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Stoppel SM, Lunestad BT, Myrmel M. The effect of enzymatic and viability dye treatment in combination with long-range PCR on assessing Tulane virus infectivity. J Virol Methods 2024; 327:114919. [PMID: 38531509 DOI: 10.1016/j.jviromet.2024.114919] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2023] [Revised: 03/22/2024] [Accepted: 03/23/2024] [Indexed: 03/28/2024]
Abstract
Human norovirus (HuNoV) is regularly involved in food-borne infections. To detect infectious HuNoV in food, RT-qPCR remains state of the art but also amplifies non-infectious virus. The present study combines pre-treatments, RNase and propidium monoazide, with three molecular analyses, including long-range PCR, to predominantly detect infectious Tulane virus (TuV), a culturable HuNoV surrogate. TuV was exposed to inactivating conditions to assess which molecular method most closely approximates the reduction in infectious virus determined by cell culture (TCID50). After thermal treatments (56 °C/5 min, 70 °C/5 min, 72 °C/20 min), TCID50 reductions of 0.3, 4.4 and 5.9 log10 were observed. UV exposure (40/100/1000 mJ/cm2) resulted in 1.1, 2.5 and 5.9 log10 reductions. Chlorine (45/100 mg/L for 1 h) reduced infectious TuV by 2.0 and 3.0 log10. After thermal inactivation standard RT-qPCR, especially with pre-treatments, showed the smallest deviation from TCID50. On average, RT-qPCR with pre-treatments deviated by 1.1-1.3 log10 from TCID50. For UV light, long-range PCR was closest to TCID50 results. Long-range reductions deviated from TCID50 by ≤0.1 log10 for mild and medium UV-conditions. However, long-range analyses often resulted in qPCR non-detects. At higher UV doses, RT-qPCR with pre-treatments differed by ≤1.0 log10 from TCID50. After chlorination the molecular methods repeatedly deviated from TCID50 by >1.0 log10, Overall, each method needs to be further optimized for the individual types of inactivation treatment.
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Affiliation(s)
- Sarah M Stoppel
- Institute of Marine Research, Section for Seafood Hazards, Nordnesgaten 50, Bergen 5005, Norway.
| | - Bjørn Tore Lunestad
- Institute of Marine Research, Section for Seafood Hazards, Nordnesgaten 50, Bergen 5005, Norway
| | - Mette Myrmel
- Norwegian University of Life Sciences, Faculty of Veterinary Medicine, Elizabeth Stephansens vei 15, Ås 1430, Norway
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Hou S, Zhao T, Yang D, Li Q, Liang L, Wang G, Ma Q. Selection and Validation of Reference Genes for Quantitative RT-PCR Analysis in Corylus heterophylla Fisch. × Corylus avellana L. PLANTS 2021; 10:plants10010159. [PMID: 33467497 PMCID: PMC7830083 DOI: 10.3390/plants10010159] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/08/2020] [Revised: 01/07/2021] [Accepted: 01/08/2021] [Indexed: 11/16/2022]
Abstract
(1) Background: the species of Corylus have sporophytic type of self-incompatibility. Several genes related to recognition reaction between pollen and stigma have been identified in hazelnuts. To better understand the self-incompatibility (SI) response, we screened the suitable reference genes by using quantitative real-time reverse transcription PCR (qRT-PCR) analysis in hazelnut for the first time. (2) Methods: the major cultivar "Dawei" was used as material. A total of 12 candidate genes were identified and their expression profiles were compared among different tissues and in response to various treatments (different times after self- and cross-pollination) by RT-qPCR. The expression stability of these 12 candidate reference genes was evaluated using geNorm, NormFinder, BestKeeper, Delta Ct, and RefFinder programs. (3) Results: the comprehensive ranking of RefFinder indicated that ChaActin, VvActin,
ChaUBQ14, and ChaEF1-α were the most suitable reference genes. According to the stability analysis of 12 candidate reference genes for each sample group based on four software packages, ChaActin and ChaEF1-α were most stable in different times after self-pollination and 4 h after self- and cross-pollination, respectively. To further validate the suitability of the reference genes identified in this study, CavPrx, which the expression profiles in Corylus have been reported, was quantified by using ChaActin and ChaEF1-α as reference genes. (4) Conclusions: our study of reference genes selection in hazelnut shows that the two reference genes, ChaActin and ChaEF1-α, are suitable for the evaluation of gene expression, and can be used for the analysis of pollen-pistil interaction in Corylus. The results supply a reliable foundation for accurate gene quantifications in Corylus species, which will facilitate the studies related to the reproductive biology in Corylus.
