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Cuellar-Quimbaya AF, Muñoz AL, Yepez-Perez Y, C IDJ, Rodríguez AK, Segura NA, Bello F, Losada-Barragán M. Quantitative detection of chikungunya, Zika, and dengue viruses by one-step real-time PCR in different cell substrates. Braz J Microbiol 2024; 55:1083-1090. [PMID: 38424268 PMCID: PMC11153482 DOI: 10.1007/s42770-023-01226-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2023] [Accepted: 12/20/2023] [Indexed: 03/02/2024] Open
Abstract
Chikungunya (CHIKV), Zika (ZIKV), and dengue viruses (DENV) are vector-borne pathogens that cause emerging and re-emerging epidemics throughout tropical and subtropical countries. The symptomatology is similar among these viruses and frequently co-circulates in the same areas, making the diagnosis arduous. Although there are different methods for detecting and quantifying pathogens, real-time reverse transcription-polymerase chain reaction (real-time RT-qPCR) has become a leading technique for detecting viruses. However, the currently developed assays frequently involve probes and high-cost reagents, limiting access in low-income countries. Therefore, this study aims to design and evaluate a quantitative one-step RT-qPCR assay to detect CHIKV, ZIKV, and DENV with high specificity, reproducibility, and low cost in multiple cell substrates. We established a DNA intercalating green dye-based RT-qPCR test that targets nsP1 of CHIKV, and NS5 gene of ZIKV, and DENV for the amplification reaction. The assay exhibited a high specificity confirmed by the melting curve analysis. No cross-reactivity was observed between the three viruses or unspecific amplification of host RNA. The sensitivity of the reaction was evaluated for each virus assay, getting a limit of detection of one RNA copy per virus. Standard curves were constructed, obtaining a reaction efficiency of ~ 100%, a correlation coefficient (R2) of ~ 0.97, and a slope of -3.3. The coefficient of variation (CV) ranged from 0.02 to 1.43. In addition, the method was optimized for viral quantification and tested in Vero, BHK-21, C6/36, LULO, and the Aedes cell lines. Thus, the DNA intercalating green dye-based RT-qPCR assay was a highly specific, sensitive, reproducible, and effective method for detecting and quantifying CHIKV, ZIKV, and DENV in different cell substrates that could also be applied in clinical samples.
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Affiliation(s)
- Andrés F Cuellar-Quimbaya
- Faculty of Science, Universidad Antonio Nariño (UAN), Sede Circunvalar. Cra. 3 Este # 47A - 15, 110231, Bogotá, Colombia
| | - Ana Luisa Muñoz
- Faculty of Science, Universidad Antonio Nariño (UAN), Sede Circunvalar. Cra. 3 Este # 47A - 15, 110231, Bogotá, Colombia
- Fundación Banco Nacional de Sangre Hemolife, Bogotá, Colombia
| | - Yoelis Yepez-Perez
- PhD Program in Biomedical and Biological Sciences, Universidad del Rosario, 111321, Bogotá, Colombia
| | - Ingrid DJiménez C
- Faculty of Science, Universidad Pedagógica y Tecnológica de Colombia (UPTC), 150003, Tunja, Colombia
| | - Anny K Rodríguez
- Faculty of Science, Universidad Antonio Nariño (UAN), Sede Circunvalar. Cra. 3 Este # 47A - 15, 110231, Bogotá, Colombia
| | - Nidya Alexandra Segura
- Faculty of Science, Universidad Pedagógica y Tecnológica de Colombia (UPTC), 150003, Tunja, Colombia
| | - Felio Bello
- Faculty of Agricultural and Livestock Sciences, Program of Veterinary Medicine, Universidad de La Salle, 110141, Bogotá, Colombia
| | - Mónica Losada-Barragán
- Faculty of Science, Universidad Antonio Nariño (UAN), Sede Circunvalar. Cra. 3 Este # 47A - 15, 110231, Bogotá, Colombia.
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Hozalski RM, Zhao X, Kim T, LaPara TM. On-site filtration of large sample volumes improves the detection of opportunistic pathogens in drinking water distribution systems. Appl Environ Microbiol 2024; 90:e0165823. [PMID: 38236032 PMCID: PMC10880612 DOI: 10.1128/aem.01658-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2023] [Accepted: 12/06/2023] [Indexed: 01/19/2024] Open
Abstract
In this study, we compared conventional vacuum filtration of small volumes through disc membranes (effective sample volumes for potable water: 0.3-1.0 L) with filtration of high volumes using ultrafiltration (UF) modules (effective sample volumes for potable water: 10.6-84.5 L) for collecting bacterial biomass from raw, finished, and tap water at seven drinking water systems. Total bacteria, Legionella spp., Legionella pneumophila, Mycobacterium spp., and Mycobacterium avium complex in these samples were enumerated using both conventional quantitative PCR (qPCR) and viability qPCR (using propidium monoazide). In addition, PCR-amplified gene fragments were sequenced for microbial community analysis. The frequency of detection (FOD) of Legionella spp. in finished and tap water samples was much greater using UF modules (83% and 77%, respectively) than disc filters (24% and 33%, respectively). The FODs for Mycobacterium spp. in raw, finished, and tap water samples were also consistently greater using UF modules than disc filters. Furthermore, the number of observed operational taxonomic units and diversity index values for finished and tap water samples were often substantially greater when using UF modules as compared to disc filters. Conventional and viability qPCR yielded similar results, suggesting that membrane-compromised cells represented a minor fraction of total bacterial biomass. In conclusion, our research demonstrates that large-volume filtration using UF modules improved the detection of opportunistic pathogens at the low concentrations typically found in public drinking water systems and that the majority of bacteria in these systems appear to be viable in spite of disinfection with free chlorine and/or chloramine.IMPORTANCEOpportunistic pathogens, such as Legionella pneumophila, are a growing public health concern. In this study, we compared sample collection and enumeration methods on raw, finished, and tap water at seven water systems throughout the State of Minnesota, USA. The results showed that on-site filtration of large water volumes (i.e., 500-1,000 L) using ultrafiltration membrane modules improved the frequency of detection of relatively rare organisms, including opportunistic pathogens, compared to the common approach of filtering about 1 L using disc membranes. Furthermore, results from viability quantitative PCR (qPCR) with propidium monoazide were similar to conventional qPCR, suggesting that membrane-compromised cells represent an insignificant fraction of microorganisms. Results from these ultrafiltration membrane modules should lead to a better understanding of the microbial ecology of drinking water distribution systems and their potential to inoculate premise plumbing systems with opportunistic pathogens where conditions are more favorable for their growth.
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Affiliation(s)
- Raymond M. Hozalski
- Department of Civil, Environmental, and Geo- Engineering, University of Minnesota Twin Cities, Minneapolis, Minnesota, USA
- Biotechnology Institute, University of Minnesota Twin Cities, St. Paul, Minnesota, USA
| | - Xiaotian Zhao
- Department of Civil, Environmental, and Geo- Engineering, University of Minnesota Twin Cities, Minneapolis, Minnesota, USA
| | - Taegyu Kim
- Department of Civil, Environmental, and Geo- Engineering, University of Minnesota Twin Cities, Minneapolis, Minnesota, USA
| | - Timothy M. LaPara
- Department of Civil, Environmental, and Geo- Engineering, University of Minnesota Twin Cities, Minneapolis, Minnesota, USA
- Biotechnology Institute, University of Minnesota Twin Cities, St. Paul, Minnesota, USA
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Shin GE, Park JY, Lee KK, Ko MK, Ku BK, Park CK, Jeoung HY. Genetic diversity of porcine reproductive and respiratory syndrome virus and evaluation of three one-step real-time RT-PCR assays in Korea. BMC Vet Res 2022; 18:327. [PMID: 36042510 PMCID: PMC9429472 DOI: 10.1186/s12917-022-03407-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2021] [Accepted: 07/29/2022] [Indexed: 11/23/2022] Open
Abstract
Background Porcine reproductive and respiratory syndrome virus (PRRSV) has caused huge economic losses in the global swine industry. Frequent genetic variations in this virus cause difficulties in controlling and accurately diagnosing PRRSV. Methods In this study, we investigated the genetic characteristics of PRRSV-1 and PRRSV-2 circulating in Korea from January 2018 to September 2021 and evaluated three one-step real-time reverse transcription polymerase chain reaction (RT-PCR) assays. Results A total of 129 lung samples were collected, consisting of 47 samples for PRRSV-1, 62 samples for PRRSV-2, and 20 PRRSV-negative samples. Nucleotide sequence analysis of open reading frames (ORFs) 5, ORF6, and ORF7 genes from PRRSV samples showed that PRRSV-1 belonged to subgroup A (43/47, 91.49%) and subgroup C (4/47, 8.51%), whereas PRRSV-2 was classified as lineage 1 (25/62, 40.32%), Korean lineage (Kor) C (13/62, 20.97%), Kor B (10/62, 16.13%), lineage 5 (9/62, 14.52%), and Kor A (5/62, 8.06%). Amino acid sequence analysis showed that the neutralizing epitope and T cell epitope of PRRSV-1, and the decoy epitope region and hypervariable regions of PRRSV-2 had evolved under positive selection pressure. In particular, the key amino acid substitutions were found at positions 102 and 104 of glycoprotein 5 (GP5) in some PRRSV-2, and at positions 10 and 70 of membrane protein (M) in most PRRSV-2. In addition, one-step real-time RT-PCR assays, comprising two commercial tests and one test recommended by the World Organization for Animal Health (OIE), were evaluated. Conclusion The results revealed that two of the real-time RT-PCR assays had high sensitivities and specificities, whereas the real-time RT-PCR assay of the OIE had low sensitivity due to mismatches between nucleotides of Korean PRRSVs and forward primers. In this study, we genetically characterized recent PRRSV occurrences and evaluated three one-step real-time RT-PCR assays used in Korea. Supplementary Information The online version contains supplementary material available at 10.1186/s12917-022-03407-0.
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Affiliation(s)
- Go-Eun Shin
- Animal Disease Diagnostic Division, Animal and Plant Quarantine Agency, Gimcheon, 39660, Korea.,College of Veterinary Medicine, Kyungbuk National University, 80, Daehak-ro, Daegu, 41566, Korea
| | - Ji-Young Park
- Animal Disease Diagnostic Division, Animal and Plant Quarantine Agency, Gimcheon, 39660, Korea
| | - Kyoung-Ki Lee
- Animal Disease Diagnostic Division, Animal and Plant Quarantine Agency, Gimcheon, 39660, Korea
| | - Mi-Kyeong Ko
- Animal Disease Diagnostic Division, Animal and Plant Quarantine Agency, Gimcheon, 39660, Korea
| | - Bok-Kyung Ku
- Animal Disease Diagnostic Division, Animal and Plant Quarantine Agency, Gimcheon, 39660, Korea
| | - Choi-Kyu Park
- College of Veterinary Medicine, Kyungbuk National University, 80, Daehak-ro, Daegu, 41566, Korea.
| | - Hye-Young Jeoung
- Animal Disease Diagnostic Division, Animal and Plant Quarantine Agency, Gimcheon, 39660, Korea.
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Development and validation of multiplex SYBR Green real-time PCR assays for detection and molecular surveillance of four tick-borne canine haemoparasites. Ticks Tick Borne Dis 2022; 13:101937. [DOI: 10.1016/j.ttbdis.2022.101937] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2021] [Revised: 02/24/2022] [Accepted: 03/07/2022] [Indexed: 12/21/2022]
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Ruiz-Ruiz S, Ponce CA, Pesantes N, Bustamante R, Gatti G, San Martin V, Gutierrez M, Bórquez P, Vargas SL, Magne F, Calderón EJ, Pérez-Brocal V, Moya A. A Real-Time PCR Assay for Detection of Low Pneumocystis jirovecii Levels. Front Microbiol 2022; 12:787554. [PMID: 35087490 PMCID: PMC8787145 DOI: 10.3389/fmicb.2021.787554] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Accepted: 12/17/2021] [Indexed: 11/13/2022] Open
Abstract
Here we report a new real-time PCR assay using SYBR Green which provides higher sensitivity for the specific detection of low levels of Pneumocystis jirovecii. To do so, two primer sets were designed, targeting the family of genes that code for the most abundant surface protein of Pneumocystis spp., namely the major surface glycoproteins (Msg), and the mitochondrial large subunit rRNA (mtLSUrRNA) multicopy gene, simultaneously detecting two regions. PCR methods are instrumental in detecting these low levels; however, current nested-PCR methods are time-consuming and complex. To validate our new real-time Msg-A/mtLSUrRNA PCR protocol, we compared it with nested-PCR based on the detection of Pneumocystis mitochondrial large subunit rRNA (mtLSUrRNA), one of the main targets used to detect this pathogen. All samples identified as positive by the nested-PCR method were found positive using our new real-time PCR protocol, which also detected P. jirovecii in three nasal aspirate samples that were negative for both rounds of nested-PCR. Furthermore, we read both rounds of the nested-PCR results for comparison and found that some samples with no PCR amplification, or with a feeble band in the first round, correlated with higher Ct values in our real-time Msg-A/mtLSUrRNA PCR. This finding demonstrates the ability of this new single-round protocol to detect low Pneumocystis levels. This new assay provides a valuable alternative for P. jirovecii detection, as it is both rapid and sensitive.
