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Vecchia AD, Rigotto C, Soliman MC, Souza FGD, Giehl IC, Spilki FR. Recovery rate of multiple enteric viruses artificially seeded in water and concentrated by adsorption-elution with negatively charged membranes: interaction and interference between different virus species. WATER SCIENCE AND TECHNOLOGY : A JOURNAL OF THE INTERNATIONAL ASSOCIATION ON WATER POLLUTION RESEARCH 2015; 72:2291-2300. [PMID: 26676018 DOI: 10.2166/wst.2015.458] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Viral concentration method by adsorption-elution with negative membranes has been widely employed for concentrating viruses from environmental samples. In order to provide an adequate assessment of its recovery efficiency, this study was conducted to assess viral recovery rates for viral species commonly found in water (HAdV-5, EV, RV, BAdV and CAV-2), quantifying viral genomes at the end of the five different steps of the process. Recovery rates were analyzed for several viruses combined in a single water sample and for each virus assayed separately. Ultrapure water samples were artificially contaminated and analyzed by real-time quantitative polymerase chain reaction (qPCR). High recovery rates were found after the final stage when assessed individually (89 to 125%) and combined in the same sample (23 to > 164%). HAdV-5 exhibited >100% recovery when assayed with human viruses and other AdVs, whereas BAdV and CAV-2 were not detected. These data suggest that recovery efficiency could be related to viral structural characteristics, their electric charges and other interactions, so that they are retained with greater or lesser efficiency when coupled. This protocol could be applied to environmental samples, since high recovery rates were observed and infectious viruses were detected at the end of the concentration process.
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Affiliation(s)
- Andréia Dalla Vecchia
- Laboratório de Microbiologia Molecular, Instituto de Ciências da Saúde, Universidade Feevale, CEP 93352-000, Novo Hamburgo, RS, Brasil E-mail:
| | - Caroline Rigotto
- Laboratório de Microbiologia Molecular, Instituto de Ciências da Saúde, Universidade Feevale, CEP 93352-000, Novo Hamburgo, RS, Brasil E-mail:
| | - Mayra Cristina Soliman
- Laboratório de Microbiologia Molecular, Instituto de Ciências da Saúde, Universidade Feevale, CEP 93352-000, Novo Hamburgo, RS, Brasil E-mail:
| | - Fernanda Gil de Souza
- Laboratório de Microbiologia Molecular, Instituto de Ciências da Saúde, Universidade Feevale, CEP 93352-000, Novo Hamburgo, RS, Brasil E-mail:
| | - Isabel Cristina Giehl
- Laboratório de Microbiologia Molecular, Instituto de Ciências da Saúde, Universidade Feevale, CEP 93352-000, Novo Hamburgo, RS, Brasil E-mail:
| | - Fernando Rosado Spilki
- Laboratório de Microbiologia Molecular, Instituto de Ciências da Saúde, Universidade Feevale, CEP 93352-000, Novo Hamburgo, RS, Brasil E-mail:
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102
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Organic substances interfere with reverse transcription-quantitative PCR-based virus detection in water samples. Appl Environ Microbiol 2014; 81:1585-93. [PMID: 25527552 DOI: 10.1128/aem.03082-14] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023] Open
Abstract
Reverse transcription (RT)-PCR-based virus detection from water samples is occasionally hampered by organic substances that are co-concentrated during virus concentration procedures. To characterize these organic substances, samples containing commercially available humic acid, which is known to inhibit RT-PCR, and river water samples were subjected to adsorption-elution-based virus concentration using an electronegative membrane. In this study, the samples before, during, and after the concentration were analyzed in terms of organic properties and virus detection efficiencies. Two out of the three humic acid solutions resulted in RT-quantitative PCR (qPCR) inhibition that caused >3-log10-unit underestimation of spiked poliovirus. Over 60% of the organics contained in the two solutions were recovered in the concentrate, while over 60% of the organics in the uninhibited solution were lost during the concentration process. River water concentrates also caused inhibition of RT-qPCR. Organic concentrations in the river water samples increased by 2.3 to 3.9 times after the virus concentration procedure. The inhibitory samples contained organic fractions in the 10- to 100-kDa size range, which are suspected to be RT-PCR inhibitors. According to excitation-emission matrices, humic acid-like and protein-like fractions were also recovered from river water concentrates, but these fractions did not seem to affect virus detection. Our findings reveal that detailed organic analyses are effective in characterizing inhibitory substances.
