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Cook LSJ, Briscoe AG, Fonseca VG, Boenigk J, Woodward G, Bass D. Microbial, holobiont, and Tree of Life eDNA/eRNA for enhanced ecological assessment. Trends Microbiol 2025; 33:48-65. [PMID: 39164135 DOI: 10.1016/j.tim.2024.07.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2024] [Revised: 07/07/2024] [Accepted: 07/08/2024] [Indexed: 08/22/2024]
Abstract
Microbial environmental DNA and RNA (collectively 'eNA') originate from a diverse and abundant array of microbes present in environmental samples. These eNA signals, largely representing whole organisms, serve as a powerful complement to signals derived from fragments or remnants of larger organisms. Integrating microbial data into the toolbox of ecosystem assessments and biotic indices therefore has the potential to transform how we use eNA data to understand biodiversity dynamics and ecosystem functions, and to inform the next generation of environmental monitoring. Incorporating holobiont and Tree of Life approaches into eNA analyses offers further holistic insight into the range of ecological interactions between microbes and other organisms, paving the way for advancing our understanding of, and ultimately manipulating ecosystem properties pertinent to environmental management, conservation, wildlife health, and food production.
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Affiliation(s)
- Lauren S J Cook
- Centre for Environment, Fisheries and Aquaculture Science, Barrack Road, Weymouth, Dorset DT4 8UB, UK; Science, The Natural History Museum, Cromwell Road, London SW7 5BD, UK; Royal Holloway University of London, Egham, Surrey TW20 0EX, UK
| | - Andrew G Briscoe
- Science, The Natural History Museum, Cromwell Road, London SW7 5BD, UK; NatureMetrics, Surrey Research Park, Guildford GU2 7HJ, UK
| | - Vera G Fonseca
- Centre for Environment, Fisheries and Aquaculture Science, Barrack Road, Weymouth, Dorset DT4 8UB, UK
| | - Jens Boenigk
- Department of Biodiversity, University of Duisburg-Essen, 45141 Essen, Universitätsstraße 5, Germany
| | - Guy Woodward
- Georgina Mace Centre for the Living Planet, Department of Life Sciences, Imperial College London, Silwood Park Campus, Ascot, Berkshire SL5 7PY, UK
| | - David Bass
- Centre for Environment, Fisheries and Aquaculture Science, Barrack Road, Weymouth, Dorset DT4 8UB, UK; Science, The Natural History Museum, Cromwell Road, London SW7 5BD, UK; Biosciences, University of Exeter, Stocker Road, Exeter EX4 4QD, UK.
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Yang J, Sun D, Xia T, Shi S, Suo J, Kuang H, Sun N, Hu H, Zheng Z, Zhou Y, Li X, Chen S, Huang H, Yan Z. Monitoring Prevalence and Persistence of Environmental Contamination by SARS-CoV-2 RNA in a Makeshift Hospital for Asymptomatic and Very Mild COVID-19 Patients. Int J Public Health 2023; 68:1605994. [PMID: 37767017 PMCID: PMC10520216 DOI: 10.3389/ijph.2023.1605994] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2023] [Accepted: 08/29/2023] [Indexed: 09/29/2023] Open
Abstract
Objective: To investigate the details of environmental contamination status by SARS-CoV-2 in a makeshift COVID-19 hospital. Methods: Environmental samples were collected from a makeshift hospital. The extent of contamination was assessed by quantitative reverse transcription polymerase chain reaction (RT-qPCR) for SARS-CoV-2 RNA from various samples. Results: There was a wide range of total collected samples contaminated with SARS-CoV-2 RNA, ranging from 8.47% to 100%. Results revealed that 70.00% of sewage from the bathroom and 48.19% of air samples were positive. The highest rate of contamination was found from the no-touch surfaces (73.07%) and the lowest from frequently touched surfaces (33.40%). The most contaminated objects were the top surfaces of patient cubic partitions (100%). The median Ct values among strongly positive samples were 33.38 (IQR, 31.69-35.07) and 33.24 (IQR, 31.33-34.34) for ORF1ab and N genes, respectively. SARS-CoV-2 relic RNA can be detected on indoor surfaces for up to 20 days. Conclusion: The findings show a higher prevalence and persistence in detecting the presence of SARS-CoV-2 in the makeshift COVID-19 hospital setting. The contamination mode of droplet deposition may be more common than contaminated touches.
