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Jiang M, Wang ALW, Be NA, Mulakken N, Nelson KL, Kantor RS. Evaluation of the Impact of Concentration and Extraction Methods on the Targeted Sequencing of Human Viruses from Wastewater. Environ Sci Technol 2024; 58:8239-8250. [PMID: 38690747 PMCID: PMC11097627 DOI: 10.1021/acs.est.4c00580] [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] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/16/2024] [Revised: 04/18/2024] [Accepted: 04/19/2024] [Indexed: 05/03/2024]
Abstract
Sequencing human viruses in wastewater is challenging due to their low abundance compared to the total microbial background. This study compared the impact of four virus concentration/extraction methods (Innovaprep, Nanotrap, Promega, and Solids extraction) on probe-capture enrichment for human viruses followed by sequencing. Different concentration/extraction methods yielded distinct virus profiles. Innovaprep ultrafiltration (following solids removal) had the highest sequencing sensitivity and richness, resulting in the successful assembly of several near-complete human virus genomes. However, it was less sensitive in detecting SARS-CoV-2 by digital polymerase chain reaction (dPCR) compared to Promega and Nanotrap. Across all preparation methods, astroviruses and polyomaviruses were the most highly abundant human viruses, and SARS-CoV-2 was rare. These findings suggest that sequencing success can be increased using methods that reduce nontarget nucleic acids in the extract, though the absolute concentration of total extracted nucleic acid, as indicated by Qubit, and targeted viruses, as indicated by dPCR, may not be directly related to targeted sequencing performance. Further, using broadly targeted sequencing panels may capture viral diversity but risks losing signals for specific low-abundance viruses. Overall, this study highlights the importance of aligning wet lab and bioinformatic methods with specific goals when employing probe-capture enrichment for human virus sequencing from wastewater.
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Affiliation(s)
- Minxi Jiang
- Department
of Civil and Environmental Engineering, University of California, Berkeley, California 94720, United States
| | - Audrey L. W. Wang
- Department
of Civil and Environmental Engineering, University of California, Berkeley, California 94720, United States
| | - Nicholas A. Be
- Physical
and Life Sciences Directorate, Lawrence
Livermore National Laboratory, Livermore, California 94550, United States
| | - Nisha Mulakken
- Computing
and Global Security Directorates, Lawrence
Livermore National Laboratory, Livermore, California 94550, United States
| | - Kara L. Nelson
- Department
of Civil and Environmental Engineering, University of California, Berkeley, California 94720, United States
| | - Rose S. Kantor
- Department
of Civil and Environmental Engineering, University of California, Berkeley, California 94720, United States
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Mantri D, Wymenga L, van Turnhout J, van Zeijl H, Zhang G. Manipulation, Sampling and Inactivation of the SARS-CoV-2 Virus Using Nonuniform Electric Fields on Micro-Fabricated Platforms: A Review. Micromachines (Basel) 2023; 14:345. [PMID: 36838044 PMCID: PMC9967285 DOI: 10.3390/mi14020345] [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] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/22/2022] [Revised: 01/21/2023] [Accepted: 01/21/2023] [Indexed: 06/18/2023]
Abstract
Micro-devices that use electric fields to trap, analyze and inactivate micro-organisms vary in concept, design and application. The application of electric fields to manipulate and inactivate bacteria and single-celled organisms has been described extensively in the literature. By contrast, the effect of such fields on viruses is not well understood. This review explores the possibility of using existing methods for manipulating and inactivating larger viruses and bacteria, for smaller viruses, such as SARS-CoV-2. It also provides an overview of the theoretical background. The findings may be used to implement new ideas and frame experimental parameters that optimize the manipulation, sampling and inactivation of SARS-CoV-2 electrically.
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Affiliation(s)
- Devashish Mantri
- Department Biomedical Engineering, Delft University of Technology, 2628 CD Delft, The Netherlands
| | - Luutzen Wymenga
- Department Microelectronics, Delft University of Technology, 2628 CD Delft, The Netherlands
| | - Jan van Turnhout
- Department Material Science Engineering, Delft University of Technology, 2628 CD Delft, The Netherlands
| | - Henk van Zeijl
- Department Microelectronics, Delft University of Technology, 2628 CD Delft, The Netherlands
| | - Guoqi Zhang
- Department Microelectronics, Delft University of Technology, 2628 CD Delft, The Netherlands
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Nourinejhad Zarghani S, Monavari M, Ehlers J, Hamacher J, Büttner C, Bandte M. Comparison of Models for Quantification of Tomato Brown Rugose Fruit Virus Based on a Bioassay Using a Local Lesion Host. Plants (Basel) 2022; 11:3443. [PMID: 36559554 PMCID: PMC9783233 DOI: 10.3390/plants11243443] [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] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/07/2022] [Revised: 11/28/2022] [Accepted: 11/30/2022] [Indexed: 06/17/2023]
Abstract
Considering the availability of serological and molecular biological methods, the bioassay has been paled into insignificance, although it is the only experimental method that can be used to demonstrate the infectivity of a virus. We compared goodness-of-fit and predictability power of five models for the quantification of tomato brown rugose fruit virus (ToBRFV) based on local lesion assays: the Kleczkowski model, Furumoto and Mickey models I and II, the Gokhale and Bald model (growth curve model), and the modified Poisson model. For this purpose, mechanical inoculations onto Nicotiana tabacum L. cv. Xanthi nc and N. glutionosa L. with defined virus concentrations were first performed with half-leaf randomization in a Latin square design. Subsequently, models were implemented using Python software and fitted to the number of local lesions. All models could fit to the data for quantifying ToBRFV based on local lesions, among which the modified Poisson model had the best prediction of virus concentration in spike samples based on local lesions, although data of individual indicator plants showed variations. More accurate modeling was obtained from the test plant N. glutinosa than from N. tabacum cv. Xanthi nc. The position of the half-leaves on the test plants had no significant effect on the number of local lesions.
