The Experts below are selected from a list of 49908 Experts worldwide ranked by ideXlab platform
Zeynep Cetecioglu - One of the best experts on this subject based on the ideXlab platform.
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benchmarking Virus Concentration methods for quantification of sars cov 2 in raw wastewater
Science of The Total Environment, 2021Co-Authors: Mohammed Hakim Jafferali, Kasra Khatami, Merve Atasoy, Madeleine Birgersson, Cecilia Williams, Zeynep CeteciogluAbstract:Wastewater-based epidemiology offers a cost-effective alternative to testing large populations for SARS-CoV-2 Virus, and may potentially be used as an early warning system for SARS-CoV-2 pandemic spread. However, Viruses are highly diluted in wastewater, and a validated method for their Concentration and further processing, and suitable reference Viruses, are the main needs to be established for reliable SARS-CoV-2 municipal wastewater detection. For this purpose, we collected wastewater from two European cities during the Covid-19 pandemic and evaluated the sensitivity of RT-qPCR detection of viral RNA after four Concentration methods (two variants of ultrafiltration-based method and two adsorption and extraction-based methods). Further, we evaluated one external (bovine corona Virus) and one internal (pepper mild mottle Virus) reference Virus. We found a consistently higher recovery of spiked Virus using the modified ultrafiltration-based method. This method also had a significantly higher efficiency (p-value <0.01) for wastewater SARS-CoV-2 detection. The ultracentrifugation method was the only method that detected SARS-CoV-2 in the wastewater of both cities. The pepper mild mottle Virus was found to function as a potentially suitable internal reference standard.
Mohammed Hakim Jafferali - One of the best experts on this subject based on the ideXlab platform.
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benchmarking Virus Concentration methods for quantification of sars cov 2 in raw wastewater
Science of The Total Environment, 2021Co-Authors: Mohammed Hakim Jafferali, Kasra Khatami, Merve Atasoy, Madeleine Birgersson, Cecilia Williams, Zeynep CeteciogluAbstract:Wastewater-based epidemiology offers a cost-effective alternative to testing large populations for SARS-CoV-2 Virus, and may potentially be used as an early warning system for SARS-CoV-2 pandemic spread. However, Viruses are highly diluted in wastewater, and a validated method for their Concentration and further processing, and suitable reference Viruses, are the main needs to be established for reliable SARS-CoV-2 municipal wastewater detection. For this purpose, we collected wastewater from two European cities during the Covid-19 pandemic and evaluated the sensitivity of RT-qPCR detection of viral RNA after four Concentration methods (two variants of ultrafiltration-based method and two adsorption and extraction-based methods). Further, we evaluated one external (bovine corona Virus) and one internal (pepper mild mottle Virus) reference Virus. We found a consistently higher recovery of spiked Virus using the modified ultrafiltration-based method. This method also had a significantly higher efficiency (p-value <0.01) for wastewater SARS-CoV-2 detection. The ultracentrifugation method was the only method that detected SARS-CoV-2 in the wastewater of both cities. The pepper mild mottle Virus was found to function as a potentially suitable internal reference standard.
Hiroyuki Katayama - One of the best experts on this subject based on the ideXlab platform.
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Concentration of Enteric Viruses in Large Volumes of Water Using a Cartridge-Type Mixed Cellulose Ester Membrane
Food and Environmental Virology, 2015Co-Authors: Akihiko Hata, Katsuhito Matsumori, Masaaki Kitajima, Hiroyuki KatayamaAbstract:A viral adsorption–elution method using a flat/disk-type electronegative membrane (diameter of 47–90 mm) has been widely utilized to concentrate Viruses in relatively small volumes of water (up to 10 L) due to limited filtration area. In the present study, we aimed to develop a Virus Concentration method that is based on the same principle and yet allows Concentration of large volumes of water using a cartridge-type electronegative membrane. We modified two electronegative membrane-based methods for this purpose (i.e., Mg^2+ method and Al^3+ method) and determined recovery efficiencies of polioVirus and murine noroVirus inoculated in water samples. The Virus recovery efficiency of the Al^3+ method substantially decreased as the volume of water sample increased. In contrast, Mg^2+ method showed stable Virus recovery efficiencies (10–54 %) even when 40 to 1,000 L of river and tap water samples were processed. The volume of the concentrate (400 mL) can be further reduced to 1.5 mL by a Centricon plus-70 centrifugal ultrafiltration device with overall recovery efficiencies of 8.8–16 %. Our results demonstrated that the newly developed Virus Concentration method enables detection of as low as 10^1 copies/L of Viruses in water samples.
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Application of Acidic Elution to Virus Concentration Using Electropositive Filters
Food and environmental virology, 2012Co-Authors: Eiji Haramoto, Hiroyuki KatayamaAbstract:The effect of the type and pH of an elution solution on the recovery of polioVirus from water by a Virus Concentration method using an electropositive filter was evaluated. The experimental results obtained indicated the potential usefulness of H2SO4 (pH 1.5–3.5) as a novel solution for Virus elution.
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Recovery of human noroVirus from water by Virus Concentration methods.