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Affiliation(s)
- Susana Ruiz-Ruiz
- Fundación para el Fomento de la Investigación Sanitaria y Biomédica de la Comunitat Valenciana (FISABIO)-Salud Pública, València, Spain.,Centro de Investigación Biomédica en Red en Epidemiología y Salud Pública (CIBEResp), Instituto de Salud Carlos III, Madrid, Spain
| | - Carolina A Ponce
- Programa de Microbiología y Micología, Facultad de Medicina, Instituto de Ciencias Biomédicas, Universidad de Chile, Santiago, Chile
| | - Nicole Pesantes
- Fundación para el Fomento de la Investigación Sanitaria y Biomédica de la Comunitat Valenciana (FISABIO)-Salud Pública, València, Spain.,Centro de Investigación Biomédica en Red en Epidemiología y Salud Pública (CIBEResp), Instituto de Salud Carlos III, Madrid, Spain
| | - Rebeca Bustamante
- Programa de Microbiología y Micología, Facultad de Medicina, Instituto de Ciencias Biomédicas, Universidad de Chile, Santiago, Chile
| | - Gianna Gatti
- Programa de Microbiología y Micología, Facultad de Medicina, Instituto de Ciencias Biomédicas, Universidad de Chile, Santiago, Chile
| | | | | | | | - Sergio L Vargas
- Programa de Microbiología y Micología, Facultad de Medicina, Instituto de Ciencias Biomédicas, Universidad de Chile, Santiago, Chile
| | - Fabien Magne
- Programa de Microbiología y Micología, Facultad de Medicina, Instituto de Ciencias Biomédicas, Universidad de Chile, Santiago, Chile
| | - Enrique J Calderón
- Centro de Investigación Biomédica en Red en Epidemiología y Salud Pública (CIBEResp), Instituto de Salud Carlos III, Madrid, Spain.,Hospital Universitario Virgen del Rocío, Instituto de Biomedicina de Sevilla, Consejo Superior de Investigaciones Científicas (CSIC), and Universidad de Sevilla, Seville, Spain
| | - Vicente Pérez-Brocal
- Fundación para el Fomento de la Investigación Sanitaria y Biomédica de la Comunitat Valenciana (FISABIO)-Salud Pública, València, Spain.,Centro de Investigación Biomédica en Red en Epidemiología y Salud Pública (CIBEResp), Instituto de Salud Carlos III, Madrid, Spain
| | - Andrés Moya
- Fundación para el Fomento de la Investigación Sanitaria y Biomédica de la Comunitat Valenciana (FISABIO)-Salud Pública, València, Spain.,Centro de Investigación Biomédica en Red en Epidemiología y Salud Pública (CIBEResp), Instituto de Salud Carlos III, Madrid, Spain.,Instituto de Biología Integrativa de Sistemas (I2Sysbio), Universitat de València and Consejo Superior de Investigaciones Científicas (CSIC), València, Spain
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Mori A, Pomari E, Deiana M, Perandin F, Caldrer S, Formenti F, Mistretta M, Orza P, Ragusa A, Piubelli C. Molecular techniques for the genomic viral RNA detection of West Nile, Dengue, Zika and Chikungunya arboviruses: a narrative review. Expert Rev Mol Diagn 2021; 21:591-612. [PMID: 33910444 DOI: 10.1080/14737159.2021.1924059] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Introduction: Molecular technology has played an important role in arboviruses diagnostics. PCR-based methods stand out in terms of sensitivity, specificity, cost, robustness, and accessibility, and especially the isothermal amplification (IA) method is ideal for field-adaptable diagnostics in resource-limited settings (RLS).Areas covered: In this review, we provide an overview of the various molecular methods for West Nile, Zika, Dengue and Chikungunya. We summarize literature works reporting the assessment and use of in house and commercial assays. We describe limitations and challenges in the usage of methods and opportunities for novel approaches such as NNext-GenerationSequencing (NGS).Expert opinion: The rapidity and accuracy of differential diagnosis is essential for a successful clinical management, particularly in co-circulation area of arboviruses. Several commercial diagnostic molecular assays are available, but many are not affordable by RLS and not usable as Point-of-care/Point-of-need (POC/PON) such as RReal-TimeRT-PCR, Array-based methods and NGS. In contrast, the IA-based system fits better for POC/PON but it is still not ideal for the multiplexing detection system. Improvement in the characterization and validation of current molecular assays is needed to optimize their translation to the point of care.
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Affiliation(s)
- Antonio Mori
- Department of Infectious-Tropical Diseases and Microbiology, IRCCS Sacro Cuore Don Calabria Hospital, Verona, Italy.,Department of Diagnostics and Public Health, University of Verona, Verona, Italy
| | - Elena Pomari
- Department of Infectious-Tropical Diseases and Microbiology, IRCCS Sacro Cuore Don Calabria Hospital, Verona, Italy
| | - Michela Deiana
- Department of Infectious-Tropical Diseases and Microbiology, IRCCS Sacro Cuore Don Calabria Hospital, Verona, Italy
| | - Francesca Perandin
- Department of Infectious-Tropical Diseases and Microbiology, IRCCS Sacro Cuore Don Calabria Hospital, Verona, Italy
| | - Sara Caldrer
- Department of Infectious-Tropical Diseases and Microbiology, IRCCS Sacro Cuore Don Calabria Hospital, Verona, Italy
| | - Fabio Formenti
- Department of Infectious-Tropical Diseases and Microbiology, IRCCS Sacro Cuore Don Calabria Hospital, Verona, Italy
| | - Manuela Mistretta
- Department of Infectious-Tropical Diseases and Microbiology, IRCCS Sacro Cuore Don Calabria Hospital, Verona, Italy
| | - Pierantonio Orza
- Department of Infectious-Tropical Diseases and Microbiology, IRCCS Sacro Cuore Don Calabria Hospital, Verona, Italy
| | - Andrea Ragusa
- Department of Infectious-Tropical Diseases and Microbiology, IRCCS Sacro Cuore Don Calabria Hospital, Verona, Italy
| | - Chiara Piubelli
- Department of Infectious-Tropical Diseases and Microbiology, IRCCS Sacro Cuore Don Calabria Hospital, Verona, Italy
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Tomar PS, Kumar JS, Patel S, Sharma S. Polymerase Spiral Reaction Assay for Rapid and Real Time Detection of West Nile Virus From Clinical Samples. Front Cell Infect Microbiol 2020; 10:426. [PMID: 32984063 PMCID: PMC7492713 DOI: 10.3389/fcimb.2020.00426] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2019] [Accepted: 07/13/2020] [Indexed: 12/02/2022] Open
Abstract
West Nile virus (WNV) is a mosquito-borne virus of public health importance. Currently, there is no FDA approved vaccine available against WNV infection in humans. Therefore, the early diagnosis of the WNV infection is important for epidemiologic control and timely clinical management in areas where multiple Flaviviruses are endemic. The present study aimed to develop reverse transcription polymerase spiral reaction (RT-PSR) assay that rapidly and accurately detects the envelope (env) gene of WNV. RT-PSR assay was optimized at 63°C for 60 min using real-time turbidimeter or visual detection by the addition of SYBR Green I dye. The standard curve for RT-PSR assay was generated using the 10-fold serial dilutions of in vitro transcribed WNV RNA. To determine the detection limit of RT-PSR assay, an amplified product of conventional RT-PCR was in vitro transcribed as per standard protocol. The detection limit of the newly developed RT-PSR assay was compared with that of conventional RT-PCR and CDC reported TaqMan real-time RT-PCR using a serial 10-fold dilution of IVT WNV RNA. The detection limit of RT-PSR was found to be 1 RNA copy, which is 100-fold higher than that of conventional RT-PCR (100 copies). This suggests that RT-PSR assay is a valuable diagnostic tool for rapid and real-time detection of WNV in acute-phase serum samples. The assay was validated with a panel of 107 WNV suspected human clinical samples with signs of acute posterior uveitis and onset of febrile illness. Out of 107 samples, 30 were found positive by RT-PSR assay. The specificities of the selected primer sets were established by the absence of cross-reactivity with other closely related members viruses of the Flaviviruses, Alphaviruses, and Morbilliviruses groups. No cross-reactivity was observed with other viruses. To best of our knowledge, this is the first report describing the RT-PSR assay for the detection of RNA virus (WNV) in clinical samples. RT-PSR is a high throughput method and more than 30 reactions can be run at once in real-time turbidimeter. PSR assay has potential to be used for a rapid screening of large number of clinical samples in endemic areas during an outbreak.
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Affiliation(s)
- Priyanka Singh Tomar
- Division of Virology, Defence Research and Development Establishment, Gwalior, India
| | - Jyoti S Kumar
- Division of Virology, Defence Research and Development Establishment, Gwalior, India
| | - Sapan Patel
- School of Studies in Botany, Jiwaji University, Gwalior, India
| | - Shashi Sharma
- Division of Virology, Defence Research and Development Establishment, Gwalior, India
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Detection of Eight Respiratory Bacterial Pathogens Based on Multiplex Real-Time PCR with Fluorescence Melting Curve Analysis. CANADIAN JOURNAL OF INFECTIOUS DISEASES & MEDICAL MICROBIOLOGY 2020; 2020:2697230. [PMID: 32184908 PMCID: PMC7061119 DOI: 10.1155/2020/2697230] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/16/2019] [Revised: 11/22/2019] [Accepted: 12/13/2019] [Indexed: 01/23/2023]
Abstract
Background and Objective. Acinetobacter baumannii, Escherichia coli, Klebsiella pneumoniae, Streptococcus pneumoniae, Haemophilus influenzae, Staphylococcus aureus, Pseudomonas aeruginosa, and Mycobacterium tuberculosis are primary respiratory bacterial pathogens contributing to morbidity and mortality in developing countries. This study evaluated the diagnostic performance of multiplex real-time PCR with fluorescence melting curve analysis (MCA) assay, which was used to detect eight respiratory bacterial pathogens simultaneously. Methods A total of 157 sputum specimens were examined by multiplex real-time with fluorescence MCA, and the results were compared with the conventional culture method. Results Multiplex real-time PCR with fluorescence MCA specifically detected and differentiated eight respiratory bacterial pathogens by different melting curve peaks for each amplification product within 2 hours and exhibited high repeatability. The limit of detection ranged from 64 to 102 CFU/mL in the multiplex PCR system. Multiplex real-time PCR with fluorescence MCA showed a sensitivity greater than 80% and a 100% specificity for each pathogen. The kappa correlation of eight bacteria ranged from 0.89 to 1.00, and the coefficient of variation ranged from 0.05% to 0.80%. Conclusions Multiplex real-time PCR with fluorescence MCA assay is a sensitive, specific, high-throughput, and cost-effective method to detect multiple bacterial pathogens simultaneously.
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Li L, Hu Z, Sun J, Guo K, Chu X, Wang X, Lu Y. Development of an EvaGreen-based real-time PCR assay for detection of Aleutian mink disease virus. J Virol Methods 2019; 275:113751. [PMID: 31639372 DOI: 10.1016/j.jviromet.2019.113751] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2017] [Revised: 10/03/2019] [Accepted: 10/11/2019] [Indexed: 11/18/2022]
Abstract
The objective of this study was to develop a rapid, sensitive and specific EvaGreen (EG)-based real-time PCR assay capable of detecting Aleutian mink disease virus (AMDV) and to evaluate the reliability of the assay for analysis of blood or tissue samples. For this assay, a pair of primers was designed based on a nonstructural protein (NS)-encoding gene of AMDV, and the identity of PCR products was identified based on a melting temperature of 82.8°C. The EG-based real-time PCR assay did not detect canine distemper virus or mink enteritis virus, and the assay could be used to detect Chinese and American AMDV strains, in contrast to a commercial TaqMan kit that could only detect American AMDV strains. The amplification efficiencies of the EG assay were 104.8% for the Chinese strain and 94.4% for the American strain, and the detection limit was 1 copy/μL of AMDV plasmid or 3 pg/μL of viral DNA (Chinese strain). The intra- and inter-assay variation coefficients of melting temperature were all lower than 0.15%, confirming the high reproducibility of the assay. Forty-five clinical blood samples were simultaneously analyzed using the EG real-time PCR, TaqMan kit and conventional PCR, and the detection rates were 91.1%, 0.0% and 86.7%, respectively. Serum samples were also collected from the corresponding blood samples and tested using the counterimmunoelectrophoresis (CIEP) assay, where positive samples accounted for 24.4% of the 45 samples. In conclusion, EG-based real-time PCR is a rapid, sensitive, universal assay that can be effectively utilized as a reliable and specific tool for detection and quantitation of AMDV.
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Affiliation(s)
- Li Li
- Heilongjiang Key Laboratory for Animal Disease Control and Pharmaceutical Development, College of Veterinary Medicine, Northeast Agricultural University, 600 Changjiang Road, Harbin 150030, PR China; Harbin Customs District P.R. China, 88 Songshan Road, Harbin 150008, PR China
| | - Zhe Hu
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, the Chinese Academy of Agriculture Sciences, 678 Haping Road, Harbin 150001, PR China
| | - Jinhui Sun
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, the Chinese Academy of Agriculture Sciences, 678 Haping Road, Harbin 150001, PR China; College of Animal Science and Technology, Northeast Agricultural University, 600 Changjiang Road, Harbin 150030, PR China
| | - Kui Guo
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, the Chinese Academy of Agriculture Sciences, 678 Haping Road, Harbin 150001, PR China
| | - Xiaoyu Chu
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, the Chinese Academy of Agriculture Sciences, 678 Haping Road, Harbin 150001, PR China
| | - Xiaojun Wang
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, the Chinese Academy of Agriculture Sciences, 678 Haping Road, Harbin 150001, PR China
| | - Yixin Lu
- Heilongjiang Key Laboratory for Animal Disease Control and Pharmaceutical Development, College of Veterinary Medicine, Northeast Agricultural University, 600 Changjiang Road, Harbin 150030, PR China.
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McGreal B, Sandanayaka M, Chooi KM, MacDiarmid R. Development of sensitive molecular assays for the detection of grapevine leafroll-associated virus 3 in an insect vector. Arch Virol 2019; 164:2333-2338. [PMID: 31187278 DOI: 10.1007/s00705-019-04310-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2019] [Accepted: 05/13/2019] [Indexed: 11/28/2022]
Abstract
Grapevine leafroll-associated virus 3 (GLRaV-3) is an economically significant virus of grapevines, with secondary spread mediated by several species of mealybug and soft scale insects. To better understand virus-vector interactions, sensitive virus detection in these insects is a key tool. In this research, two new hydrolysis-probe-based real-time assays for GLRaV-3 detection were developed and compared to three existing assays. Of the five assays compared, the one-step RT-qPCR probe-based assay was the most sensitive and reliable, with as few as 10 virus RNA copies detected. This is the first description of a real-time molecular assay for virus detection in mealybugs with such sensitivity.