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Affiliation(s)
- Sihao Hou
- Key Laboratory of Tree Breeding and Cultivation of the State Forestry and Grassland Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing 100091, China; (S.H.); (T.Z.); (D.Y.); (Q.L.); (L.L.); (G.W.)
- Hazelnut Engineering and Technical Research Center of the State Forestry and Grassland Administration, Beijing 100091, China
- National Hazelnut Industry Innovation Alliance of the State Forestry and Grassland Administration, Beijing 100091, China
| | - Tiantian Zhao
- Key Laboratory of Tree Breeding and Cultivation of the State Forestry and Grassland Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing 100091, China; (S.H.); (T.Z.); (D.Y.); (Q.L.); (L.L.); (G.W.)
- Hazelnut Engineering and Technical Research Center of the State Forestry and Grassland Administration, Beijing 100091, China
- National Hazelnut Industry Innovation Alliance of the State Forestry and Grassland Administration, Beijing 100091, China
| | - Dan Yang
- Key Laboratory of Tree Breeding and Cultivation of the State Forestry and Grassland Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing 100091, China; (S.H.); (T.Z.); (D.Y.); (Q.L.); (L.L.); (G.W.)
- Hazelnut Engineering and Technical Research Center of the State Forestry and Grassland Administration, Beijing 100091, China
- National Hazelnut Industry Innovation Alliance of the State Forestry and Grassland Administration, Beijing 100091, China
| | - Qing Li
- Key Laboratory of Tree Breeding and Cultivation of the State Forestry and Grassland Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing 100091, China; (S.H.); (T.Z.); (D.Y.); (Q.L.); (L.L.); (G.W.)
- Hazelnut Engineering and Technical Research Center of the State Forestry and Grassland Administration, Beijing 100091, China
- National Hazelnut Industry Innovation Alliance of the State Forestry and Grassland Administration, Beijing 100091, China
| | - Lisong Liang
- Key Laboratory of Tree Breeding and Cultivation of the State Forestry and Grassland Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing 100091, China; (S.H.); (T.Z.); (D.Y.); (Q.L.); (L.L.); (G.W.)
- Hazelnut Engineering and Technical Research Center of the State Forestry and Grassland Administration, Beijing 100091, China
- National Hazelnut Industry Innovation Alliance of the State Forestry and Grassland Administration, Beijing 100091, China
| | - Guixi Wang
- Key Laboratory of Tree Breeding and Cultivation of the State Forestry and Grassland Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing 100091, China; (S.H.); (T.Z.); (D.Y.); (Q.L.); (L.L.); (G.W.)
- Hazelnut Engineering and Technical Research Center of the State Forestry and Grassland Administration, Beijing 100091, China
- National Hazelnut Industry Innovation Alliance of the State Forestry and Grassland Administration, Beijing 100091, China
| | - Qinghua Ma
- Key Laboratory of Tree Breeding and Cultivation of the State Forestry and Grassland Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing 100091, China; (S.H.); (T.Z.); (D.Y.); (Q.L.); (L.L.); (G.W.)
