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Centralized and decentralized wastewater-based epidemiology to infer COVID-19 transmission - A brief review. One Health 2022; 15:100405. [PMID: 35664497 PMCID: PMC9150914 DOI: 10.1016/j.onehlt.2022.100405] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2022] [Revised: 05/26/2022] [Accepted: 05/27/2022] [Indexed: 11/22/2022] Open
Abstract
Wastewater-based epidemiology has shown to be a promising and innovative approach to measure a wide variety of illicit drugs that are consumed in the communities. In the same way as for illicit drugs, wastewater-based epidemiology is a promising approach to understand the prevalence of viruses in a community-level. The ongoing coronavirus disease 2019 (COVID-19) pandemic created an unprecedented burden on public health and diagnostic laboratories all over the world because of the need for massive laboratory testing. Many studies have shown the applicability of a centralized wastewater-based epidemiology (WBE) approach, where samples are collected at WWTPs. A more recent concept is a decentralized approach for WBE where samples are collected at different points of the sewer system and at polluted water bodies. The second being particularly important in countries where there are insufficient connections from houses to municipal sewage pipelines and thus untreated wastewater is discharged directly in environmental waters. A decentralized approach can be used to focus the value of diagnostic tests in what we call targeted-WBE, by monitoring wastewater in parts of the population where an outbreak is likely to happen, such as student dorms, retirement homes and hospitals. A combination of centralized and decentralized WBE should be considered for an affordable, sustainable, and successful WBE implementation in high-, middle- and low-income countries.
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Vitek R, do Nascimento FH, Masini JC. Polymer monoliths for the concentration of viruses from environmental waters: A review. J Sep Sci 2021; 45:134-148. [PMID: 34128332 DOI: 10.1002/jssc.202100282] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2021] [Revised: 06/09/2021] [Accepted: 06/10/2021] [Indexed: 12/13/2022]
Abstract
Even at low concentrations in environmental waters, some viruses are highly infective, making them a threat to human health. They are the leading cause of waterborne enteric diseases. In agriculture, plant viruses in irrigation and runoff water threat the crops. The low concentrations pose a challenge to early contamination detection. Thus, concentrating the virus particles into a small volume may be mandatory to achieve reliable detection in molecular techniques. This paper reviews the organic monoliths developments and their applications to concentrate virus particles from waters (waste, surface, tap, sea, and irrigation waters). Free-radical polymerization and polyaddition reactions are the most common strategies to prepare the monoliths currently used for virus concentration. Here, the routes for preparing and functionalizing both methacrylate and epoxy-based monoliths will be shortly described, following a revision of their retention mechanisms and applications in the concentration of enteric and plant viruses in several kinds of waters.
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Affiliation(s)
- Renan Vitek
- Departamento de Química Fundamental, Instituto de Química, Universidade de São Paulo, São Paulo, Brazil.,Instituto Federal de Educação Ciência e Tecnologia de Mato Grosso, Cuiabá, Brazil
| | - Fernando H do Nascimento
- Departamento de Química Fundamental, Instituto de Química, Universidade de São Paulo, São Paulo, Brazil
| | - Jorge C Masini
- Departamento de Química Fundamental, Instituto de Química, Universidade de São Paulo, São Paulo, Brazil
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Bačnik K, Kutnjak D, Pecman A, Mehle N, Tušek Žnidarič M, Gutiérrez Aguirre I, Ravnikar M. Viromics and infectivity analysis reveal the release of infective plant viruses from wastewater into the environment. WATER RESEARCH 2020; 177:115628. [PMID: 32299020 DOI: 10.1016/j.watres.2020.115628] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/22/2019] [Revised: 02/13/2020] [Accepted: 02/14/2020] [Indexed: 05/06/2023]
Abstract
Viruses represent one of the most important threats to agriculture. Several viral families include highly stable pathogens, which remain infective and can be transported long distances in water. The diversity of plant viruses in wastewater remains understudied; however, their potential impact is increasing with the increased irrigation usage of reclaimed wastewater. To determine the abundance, diversity and biological relevance of plant viruses in wastewater influents and effluents we applied an optimized virus concentration method followed by high-throughput sequencing and infectivity assays. We detected representatives of 47 plant virus species, including emerging crop threats. We also demonstrated infectivity for pathogenic and economically relevant plant viruses from the genus Tobamovirus (family Virgaviridae), which remain infective even after conventional wastewater treatment. These results demonstrate the potential of metagenomics to capture the diversity of plant viruses circulating in the environment and expose the potential risk of the uncontrolled use of reclaimed water for irrigation.