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Affiliation(s)
- Shaheen Nourinejhad Zarghani
- Division Phytomedicine, Faculty of Life Sciences, Albrecht Daniel Thaer-Institute of Agricultural and Horticultural Sciences, Humboldt-Universität zu Berlin, Lentzeallee 55-57, 14197 Berlin, Germany
| | - Mehran Monavari
- Section eScience, Federal Institute for Materials Research and Testing, Unter den Eichen 87, 12205 Berlin, Germany
| | - Jens Ehlers
- Division Phytomedicine, Faculty of Life Sciences, Albrecht Daniel Thaer-Institute of Agricultural and Horticultural Sciences, Humboldt-Universität zu Berlin, Lentzeallee 55-57, 14197 Berlin, Germany
| | - Joachim Hamacher
- INRES-Plant Pathology, Universität Bonn, Nussallee 9, 53115 Bonn, Germany
| | - Carmen Büttner
- Division Phytomedicine, Faculty of Life Sciences, Albrecht Daniel Thaer-Institute of Agricultural and Horticultural Sciences, Humboldt-Universität zu Berlin, Lentzeallee 55-57, 14197 Berlin, Germany
| | - Martina Bandte
- Division Phytomedicine, Faculty of Life Sciences, Albrecht Daniel Thaer-Institute of Agricultural and Horticultural Sciences, Humboldt-Universität zu Berlin, Lentzeallee 55-57, 14197 Berlin, Germany
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Yu L, Tian Z, Joshi DR, Yuan L, Tuladhar R, Zhang Y, Yang M. Detection of SARS-CoV-2 and Other Viruses in Wastewater: Optimization and Automation of an Aluminum Hydroxide Adsorption-Precipitation Method for Virus Concentration. ACS ES T Water 2022; 2:2175-2184. [PMID: 37552732 PMCID: PMC9115887 DOI: 10.1021/acsestwater.2c00079] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/15/2022] [Revised: 04/22/2022] [Accepted: 04/26/2022] [Indexed: 06/18/2023]
Abstract
This study aimed to provide a low-cost technique for virus detection in wastewater by improving an aluminum hydroxide adsorption-precipitation method. The releasing efficiency of viruses trapped by the aluminum hydroxide precipitates was improved by adding ethylenediaminetetraacetic acid disodium salt (EDTA-2Na) to dissolve the precipitates at a Na2EDTA·2H2O:AlCl3 molar ratio of 1.8-3.6. The recovery rates of the improved method for seven viruses, including SARS-CoV-2-abEN pseudovirus and six animal viruses, were 5.9-22.3% in tap water and 4.9-35.1% in wastewater. Rotavirus A (9.0-4.5 × 103 copies/mL), porcine circovirus type 2 (5.8-6.4 × 105 copies/mL), and porcine parvovirus (5.6-2.7 × 104 copies/mL) were detected in China's pig farm wastewater, while rotavirus A (2.0 × 103 copies/mL) was detected in hospital wastewater. SARS-CoV-2 was detected in hospital wastewater (8.4 × 102 to 1.4 × 104 copies/mL), sewage (6.4 × 10 to 2.3 × 103 copies/mL), and river water (6.6 × 10 to 9.3 × 10 copies/mL) in Nepal. The method was automized, with a rate of recovery of 4.8 ± 1.4% at a virus concentration of 102 copies/mL. Thus, the established method could be used for wastewater-based epidemiology with sufficient sensitivity in coping with the COVID-19 epidemic and other virus epidemics.
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Affiliation(s)
- Lina Yu
- State Key Laboratory of Environmental Aquatic
Chemistry, Research Center for Eco-Environmental Sciences, Chinese Academy of
Sciences, Beijing 100085, China
- Sino-Danish College, University of
Chinese Academy of Sciences, Beijing 100190,
China
- University of Chinese Academy of
Sciences, Beijing 100049, China
| | - Zhe Tian
- State Key Laboratory of Environmental Aquatic
Chemistry, Research Center for Eco-Environmental Sciences, Chinese Academy of
Sciences, Beijing 100085, China
| | - Dev Raj Joshi
- Central Department of Microbiology,
Tribhuvan University, GPO 44613 Kirtipur, Kathmandu,
Nepal
| | - Lin Yuan
- Beijing Sino-science Gene Technology
Company, Ltd., Beijing 102629, China
| | - Reshma Tuladhar
- Central Department of Microbiology,
Tribhuvan University, GPO 44613 Kirtipur, Kathmandu,
Nepal
| | - Yu Zhang
- State Key Laboratory of Environmental Aquatic
Chemistry, Research Center for Eco-Environmental Sciences, Chinese Academy of
Sciences, Beijing 100085, China
- Sino-Danish College, University of
Chinese Academy of Sciences, Beijing 100190,
China
- University of Chinese Academy of
Sciences, Beijing 100049, China
| | - Min Yang
- Sino-Danish College, University of
Chinese Academy of Sciences, Beijing 100190,
China
- University of Chinese Academy of
Sciences, Beijing 100049, China
- Key Laboratory of Drinking Water Science and Technology,
Research Center for Eco-Environmental Sciences, Chinese Academy of
Sciences, Beijing 100085, China
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Birnbaum DP, Vilardi KJ, Anderson CL, Pinto AJ, Joshi NS. Simple Affinity-Based Method for Concentrating Viruses from Wastewater Using Engineered Curli Fibers. ACS ES T Water 2022; 2:1836-1843. [PMID: 36778666 PMCID: PMC9916486 DOI: 10.1021/acsestwater.1c00208] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
Wastewater surveillance is a proven method for tracking community spread and prevalence of some infectious viral diseases. A primary concentration step is often used to enrich viral particles from wastewater prior to subsequent viral quantification and/or sequencing. Here, we present a simple procedure for concentrating viruses from wastewater using bacterial biofilm protein nanofibers known as curli fibers. Through simple genetic engineering, we produced curli fibers functionalized with single-domain antibodies (also known as nanobodies) specific for the coat protein of the model virus bacteriophage MS2. Using these modified fibers in a simple spin-down protocol, we demonstrated efficient concentration of MS2 in both phosphate-buffered saline (PBS) and in the wastewater matrix. Additionally, we produced nanobody-functionalized curli fibers capable of binding the spike protein of SARS-CoV-2, showing the versatility of the system. Our concentration protocol is simple to implement, can be performed quickly under ambient conditions, and requires only components produced through bacterial culture. We believe this technology represents an attractive alternative to existing concentration methods and warrants further research and optimization for field-relevant applications.
