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das Neves Costa LCP, Siqueira JAM, Teixeira DM, da Piedade GJL, Júnior ECS, Ferreira JL, da Silva LD, Gabbay YB. Circulation of adenovirus and other viruses in urban drainage channels: an environmental surveillance in Belém, Amazon region, Brazil. Braz J Microbiol 2023; 54:2939-2949. [PMID: 37747624 PMCID: PMC10689653 DOI: 10.1007/s42770-023-01125-9] [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: 06/15/2023] [Accepted: 09/06/2023] [Indexed: 09/26/2023] Open
Abstract
Urban channels in amazon cities are very polluted, with garbage and sewage disposal in these aquatic environments, favoring the high dissemination of waterborne viruses such as human adenovirus (HAdV). The aim of this study was to perform the detection and molecular characterization of adenovirus in urban channels and in a wastewater treatment plant located in a metropolitan city in the Amazon. Additionally, metagenomic analyses were performed to assess viral diversity. Samples were concentrated by organic flocculation, analyzed by quantitative real time PCR (qPCR) and sequenced (Sanger e next generation sequencing). Cell culture was performed to verify the viability of HAdV particles. A total of 104 samples were collected, being the HAdV positivity of 76% (79/104). Among the positive samples, 29.1% (23/79) were characterized as HAdV-F40 (87%, 20/23), HAdV-F41 (8.7%, 2/23), and HAdV-B (4.3%, 1/23). Average precipitation rates ranged from 163 to 614 mm, while the pH ranged from 6.9 to 7.6. Eight positive samples were inoculated into A549 cells and in 4 of these, was observed changes in the structure of the cell monolayer, alteration in the structure of the cell monolayer was observed, but without amplification when analyzed by PCR. The metagenomic data demonstrated the presence of 14 viral families, being the most abundant: Myoviridae (41% of available reads), Siphoviridae (24.5%), Podoviridae (14.1%), and Autographiviridae (6.9%) with more than 85% of the total number of identified reads. This study reinforcing that continuous surveillance may contribute to monitoring viral diversity in aquatic environments and provide early warning of potential outbreaks.
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Affiliation(s)
| | - Jones Anderson Monteiro Siqueira
- Virology Section, Evandro Chagas Institute, Health and Environment Surveillance Secretariat, Brazilian Ministry of Health, Ananindeua, PA, Brazil
| | - Dielle Monteiro Teixeira
- Virology Section, Evandro Chagas Institute, Health and Environment Surveillance Secretariat, Brazilian Ministry of Health, Ananindeua, PA, Brazil
| | - Guilherme Junior Leite da Piedade
- Postgraduate Program in Virology, Evandro Chagas Institute, Health and Environment Surveillance Secretariat, Brazilian Ministry of Health, Ananindeua, PA, Brazil
| | - Edivaldo Costa Sousa Júnior
- Virology Section, Evandro Chagas Institute, Health and Environment Surveillance Secretariat, Brazilian Ministry of Health, Ananindeua, PA, Brazil
| | - James Lima Ferreira
- Virology Section, Evandro Chagas Institute, Health and Environment Surveillance Secretariat, Brazilian Ministry of Health, Ananindeua, PA, Brazil
| | - Luciana Damascena da Silva
- Virology Section, Evandro Chagas Institute, Health and Environment Surveillance Secretariat, Brazilian Ministry of Health, Ananindeua, PA, Brazil
| | - Yvone Benchimol Gabbay
- Virology Section, Evandro Chagas Institute, Health and Environment Surveillance Secretariat, Brazilian Ministry of Health, Ananindeua, PA, Brazil
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2
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Gholipour S, Ghalhari MR, Nikaeen M, Rabbani D, Pakzad P, Miranzadeh MB. Occurrence of viruses in sewage sludge: A systematic review. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 824:153886. [PMID: 35182626 PMCID: PMC8848571 DOI: 10.1016/j.scitotenv.2022.153886] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/30/2021] [Revised: 01/25/2022] [Accepted: 02/11/2022] [Indexed: 05/04/2023]
Abstract
Enteric viruses are of great importance in wastewater due to their high excretion from infected individuals, low removal in wastewater treatment processes, long-time survival in the environment, and low infectious dose. Among the other viruses, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) surveillance in wastewater systems has received particular attention as a result of the current COVID-19 epidemic. Viruses adhering to solid particles in wastewater treatment processes will end up as sewage sludge, and therefore insufficient sludge treatment may result in viral particles dissemination into the environment. Here, we review data on viruses' presence in sewage sludge, their detection and concentration methods, and information on human health issues associated with sewage sludge land application. We used combinations of the following keywords in the Scopus, Web of Science (WOS), and PubMed databases, which were published between 2010 and January 21th, 2022: sludge (sewage sludge, biosolids, sewage solids, wastewater solids) and virus (enteric virus, viral particles, viral contamination, SARS-CoV-2, coronavirus). The sources were searched twice, once with and then without the common enteric virus names (adenovirus, rotavirus, norovirus, enterovirus, hepatitis A virus). Studies suggest adenovirus and norovirus as the most prevalent enteric viruses in sewage sludge. Indeed, other viruses include rotavirus, hepatitis A virus, and enterovirus were frequently found in sewage sludge samples. Untreated biological sludge and thickened sludge showed more viral contamination level than digested sludge and the lowest prevalence of viruses was reported in lime stabilized sludge. The review reveals that land application of sewage sludge may pose viral infection risks to people due to accidently ingestion of sludge or intake of crops grown in biosolids amended soil. Moreover, contamination of groundwater and/or surface water may occur due to land application of sewage sludge.