Journal of virological methods, 2009Co-Authors: Eiji Haramoto, Hiroyuki Katayama, Etsuko Utagawa, Shinichiro OhgakiAbstract:The aim of this study was to evaluate the applicability of Virus Concentration methods to detect human noroVirus (HuNoV) in water. One conventional Virus Concentration method using an electropositive filter (1MDS-method) and two methods developed by our research group using an electronegative filter (Mg-method and Al-method) were subjected to recovery tests of the HuNoV strain GII.4, which was obtained from a diarrhea patient, and polioVirus (PV) type 1 inoculated into 5 kinds of water samples. The mean recovery yields of HuNoV by the Mg-method, determined by real-time PCR, were 186%, 80%, 167%, 15%, and 39% for MilliQ water, tap water, bottled water, river water, and pond water, respectively (n=2 each), which were generally comparable to those of PV. A similar trend was observed for the Al-method (n=8 in total), suggesting that both Mg- and Al-methods can be appropriate for concentrating HuNoVs from water samples. Unlike these two methods, no clear correlation was found between the recovery of HuNoV and PV by the 1MDS-method (n=6 in total). This study is significant because it provides observations on the use of Virus Concentration methods for the detection of uncultivable HuNoV in water samples.
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Recovery of naked viral genomes in water by Virus Concentration methods.
Journal of Virological Methods, 2007Co-Authors: Eiji Haramoto, Hiroyuki Katayama, Kumiko Oguma, Shinichiro OhgakiAbstract:Abstract The recovery efficiency of naked polioVirus-RNA in water using Virus Concentration methods was determined to evaluate the possibility of detecting naked viral genomes. Two conventional Virus Concentration methods (1MDS-method and HA-method) and two methods developed by our research group (Mg-method and Al-method) were applied to recovery tests of polioVirus-RNA from four kinds of water sample, in parallel with recovery tests of polioVirus-virions. Mean recovery yields of polioVirus-RNA by the Mg-method were 5.7, 12, 3.4, and 17% for MilliQ water, tap water, secondary-treated sewage, and seawater, respectively. Meanwhile, mean recovery yields of polioVirus-virions by the Mg-method were 6.6–14.7 times higher than those of the RNA. Using the Al-method, polioVirus-RNA in MilliQ water and tap water was recovered at a higher recovery yield as compared to the Mg-method (69% from MilliQ water and 26% from tap water on average) in addition to the virions. The 1MDS-method and the HA-method did not provide as high recovery yields of the virions as the Mg-method. From these results, the Mg-method was judged most appropriate for selective detection of virions instead of naked viral genomes in water among the four methods tested.
Leera Kittigul - One of the best experts on this subject based on the ideXlab platform.
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A comparison of Virus Concentration methods for molecular detection and characterization of rotaVirus in bivalve shellfish species
Food microbiology, 2014Co-Authors: Leera Kittigul, Yutatirat Singhaboot, Porntip Chavalitshewinkoon-petmitr, Kannika Pombubpa, Chakrit HirunpetcharatAbstract:The objectives of this study were to develop a method for concentrating rotaVirus, to assess the detection rate, and to characterize the genotype of naturally occurring rotaVirus in bivalve shellfish species; including oysters (Saccostrea forskali), cockles (Anadara nodifera), and mussels (Perna viridis). The results demonstrated that an adsorption-twice elution-extraction method was less-time consuming method of concentrating the spiked rotaVirus, yielding high sensitivity of 1.14 genome copies/g of digestive tissues from all three shellfish species, as detected using an RT-nested PCR. In seeding experiments, rotaVirus as low as 1.39 genome copies was able to be detected in 4 g of digestive tissues or per sample. In the period of August 2011 to July 2012, of the 300 bivalve shellfish samples collected and tested, 24 (8.0%) were found to be contaminated with rotaVirus, the figures being: oysters, 13/100 samples; mussels, 10/100 samples; and cockles, 1/100 samples. By DNA sequencing of the RT-nested PCR products and phylogenetic analysis, the rotaViruses detected were classified into G1, lineage II (4 samples); G3 (10 samples): lineage I (3 samples), lineage IIIc (3 samples), lineage IIId (3 samples), lineage IV (1 sample); G9 (6 samples); and G12, lineage III (1 sample). These findings suggest that this Virus Concentration method provides high sensitivity for the detection of rotaVirus from the three bivalve shellfish species. The prevalence of rotaVirus and the identified genotypes contribute to the molecular epidemiology of rotaVirus in different shellfish species.
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An efficient Virus Concentration method and RT-nested PCR for detection of rotaViruses in environmental water samples.
