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Singh S, Stainton D, Tzanetakis IE. Development of Rapid and Affordable Virus-Mimicking Artificial Positive Controls. PLANT DISEASE 2024; 108:30-34. [PMID: 37578360 DOI: 10.1094/pdis-06-23-1072-sr] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/15/2023]
Abstract
A major bottleneck in the development of detection assays is the availability of positive controls. Their acquisition can be problematic, their maintenance is expensive, and without them, assays cannot be validated. Herein, we present a novel strategy for the development of virus-mimicking artificial positive controls (ViMAPCs). The time between design and application is less than 5 days, unlike alternatives which normally take several weeks to obtain and implement. The ViMAPCs provide a realistic representation of natural infection unlike alternatives and allow for an effortless recognition of laboratory-based contamination. The feasibility and adaptability of the strategy was evaluated using several RNA and DNA plant viruses. ViMAPCs can be used in diagnostics laboratories but also in the monitoring of pathogen outbreaks where rapid response is of utmost importance.
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Affiliation(s)
- Shivani Singh
- Department of Entomology and Plant Pathology, Division of Agriculture, University of Arkansas System, Fayetteville, AR 72701
| | - Daisy Stainton
- Department of Entomology and Plant Pathology, Division of Agriculture, University of Arkansas System, Fayetteville, AR 72701
| | - Ioannis E Tzanetakis
- Department of Entomology and Plant Pathology, Division of Agriculture, University of Arkansas System, Fayetteville, AR 72701
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Development of a Real-Time Loop-Mediated Isothermal Amplification Method for the Detection of West Nile Virus. Jundishapur J Microbiol 2020. [DOI: 10.5812/jjm.105443] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Background: The West Nile Virus (WNV), discovered in New York, USA in 1999 after it was first isolated in Uganda in 1937, has since spread not only in the United States but also around the world. Africa, Eurasia, Australia, and the Middle East have sporadic cases of the disease. Objectives: We aimed to find real-time reverse transcription loop-mediated isothermal amplification (RT-LAMP) assay to be more sensitive than conventional RT-PCR, and more rapid and efficient than conventional RT-PCR and real-time RT-PCR for WNV detection. Methods: A total of 32 genomic sequences from different strains of WNV were analyzed to identify conserved nucleotide sequence regions. Six WNV specific RT-LAMP primers targeting the E gene were designed. Results: The novel primer for the real-time RT-LAMP assay can detect WNV with high specificity. The efficiency of the real-time RT-LAMP assay is higher than the conventional RT-PCR and real-time RT-PCR. Real-time RT-PCR and conventional PCR require at least 30 – 40 min and 2 h, respectively, to yield results, whereas real-time RT-LAMP provides positive results in only 10 – 20 min. Conclusions: The novel primers were developed by analyzing of 32 genomic sequences of WNV strains. The primers were designed from the most conserved region of the E gene for real-time RT-LAMP. The LAMP assay is a rapid, efficient, highly sensitive, and specific tool for the identification of WNV.
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Lee JW, Won YJ, Kang LH, Lee SG, Park SW, Paik SY. Development of a real-time loop-mediated isothermal amplification method for the detection of severe fever with thrombocytopenia syndrome virus. J Microbiol 2020; 58:711-715. [PMID: 32424580 PMCID: PMC7232587 DOI: 10.1007/s12275-020-0109-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2020] [Revised: 04/14/2020] [Accepted: 04/16/2020] [Indexed: 02/06/2023]
Abstract
Severe fever with thrombocytopenia syndrome (SFTS) is being reported annually in South Korea since its first detection there in 2010. The causal agent is a negative-strand RNA virus 80–100 nm in diameter. It causes fever, thrombocytopenia, leukocytopenia, gastrointestinal symptoms, and neural symptoms. The mortality rate of SFTS was 32.6% among 172 cases reported from 2012 to 2015 in South Korea. Thus, is necessary to develop an effective diagnostic method that selectively identifies the isolates circulating in South Korea. The real-time reverse transcription loop-mediated isothermal amplification (RT-LAMP) assay is a simple, rapid, and sensitive approach for molecular diagnosis. Here, we designed novel primers for this assay and found that the technique had very high specificity, sensitivity, and efficiency. This real-time RT-LAMP approach using the novel primers developed herein can be applied for early diagnosis of SFTSV strains in South Korea to reduce the mortality rate of SFTS.