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Affiliation(s)
- Sahar Gholipour
- Department of Environmental Health Engineering, Faculty of Health, Kashan University of Medical Sciences, Kashan, Iran
| | - Mohammad Rezvani Ghalhari
- Department of Environmental Health Engineering, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran
| | - Mahnaz Nikaeen
- Department of Environmental Health Engineering, School of Health, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Davarkhah Rabbani
- Department of Environmental Health Engineering, Faculty of Health, Kashan University of Medical Sciences, Kashan, Iran
| | - Parichehr Pakzad
- Department of Environmental Health Engineering, School of Health, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Mohammad Bagher Miranzadeh
- Department of Environmental Health Engineering, Faculty of Health, Kashan University of Medical Sciences, Kashan, Iran.
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Stobnicka-Kupiec A, Gołofit-Szymczak M, Cyprowski M, Górny RL. Detection and identification of potentially infectious gastrointestinal and respiratory viruses at workplaces of wastewater treatment plants with viability qPCR/RT-qPCR. Sci Rep 2022; 12:4517. [PMID: 35296727 PMCID: PMC8924946 DOI: 10.1038/s41598-022-08452-1] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2021] [Accepted: 03/07/2022] [Indexed: 12/11/2022] Open
Abstract
This study aimed to qualitatively and quantitatively assess the prevalence of the most common respiratory and gastrointestinal viruses in the air, surface swab, and influent/effluent samples collected in wastewater treatment plants (WWTPs). Application of qPCR/RT-qPCR (quantitative polymerase chain reaction/reverse-transcription quantitative polymerase chain reaction) assays combined with PMA (propidium monoazide) dye pretreatment allowed detecting the potentially infectious and disintegrated viral particles in collected samples. In the air at workplaces in WWTPs, the most frequent isolation with the highest concentrations (reaching up to 103 gc/m3 of potentially infectious intact viral particles) were observed in case of adenoviruses (AdVs) and rotaviruses (RoVs), followed by noroviruses (NoVs). Viruses were significantly more often detected in the air samples collected with Coriolis μ impinger, than with MAS-100NT impactor. The temperature negatively (Spearman correlation: –1 < R < 0; p < 0.05), while RH (relative humidity) positively (0 < R < 1; p < 0.05) affected airborne concentrations of potentially infectious viral particles. In turn, the predominant viruses on studied surfaces were RoVs and noroviruses GII (NoV GII) with concentrations of potentially infectious virions up to 104 gc/100 cm2. In the cases of SARS-CoV-2 and presumptive SARS-CoV-2 or other coronaviruses, their concentrations reached up to 103 gc/100 cm2. The contamination level of steel surfaces in WWTPs was similar to this on plastic ones. This study revealed that the qualitative and quantitative characteristics of respiratory and gastrointestinal viruses at workplaces in WWTPs is important for proper exposure assessment and needs to be included in risk management in occupational environment with high abundance of microbial pollutants derived from wastewater.
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Affiliation(s)
- Agata Stobnicka-Kupiec
- Central Institute for Labour Protection - National Research Institute, Czerniakowska 16 Street, Warsaw, Poland.
| | - Małgorzata Gołofit-Szymczak
- Central Institute for Labour Protection - National Research Institute, Czerniakowska 16 Street, Warsaw, Poland
| | - Marcin Cyprowski
- Central Institute for Labour Protection - National Research Institute, Czerniakowska 16 Street, Warsaw, Poland
| | - Rafał L Górny
- Central Institute for Labour Protection - National Research Institute, Czerniakowska 16 Street, Warsaw, Poland
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Lima FS, Scalize PS, Gabriel EFM, Gomes RP, Gama AR, Demoliner M, Spilki FR, Vieira JDG, Carneiro LC. Escherichia coli, Species C Human Adenovirus, and Enterovirus in Water Samples Consumed in Rural Areas of Goiás, Brazil. FOOD AND ENVIRONMENTAL VIROLOGY 2022; 14:77-88. [PMID: 34792781 DOI: 10.1007/s12560-021-09504-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/21/2020] [Accepted: 11/08/2021] [Indexed: 06/13/2023]
Abstract
Rural environments lack basic sanitation services. Facilities for obtaining water and disposing sewage are often under the initiative of each resident, who may not be able to build and maintain them properly. Thus, water for human consumption is subject to fecal contamination and, consequently, the presence of waterborne pathogens, such as enteric viruses. This study evaluated fecal contamination of water samples from individual sources used for domestic water supply on small farms in the state of Goiás, Brazil. Samples were collected from 78 houses whose water sources were tubular wells, dug wells, springs, and surface waters. Escherichia coli (EC) bacteria, analyzed by the defined chromogenic substrate method, was used as a traditional indicator of fecal contamination. The enteric viruses Human mastadenovirus (HAdV) and Enterovirus (EV), analyzed by qPCR, were tested as complementary indicators of fecal contamination. At least one of these markers was found in 89.7% of the samples. Detection rates were 79.5% for EC, 52.6% for HAdV, and 5.1% for EV. The average concentration for EC was 8.82 × 101 most probable number (MPN) per 100 mL, while for HAdV and EV the concentrations were 7.51 × 105 and 1.89 × 106 genomic copies (GC) per liter, respectively. EC was the most frequent marker in ground and surface water samples. HAdV was detected significantly more frequently in groundwater than in surface water and was more efficient in indicating contamination in tubular wells. There was no association of frequencies or correlation of concentrations between EC and HAdV. HAdV indicated human fecal contamination and performed well as a complementary indicator. The results reveal that a large part of the analyzed population is vulnerable to waterborne diseases caused by enteric pathogens.
