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Singh S, Stainton D, Tzanetakis IE. Development of Rapid and Affordable Virus-Mimicking Artificial Positive Controls. PLANT DISEASE 2024; 108:30-34. [PMID: 37578360 DOI: 10.1094/pdis-06-23-1072-sr] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/15/2023]
Abstract
A major bottleneck in the development of detection assays is the availability of positive controls. Their acquisition can be problematic, their maintenance is expensive, and without them, assays cannot be validated. Herein, we present a novel strategy for the development of virus-mimicking artificial positive controls (ViMAPCs). The time between design and application is less than 5 days, unlike alternatives which normally take several weeks to obtain and implement. The ViMAPCs provide a realistic representation of natural infection unlike alternatives and allow for an effortless recognition of laboratory-based contamination. The feasibility and adaptability of the strategy was evaluated using several RNA and DNA plant viruses. ViMAPCs can be used in diagnostics laboratories but also in the monitoring of pathogen outbreaks where rapid response is of utmost importance.
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Affiliation(s)
- Shivani Singh
- Department of Entomology and Plant Pathology, Division of Agriculture, University of Arkansas System, Fayetteville, AR 72701
| | - Daisy Stainton
- Department of Entomology and Plant Pathology, Division of Agriculture, University of Arkansas System, Fayetteville, AR 72701
| | - Ioannis E Tzanetakis
- Department of Entomology and Plant Pathology, Division of Agriculture, University of Arkansas System, Fayetteville, AR 72701
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Wang HB, Du T, Lin JH, Chen XB, Tu CN. Development and evaluation of an external quality control and internal quality control containing real-time RT-PCR assay for the detection of o'nyong-nyong virus. Biologicals 2023; 84:101717. [PMID: 37801802 DOI: 10.1016/j.biologicals.2023.101717] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2022] [Revised: 06/20/2023] [Accepted: 09/25/2023] [Indexed: 10/08/2023] Open
Abstract
O'nyong-nyong fever is a mosquito-borne tropical viral disease while few molecular diagnostic tools have been established for its surveillance until now. In the current study, a single-step, dual-color real-time reverse transcription polymerase chain reaction (RT-PCR) assay which contained both external quality control (EQC) and internal quality control (IQC) prepared by armored RNA technique was developed and evaluated for the detection of o'nyong-nyong virus (ONNV). Results showed that the assay was established successfully without cross-reaction with genetically related or symptom-alike diseases, which showed high specificity of the assay. The coefficient of variation of the assay was 0.97%, far less than 5%, indicating good repeatability of the assay. The lower limit of detection of the assay could reach as low as 100 copies of genome equivalent. During evaluation, the assay could correctly detect ONNV from spiked human serum samples and Anopheles species mosquito samples, while no ONNV positive was observed either from serum samples of patients with acute febrile illness or from local Anopheles species mosquitoes, suggesting no ONNV had been transmitted locally. In conclusion, the assay could potentially provide a valuable platform for ONNV molecular detection, which may improve the preparedness for future o'nyong-nyong fever outbreaks.
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Affiliation(s)
- Hai-Bo Wang
- Key Laboratory of Emerging Infectious Disease Detection, Zhuhai International Travel Healthcare Center, Zhuhai, 519020, Guangdong, China.
| | - Tian Du
- Futian District Center for Disease Control and Prevention, Shenzhen, 518040, Guangdong, China
| | - Ji-Hong Lin
- Zhongshan International Travel Healthcare Center, Zhongshan, 528400, Guangdong, China
| | - Xin-Bin Chen
- Key Laboratory of Emerging Infectious Disease Detection, Zhuhai International Travel Healthcare Center, Zhuhai, 519020, Guangdong, China
| | - Cheng-Ning Tu
- Key Laboratory of Emerging Infectious Disease Detection, Zhuhai International Travel Healthcare Center, Zhuhai, 519020, Guangdong, China
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3
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Recombinase polymerase amplification (RPA) with lateral flow detection for three Anaplasma species of importance to livestock health. Sci Rep 2021; 11:15962. [PMID: 34354122 PMCID: PMC8342517 DOI: 10.1038/s41598-021-95402-y] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2021] [Accepted: 07/22/2021] [Indexed: 02/07/2023] Open
Abstract
Anaplasma marginale, A. ovis, and A. phagocytophilum are the causative agents of bovine anaplasmosis, ovine anaplasmosis, and granulocytic anaplasmosis, respectively. The gold standard for diagnosis of post-acute and long-term persistent infections is the serological cELISA, which does not discriminate between Anaplasma species and requires highly equipped laboratories and trained personnel. This study addresses the development of a rapid, isothermal, sensitive, species-specific RPA assays to detect three Anaplasma species in blood and cELISA A. marginale-positive serum samples. Three RPA primer and probe sets were designed targeting msp4 genes of each Anaplasma species and the internal control (GAPDH gene) for each assay. The limit of detection of gel-based or RPA-basic assays is 8.99 × 104 copies/µl = A. marginale, 5.04 × 106 copies/µl = A. ovis, and 4.58 × 103 copies/µl = A. phagocytophilum, and for each multiplex lateral flow or RPA-nfo assays is 8.99 × 103 copies/µl of A. marginale, 5.04 × 103 copies/µl of A. ovis, 4.58 × 103 copies/µl of A. phagocytophilum, and 5.51 × 103 copies/µl of internal control (GAPDH). Although none of the 80 blood samples collected from Oklahoma cattle were positive, the RPA-nfo assays detected all A. marginale cattle blood samples with varying prevalence rates of infection, 83% of the 24 cELISA A. marginale-positive serum samples, and all A. phagocytophilum cell culture samples. Overall, although early detection of three Anaplasma species was not specifically addressed, the described RPA technique represents an improvement for detection of three Anaplasma in regions where access to laboratory equipment is limited.