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Affiliation(s)
- Jae Woong Lee
- Department of Microbiology, College of Medicine, The Catholic University of Korea, Seoul, 06591, Republic of Korea
| | - Yu-Jung Won
- Department of Microbiology, College of Medicine, The Catholic University of Korea, Seoul, 06591, Republic of Korea
| | - Lae Hyung Kang
- Department of Microbiology, College of Medicine, The Catholic University of Korea, Seoul, 06591, Republic of Korea
| | - Sung-Geun Lee
- Korea Zoonosis Research Institute, Jeonbuk National University, Iksan, 54596, Republic of Korea
| | - Seung-Won Park
- Department of Biotechnology, Daegu Catholic University, Gyeongsan-si, 38430, Republic of Korea
| | - Soon-Young Paik
- Department of Microbiology, College of Medicine, The Catholic University of Korea, Seoul, 06591, Republic of Korea.
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Dimaculangan M, Wiid SC, Bester PA, Sekee TR, Burt FJ. A simple and rapid approach to prepare Sindbis and West Nile viral RNA controls for differentiation between positive samples and laboratory contamination. J Virol Methods 2020; 278:113822. [PMID: 31954734 DOI: 10.1016/j.jviromet.2020.113822] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2019] [Revised: 01/14/2020] [Accepted: 01/15/2020] [Indexed: 10/25/2022]
Abstract
Reverse transcription-polymerase chain reaction (RT-PCR) is frequently used for surveillance and diagnosis of arboviruses and emerging viruses. A disadvantage of RT-PCR assays, especially nested assays, is the potential for false-positive results caused by laboratory contamination from either positive controls or positive samples. Positive reactors usually require sequence determination for confirmation which delay timeous reporting of a result. Thus, the aim of the study was to use a simple technique to prepare a positive control allowing true positives to be differentiated from laboratory contamination based on size differentiation for conventional PCR, or melt temperatures for real time assays. A flavivirus positive control and an alphavirus positive control were prepared for two RT-PCR assays that we are currently using for arbovirus surveillance in South Africa. Primers targeting a region of the partial genes of interest cloned in pGEM®T-easy were modified at the 5' ends with non-viral nucleotides. The resulting amplicons were circularised, resulting in pGEM®T-easy constructs with 51 and 65 non-viral bases inserted into the partial flaviviral and alphaviral genes respectively and used as template for transcribing RNA. Sequence analysis was used to confirm the manipulation of the partial genes. Using virus specific primer pairs, viral RNA could be readily differentiated from the modified positive controls either by size differentiation, or melt temperature in a SYBR®Green real time RT-PCR. This study demonstrates how simple recombinant technology can be used to produce a positive control that has application in the laboratory for surveillance studies or as a diagnostic tool using synthetic genes to abrogate the requirement for handling infectious virus.
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Affiliation(s)
- Micah Dimaculangan
- Division of Virology, Faculty of the Health Sciences, University of the Free State, Bloemfontein, South Africa
| | - Siewert C Wiid
- Division of Virology, Faculty of the Health Sciences, University of the Free State, Bloemfontein, South Africa
| | - Phillip A Bester
- Division of Virology, Faculty of the Health Sciences, University of the Free State, Bloemfontein, South Africa; National Health Laboratory Service, Bloemfontein, South Africa
| | - Tumelo R Sekee
- Division of Virology, Faculty of the Health Sciences, University of the Free State, Bloemfontein, South Africa
| | - Felicity J Burt
- Division of Virology, Faculty of the Health Sciences, University of the Free State, Bloemfontein, South Africa; National Health Laboratory Service, Bloemfontein, South Africa.
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Comparison of process control viruses for use in extraction and detection of human norovirus from food matrices. Food Res Int 2015. [DOI: 10.1016/j.foodres.2015.05.027] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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Acute gastroenteritis outbreaks associated with ground-waterborne norovirus in South Korea during 2008–2012. Epidemiol Infect 2014; 142:2604-9. [DOI: 10.1017/s0950268814000247] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
SUMMARYEpidemiological and virological studies indicate that noroviruses-contaminated groundwater was the primary source of four acute gastroenteritis outbreaks in South Korea between 2008 and 2012. Furthermore, cabbage kimchi was first identified as the vehicle of transmission between groundwater and infected patients in an outbreak in 2011. The proper treatment of groundwater sources prior to use for drinking or in food preparation is necessary to prevent further outbreaks.