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Affiliation(s)
- Daniel P Birnbaum
- John A. Paulson School of Engineering and Applied Sciences, Harvard University, Cambridge, Massachusetts 02138, United States; Department of Chemistry and Chemical Biology, Northeastern University, Boston, Massachusetts 02115, United States
| | - Katherine J Vilardi
- Department of Civil and Environmental Engineering, Northeastern University, Boston, Massachusetts 02115, United States
| | - Christopher L Anderson
- Department of Civil and Environmental Engineering, Northeastern University, Boston, Massachusetts 02115, United States
| | - Ameet J Pinto
- School of Civil and Environmental Engineering, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
| | - Neel S Joshi
- Department of Chemistry and Chemical Biology, Northeastern University, Boston, Massachusetts 02115, United States
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Mashin VV, Sergeev AN, Martynova NN, Sergeev AA, Lys'ko KA, Raikov AO, Kataeva VV, Zagidullin NV. Viral Safety Issues in the Production and Manufacturing of Human Immunoglobulin Preparations from Equine Plasma/Serum. Pharm Chem J 2022; 56:532-7. [PMID: 35845147 DOI: 10.1007/s11094-022-02675-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2021] [Indexed: 11/11/2022]
Abstract
The current Russian and foreign pharmacopoeias either do not provide any information about existing types of viral diseases in horses or do not present it in full. Data of modern domestic and foreign literature was used to prepare the most complete list of viruses that cause equine diseases including 36 infectious agents, 25 of which are pathogenic for humans, 13 of the 25 of which are widespread throughout Russia. Information is provided on the magnitudes of the disease incubation periods (which are most often within one month), the external clinical signs of these diseases (which can also be asymptomatic), and the maximum possible concentrations of viruses in the blood of horses with these diseases (which can reach 8 log conventional units/mL of blood). This information is offered for use in critical production stages of heterologous immunoglobulin drugs for medical use to assure viral safety.
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Kim MJ, Baek EJ, Kim JO, Hwang JY, Kwon MG, Il Kim K. Application of iron flocculation to concentrate white spot syndrome virus in seawater. J Virol Methods 2022; 306:114554. [PMID: 35623490 DOI: 10.1016/j.jviromet.2022.114554] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2022] [Revised: 05/15/2022] [Accepted: 05/22/2022] [Indexed: 10/18/2022]
Abstract
The iron flocculation method, which comprises the Fe-virus flocculate formation-filtration-resuspension steps, is extensively used to concentrate and precipitate viruses distributed in water. To apply this method to concentrate white spot syndrome virus (WSSV) in seawater, viral genomic and infective recovery yields were compared between polyethylene sulfone (PES) and polycarbonate (PC) membrane filters and two types of resuspension buffers (oxalate and ascorbate). Viral genome quantitation was determined above a 95% limit of detection (11.48 viral DNA copies/μL) using quantitative real-time PCR. From WSSV-spiked seawater (100 to 106 viral DNA copies/mL), the viral genomic recovery yields of the PES-Oxalate, PC-Oxalate, PES-Ascorbate, and PC-Ascorbate conditions were 78.67% ± 12.90%, 84.53% ± 24.30%, 85.59% ± 16.98%, and 93.74% ± 7.44%, respectively. The detectable Fe-virus flocculates collected by the PC membrane were approximately 101 WSSV DNA copies/mL of seawater, a value more than 10-fold higher than that compared to the PES membrane filter (102 WSSV DNA copies/mL), regardless of the resuspension buffer types. WSSV resuspended with oxalate buffer caused mass mortality among whiteleg shrimp (Litopenaeus vannamei), inducing the expression of the virus envelope protein, VP28, similar to that of a native virus, suggesting stable viral activity during the resuspension process. Based on the PES-Ascorbate, WSSV particles could be successfully concentrated in seawater from shrimp farms with white spot disease outbreaks (approximately 102 WSSV DNA copies/mL). Collectively, these findings indicate that the simple and efficient method of iron flocculation is sufficient to concentrate WSSV in seawater and could be used as a non-invasive approach and one of the reasonable diagnostic processes for white spot disease surveillance.
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Affiliation(s)
- Min Jae Kim
- Department of Aquatic Life Medicine, Pukyong National University, Busan, 48513, Republic of Korea
| | - Eun Jin Baek
- Department of Aquatic Life Medicine, Pukyong National University, Busan, 48513, Republic of Korea
| | - Jae-Ok Kim
- Tongyeong Regional Office, National Fishery Products Quality Management Service (NFQS)
| | - Jee Youn Hwang
- Aquatic Disease Control Division, National Fishery Products Quality Management Service (NFQS)
| | - Mun-Gyeong Kwon
- Aquatic Disease Control Division, National Fishery Products Quality Management Service (NFQS)
| | - Kwang Il Kim
- Department of Aquatic Life Medicine, Pukyong National University, Busan, 48513, Republic of Korea.
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Bar-Or I, Yaniv K, Shagan M, Ozer E, Weil M, Indenbaum V, Elul M, Erster O, Mendelson E, Mannasse B, Shirazi R, Kramarsky-Winter E, Nir O, Abu-Ali H, Ronen Z, Rinott E, Lewis YE, Friedler E, Bitkover E, Paitan Y, Berchenko Y, Kushmaro A. Regressing SARS-CoV-2 Sewage Measurements Onto COVID-19 Burden in the Population: A Proof-of-Concept for Quantitative Environmental Surveillance. Front Public Health 2022; 9:561710. [PMID: 35047467 PMCID: PMC8762221 DOI: 10.3389/fpubh.2021.561710] [Citation(s) in RCA: 25] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2020] [Accepted: 11/18/2021] [Indexed: 01/19/2023] Open
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is an RNA virus, a member of the coronavirus family of respiratory viruses that includes severe acute respiratory syndrome coronavirus 1 (SARS-CoV-1) and the Middle East respiratory syndrome (MERS). It has had an acute and dramatic impact on health care systems, economies, and societies of affected countries during the past 8 months. Widespread testing and tracing efforts are being employed in many countries in attempts to contain and mitigate this pandemic. Recent data has indicated that fecal shedding of SARS-CoV-2 is common and that the virus RNA can be detected in wastewater. This indicates that wastewater monitoring may provide a potentially efficient tool for the epidemiological surveillance of SARS-CoV-2 infection in large populations at relevant scales. In particular, this provides important means of (i) estimating the extent of outbreaks and their spatial distributions, based primarily on in-sewer measurements, (ii) managing the early-warning system quantitatively and efficiently, and (iii) verifying disease elimination. Here we report different virus concentration methods using polyethylene glycol (PEG), alum, or filtration techniques as well as different RNA extraction methodologies, providing important insights regarding the detection of SARS-CoV-2 RNA in sewage. Virus RNA particles were detected in wastewater in several geographic locations in Israel. In addition, a correlation of virus RNA concentration to morbidity was detected in Bnei-Barak city during April 2020. This study presents a proof of concept for the use of direct raw sewage-associated virus data, during the pandemic in the country as a potential epidemiological tool.