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Affiliation(s)
- Fernando Santos Lima
- Instituto de Patologia Tropical e Saúde Pública, Universidade Federal de Goiás, Goiânia, GO, 74605-050, Brazil.
| | - Paulo Sérgio Scalize
- Escola de Engenharia Civil e Ambiental, Universidade Federal de Goiás, Goiânia, GO, 74605-220, Brazil
| | | | - Raylane Pereira Gomes
- Instituto de Patologia Tropical e Saúde Pública, Universidade Federal de Goiás, Goiânia, GO, 74605-050, Brazil
| | - Aline Rodrigues Gama
- Instituto de Patologia Tropical e Saúde Pública, Universidade Federal de Goiás, Goiânia, GO, 74605-050, Brazil
| | - Meriane Demoliner
- Laboratório de Microbiologia Molecular, Universidade Feevale, Novo Hamburgo, RS, 93352-075, Brazil
| | - Fernando Rosado Spilki
- Laboratório de Microbiologia Molecular, Universidade Feevale, Novo Hamburgo, RS, 93352-075, Brazil
| | | | - Lilian Carla Carneiro
- Instituto de Patologia Tropical e Saúde Pública, Universidade Federal de Goiás, Goiânia, GO, 74605-050, Brazil
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Anand U, Li X, Sunita K, Lokhandwala S, Gautam P, Suresh S, Sarma H, Vellingiri B, Dey A, Bontempi E, Jiang G. SARS-CoV-2 and other pathogens in municipal wastewater, landfill leachate, and solid waste: A review about virus surveillance, infectivity, and inactivation. ENVIRONMENTAL RESEARCH 2022; 203:111839. [PMID: 34358502 PMCID: PMC8332740 DOI: 10.1016/j.envres.2021.111839] [Citation(s) in RCA: 57] [Impact Index Per Article: 28.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/27/2021] [Revised: 07/15/2021] [Accepted: 08/02/2021] [Indexed: 05/18/2023]
Abstract
This review discusses the techniques available for detecting and inactivating of pathogens in municipal wastewater, landfill leachate, and solid waste. In view of the current COVID-19 pandemic, SARS-CoV-2 is being given special attention, with a thorough examination of all possible transmission pathways linked to the selected waste matrices. Despite the lack of works focused on landfill leachate, a systematic review method, based on cluster analysis, allows to analyze the available papers devoted to sewage sludge and wastewater, allowing to focalize the work on technologies able to detect and treat pathogens. In this work, great attention is also devoted to infectivity and transmission mechanisms of SARS-CoV-2. Moreover, the literature analysis shows that sewage sludge and landfill leachate seem to have a remote chance to act as a virus transmission route (pollution-to-human transmission) due to improper collection and treatment of municipal wastewater and solid waste. However due to the incertitude about virus infectivity, these possibilities cannot be excluded and need further investigation. As a conclusion, this paper shows that additional research is required not only on the coronavirus-specific disinfection, but also the regular surveillance or monitoring of viral loads in sewage sludge, wastewater, and landfill leachate. The disinfection strategies need to be optimized in terms of dosage and potential adverse impacts like antimicrobial resistance, among many other factors. Finally, the presence of SARS-CoV-2 and other pathogenic microorganisms in sewage sludge, wastewater, and landfill leachate can hamper the possibility to ensure safe water and public health in economically marginalized countries and hinder the realization of the United Nations' sustainable development goals (SDGs).
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Affiliation(s)
- Uttpal Anand
- Department of Life Sciences and the National Institute for Biotechnology in the Negev, Ben-Gurion University of the Negev, Beer-Sheva, 84105, Israel
| | - Xuan Li
- School of Civil, Mining and Environmental Engineering, University of Wollongong, Australia
| | - Kumari Sunita
- Department of Botany, Deen Dayal Upadhyay Gorakhpur University, Gorakhpur, Uttar Pradesh, 273009, India
| | - Snehal Lokhandwala
- Department of Environmental Science & Technology, Shroff S.R. Rotary Institute of Chemical Technology, UPL University of Sustainable Technology, Ankleshwar, Gujarat, 393135, India
| | - Pratibha Gautam
- Department of Environmental Science & Technology, Shroff S.R. Rotary Institute of Chemical Technology, UPL University of Sustainable Technology, Ankleshwar, Gujarat, 393135, India
| | - S Suresh
- Department of Chemical Engineering, Maulana Azad National Institute of Technology, Bhopal, 462 003, Madhya Pradesh, India
| | - Hemen Sarma
- Department of Botany, Nanda Nath Saikia College, Dhodar Ali, Titabar, 785630, Assam, India
| | - Balachandar Vellingiri
- Human Molecular Cytogenetics and Stem Cell Laboratory, Department of Human Genetics and Molecular Biology, Bharathiar University, Coimbatore, 641-046, India
| | - Abhijit Dey
- Department of Life Sciences, Presidency University, 86/1 College Street, Kolkata, 700073, West Bengal, India
| | - Elza Bontempi
- INSTM and Chemistry for Technologies Laboratory, Department of Mechanical and Industrial Engineering, University of Brescia, Via Branze, 38, 25123, Brescia, Italy.
| | - Guangming Jiang
- School of Civil, Mining and Environmental Engineering, University of Wollongong, Australia; Illawarra Health and Medical Research Institute (IHMRI), University of Wollongong, Wollongong, Australia.