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Affiliation(s)
- Brogan McGreal
- The New Zealand Institute for Plant and Food Research Limited, Private Bag 92169, Auckland Mail Centre, Auckland, 1142, New Zealand. .,School of Biological Sciences, The University of Auckland, Auckland, New Zealand.
| | - Manoharie Sandanayaka
- The New Zealand Institute for Plant and Food Research Limited, Private Bag 92169, Auckland Mail Centre, Auckland, 1142, New Zealand
| | - Kar Mun Chooi
- The New Zealand Institute for Plant and Food Research Limited, Private Bag 92169, Auckland Mail Centre, Auckland, 1142, New Zealand
| | - Robin MacDiarmid
- The New Zealand Institute for Plant and Food Research Limited, Private Bag 92169, Auckland Mail Centre, Auckland, 1142, New Zealand.,School of Biological Sciences, The University of Auckland, Auckland, New Zealand
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11
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Aloisio M, Morelli M, Elicio V, Saldarelli P, Ura B, Bortot B, Severini G, Minafra A. Detection of four regulated grapevine viruses in a qualitative, single tube real-time PCR with melting curve analysis. J Virol Methods 2018; 257:42-47. [DOI: 10.1016/j.jviromet.2018.04.008] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2017] [Revised: 04/06/2018] [Accepted: 04/08/2018] [Indexed: 10/17/2022]
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12
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Beloor J, Maes N, Ullah I, Uchil P, Jackson A, Fikrig E, Lee SK, Kumar P. Small Interfering RNA-Mediated Control of Virus Replication in the CNS Is Therapeutic and Enables Natural Immunity to West Nile Virus. Cell Host Microbe 2018; 23:549-556.e3. [PMID: 29606496 DOI: 10.1016/j.chom.2018.03.001] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2017] [Revised: 01/21/2018] [Accepted: 02/28/2018] [Indexed: 12/30/2022]
Abstract
No vaccines or therapeutics are licensed for West Nile virus (WNV), a mosquito-transmitted neuroencephalitic flavivirus. The small interfering RNA siFvEJW targets a conserved sequence within the WNV E protein and limits virus infection. Using a rabies virus-derived neuron-targeting peptide (RVG9R) and an intranasal route for delivering siFvEJW to the CNS, we demonstrate that treatment of WNV-infected mice at late stages of neuroinvasive disease results in recovery. Selectively targeting virus in the CNS lowers viral burdens in the brain, reduces neuropathology, and results in a 90% survival rate at 5-6 days post-infection (when viral titers peak in the CNS), while placebo-treated mice succumb by days 9-10. Importantly, CNS virus clearance is achieved by humoral and cell-mediated immune responses to WNV infection in peripheral tissues, which also engender sterilizing immunity against subsequent WNV infection. These results indicate that intranasal RVG9R-siRNA treatment offers efficient late-stage therapy and facilitates natural long-term immunity against neuroinvasive flaviviruses.
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Affiliation(s)
- Jagadish Beloor
- Department of Internal Medicine, Section of Infectious Diseases, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Nyree Maes
- Department of Internal Medicine, Section of Infectious Diseases, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Irfan Ullah
- Department of Bioengineering and Institute of Nanoscience and Technology, Hanyang University, Seoul 133-791, Korea
| | - Pradeep Uchil
- Department of Microbial Pathogenesis, Yale University School of Medicine, New Haven, CT 06510, USA
| | - Andrew Jackson
- Department of Internal Medicine, Section of Infectious Diseases, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Erol Fikrig
- Department of Internal Medicine, Section of Infectious Diseases, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Sang Kyung Lee
- Department of Bioengineering and Institute of Nanoscience and Technology, Hanyang University, Seoul 133-791, Korea.
| | - Priti Kumar
- Department of Internal Medicine, Section of Infectious Diseases, Yale University School of Medicine, New Haven, CT 06520, USA.
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13
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Westmoreland KD, Montgomery ND, Stanley CC, El-Mallawany NK, Wasswa P, van der Gronde T, Mtete I, Butia M, Itimu S, Chasela M, Mtunda M, Kampani C, Liomba NG, Tomoka T, Dhungel BM, Sanders MK, Krysiak R, Kazembe P, Dittmer DP, Fedoriw Y, Gopal S. Plasma Epstein-Barr virus DNA for pediatric Burkitt lymphoma diagnosis, prognosis and response assessment in Malawi. Int J Cancer 2017; 140:2509-2516. [PMID: 28268254 PMCID: PMC5386821 DOI: 10.1002/ijc.30682] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2016] [Accepted: 02/20/2017] [Indexed: 12/26/2022]
Abstract
Point-of-care tools are needed in sub-Saharan Africa (SSA) to improve pediatric Burkitt lymphoma (BL) diagnosis and treatment. We evaluated plasma Epstein-Barr virus (pEBV) DNA as a pediatric BL biomarker in Malawi. Prospectively enrolled children with BL were compared to classical Hodgkin lymphoma (cHL) and nonlymphoma diagnoses. Pediatric BL patients received standardized chemotherapy and supportive care. pEBV DNA was measured at baseline, mid-treatment, and treatment completion. Of 121 assessed children, pEBV DNA was detected in 76/88 (86%) with BL, 16/17 (94%) with cHL, and 2/16 (12%) with nonlymphoma, with proportions higher in BL versus nonlymphoma (p < 0.001) and similar in BL versus cHL (p = 0.69). If detected, median pEBV DNA was 6.1 log10 copies/mL for BL, 4.8 log10 copies/mL for cHL, and 3.4 log10 copies/mL for nonlymphoma, with higher levels in BL versus cHL (p = 0.029), and a trend toward higher levels in BL versus nonlymphoma (p = 0.062). pEBV DNA declined during treatment in the cohort overall and increased in several children before clinical relapse. Twelve-month overall survival was 40% in the cohort overall, and for children with baseline pEBV detected, survival was worse if baseline pEBV DNA was ≥6 log10 copies/mL versus <6 log10 copies/mL (p = 0.0002), and also if pEBV DNA was persistently detectable at mid-treatment versus undetectable (p = 0.041). Among children with baseline pEBV DNA detected, viremia was the only significant risk factor for death by 12 months in multivariate analyses (adjusted hazard ratio 1.35 per log10 copies/mL, 95% CI 1.04-1.75, p = 0.023). Quantitative pEBV DNA has potential utility for diagnosis, prognosis, and response assessment for pediatric BL in SSA.
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Affiliation(s)
| | | | | | | | | | | | - Idah Mtete
- Baylor College of Medicine Children’s Foundation Malawi, Lilongwe, Malawi
| | - Mercy Butia
- Baylor College of Medicine Children’s Foundation Malawi, Lilongwe, Malawi
| | | | - Mary Chasela
- Baylor College of Medicine Children’s Foundation Malawi, Lilongwe, Malawi
| | - Mary Mtunda
- Baylor College of Medicine Children’s Foundation Malawi, Lilongwe, Malawi
| | | | | | - Tamiwe Tomoka
- UNC Project-Malawi, Lilongwe, Malawi
- University of Malawi College of Medicine, Blantyre, Malawi
| | | | | | | | - Peter Kazembe
- Baylor College of Medicine Children’s Foundation Malawi, Lilongwe, Malawi
| | | | | | - Satish Gopal
- UNC Project-Malawi, Lilongwe, Malawi
- University of North Carolina, Chapel Hill, USA
- University of Malawi College of Medicine, Blantyre, Malawi
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14
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Tolardo AL, Souza WMD, Romeiro MF, Vieira LC, Luna LKDS, Henriques DA, Araujo JD, Siqueira CEH, Colombo TE, Aquino VH, Fonseca BALD, Bronzoni RVDM, Nogueira ML, Durigon EL, Figueiredo LTM. A real-time reverse transcriptase polymerase chain reaction for detection and quantification of Vesiculovirus. Mem Inst Oswaldo Cruz 2017; 111:385-90. [PMID: 27276185 PMCID: PMC4909037 DOI: 10.1590/0074-02760150456] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2015] [Accepted: 05/06/2016] [Indexed: 01/01/2023] Open
Abstract
Vesiculoviruses (VSV) are zoonotic viruses that cause vesicular stomatitis disease in cattle, horses and pigs, as well as sporadic human cases of acute febrile illness. Therefore, diagnosis of VSV infections by reliable laboratory techniques is important to allow a proper case management and implementation of strategies for the containment of virus spread. We show here a sensitive and reproducible real-time reverse transcriptase polymerase chain reaction (RT-PCR) for detection and quantification of VSV. The assay was evaluated with arthropods and serum samples obtained from horses, cattle and patients with acute febrile disease. The real-time RT-PCR amplified the Piry, Carajas, Alagoas and Indiana Vesiculovirus at a melting temperature 81.02 ± 0.8ºC, and the sensitivity of assay was estimated in 10 RNA copies/mL to the Piry Vesiculovirus. The viral genome has been detected in samples of horses and cattle, but not detected in human sera or arthropods. Thus, this assay allows a preliminary differential diagnosis of VSV infections.
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Affiliation(s)
- Aline Lavado Tolardo
- Universidade de São Paulo, Universidade de São Paulo, Faculdade de Medicina de Ribeirão Preto, Centro de Pesquisa em Virologia, Ribeirão Preto SP , Brasil, Universidade de São Paulo, Faculdade de Medicina de Ribeirão Preto, Centro de Pesquisa em Virologia, Ribeirão Preto, SP, Brasil
| | - William Marciel de Souza
- Universidade de São Paulo, Universidade de São Paulo, Faculdade de Medicina de Ribeirão Preto, Centro de Pesquisa em Virologia, Ribeirão Preto SP , Brasil, Universidade de São Paulo, Faculdade de Medicina de Ribeirão Preto, Centro de Pesquisa em Virologia, Ribeirão Preto, SP, Brasil
| | - Marilia Farignoli Romeiro
- Universidade de São Paulo, Universidade de São Paulo, Faculdade de Medicina de Ribeirão Preto, Centro de Pesquisa em Virologia, Ribeirão Preto SP , Brasil, Universidade de São Paulo, Faculdade de Medicina de Ribeirão Preto, Centro de Pesquisa em Virologia, Ribeirão Preto, SP, Brasil
| | - Luiz Carlos Vieira
- Universidade de São Paulo, Universidade de São Paulo, Faculdade de Medicina de Ribeirão Preto, Centro de Pesquisa em Virologia, Ribeirão Preto SP , Brasil, Universidade de São Paulo, Faculdade de Medicina de Ribeirão Preto, Centro de Pesquisa em Virologia, Ribeirão Preto, SP, Brasil
| | - Luciano Kleber de Souza Luna
- Universidade de São Paulo, Universidade de São Paulo, Faculdade de Medicina de Ribeirão Preto, Centro de Pesquisa em Virologia, Ribeirão Preto SP , Brasil, Universidade de São Paulo, Faculdade de Medicina de Ribeirão Preto, Centro de Pesquisa em Virologia, Ribeirão Preto, SP, Brasil
| | - Dyana Alves Henriques
- Universidade de São Paulo, Universidade de São Paulo, Instituto de Ciências Biomédicas, Laboratório de Virologia Clínica e Molecular, São Paulo SP , Brasil, Universidade de São Paulo, Instituto de Ciências Biomédicas, Laboratório de Virologia Clínica e Molecular, São Paulo, SP, Brasil
| | - Jansen de Araujo
- Universidade de São Paulo, Universidade de São Paulo, Instituto de Ciências Biomédicas, Laboratório de Virologia Clínica e Molecular, São Paulo SP , Brasil, Universidade de São Paulo, Instituto de Ciências Biomédicas, Laboratório de Virologia Clínica e Molecular, São Paulo, SP, Brasil
| | - Carlos Eduardo Hassegawa Siqueira
- Universidade Federal de Mato Grosso, Universidade Federal de Mato Grosso, Instituto de Ciências da Saúde, Centro Universitário de Sinop, Sinop MT , Brasil, Universidade Federal de Mato Grosso, Instituto de Ciências da Saúde, Centro Universitário de Sinop, Sinop, MT, Brasil
| | - Tatiana Elias Colombo
- Faculdade de Medicina de São José do Rio Preto, Faculdade de Medicina de São José do Rio Preto, Laboratório de Pesquisa em Virologia, São José do Rio Preto SP , Brasil, Faculdade de Medicina de São José do Rio Preto, Laboratório de Pesquisa em Virologia, São José do Rio Preto, SP, Brasil
| | - Victor Hugo Aquino
- Universidade de São Paulo, Universidade de São Paulo, Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Departamento de Análises Clínicas, Toxicológicas e Bromatológicas, Ribeirão Preto SP , Brasil, Universidade de São Paulo, Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Departamento de Análises Clínicas, Toxicológicas e Bromatológicas, Laboratório de Virologia, Ribeirão Preto, SP, Brasil
| | - Benedito Antonio Lopes da Fonseca
- Universidade de São Paulo, Universidade de São Paulo, Faculdade de Medicina de Ribeirão Preto, Centro de Pesquisa em Virologia, Ribeirão Preto SP , Brasil, Universidade de São Paulo, Faculdade de Medicina de Ribeirão Preto, Centro de Pesquisa em Virologia, Ribeirão Preto, SP, Brasil
| | - Roberta Vieira de Morais Bronzoni
- Universidade Federal de Mato Grosso, Universidade Federal de Mato Grosso, Instituto de Ciências da Saúde, Centro Universitário de Sinop, Sinop MT , Brasil, Universidade Federal de Mato Grosso, Instituto de Ciências da Saúde, Centro Universitário de Sinop, Sinop, MT, Brasil
| | - Maurício Lacerda Nogueira
- Faculdade de Medicina de São José do Rio Preto, Faculdade de Medicina de São José do Rio Preto, Laboratório de Pesquisa em Virologia, São José do Rio Preto SP , Brasil, Faculdade de Medicina de São José do Rio Preto, Laboratório de Pesquisa em Virologia, São José do Rio Preto, SP, Brasil
| | - Edison Luiz Durigon
- Universidade de São Paulo, Universidade de São Paulo, Instituto de Ciências Biomédicas, Laboratório de Virologia Clínica e Molecular, São Paulo SP , Brasil, Universidade de São Paulo, Instituto de Ciências Biomédicas, Laboratório de Virologia Clínica e Molecular, São Paulo, SP, Brasil
| | - Luiz Tadeu Moraes Figueiredo
- Universidade de São Paulo, Universidade de São Paulo, Faculdade de Medicina de Ribeirão Preto, Centro de Pesquisa em Virologia, Ribeirão Preto SP , Brasil, Universidade de São Paulo, Faculdade de Medicina de Ribeirão Preto, Centro de Pesquisa em Virologia, Ribeirão Preto, SP, Brasil
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15
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Pawar SS, Meshram CD, Singh NK, Saini M, Mishra BP, Gupta PK. EvaGreen-based Multiplex Real-time PCR Assay for Rapid Differentiation of Wild-Type and Glycoprotein E-Deleted Bovine Herpesvirus-1 Strains. Anim Biotechnol 2017; 28:248-252. [PMID: 28060576 DOI: 10.1080/10495398.2016.1268620] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
Bovine herpesvirus-1 (BoHV-1) is an important viral pathogen causing significant economic losses to the cattle industry. Glycoprotein E-deleted marker vaccines form the basis for BoHV-1 control programs widely, wherein detection and differentiation of wild-type and gE-deleted vaccine strains is of crucial importance for proper disease management. In the present study, we report an EvaGreen-based multiplex real-time polymerase chain reaction (EGRT-PCR) assay for rapid differentiation of wild-type and glycoprotein E-deleted strains of BoHV-1. The EGRT-PCR assay could simultaneously detect two viral genes (glycoprotein B and E) and an internal positive control gene (bovine growth hormone- bGH), in a single-tube reaction. The analytical sensitivity of the EGRT-PCR assay was as little as 10 copies of the BoHV-1 DNA per reaction. The modified real-time PCR assay could successfully differentiate wild-type and gE-deleted BoHV-1 strains based on gene specific melting temperatures (Tm) peaks. Our results have shown that the EGRT-PCR developed in this study might prove to be a promising tool in disease management by enabling rapid differentiation of wild-type and gE-deleted strains of BoHV-1.