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Dehghan Esmat Abadi M, Motalebzadeh H, Barati M, Yaghobi M. Designing Two Synthetic Constructs for Real Time PCR Detection of Francisella tularensis and Ebola Virus. Avicenna J Med Biotechnol 2021; 13:92-97. [PMID: 34012525 PMCID: PMC8112141 DOI: 10.18502/ajmb.v13i2.5528] [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] [Indexed: 11/24/2022] Open
Abstract
Background: Generally, timely diagnosis of micro-organisms is very important to prevent many diseases. Many methods can detect micro-organisms like culture-based methods and molecular methods. The molecular methods are usually preferred because they provide fast and reliable results. In some cases, microbial strains are not accessible, and there is no safety to work with them; therefore, synthetic constructs which are designed according to the available sequences in databases can be used as a positive control for detection of them. Methods: In this study, a synthetic construct was designed for molecular detection of Francisella tularensis (F. tularensis) and the Ebola virus by multiplex real-time PCR reaction. For this, sequences were taken from databases and then multiple alignments were done by software. Also, conventional PCR and two models of real-time PCR (SYBR green and TaqMan) were applied. Finally, multiplex real-time PCR was performed. Results: The synthetic construct was designed and used for conventional PCR and multiplex PCR. The results of common PCR showed a single band at 148 bp and 167 bp in 1.5% agarose gel stained by ethidium bromide for F. tularensis and Ebola virus, respectively. Also, a dual-band at 148 and 167 bp was observed in multiplex PCR. Results of real-time PCR showed a limit of detection about 0.1 pg of plasmid/μl. Conclusion: In conclusion, the designed construct can be used as a positive control for an accurate diagnosis of these micro-organisms without any biological danger for laboratory staff. So, this method is useful for diagnosis of these agents in food, water, and blood samples.
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Affiliation(s)
| | - Hesam Motalebzadeh
- Department of Medical Biotechnology, Faculty of Allied Medical Sciences, Iran University of Medical Sciences, Tehran, Iran
| | - Mahmoud Barati
- Department of Genetics, Faculty of Basic Sciences, Science and Research Branch, Islamic Azad University, Tehran, Iran
| | - Mohammadali Yaghobi
- Faculty of Chemistry and Chemical Engineering, Malek Ashtar University of Technology, Tehran, Iran
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Arif M, Busot GY, Mann R, Rodoni B, Stack JP. Multiple internal controls enhance reliability for PCR and real time PCR detection of Rathayibacter toxicus. Sci Rep 2021; 11:8365. [PMID: 33863977 PMCID: PMC8052354 DOI: 10.1038/s41598-021-87815-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2019] [Accepted: 03/26/2021] [Indexed: 01/05/2023] Open
Abstract
Rathayibacter toxicus is a toxigenic bacterial plant pathogen indigenous to Australia and South Africa. A threat to livestock industries globally, the bacterium was designated a U.S. Select Agent. Biosecurity and phytosanitary concerns arise due to the international trade of seed and hay that harbor the bacterium. Accurate diagnostic protocols to support phytosanitary decisions, delineate areas of freedom, and to support research are required to address those concerns. Whole genomes of three genetic populations of R. toxicus were sequenced (Illumina MiSeq platforms), assembled and genomic regions unique to each population identified. Highly sensitive and specific TaqMan qPCR and multiplex endpoint PCR assays were developed for the detection and identification of R. toxicus to the population level of discrimination. Specificity was confirmed with appropriate inclusivity and exclusivity panels; no cross reactivity was observed. The endpoint multiplex PCR and TaqMan qPCR assays detected 10 fg and 1 fg of genomic DNA, respectively. To enhance reliability and increase confidence in results, three types of internal controls with no or one extra primer were developed and incorporated into each assay to detect both plant and artificial internal controls. Assays were validated by blind ring tests with multiple operators in three international laboratories.