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Affiliation(s)
- Katarina Bačnik
- National Institute of Biology, Department of Biotechnology and Systems Biology, Večna pot 111, 1000, Ljubljana, Slovenia; Jožef Stefan International Postgraduate School, Jamova cesta 39, 1000, Ljubljana, Slovenia
| | - Denis Kutnjak
- National Institute of Biology, Department of Biotechnology and Systems Biology, Večna pot 111, 1000, Ljubljana, Slovenia
| | - Anja Pecman
- National Institute of Biology, Department of Biotechnology and Systems Biology, Večna pot 111, 1000, Ljubljana, Slovenia; Jožef Stefan International Postgraduate School, Jamova cesta 39, 1000, Ljubljana, Slovenia
| | - Nataša Mehle
- National Institute of Biology, Department of Biotechnology and Systems Biology, Večna pot 111, 1000, Ljubljana, Slovenia
| | - Magda Tušek Žnidarič
- National Institute of Biology, Department of Biotechnology and Systems Biology, Večna pot 111, 1000, Ljubljana, Slovenia
| | - Ion Gutiérrez Aguirre
- National Institute of Biology, Department of Biotechnology and Systems Biology, Večna pot 111, 1000, Ljubljana, Slovenia
| | - Maja Ravnikar
- National Institute of Biology, Department of Biotechnology and Systems Biology, Večna pot 111, 1000, Ljubljana, Slovenia; University of Nova Gorica, Vipavska cesta, 5000, Nova Gorica, Slovenia.
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Dobnik D, Kogovšek P, Jakomin T, Košir N, Tušek Žnidarič M, Leskovec M, Kaminsky SM, Mostrom J, Lee H, Ravnikar M. Accurate Quantification and Characterization of Adeno-Associated Viral Vectors. Front Microbiol 2019; 10:1570. [PMID: 31379763 PMCID: PMC6650692 DOI: 10.3389/fmicb.2019.01570] [Citation(s) in RCA: 56] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2018] [Accepted: 06/24/2019] [Indexed: 12/18/2022] Open
Abstract
One of the main challenges in the gene therapy viral vector development is to establish an optimized process for its large scale production. This requires optimization for upstream and downstream processes as well as methods that enable the step-by step analytical characterization of the virus, the results of which inform the iterative refinement of production for yield, purity and potency. The biggest problem here is a plethora of viral vector formulations, many of which interfere with analytical techniques. We took adeno-associated virus (AAV) as an example and showed benefits of combined use of molecular methods and transmission electron microscopy (TEM) for viral vectors' characterization and quantification. Results of the analyses showed that droplet digital PCR (ddPCR) performs better than quantitative real-time PCR (qPCR), in terms of robustness and assay variance, and this was especially relevant for partially purified (in-process) samples. Moreover, we demonstrate the importance of sample preparation prior to PCR analysis. We evaluated viral structure, presence of aggregates and impurities with TEM analysis and found that these impacted the differences in viral titers observed by qPCR and ddPCR and could be altered by sample preparation. These results serve as a guide for the establishment of the analytical methods required to provide measures of identity and purity for AAV viral vectors.
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Affiliation(s)
- David Dobnik
- Department of Biotechnology and Systems Biology, National Institute of Biology, Ljubljana, Slovenia
| | - Polona Kogovšek
- Department of Biotechnology and Systems Biology, National Institute of Biology, Ljubljana, Slovenia
| | - Tjaša Jakomin
- Department of Biotechnology and Systems Biology, National Institute of Biology, Ljubljana, Slovenia
| | - Nejc Košir
- Department of Biotechnology and Systems Biology, National Institute of Biology, Ljubljana, Slovenia
| | - Magda Tušek Žnidarič
- Department of Biotechnology and Systems Biology, National Institute of Biology, Ljubljana, Slovenia
| | | | - Stephen M. Kaminsky
- Belfer Gene Therapy Core Facility, Department of Genetic Medicine, Weill Medical College of Cornell University, New York, NY, United States
| | - Janet Mostrom
- Belfer Gene Therapy Core Facility, Department of Genetic Medicine, Weill Medical College of Cornell University, New York, NY, United States
| | - Hyunmi Lee
- Belfer Gene Therapy Core Facility, Department of Genetic Medicine, Weill Medical College of Cornell University, New York, NY, United States
| | - Maja Ravnikar
- Department of Biotechnology and Systems Biology, National Institute of Biology, Ljubljana, Slovenia
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Abstract
Viruses represent the most abundant and diverse of the biological entities in environmental waters, including the seas and probably also freshwater systems. They are important players in ecological networks in waters and influence global biochemical cycling and community composition dynamics. Among the many diverse viruses from terrestrial environments found in environmental waters, some are plant, animal, and/or human pathogens. The majority of pathogenic viral species found in waters are very stable and can survive outside host cells for long periods. The occurrence of such viruses in environmental waters has raised concerns because of the confirmation of the infectivity of waterborne viruses even at very low concentrations. This chapter focuses mainly on the survival of human, animal, and plant pathogenic viruses in aqueous environments, the possibility of their water-mediated transmission, the ecological implications of viruses in water, the methods adapted for detecting such viruses, and how to minimize the risk of viruses spreading through water.
