Diseases Laboratory, Harry Butler Institute, Murdoch University, Perth, Australia
| | - Katja Spiess
- Virus Research and Development Laboratory, Virus & Microbiological Special Diagnostics, Statens Serum Institut, Copenhagen, Denmark
| | - Man-Hung Eric Tang
- Sequencing and Bioinformatics, Bacteria, Parasites & Fungi, Statens Serum Institut, Copenhagen, Denmark
| | | | - Thomas Emil Andersen
- Department of Clinical Microbiology, Odense University Hospital, Odense, Denmark
- Research Unit for Clinical Microbiology, University of Southern Denmark, Odense, Denmark
| | - Silje Vermedal Hoegh
- Department of Clinical Microbiology, Odense University Hospital, Odense, Denmark
| | - Rune Micha Pedersen
- Department of Clinical Microbiology, Odense University Hospital, Odense, Denmark
- Research Unit for Clinical Microbiology, University of Southern Denmark, Odense, Denmark
| | - Marianne Nielsine Skov
- Department of Clinical Microbiology, Odense University Hospital, Odense, Denmark
- Research Unit for Clinical Microbiology, University of Southern Denmark, Odense, Denmark
| | - Kat Steinke
- Department of Clinical Microbiology, Odense University Hospital, Odense, Denmark
| | - Thomas Vognbjerg Sydenham
- Department of Clinical Microbiology, Odense University Hospital, Odense, Denmark
- Research Unit for Clinical Microbiology, University of Southern Denmark, Odense, Denmark
| | - Morten Hoppe
- Department of Clinical Microbiology, Copenhagen University Hospital, Herlev and Gentofte, Denmark
| | - Lene Nielsen
- Department of Clinical Microbiology, Copenhagen University Hospital, Herlev and Gentofte, Denmark
| | - Tyra Grove Krause
- Epidemiological Infectious Disease Preparedness, Statens Serum Institut, Copenhagen, Denmark
| | | | - Pikka Jokelainen
- Infectious Disease Preparedness, Statens Serum Institut, Copenhagen, Denmark
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