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Affiliation(s)
- Mohammad Arif
- Department of Plant and Environmental Protection Sciences, University of Hawaii At Manoa, Honolulu, HI, USA.,Department of Plant Pathology, Great Plains Diagnostic Network, Kansas State University, 4024 Throckmorton Plant Sciences Center, Manhattan, KS, 66506-5502, USA.,Plant Biosecurity Cooperative Research Centre, Canberra, Australia
| | - Grethel Y Busot
- Department of Plant Pathology, Great Plains Diagnostic Network, Kansas State University, 4024 Throckmorton Plant Sciences Center, Manhattan, KS, 66506-5502, USA.,Plant Biosecurity Cooperative Research Centre, Canberra, Australia.,Inari Agricultural Inc., One Kendall Square, Cambridge, MA, USA
| | - Rachel Mann
- Department of Economic Development, Jobs, Transport and Resources, Biosciences Research Division, Bundoora, VIC, Australia.,Plant Biosecurity Cooperative Research Centre, Canberra, Australia
| | - Brendan Rodoni
- Department of Economic Development, Jobs, Transport and Resources, Biosciences Research Division, Bundoora, VIC, Australia.,Plant Biosecurity Cooperative Research Centre, Canberra, Australia
| | - James P Stack
- Department of Plant Pathology, Great Plains Diagnostic Network, Kansas State University, 4024 Throckmorton Plant Sciences Center, Manhattan, KS, 66506-5502, USA. .,Plant Biosecurity Cooperative Research Centre, Canberra, Australia.
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Dobhal S, Olson JD, Arif M, Garcia Suarez JA, Ochoa-Corona FM. A simplified strategy for sensitive detection of Rose rosette virus compatible with three RT-PCR chemistries. J Virol Methods 2016; 232:47-56. [PMID: 26850142 DOI: 10.1016/j.jviromet.2016.01.013] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2015] [Revised: 12/12/2015] [Accepted: 01/31/2016] [Indexed: 11/29/2022]
Abstract
Rose rosette disease is a disorder associated with infection by Rose rosette virus (RRV), a pathogen of roses that causes devastating effects on most garden cultivated varieties, and the wild invasive rose especially Rosa multiflora. Reliable and sensitive detection of this disease in early phases is needed to implement proper control measures. This study assesses a single primer-set based detection method for RRV and demonstrates its application in three different chemistries: Endpoint RT-PCR, TaqMan-quantitative RT-PCR (RT-qPCR) and SYBR Green RT-qPCR with High Resolution Melting analyses. A primer set (RRV2F/2R) was designed from consensus sequences of the nucleocapsid protein gene p3 located in the RNA 3 region of RRV. The specificity of primer set RRV2F/2R was validated in silico against published GenBank sequences and in-vitro against infected plant samples and an exclusivity panel of near-neighbor and other viruses that commonly infect Rosa spp. The developed assay is sensitive with a detection limit of 1fg from infected plant tissue. Thirty rose samples from 8 different states of the United States were tested using the developed methods. The developed methods are sensitive and reliable, and can be used by diagnostic laboratories for routine testing and disease management decisions.
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Affiliation(s)
- Shefali Dobhal
- National Institute for Microbial Forensics & Food and Agricultural Biosecurity, Stillwater, OK, USA; Department of Entomology and Plant Pathology, Oklahoma State University, Stillwater, OK, USA
| | - Jennifer D Olson
- Department of Entomology and Plant Pathology, Oklahoma State University, Stillwater, OK, USA
| | - Mohammad Arif
- National Institute for Microbial Forensics & Food and Agricultural Biosecurity, Stillwater, OK, USA; Department of Entomology and Plant Pathology, Oklahoma State University, Stillwater, OK, USA
| | - Johnny A Garcia Suarez
- National Institute for Microbial Forensics & Food and Agricultural Biosecurity, Stillwater, OK, USA; Department of Entomology and Plant Pathology, Oklahoma State University, Stillwater, OK, USA; Departamento de Ciencias de la Vida y de la Agricultura, Universidad de las Fuerzas Armadas ESPE, Sangolquí, Ecuador
| | - Francisco M Ochoa-Corona
- National Institute for Microbial Forensics & Food and Agricultural Biosecurity, Stillwater, OK, USA; Department of Entomology and Plant Pathology, Oklahoma State University, Stillwater, OK, USA.