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6
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Nozza E, Valentini S, Melzi G, Vecchi R, Corsini E. Advances on the immunotoxicity of outdoor particulate matter: A focus on physical and chemical properties and respiratory defence mechanisms. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 780:146391. [PMID: 33774291 DOI: 10.1016/j.scitotenv.2021.146391] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/10/2020] [Revised: 02/16/2021] [Accepted: 03/07/2021] [Indexed: 06/12/2023]
Abstract
Particulate matter (PM) is acknowledged to have multiple detrimental effects on human health. In this review, we report literature results on the possible link between outdoor PM and health outcomes with a focus on pulmonary infections and the mechanisms responsible for observed negative effects. PM physical and chemical properties, such as size and chemical composition, as well as major emission sources are described for a more comprehensive view about the role played by atmospheric PM in the observed adverse health effects; to this aim, major processes leading to the deposition of PM in the respiratory tract and how this can pave the way to the onset of pathologies are also presented. From the literature works here reviewed, two ways in which PM can threaten human health promoting respiratory infectious diseases are mostly taken into account. The first pathway is related to an enhanced susceptibility and here we will also report on molecular mechanisms in the lung immune system responsible for the augmented susceptibility to pathogens, such as the damage of mechanical defensive barriers, the alteration of the innate immune response, and the generation of oxidative stress. The second one deals with the relationship between infectious agents and PM; here we recall that viruses and bacteria (BioPM) are themselves part of atmospheric PM and are collected during sampling together with particles of different origin; so, data should be analysed with caution in order to avoid any false cause-effect relation. To face these issues a multidisciplinary approach is mandatory as also evident from the ongoing research about the mechanisms hypothesized for the SARS-CoV-2 airborne spreading, which is still controversial and claims for further investigation. Therefore, we preferred not to include papers dealing with SARS-CoV-2.
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Affiliation(s)
- E Nozza
- Department of Environmental Science and Policy, Università degli Studi di Milano, via Balzaretti 9, 20133 Milan, Italy; Department of Physics, Università degli Studi di Milano, via Celoria 16, 20133 Milan, Italy
| | - S Valentini
- Department of Physics, Università degli Studi di Milano, via Celoria 16, 20133 Milan, Italy
| | - G Melzi
- Department of Pharmacological and Biomolecular Sciences (DiSFeB), Università degli Studi di Milano, via Balzaretti 9, 20133 Milan, Italy
| | - R Vecchi
- Department of Physics, Università degli Studi di Milano, via Celoria 16, 20133 Milan, Italy.
| | - E Corsini
- Department of Environmental Science and Policy, Università degli Studi di Milano, via Balzaretti 9, 20133 Milan, Italy
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Functionalized Surfaces as a Tool for Virus Sensing: A Demonstration of Human mastadenovirus Detection in Environmental Waters. CHEMOSENSORS 2021. [DOI: 10.3390/chemosensors9020019] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
The main goal of this study was to apply magnetic bead surface functionalization in the form of immunomagnetic separation (IMS) combined with real-time polymerase chain reaction (qPCR) (IMS-qPCR) to detect Human mastadenovirus species C (HAdV-C) and F (HAdV-F) in water samples. The technique efficiency was compared to a nonfunctionalized method (ultracentrifugation) followed by laboratory detection. Tests were carried out to standardize IMS parameters followed by tests on 15 water samples concentrated by IMS and ultracentrifugation. Microscopic analyses detected a successful beads–antibody attachment. HAdV was detected up to dilutions of 10−6 by IMS-qPCR, and samples concentrated by IMS were able to infect cell cultures. In water samples, HAdV-C was detected in 60% (monoclonal) and 47% (polyclonal) by IMS-qPCR, while 13% of samples concentrated by ultracentrifugation gave a positive result. HAdV-F was positive in 27% of samples by IMS-qPCR (polyclonal) and ultracentrifugation and 20% by IMS-qPCR (monoclonal). The rate of detection varied from 4.55 × 102 to 5.83 × 106 genomic copies/L for IMS-qPCR and from 2.00 × 102 to 2.11 × 103 GC/L for ultracentrifugation. IMS showed to be a more effective concentration technique for HAdV than ultracentrifugation, improving the assessment of infectious HAdV in water resources.
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8
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Urban-Rural Differences in Respiratory Tract Infections in Medieval and Early Modern Polish Subadult Samples. BIOARCHAEOLOGY AND SOCIAL THEORY 2020. [DOI: 10.1007/978-3-030-53417-2_10] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
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9
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Hamza IA, Bibby K. Critical issues in application of molecular methods to environmental virology. J Virol Methods 2019; 266:11-24. [PMID: 30659861 DOI: 10.1016/j.jviromet.2019.01.008] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2018] [Revised: 01/15/2019] [Accepted: 01/16/2019] [Indexed: 12/16/2022]
Abstract
Waterborne diseases have significant public health and socioeconomic implications worldwide. Many viral pathogens are commonly associated with water-related diseases, namely enteric viruses. Also, novel recently discovered human-associated viruses have been shown to be a causative agent of gastroenteritis or other clinical symptoms. A wide range of analytical methods is available for virus detection in environmental water samples. Viral isolation is historically carried out via propagation on permissive cell lines; however, some enteric viruses are difficult or not able to propagate on existing cell lines. Real-time polymerase chain reaction (qPCR) screening of viral nucleic acid is routinely used to investigate virus contamination in water due to the high sensitivity and specificity. Additionally, the introduction of metagenomic approaches into environmental virology has facilitated the discovery of viruses that cannot be grown in cell culture. This review (i) highlights the applications of molecular techniques in environmental virology such as PCR and its modifications to overcome the critical issues associated with the inability to discriminate between infectious viruses and nonviable viruses, (ii) outlines the strengths and weaknesses of Nucleic Acid Sequence Based Amplification (NASBA) and microarray, (iii) discusses the role of digital PCR as an emerging water quality monitoring assay and its advantages over qPCR, (iv) addresses the viral metagenomics in terms of detecting emerging viral pathogens and diversity in aquatic environment. Indeed, there are many challenges for selecting methods to detect classic and emerging viruses in environmental samples. While the existing techniques have revealed the importance and diversity of viruses in the water environment, further developments are necessary to enable more rapid and accurate methodologies for viral water quality monitoring and regulation.