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Joung HK, Han SH, Park SJ, Jheong WH, Ahn TS, Lee JB, Jeong YS, Jang KL, Lee GC, Rhee OJ, Park JW, Paik SY. Nationwide surveillance for pathogenic microorganisms in groundwater near carcass burials constructed in South Korea in 2010. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2013; 10:7126-43. [PMID: 24351737 PMCID: PMC3881157 DOI: 10.3390/ijerph10127126] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/15/2013] [Revised: 11/27/2013] [Accepted: 11/28/2013] [Indexed: 11/17/2022]
Abstract
Widespread outbreaks of foot-and-mouth disease and avian influenza occurred in South Korea during 2010. In response to the culling of many animals to attenuate the spread of disease, South Korea used mass burial sites to dispose of the large number of carcasses; consequently, concerns about groundwater contamination by leachate from these burial sites are increasing. Groundwater is one of the main sources of drinking water, and its cleanliness is directly related to public health. Thus, this study aimed to evaluate the safety of groundwater around the burial sites (total of 600 sites). A total of 1,200 groundwater samples were collected though the country, and microbial analysis was conducted during two time periods: during the spring (n = 600; April to June 2012) and after rainfall (n = 600; August to October, 2012; fall). Fecal coliform and Escherichia coli were detected in 173 (14.4%) and 85 (7.1%) of the 1,200 samples, respectively. Salmonella spp. and Shigella spp. each were detected only once (0.083%). Clostridium perfringens was detected from 7 groundwater samples (0.583%), and E. coli O157:H7 was not detected. With respect to norovirus, only the GII type was detected from six groundwater samples (0.5%), and enterovirus was detected in 15 groundwater samples (1.25%). The frequency of E. coli that we detected was lower than that found in previous studies conducted in South Korea, but we detected higher frequency of fecal coliform than that observed in a previous report. The contamination frequencies of Salmonella spp. and Shigella spp. were very low, but C. perfringens, which could be an indicator of fecal pollution, was detected in seven regions. Overall, the results of the present study indicate a low possibility of contamination from burial sites. However, consistent monitoring is required to prevent microbial contamination of groundwater near the burial sites.
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Affiliation(s)
- Ha Kyung Joung
- Department of Microbiology, College of Medicine, the Catholic University of Korea, 505 Banpo-dong Seocho-gu, Seoul 137-701, Korea; E-Mails: (H.K.J.); (S.H.H.)
| | - Sang Ha Han
- Department of Microbiology, College of Medicine, the Catholic University of Korea, 505 Banpo-dong Seocho-gu, Seoul 137-701, Korea; E-Mails: (H.K.J.); (S.H.H.)
| | - Su-Jung Park
- Environmental Infrastructure Research Department, National Institute of Environmental Research, Incheon 404-170, Korea; E-Mails: psj12@korea,kr (S.-J.P.); (W.-H.J.)
| | - Weon-Hwa Jheong
- Environmental Infrastructure Research Department, National Institute of Environmental Research, Incheon 404-170, Korea; E-Mails: psj12@korea,kr (S.-J.P.); (W.-H.J.)
| | - Tae Seok Ahn
- Department of Environmental Science, Kangwon National University, Chuncheon-si, Gangwon-do 200-701, Korea; E-Mail:
| | - Joong-Bok Lee
- Department of Infectious Disease, College of Veterinary Medicine, Konkuk University, Gwangiin-gu, Seoul 143-701, Korea; E-Mail:
| | - Yong-Seok Jeong
- Department of Biology, College of Sciences, Kyung Hee University, 26, Kyungheedaero, Dongdaemun-gu, Seoul 130-701, Korea; E-Mail:
| | - Kyung Lib Jang
- Department of Microbiology, College of Natural Sciences, Pusan National University, Busan 609-735, Korea; E-Mail:
| | - Gyu-Cheol Lee
- Water Analysis and Research Center, Korea Institute of Water and Environment, Korea Water Resources Corp., Daejeon 306-711, Korea; E-Mail:
| | - Ok-Jae Rhee
- DK EcoV Environmental Microbiology Lab, Biotechnology Business Incubating Center, Dankook University, Chungnam 330-714, Korea; E-Mail:
| | | | - Soon Young Paik
- Department of Microbiology, College of Medicine, the Catholic University of Korea, 505 Banpo-dong Seocho-gu, Seoul 137-701, Korea; E-Mails: (H.K.J.); (S.H.H.)