- Hazelnut Engineering and Technical Research Center of the State Forestry and Grassland Administration, Beijing 100091, China
- National Hazelnut Industry Innovation Alliance of the State Forestry and Grassland Administration, Beijing 100091, China
- Correspondence: ; Tel.: +86-1381-139-0689
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Ailavadi S, Davidson PM, Morgan MT, D'Souza DH. Thermal Inactivation Kinetics of Tulane Virus in Cell-Culture Medium and Spinach. J Food Sci 2019; 84:557-563. [DOI: 10.1111/1750-3841.14461] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2018] [Revised: 11/25/2018] [Accepted: 01/12/2019] [Indexed: 11/29/2022]
Affiliation(s)
- Sukriti Ailavadi
- Dept. of Food Science; Univ. of Tennessee; 2605 River Drive Knoxville TN 37996 U.S.A
| | - P. Michael Davidson
- Dept. of Food Science; Univ. of Tennessee; 2605 River Drive Knoxville TN 37996 U.S.A
| | - Mark T. Morgan
- Dept. of Food Science; Univ. of Tennessee; 2605 River Drive Knoxville TN 37996 U.S.A
| | - Doris H. D'Souza
- Dept. of Food Science; Univ. of Tennessee; 2605 River Drive Knoxville TN 37996 U.S.A
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4
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Predictive models for thermal inactivation of human norovirus and surrogates in strawberry puree. Food Control 2019. [DOI: 10.1016/j.foodcont.2018.08.031] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
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Tian P, Yang D, Shan L, Li Q, Liu D, Wang D. Estimation of Human Norovirus Infectivity from Environmental Water Samples by In Situ Capture RT-qPCR Method. FOOD AND ENVIRONMENTAL VIROLOGY 2018; 10:29-38. [PMID: 28856596 DOI: 10.1007/s12560-017-9317-1] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/08/2017] [Accepted: 08/12/2017] [Indexed: 05/05/2023]
Abstract
Human noroviruses (HuNoVs) are highly infectious viruses for which water is an important medium of transmission. In this study, we explored a new in situ capture RT-qPCR (ISC-RT-qPCR) methodology to estimate the infectivity of HuNoV in environmental water samples. This assay was based on capturing encapsidated HuNoV by viral receptors, followed by in situ amplification of the captured viral genomes by RT-qPCR. We demonstrated that the ISC-RT-qPCR did not capture and enable signal amplification of heat-denatured Tulane Virus (TV) and HuNoVs. We further demonstrated that the sensitivity of ISC-RT-qPCR was equal or better than that of conventional RT-qPCR procedures for the detection of HuNoV GI and GII. We then utilized the ISC-RT-qPCR to detect HuNoV in environmental water samples for comparison against that from a conventional RT-qPCR procedure. TV was used as a process control virus. While complete inhibition of TV genomic signal was observed in 27% of samples tested by RT-qPCR, no inhibition of TV genomic signal was observed by ISC-RT-qPCR. From 72 samples tested positive for HuNoV GI signal by RT-qPCR, only 20 (27.8%) of these samples tested positive by ISC-RT-qPCR, suggesting that 72.2% of RT-qPCR-positive samples were unlikely to be infectious. From 16 samples tested positive for HuNoV GII signal by RT-qPCR, only one of these samples tested positive by ISC-RT-qPCR. Five samples that had initially tested negative for HuNoV GII signal by RT-qPCR, was tested as positive by ISC-RT-qPCR. Overall, ISC-RT-qPCR method provided an alternative assay to estimate infectivity of HuNoV in environmental samples.
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Affiliation(s)
- Peng Tian
- Produce Safety and Microbiology Research Unit, Western Regional Research Center, Agricultural Research Service, United States Department of Agriculture, 800 Buchanan St., Albany, CA, 94710-1105, USA.
| | - David Yang
- Produce Safety and Microbiology Research Unit, Western Regional Research Center, Agricultural Research Service, United States Department of Agriculture, 800 Buchanan St., Albany, CA, 94710-1105, USA
| | - Lei Shan
- Produce Safety and Microbiology Research Unit, Western Regional Research Center, Agricultural Research Service, United States Department of Agriculture, 800 Buchanan St., Albany, CA, 94710-1105, USA
| | - Qianqian Li
- Department of Bioengineering, Shanghai Institute of Technology, Shanghai, 100 Haiquan Road, Fengxian District, Shanghai, 201418, People's Republic of China
| | - Danlei Liu
- MOST-USDA Joint Research Center for Food Safety & Bor Luh Food Safety Center, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 200240, People's Republic of China
| | - Dapeng Wang
- MOST-USDA Joint Research Center for Food Safety & Bor Luh Food Safety Center, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 200240, People's Republic of China
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Li Q, Wang D, Yang D, Shan L, Tian P. Binding of Escherichia coli Does Not Protect Tulane Virus from Heat-Inactivation Regardless the Expression of HBGA-Like Molecules. Front Microbiol 2017; 8:1746. [PMID: 28983282 PMCID: PMC5613088 DOI: 10.3389/fmicb.2017.01746] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2017] [Accepted: 08/28/2017] [Indexed: 12/14/2022] Open
Abstract