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Affiliation(s)
- Sachin S Pawar
- a Division of Veterinary Biotechnology , Indian Veterinary Research Institute , Izatnagar , India
| | - Chetan D Meshram
- a Division of Veterinary Biotechnology , Indian Veterinary Research Institute , Izatnagar , India
| | - Niraj K Singh
- b School of Animal Biotechnology , Guru Angad Dev Veterinary and Animal Sciences University , Ludhiana , India
| | - Mohini Saini
- c Division of Biochemistry , Indian Veterinary Research Institute , Izatnagar , India
| | - B P Mishra
- a Division of Veterinary Biotechnology , Indian Veterinary Research Institute , Izatnagar , India
| | - Praveen K Gupta
- a Division of Veterinary Biotechnology , Indian Veterinary Research Institute , Izatnagar , India
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16
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Jiang S, He Y, Zhang Y, Zhang X, Jiang L, Wang Z, Zhu Q, Ma X. Assessment of self-produced PCR methods for the detection ofToxoplasma gondiiDNA in meat. J Food Saf 2016. [DOI: 10.1111/jfs.12330] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Shoufu Jiang
- Department of Parasitic Disease Control; Shanghai Municipal Center for Disease Control and Prevention; Shanghai 200336 China
| | - Yanyan He
- Department of Parasitic Disease Control; Shanghai Municipal Center for Disease Control and Prevention; Shanghai 200336 China
| | - Yaoguang Zhang
- Department of Parasitic Disease Control; Shanghai Municipal Center for Disease Control and Prevention; Shanghai 200336 China
| | - Xiaoping Zhang
- Department of Parasitic Disease Control; Shanghai Municipal Center for Disease Control and Prevention; Shanghai 200336 China
| | - Li Jiang
- Department of Parasitic Disease Control; Shanghai Municipal Center for Disease Control and Prevention; Shanghai 200336 China
| | - Zhenyu Wang
- Department of Parasitic Disease Control; Shanghai Municipal Center for Disease Control and Prevention; Shanghai 200336 China
| | - Qian Zhu
- Department of Parasitic Disease Control; Shanghai Municipal Center for Disease Control and Prevention; Shanghai 200336 China
| | - Xiaojiang Ma
- Department of Parasitic Disease Control; Shanghai Municipal Center for Disease Control and Prevention; Shanghai 200336 China
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17
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Lamaningao P, Kanda S, Laimanivong S, Shimono T, Darcy AW, Phyaluanglath A, Mishima N, Nishiyama T. Development of a PCR Assay for Diagnosing Trematode (Opisthorchis and Haplorchis) Infections in Human Stools. Am J Trop Med Hyg 2016; 96:221-228. [PMID: 27821695 DOI: 10.4269/ajtmh.16-0165] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2016] [Accepted: 09/22/2016] [Indexed: 01/20/2023] Open
Abstract
We developed a combined conventional polymerase chain reaction (PCR) and real-time PCR (qPCR)-based assay for detecting and discriminating between Opisthorchis viverrini and Haplorchis taichui parasite infections. The first PCR amplifies the mitochondrial cytochrome c oxidase subunit I (COI) genes of parasites, and differential diagnosis is achieved by performing qPCR with specific primers and SYBR Green I. The detection limit of the assay was found to be 2.0 × 102 plasmid copies in a test in which a stool sample was spiked with a single egg, which is equivalent to 5 eggs per gram (EPG). The testing of 34 clinical stool samples that had been demonstrated to contain "Opisthorchis-like" eggs by microscopy showed that the novel assay exhibited a sensitivity of 100% for "Opisthorchis-like" parasitic infections, and 71% and 91% of these samples were found to be infected with O. viverrini and H. taichui, respectively. A further four parasitic infections were diagnosed in the 16 negative samples, and the microscopic findings of these samples were confirmed to be false negatives by sequencing analysis. The assay also displayed high specificity during the testing of 10 samples containing other common parasites. The fact that our qPCR SYBR Green I-based assay detected submicroscopic traces of parasitic DNA and was able to differentiate between parasites that produce eggs with similar morphologies indicates that it has a good potential for development of diagnostic application to use in areas where multiple parasites coexist.
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Affiliation(s)
- Pheophet Lamaningao
- Department of Public Health, Kansai Medical University, Osaka, Japan. .,Regenerative Research Center for Intractable Diseases, Kansai Medical University, Osaka, Japan
| | - Seiji Kanda
- Department of Public Health, Kansai Medical University, Osaka, Japan. .,Regenerative Research Center for Intractable Diseases, Kansai Medical University, Osaka, Japan
| | - Sakhone Laimanivong
- Center of Malariology, Parasitology, and Entomology, Ministry of Health, Vientiane, Lao People's Democratic Republic
| | - Takaki Shimono
- Department of Public Health, Kansai Medical University, Osaka, Japan.,Regenerative Research Center for Intractable Diseases, Kansai Medical University, Osaka, Japan
| | | | - Amphay Phyaluanglath
- Clinical Laboratory, Mahosot Hospital, Ministry of Health, Vientiane, Lao People's Democratic Republic
| | - Nobuyuki Mishima
- Department of Public Health, Kansai Medical University, Osaka, Japan
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18
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Li J, Li W, Mao L, Hao F, Yang L, Zhang W, Jiang J. Rapid detection of novel caprine parainfluenza virus type 3 (CPIV3) using a TaqMan-based RT-qPCR. J Virol Methods 2016; 236:126-131. [PMID: 27448824 DOI: 10.1016/j.jviromet.2016.07.016] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2016] [Revised: 07/17/2016] [Accepted: 07/18/2016] [Indexed: 12/22/2022]
Abstract
Parainfluenza virus type 3 (PIV3) is one of the most important respiratory pathogens for humans and many animals. A novel caprine PIV3 (CPIV3) was recently identified and isolated from Chinese goat flocks with respiratory disease. In order to develop rapid and sensitive methods for CPIV3 detection in infected goats, a TaqMan RT-qPCR was established in this study based on the primers and probe designed to amplify a 150 nucleotide-long region located within the M gene of the virus. The method was able to detect about 1.0×10(1) DNA copies/μL with an efficiency of 99.6% and a R(2) value of 0.997. There were no cross-reaction observed using this technique against peste des petits ruminants virus (PPRV), border disease virus (BDV), bluetongue virus (BTV) and bovine viral diarrhea virus (BVDV). One hundred and fourteen samples, including nasal swabs, feces swabs, sera, hearts, livers, spleens, lungs, kidneys, tracheas and hilar lymph nodes (HLNs) from six challenged goats, were evaluated by this technique. Using TaqMan RT-qPCR, CPIV3 was positively detected in 51 of 114 samples (44.74%), which was higher than RT-PCR (27.19%, 31/114) and virus isolation (14.9%, 17/114), respectively. The method also gave higher positive detection rate (35%, 42/120) than RT-PCR (28.33%, 34/120) from clinical samples. These data indicated that this method could be used for faster and more accurate monitoring of viral load, disease progression and vaccination efficacy of CPIV3 in goat flocks.
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Affiliation(s)
- Jizong Li
- Institute of Veterinary Medicine, Jiangsu Academy of Agricultural Sciences, Key Laboratory of Veterinary Biological Engineering and Technology, Ministry of Agriculture, National Center for Engineering Research of Veterinary Bio-products, Nanjing 210014, China
| | - Wenliang Li
- Institute of Veterinary Medicine, Jiangsu Academy of Agricultural Sciences, Key Laboratory of Veterinary Biological Engineering and Technology, Ministry of Agriculture, National Center for Engineering Research of Veterinary Bio-products, Nanjing 210014, China
| | - Li Mao
- Institute of Veterinary Medicine, Jiangsu Academy of Agricultural Sciences, Key Laboratory of Veterinary Biological Engineering and Technology, Ministry of Agriculture, National Center for Engineering Research of Veterinary Bio-products, Nanjing 210014, China
| | - Fei Hao
- Institute of Veterinary Medicine, Jiangsu Academy of Agricultural Sciences, Key Laboratory of Veterinary Biological Engineering and Technology, Ministry of Agriculture, National Center for Engineering Research of Veterinary Bio-products, Nanjing 210014, China
| | - Leilei Yang
- Institute of Veterinary Medicine, Jiangsu Academy of Agricultural Sciences, Key Laboratory of Veterinary Biological Engineering and Technology, Ministry of Agriculture, National Center for Engineering Research of Veterinary Bio-products, Nanjing 210014, China
| | - Wenwen Zhang
- Institute of Veterinary Medicine, Jiangsu Academy of Agricultural Sciences, Key Laboratory of Veterinary Biological Engineering and Technology, Ministry of Agriculture, National Center for Engineering Research of Veterinary Bio-products, Nanjing 210014, China
| | - Jieyuan Jiang
- Institute of Veterinary Medicine, Jiangsu Academy of Agricultural Sciences, Key Laboratory of Veterinary Biological Engineering and Technology, Ministry of Agriculture, National Center for Engineering Research of Veterinary Bio-products, Nanjing 210014, China.
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19
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Jiménez-Clavero MA, Agüero M, Rojo G, Gómez-Tejedor C. A New Fluorogenic Real-Time RT-PCR Assay for Detection of Lineage 1 and Lineage 2 West Nile Viruses. J Vet Diagn Invest 2016; 18:459-62. [PMID: 17037613 DOI: 10.1177/104063870601800505] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
West Nile virus represents an emerging threat for animal and human health worldwide. This virus exhibits a marked genetic variation, with at least 2 distinct evolutionary lineages. Lineage 1 has been recognized in Africa, Asia, Europe, Oceania, and more recently in the Americas, whereas lineage 2 is restricted to Africa. Perhaps for this reason, the available real-time RT-PCR methods for detecting West Nile virus genome have mainly focused on lineage 1. However, both viruses may potentially be spread beyond their endemic areas by migratory birds. This report describes a new real-time reverse transcription-PCR (RT-PCR) method based on a 59-Taq nuclease-39 minor groove binder DNA probe (TaqMan MGBE) that allows the detection of a wide range of West Nile virus isolates, including both lineages 1 and 2. This method was able to detect West Nile viruses from different origins (North and Central Africa, Middle East, Europe, and North America), whereas other flaviviruses (Usutu, Dengue, Yellow fever) analyzed in parallel remained negative. The sensitivity achieved by this assay was 1022-1023 pfu/tube. This method, which can be performed in 96-well format, could be suitable for the large-scale surveillance of West Nile virus in areas where both lineages can potentially spread.
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Affiliation(s)
- Miguel Angel Jiménez-Clavero
- Departamento de Enfermedades Emergentes, Laboratorio Central de Veterinaria, Ctra. Algete, km 8, 28110, Algete (Madrid), Spain.
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20
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David S, Abraham AM. Epidemiological and clinical aspects on West Nile virus, a globally emerging pathogen. Infect Dis (Lond) 2016; 48:571-86. [PMID: 27207312 DOI: 10.3109/23744235.2016.1164890] [Citation(s) in RCA: 56] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
BACKGROUND Since the isolation of West Nile virus (WNV) in 1937, in Uganda, it has spread globally, causing significant morbidity and mortality. While birds serve as amplifier hosts, mosquitoes of the Culex genus function as vectors. Humans and horses are dead end hosts. The clinical manifestations of West Nile infection in humans range from asymptomatic illness to West Nile encephalitis. METHODS The laboratory offers an array of tests, the preferred method being detection of RNA and serum IgM for WNV, which, if detected, confirms the clinical diagnosis. Although no definitive antiviral therapy and vaccine are available for humans, many approaches are being studied. STUDY This article will review the current literature of the natural cycle, geographical distribution, virology, replication cycle, molecular epidemiology, pathogenesis, laboratory diagnosis, clinical manifestations, blood donor screening for WNV, treatment, prevention and vaccines.
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Affiliation(s)
- Shoba David
- a Department of Clinical Virology , Christian Medical College , Vellore , Tamil Nadu , India
| | - Asha Mary Abraham
- a Department of Clinical Virology , Christian Medical College , Vellore , Tamil Nadu , India
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21
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Detection of dengue, west Nile virus, rickettsiosis and leptospirosis by a new real-time PCR strategy. SPRINGERPLUS 2016; 5:671. [PMID: 27350908 PMCID: PMC4899400 DOI: 10.1186/s40064-016-2318-y] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/29/2015] [Accepted: 05/10/2016] [Indexed: 02/07/2023]
Abstract
Dengue virus (DENV) infection causes sudden fever along with several nonspecific signs and symptoms and in severe cases, death. DENV is transmitted to people by Aedes aegypti and Ae. albopictus mosquitoes, whose populations increase during rainy season. West Nile Virus (WNV), Rickettsia spp. and Leptospira spp. are fever-causing pathogens that share many of the initial symptoms of DENV infection and also thrive in the rainy season. Outbreaks in some regions may be due to any of these pathogens that can co-circulate. Plus, they are clinically indistinguishable until severe symptoms appear, even though these diseases should be treated differently. An effective differential diagnosis would help clinicians and vector control departments to make right decisions for control and treatment of these diseases. Therefore, we developed four different SYBR green®-based reverse transcription quantitative PCR (RT-qPCR) assays for simultaneous detection of DENV, WNV, Rickettsia spp. and Leptospira spp. The assay has been optimized to yield results in less than 1 h; and in order to reduce contamination risk, all reagents were premixed and lyophilized on 96 well plates and thus only requires the addition of water and total nucleic acids from the sample. Sensitivities of the assays were less than 100 copies of nucleic acid targeted for these four pathogens. Assays did not show cross reactivity with any of the four pathogens nor to human nucleic acids. We are presenting a sensitive and selective kit that detects four relevant pathogens from tropical regions, that is quick, cost-effective and easy to use.