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Affiliation(s)
- Itay Bar-Or
- Central Virology Lab, Ministry of Health, Sheba Medical Center, Jerusalem, Israel
| | - Karin Yaniv
- Avram and Stella Goldstein-Goren, Department of Biotechnology Engineering, Ben-Gurion University of the Negev, Beer Sheva, Israel
| | - Marilou Shagan
- Avram and Stella Goldstein-Goren, Department of Biotechnology Engineering, Ben-Gurion University of the Negev, Beer Sheva, Israel
| | - Eden Ozer
- Department of Life Sciences, Ben-Gurion University of the Negev, Beer Sheva, Israel
| | - Merav Weil
- Central Virology Lab, Ministry of Health, Sheba Medical Center, Jerusalem, Israel
| | - Victoria Indenbaum
- Central Virology Lab, Ministry of Health, Sheba Medical Center, Jerusalem, Israel
| | - Michal Elul
- Central Virology Lab, Ministry of Health, Sheba Medical Center, Jerusalem, Israel
| | - Oran Erster
- Central Virology Lab, Ministry of Health, Sheba Medical Center, Jerusalem, Israel
| | - Ella Mendelson
- Central Virology Lab, Ministry of Health, Sheba Medical Center, Jerusalem, Israel
- School of Public Health, Sackler Faculty of Medicine, Tel-Aviv University, Tel Aviv, Israel
| | - Batya Mannasse
- Central Virology Lab, Ministry of Health, Sheba Medical Center, Jerusalem, Israel
| | - Rachel Shirazi
- Central Virology Lab, Ministry of Health, Sheba Medical Center, Jerusalem, Israel
| | - Esti Kramarsky-Winter
- Avram and Stella Goldstein-Goren, Department of Biotechnology Engineering, Ben-Gurion University of the Negev, Beer Sheva, Israel
| | - Oded Nir
- Zuckerberg Institute for Water Research (ZIWR), Blaustein Institutes for Desert Research, Ben-Gurion University of the Negev, Sde Boker, Israel
| | - Hala Abu-Ali
- Zuckerberg Institute for Water Research (ZIWR), Blaustein Institutes for Desert Research, Ben-Gurion University of the Negev, Sde Boker, Israel
| | - Zeev Ronen
- Zuckerberg Institute for Water Research (ZIWR), Blaustein Institutes for Desert Research, Ben-Gurion University of the Negev, Sde Boker, Israel
| | - Ehud Rinott
- Maccabi Healthcare Services, Tel-Aviv, Israel
| | - Yair E. Lewis
- Faculty of Medicine, Technion–Israel Institute of Technology, Haifa, Israel
| | - Eran Friedler
- Faculty of Civil and Environmental Engineering, Technion–Israel Institute of Technology, Haifa, Israel
| | - Eden Bitkover
- Department of Chemical Engineering, Technion–Israel Institute of Technology, Haifa, Israel
| | - Yossi Paitan
- Clinical Microbiology Laboratory, Meir Medical Center, Kfar Saba, Israel
| | - Yakir Berchenko
- Department of Industrial Engineering and Management, Ben-Gurion University of the Negev, Beer Sheva, Israel
| | - Ariel Kushmaro
- Avram and Stella Goldstein-Goren, Department of Biotechnology Engineering, Ben-Gurion University of the Negev, Beer Sheva, Israel
- The Ilse Katz Center for Meso and Nanoscale Science and Technology, Ben-Gurion University of the Negev, Beer Sheva, Israel
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Mondal S, Wintermantel WM, Gray SM. Virus and helper component interactions favour the transmission of recombinant potato virus Y strains. J Gen Virol 2021; 102. [PMID: 34161221 DOI: 10.1099/jgv.0.001620] [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] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
In recent years, several recombinant strains of potato virus Y, notably PVYNTN and PVYN:O have displaced the ordinary strain, PVYO, and emerged as the predominant strains affecting the USA potato crop. Previously we reported that recombinant strains were transmitted more efficiently than PVYO when they were acquired sequentially, regardless of acquisition order. In another recent study, we showed that PVYNTN binds preferentially to the aphid stylet over PVYO when aphids feed on a mixture of PVYO and PVYNTN. To understand the mechanism of this transmission bias as well as preferential virus binding, we separated virus and active helper component proteins (HC), mixed them in homologous and heterologous combinations, and then fed them to aphids using Parafilm sachets. Mixtures of PVYO HC with either PVYN:O or PVYNTN resulted in efficient transmission. PVYN:O HC also facilitated the transmission of PVYO and PVYNTN, albeit with reduced efficiency. PVYNTN HC failed to facilitate transmission of either PVYO or PVYN:O. When PVYO HC or PVYN:O HC was mixed with equal amounts of the two viruses, both viruses in all combinations were transmitted at high efficiencies. In contrast, no transmission occurred when combinations of viruses were mixed with PVYNTN HC. Further study evaluated transmission using serial dilutions of purified virus mixed with HCs. While PVYNTN HC only facilitated the transmission of the homologous virus, the HCs of PVYO and PVYN:O facilitated the transmission of all strains tested. This phenomenon has likely contributed to the increase in the recombinant strains affecting the USA potato crop.