Histo-blood group antigens (HBGAs) are considered as receptors/co-receptors for human norovirus (HuNoV). It has been reported that binding of HuNoV-derived virus-like particles (VLPs) to HBGA-like molecules-expressing bacteria increased the stability of VLPs to heat-denaturation (HD). In this study, we tested for HBGA-like-binding-conveyed protection against HD on viral replication using Tulane virus (TV) and Escherichia coli O86:H2 (O86:H2), with E. coli K-12 (K-12) used as a control. Expression of HBGA type B was confirmed by ELISA in O86:H2 but not in K-12. Binding of TV was confirmed by ELISA in O86:H2 (P/N = 2.23) but not in K-12 (P/N = 1.90). Pre-incubation of TV with free HBGA could completely inhibit its ability to bind to O86:H2 (p = 0.004), while producing no significant change in its ability to bind K-12 (p = 0.635). We utilized a bacterial-capture-RT-qPCR procedure to confirm that both bacterial strains were capable of binding TV, and that O86:H2 exhibited fivefold greater binding capacity than K-12. Pre-incubation of TV with free HBGA would partially inhibit the binding of TV to O86:H2 (p = 0.047). In contrast, not only did pre-incubation of TV with free HBGA not inhibit the binding of TV to K-12, binding was slightly enhanced (p = 0.13). The viral infectivity assay allowed us to conduct a direct evaluation of the ability of HBGA-like-bound bacteria to confer HD protection to TV. Prior to inoculate to LLC-MK2 cells, TV was incubated with each bacterial strain at ratios of 1:0, 1:1 and 100:1, then both partially and fully HD. The viral amplification was quantitated by RT-qPCR 48 h later. The binding of bacteria to TV reduced viral replication in a dose-dependent matter. We found that neither bound O86:H2 nor K-12 conferred protection of TV against partial or full HD conditions. Partial HD reduction of viral replication was not significantly impacted by the binding of either bacterial strain, with infectivity losses of 99.03, 99.42, 96.32, 96.10, and 98.88% for TV w/o bacteria, TV w/O86:H2 (1:1), TV w/O86:H2 (100:1), TV w/K-12 (1:1), and TV w/K-12 (100:1), respectively. Full HD reduction of viral replication was not impacted by the binding of either bacterial strain, as full loss of infectivity was observed in all cases.
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Affiliation(s)
- Qianqian Li
- Department of Bioengineering, Shanghai Institute of TechnologyShanghai, China.,Produce Safety and Microbiology Research Unit, Western Regional Research Center, Agricultural Research Service, United States Department of Agriculture, AlbanyCA, United States
| | - Dapeng Wang
- MOST-USDA Joint Research Center for Food Safety, School of Agriculture and Biology, Shanghai Jiao Tong UniversityShanghai, China
| | - David Yang
- Produce Safety and Microbiology Research Unit, Western Regional Research Center, Agricultural Research Service, United States Department of Agriculture, AlbanyCA, United States
| | - Lei Shan
- Produce Safety and Microbiology Research Unit, Western Regional Research Center, Agricultural Research Service, United States Department of Agriculture, AlbanyCA, United States
| | - Peng Tian
- Produce Safety and Microbiology Research Unit, Western Regional Research Center, Agricultural Research Service, United States Department of Agriculture, AlbanyCA, United States
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Wang M, Rong S, Tian P, Zhou Y, Guan S, Li Q, Wang D. Bacterial Surface-Displayed GII.4 Human Norovirus Capsid Proteins Bound to HBGA-Like Molecules in Romaine Lettuce. Front Microbiol 2017; 8:251. [PMID: 28265267 PMCID: PMC5316531 DOI: 10.3389/fmicb.2017.00251] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2017] [Accepted: 02/06/2017] [Indexed: 11/13/2022] Open
Abstract
Human Noroviruses (HuNoVs) are the main cause of non-bacterial gastroenteritis. Contaminated produce is a main vehicle for dissemination of HuNoVs. In this study, we used an ice nucleation protein mediated surface display system to present the protruding domain of GII.4 HuNoV capsid protein on bacterial surface and used it as a new strategy to explore interaction between HuNoV protein and receptor candidates from romaine lettuce. The surface-displayed HuNoV proteins were confirmed on the surface of the transformed bacteria by an immunofluorescence assay. The distribution patterns of the surface-displayed HuNoV proteins in romaine lettuce were identified through a confocal immunofluorescence assay. The surface-displayed HuNoV proteins could be found in the stomata, and the surfaces of vein and leaf of romaine lettuce. The surface-displayed HuNoV proteins could be captured by an ELISA assay utilizing extract from leaf (LE) or vein (VE). The binding of the surface-displayed HuNoV proteins to LE or VE could be competitively blocked by histo-blood group antigens from human saliva. In addition, the binding of the surface-displayed HuNoV proteins to LE or VE could also be attenuated by heat denaturation of lettuce proteins, and abolished by oxidation of lettuce carbohydrates. The results indicated that histo-blood group antigen-like molecules in LE or VE were involved in the binding of the surface-displayed HuNoV proteins to romaine lettuce. All data demonstrated that the surface-displayed HuNoV proteins could be utilized in a new and simple system for investigation of the interaction between the HuNoVs and their candidate ligands.
