1
|
Fernandez-Cassi X, Kohn T. Comparison of Three Viral Nucleic Acid Preamplification Pipelines for Sewage Viral Metagenomics. Food Environ Virol 2024:10.1007/s12560-024-09594-3. [PMID: 38647859 DOI: 10.1007/s12560-024-09594-3] [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] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/19/2023] [Accepted: 03/01/2024] [Indexed: 04/25/2024]
Abstract
Viral metagenomics is a useful tool for detecting multiple human viruses in urban sewage. However, more refined protocols are required for its effective use in disease surveillance. In this study, we investigated the performance of three different preamplification pipelines (specific to RNA viruses, DNA viruses or both) for viral genome sequencing using spiked-in Phosphate Buffered Saline and sewage samples containing known concentrations of viruses. We found that compared to the pipeline targeting all genome types, the RNA pipeline performed better in detecting RNA viruses in both spiked and unspiked sewage samples, allowing the detection of various mammalian viruses including members from the Reoviridae, Picornaviridae, Astroviridae and Caliciviridae. However, the DNA-specific pipeline did not improve the detection of mammalian DNA viruses. We also measured viral recovery by quantitative reverse transcription polymerase chain reaction and assessed the impact of genetic background (non-viral genetic material) on viral coverage. Our results indicate that viral recoveries were generally lower in sewage (average of 11.0%) and higher in Phosphate Buffered Saline (average of 23.4%) for most viruses. Additionally, spiked-in viruses showed lower genome coverage in sewage, demonstrating the negative effect of genetic background on sequencing. Finally, correlation analysis revealed a relationship between virus concentration and genome normalized reads per million, indicating that viral metagenomic sequencing can be semiquantitative.
Collapse
Affiliation(s)
- Xavier Fernandez-Cassi
- Laboratory of Environmental Chemistry, School of Architecture, Civil and Environmental Engineering, École Polytechnique Fédérale de Lausanne (EPFL), Vaud, Lausanne, Switzerland.
- Departament of Biology, Healthcare and Environment, Faculty of Pharmacy and Food Sciences, University of Barcelona (UB), Barcelona, Catalunya, Spain.
| | - Tamar Kohn
- Laboratory of Environmental Chemistry, School of Architecture, Civil and Environmental Engineering, École Polytechnique Fédérale de Lausanne (EPFL), Vaud, Lausanne, Switzerland
| |
Collapse
|
2
|
Li C, Sylvestre É, Fernandez-Cassi X, Julian TR, Kohn T. Waterborne virus transport and the associated risks in a large lake. Water Res 2023; 229:119437. [PMID: 36476383 DOI: 10.1016/j.watres.2022.119437] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [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: 08/24/2022] [Revised: 11/04/2022] [Accepted: 11/26/2022] [Indexed: 06/17/2023]
Abstract
Waterborne enteric viruses in lakes, especially at recreational water sites, may have a negative impact on human health. However, their fate and transport in lakes are poorly understood. In this study, we propose a coupled water quality and quantitative microbial risk assessment (QMRA) model to study the transport, fate and infection risk of four common waterborne viruses (adenovirus, enterovirus, norovirus and rotavirus), using Lake Geneva as a study site. The measured virus load in raw sewage entering the lake was used as the source term in the water quality simulations for a hypothetical scenario of discharging raw wastewater at the lake surface. After discharge into the lake, virus inactivation was modeled as a function of water temperature and solar irradiance that varied both spatially and temporally during transport throughout the lake. Finally, the probability of infection, while swimming at a popular beach, was quantified and compared among the four viruses. Norovirus was found to be the most abundant virus that causes an infection probability that is at least 10 times greater than the other viruses studied. Furthermore, environmental inactivation was found to be an essential determinant in the infection risks posed by viruses to recreational water users. We determined that infection risks by enterovirus and rotavirus could be up to 1000 times lower when virus inactivation by environmental stressors was accounted for compared with the scenarios considering hydrodynamic transport only. Finally, the model highlighted the role of the wind field in conveying the contamination plume and hence in determining infection probability. Our simulations revealed that for beaches located west of the sewage discharge, the infection probability under eastward wind was 43% lower than that under westward wind conditions. This study highlights the potential of combining water quality simulation and virus-specific risk assessment for a safe water resources usage and management.
Collapse
Affiliation(s)
- Chaojie Li
- Laboratory of Environmental Chemistry, School of Architecture, Civil and Environmental Engineering, (ENAC), École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Émile Sylvestre
- Department Environmental Microbiology, Eawag-Swiss Federal Institute of Aquatic Science and Technology, Dübendorf, Switzerland
| | - Xavier Fernandez-Cassi
- Laboratory of Environmental Chemistry, School of Architecture, Civil and Environmental Engineering, (ENAC), École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Timothy R Julian
- Department Environmental Microbiology, Eawag-Swiss Federal Institute of Aquatic Science and Technology, Dübendorf, Switzerland; Swiss Tropical and Public Health Institute, Basel, Switzerland; University of Basel, Basel, Switzerland
| | - Tamar Kohn
- Laboratory of Environmental Chemistry, School of Architecture, Civil and Environmental Engineering, (ENAC), École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland.
| |
Collapse
|
3
|
Cariti F, Tuñas Corzon A, Fernandez-Cassi X, Ganesanandamoorthy P, Ort C, Julian TR, Kohn T. Wastewater Reveals the Spatiotemporal Spread of SARS-CoV-2 in the Canton of Ticino (Switzerland) during the Onset of the COVID-19 Pandemic. ACS ES T Water 2022; 2:2194-2200. [PMID: 36398130 PMCID: PMC9664445 DOI: 10.1021/acsestwater.2c00082] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
Wastewater-based epidemiology (WBE) has emerged as an effective tool for monitoring SARS-CoV-2 dynamics during the COVID-19 pandemic. Here, we add a spatial component to WBE and use it to investigate SARS-CoV-2 spread in the canton of Ticino during the onset of the pandemic in Switzerland (end of February 2020 to beginning of March 2020). Ticino is located at the border to Northern Italy, where a large COVID-19 outbreak occurred in February 2020. Not surprisingly, Ticino was the site of the first clinically confirmed COVID-19 case in Switzerland. We retrospectively analyzed daily influent samples from nine wastewater treatment plants in Ticino that jointly cover an area of 20 km × 60 km and 351,000 people (>99% of the population). Our result is a fine-grained view of the spatiotemporal evolution of the COVID-19 pandemic in this canton. The wastewater analysis revealed that by February 29, 2020, SARS-CoV-2 had already spread to all catchments. At the same time, only four individual cases had been clinically confirmed across the region served by the treatment plants investigated. Our results demonstrate that WBE could serve as a versatile tool to monitor the introduction and spread of an infectious agent on a regional scale. To fully exploit its utility, WBE should be implemented in real time and become an integral part of future disease surveillance efforts.
Collapse
Affiliation(s)
- Federica Cariti
- Laboratory
of Environmental Chemistry, School of Architecture, Civil and Environmental
Engineering, École Polytechnique
Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland
| | - Alex Tuñas Corzon
- Laboratory
of Environmental Chemistry, School of Architecture, Civil and Environmental
Engineering, École Polytechnique
Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland
| | - Xavier Fernandez-Cassi
- Laboratory
of Environmental Chemistry, School of Architecture, Civil and Environmental
Engineering, École Polytechnique
Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland
| | | | - Christoph Ort
- Eawag, Swiss
Federal Institute of Aquatic Science and Technology, 8600 Dübendorf, Switzerland
| | - Timothy R. Julian
- Eawag, Swiss
Federal Institute of Aquatic Science and Technology, 8600 Dübendorf, Switzerland
- Swiss
Tropical and Public Health Institute, CH-4051 Basel, Switzerland
- University
of Basel, CH-4055 Basel, Switzerland
| | - Tamar Kohn
- Laboratory
of Environmental Chemistry, School of Architecture, Civil and Environmental
Engineering, École Polytechnique
Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland
| |
Collapse
|
4
|
Jahn K, Dreifuss D, Topolsky I, Kull A, Ganesanandamoorthy P, Fernandez-Cassi X, Bänziger C, Devaux AJ, Stachler E, Caduff L, Cariti F, Corzón AT, Fuhrmann L, Chen C, Jablonski KP, Nadeau S, Feldkamp M, Beisel C, Aquino C, Stadler T, Ort C, Kohn T, Julian TR, Beerenwinkel N. Early detection and surveillance of SARS-CoV-2 genomic variants in wastewater using COJAC. Nat Microbiol 2022. [PMID: 35851854 DOI: 10.1101/2021.01.08.21249379] [Citation(s) in RCA: 27] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/13/2023]
Abstract
The continuing emergence of SARS-CoV-2 variants of concern and variants of interest emphasizes the need for early detection and epidemiological surveillance of novel variants. We used genomic sequencing of 122 wastewater samples from three locations in Switzerland to monitor the local spread of B.1.1.7 (Alpha), B.1.351 (Beta) and P.1 (Gamma) variants of SARS-CoV-2 at a population level. We devised a bioinformatics method named COJAC (Co-Occurrence adJusted Analysis and Calling) that uses read pairs carrying multiple variant-specific signature mutations as a robust indicator of low-frequency variants. Application of COJAC revealed that a local outbreak of the Alpha variant in two Swiss cities was observable in wastewater up to 13 d before being first reported in clinical samples. We further confirmed the ability of COJAC to detect emerging variants early for the Delta variant by analysing an additional 1,339 wastewater samples. While sequencing data of single wastewater samples provide limited precision for the quantification of relative prevalence of a variant, we show that replicate and close-meshed longitudinal sequencing allow for robust estimation not only of the local prevalence but also of the transmission fitness advantage of any variant. We conclude that genomic sequencing and our computational analysis can provide population-level estimates of prevalence and fitness of emerging variants from wastewater samples earlier and on the basis of substantially fewer samples than from clinical samples. Our framework is being routinely used in large national projects in Switzerland and the UK.