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Affiliation(s)
- Shaonpius Mondal
- Plant Pathology and Plant-Microbe Biology Section, School of Integrative Plant Science, Cornell University, Ithaca, NY 14853-5904, USA
- Present address: USDA-ARS, Crop Improvement and Protection Research Unit, CA 93905, Salinas, USA
| | | | - Stewart M Gray
- Plant Pathology and Plant-Microbe Biology Section, School of Integrative Plant Science, Cornell University, Ithaca, NY 14853-5904, USA
- USDA-ARS, Emerging Pests and Pathogen Research Unit, Ithaca, NY 14853-5904, USA
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Möckel M, Corman VM, Stegemann MS, Hofmann J, Stein A, Jones TC, Gastmeier P, Seybold J, Offermann R, Bachmann U, Lindner T, Bauer W, Drosten C, Rosen A, Somasundaram R. SARS-CoV-2 antigen rapid immunoassay for diagnosis of COVID-19 in the emergency department. Biomarkers 2021; 26:213-220. [PMID: 33455451 PMCID: PMC7898296 DOI: 10.1080/1354750x.2021.1876769] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Background In the emergency department (ED) setting, rapid testing for SARS-CoV-2 is likely associated with advantages to patients and healthcare workers, for example, enabling early but rationale use of limited isolation resources. Most recently, several SARS-CoV-2 rapid point-of-care antigen tests (AGTEST) became available. There is a growing need for data regarding their clinical utility and performance in the diagnosis of SARS-CoV-2 infection in the real life setting EDs. Methods We implemented AGTEST (here: Roche/SD Biosensor) in all four adult and the one paediatric EDs at Charité – Universitätsmedizin Berlin in our diagnostic testing strategy. Test indication was limited to symptomatic suspected COVID-19 patients. Detailed written instructions on who to test were distributed and testing personnel were trained in proper specimen collection and handling. In each suspected COVID-19 patient, two sequential deep oro-nasopharyngeal swabs were obtained for viral tests. The first swab was collected for nucleic acid testing through SARS-CoV-2 real-time reverse transcriptase (rt)-PCR diagnostic panel (PCRTEST) in the central laboratory. The second swab was collected to perform the AGTEST. Analysis of routine data was prospectively planned and data were retrieved from the medical records after the inclusion period in the adult or paediatric ED. Diagnostic performance was calculated using the PCRTEST as reference standard. False negative and false positive AGTEST results were analysed individually and compared with viral concentrations derived from the calibrated PCRTEST. Results We included n = 483 patients including n = 202 from the paediatric ED. N = 10 patients had to be excluded due to missing data and finally n = 473 patients were analysed. In the adult cohort, the sensitivity of the AGTEST was 75.3 (95%CI: 65.8/83.4)% and the specificity was 100 (95%CI: 98.4/100)% with a SARS-CoV-2 prevalence of 32.8%; the positive predictive value was 100 (95%CI: 95.7/100)% and the negative predictive value 89.2 (95%CI: 84.5/93.9)%. In the paediatric cohort, the sensitivity was 72.0 (95%CI: 53.3/86.7)%, the specificity was 99.4 (95%CI:97.3/99.9)% with a prevalence of 12.4%; the positive predictive value was 94.7 (95%CI: 78.3/99.7)% and the negative predictive value was 96.2 (95%CI:92.7/98.3)%. Thus, n = 22 adult and n = 7 paediatric patients showed false negative AGTEST results and only one false positive AGTEST occurred, in the paediatric cohort. Calculated viral concentrations from the rt-PCR lay between 3.16 and 9.51 log10 RNA copies/mL buffer. All false negative patients in the adult ED cohort, who had confirmed symptom onset at least seven days earlier had less than 5 × 105 RNA copies/mL buffer. Conclusions We conclude that the use of AGTEST among symptomatic patients in the emergency setting is useful for the early identification of COVID-19, but patients who test negative require confirmation by PCRTEST and must stay isolated until this result becomes available. Adult patients with a false negative AGTEST and symptom onset at least one week earlier have typically a low SARS-CoV-2 RNA concentration and are likely no longer infectious.
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Affiliation(s)
- Martin Möckel
- Department of Emergency and Acute Medicine, Campus Mitte and Virchow, Charité - Universitätsmedizin Berlin, Berlin, Germany
| | - Victor M Corman
- Institute of Virology, Charité - Universitätsmedizin Berlin, Berlin, Germany.,German Centre for Infection Research (DZIF), Charité - Universitätsmedizin Berlin, Berlin, Germany
| | - Miriam S Stegemann
- Department of Infectious Diseases and Respiratory Medicine, Charité - Universitätsmedizin Berlin, Berlin, Germany
| | - Jörg Hofmann
- Institute of Virology, Charité - Universitätsmedizin Berlin, Berlin, Germany.,Labor Berlin - Charité Vivantes GmbH, Charité - Universitätsmedizin Berlin, Berlin, Germany
| | - Angela Stein
- Labor Berlin - Charité Vivantes GmbH, Charité - Universitätsmedizin Berlin, Berlin, Germany
| | - Terry C Jones
- Institute of Virology, Charité - Universitätsmedizin Berlin, Berlin, Germany
| | - Petra Gastmeier
- Institute for Hygiene and Environmental Medicine, Charité - Universitätsmedizin Berlin, Berlin, Germany
| | - Joachim Seybold
- Medical Directorate, Charité - Universitätsmedizin Berlin, Berlin, Germany
| | - Ralf Offermann
- Department of Emergency and Acute Medicine, Campus Mitte and Virchow, Charité - Universitätsmedizin Berlin, Berlin, Germany
| | - Ulrike Bachmann
- Department of Emergency and Acute Medicine, Campus Mitte and Virchow, Charité - Universitätsmedizin Berlin, Berlin, Germany
| | - Tobias Lindner
- Department of Emergency and Acute Medicine, Campus Mitte and Virchow, Charité - Universitätsmedizin Berlin, Berlin, Germany
| | - Wolfgang Bauer
- Department of Emergency and Acute Medicine, Campus Benjamin Franklin, Charité - Universitätsmedizin Berlin, Berlin, Germany
| | - Christian Drosten
- Institute of Virology, Charité - Universitätsmedizin Berlin, Berlin, Germany
| | - Alexander Rosen
- Department of Pediatrics, Division of Pulmonology Immunology and Critical Care Medicine, Charité - Universitätsmedizin Berlin, Berlin, Germany
| | - Rajan Somasundaram
- Department of Emergency and Acute Medicine, Campus Benjamin Franklin, Charité - Universitätsmedizin Berlin, Berlin, Germany
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11
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Dumke R, de la Cruz Barron M, Oertel R, Helm B, Kallies R, Berendonk TU, Dalpke A. Evaluation of Two Methods to Concentrate SARS-CoV-2 from Untreated Wastewater. Pathogens 2021; 10:pathogens10020195. [PMID: 33673032 PMCID: PMC7917696 DOI: 10.3390/pathogens10020195] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2020] [Revised: 02/08/2021] [Accepted: 02/09/2021] [Indexed: 12/18/2022] Open
Abstract
Use of wastewater-based epidemiology as a tool to record and manage the course of SARS-CoV-2 infections in human populations requires information about the efficiency of methods to concentrate the virus from wastewater. In the present study, we spiked untreated wastewater with quantified SARS-CoV-2 positive clinical material and enriched the virus by polyethylene glycol precipitation and ultrafiltration with Vivaspin 10 kDa MWCO columns. SARS-CoV-2 was detected and quantified by reverse transcription quantitative PCR (E- and S-gene) and droplet digital PCR. The concentration of virus with precipitation resulted in mean recoveries between 59.4% and 63.7% whereas rates from 33.0% to 42.6% after ultrafiltration of samples were demonstrated. The results suggest that the use of both methods allows an effective and practicable enrichment of SARS-CoV-2 from raw wastewater.
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Affiliation(s)
- Roger Dumke
- Institute of Medical Microbiology and Virology, Technische Universität Dresden, Fetscherstrasse 74, 01307 Dresden, Germany;
- Correspondence:
| | - Magali de la Cruz Barron
- Institute of Hydrobiology, Technische Universität Dresden, Helmholtzstrasse 10, 01069 Dresden, Germany; (M.d.l.C.B.); (T.U.B.)