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Affiliation(s)
- Ibrahim Ahmed Hamza
- Department of Water Pollution Research, National Research Centre, Cairo, Egypt.
| | - Kyle Bibby
- Department of Civil & Environmental Engineering & Earth Sciences, University of Notre Dame, USA
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10
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Peteffi GP, Fleck JD, Kael IM, Girardi V, Bündchen R, Krajeski DM, Demoliner M, Silva FP, da Rosa DC, Antunes MV, Linden R. Caffeine levels as a predictor of Human mastadenovirus presence in surface waters-a case study in the Sinos River basin-Brazil. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2018; 25:15774-15784. [PMID: 29582324 DOI: 10.1007/s11356-018-1649-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/28/2017] [Accepted: 02/28/2018] [Indexed: 06/08/2023]
Abstract
The presence of caffeine in environmental water samples is almost entirely human-related, given that there are virtually no industrial or agricultural releases. Caffeine has already been proposed as an anthropogenic marker for wastewater contamination of surface waters. The aim of this study was to evaluate if caffeine concentrations in water can be a predictor of virological and bacteriological contamination. Water samples were taken at three sampling sites from urban water streams from the hydrographic basin of the Sinos River (Brazil) monthly in the period of May 9th, 2016 to April 11th, 2017 (n = 36). Concentrations of Human mastadenovirus (HAdV-F and HAdV-C), fecal coliforms, and caffeine were measured in all collected samples. Concentrations of caffeine in water were strongly correlated with HAdV-F (rs = 0.704, p = 0.000). This study, for the first time, characterized caffeine concentrations in water as predictors of virus presence, with cut-off values presenting 92.9% specificity and 95.5% sensitivity for HAdV-F and 66.7% specificity and 80% sensitivity for HAdV-C. Considering its marked chemical stability and ease of quantification, caffeine concentrations can be used as a comprehensive marker of human contamination of water resources, also being predictive of bacteriological and virological concentrations.
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Affiliation(s)
- Giovana Piva Peteffi
- Laboratory of Analytical Toxicology, Universidade Feevale, ERS 239, 2755, Vila Nova, Novo Hamburgo, 93352-000, Brazil.
- Graduate Program in Environmental Quality, Universidade Feevale, ERS 239, 2755, Novo Hamburgo, 93352-000, Brazil.
- , Novo Hamburgo, Brazil.
| | - Juliane Deise Fleck
- Graduate Program in Environmental Quality, Universidade Feevale, ERS 239, 2755, Novo Hamburgo, 93352-000, Brazil
- Laboratory of Molecular Microbiology, Universidade Feevale, ERS 239, 2755, Novo Hamburgo, 93352-000, Brazil
| | - Igor Mendes Kael
- Laboratory of Analytical Toxicology, Universidade Feevale, ERS 239, 2755, Vila Nova, Novo Hamburgo, 93352-000, Brazil
| | - Viviane Girardi
- Graduate Program in Environmental Quality, Universidade Feevale, ERS 239, 2755, Novo Hamburgo, 93352-000, Brazil
- Laboratory of Molecular Microbiology, Universidade Feevale, ERS 239, 2755, Novo Hamburgo, 93352-000, Brazil
| | - Raquel Bündchen
- Laboratory of Molecular Microbiology, Universidade Feevale, ERS 239, 2755, Novo Hamburgo, 93352-000, Brazil
| | - Daiane Metz Krajeski
- Laboratory of Molecular Microbiology, Universidade Feevale, ERS 239, 2755, Novo Hamburgo, 93352-000, Brazil
| | - Meriane Demoliner
- Laboratory of Molecular Microbiology, Universidade Feevale, ERS 239, 2755, Novo Hamburgo, 93352-000, Brazil
| | - Francini Pereira Silva
- Laboratory of Molecular Microbiology, Universidade Feevale, ERS 239, 2755, Novo Hamburgo, 93352-000, Brazil
| | - Débora Couto da Rosa
- Laboratory of Molecular Microbiology, Universidade Feevale, ERS 239, 2755, Novo Hamburgo, 93352-000, Brazil
| | - Marina Venzon Antunes
- Laboratory of Analytical Toxicology, Universidade Feevale, ERS 239, 2755, Vila Nova, Novo Hamburgo, 93352-000, Brazil
| | - Rafael Linden
- Laboratory of Analytical Toxicology, Universidade Feevale, ERS 239, 2755, Vila Nova, Novo Hamburgo, 93352-000, Brazil
- Graduate Program in Environmental Quality, Universidade Feevale, ERS 239, 2755, Novo Hamburgo, 93352-000, Brazil
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11