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22
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Babu B, Jeyaprakash A, Jones D, Schubert TS, Baker C, Washburn BK, Miller SH, Poduch K, Knox GW, Ochoa-Corona FM, Paret ML. Development of a rapid, sensitive TaqMan real-time RT-PCR assay for the detection of Rose rosette virus using multiple gene targets. J Virol Methods 2016; 235:41-50. [PMID: 27210549 DOI: 10.1016/j.jviromet.2016.05.010] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2015] [Revised: 05/02/2016] [Accepted: 05/15/2016] [Indexed: 12/30/2022]
Abstract
Rose rosette virus (RRV), belonging to the genus Emaravirus, is a highly destructive pathogen that causes rose rosette disease. The disease is a major concern for the rose industry in the U.S. due to the lack of highly sensitive methods for early detection of RRV. This is critical, as early identification of the infected plants and eradication is necessary in minimizing the risks associated with the spread of the disease. A highly reliable, specific and sensitive detection assay is thus required to test and confirm the presence of RRV in suspected plant samples. In this study a TaqMan real-time reverse transcription-polymerase chain reaction (RT-PCR) assay was developed for the detection of RRV from infected roses, utilizing multiple gene targets. Four pairs of primers and probes; two of them (RRV_2-1 and RRV_2-2) based on the consensus sequences of the glycoprotein gene (RNA2) and the other two (RRV_3-2 and RRV_3-5) based on the nucleocapsid gene (RNA3) were designed. The specificity of the primers and probes was evaluated against other representative viruses infecting roses, belonging to the genera Alfamovirus, Cucumovirus, Ilarvirus, Nepovirus, Tobamovirus, and Tospovirus and one Emaravirus (Wheat mosaic virus). Dilution assays using the in vitro transcripts (spiked with total RNA from healthy plants, and non-spiked) showed that all the primers and probes are highly sensitive in consistently detecting RRV with a detection limit of 1 fg. Testing of the infected plants over a period of time (three times in monthly intervals) indicated high reproducibility, with the primer/probe RRV_3-5 showing 100% positive detection, while RRV_2-1, RRV_2-2 and RRV_3-2 showed 90% positive detection. The developed real-time RT-PCR assay is reliable, highly sensitive, and can be easily used in diagnostic laboratories for testing and confirmation of RRV.
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Affiliation(s)
- Binoy Babu
- North Florida Research and Education Center, Institute of Food and Agricultural Sciences, University of Florida, Quincy, FL 32351, United States.
| | - Ayyamperumal Jeyaprakash
- Division of Plant Industry, Florida Department of Agriculture and Consumer Services, Gainesville, FL 32608, United States
| | - Debra Jones
- Division of Plant Industry, Florida Department of Agriculture and Consumer Services, Gainesville, FL 32608, United States
| | - Timothy S Schubert
- Division of Plant Industry, Florida Department of Agriculture and Consumer Services, Gainesville, FL 32608, United States
| | - Carlye Baker
- Division of Plant Industry, Florida Department of Agriculture and Consumer Services, Gainesville, FL 32608, United States
| | - Brian K Washburn
- Department of Biological Science, Florida State University, Tallahassee, FL 32306, United States
| | - Steven H Miller
- Department of Biological Science, Florida State University, Tallahassee, FL 32306, United States
| | - Kristina Poduch
- Department of Biological Science, Florida State University, Tallahassee, FL 32306, United States
| | - Gary W Knox
- North Florida Research and Education Center, Institute of Food and Agricultural Sciences, University of Florida, Quincy, FL 32351, United States
| | - Francisco M Ochoa-Corona
- Department of Entomology and Plant Pathology, Oklahoma State University, Stillwater, OK 74078, United States
| | - Mathews L Paret
- North Florida Research and Education Center, Institute of Food and Agricultural Sciences, University of Florida, Quincy, FL 32351, United States.
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23
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Zheng X, Liu G, Opriessnig T, Wang Z, Yang Z, Jiang Y. Rapid detection and grouping of porcine bocaviruses by an EvaGreen(®) based multiplex real-time PCR assay using melting curve analysis. Mol Cell Probes 2016; 30:195-204. [PMID: 27180269 DOI: 10.1016/j.mcp.2016.05.001] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2016] [Revised: 05/08/2016] [Accepted: 05/10/2016] [Indexed: 01/20/2023]
Abstract
Several novel porcine bocaviruses (PBoVs) have been identified in pigs in recent years and association of these viruses with respiratory signs or diarrhea has been suggested. In this study, an EvaGreen(®)-based multiplex real-time PCR (EG-mPCR) with melting curve analysis was developed for simultaneous detection and grouping of novel PBoVs into the same genogroups G1, G2 and G3. Each target produced a specific amplicon with a melting peak of 81.3 ± 0.34 °C for PBoV G1, 78.2 ± 0.37 °C for PBoV G2, and 85.0 ± 0.29 °C for PBoV G3. Non-specific reactions were not observed when other pig viruses were used to assess the EG-mPCR assay. The sensitivity of the EG-mPCR assay using purified plasmid constructs containing the specific viral target fragments was 100 copies for PBoV G1, 50 for PBoV G2 and 100 for PBoV G3. The assay is able to detect and distinguish three PBoV groups with intra-assay and inter-assay variations ranging from 0.13 to 1.59%. The newly established EG-mPCR assay was validated with 227 field samples from pigs. PBoV G1, G2 and G3 was detected in 15.0%, 25.1% and 41.9% of the investigated samples and coinfections of two or three PBoV groups were also detected in 25.1% of the cases, indicating that all PBoV groups are prevalent in Chinese pigs. The agreement of the EG-mPCR assay with an EvaGreen-based singleplex real-time PCR (EG-sPCR) assay was 99.1%. This EG-mPCR will serve as a rapid, sensitive, reliable and cost effective alternative for routine surveillance testing of multiple PBoVs in pigs and will enhance our understanding of the epidemiological features and possible also pathogenetic changes associated with these viruses in pigs.
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Affiliation(s)
- Xiaowen Zheng
- College of Life Sciences, Zhejiang Sci-Tech University, Hangzhou, China
| | - Gaopeng Liu
- College of Life Sciences, Zhejiang Sci-Tech University, Hangzhou, China
| | - Tanja Opriessnig
- The Roslin Institute and The Royal (Dick) School of Veterinary Studies, University of Edinburgh, Midlothian EH25 9RG, UK; Department of Veterinary Diagnostic and Production Animal Medicine, College of Veterinary Medicine, Iowa State University, Ames, IA, USA
| | - Zining Wang
- College of Life Sciences, Zhejiang Sci-Tech University, Hangzhou, China
| | - Zongqi Yang
- College of Life Sciences, Zhejiang Sci-Tech University, Hangzhou, China
| | - Yonghou Jiang
- College of Life Sciences, Zhejiang Sci-Tech University, Hangzhou, China.
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24
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Dash PK, Agarwal A, Sharma S, Saha A, Joshi G, Gopalan N, Sukumaran D, Parida MM. Development of a SYBR green I-based quantitative RT-PCR for Ross River virus: Application in vector competence studies and antiviral drug evaluation. J Virol Methods 2016; 234:107-14. [PMID: 27105737 PMCID: PMC7119768 DOI: 10.1016/j.jviromet.2016.04.011] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2016] [Revised: 04/14/2016] [Accepted: 04/15/2016] [Indexed: 11/16/2022]
Abstract
Ross River virus (RRV) is an emerging Alphavirus and is presently endemic in many parts of Oceania. Keeping in mind its emergence, we developed a molecular detection system and utilized it to study vector competence and evaluate activity of antiviral compounds against RRV. A SYBR Green I-based quantitative RT-PCR for detection of RRV was developed targeting the E2 gene, with a detection limit of 100 RNA copies/reaction. The specificity was confirmed with closely related Alphaviruses and Flaviviruses. The assay was applied to study the vector competence of Indian Aedes aegypti for RRV, which revealed 100% infection and dissemination rate with 75% transmission rate. Viral RNA was found in saliva as early as 3day post infection (dpi). Further application of the assay in antiviral drug evaluation revealed the superior in vitro activity of ribavirin compared to chloroquine in Vero cells. Successful demonstration of this assay to detect RRV in low titre mosquito samples makes it a sensitive tool in vector surveillance. This study also showed that Indian Ae. aegypti are well competent to transmit RRV highlighting the risk of its introduction to naïve territories across continents. Further validation of this assay, revealed its utility in screening of potential antivirals against RRV.
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Affiliation(s)
- Paban Kumar Dash
- Division of Virology, Defence R and D Establishment, Jhansi Road, Gwalior 474 002, M.P., India.
| | - Ankita Agarwal
- Division of Virology, Defence R and D Establishment, Jhansi Road, Gwalior 474 002, M.P., India
| | - Shashi Sharma
- Division of Virology, Defence R and D Establishment, Jhansi Road, Gwalior 474 002, M.P., India
| | - Amrita Saha
- Division of Virology, Defence R and D Establishment, Jhansi Road, Gwalior 474 002, M.P., India
| | - Gaurav Joshi
- Division of Virology, Defence R and D Establishment, Jhansi Road, Gwalior 474 002, M.P., India
| | - Natarajan Gopalan
- Vector Management Division, Defence R and D Establishment, Jhansi Road, Gwalior 474 002, M.P., India
| | - Devanathan Sukumaran
- Vector Management Division, Defence R and D Establishment, Jhansi Road, Gwalior 474 002, M.P., India
| | - Man Mohan Parida
- Division of Virology, Defence R and D Establishment, Jhansi Road, Gwalior 474 002, M.P., India
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25
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Nagy A, Černíková L, Vitásková E, Křivda V, Dán Á, Dirbáková Z, Jiřincová H, Procházka B, Sedlák K, Havlíčková M. MeltMan: Optimization, Evaluation, and Universal Application of a qPCR System Integrating the TaqMan qPCR and Melting Analysis into a Single Assay. PLoS One 2016; 11:e0151204. [PMID: 27031831 PMCID: PMC4816343 DOI: 10.1371/journal.pone.0151204] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2015] [Accepted: 02/23/2016] [Indexed: 12/05/2022] Open
Abstract
In the present work, we optimised and evaluated a qPCR system integrating 6-FAM (6-carboxyfluorescein)-labelled TaqMan probes and melting analysis using the SYTO 82 (S82) DNA binding dye in a single reaction. We investigated the influence of the S82 on various TaqMan and melting analysis parameters and defined its optimal concentration. In the next step, the method was evaluated in 36 different TaqMan assays with a total of 729 paired reactions using various DNA and RNA templates, including field specimens. In addition, the melting profiles of interest were correlated with the electrophoretic patterns. We proved that the S82 is fully compatible with the FAM-TaqMan system. Further, the advantages of this approach in routine diagnostic TaqMan qPCR were illustrated with practical examples. These included solving problems with flat or other atypical amplification curves or even false negativity as a result of probe binding failure. Our data clearly show that the integration of the TaqMan qPCR and melting analysis into a single assay provides an additional control option as well as the opportunity to perform more complex analyses, get more data from the reactions, and obtain analysis results with higher confidence.
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Affiliation(s)
- Alexander Nagy
- Laboratory of Molecular Methods, State Veterinary Institute Prague, Prague, Czech Republic
- National Reference Laboratory for Influenza, National Institute of Public Health, Prague, Czech Republic
- * E-mail:
| | - Lenka Černíková
- Laboratory of Molecular Methods, State Veterinary Institute Prague, Prague, Czech Republic
| | - Eliška Vitásková
- Laboratory of Molecular Methods, State Veterinary Institute Prague, Prague, Czech Republic
| | - Vlastimil Křivda
- Laboratory of Molecular Methods, State Veterinary Institute Prague, Prague, Czech Republic
- Department of Virology and Serology, State Veterinary Institute Prague, Prague, Czech Republic
| | - Ádám Dán
- National Food Chain Safety Office, Veterinary Diagnostic Directorate, Molecular Biology Laboratory, Budapest, Hungary
| | - Zuzana Dirbáková
- Department of Virology, State Veterinary Institute Zvolen, Zvolen, Slovak Republic
| | - Helena Jiřincová
- National Reference Laboratory for Influenza, National Institute of Public Health, Prague, Czech Republic
| | - Bohumír Procházka
- Department of Informatics and Biostatistics, National Institute of Public Health, Prague, Czech Republic
| | - Kamil Sedlák
- Department of Virology and Serology, State Veterinary Institute Prague, Prague, Czech Republic
| | - Martina Havlíčková
- National Reference Laboratory for Influenza, National Institute of Public Health, Prague, Czech Republic
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26
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A real time Taqman RT-PCR for the detection of rabbit hemorrhagic disease virus 2 (RHDV2). J Virol Methods 2015; 219:90-95. [DOI: 10.1016/j.jviromet.2015.03.017] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2015] [Revised: 03/06/2015] [Accepted: 03/18/2015] [Indexed: 11/23/2022]
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27
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Zhang Z, Liu S, Ma C, Zhao P, Cui Z. Absolute quantification of a very virulent Marek's disease virus dynamic quantity and distributions in different tissues. Poult Sci 2015; 94:1150-7. [PMID: 25834249 DOI: 10.3382/ps/pev063] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/01/2015] [Indexed: 11/20/2022] Open
Abstract
Chickens infected with Marek's disease virus (MDV) carry the virus consistently for a long time, which increases the incidence and rate of virus-induced multi-organ tumors and increases its potential for horizontal transmission. There is a positive correlation between very virulent (vv) MDV quantity and the pathology. The purpose of this study was to determine the vvMDV loads dynamics in different phases, and the correlation between the viral quantity and tumor development. We used a SYBR Green duplex real-time quantitative PCR (q-PCR) assay to detect and quantify MDV loads and distributions in different tissues, targeting the Eco-Q protein gene (meq) of the virus and the house-keeping ovotransferrin (ovo) gene of chickens. The q-PCR was performed using different tissue DNA preparations derived from chickens which were infected with 1,000 pfu of the SDWJ1302 strain and tissue samples were collected from control and MDV-infected birds on 7, 10, 15, 21, 28, 40, 60, and 90 d post-infection (DPI). The data indicated that the MDV genome was almost quantifiable in immune organs of infected chickens as early as 7 DPI, and the number of MDV genome copies in the blood and different organs peaked by 28 DPI, but then gradually decreased by 40 DPI. The levels of viral quantity in the lymphocytes, liver, and spleen were all higher than those in other organs, and that in the feather follicles was the highest among different phases of MDV infection. The vvMDV could still be detected in peripheral blood and tissues by 90 DPI, and the vast existence of virus will stimulate tissue destruction. The data provided further evidence of viral infection involving multi-organ distribution and mainly involving immune organ proliferation, resulting in immunosuppression.