- Department of River Ecology, Helmholtz Centre for Environmental Research—UFZ, Brückstrasse 3a, 39114 Magdeburg, Germany
| | - Reinhard Oertel
- Institute of Clinical Pharmacology, Technische Universität Dresden, Fetscherstrasse 74, 01307 Dresden, Germany;
| | - Björn Helm
- Institute of Urban and Industrial Water Management, Technische Universität Dresden, Helmholtzstrasse 10, 01069 Dresden, Germany;
| | - Rene Kallies
- Department of Environmental Microbiology, Helmholtz Centre for Environmental Research—UFZ, Permoserstrasse 15, 04318 Leipzig, Germany;
| | - Thomas U. Berendonk
- Institute of Hydrobiology, Technische Universität Dresden, Helmholtzstrasse 10, 01069 Dresden, Germany; (M.d.l.C.B.); (T.U.B.)
| | - Alexander Dalpke
- Institute of Medical Microbiology and Virology, Technische Universität Dresden, Fetscherstrasse 74, 01307 Dresden, Germany;
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12
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Bar-Or I, Yaniv K, Shagan M, Ozer E, Weil M, Indenbaum V, Elul M, Erster O, Mendelson E, Mannasse B, Shirazi R, Kramarsky-Winter E, Nir O, Abu-Ali H, Ronen Z, Rinott E, Lewis YE, Friedler E, Bitkover E, Paitan Y, Berchenko Y, Kushmaro A. Regressing SARS-CoV-2 Sewage Measurements Onto COVID-19 Burden in the Population: A Proof-of-Concept for Quantitative Environmental Surveillance. Front Public Health 2021. [PMID: 35047467 DOI: 10.1101/2020.04.26.20073569] [Citation(s) in RCA: 50] [Impact Index Per Article: 16.7] [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: 05/11/2023] Open
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is an RNA virus, a member of the coronavirus family of respiratory viruses that includes severe acute respiratory syndrome coronavirus 1 (SARS-CoV-1) and the Middle East respiratory syndrome (MERS). It has had an acute and dramatic impact on health care systems, economies, and societies of affected countries during the past 8 months. Widespread testing and tracing efforts are being employed in many countries in attempts to contain and mitigate this pandemic. Recent data has indicated that fecal shedding of SARS-CoV-2 is common and that the virus RNA can be detected in wastewater. This indicates that wastewater monitoring may provide a potentially efficient tool for the epidemiological surveillance of SARS-CoV-2 infection in large populations at relevant scales. In particular, this provides important means of (i) estimating the extent of outbreaks and their spatial distributions, based primarily on in-sewer measurements, (ii) managing the early-warning system quantitatively and efficiently, and (iii) verifying disease elimination. Here we report different virus concentration methods using polyethylene glycol (PEG), alum, or filtration techniques as well as different RNA extraction methodologies, providing important insights regarding the detection of SARS-CoV-2 RNA in sewage. Virus RNA particles were detected in wastewater in several geographic locations in Israel. In addition, a correlation of virus RNA concentration to morbidity was detected in Bnei-Barak city during April 2020. This study presents a proof of concept for the use of direct raw sewage-associated virus data, during the pandemic in the country as a potential epidemiological tool.
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Affiliation(s)
- Itay Bar-Or
- Central Virology Lab, Ministry of Health, Sheba Medical Center, Jerusalem, Israel
| | - Karin Yaniv
- Avram and Stella Goldstein-Goren, Department of Biotechnology Engineering, Ben-Gurion University of the Negev, Beer Sheva, Israel
| | - Marilou Shagan
- Avram and Stella Goldstein-Goren, Department of Biotechnology Engineering, Ben-Gurion University of the Negev, Beer Sheva, Israel
| | - Eden Ozer
- Department of Life Sciences, Ben-Gurion University of the Negev, Beer Sheva, Israel
| | - Merav Weil
- Central Virology Lab, Ministry of Health, Sheba Medical Center, Jerusalem, Israel
| | - Victoria Indenbaum
- Central Virology Lab, Ministry of Health, Sheba Medical Center, Jerusalem, Israel
| | - Michal Elul
- Central Virology Lab, Ministry of Health, Sheba Medical Center, Jerusalem, Israel
| | - Oran Erster
- Central Virology Lab, Ministry of Health, Sheba Medical Center, Jerusalem, Israel
| | - Ella Mendelson
- Central Virology Lab, Ministry of Health, Sheba Medical Center, Jerusalem, Israel
- School of Public Health, Sackler Faculty of Medicine, Tel-Aviv University, Tel Aviv, Israel
| | - Batya Mannasse
- Central Virology Lab, Ministry of Health, Sheba Medical Center, Jerusalem, Israel
| | - Rachel Shirazi
- Central Virology Lab, Ministry of Health, Sheba Medical Center, Jerusalem, Israel
| | - Esti Kramarsky-Winter
- Avram and Stella Goldstein-Goren, Department of Biotechnology Engineering, Ben-Gurion University of the Negev, Beer Sheva, Israel
| | - Oded Nir
- Zuckerberg Institute for Water Research (ZIWR), Blaustein Institutes for Desert Research, Ben-Gurion University of the Negev, Sde Boker, Israel
| | - Hala Abu-Ali
- Zuckerberg Institute for Water Research (ZIWR), Blaustein Institutes for Desert Research, Ben-Gurion University of the Negev, Sde Boker, Israel
| | - Zeev Ronen
- Zuckerberg Institute for Water Research (ZIWR), Blaustein Institutes for Desert Research, Ben-Gurion University of the Negev, Sde Boker, Israel
| | - Ehud Rinott
- Maccabi Healthcare Services, Tel-Aviv, Israel
| | - Yair E Lewis
- Faculty of Medicine, Technion-Israel Institute of Technology, Haifa, Israel
| | - Eran Friedler
- Faculty of Civil and Environmental Engineering, Technion-Israel Institute of Technology, Haifa, Israel
| | - Eden Bitkover
- Department of Chemical Engineering, Technion-Israel Institute of Technology, Haifa, Israel
| | - Yossi Paitan
- Clinical Microbiology Laboratory, Meir Medical Center, Kfar Saba, Israel
| | - Yakir Berchenko
- Department of Industrial Engineering and Management, Ben-Gurion University of the Negev, Beer Sheva, Israel
| | - Ariel Kushmaro
- Avram and Stella Goldstein-Goren, Department of Biotechnology Engineering, Ben-Gurion University of the Negev, Beer Sheva, Israel
- The Ilse Katz Center for Meso and Nanoscale Science and Technology, Ben-Gurion University of the Negev, Beer Sheva, Israel
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13
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Bar-Or I, Yaniv K, Shagan M, Ozer E, Weil M, Indenbaum V, Elul M, Erster O, Mendelson E, Mannasse B, Shirazi R, Kramarsky-Winter E, Nir O, Abu-Ali H, Ronen Z, Rinott E, Lewis YE, Friedler E, Bitkover E, Paitan Y, Berchenko Y, Kushmaro A. Regressing SARS-CoV-2 Sewage Measurements Onto COVID-19 Burden in the Population: A Proof-of-Concept for Quantitative Environmental Surveillance. Front Public Health 2021. [PMID: 35047467 DOI: 10.1101/2020.04.26.20073569v1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/22/2023] Open
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is an RNA virus, a member of the coronavirus family of respiratory viruses that includes severe acute respiratory syndrome coronavirus 1 (SARS-CoV-1) and the Middle East respiratory syndrome (MERS). It has had an acute and dramatic impact on health care systems, economies, and societies of affected countries during the past 8 months. Widespread testing and tracing efforts are being employed in many countries in attempts to contain and mitigate this pandemic. Recent data has indicated that fecal shedding of SARS-CoV-2 is common and that the virus RNA can be detected in wastewater. This indicates that wastewater monitoring may provide a potentially efficient tool for the epidemiological surveillance of SARS-CoV-2 infection in large populations at relevant scales. In particular, this provides important means of (i) estimating the extent of outbreaks and their spatial distributions, based primarily on in-sewer measurements, (ii) managing the early-warning system quantitatively and efficiently, and (iii) verifying disease elimination. Here we report different virus concentration methods using polyethylene glycol (PEG), alum, or filtration techniques as well as different RNA extraction methodologies, providing important insights regarding the detection of SARS-CoV-2 RNA in sewage. Virus RNA particles were detected in wastewater in several geographic locations in Israel. In addition, a correlation of virus RNA concentration to morbidity was detected in Bnei-Barak city during April 2020. This study presents a proof of concept for the use of direct raw sewage-associated virus data, during the pandemic in the country as a potential epidemiological tool.