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Girardi V, Demoliner M, Rigotto C, Schneider VE, Paesi S, Spilki FR. Assessment of diversity of adenovirus DNA polymerase gene in recreational waters facilitated by ultracentrifugal concentration. JOURNAL OF WATER AND HEALTH 2018; 16:102-111. [PMID: 29424724 DOI: 10.2166/wh.2017.144] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Adenoviruses (AdV) are related to respiratory and gastrointestinal diseases in animals and human beings. Their wide genetic diversity in water bodies and their resistance to environmental conditions allow the use of AdV as a reliable marker for detection of fecal contamination. In this work, the diversity of AdV along Belo Stream - in the city of Caxias do Sul, Rio Grande do Sul, Brazil - was evaluated. Samples were compared in both concentrated and unconcentrated forms. The identification of different AdV species was performed by amplifying a partial sequence of the DNA polymerase gene. AdV was detected in 24 out of 55 concentrated samples (43.6%) and the following species were identified: human adenovirus (HAdV) species C (4/55; 7.2%), D (6/55; 10.9%), E (2/55; 3.6%), and F (9/55; 16.3%). AdV related to other mammalian hosts, such as bovine adenovirus (1/55, 1.8%) and murine adenovirus (2/55, 3.6%), have also been identified; 23.6% (13/55) of the unconcentrated samples were positive, and identified as HAdV species C (6/55, 10.9%), D (1/55, 1.8%), and F (6/55, 10.9%). Results obtained evidenced the presence and the great diversity of AdV, mainly of human origin, circulating in Belo Stream. As expected, the concentration step performed helped to detect AdV in more samples.
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Affiliation(s)
- Viviane Girardi
- Laboratório de Microbiologia Molecular, Universidade Feevale, ERS 239 n° 2755, Novo Hamburgo, RS 93352-000, Brasil E-mail:
| | - Meriane Demoliner
- Laboratório de Microbiologia Molecular, Universidade Feevale, ERS 239 n° 2755, Novo Hamburgo, RS 93352-000, Brasil E-mail:
| | - Caroline Rigotto
- Laboratório de Microbiologia Molecular, Universidade Feevale, ERS 239 n° 2755, Novo Hamburgo, RS 93352-000, Brasil E-mail:
| | - Vania Elisabete Schneider
- Instituto de Saneamento Ambiental (ISAM), Universidade de Caxias do Sul, Rua Francisco Getúlio Vargas, n° 1130, Caxias do Sul, RS 95070-560, Brasil
| | - Suelen Paesi
- Laboratório de Diagnóstico Molecular, Instituto de Biotecnologia, Universidade de Caxias do Sul, Rua Francisco Getúlio Vargas, n° 1130, Caxias do Sul, RS 95070-560, Brasil
| | - Fernando Rosado Spilki
- Laboratório de Microbiologia Molecular, Universidade Feevale, ERS 239 n° 2755, Novo Hamburgo, RS 93352-000, Brasil E-mail:
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Turgeon N, Michel K, Ha TL, Robine E, Moineau S, Duchaine C. Resistance of Aerosolized Bacterial Viruses to Four Germicidal Products. PLoS One 2016; 11:e0168815. [PMID: 28030577 PMCID: PMC5193356 DOI: 10.1371/journal.pone.0168815] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2016] [Accepted: 12/06/2016] [Indexed: 01/05/2023] Open
Abstract
Viral diseases can spread through a variety of routes including aerosols. Yet, limited data are available on the efficacy of aerosolized chemicals to reduce viral loads in the air. Bacteriophages (phages) are often used as surrogates for hazardous viruses in aerosol studies because they are inexpensive, easy to handle, and safe for laboratory workers. Moreover, several of these bacterial viruses display physical characteristics similar to pathogenic human and animal viruses, like morphological size, type of nucleic acids, capsid morphology, and the presence of an envelope. In this study, the efficacy of four chemicals was evaluated on four airborne phages at two different relative humidity levels. Non-tailed bacteriophages MS2 (single-stranded RNA), ϕ6 (double-stranded RNA, enveloped), PR772 (double-stranded DNA), and ϕX174 (single-stranded DNA) were first aerosolized in a 55L rotative environmental chamber at 19°C with 25% and 50% relative humidity. Then, hydrogen peroxide, Eugenol (phenylpropene used in commercial perfumes and flavorings), Mist® (automobile disinfectant containing Triethylene glycol), and Pledge® (multisurface disinfectant containing Isopropanol, n-Alkyl Dimethyl Benzyl Amonium Chlorides, and n-Alkyl Dimethyl Ethylbenzyl Ammonium Chloride) were nebulized with the phages using a separate nebulizer. Aerosols were maintained in suspension during 10 minutes, 1 hour, and 2 hours. Viral aerosols were sampled using an SKC BioSampler and samples were analyzed using qPCR and plaque assays. The resistance levels of the four phages varied depending on the relative humidity (RH) and germicidal products tested. Phage MS2 was the most stable airborne virus under the environmental conditions tested while phage PR772 was the least stable. Pledge® and Eugenol reduced the infectivity of all airborne phages tested. At 25% RH, Pledge® and Eugenol were more effective at reducing infectivity of RNA phages ϕ6 and MS2. At 50% RH, Pledge® was the most effective agent against phage MS2. These findings illustrate that various airborne viruses should be tested to demonstrate the effectiveness of germicidal treatments. This research also provides a set of parameters for testing germicidal products in large-scale settings to reduce the risk of virus transmission.