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Affiliation(s)
- Zhenjie Zhang
- Collaborative Innovation Center for the Origin and Control of Emerging Infectious Diseases, Taishan Medical College, Taian 271000, China
| | - Shaoqiong Liu
- College of Veterinary Medicine, Shandong Agricultural University, Taian 271018, China
| | - Chengtai Ma
- College of Veterinary Medicine, Shandong Agricultural University, Taian 271018, China
| | - Peng Zhao
- College of Veterinary Medicine, Shandong Agricultural University, Taian 271018, China
| | - Zhizhong Cui
- College of Veterinary Medicine, Shandong Agricultural University, Taian 271018, China
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28
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Chugh PE, Damania BA, Dittmer DP. Toll-like receptor-3 is dispensable for the innate microRNA response to West Nile virus (WNV). PLoS One 2014; 9:e104770. [PMID: 25127040 PMCID: PMC4134228 DOI: 10.1371/journal.pone.0104770] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2014] [Accepted: 07/16/2014] [Indexed: 12/28/2022] Open
Abstract
The innate immune response to West Nile virus (WNV) infection involves recognition through toll-like receptors (TLRs) and RIG-I-like receptors (RLRs), leading to establishment of an antiviral state. MiRNAs (miRNAs) have been shown to be reliable biomarkers of TLR activation. Here, we sought to evaluate the contribution of TLR3 and miRNAs to the host response to WNV infection. We first analyzed HEK293-NULL and HEK293-TLR3 cells for changes in the innate immune response to infection. The presence of TLR3 did not seem to affect WNV load, infectivity or phosphorylation of IRF3. Analysis of experimentally validated NFκB-responsive genes revealed a WNV-induced signature largely independent of TLR3. Since miRNAs are involved in viral pathogenesis and the innate response to infection, we sought to identify changes in miRNA expression upon infection in the presence or absence of TLR3. MiRNA profiling revealed 70 miRNAs induced following WNV infection in a TLR3-independent manner. Further analysis of predicted gene targets of WNV signature miRNAs revealed genes highly associated with pathways regulating cell death, viral pathogenesis and immune cell trafficking.
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Affiliation(s)
- Pauline E. Chugh
- Department of Microbiology and Immunology, Lineberger Comprehensive Cancer Center, Center for AIDS Research, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Blossom A. Damania
- Department of Microbiology and Immunology, Lineberger Comprehensive Cancer Center, Center for AIDS Research, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Dirk P. Dittmer
- Department of Microbiology and Immunology, Lineberger Comprehensive Cancer Center, Center for AIDS Research, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
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29
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Yamane D, McGivern DR, Wauthier E, Yi M, Madden VJ, Welsch C, Antes I, Wen Y, Chugh PE, McGee CE, Widman DG, Misumi I, Bandyopadhyay S, Kim S, Shimakami T, Oikawa T, Whitmire JK, Heise MT, Dittmer DP, Kao CC, Pitson SM, Merrill AH, Reid LM, Lemon SM. Regulation of the hepatitis C virus RNA replicase by endogenous lipid peroxidation. Nat Med 2014; 20:927-35. [PMID: 25064127 PMCID: PMC4126843 DOI: 10.1038/nm.3610] [Citation(s) in RCA: 114] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2014] [Accepted: 05/23/2014] [Indexed: 02/07/2023]
Abstract
Although oxidative tissue injury often accompanies viral infection, there is little understanding of how it influences virus replication. We show that multiple hepatitis C virus (HCV) genotypes are exquisitely sensitive to oxidative membrane damage, a property distinguishing them from other pathogenic RNA viruses. Lipid peroxidation, regulated in part through sphingosine kinase 2, severely restricts HCV replication in Huh-7 cells and primary human hepatoblasts. Endogenous oxidative membrane damage lowers the 50% effective concentration of direct-acting antivirals, suggesting critical regulation of the conformation of the NS3/4A protease and NS5B polymerase, membrane-bound HCV replicase components. Resistance to lipid peroxidation maps genetically to trans-membrane and membrane-proximal residues within these proteins, and is essential for robust replication in cell culture, as exemplified by the atypical JFH1 strain. Thus, the typical, wild-type HCV replicase is uniquely regulated by lipid peroxidation, providing a novel mechanism for attenuating replication in stressed tissue and possibly facilitating long-term viral persistence.
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Affiliation(s)
- Daisuke Yamane
- 1] Department of Medicine, Division of Infectious Diseases, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA. [2] Lineberger Comprehensive Cancer Center, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - David R McGivern
- 1] Department of Medicine, Division of Infectious Diseases, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA. [2] Lineberger Comprehensive Cancer Center, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Eliane Wauthier
- 1] Lineberger Comprehensive Cancer Center, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA. [2] Department of Cell Biology and Physiology, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - MinKyung Yi
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, Texas, USA
| | - Victoria J Madden
- Department of Pathology, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Christoph Welsch
- Department of Internal Medicine I, J.W. Goethe University Hospital, Frankfurt, Germany
| | - Iris Antes
- Center for Integrated Protein Science Munich (CIPSM), Department of Life Sciences, Technical University Munich, Freising, Germany
| | - Yahong Wen
- Department of Molecular and Cellular Biochemistry, Indiana University, Bloomington, Indiana, USA
| | - Pauline E Chugh
- 1] Lineberger Comprehensive Cancer Center, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA. [2] Department of Microbiology and Immunology, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Charles E McGee
- Department of Genetics, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Douglas G Widman
- Department of Epidemiology, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Ichiro Misumi
- Department of Genetics, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Sibali Bandyopadhyay
- 1] School of Biology, Georgia Institute of Technology, Atlanta, Georgia, USA. [2] Parker H. Petit Institute for Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, Georgia, USA
| | - Seungtaek Kim
- 1] Department of Medicine, Division of Infectious Diseases, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA. [2] Lineberger Comprehensive Cancer Center, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA. [3] Severance Biomedical Science Institute, Yonsei University College of Medicine, Seoul, Korea
| | - Tetsuro Shimakami
- 1] Department of Medicine, Division of Infectious Diseases, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA. [2] Lineberger Comprehensive Cancer Center, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Tsunekazu Oikawa
- 1] Lineberger Comprehensive Cancer Center, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA. [2] Department of Cell Biology and Physiology, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Jason K Whitmire
- 1] Lineberger Comprehensive Cancer Center, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA. [2] Department of Microbiology and Immunology, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA. [3] Department of Genetics, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Mark T Heise
- 1] Lineberger Comprehensive Cancer Center, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA. [2] Department of Genetics, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Dirk P Dittmer
- 1] Lineberger Comprehensive Cancer Center, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA. [2] Department of Microbiology and Immunology, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - C Cheng Kao
- Department of Molecular and Cellular Biochemistry, Indiana University, Bloomington, Indiana, USA
| | - Stuart M Pitson
- Centre for Cancer Biology, SA Pathology, Adelaide, South Australia, Australia
| | - Alfred H Merrill
- 1] School of Biology, Georgia Institute of Technology, Atlanta, Georgia, USA. [2] Parker H. Petit Institute for Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, Georgia, USA
| | - Lola M Reid
- 1] Lineberger Comprehensive Cancer Center, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA. [2] Department of Cell Biology and Physiology, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Stanley M Lemon
- 1] Department of Medicine, Division of Infectious Diseases, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA. [2] Lineberger Comprehensive Cancer Center, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA. [3] Department of Microbiology and Immunology, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
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30
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Hirota J, Shimizu S, Shibahara T. Application of West Nile virus diagnostic techniques. Expert Rev Anti Infect Ther 2014; 11:793-803. [PMID: 23977935 DOI: 10.1586/14787210.2013.814824] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
West Nile virus (WNV) is an enveloped RNA virus in the family Flaviviridae and belongs to Japanese encephalitis virus serocomplex group. The WNV has a wide geographic distribution that includes Africa, Europe, Asia, America and Australia. Recently, it has re-emerged as an important pathogenic organism, illustrated by the series of WNV outbreaks in North America and in Europe. Several hundred people are sacrificed by WNV infection every year. WNV can infect many mammals, birds, reptiles and amphibians. A variety of diagnoses for WNV infection have been developed, such as virus isolation, nucleotide amplification, antigen detection and serology. Flaviviruses, including WNV, share common nucleotide sequences and antigenic epitopes. Understanding these properties that can influence cross-reactivity is important for accurate diagnosis, especially because areas with multiple flaviviruses are currently expanding. Herein, the authors outline the different diagnostic methods for detecting WNV infection as well as important considerations in using these methods.
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Affiliation(s)
- Jiro Hirota
- National Institute of Animal Health, National Agriculture and Food Research Organization, 3-1-5 Kannondai, Tsukuba, Ibaraki 305-0856, Japan
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31
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Liegler T, Abdel-Mohsen M, Bentley LG, Atchison R, Schmidt T, Javier J, Mehrotra M, Eden C, Glidden DV, McMahan V, Anderson PL, Li P, Wong JK, Buchbinder S, Guanira JV, Grant RM. HIV-1 drug resistance in the iPrEx preexposure prophylaxis trial. J Infect Dis 2014; 210:1217-27. [PMID: 24740633 PMCID: PMC4176446 DOI: 10.1093/infdis/jiu233] [Citation(s) in RCA: 63] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
BACKGROUND The iPrEx study demonstrated that combination oral emtricitabine and tenofovir disoproxil fumarate (FTC/TDF) as preexposure prophylaxis (PrEP) protects against HIV acquisition in men who have sex with men and transgender women. Selection for drug resistance could offset PrEP benefits. METHODS Phenotypic and genotypic clinical resistance assays characterized major drug resistant mutations. Minor variants with FTC/TDF mutations K65R, K70E, M184V/I were measured using 454 deep sequencing and a novel allele-specific polymerase chain reaction (AS-PCR) diagnostic tolerant to sequence heterogeneity. RESULTS Control of primer-binding site heterogeneity resulted in improved accuracy of minor variant measurements by AS-PCR. Of the 48 on-study infections randomized to FTC/TDF, none showed FTC/TDF mutations by clinical assays despite detectable drug levels in 8 participants. Two randomized to FTC/TDF had minor variant M184I detected at 0.53% by AS-PCR or 0.75% by deep sequencing, only 1 of which had low but detectable drug levels. Among those with acute infection at randomization to FTC/TDF, M184V or I mutations that were predominant at seroconversion waned to background levels within 24 weeks after discontinuing drug. CONCLUSIONS Drug resistance was rare in iPrEx on-study FTC/TDF-randomized seroconverters, and only as low-frequency minor variants. FTC resistance among those initiating PrEP with acute infection waned rapidly after drug discontinuation. Clinical Trials Registration.NCT00458393.
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Affiliation(s)
- Teri Liegler
- Department of Medicine, University of California AIDS Research Institute, University of California
| | | | | | | | | | | | | | | | - David V Glidden
- Department of Epidemiology, University of California, San Francisco
| | | | - Peter L Anderson
- Department of Pharmaceutical Sciences, University of Colorado Denver, Aurora
| | - Peilin Li
- Veterans Affairs Medical Center, San Francisco
| | | | - Susan Buchbinder
- Bridge HIV, San Francisco Department of Public Health, California
| | | | - Robert M Grant
- Department of Medicine, University of California J. David Gladstone Institutes
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Kumar JS, Saxena D, Parida M. Development and comparative evaluation of SYBR Green I-based one-step real-time RT-PCR assay for detection and quantification of West Nile virus in human patients. Mol Cell Probes 2014; 28:221-7. [PMID: 24732288 DOI: 10.1016/j.mcp.2014.03.005] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2013] [Revised: 03/05/2014] [Accepted: 03/16/2014] [Indexed: 11/27/2022]
Abstract
The recent outbreaks of West Nile Virus (WNV) in the Northeastern American continents and other regions of the world have made it essential to develop an efficient protocol for surveillance of WN virus. Nucleic acid based techniques like, RT-PCR have the advantage of sensitivity, specificity and rapidity. A one step single tube Env gene specific real-time RT-PCR was developed for early and reliable clinical diagnosis of WNV infection in clinical samples. The applicability of this assay for clinical diagnosis was validated with 105 suspected acute-phase serum and plasma samples from the recent epidemic of mysterious fever in Tamil Nadu, India in 2009-10. The comparative evaluation revealed the higher sensitivity of real-time RT-PCR assay by picking up 4 additional samples with low copy number of template in comparison to conventional RT-PCR. All the real-time positive samples further confirmed by CDC reported TaqMan real-time RT-PCR and quantitative real-time RT-PCR assays for the simultaneous detection of WNV lineage 1 and 2 strains. The quantitation of the viral load samples was done using a standard curve. These findings demonstrated that the assay has the potential usefulness for clinical diagnosis due to detection and quantification of WNV in acute-phase patient serum samples.
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Affiliation(s)
- Jyoti S Kumar
- Division of Virology, Defence Research and Development Establishment (DRDE), Jhansi Road, Gwalior 474002, MP, India.
| | - Divyasha Saxena
- Division of Virology, Defence Research and Development Establishment (DRDE), Jhansi Road, Gwalior 474002, MP, India
| | - Manmohan Parida
- Division of Virology, Defence Research and Development Establishment (DRDE), Jhansi Road, Gwalior 474002, MP, India
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Zhu Z, Fan H, Qi X, Qi Y, Shi Z, Wang H, Cui L, Zhou M. Development and evaluation of a SYBR green-based real time RT-PCR assay for detection of the emerging avian influenza A (H7N9) virus. PLoS One 2013; 8:e80028. [PMID: 24278234 PMCID: PMC3835827 DOI: 10.1371/journal.pone.0080028] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2013] [Accepted: 09/27/2013] [Indexed: 11/19/2022] Open
Abstract
Most recently a novel avian-origin influenza A (H7N9) virus emerged in China and has been associated with lots of human infection and fatal cases. Genetic analysis of the viral genome revealed that this reassortant virus might be better adapted to humans than other avian influenza viruses. Molecular diagnostic methods are thus urgently needed in public health laboratories. In this study, a SYBR green-based one-step real time reverse transcription-PCR (RT-PCR) was developed to detect the novel H7N9 virus. The primer pairs on the basis of the hemagglutinin and neuraminidase gene sequences of H7N9 viruses amplified subtype-specific fragments with Tm values of 80.77±0.06°C for H7 and 81.20±0.17°C for N9 respectively. The standard curves showed a dynamic linear range across 6 log units of RNA copy number (106 to 101 copies/ µl) with a detection limit of 10 copies per reaction for both H7 and N9 assays by using serial ten-fold diluted in-vitro transcribed viral RNA. In addition, no cross-reactivity was observed with seasonal H1N1, H1N1 pdm09, H3N2, H5N1 and H9N2 viruses as well as other human respiratory viruses. When the assay was further evaluated in H7N9 virus infected clinical samples, positive amplification signals were obtained in all of the specimens with the accordance between H7 and N9 assays. Therefore, the established SYBR green-based real time RT-PCR assay could provide a rapid, sensitive, specific and reliable alternative approach with lower costs for high throughput screening of suspected samples from humans, animals and environments in first line public health laboratories.