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103
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Furtak VA, Dabrazhynetskaya A, Volokhov DV, Chizhikov V. Use of tangential flow filtration for improving detection of viral adventitious agents in cell substrates. Biologicals 2014; 43:23-30. [PMID: 25432087 DOI: 10.1016/j.biologicals.2014.10.005] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2014] [Revised: 10/03/2014] [Accepted: 10/27/2014] [Indexed: 11/28/2022] Open
Abstract
In this study, we assessed the feasibility of tangential flow filtration (TFF) for primary concentration of viral adventitious agents (AAs) from large volumes of cell substrate-derived samples, such as cell-free Chinese hamster ovary (CHO) culture supernatants (500 mL) and CHO cell lysates (50 mL), prior to virus detection in them by nucleic acid-based methods (i.e., qPCR and massively parallel sequencing (MPS). The study was conducted using the samples spiked with four model DNA viruses (bovine herpesvirus type 4, human adenovirus type 5, simian polyomavirus SV-40, and bovine parvovirus). The results showed that the combined TFF/MPS approach enables reliable detection of as low as 1000 genome equivalents (GE) of each of the four viruses spiked into the cell substrate samples. The final achieved sensitivities of 2 GE/mL for cell culture supernatant and 20 GE/mL for cell lysate make this approach more sensitive than virus-specific PCR and qPCR assays. The study results allowed us to propose that TFF might be useful and valuable method for simple and rapid concentration of potential AAs in cell substrate samples prior to AAs detection by conventional in vivo, in vitro, or molecular methods.
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Affiliation(s)
- Vyacheslav A Furtak
- Center for Biologics Evaluation and Research, Food and Drug Administration, 10903 New Hampshire Avenue, Silver Spring, MD, USA
| | - Alena Dabrazhynetskaya
- Center for Biologics Evaluation and Research, Food and Drug Administration, 10903 New Hampshire Avenue, Silver Spring, MD, USA
| | - Dmitriy V Volokhov
- Center for Biologics Evaluation and Research, Food and Drug Administration, 10903 New Hampshire Avenue, Silver Spring, MD, USA
| | - Vladimir Chizhikov
- Center for Biologics Evaluation and Research, Food and Drug Administration, 10903 New Hampshire Avenue, Silver Spring, MD, USA.
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104
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105
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Ranking filter methods for concentrating pathogens in lake water. Appl Environ Microbiol 2014; 79:5418-9. [PMID: 23926086 DOI: 10.1128/aem.01430-13] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
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106
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Butot S, Zuber S, Baert L. Sample preparation prior to molecular amplification: complexities and opportunities. Curr Opin Virol 2014; 4:66-70. [PMID: 24441295 DOI: 10.1016/j.coviro.2013.12.004] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2013] [Revised: 12/02/2013] [Accepted: 12/12/2013] [Indexed: 02/01/2023]
Abstract
Molecular amplification using Reverse Transcription quantitative Polymerase Chain Reaction (RT-qPCR) is currently considered as the gold standard to detect enteric human pathogenic viruses such as norovirus and hepatitis A virus in food and water. However, the molecular-based detection requires an adequate sampling strategy and a sample preparation specific for viruses. Sampling for enteric human viruses in water and food should not necessarily follow bacterial sampling plans. The development of a reference detection method including sample preparation as proposed in ISO/TS 15216 represents a milestone to facilitate the evaluation of the performance and eventually validation of future virus detection methods. The potential viral infectivity linked to a positive PCR result is a remaining issue and pretreatments allowing the differentiation of infectious viruses would be useful for future risk assessments.