Collapse
Affiliation(s)
- Katharina Jahn
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland
- SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - David Dreifuss
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland
- SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Ivan Topolsky
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland
- SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Anina Kull
- Eawag, Swiss Federal Institute of Aquatic Science and Technology, Dübendorf, Switzerland
| | | | - Xavier Fernandez-Cassi
- Laboratory of Environmental Chemistry, School of Architecture, Civil and Environmental Engineering, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Carola Bänziger
- Eawag, Swiss Federal Institute of Aquatic Science and Technology, Dübendorf, Switzerland
| | - Alexander J Devaux
- Eawag, Swiss Federal Institute of Aquatic Science and Technology, Dübendorf, Switzerland
| | - Elyse Stachler
- Eawag, Swiss Federal Institute of Aquatic Science and Technology, Dübendorf, Switzerland
| | - Lea Caduff
- Eawag, Swiss Federal Institute of Aquatic Science and Technology, Dübendorf, Switzerland
| | - Federica Cariti
- Laboratory of Environmental Chemistry, School of Architecture, Civil and Environmental Engineering, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Alex Tuñas Corzón
- Laboratory of Environmental Chemistry, School of Architecture, Civil and Environmental Engineering, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Lara Fuhrmann
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland
- SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Chaoran Chen
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland
- SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Kim Philipp Jablonski
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland
- SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Sarah Nadeau
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland
- SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Mirjam Feldkamp
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland
| | - Christian Beisel
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland
| | - Catharine Aquino
- Functional Genomics Center Zurich, ETH Zurich, Zurich, Switzerland
| | - Tanja Stadler
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland
- SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Christoph Ort
- Eawag, Swiss Federal Institute of Aquatic Science and Technology, Dübendorf, Switzerland
| | - Tamar Kohn
- Laboratory of Environmental Chemistry, School of Architecture, Civil and Environmental Engineering, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Timothy R Julian
- Eawag, Swiss Federal Institute of Aquatic Science and Technology, Dübendorf, Switzerland
- Swiss Tropical and Public Health Institute, Basel, Switzerland
- University of Basel, Basel, Switzerland
| | - Niko Beerenwinkel
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland.
- SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland.
| |
Collapse
|
5
|
Huisman JS, Scire J, Caduff L, Fernandez-Cassi X, Ganesanandamoorthy P, Kull A, Scheidegger A, Stachler E, Boehm AB, Hughes B, Knudson A, Topol A, Wigginton KR, Wolfe MK, Kohn T, Ort C, Stadler T, Julian TR. Wastewater-Based Estimation of the Effective Reproductive Number of SARS-CoV-2. Environ Health Perspect 2022; 130:57011. [PMID: 35617001 PMCID: PMC9135136 DOI: 10.1289/ehp10050] [Citation(s) in RCA: 46] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/29/2021] [Revised: 04/09/2022] [Accepted: 04/26/2022] [Indexed: 05/05/2023]
Abstract
BACKGROUND The effective reproductive number, R e , is a critical indicator to monitor disease dynamics, inform regional and national policies, and estimate the effectiveness of interventions. It describes the average number of new infections caused by a single infectious person through time. To date, R e estimates are based on clinical data such as observed cases, hospitalizations, and/or deaths. These estimates are temporarily biased when clinical testing or reporting strategies change. OBJECTIVES We show that the dynamics of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) RNA in wastewater can be used to estimate R e in near real time, independent of clinical data and without the associated biases. METHODS We collected longitudinal measurements of SARS-CoV-2 RNA in wastewater in Zurich, Switzerland, and San Jose, California, USA. We combined this data with information on the temporal dynamics of shedding (the shedding load distribution) to estimate a time series proportional to the daily COVID-19 infection incidence. We estimated a wastewater-based R e from this incidence. RESULTS The method to estimate R e from wastewater worked robustly on data from two different countries and two wastewater matrices. The resulting estimates were as similar to the R e estimates from case report data as R e estimates based on observed cases, hospitalizations, and deaths are among each other. We further provide details on the effect of sampling frequency and the shedding load distribution on the ability to infer R e . DISCUSSION To our knowledge, this is the first time R e has been estimated from wastewater. This method provides a low-cost, rapid, and independent way to inform SARS-CoV-2 monitoring during the ongoing pandemic and is applicable to future wastewater-based epidemiology targeting other pathogens. https://doi.org/10.1289/EHP10050.
Collapse
Affiliation(s)
- Jana S. Huisman
- Department of Environmental Systems Science, ETH Zurich, Swiss Federal Institute of Technology, Zurich, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
- Department of Biosystems Science and Engineering, ETH Zurich, Swiss Federal Institute of Technology, Basel, Switzerland
| | - Jérémie Scire
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
- Department of Biosystems Science and Engineering, ETH Zurich, Swiss Federal Institute of Technology, Basel, Switzerland
| | - Lea Caduff
- Eawag, Swiss Federal Institute of Aquatic Science and Technology, Dübendorf, Switzerland
| | - Xavier Fernandez-Cassi
- Laboratory of Environmental Chemistry, School of Architecture, Civil and Environmental Engineering, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | | | - Anina Kull
- Eawag, Swiss Federal Institute of Aquatic Science and Technology, Dübendorf, Switzerland
| | - Andreas Scheidegger
- Eawag, Swiss Federal Institute of Aquatic Science and Technology, Dübendorf, Switzerland
| | - Elyse Stachler
- Eawag, Swiss Federal Institute of Aquatic Science and Technology, Dübendorf, Switzerland
| | - Alexandria B. Boehm
- Department of Civil and Environmental Engineering, Stanford University, Stanford, California, USA
| | | | - Alisha Knudson
- Verily Life Sciences, South San Francisco, California, USA
| | - Aaron Topol
- Verily Life Sciences, South San Francisco, California, USA
| | - Krista R. Wigginton
- Department of Civil and Environmental Engineering, University of Michigan, Ann Arbor, Michigan, USA
| | - Marlene K. Wolfe
- Department of Civil and Environmental Engineering, Stanford University, Stanford, California, USA
| | - Tamar Kohn
- Laboratory of Environmental Chemistry, School of Architecture, Civil and Environmental Engineering, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Christoph Ort
- Eawag, Swiss Federal Institute of Aquatic Science and Technology, Dübendorf, Switzerland
| | - Tanja Stadler
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
- Department of Biosystems Science and Engineering, ETH Zurich, Swiss Federal Institute of Technology, Basel, Switzerland
| | - Timothy R. Julian
- Eawag, Swiss Federal Institute of Aquatic Science and Technology, Dübendorf, Switzerland
- Swiss Tropical and Public Health Institute, Basel, Switzerland
- University of Basel, Basel, Switzerland
| |
Collapse
|
6
|
Huisman JS, Scire J, Caduff L, Fernandez-Cassi X, Ganesanandamoorthy P, Kull A, Scheidegger A, Stachler E, Boehm AB, Hughes B, Knudson A, Topol A, Wigginton KR, Wolfe MK, Kohn T, Ort C, Stadler T, Julian TR. Wastewater-Based Estimation of the Effective Reproductive Number of SARS-CoV-2. Environ Health Perspect 2022; 130:57011. [PMID: 35617001 DOI: 10.1101/2021.04.29.21255961] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
BACKGROUND The effective reproductive number, Re, is a critical indicator to monitor disease dynamics, inform regional and national policies, and estimate the effectiveness of interventions. It describes the average number of new infections caused by a single infectious person through time. To date, Re estimates are based on clinical data such as observed cases, hospitalizations, and/or deaths. These estimates are temporarily biased when clinical testing or reporting strategies change. OBJECTIVES We show that the dynamics of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) RNA in wastewater can be used to estimate Re in near real time, independent of clinical data and without the associated biases. METHODS We collected longitudinal measurements of SARS-CoV-2 RNA in wastewater in Zurich, Switzerland, and San Jose, California, USA. We combined this data with information on the temporal dynamics of shedding (the shedding load distribution) to estimate a time series proportional to the daily COVID-19 infection incidence. We estimated a wastewater-based Re from this incidence. RESULTS The method to estimate Re from wastewater worked robustly on data from two different countries and two wastewater matrices. The resulting estimates were as similar to the Re estimates from case report data as Re estimates based on observed cases, hospitalizations, and deaths are among each other. We further provide details on the effect of sampling frequency and the shedding load distribution on the ability to infer Re. DISCUSSION To our knowledge, this is the first time Re has been estimated from wastewater. This method provides a low-cost, rapid, and independent way to inform SARS-CoV-2 monitoring during the ongoing pandemic and is applicable to future wastewater-based epidemiology targeting other pathogens. https://doi.org/10.1289/EHP10050.
Collapse
Affiliation(s)
- Jana S Huisman
- Department of Environmental Systems Science, ETH Zurich, Swiss Federal Institute of Technology, Zurich, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
- Department of Biosystems Science and Engineering, ETH Zurich, Swiss Federal Institute of Technology, Basel, Switzerland
| | - Jérémie Scire
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
- Department of Biosystems Science and Engineering, ETH Zurich, Swiss Federal Institute of Technology, Basel, Switzerland
| | - Lea Caduff
- Eawag, Swiss Federal Institute of Aquatic Science and Technology, Dübendorf, Switzerland
| | - Xavier Fernandez-Cassi
- Laboratory of Environmental Chemistry, School of Architecture, Civil and Environmental Engineering, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | | | - Anina Kull
- Eawag, Swiss Federal Institute of Aquatic Science and Technology, Dübendorf, Switzerland
| | - Andreas Scheidegger
- Eawag, Swiss Federal Institute of Aquatic Science and Technology, Dübendorf, Switzerland
| | - Elyse Stachler
- Eawag, Swiss Federal Institute of Aquatic Science and Technology, Dübendorf, Switzerland
| | - Alexandria B Boehm
- Department of Civil and Environmental Engineering, Stanford University, Stanford, California, USA
| | | | - Alisha Knudson
- Verily Life Sciences, South San Francisco, California, USA
| | - Aaron Topol
- Verily Life Sciences, South San Francisco, California, USA
| | - Krista R Wigginton
- Department of Civil and Environmental Engineering, University of Michigan, Ann Arbor, Michigan, USA
| | - Marlene K Wolfe
- Department of Civil and Environmental Engineering, Stanford University, Stanford, California, USA
| | - Tamar Kohn
- Laboratory of Environmental Chemistry, School of Architecture, Civil and Environmental Engineering, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Christoph Ort
- Eawag, Swiss Federal Institute of Aquatic Science and Technology, Dübendorf, Switzerland
| | - Tanja Stadler
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
- Department of Biosystems Science and Engineering, ETH Zurich, Swiss Federal Institute of Technology, Basel, Switzerland
| | - Timothy R Julian
- Eawag, Swiss Federal Institute of Aquatic Science and Technology, Dübendorf, Switzerland
- Swiss Tropical and Public Health Institute, Basel, Switzerland
- University of Basel, Basel, Switzerland
| |
Collapse
|
7
|
Olive M, Moerman F, Fernandez-Cassi X, Altermatt F, Kohn T. Removal of Waterborne Viruses by Tetrahymena pyriformis Is Virus-Specific and Coincides with Changes in Protist Swimming Speed. Environ Sci Technol 2022; 56:4062-4070. [PMID: 35258957 PMCID: PMC8988290 DOI: 10.1021/acs.est.1c05518] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/20/2021] [Revised: 02/23/2022] [Accepted: 02/24/2022] [Indexed: 05/20/2023]
Abstract
Biological treatment of waterborne viruses, specifically grazing of viruses by protists, can enhance microbial water quality while avoiding the production of toxic byproducts and high energy costs. However, tangible applications are limited by the lack of understanding of the underlying mechanisms. Here, we examined the feeding behavior of Tetrahymena pyriformis ciliates on 13 viruses, including bacteriophages, enteric viruses, and respiratory viruses. Significant differences in virus removal by T. pyriformis were observed, ranging from no removal (Qbeta, coxsackievirus B5) to ≥2.7 log10 (JC polyomavirus) after 48 h of co-incubation of the protist with the virus. Removal rates were conserved even when protists were co-incubated with multiple viruses simultaneously. Video analysis revealed that the extent of virus removal was correlated with an increase in the protists' swimming speed, a behavioral trait consistent with the protists' response to the availability of food. Protistan feeding may be driven by a virus' hydrophobicity but was independent of virus size or the presence of a lipid envelope.