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Gonçalves J, Gutiérrez-Aguirre I, Balasubramanian MN, Zagorščak M, Ravnikar M, Turk V. Surveillance of human enteric viruses in coastal waters using concentration with methacrylate monolithic supports prior to detection by RT-qPCR. MARINE POLLUTION BULLETIN 2018; 128:307-317. [PMID: 29571377 PMCID: PMC5884306 DOI: 10.1016/j.marpolbul.2018.01.040] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/17/2017] [Revised: 12/07/2017] [Accepted: 01/18/2018] [Indexed: 05/04/2023]
Abstract
This is the first surveillance study using methacrylate monolithic supports to concentrate environmental coastal water samples, prior to molecular target detection by RT-qPCR. Rotaviruses (RoV) and Noroviruses (NoV) were monitored in a polluted area at the Bay of Koper (Gulf of Trieste, Northern Adriatic Sea) and at a nearby bathing area and mussel farm areas. RoV and NoV are released into the Bay of Koper, with higher rates close to the discharge of the wastewater treatment plant, however, they can be detected at recreational and mussel farming areas. Our results showed that water bodies considered safe based on FC concentrations, can still have low, yet potentially infective, concentrations of human viruses.
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Affiliation(s)
- José Gonçalves
- Marine Biology Station Piran, National Institute of Biology, Fornače 41, SI-6330 Piran, Slovenia; Department of Biotechnology and Systems Biology, National Institute of Biology, Večna Pot 111, SI-1000 Ljubljana, Slovenia.
| | - Ion Gutiérrez-Aguirre
- Department of Biotechnology and Systems Biology, National Institute of Biology, Večna Pot 111, SI-1000 Ljubljana, Slovenia
| | | | - Maja Zagorščak
- Department of Biotechnology and Systems Biology, National Institute of Biology, Večna Pot 111, SI-1000 Ljubljana, Slovenia
| | - Maja Ravnikar
- Department of Biotechnology and Systems Biology, National Institute of Biology, Večna Pot 111, SI-1000 Ljubljana, Slovenia
| | - Valentina Turk
- Marine Biology Station Piran, National Institute of Biology, Fornače 41, SI-6330 Piran, Slovenia; University of Nova Gorica, Vipavska 15, SI-5000 Nova Gorica, Slovenia
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Gutiérrez-Aguirre I, Kutnjak D, Rački N, Rupar M, Ravnikar M. Monolith Chromatography as Sample Preparation Step in Virome Studies of Water Samples. Methods Mol Biol 2018; 1746:63-75. [PMID: 29492887 DOI: 10.1007/978-1-4939-7683-6_6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Viruses exist in aquatic media and many of them use this media as transmission route. Next-generation sequencing (NGS) technologies have opened new doors in virus research, allowing also to reveal a hidden diversity of viral species in aquatic environments. Not surprisingly, many of the newly discovered viruses are found in environmental fresh and marine waters. One of the problems in virome research can be the low amount of viral nucleic acids present in the sample in contrast to the background ones (host, eukaryotic, prokaryotic, environmental). Therefore, virus enrichment prior to NGS is necessary in many cases. In water samples, an added problem resides in the low concentration of viruses typically present in aquatic media. Different concentration strategies have been used to overcome such limitations. CIM monoliths are a new generation of chromatographic supports that due to their particular structural characteristics are very efficient in concentration and purification of viruses. In this chapter, we describe the use of CIM monolithic chromatography for sample preparation step in NGS studies targeting viruses in fresh or marine water. The step-by-step protocol will include a case study where CIM concentration was used to study the virome of a wastewater sample using NGS.
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Affiliation(s)
- Ion Gutiérrez-Aguirre
- Department of Biotechnology and Systems Biology, National Institute of Biology, Ljubljana, Slovenia.
| | - Denis Kutnjak
- Department of Biotechnology and Systems Biology, National Institute of Biology, Ljubljana, Slovenia
| | - Nejc Rački
- Lek Pharmaceuticals d.d., Menges, Slovenia
| | | | - Maja Ravnikar
- Department of Biotechnology and Systems Biology, National Institute of Biology, Ljubljana, Slovenia
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Krajacic M, Ravnikar M, Štrancar A, Gutiérrez-Aguirre I. Application of monolithic chromatographic supports in virus research. Electrophoresis 2017; 38:2827-2836. [DOI: 10.1002/elps.201700152] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2017] [Revised: 04/28/2017] [Accepted: 05/03/2017] [Indexed: 11/05/2022]
Affiliation(s)
- Mladen Krajacic
- Department of Biology; Faculty of Science; University of Zagreb; Zagreb Croatia
| | - Maja Ravnikar
- Department of Biotechnology and Systems Biology; National Institute of Biology; Ljubljana Slovenia
| | | | - Ion Gutiérrez-Aguirre
- Department of Biotechnology and Systems Biology; National Institute of Biology; Ljubljana Slovenia
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