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Affiliation(s)
- Zheng Zhu
- Institute of Pathogenic Microbiology, Jiangsu Provincial Center for Disease Control and Prevention, Key Laboratory of Enteric Pathogenic Microbiology, Ministry of Health, Nanjing, China
| | - Huan Fan
- Institute of Pathogenic Microbiology, Jiangsu Provincial Center for Disease Control and Prevention, Key Laboratory of Enteric Pathogenic Microbiology, Ministry of Health, Nanjing, China
| | - Xian Qi
- Department of Acute Infectious Diseases Control and Prevention, Jiangsu Provincial Center for Disease Control and Prevention, Nanjing, China
| | - Yuhua Qi
- Institute of Pathogenic Microbiology, Jiangsu Provincial Center for Disease Control and Prevention, Key Laboratory of Enteric Pathogenic Microbiology, Ministry of Health, Nanjing, China
| | - Zhiyang Shi
- Institute of Pathogenic Microbiology, Jiangsu Provincial Center for Disease Control and Prevention, Key Laboratory of Enteric Pathogenic Microbiology, Ministry of Health, Nanjing, China
| | - Hua Wang
- Institute of Pathogenic Microbiology, Jiangsu Provincial Center for Disease Control and Prevention, Key Laboratory of Enteric Pathogenic Microbiology, Ministry of Health, Nanjing, China
| | - Lunbiao Cui
- Institute of Pathogenic Microbiology, Jiangsu Provincial Center for Disease Control and Prevention, Key Laboratory of Enteric Pathogenic Microbiology, Ministry of Health, Nanjing, China
- * E-mail: (LC); (MZ)
| | - Minghao Zhou
- Institute of Pathogenic Microbiology, Jiangsu Provincial Center for Disease Control and Prevention, Key Laboratory of Enteric Pathogenic Microbiology, Ministry of Health, Nanjing, China
- * E-mail: (LC); (MZ)
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Sambri V, Capobianchi MR, Cavrini F, Charrel R, Donoso-Mantke O, Escadafal C, Franco L, Gaibani P, Gould EA, Niedrig M, Papa A, Pierro A, Rossini G, Sanchini A, Tenorio A, Varani S, Vázquez A, Vocale C, Zeller H. Diagnosis of west nile virus human infections: overview and proposal of diagnostic protocols considering the results of external quality assessment studies. Viruses 2013; 5:2329-48. [PMID: 24072061 PMCID: PMC3814591 DOI: 10.3390/v5102329] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2013] [Revised: 08/28/2013] [Accepted: 09/09/2013] [Indexed: 01/14/2023] Open
Abstract
West Nile virus, genus Flavivirus, is transmitted between birds and occasionally other animals by ornithophilic mosquitoes. This virus also infects humans causing asymptomatic infections in about 85% of cases and <1% of clinical cases progress to severe neuroinvasive disease. The virus also presents a threat since most infections remain unapparent. However, the virus contained in blood and organs from asymptomatically infected donors can be transmitted to recipients of these infectious tissues. This paper reviews the presently available methods to achieve the laboratory diagnosis of West Nile virus infections in humans, discussing the most prominent advantages and disadvantages of each in light of the results obtained during four different External Quality Assessment studies carried out by the European Network for ‘Imported’ Viral Diseases (ENIVD).
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Affiliation(s)
- Vittorio Sambri
- Operative Unit of Clinical Microbiology, Regional Reference Centre for Microbiological Emergencies, S. Orsola-Malpighi University Hospital, Bologna 40138, Italy; E-Mails: (V.S.); (F.C.); (P.G.); (A.P.); (G.R.); (S.V.); (C.V.)
- Author to whom correspondence should be addressed; E-Mail: ; Tel.: +39-331-8687352
| | - Maria R. Capobianchi
- National Institute for Infectious Diseases (INMI) “L. Spallanzani”, Rome 00149, Italy; E-Mail:
| | - Francesca Cavrini
- Operative Unit of Clinical Microbiology, Regional Reference Centre for Microbiological Emergencies, S. Orsola-Malpighi University Hospital, Bologna 40138, Italy; E-Mails: (V.S.); (F.C.); (P.G.); (A.P.); (G.R.); (S.V.); (C.V.)
| | - Rémi Charrel
- UMR_D 190 “Emergence des Pathologies Virales”, APHM Public Hospitals of Marseille, EHESP French School of Public Health & IHU Mediterranee Infection, IRD French Institute of Research for Development, Aix Marseille University, 13005, Marseille, France; E-Mail: (R.C.)
| | - Olivier Donoso-Mantke
- Centre for Biological Threats and Special Pathogens (ZBS-1), Robert Koch-Institut, Berlin 13353, Germany; E-Mails: (O.D.-M.); (C.E.); (M.N.); (A.S.)
| | - Camille Escadafal
- Centre for Biological Threats and Special Pathogens (ZBS-1), Robert Koch-Institut, Berlin 13353, Germany; E-Mails: (O.D.-M.); (C.E.); (M.N.); (A.S.)
| | - Leticia Franco
- National Microbiology Centre, Instituto de Salud Carlos III, Madrid 28220, Spain; E-Mails: (L.F.); (A.T.); (A.V.)
| | - Paolo Gaibani
- Operative Unit of Clinical Microbiology, Regional Reference Centre for Microbiological Emergencies, S. Orsola-Malpighi University Hospital, Bologna 40138, Italy; E-Mails: (V.S.); (F.C.); (P.G.); (A.P.); (G.R.); (S.V.); (C.V.)
| | - Ernest A. Gould
- UMR_D 190 “Emergence des Pathologies Virales”, APHM Public Hospitals of Marseille, EHESP French School of Public Health & IHU Mediterranee Infection, IRD French Institute of Research for Development, Aix Marseille University, 13005, Marseille, France; E-Mail: (R.C.)
- NERC Centre for Ecology and Hydrology, Wallingford, Oxon OX10 8BB, UK; E-Mail: (E.A.G.)
| | - Matthias Niedrig
- Centre for Biological Threats and Special Pathogens (ZBS-1), Robert Koch-Institut, Berlin 13353, Germany; E-Mails: (O.D.-M.); (C.E.); (M.N.); (A.S.)
| | - Anna Papa
- Department of Microbiology, Medical School, Aristotle University of Thessaloniki, Thessaloniki 54124, Greece; E-Mail:
| | - Anna Pierro
- Operative Unit of Clinical Microbiology, Regional Reference Centre for Microbiological Emergencies, S. Orsola-Malpighi University Hospital, Bologna 40138, Italy; E-Mails: (V.S.); (F.C.); (P.G.); (A.P.); (G.R.); (S.V.); (C.V.)
| | - Giada Rossini
- Operative Unit of Clinical Microbiology, Regional Reference Centre for Microbiological Emergencies, S. Orsola-Malpighi University Hospital, Bologna 40138, Italy; E-Mails: (V.S.); (F.C.); (P.G.); (A.P.); (G.R.); (S.V.); (C.V.)
| | - Andrea Sanchini
- Centre for Biological Threats and Special Pathogens (ZBS-1), Robert Koch-Institut, Berlin 13353, Germany; E-Mails: (O.D.-M.); (C.E.); (M.N.); (A.S.)
- European Public Health Microbiology Training Programme (EUPHEM), European Centre for Disease Prevention and Control, Stockholm 171 83, Sweden
| | - Antonio Tenorio
- National Microbiology Centre, Instituto de Salud Carlos III, Madrid 28220, Spain; E-Mails: (L.F.); (A.T.); (A.V.)
| | - Stefania Varani
- Operative Unit of Clinical Microbiology, Regional Reference Centre for Microbiological Emergencies, S. Orsola-Malpighi University Hospital, Bologna 40138, Italy; E-Mails: (V.S.); (F.C.); (P.G.); (A.P.); (G.R.); (S.V.); (C.V.)
| | - Ana Vázquez
- National Microbiology Centre, Instituto de Salud Carlos III, Madrid 28220, Spain; E-Mails: (L.F.); (A.T.); (A.V.)
| | - Caterina Vocale
- Operative Unit of Clinical Microbiology, Regional Reference Centre for Microbiological Emergencies, S. Orsola-Malpighi University Hospital, Bologna 40138, Italy; E-Mails: (V.S.); (F.C.); (P.G.); (A.P.); (G.R.); (S.V.); (C.V.)
| | - Herve Zeller
- European Centre for Disease Prevention and Control, Stockholm 171 83, Sweden; E-Mail:
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Development of a one-step SYBR Green I real-time RT-PCR assay for the detection and quantitation of Araraquara and Rio Mamore hantavirus. Viruses 2013; 5:2272-81. [PMID: 24056673 PMCID: PMC3798901 DOI: 10.3390/v5092272] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2013] [Revised: 09/10/2013] [Accepted: 09/17/2013] [Indexed: 01/09/2023] Open
Abstract
Hantaviruses are members of the family Bunyaviridae and are an emerging cause of disease worldwide with high lethality in the Americas. In Brazil, the diagnosis for hantaviruses is based on immunologic techniques associated with conventional RT-PCR. A novel one-step SYBR Green real-time RT-PCR was developed for the detection and quantitation of Araraquara hantavirus (ARAV) and Rio Mamore hantavirus (RIOMV). The detection limit of assay was 10copies/µL of RNA in vitro transcribed of segment S. The specificity of assay was evaluated by melting curve analysis, which showed that the Araraquara virus amplified product generated a melt peak at 80.83 ± 0.89 °C without generating primer-dimers or non-specific products. The assay was more sensitive than conventional RT-PCR and we detected two samples undetected by conventional RT-PCR. The one-step SYBR Green real-time quantitative RT-PCR is specific, sensible and reproducible, which makes it a powerful tool in both diagnostic applications and general research of ARAV and RIOMV and possibly other Brazilian hantaviruses.
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Bhullar SS, Chandak NH, Purohit HJ, Taori GM, Daginawala HF, Kashyap RS. Determination of viral load by quantitative real-time PCR in herpes simplex encephalitis patients. Intervirology 2013; 57:1-7. [PMID: 23988484 DOI: 10.1159/000351521] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2012] [Accepted: 04/04/2013] [Indexed: 11/19/2022] Open
Abstract
OBJECTIVE Human herpesviruses cause various acute, subacute, and chronic disorders of the central nervous system and peripheral nervous systems in adults and children. The objective of the present study is to summarize the experience gained with the estimation of viral load in the central nervous system of children and adults with herpes simplex encephalitis (HSE) admitted to a neurological institute at Nagpur, India, by quantitative real-time PCR (qPCR) assay within the past 4 years. METHODS The qPCR assay was evaluated retrospectively in 242 cerebrospinal fluid (CSF) samples from patients. Evaluation of possible relationships was done between the herpes simplex virus (HSV) DNA concentration in CSF with that of patients' clinical and laboratory manifestations. The prevalence of the type of HSV in the study population was also determined using type-specific real-time PCR analysis. RESULTS AND CONCLUSIONS Real-time analysis using type-specific primers revealed the presence of predominantly HSV-1 genotype in the study population. The qPCR results show that in patients with higher viral loads in their CSF, a greater number of cases were associated with the presence of lesions in the brain as revealed by computed tomography/magnetic resonance imaging scan. They required acyclovir therapy for a longer duration and had a poorer clinical outcome than the patients with lower viral loads in their CSF.
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Affiliation(s)
- Shradha S Bhullar
- Biochemistry Research Laboratory, Central India Institute of Medical Sciences, Nagpur, India
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37
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Agarwal A, Singh AK, Sharma S, Soni M, Thakur AK, Gopalan N, Parida MM, Rao PVL, Dash PK. Application of real-time RT-PCR in vector surveillance and assessment of replication kinetics of an emerging novel ECSA genotype of Chikungunya virus in Aedes aegypti. J Virol Methods 2013; 193:419-25. [PMID: 23850695 DOI: 10.1016/j.jviromet.2013.07.004] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2013] [Revised: 06/28/2013] [Accepted: 07/03/2013] [Indexed: 12/16/2022]
Abstract
Chikungunya has emerged as one of the most important arboviral infection of global significance. Expansion of Chikungunya virus endemic areas can be ascribed to naive population, increasing vector population and adaptability of virus to new vector. In this study, a SYBR Green I based quantitative RT-PCR assay was developed. The assay was found to be 10-fold more sensitive than conventional RT-PCR and no cross reactivity was observed with related alphaviruses and flaviviruses. The detection efficiency of the assay was impervious to mosquitoes of different pool sizes. Vector surveillance has resulted in detection of CHIKV RNA in Aedes aegypti, confirming its vectorial potential for CHIKV in northern India. The assessment of the assay was further carried out by studying the competence of Indian Ae. aegypti for CHIKV, which revealed 100% infection rate and dissemination rate with 60% transmission rate. The replication kinetics of CHIKV in different anatomical sites of Ae. aegypti revealed highest titre at day 6 post infection in midgut and at day 10 post infection in saliva, legs and wings. The implementation of the assay in detecting lower viral load makes it a remarkable tool for surveillance of virus activity in mosquitoes.
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Affiliation(s)
- Ankita Agarwal
- Division of Virology, Defence Research and Development Establishment, Jhansi Road, Gwalior 474 002, M.P., India
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Generic and sequence-variant specific molecular assays for the detection of the highly variable Grapevine leafroll-associated virus 3. J Virol Methods 2013; 189:20-9. [DOI: 10.1016/j.jviromet.2012.12.018] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2012] [Revised: 12/17/2012] [Accepted: 12/19/2012] [Indexed: 11/19/2022]
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Sekaran SD, Artsob H. Molecular diagnostics for the detection of human flavivirus infections. ACTA ACUST UNITED AC 2013; 1:521-30. [PMID: 23496358 DOI: 10.1517/17530059.1.4.521] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
Flaviviruses constitute a genus of viruses that are important etiologic agents of human disease, causing clinical disease ranging from fever to severe manifestations, such as encephalitis and hemorrhagic fever. Serology is presently the most frequently used means of diagnosing flavivirus infections. However, other diagnostic tests may be employed, such as molecular detection, virus isolation and antigen-capture procedures. The applicability of the latter three diagnostic procedures can be expected to vary depending upon the infecting flavivirus, as some flaviviruses, such as dengue, display high and long-term viremias, whereas other flaviviruses produce no, or barely detectable, viremias. Molecular diagnostic techniques have been successfully applied to the diagnosis of flavivirus infections and have the advantage of rapidity, sensitivity and specific identification of the infecting virus. However, it is important to ensure that the right detection tools are employed (for example, appropriate primers and probes to detect the specific virus) and that the laboratory maintains a high proficiency in their testing procedures. Some of the studies that have been employed in the diagnosis of flavivirus infections are reviewed in this article. It seems that there is the potential to develop testing algorithms that successfully employ molecular diagnostics alone or in conjunction with other laboratory techniques for the diagnosis of acute human flavivirus infections.