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Arif M, Opit G, Mendoza-Yerbafría A, Dobhal S, Li Z, Kučerová Z, Ochoa-Corona FM. Array of Synthetic Oligonucleotides to Generate Unique Multi-Target Artificial Positive Controls and Molecular Probe-Based Discrimination of Liposcelis Species. PLoS One 2015; 10:e0129810. [PMID: 26086728 PMCID: PMC4472718 DOI: 10.1371/journal.pone.0129810] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2015] [Accepted: 05/13/2015] [Indexed: 11/23/2022] Open
Abstract
Several species of the genus Liposcelis are common insect pests that cause serious qualitative and quantitative losses to various stored grains and processed grain products. They also can contaminate foods, transmit pathogenic microorganisms and cause allergies in humans. The common occurrence of multi-species infestations and the fact that it is difficult to identify and discriminate Liposcelis spp. make accurate, rapid detection and discriminatory tools absolutely necessary for confirmation of their identity. In this study, PCR primers and probes specific to different Liposcelis spp. were designed based on nucleotide sequences of the cytochrome oxidase 1 (CO1) gene. Primer sets ObsCo13F/13R, PeaCo15F/14R, BosCO7F/7R, BruCo5F/5R, and DecCo11F/11R were used to specifically detect Liposcelis obscura Broadhead, Liposcelis pearmani Lienhard, Liposcelis bostrychophila Badonnel, Liposcelis brunnea Motschulsky and Liposcelis decolor (Pearman) in multiplex endpoint PCRs, which amplified products of 438-, 351-, 191-, 140-, and 87-bp, respectively. In multiplex TaqMan qPCR assays, orange, yellow, red, crimson and green channels corresponding to reporter dyes 6-ROXN, HEX, Cy5, Quasar705 and 6-FAM specifically detected L. obscura, L. brunnea, L. bostrychophila, L. pearmani and L. decolor, respectively. All developed primer and probe sets allowed specific amplification of corresponding targeted Liposcelis species. The development of multiplex endpoint PCR and multiplex TaqMan qPCR will greatly facilitate psocid identification and their management. The use of APCs will streamline and standardize PCR assays. APC will also provide the opportunity to have all positive controls in a single tube, which reduces maintenance cost and labor, but increases the accuracy and reliability of the assays. These novel methods from our study will have applications in pest management, biosecurity, quarantine, food safety, and routine diagnostics.
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Affiliation(s)
- Mohammad Arif
- National Institute for Microbial Forensics & Food and Agricultural Biosecurity, 127 Noble Research Center, Oklahoma State University, Stillwater, Oklahoma, 74078, United States of America
- Department of Entomology and Plant Pathology, 127 Noble Research Center, Oklahoma State University, Stillwater, Oklahoma, 74078, United States of America
| | - George Opit
- Department of Entomology and Plant Pathology, 127 Noble Research Center, Oklahoma State University, Stillwater, Oklahoma, 74078, United States of America
- * E-mail: (GO); (FMOC)
| | - Abigail Mendoza-Yerbafría
- National Institute for Microbial Forensics & Food and Agricultural Biosecurity, 127 Noble Research Center, Oklahoma State University, Stillwater, Oklahoma, 74078, United States of America
- Department of Entomology and Plant Pathology, 127 Noble Research Center, Oklahoma State University, Stillwater, Oklahoma, 74078, United States of America
| | - Shefali Dobhal
- National Institute for Microbial Forensics & Food and Agricultural Biosecurity, 127 Noble Research Center, Oklahoma State University, Stillwater, Oklahoma, 74078, United States of America
- Department of Entomology and Plant Pathology, 127 Noble Research Center, Oklahoma State University, Stillwater, Oklahoma, 74078, United States of America
| | - Zhihong Li
- Department of Entomology, College of Agriculture and Biotechnology, China Agricultural University, Yuanmingyuan West Road 2, Beijing, 100193, PR China
| | - Zuzana Kučerová
- Crop Research Institute, Drnovská 507, 161 06, Prague, 6, Czech Republic
| | - Francisco M. Ochoa-Corona
- National Institute for Microbial Forensics & Food and Agricultural Biosecurity, 127 Noble Research Center, Oklahoma State University, Stillwater, Oklahoma, 74078, United States of America
- Department of Entomology and Plant Pathology, 127 Noble Research Center, Oklahoma State University, Stillwater, Oklahoma, 74078, United States of America
- * E-mail: (GO); (FMOC)
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