Collapse
Affiliation(s)
- Margot Olive
- Laboratory
of Environmental Chemistry, School of Architecture, Civil and Environmental
Engineering (ENAC), Ecole Polytechnique
Federale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland
| | - Felix Moerman
- Department
of Aquatic Ecology, EAWAG, Swiss Federal
Institute of Aquatic Science and Technology, CH-8600 Dübendorf, Switzerland
- Department
of Evolutionary Biology and Environmental Studies, University of Zurich, Winterthurerstrasse 190, 8057 Zürich, Switzerland
| | - Xavier Fernandez-Cassi
- Laboratory
of Environmental Chemistry, School of Architecture, Civil and Environmental
Engineering (ENAC), Ecole Polytechnique
Federale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland
| | - Florian Altermatt
- Department
of Aquatic Ecology, EAWAG, Swiss Federal
Institute of Aquatic Science and Technology, CH-8600 Dübendorf, Switzerland
- Department
of Evolutionary Biology and Environmental Studies, University of Zurich, Winterthurerstrasse 190, 8057 Zürich, Switzerland
| | - Tamar Kohn
- Laboratory
of Environmental Chemistry, School of Architecture, Civil and Environmental
Engineering (ENAC), Ecole Polytechnique
Federale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland
- E-mail:
| |
Collapse
|
8
|
Fernandez-Cassi X, Timoneda N, Martínez-Puchol S, Rusiñol M, Rodriguez-Manzano J, Figuerola N, Bofill-Mas S, Abril JF, Girones R. Corrigendum to "Metagenomics for the study of viruses in urban sewage as a tool for public health surveillance" [Sci. Total Environ. 618 (2016) 870-880 10.1016/j.scitotenv.2017.08.249]. Sci Total Environ 2022; 814:152530. [PMID: 34995880 DOI: 10.1016/j.scitotenv.2021.152530] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Affiliation(s)
- X Fernandez-Cassi
- Department of Genetics, Microbiology and Statistics, Faculty of Biology, University of Barcelona, Barcelona, Catalonia, Spain.
| | - N Timoneda
- Department of Genetics, Microbiology and Statistics, Faculty of Biology, University of Barcelona, Barcelona, Catalonia, Spain; Computational Genomics Lab and Institute of Biomedicine (IBUB), University of Barcelona, Barcelona, Catalonia, Spain
| | - S Martínez-Puchol
- Department of Genetics, Microbiology and Statistics, Faculty of Biology, University of Barcelona, Barcelona, Catalonia, Spain
| | - M Rusiñol
- Department of Genetics, Microbiology and Statistics, Faculty of Biology, University of Barcelona, Barcelona, Catalonia, Spain
| | - J Rodriguez-Manzano
- Centre for Bio - Inspired Technology, Department of Electrica land Electronic Engineering, Imperial College London, London, United Kingdom
| | - N Figuerola
- Department of Genetics, Microbiology and Statistics, Faculty of Biology, University of Barcelona, Barcelona, Catalonia, Spain
| | - S Bofill-Mas
- Department of Genetics, Microbiology and Statistics, Faculty of Biology, University of Barcelona, Barcelona, Catalonia, Spain
| | - J F Abril
- Department of Genetics, Microbiology and Statistics, Faculty of Biology, University of Barcelona, Barcelona, Catalonia, Spain; Computational Genomics Lab and Institute of Biomedicine (IBUB), University of Barcelona, Barcelona, Catalonia, Spain
| | - R Girones
- Department of Genetics, Microbiology and Statistics, Faculty of Biology, University of Barcelona, Barcelona, Catalonia, Spain.
| |
Collapse
|
9
|
Caduff L, Dreifuss D, Schindler T, Devaux AJ, Ganesanandamoorthy P, Kull A, Stachler E, Fernandez-Cassi X, Beerenwinkel N, Kohn T, Ort C, Julian TR. Inferring transmission fitness advantage of SARS-CoV-2 variants of concern from wastewater samples using digital PCR, Switzerland, December 2020 through March 2021. Euro Surveill 2022; 27:2100806. [PMID: 35272748 PMCID: PMC8915404 DOI: 10.2807/1560-7917.es.2022.27.10.2100806] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [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: 04/19/2023] Open
Abstract
BackgroundThroughout the COVID-19 pandemic, SARS-CoV-2 genetic variants of concern (VOCs) have repeatedly and independently arisen. VOCs are characterised by increased transmissibility, increased virulence or reduced neutralisation by antibodies obtained from prior infection or vaccination. Tracking the introduction and transmission of VOCs relies on sequencing, typically whole genome sequencing of clinical samples. Wastewater surveillance is increasingly used to track the introduction and spread of SARS-CoV-2 variants through sequencing approaches.AimHere, we adapt and apply a rapid, high-throughput method for detection and quantification of the relative frequency of two deletions characteristic of the Alpha, Beta, and Gamma VOCs in wastewater.MethodsWe developed drop-off RT-dPCR assays and an associated statistical approach implemented in the R package WWdPCR to analyse temporal dynamics of SARS-CoV-2 signature mutations (spike Δ69-70 and ORF1a Δ3675-3677) in wastewater and quantify transmission fitness advantage of the Alpha VOC.ResultsBased on analysis of Zurich wastewater samples, the estimated transmission fitness advantage of SARS-CoV-2 Alpha based on the spike Δ69-70 was 0.34 (95% confidence interval (CI): 0.30-0.39) and based on ORF1a Δ3675-3677 was 0.53 (95% CI: 0.49-0.57), aligning with the transmission fitness advantage of Alpha estimated by clinical sample sequencing in the surrounding canton of 0.49 (95% CI: 0.38-0.61).ConclusionDigital PCR assays targeting signature mutations in wastewater offer near real-time monitoring of SARS-CoV-2 VOCs and potentially earlier detection and inference on transmission fitness advantage than clinical sequencing.
Collapse
Affiliation(s)
- Lea Caduff
- Eawag, Swiss Federal Institute of Aquatic Science and Technology, Dübendorf, Switzerland
| | - David Dreifuss
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland
- SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Tobias Schindler
- Swiss Tropical and Public Health Institute, Basel, Switzerland
- University of Basel, Basel, Switzerland
| | - Alexander J Devaux
- Eawag, Swiss Federal Institute of Aquatic Science and Technology, Dübendorf, Switzerland
| | | | - Anina Kull
- Eawag, Swiss Federal Institute of Aquatic Science and Technology, Dübendorf, Switzerland
| | - Elyse Stachler
- Eawag, Swiss Federal Institute of Aquatic Science and Technology, Dübendorf, Switzerland
| | - Xavier Fernandez-Cassi
- Laboratory of Environmental Chemistry, School of Architecture, Civil and Environmental Engineering, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Niko Beerenwinkel
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland
- SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Tamar Kohn
- Laboratory of Environmental Chemistry, School of Architecture, Civil and Environmental Engineering, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Christoph Ort
- Eawag, Swiss Federal Institute of Aquatic Science and Technology, Dübendorf, Switzerland
| | - Timothy R Julian
- Eawag, Swiss Federal Institute of Aquatic Science and Technology, Dübendorf, Switzerland
- Swiss Tropical and Public Health Institute, Basel, Switzerland
- University of Basel, Basel, Switzerland
| |
Collapse
|
10
|
Fernandez-Cassi X, Scheidegger A, Bänziger C, Cariti F, Tuñas Corzon A, Ganesanandamoorthy P, Lemaitre JC, Ort C, Julian TR, Kohn T. Wastewater monitoring outperforms case numbers as a tool to track COVID-19 incidence dynamics when test positivity rates are high. Water Res 2021; 200:117252. [PMID: 34048984 PMCID: PMC8126994 DOI: 10.1016/j.watres.2021.117252] [Citation(s) in RCA: 73] [Impact Index Per Article: 24.3] [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: 03/27/2021] [Revised: 05/10/2021] [Accepted: 05/11/2021] [Indexed: 05/16/2023]
Abstract
Wastewater-based epidemiology (WBE) has been shown to coincide with, or anticipate, confirmed COVID-19 case numbers. During periods with high test positivity rates, however, case numbers may be underreported, whereas wastewater does not suffer from this limitation. Here we investigated how the dynamics of new COVID-19 infections estimated based on wastewater monitoring or confirmed cases compare to true COVID-19 incidence dynamics. We focused on the first pandemic wave in Switzerland (February to April, 2020), when test positivity ranged up to 26%. SARS-CoV-2 RNA loads were determined 2-4 times per week in three Swiss wastewater treatment plants (Lugano, Lausanne and Zurich). Wastewater and case data were combined with a shedding load distribution and an infection-to-case confirmation delay distribution, respectively, to estimate infection incidence dynamics. Finally, the estimates were compared to reference incidence dynamics determined by a validated compartmental model. Incidence dynamics estimated based on wastewater data were found to better track the timing and shape of the reference infection peak compared to estimates based on confirmed cases. In contrast, case confirmations provided a better estimate of the subsequent decline in infections. Under a regime of high-test positivity rates, WBE thus provides critical information that is complementary to clinical data to monitor the pandemic trajectory.