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Affiliation(s)
- Ming Wang
- Department of Bioengineering, Shanghai Institute of Technology Shanghai, China
| | - Shaofeng Rong
- Department of Bioengineering, Shanghai Institute of Technology Shanghai, China
| | - Peng Tian
- Produce Safety and Microbiology Research Unit, Western Regional Research Center, Agricultural Research Service - United States Department of Agriculture, Albany CA, USA
| | - Yue Zhou
- Department of Bioengineering, Shanghai Institute of Technology Shanghai, China
| | - Shimin Guan
- Department of Bioengineering, Shanghai Institute of Technology Shanghai, China
| | - Qianqian Li
- Department of Bioengineering, Shanghai Institute of Technology Shanghai, China
| | - Dapeng Wang
- MOST-USDA Joint Research Center for Food Safety, School of Agriculture and Biology, Shanghai Jiao Tong University Shanghai, China
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Ho J, Seidel M, Niessner R, Eggers J, Tiehm A. Long amplicon (LA)-qPCR for the discrimination of infectious and noninfectious phix174 bacteriophages after UV inactivation. WATER RESEARCH 2016; 103:141-148. [PMID: 27450352 DOI: 10.1016/j.watres.2016.07.032] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/04/2016] [Revised: 07/11/2016] [Accepted: 07/13/2016] [Indexed: 05/19/2023]
Abstract
Waterborne viruses are increasingly being considered in risk assessment schemes. In general, virus detection by culture methods is time consuming. In contrast, detection by quantitative polymerase chain reaction (qPCR) is more rapid and therefore, more suitable for monitoring. At present, qPCR lacks the essential ability for discriminating between infectious and non-infectious viruses, thus limiting its applicability for monitoring disinfection processes. In this study, a method was developed to quantify UV inactivation by long amplicon (LA)-qPCR. Bacteriophage phiX174 was used as a surrogate for human pathogenic viruses. A qPCR protocol was developed with new sets of primers, resulting in amplicon lengths of 108, 250, 456, 568, 955, 1063, 1544, and 1764 nucleotides. The log reduction of gene copies increased with increasing amplicon length. Additional treatment with the intercalating dye, PMA, had no effect, indicating that the bacteriophage capsids were not damaged by low pressure UV irradiation. A qPCR of nearly the complete genome (approx. 5000 nucleotides) showed similar results to the plaque assay. The log reduction in qPCR correlates with [specific amplicon length x UV dose]. The normalized DNA effect constant can be applied to calculate phiX174 inactivation based on qPCR detection.
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Affiliation(s)
- Johannes Ho
- DVGW-Technologiezentrum Wasser (TZW), Department Microbiology and Molecular Biology, Karlsruher Str. 84, Karlsruhe, Germany
| | - Michael Seidel
- Chair of Analytical Chemistry and Institute of Hydrochemistry, Technical University of Munich, Marchioninistr. 17, 81377 Munich, Germany
| | - Reinhard Niessner
- Chair of Analytical Chemistry and Institute of Hydrochemistry, Technical University of Munich, Marchioninistr. 17, 81377 Munich, Germany
| | - Jutta Eggers
- DVGW-Technologiezentrum Wasser (TZW), Department Technology and Economics, Karlsruher Str. 84, Karlsruhe, Germany
| | - Andreas Tiehm
- DVGW-Technologiezentrum Wasser (TZW), Department Microbiology and Molecular Biology, Karlsruher Str. 84, Karlsruhe, Germany.
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