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Affiliation(s)
- Nathalie Turgeon
- Centre de recherche de l’Institut universitaire de cardiologie et de pneumologie de Québec-Université Laval, Québec, Québec, Canada
- Département de biochimie, de microbiologie et de bio-informatique, Faculté des sciences et de génie, Université Laval, Québec, Québec, Canada
| | - Kevin Michel
- Centre de recherche de l’Institut universitaire de cardiologie et de pneumologie de Québec-Université Laval, Québec, Québec, Canada
- Département de biochimie, de microbiologie et de bio-informatique, Faculté des sciences et de génie, Université Laval, Québec, Québec, Canada
| | - Thi-Lan Ha
- Centre Scientifique et Technique du Bâtiment, Champs-sur-Marne, Marne la Vallée cedex, France
| | - Enric Robine
- Centre Scientifique et Technique du Bâtiment, Champs-sur-Marne, Marne la Vallée cedex, France
| | - Sylvain Moineau
- Département de biochimie, de microbiologie et de bio-informatique, Faculté des sciences et de génie, Université Laval, Québec, Québec, Canada
- Félix d’Hérelle Reference Center for Bacterial Viruses and GREB, Faculté de médecine dentaire, Université Laval, Québec, Québec, Canada
| | - Caroline Duchaine
- Centre de recherche de l’Institut universitaire de cardiologie et de pneumologie de Québec-Université Laval, Québec, Québec, Canada
- Département de biochimie, de microbiologie et de bio-informatique, Faculté des sciences et de génie, Université Laval, Québec, Québec, Canada
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13
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Calusinska M, Marynowska M, Goux X, Lentzen E, Delfosse P. Analysis of dsDNA and RNA viromes in methanogenic digesters reveals novel viral genetic diversity. Environ Microbiol 2016; 18:1162-75. [PMID: 26568175 PMCID: PMC7163765 DOI: 10.1111/1462-2920.13127] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2014] [Revised: 08/17/2015] [Accepted: 11/06/2015] [Indexed: 01/08/2023]
Abstract
Although viruses are not the key players of the anaerobic digestion process, they may affect the dynamics of bacterial and archaeal populations involved in biogas production. Until now viruses have received very little attention in this specific habitat; therefore, as a first step towards their characterization, we optimized a virus filtration protocol from anaerobic sludge. Afterwards, to assess dsDNA and RNA viral diversity in sludge samples from nine different reactors fed either with waste water, agricultural residues or solid municipal waste plus agro‐food residues, we performed metagenomic analyses. As a result we showed that, while the dsDNA viromes (21 assigned families in total) were dominated by dsDNA phages of the order Caudovirales, RNA viruses (14 assigned families in total) were less diverse and were for the main part plant‐infecting viruses. Interestingly, less than 2% of annotated contigs were assigned as putative human and animal pathogens. Our study greatly extends the existing view of viral genetic diversity in methanogenic reactors and shows that these viral assemblages are distinct not only among the reactor types but also from nearly 30 other environments already studied, including the human gut, fermented food, deep sea sediments and other aquatic habitats.
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Affiliation(s)
- Magdalena Calusinska
- Luxembourg Institute of Science and Technology, Environmental Research and Innovation (ERIN), 41 rue du Brill, L-4422, Belvaux, Luxembourg
| | - Martyna Marynowska
- Luxembourg Institute of Science and Technology, Environmental Research and Innovation (ERIN), 41 rue du Brill, L-4422, Belvaux, Luxembourg.,Intercollegiate Faculty of Biotechnology, University of Gdansk and Medical University of Gdansk, ul. Kladki 24, 80-822, Gdansk, Poland
| | - Xavier Goux
- Luxembourg Institute of Science and Technology, Environmental Research and Innovation (ERIN), 41 rue du Brill, L-4422, Belvaux, Luxembourg
| | - Esther Lentzen
- Luxembourg Institute of Science and Technology, Materials Research and Technology (MRT), 41 rue du Brill, L-4422, Belvaux, Luxembourg
| | - Philippe Delfosse
- Luxembourg Institute of Science and Technology, Environmental Research and Innovation (ERIN), 41 rue du Brill, L-4422, Belvaux, Luxembourg
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Kuo HW, Chen LZ, Shih MH. High prevalence of type 41 and high sequence diversity of partial hexon gene of human adenoviruses in municipal raw sewage and activated sludge. J Appl Microbiol 2015; 119:1181-95. [PMID: 26189615 DOI: 10.1111/jam.12907] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2015] [Revised: 06/24/2015] [Accepted: 07/04/2015] [Indexed: 11/29/2022]
Abstract
AIM This study was aimed to assess seasonal/geographical distribution and sequence diversity of partial hexon gene for human adenoviruses (HAdVs) within raw sewages (RS) and activated sludges (AS). METHODS AND RESULTS Assessments were based on high-throughput sequencing (HTS) for polymerase chain reaction (PCR)-amplified 128-bp partial hexon gene fragments and followed by principal coordinate analyses (PCoA) for revealed sequences. Sequencing results showed that the majority of sequences (>90%) for the RS or AS samples were identical to HAdV type 41 of species F, while rest of few sequences belonged to HAdV species-D and -C were only occurred rarely without significant seasonal/geographical variation. The partial hexon genes were highly diverse as many sequence types and operational taxonomic unit groups were noticed among the matched sequences. CONCLUSIONS This study demonstrated that HAdV-41 was constantly appeared in the RS and AS samples from Taiwan throughout the year without significant seasonal or geographical variations; but, had high sequence diverse noticed for the 128-bp partial hexon gene fragments. SIGNIFICANCE AND IMPACT OF THE STUDY High-throughput-sequencing results provided better insights of HAdV distribution and genetic diversity for raw sewage and AS samples allowing some probable biases for cloning-sequencing approach to be defeated and further providing public health awareness regarding viral-contaminated sewages or sludges.