Collapse
Affiliation(s)
- Xavier Fernandez-Cassi
- Laboratory of Environmental Chemistry, School of Architecture, Civil and Environmental Engineering, École Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland
| | - Andreas Scheidegger
- Swiss Federal Institute of Aquatic Science and Technology (Eawag), 8600 Dübendorf, Switzerland
| | - Carola Bänziger
- Swiss Federal Institute of Aquatic Science and Technology (Eawag), 8600 Dübendorf, Switzerland
| | - Federica Cariti
- Laboratory of Environmental Chemistry, School of Architecture, Civil and Environmental Engineering, École Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland
| | - Alex Tuñas Corzon
- Laboratory of Environmental Chemistry, School of Architecture, Civil and Environmental Engineering, École Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland
| | | | - Joseph C Lemaitre
- Laboratory of Ecohydrology, School of Architecture, Civil and Environmental Engineering, École Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland
| | - Christoph Ort
- Swiss Federal Institute of Aquatic Science and Technology (Eawag), 8600 Dübendorf, Switzerland
| | - Timothy R Julian
- Laboratory of Environmental Chemistry, School of Architecture, Civil and Environmental Engineering, École Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland; Swiss Tropical and Public Health Institute, CH-4051 Basel, Switzerland; University of Basel, CH-4055 Basel, Switzerland
| | - Tamar Kohn
- Laboratory of Environmental Chemistry, School of Architecture, Civil and Environmental Engineering, École Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland.
| |
Collapse
|
11
|
Fernandez-Cassi X, Scheidegger A, Bänziger C, Cariti F, Tuñas Corzon A, Ganesanandamoorthy P, Lemaitre JC, Ort C, Julian TR, Kohn T. Wastewater monitoring outperforms case numbers as a tool to track COVID-19 incidence dynamics when test positivity rates are high. Water Res 2021; 200:117252. [PMID: 34048984 DOI: 10.1101/2021.03.25.21254344] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [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: 03/27/2021] [Revised: 05/10/2021] [Accepted: 05/11/2021] [Indexed: 05/18/2023]
Abstract
Wastewater-based epidemiology (WBE) has been shown to coincide with, or anticipate, confirmed COVID-19 case numbers. During periods with high test positivity rates, however, case numbers may be underreported, whereas wastewater does not suffer from this limitation. Here we investigated how the dynamics of new COVID-19 infections estimated based on wastewater monitoring or confirmed cases compare to true COVID-19 incidence dynamics. We focused on the first pandemic wave in Switzerland (February to April, 2020), when test positivity ranged up to 26%. SARS-CoV-2 RNA loads were determined 2-4 times per week in three Swiss wastewater treatment plants (Lugano, Lausanne and Zurich). Wastewater and case data were combined with a shedding load distribution and an infection-to-case confirmation delay distribution, respectively, to estimate infection incidence dynamics. Finally, the estimates were compared to reference incidence dynamics determined by a validated compartmental model. Incidence dynamics estimated based on wastewater data were found to better track the timing and shape of the reference infection peak compared to estimates based on confirmed cases. In contrast, case confirmations provided a better estimate of the subsequent decline in infections. Under a regime of high-test positivity rates, WBE thus provides critical information that is complementary to clinical data to monitor the pandemic trajectory.
Collapse
Affiliation(s)
- Xavier Fernandez-Cassi
- Laboratory of Environmental Chemistry, School of Architecture, Civil and Environmental Engineering, École Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland
| | - Andreas Scheidegger
- Swiss Federal Institute of Aquatic Science and Technology (Eawag), 8600 Dübendorf, Switzerland
| | - Carola Bänziger
- Swiss Federal Institute of Aquatic Science and Technology (Eawag), 8600 Dübendorf, Switzerland
| | - Federica Cariti
- Laboratory of Environmental Chemistry, School of Architecture, Civil and Environmental Engineering, École Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland
| | - Alex Tuñas Corzon
- Laboratory of Environmental Chemistry, School of Architecture, Civil and Environmental Engineering, École Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland
| | | | - Joseph C Lemaitre
- Laboratory of Ecohydrology, School of Architecture, Civil and Environmental Engineering, École Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland
| | - Christoph Ort
- Swiss Federal Institute of Aquatic Science and Technology (Eawag), 8600 Dübendorf, Switzerland
| | - Timothy R Julian
- Laboratory of Environmental Chemistry, School of Architecture, Civil and Environmental Engineering, École Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland; Swiss Tropical and Public Health Institute, CH-4051 Basel, Switzerland; University of Basel, CH-4055 Basel, Switzerland
| | - Tamar Kohn
- Laboratory of Environmental Chemistry, School of Architecture, Civil and Environmental Engineering, École Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland.
| |
Collapse
|
12
|
Ismail NS, Olive M, Fernandez-Cassi X, Bachmann V, Kohn T. Viral Transfer and Inactivation through Zooplankton Trophic Interactions. Environ Sci Technol 2020; 54:9418-9426. [PMID: 32662638 DOI: 10.1021/acs.est.0c02545] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
Waterborne viruses are responsible for numerous diseases and are abundant in aquatic systems. Understanding the fate of viruses in natural systems has important implications for human health. This research quantifies the uptake of the bacteriophage T4 and the enteric virus echovirus 11 when exposed to the filter feeders Tetrahymena pyriformis and Daphnia magna, and also examines the potential of viral transfer due to trophic interactions. Experiments co-incubating each species with the viruses over 72-96 h showed up to a 4 log virus removal for T. pyriformis, while direct viral uptake by D. magna was not observed. However, viral uptake by D. magna occurred indirectly by viral transfer from prey to predator, through D. magna feeding on virus-loaded T. pyriformis. This prey-predator interaction resulted in a 1 log additional virus removal compared to removal by T. pyriformis alone. Incomplete viral inactivation by D. magna was observed through recovery of infective viruses from the daphnid tissue. This research furthers our understanding of the impacts of zooplankton filter feeding on viral inactivation and shows the potential for viral transfer through the food chain. The viral-zooplankton interactions observed in these studies indicate that zooplankton may improve water quality through viral uptake or may serve as vectors for infection by accumulating viruses.
Collapse
Affiliation(s)
- Niveen S Ismail
- Picker Engineering Program, Smith College, Northampton, Massachusetts 01063, United States
| | - Margot Olive
- Laboratory of Environmental Chemistry, School of Architecture, Civil and Environmental Engineering (ENAC), École Polytechnique Fédérale de Lausanne (EPFL), 1015 Lausanne, Switzerland
| | - Xavier Fernandez-Cassi
- Laboratory of Environmental Chemistry, School of Architecture, Civil and Environmental Engineering (ENAC), École Polytechnique Fédérale de Lausanne (EPFL), 1015 Lausanne, Switzerland
| | - Virginie Bachmann
- Laboratory of Environmental Chemistry, School of Architecture, Civil and Environmental Engineering (ENAC), École Polytechnique Fédérale de Lausanne (EPFL), 1015 Lausanne, Switzerland
| | - Tamar Kohn
- Laboratory of Environmental Chemistry, School of Architecture, Civil and Environmental Engineering (ENAC), École Polytechnique Fédérale de Lausanne (EPFL), 1015 Lausanne, Switzerland
| |
Collapse
|
13
|
Rusiñol M, Fernandez-Cassi X, Timoneda N, Carratalà A, Abril JF, Silvera C, Figueras MJ, Gelati E, Rodó X, Kay D, Wyn-Jones P, Bofill-Mas S, Girones R. Corrigendum to "Evidence of viral dissemination and seasonality in a Mediterranean river catchment: implications for water pollution management" [J. Environ. Manag. 159 (2015) 58-67]. J Environ Manage 2018; 223:1100. [PMID: 29807682 DOI: 10.1016/j.jenvman.2018.05.047] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Affiliation(s)
- M Rusiñol
- Laboratory of Virus Contaminants of Water and Food, Department of Microbiology, University of Barcelona, Barcelona, Catalonia, Spain
| | - X Fernandez-Cassi
- Laboratory of Virus Contaminants of Water and Food, Department of Microbiology, University of Barcelona, Barcelona, Catalonia, Spain
| | - N Timoneda
- Institute of Biomedicine of the University of Barcelona (IBUB), University of Barcelona, Barcelona, Catalonia, Spain
| | - A Carratalà
- Laboratory of Virus Contaminants of Water and Food, Department of Microbiology, University of Barcelona, Barcelona, Catalonia, Spain
| | - J F Abril
- Computational Genomics Laboratory, Department of Genetics, University of Barcelona, Barcelona, Catalonia, Spain
| | - C Silvera
- Microbiology Unit, Faculty of Medicine and Health Sciences, IISPV, University Rovira and Virgili, Reus, Catalonia, Spain
| | - M J Figueras
- Microbiology Unit, Faculty of Medicine and Health Sciences, IISPV, University Rovira and Virgili, Reus, Catalonia, Spain
| | - E Gelati
- Catalan Institute of Climate Sciences (IC3), Barcelona, Catalonia, Spain
| | - X Rodó
- Catalan Institute of Climate Sciences (IC3), Barcelona, Catalonia, Spain
| | - D Kay
- Institute of Geography and Earth Sciences (IGES), Aberystwyth University, Aberystwyth, United Kingdom
| | - P Wyn-Jones
- Institute of Geography and Earth Sciences (IGES), Aberystwyth University, Aberystwyth, United Kingdom
| | - S Bofill-Mas
- Laboratory of Virus Contaminants of Water and Food, Department of Microbiology, University of Barcelona, Barcelona, Catalonia, Spain
| | - R Girones
- Laboratory of Virus Contaminants of Water and Food, Department of Microbiology, University of Barcelona, Barcelona, Catalonia, Spain.
| |
Collapse
|
14
|
Abstract
Novel foods could represent a sustainable alternative to traditional farming and conventional foodstuffs. Starting in 2018, Regulation (EU) 2283/2015 entered into force, laying down provisions for the approval of novel foods in Europe, including insects. This Approved Regulation establishes the requirements that enable Food Business Operators to bring new foods into the EU market, while ensuring high levels of food safety for European consumers. The present risk profile tackles the hazards for one of the most promising novel food insects, the house cricket (Acheta domesticus). The risk profile envisages a closed A. domesticus crickets rearing system, under Hazard Analysis and Critical Control Points (HACCP) and good farming practices (GFP), in contrast with open cricket farms. The methodology used involves screening the literature and identifying possible hazards, followed by adding relevant inclusion criteria for the evidence obtained. These criteria include animal health and food safety aspects, for the entire lifespan of crickets, based on the farm to fork One Health principle. When data were scarce, comparative evidence from close relatives of the Orthoptera genus was used (e.g. grasshoppers, locusts and other cricket species). Nevertheless, significant data gaps in animal health and food safety are present. Even if HACCP‐type systems are implemented, the risk profile identifies the following considerable concerns: (1) high total aerobic bacterial counts; (2) survival of spore‐forming bacteria following thermal processing; (3) allergenicity of insects and insect‐derived products; and (4) the bioaccumulation of heavy metals (e.g. cadmium). Other hazards like parasites, fungi, viruses, prions, antimicrobial resistance and toxins are ranked as low risk. For some hazards, a need for additional evidence is highlighted.