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Affiliation(s)
- Sophie Butot
- Food Safety and Quality Competence Pillar, Nestlé Research Centre, Vers-chez-les-Blanc, Box 44, 1000 Lausanne 26, Switzerland.
| | - Sophie Zuber
- Food Safety and Quality Competence Pillar, Nestlé Research Centre, Vers-chez-les-Blanc, Box 44, 1000 Lausanne 26, Switzerland
| | - Leen Baert
- Food Safety and Quality Competence Pillar, Nestlé Research Centre, Vers-chez-les-Blanc, Box 44, 1000 Lausanne 26, Switzerland
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107
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Reply to "ranking filter methods for concentrating pathogens in lake water". Appl Environ Microbiol 2013; 79:5420-1. [PMID: 23926087 DOI: 10.1128/aem.01559-13] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
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108
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Cadiere A, Couturaud B, Boismard J, Le Cann P, Gérard A, Mas A, Faye C, Garrelly L, Roig B. Assessment of poly-l
-lysine dendrigrafts for virus concentration in water: use of MS2 bacteriophage as proof of concept. J Appl Microbiol 2013; 115:290-7. [DOI: 10.1111/jam.12209] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2012] [Revised: 03/22/2013] [Accepted: 03/25/2013] [Indexed: 11/26/2022]
Affiliation(s)
- A. Cadiere
- EHESP Rennes; Sorbonne Paris Cité; F- 35043 Rennes Cedex France
- INSERM; UMR IRSET Institut de recherche sur la santé l'environnement et le travail - 1085; LERES; F- 35043 Rennes France
| | - B. Couturaud
- Institut Charles Gerhardt, Montpellier; UMR5253 CNRS-UM2-ENSCM-UM1; Equipe IAM, UM2; Montpellier cedex 5 France
| | - J. Boismard
- EHESP Rennes; Sorbonne Paris Cité; F- 35043 Rennes Cedex France
| | - P. Le Cann
- EHESP Rennes; Sorbonne Paris Cité; F- 35043 Rennes Cedex France
- INSERM; UMR IRSET Institut de recherche sur la santé l'environnement et le travail - 1085; LERES; F- 35043 Rennes France
| | - A. Gérard
- EHESP Rennes; Sorbonne Paris Cité; F- 35043 Rennes Cedex France
- INSERM; UMR IRSET Institut de recherche sur la santé l'environnement et le travail - 1085; LERES; F- 35043 Rennes France
| | - A. Mas
- Institut Charles Gerhardt, Montpellier; UMR5253 CNRS-UM2-ENSCM-UM1; Equipe IAM, UM2; Montpellier cedex 5 France
| | - C. Faye
- COLCOM SARL; Montpellier France
| | | | - B. Roig
- EHESP Rennes; Sorbonne Paris Cité; F- 35043 Rennes Cedex France
- INSERM; UMR IRSET Institut de recherche sur la santé l'environnement et le travail - 1085; LERES; F- 35043 Rennes France
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109
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Gentry-Shields J, Stewart JR. Similar concentration and extraction recoveries allow for use of turnip crinkle virus as a process control for enteroviruses in water. J Virol Methods 2013; 189:250-7. [PMID: 23466632 DOI: 10.1016/j.jviromet.2013.02.013] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2012] [Revised: 02/21/2013] [Accepted: 02/25/2013] [Indexed: 01/30/2023]
Abstract
Enteric viruses are etiological agents of waterborne disease that may be detected using molecular techniques such as PCR. However, processing water samples in preparation for PCR typically involves concentration of samples and extraction of nucleic acids, steps that have low and variable recovery efficiencies. This study evaluated a plant virus, turnip crinkle virus (TCV), for its ability to serve as a process control for human enteroviruses during concentration and extraction procedures. Enteroviruses and TCV have similar sizes and morphologies, and both contain single stranded, positive-sense RNA genomes. Results from the study demonstrate that the tested viruses experience similar losses during sample processing. Virus recoveries averaged 0.03% for EV and 0.02% for TCV from DI water, and 0.004% for EV and 0.009% for TCV from a creek sample. Surface water and wastewater samples from around the U.S. were evaluated for the presence of TCV to ensure the virus is not present in environmental samples. All were negative. With similar recovery efficiencies to EV, TCV may be a suitable process control for enteroviruses in environmental water samples in the U.S. Use of process controls as proposed in this study would allow better detection and quantitation methods to be employed in water quality monitoring.
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Affiliation(s)
- Jennifer Gentry-Shields
- Department of Environmental Sciences and Engineering, Gillings School of Global Public Health, University of North Carolina, Chapel Hill, NC 27599-7431, USA.
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