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Lee BR, Lee SG, Park JH, Kim KY, Ryu SR, Rhee OJ, Park JW, Lee JS, Paik SY. Norovirus contamination levels in ground water treatment systems used for food-catering facilities in South Korea. Viruses 2013; 5:1646-54. [PMID: 23820792 PMCID: PMC3738952 DOI: 10.3390/v5071646] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2013] [Revised: 06/11/2013] [Accepted: 06/13/2013] [Indexed: 11/30/2022] Open
Abstract
This study aimed to inspect norovirus contamination of groundwater treatment systems used in food-catering facilities located in South Korea. A nationwide study was performed in 2010. Water samples were collected and, for the analysis of water quality, the temperature, pH, turbidity, and residual chlorine content were assessed. To detect norovirus genotypes GI and GII, RT-PCR and semi-nested PCR were performed with specific NV-GI and NV-GII primer sets, respectively. The PCR products amplified from the detected strains were then subjected to sequence analyses. Of 1,090 samples collected in 2010, seven (0.64%) were found to be norovirus-positive. Specifically, one norovirus strain was identified to have the GI-6 genotype, and six GII strains had the GII, GII-3, GII-4, and GII-17 genotypes. The very low detection rate of norovirus most likely reflects the preventative measures used. However, this virus can spread rapidly from person to person in crowded, enclosed places such as the schools investigated in this study. To promote better public health and sanitary conditions, it is necessary to periodically monitor noroviruses that frequently cause epidemic food poisoning in South Korea.
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Affiliation(s)
- Bo-Ram Lee
- Department of Microbiology, College of Medicine, the Catholic University of Korea, Seoul 137-701, Korea; E-Mail:
| | - Sung-Geun Lee
- Korea Zoonosis Research Institute, Chonbuk National University, Jeonju 561-756, Korea; E-Mail:
| | - Jong-Hyun Park
- Department of Food Science and Biotechnology, Kyungwon University, Seongnam 461-701, Korea; E-Mail:
| | - Kwang-Yup Kim
- Department of Food Science and Technology, Chungbuk National University Korea, Chongju 361-763, Korea; E-Mail:
| | - Sang-Ryeol Ryu
- Department of Food Science and Biotechnology, Seoul National University Korea, Seoul 151-742, Korea; E-Mail:
| | - Ok-Jae Rhee
- DK EcoV Environmental Microbiology Lab, Biotechnology Business Incubating Center, Dankook University, Chungnam 330-714, Korea; E-Mail:
| | - Jeong-Woong Park
- Sanigen Co. Ltd., Juan-dong, Gwacheon-si, Gyeonggi-do 427-070, Korea; E-Mail:
| | - Jeong-Su Lee
- Food Microbiology Division, Food Safety Evaluation Department, National Institute of Food and Drug Safety Evaluation, Osong 363-700, Korea; E-Mail:
| | - Soon-Young Paik
- Department of Microbiology, College of Medicine, the Catholic University of Korea, Seoul 137-701, Korea; E-Mail:
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Abstract
Global aquaculture production of turbot has rapidly increased worldwide in the last decade and it is expected to have even bigger growth in the next years due to new farms operating. The losses caused by pathogen infections have grown at the same time as the production of this species. Parasitological infections are among the main relevant pathologies associated with its culture and produce serious losses in aquaculture, reduce the growth rate in fish and may lead to unmarketable fish due to skeletal muscle abnormalities in cases with high intensity of infection. The microsporidian parasite Tetramicra brevifilum causes severe infections and generates major losses in farmed turbot. Infections are difficult to control due to spore longevity and its direct transmission. To facilitate the infection management, an effective tool for fast detection and identification of T. brevifilum is needed. This study provides a molecular methodology of fast Real-Time PCR for T. brevifilum detection to the aquaculture industry, useful for routine control of T. brevifilum at turbot farms. The method is characterized by its high specificity and sensitivity, and it can be applied to cultured turbot for parasite detection regardless of the life-cycle stage of the pathogen or the infection intensity.