Collapse
|
15
|
Torres C, Barrios ME, Cammarata RV, Victoria M, Fernandez-Cassi X, Bofill-Mas S, Colina R, Blanco Fernández MD, Mbayed VA. Phylodynamics of Merkel-cell polyomavirus and human polyomavirus 6: A long-term history with humans. Mol Phylogenet Evol 2018; 126:210-220. [PMID: 29680507 DOI: 10.1016/j.ympev.2018.04.025] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [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: 10/26/2017] [Revised: 04/06/2018] [Accepted: 04/16/2018] [Indexed: 01/10/2023]
Abstract
New human polyomaviruses have been described in the last years, including the Merkel-cell polyomavirus (MCPyV; Human polyomavirus 5) and the Human polyomavirus 6 (HPyV6). Although their infection is usually asymptomatic, in immunocompromised host can cause life-threatening pathologies, such as the Merkel cell carcinoma, an aggressive skin neoplasia associated to the MCPyV. Despite being prevalent viruses in population, epidemiological data from South America are scarce, as well as the characterization of the viral types circulating and their origin. The aims of this work were to describe MCPyV and HPyV6 from environmental samples with different geographical origin and to analyze their phylogenetic and evolutionary histories, particularly for MCPyV. Partial and complete genome sequences were obtained from sewage samples from Argentina, Uruguay and Spain. A total number of 87 sequences were obtained for MCPyV and 33 for HPyV6. Phylogenetic analysis showed that MCPyV sequences distributed according to their geographic origin in Europe/North America, Africa, Asia, South America and Oceania groups, suggesting that viral diversification might have followed human migrations across the globe. In particular, viruses from Argentina associated with Europe/North America and South America genotypes, whereas those from Uruguay and Spain also grouped with Africa genotype, reflecting the origin of the current population in each country, which could arrive not only during ancient human migration but also during recent migratory events. In addition, the South American group presented a high level of clusterization, showing internal clusters that could be related to specific locations, such as French Guiana and Brazil or the Southern region into South America, such as Argentina and Uruguay, suggesting a long term evolutionary process in the region. Additionally, in this work, we carried out the first analysis about the evolutionary history of MCPyV trough the integration of phylogenetic, epidemiological and historical data. Since a strong association is observed between the phylogenetic relationships and the origin of the sampled population, this analysis was based on the hypothesis of co-divergence between the virus and human populations. This analysis resulted in a substitution rate of 5.1 × 10-8 s/s/y (∼5.1% of divergence per million years) for the complete genome of MCPyV, which is in the range of those estimated for other double-stranded DNA viruses. Regarding HPyV6, a South American group with clusterization was observed (sequences from Uruguay). Meanwhile, sequences from Argentina grouped with European ones (France and Spain) and remained separated from those isolated in China, USA or Australia. The analysis of viruses from the environment allowed us to deep characterize prevalent infections in different geographic regions, reveling that viruses circulating in each population reflected its origin and that there are specific lineages associated with South America.
Collapse
Affiliation(s)
- Carolina Torres
- Universidad de Buenos Aires, Facultad de Farmacia y Bioquímica, Departamento de Microbiología, Inmunología y Biotecnología, Cátedra de Virología, Buenos Aires, Argentina; CONICET, Buenos Aires, Argentina.
| | - Melina Elizabeth Barrios
- Universidad de Buenos Aires, Facultad de Farmacia y Bioquímica, Departamento de Microbiología, Inmunología y Biotecnología, Cátedra de Virología, Buenos Aires, Argentina; CONICET, Buenos Aires, Argentina
| | - Robertina Viviana Cammarata
- Universidad de Buenos Aires, Facultad de Farmacia y Bioquímica, Departamento de Microbiología, Inmunología y Biotecnología, Cátedra de Virología, Buenos Aires, Argentina; CONICET, Buenos Aires, Argentina
| | - Matías Victoria
- Laboratorio de Virología Molecular, CENUR Litoral Norte, Sede Salto, Universidad de la República, Uruguay
| | - Xavier Fernandez-Cassi
- Laboratory of Virus Contaminants of Water and Food, Department of Genetics, Microbiology and Statistics, University of Barcelona, Barcelona, Catalonia, Spain
| | - Silvia Bofill-Mas
- Laboratory of Virus Contaminants of Water and Food, Department of Genetics, Microbiology and Statistics, University of Barcelona, Barcelona, Catalonia, Spain
| | - Rodney Colina
- Laboratorio de Virología Molecular, CENUR Litoral Norte, Sede Salto, Universidad de la República, Uruguay
| | - María Dolores Blanco Fernández
- Universidad de Buenos Aires, Facultad de Farmacia y Bioquímica, Departamento de Microbiología, Inmunología y Biotecnología, Cátedra de Virología, Buenos Aires, Argentina; CONICET, Buenos Aires, Argentina
| | - Viviana Andrea Mbayed
- Universidad de Buenos Aires, Facultad de Farmacia y Bioquímica, Departamento de Microbiología, Inmunología y Biotecnología, Cátedra de Virología, Buenos Aires, Argentina; CONICET, Buenos Aires, Argentina
| |
Collapse
|
16
|
Torres C, Barrios M, Cammarata R, Victoria M, Fernandez-Cassi X, Bofill-Mas S, Colina R, Blanco Fernández M, Mbayed V. A45 Merkel-cell polyomavirus and human polyomavirus 6 in Argentina, Uruguay, and Spain: Deep characterization of the South American types. Virus Evol 2018. [PMCID: PMC5905361 DOI: 10.1093/ve/vey010.044] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Affiliation(s)
- C Torres
- Virology Chair, School of Pharmacy and Biochemistry, University of Buenos Aires, Buenos Aires, Argentina
- CONICET, Buenos Aires, Argentina
| | - M Barrios
- Virology Chair, School of Pharmacy and Biochemistry, University of Buenos Aires, Buenos Aires, Argentina
| | - R Cammarata
- Virology Chair, School of Pharmacy and Biochemistry, University of Buenos Aires, Buenos Aires, Argentina
- CONICET, Buenos Aires, Argentina
| | - M Victoria
- University of the Republic, Salto, Uruguay
| | | | | | - R Colina
- University of the Republic, Salto, Uruguay
| | - M Blanco Fernández
- Virology Chair, School of Pharmacy and Biochemistry, University of Buenos Aires, Buenos Aires, Argentina
- CONICET, Buenos Aires, Argentina
| | - V Mbayed
- Virology Chair, School of Pharmacy and Biochemistry, University of Buenos Aires, Buenos Aires, Argentina
- CONICET, Buenos Aires, Argentina
| |
Collapse
|
17
|
Fernandez-Cassi X, Timoneda N, Martínez-Puchol S, Rusiñol M, Rodriguez-Manzano J, Figuerola N, Bofill-Mas S, Abril JF, Girones R. Metagenomics for the study of viruses in urban sewage as a tool for public health surveillance. Sci Total Environ 2018; 618:870-880. [PMID: 29108696 DOI: 10.1016/j.scitotenv.2017.08.249] [Citation(s) in RCA: 85] [Impact Index Per Article: 14.2] [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: 06/02/2017] [Revised: 08/23/2017] [Accepted: 08/24/2017] [Indexed: 04/14/2023]
Abstract
The application of next-generation sequencing (NGS) techniques for the identification of viruses present in urban sewage has not been fully explored. This is partially due to a lack of reliable and sensitive protocols for studying viral diversity and to the highly complex analysis required for NGS data processing. One important step towards this goal is finding methods that can efficiently concentrate viruses from sewage samples. Here the application of a virus concentration method based on skimmed milk organic flocculation (SMF) using 10L of sewage collected in different seasons enabled the detection of many viruses. However, some viruses, such as human adenoviruses, could not always be detected using metagenomics, even when quantitative PCR (qPCR) assessments were positive. A targeted metagenomic assay for adenoviruses was conducted and 59.41% of the obtained reads were assigned to murine adenoviruses. However, up to 20 different human adenoviruses (HAdV) were detected by this targeted assay being the most abundant HAdV-41 (29.24%) and HAdV-51 (1.63%). To improve metagenomics' sensitivity, two different protocols for virus concentration were comparatively analysed: an ultracentrifugation protocol and a lower-volume SMF protocol. The sewage virome contained 41 viral families, including pathogenic viral species from families Caliciviridae, Adenoviridae, Astroviridae, Picornaviridae, Polyomaviridae, Papillomaviridae and Hepeviridae. The contribution of urine to sewage metavirome seems to be restricted to a few specific DNA viral families, including the polyomavirus and papillomavirus species. In experimental infections with sewage in a rhesus macaque model, infective human hepatitis E and JC polyomavirus were identified. Urban raw sewage consists of the excreta of thousands of inhabitants; therefore, it is a representative sample for epidemiological surveillance purposes. The knowledge of the metavirome is of significance to public health, highlighting the presence of viral strains that are circulating within a population while acting as a complex matrix for viral discovery.
Collapse
Affiliation(s)
- X Fernandez-Cassi
- Department of Genetics, Microbiology and Statistics, Faculty of Biology, University of Barcelona, Barcelona, Catalonia, Spain.
| | - N Timoneda
- Department of Genetics, Microbiology and Statistics, Faculty of Biology, University of Barcelona, Barcelona, Catalonia, Spain; Computational Genomics Lab, University of Barcelona and Institute of Biomedicine (IBUB), University of Barcelona, Barcelona, Catalonia, Spain
| | - S Martínez-Puchol
- Department of Genetics, Microbiology and Statistics, Faculty of Biology, University of Barcelona, Barcelona, Catalonia, Spain
| | - M Rusiñol
- Department of Genetics, Microbiology and Statistics, Faculty of Biology, University of Barcelona, Barcelona, Catalonia, Spain
| | - J Rodriguez-Manzano
- Centre for Bio-Inspired Technology, Department of Electrical and Electronic Engineering, Imperial College London, London, United Kingdom
| | - N Figuerola
- Department of Genetics, Microbiology and Statistics, Faculty of Biology, University of Barcelona, Barcelona, Catalonia, Spain
| | - S Bofill-Mas
- Department of Genetics, Microbiology and Statistics, Faculty of Biology, University of Barcelona, Barcelona, Catalonia, Spain
| | - J F Abril
- Department of Genetics, Microbiology and Statistics, Faculty of Biology, University of Barcelona, Barcelona, Catalonia, Spain; Computational Genomics Lab, University of Barcelona and Institute of Biomedicine (IBUB), University of Barcelona, Barcelona, Catalonia, Spain
| | - R Girones
- Department of Genetics, Microbiology and Statistics, Faculty of Biology, University of Barcelona, Barcelona, Catalonia, Spain
| |
Collapse
|
18
|
Fernandez-Cassi X, Timoneda N, Gonzales-Gustavson E, Abril JF, Bofill-Mas S, Girones R. A metagenomic assessment of viral contamination on fresh parsley plants irrigated with fecally tainted river water. Int J Food Microbiol 2017. [PMID: 28646670 DOI: 10.1016/j.ijfoodmicro.2017.06.001] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Microbial food-borne diseases are still frequently reported despite the implementation of microbial quality legislation to improve food safety. Among all the microbial agents, viruses are the most important causative agents of food-borne outbreaks. The development and application of a new generation of sequencing techniques to test for viral contaminants in fresh produce is an unexplored field that allows for the study of the viral populations that might be transmitted by the fecal-oral route through the consumption of contaminated food. To advance this promising field, parsley was planted and grown under controlled conditions and irrigated using contaminated river water. Viruses polluting the irrigation water and the parsley leaves were studied by using metagenomics. To address possible contamination due to sample manipulation, library preparation, and other sources, parsley plants irrigated with nutritive solution were used as a negative control. In parallel, viruses present in the river water used for plant irrigation were analyzed using the same methodology. It was possible to assign viral taxons from 2.4 to 74.88% of the total reads sequenced depending on the sample. Most of the viral reads detected in the river water were related to the plant viral families Tymoviridae (66.13%) and Virgaviridae (14.45%) and the phage viral families Myoviridae (5.70%), Siphoviridae (5.06%), and Microviridae (2.89%). Less than 1% of the viral reads were related to viral families that infect humans, including members of the Adenoviridae, Reoviridae, Picornaviridae and Astroviridae families. On the surface of the parsley plants, most of the viral reads that were detected were assigned to the Dicistroviridae family (41.52%). Sequences related to important viral pathogens, such as the hepatitis E virus, several picornaviruses from species A and B as well as human sapoviruses and GIV noroviruses were detected. The high diversity of viral sequences found in the parsley plants suggests that irrigation on fecally-tainted food may have a role in the transmission of a wide diversity of viral families. This finding reinforces the idea that the best way to avoid food-borne viral diseases is to introduce good field irrigation and production practices. New strains have been identified that are related to the Picornaviridae and distantly related to the Hepeviridae family. However, the detection of a viral genome alone does not necessarily indicate there is a risk of infection or disease development. Thus, further investigation is crucial for correlating the detection of viral metagenomes in samples with the risk of infection. There is also an urgent need to develop new methods to improve the sensitivity of current Next Generation Sequencing (NGS) techniques in the food safety area.