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Affiliation(s)
- Itay Bar-Or
- Central Virology Lab, Ministry of Health, Sheba Medical Center, Jerusalem, Israel
| | - Karin Yaniv
- Avram and Stella Goldstein-Goren, Department of Biotechnology Engineering, Ben-Gurion University of the Negev, Beer Sheva, Israel
| | - Marilou Shagan
- Avram and Stella Goldstein-Goren, Department of Biotechnology Engineering, Ben-Gurion University of the Negev, Beer Sheva, Israel
| | - Eden Ozer
- Department of Life Sciences, Ben-Gurion University of the Negev, Beer Sheva, Israel
| | - Merav Weil
- Central Virology Lab, Ministry of Health, Sheba Medical Center, Jerusalem, Israel
| | - Victoria Indenbaum
- Central Virology Lab, Ministry of Health, Sheba Medical Center, Jerusalem, Israel
| | - Michal Elul
- Central Virology Lab, Ministry of Health, Sheba Medical Center, Jerusalem, Israel
| | - Oran Erster
- Central Virology Lab, Ministry of Health, Sheba Medical Center, Jerusalem, Israel
| | - Ella Mendelson
- Central Virology Lab, Ministry of Health, Sheba Medical Center, Jerusalem, Israel
- School of Public Health, Sackler Faculty of Medicine, Tel-Aviv University, Tel Aviv, Israel
| | - Batya Mannasse
- Central Virology Lab, Ministry of Health, Sheba Medical Center, Jerusalem, Israel
| | - Rachel Shirazi
- Central Virology Lab, Ministry of Health, Sheba Medical Center, Jerusalem, Israel
| | - Esti Kramarsky-Winter
- Avram and Stella Goldstein-Goren, Department of Biotechnology Engineering, Ben-Gurion University of the Negev, Beer Sheva, Israel
| | - Oded Nir
- Zuckerberg Institute for Water Research (ZIWR), Blaustein Institutes for Desert Research, Ben-Gurion University of the Negev, Sde Boker, Israel
| | - Hala Abu-Ali
- Zuckerberg Institute for Water Research (ZIWR), Blaustein Institutes for Desert Research, Ben-Gurion University of the Negev, Sde Boker, Israel
| | - Zeev Ronen
- Zuckerberg Institute for Water Research (ZIWR), Blaustein Institutes for Desert Research, Ben-Gurion University of the Negev, Sde Boker, Israel
| | - Ehud Rinott
- Maccabi Healthcare Services, Tel-Aviv, Israel
| | - Yair E Lewis
- Faculty of Medicine, Technion-Israel Institute of Technology, Haifa, Israel
| | - Eran Friedler
- Faculty of Civil and Environmental Engineering, Technion-Israel Institute of Technology, Haifa, Israel
| | - Eden Bitkover
- Department of Chemical Engineering, Technion-Israel Institute of Technology, Haifa, Israel
| | - Yossi Paitan
- Clinical Microbiology Laboratory, Meir Medical Center, Kfar Saba, Israel
| | - Yakir Berchenko
- Department of Industrial Engineering and Management, Ben-Gurion University of the Negev, Beer Sheva, Israel
| | - Ariel Kushmaro
- Avram and Stella Goldstein-Goren, Department of Biotechnology Engineering, Ben-Gurion University of the Negev, Beer Sheva, Israel
- The Ilse Katz Center for Meso and Nanoscale Science and Technology, Ben-Gurion University of the Negev, Beer Sheva, Israel
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14
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Abstract
Nearly all lethal viral outbreaks in the past two decades were caused by newly emerging viruses. Viruses are often studied by electron microscopy (EM), which provides new high-resolution data on the structure of viral particles relevant to both fundamental virology and practical pharmaceutical nanobiotechnology. Electron microscopy is also applied to ecological studies to detect viruses in the environment, to analysis of technological processes in the production of vaccines and other biotechnological components, and to diagnostics. Despite the advances in more sensitive methods, electron microscopy is still in active use for diagnostics. The main advantage of EM is the lack of specificity to any group of viruses, which allows working with unknown materials. However, the main limitation of the method is the relatively high detection limit (107 particles/mL), requiring viral material to be concentrated. There is no most effective universal method to concentrate viruses. Various combinations of methods and approaches are used depending on the virus and the goal. A modern virus concentration protocol involves precipitation, centrifugation, filtration, and chromatography. Here we describe the main concentrating techniques exemplified for different viruses. Effective elution techniques are required to disrupt the bonds between filter media and viruses in order to increase recovery. The paper reviews studies on unique traps, magnetic beads, and composite polyaniline and carbon nanotubes, including those of changeable size to concentrate viral particles. It also describes centrifugal concentrators to concentrate viruses on a polyethersulfone membrane. Our review suggests that the method to concentrate viruses and other nanoparticles should be chosen with regard to objectives of the study and the equipment status of the laboratory.