Journal of virological methods, 2004Co-Authors: Leera Kittigul, Som Ekchaloemkiet, Fuangfa Utrarachkij, Kanokrat Siripanichgon, Dusit Sujirarat, Supornvit Pungchitton, Augsana BoonthumAbstract:Water samples were concentrated by the modified adsorption-elution technique followed by speedVac reConcentration of the filter eluates. Reverse transcriptase-nested polymerase chain reaction (RT-nested PCR) was used to detect rotaVirus RNA in concentrates of the water. The detection limit of the rotaVirus determined by RT-nested PCR alone was about 1.67 plaque forming units (PFU) per RT-PCR assay and that by RT-nested PCR combined with Concentration from 1l seeded tap water sample was 1.46 plaque forming units per assay. Water samples were collected from various sources, concentrated, and determined rotaVirus RNA. Of 120 water samples, rotaVirus RNA was detected in 20 samples (16.7%); 2/10 (20%) of the river samples, 8/30 (26.7%) of the canal samples, and 10/40 (25%) of the sewage samples but was not found in any tap water samples (0/40). Only three water samples were positive for rotaVirus antigen determined using an enzyme-linked immunosorbent assay (ELISA). Alignment analysis of the sequenced PCR product (346-bp fragment) was performed in eight rotaVirus-positive samples using the rotaVirus sequence deposited in the GenBank. All samples gave the correct VP7 sequence. Results of analysis showed two samples similar to human rotaVirus (97-98%), five similar to rotaVirus G9 sequence (94-99%), and one sample similar to animal rotaVirus (97%). PCR inhibitors were not observed in any concentrated water samples. In all 20 (of 120) samples where rotaViruses were found, fecal coliforms including Escherichia coli were also found, but of the samples testing negative for rotaViruses, 76 were fecal coliforms positive and 69 were E. coli positive. The combination of the Virus Concentration method and RT-nested PCR described below made it possible to effectively detect rotaViruses in environmental water samples.
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An efficient Virus Concentration method and RT-nested PCR for detection of rotaViruses in environmental water samples.
Journal of Virological Methods, 2004Co-Authors: Leera Kittigul, Som Ekchaloemkiet, Fuangfa Utrarachkij, Kanokrat Siripanichgon, Dusit Sujirarat, Supornvit Pungchitton, Augsana BoonthumAbstract:Water samples were concentrated by the modified adsorption–elution technique followed by speedVac reConcentration of the filter eluates. Reverse transcriptase-nested polymerase chain reaction (RT-nested PCR) was used to detect rotaVirus RNA in concentrates of the water. The detection limit of the rotaVirus determined by RT-nested PCR alone was about 1.67 plaque forming units (PFU) per RT-PCR assay and that by RT-nested PCR combined with Concentration from 1 l seeded tap water sample was 1.46 plaque forming units per assay. Water samples were collected from various sources, concentrated, and determined rotaVirus RNA. Of 120 water samples, rotaVirus RNA was detected in 20 samples (16.7%); 2/10 (20%) of the river samples, 8/30 (26.7%) of the canal samples, and 10/40 (25%) of the sewage samples but was not found in any tap water samples (0/40). Only three water samples were positive for rotaVirus antigen determined using an enzyme-linked immunosorbent assay (ELISA). Alignment analysis of the sequenced PCR product (346-bp fragment) was performed in eight rotaVirus-positive samples using the rotaVirus sequence deposited in the GenBank. All samples gave the correct VP7 sequence. Results of analysis showed two samples similar to human rotaVirus (97–98%), five similar to rotaVirus G9 sequence (94–99%), and one sample similar to animal rotaVirus (97%). PCR inhibitors were not observed in any concentrated water samples. In all 20 (of 120) samples where rotaViruses were found, fecal coliforms including Escherichia coli were also found, but of the samples testing negative for rotaViruses, 76 were fecal coliforms positive and 69 were E. coli positive. The combination of the Virus Concentration method and RT-nested PCR described below made it possible to effectively detect rotaViruses in environmental water samples. © 2004 Elsevier B.V. All rights reserved.
Cecilia Williams - One of the best experts on this subject based on the ideXlab platform.
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benchmarking Virus Concentration methods for quantification of sars cov 2 in raw wastewater
Science of The Total Environment, 2021Co-Authors: Mohammed Hakim Jafferali, Kasra Khatami, Merve Atasoy, Madeleine Birgersson, Cecilia Williams, Zeynep CeteciogluAbstract:Wastewater-based epidemiology offers a cost-effective alternative to testing large populations for SARS-CoV-2 Virus, and may potentially be used as an early warning system for SARS-CoV-2 pandemic spread. However, Viruses are highly diluted in wastewater, and a validated method for their Concentration and further processing, and suitable reference Viruses, are the main needs to be established for reliable SARS-CoV-2 municipal wastewater detection. For this purpose, we collected wastewater from two European cities during the Covid-19 pandemic and evaluated the sensitivity of RT-qPCR detection of viral RNA after four Concentration methods (two variants of ultrafiltration-based method and two adsorption and extraction-based methods). Further, we evaluated one external (bovine corona Virus) and one internal (pepper mild mottle Virus) reference Virus. We found a consistently higher recovery of spiked Virus using the modified ultrafiltration-based method. This method also had a significantly higher efficiency (p-value <0.01) for wastewater SARS-CoV-2 detection. The ultracentrifugation method was the only method that detected SARS-CoV-2 in the wastewater of both cities. The pepper mild mottle Virus was found to function as a potentially suitable internal reference standard.