Collapse
Affiliation(s)
- X Fernandez-Cassi
- Laboratory of Virus Contaminants of Water and Food, Department of Genetics, Microbiology and Statistics, University of Barcelona, Barcelona, Catalonia, Spain.
| | - N Timoneda
- Laboratory of Virus Contaminants of Water and Food, Department of Genetics, Microbiology and Statistics, University of Barcelona, Barcelona, Catalonia, Spain; Computational Genomics Lab, Department of Genetics, Microbiology and Statistics, University of Barcelona, Barcelona, Catalonia, Spain; Institute of Biomedicine (IBUB), University of Barcelona, Barcelona, Catalonia, Spain
| | - E Gonzales-Gustavson
- Laboratory of Virus Contaminants of Water and Food, Department of Genetics, Microbiology and Statistics, University of Barcelona, Barcelona, Catalonia, Spain
| | - J F Abril
- Computational Genomics Lab, Department of Genetics, Microbiology and Statistics, University of Barcelona, Barcelona, Catalonia, Spain; Institute of Biomedicine (IBUB), University of Barcelona, Barcelona, Catalonia, Spain
| | - S Bofill-Mas
- Laboratory of Virus Contaminants of Water and Food, Department of Genetics, Microbiology and Statistics, University of Barcelona, Barcelona, Catalonia, Spain
| | - R Girones
- Laboratory of Virus Contaminants of Water and Food, Department of Genetics, Microbiology and Statistics, University of Barcelona, Barcelona, Catalonia, Spain
| |
Collapse
|
19
|
Gonzales-Gustavson E, Timoneda N, Fernandez-Cassi X, Caballero A, Abril JF, Buti M, Rodriguez-Frias F, Girones R. Identification of sapovirus GV.2, astrovirus VA3 and novel anelloviruses in serum from patients with acute hepatitis of unknown aetiology. PLoS One 2017; 12:e0185911. [PMID: 28982120 PMCID: PMC5628893 DOI: 10.1371/journal.pone.0185911] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2017] [Accepted: 09/21/2017] [Indexed: 12/14/2022] Open
Abstract
Hepatitis is a general term meaning inflammation of the liver, which can be caused by a variety of viruses. However, a substantial number of cases remain with unknown aetiology. We analysed the serum of patients with clinical signs of hepatitis using a metagenomics approach to characterize their viral species composition. Four pools of patients with hepatitis without identified aetiological agents were evaluated. Additionally, one pool of patients with hepatitis E (HEV) and pools of healthy volunteers were included as controls. A high diversity of anelloviruses, including novel sequences, was found in pools from patients with hepatitis of unknown aetiology. Moreover, viruses recently associated with gastroenteritis as sapovirus GV.2 and astrovirus VA3 were also detected only in those pools. Besides, most of the HEV genome was recovered from the HEV pool. Finally, GB virus C and human endogenous retrovirus were found in the HEV and healthy pools. Our study provides an overview of the virome in serum from hepatitis patients suggesting a potential role of these viruses not previously described in cases of hepatitis. However, further epidemiologic studies are necessary to confirm their contribution to the development of hepatitis.
Collapse
Affiliation(s)
- Eloy Gonzales-Gustavson
- Laboratory of Virus Contaminants of Water and Food, Department of Genetics, Microbiology and Statistics, Faculty of Biology, University of Barcelona, Barcelona, Catalonia, Spain
| | - N. Timoneda
- Laboratory of Virus Contaminants of Water and Food, Department of Genetics, Microbiology and Statistics, Faculty of Biology, University of Barcelona, Barcelona, Catalonia, Spain
- Computational Genomics Lab, Department of Genetics, Microbiology and Statistics, Faculty of Biology, University of Barcelona, Barcelona, Catalonia, Spain
- Institut de Biomedicina de la Universitat de Barcelona (IBUB), Barcelona, Catalonia, Spain
| | - X. Fernandez-Cassi
- Laboratory of Virus Contaminants of Water and Food, Department of Genetics, Microbiology and Statistics, Faculty of Biology, University of Barcelona, Barcelona, Catalonia, Spain
| | - A. Caballero
- Hospital Universitari Vall d’Hebron and CIBEREHD del Instituto Carlos III, Barcelona, Catalonia, Spain
| | - J. F. Abril
- Computational Genomics Lab, Department of Genetics, Microbiology and Statistics, Faculty of Biology, University of Barcelona, Barcelona, Catalonia, Spain
- Institut de Biomedicina de la Universitat de Barcelona (IBUB), Barcelona, Catalonia, Spain
| | - M. Buti
- Hospital Universitari Vall d’Hebron and CIBEREHD del Instituto Carlos III, Barcelona, Catalonia, Spain
| | - F. Rodriguez-Frias
- Hospital Universitari Vall d’Hebron and CIBEREHD del Instituto Carlos III, Barcelona, Catalonia, Spain
| | - R. Girones
- Laboratory of Virus Contaminants of Water and Food, Department of Genetics, Microbiology and Statistics, Faculty of Biology, University of Barcelona, Barcelona, Catalonia, Spain
- * E-mail:
| |
Collapse
|
20
|
Hjelmsø MH, Hellmér M, Fernandez-Cassi X, Timoneda N, Lukjancenko O, Seidel M, Elsässer D, Aarestrup FM, Löfström C, Bofill-Mas S, Abril JF, Girones R, Schultz AC. Evaluation of Methods for the Concentration and Extraction of Viruses from Sewage in the Context of Metagenomic Sequencing. PLoS One 2017; 12:e0170199. [PMID: 28099518 PMCID: PMC5242460 DOI: 10.1371/journal.pone.0170199] [Citation(s) in RCA: 85] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2016] [Accepted: 01/02/2017] [Indexed: 01/18/2023] Open
Abstract
Viral sewage metagenomics is a novel field of study used for surveillance, epidemiological studies, and evaluation of waste water treatment efficiency. In raw sewage human waste is mixed with household, industrial and drainage water, and virus particles are, therefore, only found in low concentrations. This necessitates a step of sample concentration to allow for sensitive virus detection. Additionally, viruses harbor a large diversity of both surface and genome structures, which makes universal viral genomic extraction difficult. Current studies have tackled these challenges in many different ways employing a wide range of viral concentration and extraction procedures. However, there is limited knowledge of the efficacy and inherent biases associated with these methods in respect to viral sewage metagenomics, hampering the development of this field. By the use of next generation sequencing this study aimed to evaluate the efficiency of four commonly applied viral concentrations techniques (precipitation with polyethylene glycol, organic flocculation with skim milk, monolithic adsorption filtration and glass wool filtration) and extraction methods (Nucleospin RNA XS, QIAamp Viral RNA Mini Kit, NucliSENS® miniMAG®, or PowerViral® Environmental RNA/DNA Isolation Kit) to determine the viriome in a sewage sample. We found a significant influence of concentration and extraction protocols on the detected viriome. The viral richness was largest in samples extracted with QIAamp Viral RNA Mini Kit or PowerViral® Environmental RNA/DNA Isolation Kit. Highest viral specificity were found in samples concentrated by precipitation with polyethylene glycol or extracted with Nucleospin RNA XS. Detection of viral pathogens depended on the method used. These results contribute to the understanding of method associated biases, within the field of viral sewage metagenomics, making evaluation of the current literature easier and helping with the design of future studies.