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Lee GC, Jheong WH, Jung GS, Oh SA, Kim MJ, Rhee OJ, Park S, Lee CH. Detection and molecular characterization of human noroviruses in Korean groundwater between 2008 and 2010. FOOD AND ENVIRONMENTAL VIROLOGY 2012; 4:115-123. [PMID: 23412838 DOI: 10.1007/s12560-012-9084-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/17/2012] [Accepted: 06/25/2012] [Indexed: 06/01/2023]
Abstract
RT-PCR, nucleotide sequencing, and phylogenetic analysis were performed for genotyping and molecular characterization of noroviruses isolated from Korean groundwater. Among 160 samples collected from 80 sites between 2008 and 2010, 14 samples (8.7 %) from 12 sites were positive for noroviruses (NoVs). The percentages of NoV-positive samples in 2008, 2009, and 2010 were 22.2, 3.2, and 0 %, respectively, representing a yearly decrease. GII-positive samples (n = 9, 5.6 %) outnumbered GI-positive samples (n = 5, 3.1 %). The genotypes of the GI NoVs were GI.2, GI.5, and GI.6, and the genotypes of the GII NoVs were all GII.4. One sample, HM623465, was very similar to CUK-3 and CBNU2 and two GII.4 sequences isolated from the stool of Korean gastroenteritis patients. A BLASTN search revealed several nucleotide sequences highly similar to those of NoVs isolated in this study. The original isolation sources for these similar NoVs were mostly stool (n = 731, 80.0 %) and groundwater (n = 135, 14.8 %), and all the countries from which they were isolated were almost in Asia (96.0 %); specifically, China (n = 192, 21.0 %), Japan (n = 383, 41.9 %), Korea (n = 296, 32.4 %), and other Asian countries (n = 6, 0.7 %). These results suggest that Korean groundwater might be contaminated with NoVs from the stool of infected patients and that these NoVs in turn cause new cases of gastroenteritis through a typical fecal-oral route with region-specific circulation. Therefore, it is important to properly treat sewage, which may include waterborne viruses and manage point sources in groundwater for national health and sanitation. In addition, continuous molecular surveillance remains important for understanding circulating NoVs.
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Affiliation(s)
- Gyu-Cheol Lee
- K-water, Water Analysis and Research Center, Daejeon, 306-711, Republic of Korea
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Lee GC, Jung GS, Lee CH. Complete genomic sequence analysis of norovirus isolated from South Korea. Virus Genes 2012; 45:225-36. [PMID: 22752565 DOI: 10.1007/s11262-012-0779-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2012] [Accepted: 06/18/2012] [Indexed: 01/26/2023]
Abstract
The complete nucleotide and deduced amino acid sequences of the RNA genome of a recently isolated norovirus (NoV) from Korea, designated Hu/GII-4/CBNU2/2007/KR (CBNU2), were determined and characterized by phylogenetic comparison with several genetically diverse NoV sequences. The RNA genome of CBNU2 is 7,560 nucleotides in length, excluding the 3' poly (A) tract. It includes three open reading frames (ORFs): ORF1, which encodes the nonstructural polyprotein (5-5,104); ORF2, which encodes VP1 (5,085-6,707); and ORF3, which encodes VP2 (6,707-7,513). ORF2-based phylogenetic analysis revealed that CBNU2 belonged to the GII.4 genotype, the most prevalent genotype, and formed a cluster with NoVs isolated from Asian regions, between 2006 and 2008. Comparative analysis with the consensus sequence of 207 completely sequenced NoV genomes showed 47 mismatched nucleotides: 26 in ORF1, 14 in ORF2, and 7 in ORF3, resulting in 8 amino acid changes: 3 in ORF1, 2 in ORF2, and 3 in ORF3. Phylogenetic analysis with full genome ORF1, ORF2, and ORF3 nucleotide sequences obtained from CBNU2 and each of the other representative NoV genomes suggested that CBNU2 had not undergone recombination with any of the other NoVs. A SimPlot analysis further supported this finding.
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Affiliation(s)
- Gyu-Cheol Lee
- Water Analysis and Research Center, K-water, Daejeon 306-711, Republic of Korea
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Lee MJ, Kim WH, Cho HG, Lee SS. Epidemiological Study of Ground-waterborne Norovirus GI.3-associated Gastroenteritis Outbreaks in Gyeonggi Province of South Korea in May 2011. ACTA ACUST UNITED AC 2012. [DOI: 10.4167/jbv.2012.42.3.232] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Affiliation(s)
- Myung-Jin Lee
- Gyeonggi-do Institute of Health & Environment 95, Pajangcheon st, Jangan-gu, Suwon-city, Gyeonggi-do, Korea
- Department of Biology, Kyonggi University Graduate School 94-6, Iui-dong Yeongtong-gu, Suwon-city, Gyeonggi-do, Korea
| | - Woon-Ho Kim
- Gyeonggi-do Institute of Health & Environment 95, Pajangcheon st, Jangan-gu, Suwon-city, Gyeonggi-do, Korea
| | - Han-Gil Cho
- Gyeonggi-do Institute of Health & Environment 95, Pajangcheon st, Jangan-gu, Suwon-city, Gyeonggi-do, Korea
| | - Sang-Seob Lee
- Department of Biology, Kyonggi University Graduate School 94-6, Iui-dong Yeongtong-gu, Suwon-city, Gyeonggi-do, Korea
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