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Affiliation(s)
- Shamala Devi Sekaran
- University of Malaya, Department of Medical Microbiology, Faculty of Medicine, 50603 Kuala Lumpur, Malaysia
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Monti M, Martini M, Tedeschi R. EvaGreen real-time PCR protocol for specific 'Candidatus Phytoplasma mali' detection and quantification in insects. Mol Cell Probes 2013; 27:129-36. [PMID: 23474195 DOI: 10.1016/j.mcp.2013.02.001] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2012] [Revised: 02/09/2013] [Accepted: 02/19/2013] [Indexed: 10/27/2022]
Abstract
In this paper the validation and implementation of a Real-time PCR protocol based on ribosomal protein genes has been carried out for sensitive and specific quantification of 'Candidatus (Ca.) Phytoplasma mali' (apple proliferation phytoplasma, APP) in insects. The method combines the use of EvaGreen(®) dye as chemistry detection system and the specific primer pair rpAP15f-mod/rpAP15r3, which amplifies a fragment of 238 bp of the ribosomal protein rplV (rpl22) gene of APP. Primers specificity was demonstrated by running in the same Real-time PCR 'Ca. Phytoplasma mali' samples with phytoplasmas belonging to the same group (16SrX) as 'Ca. Phytoplasma pyri' and 'Ca. Phytoplasma prunorum', and also phytoplasmas from different groups, as 'Ca. Phytoplasma phoenicium' (16SrIX) and Flavescence dorée phytoplasma (16SrV). 'Ca. Phytoplasma mali' titre in insects was quantified using a specific approach, which relates the concentration of the phytoplasma to insect 18S rDNA. Absolute quantification of APP and insect 18S rDNA were calculated using standard curves prepared from serial dilutions of plasmids containing rplV-rpsC and a portion of 18S rDNA genes, respectively. APP titre in insects was expressed as genome units (GU) of phytoplasma per picogram (pg) of individual insect 18S rDNA. 'Ca. Phytoplasma mali' concentration in examined samples (Cacopsylla melanoneura overwintered adults) ranged from 5.94 × 10(2) to 2.51 × 10(4) GU/pg of insect 18S rDNA. Repeatability and reproducibility of the method were also evaluated by calculation of the coefficient of variation (CV%) of GU of phytoplasma and pg of 18S rDNA fragment for both assays. CV less than 14% and 9% (for reproducibility test) and less than 10 and 11% (for repeatability test) were obtained for phytoplasma and insect qPCR assays, respectively. Sensitivity of the method was also evaluated, in comparison with conventional 16S rDNA-based nested-PCR procedure. The method described has been demonstrated reliable, sensitive and specific for the quantification of 'Ca. Phytoplasma mali' in insects. The possibility to study the trend of phytoplasma titre in the vectors will allow a deepen investigation on the epidemiology of the disease.
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Affiliation(s)
- Monia Monti
- Dipartimento di Scienze Agrarie, Forestali e Alimentari DISAFA, University of Torino, Via Leonardo da Vinci 44, 10095 Grugliasco TO, Italy
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Cheng J, Jiang Y, Rao P, Wu H, Dong Q, Wu Z, Ding X, Guo J. Development of a single-tube multiplex real-time PCR for detection and identification of five pathogenic targets by using melting-curve analysis with EvaGreen. Arch Virol 2012; 158:379-86. [PMID: 23053522 DOI: 10.1007/s00705-012-1493-6] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2012] [Accepted: 08/21/2012] [Indexed: 12/18/2022]
Abstract
SYBR Green I (SG) is widely used in real-time PCR applications as an intercalating dye. Preferential binding of SG during PCR and inhibition of PCR often result in failure to detect multiple amplicons in multiplex reactions. In the present study, a novel single-tube, multiplex real-time PCR with EvaGreen dye (EG) was developed and evaluated for simultaneous detection of pathogenic targets by using five potato viruses as models. The PCR products obtained using five sets of specific primers were analyzed by melting curve analysis. The assay could specifically detect and differentiate the five potato viruses by producing a distinct peak for each amplification product and exhibited a high reproducibility with coefficients of variation from 0.01 to 0.25 %. Detection sensitivity of the assay ranged from 100 to 500 copies/μL for each virus. The results of this study demonstrate that multiplex real-time PCR and melting-curve analysis with EG is a sensitive, specific and inexpensive method for simultaneous detection of multiple pathogens.
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Affiliation(s)
- Juhui Cheng
- College of Life Sciences, Zhejiang Sci-Tech University, 2nd street, Xiasha, Hangzhou, 310018, China
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Shang D, Hughes SA, Horner M, Bruce MJ, Dong Y, Carey I, Suddle AR, Agarwal K, Harrison PM, Atkins M. Development and validation of an efficient in-house real-time reverse transcription polymerase chain reaction assay for the quantitative detection of serum hepatitis delta virus RNA in a diverse South London population. J Virol Methods 2012; 184:55-62. [DOI: 10.1016/j.jviromet.2012.05.008] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2011] [Revised: 05/01/2012] [Accepted: 05/10/2012] [Indexed: 12/14/2022]
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Development of real-time PCR array for simultaneous detection of eight human blood-borne viral pathogens. PLoS One 2012; 7:e43246. [PMID: 22912836 PMCID: PMC3422334 DOI: 10.1371/journal.pone.0043246] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2012] [Accepted: 07/18/2012] [Indexed: 01/12/2023] Open
Abstract
BACKGROUND Real-time PCR array for rapid detection of multiple viral pathogens should be highly useful in cases where the sample volume and the time of testing are limited, i.e. in the eligibility testing of tissue and organ donors. FINDINGS We developed a real-time PCR array capable of simultaneously detecting eight human viral pathogens: human immunodeficiency virus types 1 and 2 (HIV-1 and -2), hepatitis B virus (HBV), hepatitis C virus (HCV), human T-cell leukemia virus-1 and -2 (HTLV-1 and -2), vaccinia virus (VACV) and West Nile virus (WNV). One hundred twenty (120) primers were designed using a combination of bioinformatics approaches, and, after experimental testing, 24 primer sets targeting eight viral pathogens were selected to set up the array with SYBR Green chemistry. The specificity and sensitivity of the virus-specific primer sets selected for the array were evaluated using analytical panels with known amounts of viruses spiked into human plasma. The array detected: 10 genome equivalents (geq)/ml of HIV-2 and HCV, 50 geq of HIV-1 (subtype B), HBV (genotype A) and WNV. It detected 100-1,000 geq/ml of plasma of HIV-1 subtypes (A - G), group N and CRF (AE and AG) isolates. Further evaluation with a panel consisting of 28 HIV-1 and HIV-2 clinical isolates revealed no cross-reactivity of HIV-1 or HIV-2 specific primers with another type of HIV. All 28 viral isolates were identified with specific primer sets targeting the most conserved genome areas. The PCR array correctly identified viral infections in a panel of 17 previously quantified clinical plasma samples positive for HIV-1, HCV or HBV at as low as several geq per PCR reaction. CONCLUSIONS The viral array described here demonstrated adequate performance in the testing of donors' clinical samples. Further improvement in its sensitivity for the broad spectrum of HIV-1 subtypes is under development.
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Armstrong PM, Prince N, Andreadis TG. Development of a multi-target TaqMan assay to detect eastern equine encephalitis virus variants in mosquitoes. Vector Borne Zoonotic Dis 2012; 12:872-6. [PMID: 22835151 DOI: 10.1089/vbz.2012.1008] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
Abstract
Disease outbreaks caused by eastern equine encephalitis virus (EEEV; Togaviridae, Alphavirus) may be prevented by implementing effective surveillance and intervention strategies directed against the mosquito vector. Methods for EEEV detection in mosquitoes include a real-time reverse transcriptase PCR technique (TaqMan assay), but we report its failure to detect variants isolated in Connecticut in 2011, due to a single base-pair mismatch in the probe-binding site. To improve the molecular detection of EEEV, we developed a multi-target TaqMan assay by adding a second primer/probe set to provide redundant targets for EEEV detection. The multi-target TaqMan assay had similar performance characteristics to the conventional assay, but also detected newly-evolving strains of EEEV. The approach described here increases the reliability of the TaqMan assay by creating back-up targets for virus detection without sacrificing sensitivity or specificity.
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Affiliation(s)
- Philip M Armstrong
- Center for Vector Biology and Zoonotic Diseases, The Connecticut Agricultural Experiment Station, New Haven, Connecticut 06504, USA.
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Pérez LJ, Díaz de Arce H, Cilloni F, Salviato A, Marciano S, Perera C, Salomoni A, Beato M, Romero A, Capua I, Cattoli G. An SYBR Green-based real-time RT-PCR assay for the detection of H5 hemagglutinin subtype avian influenza virus. Mol Cell Probes 2012; 26:137-45. [DOI: 10.1016/j.mcp.2012.02.001] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2011] [Revised: 02/01/2012] [Accepted: 02/21/2012] [Indexed: 12/01/2022]
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Development of SYBR Green I based real-time PCR assays for quantitative detection of Rice tungro bacilliform virus and Rice tungro spherical virus. J Virol Methods 2012; 181:86-92. [DOI: 10.1016/j.jviromet.2012.01.018] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2011] [Revised: 01/16/2012] [Accepted: 01/24/2012] [Indexed: 11/24/2022]
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De Filette M, Ulbert S, Diamond M, Sanders NN. Recent progress in West Nile virus diagnosis and vaccination. Vet Res 2012; 43:16. [PMID: 22380523 PMCID: PMC3311072 DOI: 10.1186/1297-9716-43-16] [Citation(s) in RCA: 97] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2011] [Accepted: 03/01/2012] [Indexed: 01/22/2023] Open
Abstract
West Nile virus (WNV) is a positive-stranded RNA virus belonging to the Flaviviridae family, a large family with 3 main genera (flavivirus, hepacivirus and pestivirus). Among these viruses, there are several globally relevant human pathogens including the mosquito-borne dengue virus (DENV), yellow fever virus (YFV), Japanese encephalitis virus (JEV) and West Nile virus (WNV), as well as tick-borne viruses such as tick-borne encephalitis virus (TBEV). Since the mid-1990s, outbreaks of WN fever and encephalitis have occurred throughout the world and WNV is now endemic in Africa, Asia, Australia, the Middle East, Europe and the Unites States. This review describes the molecular virology, epidemiology, pathogenesis, and highlights recent progress regarding diagnosis and vaccination against WNV infections.
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Affiliation(s)
- Marina De Filette
- Laboratory of Gene Therapy, Faculty of Veterinary Sciences, Ghent University, Heidestraat 19, 9820 Merelbeke, Belgium.
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Dash PK, Boutonnier A, Prina E, Sharma S, Reiter P. Development of a SYBR green I based RT-PCR assay for yellow fever virus: application in assessment of YFV infection in Aedes aegypti. Virol J 2012; 9:27. [PMID: 22264275 PMCID: PMC3296605 DOI: 10.1186/1743-422x-9-27] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2011] [Accepted: 01/22/2012] [Indexed: 12/23/2022] Open
Abstract
BACKGROUND Yellow Fever virus (YFV) is an important arboviral pathogen in much of sub-Saharan Africa and the tropical Americas. It is the prototype member of the genus Flavivirus and is transmitted primarily by Aedes (Stegomyia) mosquitoes. The incidence of human infections in endemic areas has risen in recent years. Prompt and dependable identification of YFV is a critical component of response to suspect cases. RESULTS We developed a one-step SYBR Green I-based real-time quantitative RT-PCR (qRT-PCR) assay targeting the 5'NTR and capsid-gene junction--for rapid detection and quantification of YFV. The detection limit was 1 PFU/mL, 10-fold more sensitive than conventional RT-PCR, and there was no cross-reactivity with closely related flaviviruses or with alphaviruses. Viral load in samples was determined by standard curve plotted from cycle threshold (Ct) values and virus concentration. The efficacy of the assay in mosquitoes was assessed with spiked samples. The utility of the assay for screening of pooled mosquitoes was also confirmed. Replication of a Cameroon isolate of YFV in Ae. aegypti revealed a marked variation in susceptibility among different colonies at different days post infection (pi). CONCLUSIONS The SYBR Green-1 based qRT-PCR assay is a faster, simpler, more sensitive and less expensive procedure for detection and quantification of YFV than other currently used methods.
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Affiliation(s)
- Paban Kumar Dash
- Institut Pasteur, Insects and Infectious Disease Unit, CNRS URA 3012, 25 rue du Docteur Roux, 75724 Paris, France
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Shukla J, Saxena D, Rathinam S, Lalitha P, Joseph CR, Sharma S, Soni M, Rao P, Parida M. Molecular detection and characterization of West Nile virus associated with multifocal retinitis in patients from southern India. Int J Infect Dis 2012; 16:e53-9. [DOI: 10.1016/j.ijid.2011.09.020] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2011] [Revised: 08/30/2011] [Accepted: 09/28/2011] [Indexed: 11/29/2022] Open
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Abreu PMV, Piccin JG, Rodrigues SP, Buss DS, Ventura JA, Fernandes PMB. Molecular diagnosis of Papaya meleira virus (PMeV) from leaf samples of Carica papaya L. using conventional and real-time RT-PCR. J Virol Methods 2011; 180:11-7. [PMID: 22193169 DOI: 10.1016/j.jviromet.2011.12.003] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2011] [Revised: 12/01/2011] [Accepted: 12/06/2011] [Indexed: 01/02/2023]
Abstract
Papaya meleira virus (PMeV) is the causal agent of papaya sticky disease. This study describes two methods for molecular diagnosis of PMeV using conventional and real-time PCR. These methods were shown to be more efficient than current methods of viral detection using extraction of PMeV dsRNA and observation of symptoms in the field. The methods described here were used to evaluate the effect of inoculation of papaya plants with purified PMeV dsRNA on the progress of PMeV infection. A single inoculation with PMeV dsRNA was observed to delay the progress of the virus infection by several weeks. The possibility of vertical transmission of PMeV was also investigated. No evidence was found for PMeV transmission through seeds collected from diseased fruit. The implications of these results for the epidemiology of PMeV and the management of papaya sticky disease are discussed.
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Affiliation(s)
- Paolla M V Abreu
- Núcleo de Biotecnologia, Universidade Federal do Espírito Santo, Av. Marechal Campos, 1468, 29040-090, Vitória, ES, Brazil
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