Collapse
Affiliation(s)
- Mathis Hjort Hjelmsø
- Research Group for Genomic Epidemiology, The National Food Institute, Technical University of Denmark, Kongens Lyngby, Denmark
- * E-mail:
| | - Maria Hellmér
- Division of Microbiology and Production, The National Food Institute, Technical University of Denmark, Søborg, Denmark
| | - Xavier Fernandez-Cassi
- Laboratory of Virus Contaminants of Water and Food, Department of Genetics, Microbiology, and Statistics, University of Barcelona, Barcelona, Catalonia, Spain
| | - Natàlia Timoneda
- Laboratory of Virus Contaminants of Water and Food, Department of Genetics, Microbiology, and Statistics, University of Barcelona, Barcelona, Catalonia, Spain
- Institute of Biomedicine of the University of Barcelona, University of Barcelona, Barcelona, Catalonia, Spain
| | - Oksana Lukjancenko
- Research Group for Genomic Epidemiology, The National Food Institute, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Michael Seidel
- Institute of Hydrochemistry, Chair of Analytical Chemistry, Technical University of Munich, Munich, Germany
| | - Dennis Elsässer
- Institute of Hydrochemistry, Chair of Analytical Chemistry, Technical University of Munich, Munich, Germany
| | - Frank M. Aarestrup
- Research Group for Genomic Epidemiology, The National Food Institute, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Charlotta Löfström
- Division of Microbiology and Production, The National Food Institute, Technical University of Denmark, Søborg, Denmark
| | - Sílvia Bofill-Mas
- Laboratory of Virus Contaminants of Water and Food, Department of Genetics, Microbiology, and Statistics, University of Barcelona, Barcelona, Catalonia, Spain
| | - Josep F. Abril
- Laboratory of Virus Contaminants of Water and Food, Department of Genetics, Microbiology, and Statistics, University of Barcelona, Barcelona, Catalonia, Spain
- Institute of Biomedicine of the University of Barcelona, University of Barcelona, Barcelona, Catalonia, Spain
| | - Rosina Girones
- Laboratory of Virus Contaminants of Water and Food, Department of Genetics, Microbiology, and Statistics, University of Barcelona, Barcelona, Catalonia, Spain
| | - Anna Charlotte Schultz
- Division of Microbiology and Production, The National Food Institute, Technical University of Denmark, Søborg, Denmark
| |
Collapse
|
21
|
Fernandez-Cassi X, Silvera C, Cervero-Aragó S, Rusiñol M, Latif-Eugeni F, Bruguera-Casamada C, Civit S, Araujo RM, Figueras MJ, Girones R, Bofill-Mas S. Evaluation of the microbiological quality of reclaimed water produced from a lagooning system. Environ Sci Pollut Res Int 2016; 23:16816-33. [PMID: 27194016 DOI: 10.1007/s11356-016-6812-0] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [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: 01/07/2016] [Accepted: 05/02/2016] [Indexed: 05/07/2023]
Abstract
The use of lagooning as a complementary natural method of treating secondary effluents of wastewater treatment plants has been employed as an affordable and easy means of producing reclaimed water. However, using reclaimed water for some purposes, for example, for food irrigation, presents some risks if the effluents contain microbial pathogens. Classical bacterial indicators that are used to assess faecal contamination in water do not always properly indicate the presence of bacterial or viral pathogens. In the current study, the presence of faecal indicator bacteria (FIB), heterotrophic bacterial counts (HBC), pathogens and opportunistic pathogens, such as Legionella spp., Aeromonas spp., Arcobacter spp., free-living amoeba (FLA), several viral indicators (human adenovirus and polyomavirus JC) and viral pathogens (noroviruses and hepatitis E virus) were analysed for 1 year in inlet and outlet water to assess the removal efficiency of a lagooning system. We observed 2.58 (1.17-4.59) and 1.65 (0.15-3.14) log reductions in Escherichia coli (EC) and intestinal enterococci (IE), respectively, between the inlet and outlet samples. Genomic copies of the viruses were log reduced by 1.18 (0.24-2.93), 0.64 (0.12-1.97), 0.45 (0.04-2.54) and 0.72 (0.22-2.50) for human adenovirus (HAdV), JC polyomavirus (JCPyV) and human noroviruses (NoV GI and GII), respectively. No regrowth of opportunistic pathogens was observed within the system. FLA, detected in all samples, did not show a clear trend. The reduction of faecal pathogens was irregular with 6 out of 12 samples and 4 out of 12 samples exceeding the EC and IE values, specified in the Spanish legislation for reclaimed water (RD 1620/2007). This data evidences that there is a need for more studies to evaluate the removal mechanisms of lagooning systems in order to optimize pathogen reduction. Moreover, surveillance of water used to irrigate raw edible vegetables should be conducted to ensure the fulfilment of the microbial requirements for the production of safe reclaimed water.
Collapse
Affiliation(s)
- X Fernandez-Cassi
- Department of Microbiology, Faculty of Biology, University of Barcelona, Barcelona, Spain.
| | - C Silvera
- Unitat de Microbiologia, Departament de Ciènces Médiques Bàsiques, Facultat de Medicina i Ciències de la Salut, IISPV, Universitat Rovira i Virgili, Reus, Spain
| | - S Cervero-Aragó
- Department of Microbiology, Faculty of Biology, University of Barcelona, Barcelona, Spain
- Water Hygiene, Institute for Hygiene and Applied Immunology, Medical University of Vienna, Vienna, Austria
- ICC Water and Health, Vienna, Austria
| | - M Rusiñol
- Department of Microbiology, Faculty of Biology, University of Barcelona, Barcelona, Spain
| | - F Latif-Eugeni
- Unitat de Microbiologia, Departament de Ciènces Médiques Bàsiques, Facultat de Medicina i Ciències de la Salut, IISPV, Universitat Rovira i Virgili, Reus, Spain
| | - C Bruguera-Casamada
- Department of Microbiology, Faculty of Biology, University of Barcelona, Barcelona, Spain
| | - S Civit
- Department of Statistics, Faculty of Biology, University of Barcelona, Barcelona, Spain
| | - R M Araujo
- Department of Microbiology, Faculty of Biology, University of Barcelona, Barcelona, Spain
| | - M J Figueras
- Unitat de Microbiologia, Departament de Ciènces Médiques Bàsiques, Facultat de Medicina i Ciències de la Salut, IISPV, Universitat Rovira i Virgili, Reus, Spain
| | - R Girones
- Department of Microbiology, Faculty of Biology, University of Barcelona, Barcelona, Spain
| | - S Bofill-Mas
- Department of Microbiology, Faculty of Biology, University of Barcelona, Barcelona, Spain
| |
Collapse
|
22
|
Mayer RE, Bofill-Mas S, Egle L, Reischer GH, Schade M, Fernandez-Cassi X, Fuchs W, Mach RL, Lindner G, Kirschner A, Gaisbauer M, Piringer H, Blaschke AP, Girones R, Zessner M, Sommer R, Farnleitner AH. Occurrence of human-associated Bacteroidetes genetic source tracking markers in raw and treated wastewater of municipal and domestic origin and comparison to standard and alternative indicators of faecal pollution. Water Res 2016; 90:265-276. [PMID: 26745175 PMCID: PMC4884448 DOI: 10.1016/j.watres.2015.12.031] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/22/2015] [Revised: 12/13/2015] [Accepted: 12/17/2015] [Indexed: 05/19/2023]
Abstract
This was a detailed investigation of the seasonal occurrence, dynamics, removal and resistance of human-associated genetic Bacteroidetes faecal markers (GeBaM) compared with ISO-based standard faecal indicator bacteria (SFIB), human-specific viral faecal markers and one human-associated Bacteroidetes phage in raw and treated wastewater of municipal and domestic origin. Characteristics of the selected activated sludge wastewater treatment plants (WWTPs) from Austria and Germany were studied in detail (WWTPs, n = 13, connected populations from 3 to 49000 individuals), supported by volume-proportional automated 24-h sampling and chemical water quality analysis. GeBaM were consistently detected in high concentrations in raw (median log10 8.6 marker equivalents (ME) 100 ml(-1)) and biologically treated wastewater samples (median log10 6.2-6.5 ME 100 ml(-1)), irrespective of plant size, type and time of the season (n = 53-65). GeBaM, Escherichia coli, and enterococci concentrations revealed the same range of statistical variability for raw (multiplicative standard deviations s* = 2.3-3.0) and treated wastewater (s* = 3.7-4.5), with increased variability after treatment. Clostridium perfringens spores revealed the lowest variability for raw wastewater (s* = 1.5). In raw wastewater correlations among microbiological parameters were only detectable between GeBaM, C. perfringens and JC polyomaviruses. Statistical associations amongst microbial parameters increased during wastewater treatment. Two plants with advanced treatment were also investigated, revealing a minimum log10 5.0 (10th percentile) reduction of GeBaM in the activated sludge membrane bioreactor, but no reduction of the genetic markers during UV irradiation (254 nm). This study highlights the potential of human-associated GeBaM to complement wastewater impact monitoring based on the determination of SFIB. In addition, human-specific JC polyomaviruses and adenoviruses seem to be a valuable support if highly specific markers are needed.
Collapse
Affiliation(s)
- R E Mayer
- Institute of Chemical Engineering, Research Division Biotechnology and Microbiology, Research Group Environmental Microbiology and Molecular Ecology, Vienna University of Technology, Gumpendorfer Straße 1a/166-5-2, A-1060, Vienna, Austria; InterUniversity Cooperation Centre for Water and Health, Austria
| | - S Bofill-Mas
- Laboratory of Virus Contaminants of Water and Food, Department of Microbiology, Faculty of Biology, University of Barcelona, Av. Diagonal 643, Barcelona, 08028, Spain
| | - L Egle
- Institute for Water Quality Resources and Waste Management, Vienna University of Technology, Karlsplatz 13/226, 1040, Vienna, Austria; Center of Water Resource Systems, Vienna University of Technology, Karlsplatz 13/222, 1040, Vienna, Austria
| | - G H Reischer
- Institute of Chemical Engineering, Research Division Biotechnology and Microbiology, Research Group Environmental Microbiology and Molecular Ecology, Vienna University of Technology, Gumpendorfer Straße 1a/166-5-2, A-1060, Vienna, Austria; InterUniversity Cooperation Centre for Water and Health, Austria
| | - M Schade
- Bavarian Environment Agency, Bürgermeister-Ulrich-Straße 160, 86179, Augsburg, Germany
| | - X Fernandez-Cassi
- Laboratory of Virus Contaminants of Water and Food, Department of Microbiology, Faculty of Biology, University of Barcelona, Av. Diagonal 643, Barcelona, 08028, Spain
| | - W Fuchs
- Department of Environmental Biotechnology at IFA, University of Natural Resources and Life Sciences, Gregor-Mendel-Straße 33, 1180, Vienna, Austria
| | - R L Mach
- Institute of Chemical Engineering, Research Division Biotechnology and Microbiology, Research Group Environmental Microbiology and Molecular Ecology, Vienna University of Technology, Gumpendorfer Straße 1a/166-5-2, A-1060, Vienna, Austria; InterUniversity Cooperation Centre for Water and Health, Austria
| | - G Lindner
- InterUniversity Cooperation Centre for Water and Health, Austria; Medical University Vienna, Institute for Hygiene and Applied Immunology, Water Hygiene, Kinderspitalgasse 15, A-1090, Vienna, Austria
| | - A Kirschner
- InterUniversity Cooperation Centre for Water and Health, Austria; Medical University Vienna, Institute for Hygiene and Applied Immunology, Water Hygiene, Kinderspitalgasse 15, A-1090, Vienna, Austria
| | - M Gaisbauer
- Schreiber-AWATEC Umwelttechnik GmbH, Bergmillergasse 3/1, 1140, Vienna, Austria
| | - H Piringer
- VRVis Research Center, Donau-City-Strasse 1, 1220, Vienna, Austria
| | - A P Blaschke
- InterUniversity Cooperation Centre for Water and Health, Austria; Center of Water Resource Systems, Vienna University of Technology, Karlsplatz 13/222, 1040, Vienna, Austria
| | - R Girones
- Laboratory of Virus Contaminants of Water and Food, Department of Microbiology, Faculty of Biology, University of Barcelona, Av. Diagonal 643, Barcelona, 08028, Spain
| | - M Zessner
- Institute for Water Quality Resources and Waste Management, Vienna University of Technology, Karlsplatz 13/226, 1040, Vienna, Austria; Center of Water Resource Systems, Vienna University of Technology, Karlsplatz 13/222, 1040, Vienna, Austria
| | - R Sommer
- InterUniversity Cooperation Centre for Water and Health, Austria; Medical University Vienna, Institute for Hygiene and Applied Immunology, Water Hygiene, Kinderspitalgasse 15, A-1090, Vienna, Austria.