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Affiliation(s)
- H-W Kuo
- Department of Environmental Science and Engineering, Tunghai University, Taichung, Taiwan
| | - L-Z Chen
- Department of Environmental Science and Engineering, Tunghai University, Taichung, Taiwan
| | - M-H Shih
- Department of Environmental Science and Engineering, Tunghai University, Taichung, Taiwan
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15
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Ogorzaly L, Walczak C, Galloux M, Etienne S, Gassilloud B, Cauchie HM. Human Adenovirus Diversity in Water Samples Using a Next-Generation Amplicon Sequencing Approach. FOOD AND ENVIRONMENTAL VIROLOGY 2015; 7:112-121. [PMID: 25917314 DOI: 10.1007/s12560-015-9194-4] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/18/2014] [Accepted: 03/30/2015] [Indexed: 05/18/2023]
Abstract
This study aims to establish a straightforward and original workflow for high-throughput typing of human adenoviruses (HAdVs) in environmental samples. Occurrence of HAdVs in water is well documented worldwide, but data on diversity of HAdV types circulating in water are scarcely available. Here, the characterisation of viral particles was performed by determination of amplicon sequences using a next-generation sequencing (NGS) approach. Adenoviral DNA was either directly isolated from wastewater or river water concentrates or after a cell culture passage. Genome amplification targeted a hyper variable region of the hexon gene, allowing the discrimination of the 54 human adenoviral types described until now. After read generation on the benchtop MiSeq platform (Illumina), data were analysed using the Mothur software for identification of all HAdV species and types simultaneously present in a unique sample. NGS results showed a relatively wide HAdV diversity of up to six types in one sample, whereas Sanger sequencing always only retrieved the dominant one. Detected types included HAdV-1, HAdV-2, HAdV-3, HAdV-6, HAdV-12, HAdV-31, HAdV-40 and HAdV-41, HAdV-41 being the most abundant in tested samples. In addition, the influence of the cell line (A549 vs 293A cells) on the infectious HAdV typing results was clearly determined. The 293A appeared to be the most suitable cell line allowing the detection of a larger diversity of infectious HAdVs and reflecting a more realistic initial species distribution than using the A549 cells. These findings demonstrated the feasibility of amplicon sequencing NGS approach to identify viruses in complex environmental water samples.
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Affiliation(s)
- Leslie Ogorzaly
- Department of Environmental Research and Innovation (ERIN), Luxembourg Institute of Science and Technology (LIST), 41, rue du Brill, 4422, Belvaux, Luxembourg,
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Aw TG, Howe A, Rose JB. Metagenomic approaches for direct and cell culture evaluation of the virological quality of wastewater. J Virol Methods 2014; 210:15-21. [DOI: 10.1016/j.jviromet.2014.09.017] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2014] [Revised: 09/15/2014] [Accepted: 09/16/2014] [Indexed: 10/24/2022]
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BIBBY KYLE, PECCIA JORDAN. Identification of viral pathogen diversity in sewage sludge by metagenome analysis. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2013; 47:1945-51. [PMID: 23346855 PMCID: PMC3963146 DOI: 10.1021/es305181x] [Citation(s) in RCA: 239] [Impact Index Per Article: 21.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
The large diversity of viruses that exist in human populations are potentially excreted into sewage collection systems and concentrated in sewage sludge. In the U.S., the primary fate of processed sewage sludge (class B biosolids) is application to agricultural land as a soil amendment. To characterize and understand infectious risks associated with land application, and to describe the diversity of viruses in human populations, shotgun viral metagenomics was applied to 10 sewage sludge samples from 5 wastewater treatment plants throughout the continental U.S, each serving between 100,000 and 1,000,000 people. Nearly 330 million DNA sequences were produced and assembled, and annotation resulted in identifying 43 (26 DNA, 17 RNA) different types of human viruses in sewage sludge. Novel insights include the high abundance of newly emerging viruses (e.g., Coronavirus HKU1, Klassevirus, and Cosavirus) the strong representation of respiratory viruses, and the relatively minor abundance and occurrence of Enteroviruses. Viral metagenome sequence annotations were reproducible and independent PCR-based identification of selected viruses suggests that viral metagenomes were a conservative estimate of the true viral occurrence and diversity. These results represent the most complete description of human virus diversity in any wastewater sample to date, provide engineers and environmental scientists with critical information on important viral agents and routes of infection from exposure to wastewater and sewage sludge, and represent a significant leap forward in understanding the pathogen content of class B biosolids.
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Affiliation(s)
- KYLE BIBBY
- Department of Chemical and Environmental Engineering, Yale University, Mason Laboratory, 9 Hillhouse Avenue, P.O. Box 208286, New Haven, CT 06520
| | - JORDAN PECCIA
- Department of Chemical and Environmental Engineering, Yale University, Mason Laboratory, 9 Hillhouse Avenue, P.O. Box 208286, New Haven, CT 06520
- Corresponding author tel: (203) 432-4385; fax: (203) 432-4387;
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