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Affiliation(s)
- Jinyan Yang
- Department of Disease Prevention and Control, Hainan Hospital of People’s Liberation Army of China General Hospital, Sanya, China
| | - Dan Sun
- Department of Disease Prevention and Control, Hainan Hospital of People’s Liberation Army of China General Hospital, Sanya, China
| | - Tingting Xia
- Department of Disease Prevention and Control, Hainan Hospital of People’s Liberation Army of China General Hospital, Sanya, China
| | - Shi Shi
- Department of Disease Prevention and Control, Hainan Hospital of People’s Liberation Army of China General Hospital, Sanya, China
| | - Jijiang Suo
- Department of Disease Prevention and Control, Hainan Hospital of People’s Liberation Army of China General Hospital, Sanya, China
| | - Huihui Kuang
- Department of Laboratory Medicine, Hainan Hospital of People’s Liberation Army of China General Hospital, Sanya, China
| | - Nana Sun
- Department of Laboratory Medicine, Hainan Hospital of People’s Liberation Army of China General Hospital, Sanya, China
| | - Hongyan Hu
- Department of Laboratory Medicine, Hainan Hospital of People’s Liberation Army of China General Hospital, Sanya, China
| | - Zhecheng Zheng
- Department of Health Economics Management, Hainan Hospital of People’s Liberation Army of China General Hospital, Sanya, China
| | - Yang Zhou
- Department of Health Economics Management, Hainan Hospital of People’s Liberation Army of China General Hospital, Sanya, China
| | - Xiaocui Li
- Department of Cardiology, Hainan Hospital of People’s Liberation Army of China General Hospital, Sanya, China
| | - Shaojuan Chen
- Department of Cardiology, Hainan Hospital of People’s Liberation Army of China General Hospital, Sanya, China
| | - Haiqiang Huang
- Department of Radiotherapy, Hainan Hospital of People’s Liberation Army of China General Hospital, Sanya, China
| | - Zhongqiang Yan
- Department of Disease Prevention and Control, The Second Medical Center of People’s Liberation Army of China General Hospital, Beijing, China
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Atoui A, Cordevant C, Chesnot T, Gassilloud B. SARS-CoV-2 in the environment: Contamination routes, detection methods, persistence and removal in wastewater treatment plants. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 881:163453. [PMID: 37059142 PMCID: PMC10091716 DOI: 10.1016/j.scitotenv.2023.163453] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/30/2022] [Revised: 04/07/2023] [Accepted: 04/07/2023] [Indexed: 06/01/2023]
Abstract
The present study reviewed the occurrence of SARS-CoV-2 RNA and the evaluation of virus infectivity in feces and environmental matrices. The detection of SARS-CoV-2 RNA in feces and wastewater samples, reported in several studies, has generated interest and concern regarding the possible fecal-oral route of SARS-CoV-2 transmission. To date, the presence of viable SARS-CoV-2 in feces of COVID-19 infected people is not clearly confirmed although its isolation from feces of six different patients. Further, there is no documented evidence on the infectivity of SARS-CoV-2 in wastewater, sludge and environmental water samples, although the viral genome has been detected in these matrices. Decay data revealed that SARS-CoV-2 RNA persisted longer than infectious particle in all aquatic environment, indicating that genome quantification of SARS-CoV-2 does not imply the presence of infective viral particles. In addition, this review also outlined the fate of SARS-CoV-2 RNA during the different steps in the wastewater treatment plant and focusing on the virus elimination along the sludge treatment line. Studies showed complete removal of SARS-CoV-2 during the tertiary treatment. Moreover, thermophilic sludge treatments present high efficiency in SARS-CoV-2 inactivation. Further studies are required to provide more evidence with respect to the inactivation behavior of infectious SARS-CoV-2 in different environmental matrices and to examine factors affecting SARS-CoV-2 persistence.
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Affiliation(s)
- Ali Atoui
- ANSES, Nancy Laboratory for Hydrology, Water Microbiology Unit, 40, rue Lionnois, 54 000 Nancy, France.
| | - Christophe Cordevant
- ANSES, Strategy and Programs Department, Research and Reference Division, Maisons-Alfort F-94 700, France
| | - Thierry Chesnot
- ANSES, Nancy Laboratory for Hydrology, Water Microbiology Unit, 40, rue Lionnois, 54 000 Nancy, France
| | - Benoît Gassilloud
- ANSES, Nancy Laboratory for Hydrology, Water Microbiology Unit, 40, rue Lionnois, 54 000 Nancy, France
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An Overview on Exploitation of Graphene-Based Membranes: From Water Treatment to Medical Industry, Including Recent Fighting against COVID-19. Microorganisms 2023; 11:microorganisms11020310. [PMID: 36838275 PMCID: PMC9967324 DOI: 10.3390/microorganisms11020310] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2022] [Revised: 01/20/2023] [Accepted: 01/21/2023] [Indexed: 01/26/2023] Open
Abstract
Graphene and its derivatives have lately been the subject of increased attention for different environmental applications of membrane technology such as water treatment and air filtration, exploiting their antimicrobial and antiviral activity. They are interesting candidates as membrane materials for their outstanding mechanical and chemical stability and for their thin two-dimensional (2D) nanostructure with potential pore engineering for advanced separation. All these applications have evolved and diversified from discovery to today, and now graphene and graphene derivatives also offer fascinating opportunities for the fight against infective diseases such as COVID-19 thanks to their antimicrobial and antiviral properties. This paper presents an overview of graphene-based 2D materials, their preparation and use as membrane material for applications in water treatment and in respiratory protection devices.
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