| | - A H Farnleitner
- Institute of Chemical Engineering, Research Division Biotechnology and Microbiology, Research Group Environmental Microbiology and Molecular Ecology, Vienna University of Technology, Gumpendorfer Straße 1a/166-5-2, A-1060, Vienna, Austria; InterUniversity Cooperation Centre for Water and Health, Austria
| |
Collapse
|
23
|
Rusiñol M, Fernandez-Cassi X, Timoneda N, Carratalà A, Abril JF, Silvera C, Figueras MJ, Gelati E, Rodó X, Kay D, Wyn-Jones P, Bofill-Mas S, Girones R. Evidence of viral dissemination and seasonality in a Mediterranean river catchment: Implications for water pollution management. J Environ Manage 2015; 159:58-67. [PMID: 26046988 DOI: 10.1016/j.jenvman.2015.05.019] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [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: 11/25/2014] [Revised: 05/13/2015] [Accepted: 05/16/2015] [Indexed: 05/20/2023]
Abstract
Conventional wastewater treatment does not completely remove and/or inactive viruses; consequently, viruses excreted by the population can be detected in the environment. This study was undertaken to investigate the distribution and seasonality of human viruses and faecal indicator bacteria (FIB) in a river catchment located in a typical Mediterranean climate region and to discuss future trends in relation to climate change. Sample matrices included river water, untreated and treated wastewater from a wastewater treatment plant within the catchment area, and seawater from potentially impacted bathing water. Five viruses were analysed in the study. Human adenovirus (HAdV) and JC polyomavirus (JCPyV) were analysed as indicators of human faecal contamination of human pathogens; both were reported in urban wastewater (mean values of 10(6) and 10(5) GC/L, respectively), river water (10(3) and 10(2) GC/L) and seawater (10(2) and 10(1) GC/L). Human Merkel Cell polyomavirus (MCPyV), which is associated with Merkel Cell carcinoma, was detected in 75% of the raw wastewater samples (31/37) and quantified by a newly developed quantitative polymerase chain reaction (qPCR) assay with mean concentrations of 10(4) GC/L. This virus is related to skin cancer in susceptible individuals and was found in 29% and 18% of river water and seawater samples, respectively. Seasonality was only observed for norovirus genogroup II (NoV GGII), which was more abundant in cold months with levels up to 10(4) GC/L in river water. Human hepatitis E virus (HEV) was detected in 13.5% of the wastewater samples when analysed by nested PCR (nPCR). Secondary biological treatment (i.e., activated sludge) and tertiary sewage disinfection including chlorination, flocculation and UV radiation removed between 2.22 and 4.52 log10 of the viral concentrations. Climate projections for the Mediterranean climate areas and the selected river catchment estimate general warming and changes in precipitation distribution. Persistent decreases in precipitation during summer can lead to a higher presence of human viruses because river and sea water present the highest viral concentrations during warmer months. In a global context, wastewater management will be the key to preventing environmental dispersion of human faecal pathogens in future climate change scenarios.
Collapse
Affiliation(s)
- Marta Rusiñol
- Laboratory of Virus Contaminants of Water and Food, Department of Microbiology, University of Barcelona, Barcelona, Catalonia, Spain
| | - Xavier Fernandez-Cassi
- Laboratory of Virus Contaminants of Water and Food, Department of Microbiology, University of Barcelona, Barcelona, Catalonia, Spain
| | - Natàlia Timoneda
- Laboratory of Virus Contaminants of Water and Food, Department of Microbiology, University of Barcelona, Barcelona, Catalonia, Spain; Institute of Biomedicine of the University of Barcelona (IBUB), University of Barcelona, Barcelona, Catalonia, Spain
| | - Anna Carratalà
- Laboratory of Virus Contaminants of Water and Food, Department of Microbiology, University of Barcelona, Barcelona, Catalonia, Spain
| | - Josep Francesc Abril
- Institute of Biomedicine of the University of Barcelona (IBUB), University of Barcelona, Barcelona, Catalonia, Spain; Computational Genomics Laboratory, Department of Genetics, University of Barcelona, Barcelona, Catalonia, Spain
| | - Carolina Silvera
- Microbiology Unit, Faculty of Medicine and Health Sciences, IISPV, University Rovira and Virgili, Reus, Catalonia, Spain
| | - Maria José Figueras
- Microbiology Unit, Faculty of Medicine and Health Sciences, IISPV, University Rovira and Virgili, Reus, Catalonia, Spain
| | - Emiliano Gelati
- Catalan Institute of Climate Sciences (IC3), Barcelona, Catalonia, Spain
| | - Xavier Rodó
- Catalan Institute of Climate Sciences (IC3), Barcelona, Catalonia, Spain
| | - David Kay
- Institute of Geography and Earth Sciences (IGES), Aberystwyth University, Aberystwyth, United Kingdom
| | - Peter Wyn-Jones
- Institute of Geography and Earth Sciences (IGES), Aberystwyth University, Aberystwyth, United Kingdom
| | - Sílvia Bofill-Mas
- Laboratory of Virus Contaminants of Water and Food, Department of Microbiology, University of Barcelona, Barcelona, Catalonia, Spain
| | - Rosina Girones
- Laboratory of Virus Contaminants of Water and Food, Department of Microbiology, University of Barcelona, Barcelona, Catalonia, Spain.
| |
Collapse
|
24
|
Sales-Ortells H, Fernandez-Cassi X, Timoneda N, Dürig W, Girones R, Medema G. Health risks derived from consumption of lettuces irrigated with tertiary effluent containing norovirus. Food Res Int 2015. [DOI: 10.1016/j.foodres.2014.08.018] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
|
25
|
Rusiñol M, Fernandez-Cassi X, Hundesa A, Vieira C, Kern A, Eriksson I, Ziros P, Kay D, Miagostovich M, Vargha M, Allard A, Vantarakis A, Wyn-Jones P, Bofill-Mas S, Girones R. Application of human and animal viral microbial source tracking tools in fresh and marine waters from five different geographical areas. Water Res 2014; 59:119-29. [PMID: 24793110 DOI: 10.1016/j.watres.2014.04.013] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.3] [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: 01/19/2014] [Revised: 02/24/2014] [Accepted: 04/06/2014] [Indexed: 05/21/2023]
Abstract
Integrated river basin management planning to mitigate the impacts of economic, demographic and climate change is an important issue for the future protection of water resources. Identifying sources of microbial contamination via the emerging science of Microbial Source Tracking (MST) plays a key role in risk assessment and the design of remediation strategies. Following an 18-month surveillance program within the EU-FP7-funded VIROCLIME project, specific MST tools were used to assess human markers such as adenoviruses (HAdV) and JC polyomaviruses (JCPyV) and porcine and bovine markers such as porcine adenoviruses (PAdV) and bovine polyomaviruses (BPyV) via quantification with real-time PCR to analyze surface water collected from five sites within different climatic zones: the Negro River (Brazil), Glafkos River (Greece), Tisza River (Hungary), Llobregat River (Spain) and Umeälven River (Sweden). The utility of the viral MST tools and the prevalence and abundance of specific human and animal viruses in the five river catchments and adjacent seawater, which is impacted by riverine contributions from the upstream catchments, were examined. In areas where no sanitation systems have been implemented, sewage can directly enter surface waters, and river water exhibited high viral loads; HAdV and JCPyV could be detected at mean concentrations of 10(5) and 10(4) Genome Copies/Liter (GC/L), respectively. In general, river water samples upstream of urban discharges presented lower human viral loads than downstream sampling sites, and those differences appeared to increase with urban populations but decrease in response to high river flow, as the elevated river water volume dilutes microbial loads. During dry seasons, river water flow decreases dramatically, and secondary effluents can represent the bulk of the riverine discharge. We also observed that ice cover that formed over the river during the winter in the studied areas in North Europe could preserve viral stability due to the low temperatures and/or the lack of solar inactivation. Porcine and bovine markers were detected where intensive livestock and agricultural activities were present; mean concentration values of 10(3) GC/L indicated that farms were sometimes unexpected and important sources of fecal contamination in water. During spring and summer, when livestock is outdoors and river flows are low, animal pollution increases due to diffuse contamination and direct voiding of feces onto the catchment surface. The field studies described here demonstrate the dynamics of fecal contamination in all catchments studied, and the data obtained is currently being used to develop dissemination models of fecal contamination in water with respect to future climate change scenarios. The results concerning human and animal targets presented in this study demonstrate the specificity and applicability of the viral quantitative parameters developed to widely divergent geographical areas and their high interest as new indicators of human and animal fecal contamination in water and as MST tools.
Collapse
Affiliation(s)
- Marta Rusiñol
- Laboratory of Virus Contaminants of Water and Food, Department of Microbiology, University of Barcelona, Barcelona, Spain
| | - Xavier Fernandez-Cassi
- Laboratory of Virus Contaminants of Water and Food, Department of Microbiology, University of Barcelona, Barcelona, Spain
| | - Ayalkibet Hundesa
- Laboratory of Virus Contaminants of Water and Food, Department of Microbiology, University of Barcelona, Barcelona, Spain
| | - Carmen Vieira
- Laboratory of Comparative and Environmental Virology, Oswaldo Cruz Institute, Rio de Janeiro, Brazil
| | - Anita Kern
- Department of Water Microbiology, National Institute for Environmental Health, Budapest, Hungary
| | | | - Panos Ziros
- Environmental Microbiology Unit, Department of Public Health, Medical School, University of Patras, Patras, Greece
| | - David Kay
- Institute of Geography and Earth Sciences (IGES), Aberystwyth University, Durham City, United Kingdom
| | - Marize Miagostovich
- Laboratory of Comparative and Environmental Virology, Oswaldo Cruz Institute, Rio de Janeiro, Brazil
| | - Marta Vargha
- Department of Water Microbiology, National Institute for Environmental Health, Budapest, Hungary
| | - Annika Allard
- Department of Virology, Umeå University, Umeå, Sweden
| | - Apostolos Vantarakis
- Environmental Microbiology Unit, Department of Public Health, Medical School, University of Patras, Patras, Greece
| | - Peter Wyn-Jones
- Institute of Geography and Earth Sciences (IGES), Aberystwyth University, Durham City, United Kingdom
| | - Sílvia Bofill-Mas
- Laboratory of Virus Contaminants of Water and Food, Department of Microbiology, University of Barcelona, Barcelona, Spain
| | - Rosina Girones
- Laboratory of Virus Contaminants of Water and Food, Department of Microbiology, University of Barcelona, Barcelona, Spain.
| |
Collapse
|