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Affiliation(s)
- I D Petrova
- State Research Center of Virology and Biotechnology "Vector", Rospotrebnadzor, Koltsovo, Novosibirsk region, Russia
| | - B N Zaitsev
- State Research Center of Virology and Biotechnology "Vector", Rospotrebnadzor, Koltsovo, Novosibirsk region, Russia
| | - O S Taranov
- State Research Center of Virology and Biotechnology "Vector", Rospotrebnadzor, Koltsovo, Novosibirsk region, Russia
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15
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Abstract
We recently demonstrated how various enveloped viruses can be efficiently concentrated using magnetic beads coated with an anionic polymer, poly(methyl vinyl ether-maleic anhydrate). However, the exact mechanism of interaction between the virus particles and anionic beads remains unclear. To further investigate whether these magnetic anionic beads specifically bind to the viral envelope, we examined their potential interaction with a nonenveloped virus (adenovirus). The beads were incubated with either adenovirus-infected cell culture medium or nasal aspirates from adenovirus-infected individuals and then separated from the supernatant by applying a magnetic field. After thoroughly washing the beads, adsorption of adenovirus was confirmed by a variety of techniques, including immunochromatography, polymerase chain reaction, Western blotting, and cell culture infection assays. These detection methods positively identified the hexon and penton capsid proteins of adenovirus along with the viral genome on the magnetic beads. Furthermore, various types of adenovirus including Types 5, 6, 11, 19, and 41 were captured using the magnetic bead procedure. Our bead capture method was also found to increase the sensitivity of viral detection. Adenovirus below the detectable limit for immunochromatography was efficiently concentrated using the magnetic bead procedure, allowing the virus to be successfully detected using this methodology. Moreover, these findings clearly demonstrate that a viral envelope is not required for binding to the anionic magnetic beads. Taken together, our results show that this capture procedure increases the sensitivity of detection of adenovirus and would, therefore, be a valuable tool for analyzing both clinical and experimental samples.
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Affiliation(s)
- Akikazu Sakudo
- Department of Virology, Research Institute for Microbial Diseases, Osaka University, Yamadaoka, Suita, Osaka, Japan
| | | | - Kazuyoshi Ikuta
- Department of Virology, Research Institute for Microbial Diseases, Osaka University, Yamadaoka, Suita, Osaka, Japan; Kanonji Institute, The Research Foundation for Microbial Diseases of Osaka University, Kanonji, Kagawa, Japan
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16
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Poma HR, Rajal VB, Blanco Fernández MD, Barril PA, Giordano MO, Masachessi G, Martínez LC, Isa MB, Freire MC, López Riviello G, Cisterna D, Nates SV, Mbayed VA. Evaluation of concentration efficiency of the Pseudomonas aeruginosa phage PP7 in various water matrixes by different methods. Environ Monit Assess 2013; 185:2565-76. [PMID: 22763654 PMCID: PMC5705224 DOI: 10.1007/s10661-012-2731-9] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [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: 01/27/2012] [Accepted: 06/11/2012] [Indexed: 05/17/2023]
Abstract
Enteric viruses monitoring in surface waters requires the concentration of viruses before detection assays. The aim of this study was to evaluate different methods in terms of recovery efficiencies of bacteriophage PP7 of Pseudomonas aeruginosa, measured by real-time PCR, using it as a viral control process in water analysis. Different nucleic acid extraction methods (silica-guanidinium thiocyanate, a commercial kit (Qiagen Viral RNA Kit) and phenol-chloroform with alcohol precipitation) exhibited very low recovery efficiencies (0.08-4.18 %), being the most efficient the commercial kit used for subsequent experiments. To evaluate the efficiency of three concentration methods, PBS (as model for clean water) and water samples from rivers were seeded to reach high (HC, 10(6) pfu ml(-1)) and low concentrations (LC, 10(4) pfu ml(-1)) of PP7. Tangential ultrafiltration proved to be more efficient (50.36 ± 12.91, 17.21 ± 9.22 and 12.58 ± 2.35 % for HC in PBS and two river samples, respectively) than adsorption-elution with negatively charged membranes (1.00 ± 1.34, 2.79 ± 2.62 and 0.05 ± 0.08 % for HC in PBS and two river samples, respectively) and polyethylene glycol precipitation (15.95 ± 7.43, 4.01 ± 1.12 and 3.91 ± 0.54 %, for HC in PBS and two river samples, respectively), being 3.2-50.4 times more efficient than the others for PBS and 2.7-252 times for river samples. Efficiencies also depended on the initial virus concentration and aqueous matrixes composition. In consequence, the incorporation of an internal standard like PP7 along the process is useful as a control of the water concentration procedure, the nucleic acid extraction, the presence of inhibitors and the variability of the recovery among replicas, and for the calculation of the sample limit of detection. Thus, the use of a process control, as presented here, is crucial for the accurate quantification of viral contamination.
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Affiliation(s)
- Hugo Ramiro Poma
- INIQUI-CONICET, Universidad Nacional de Salta, Av. Bolivia 5150, Salta, 4400, Argentina
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17
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Abstract
The abilities of hybridization probes to detect all human adenovirus types and to identify enteric adenovirus types were evaluated. The efficiency of hybridization was compared to other tests currently in routine laboratory use on clinical specimens from young children with gastroenteritis. Probes were derived from various regions of the adenovirus types 2 and 41 genomes, and were evaluated by hybridization with a series of DNA quantities from 1 microgram to 10 pg of one adenovirus type from each human subgenus, lambda phage, and HEp 2 cells. The sensitivity of hybridization with the HPII probe (92.7%), containing the conserved hexon gene, compared well with EM (54.6%), culture and neutralization (45.5%), and enzyme immunoassay (61.8%). The sensitivity of detection of enteric adenovirus isolates by the cloned Bg/II D fragment probe (92.9%) and by a synthetic probe (85.7%), manufactured from type-specific sequences of the Ad41 hexon gene were comparable to Ad40/Ad41 specific enzyme immunoassay (84.6%). Hybridization was found to be a sensitive method of adenovirus detection in comparison to traditional methods of laboratory diagnosis. Synthetic oligonucleotides enable specific detection of individual enteric adenovirus types. Hybridization had additional advantages over other tests in identifying cases of infection with more than one adenovirus type and in allowing an estimate of the concentration of adenovirus in the specimen.
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Affiliation(s)
- T H Scott-Taylor
- Cadham Provincial Laboratory, University of Manitoba, Winnipeg, Canada
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