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Sharma N, Jamwal VL, Nagial S, Ranjan M, Rath D, Gandhi SG. Current status of diagnostic assays for emerging zoonotic viruses: Nipah and Hendra. Expert Rev Mol Diagn 2024:1-13. [PMID: 38924448 DOI: 10.1080/14737159.2024.2368591] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2023] [Accepted: 06/12/2024] [Indexed: 06/28/2024]
Abstract
INTRODUCTION Nipah and Hendra viruses belong to the Paramyxoviridae family, which pose a significant threat to human health, with sporadic outbreaks causing severe morbidity and mortality. Early symptoms include fever, cough, sore throat, and headache, which offer little in terms of differential diagnosis. There are no specific therapeutics and vaccines for these viruses. AREAS COVERED This review comprehensively covers a spectrum of diagnostic techniques for Nipah and Hendra virus infections, discussed in conjunction with appropriate type of samples during the progression of infection. Serological assays, reverse transcriptase Real-Time PCR assays, and isothermal amplification assays are discussed in detail, along with a listing of few commercially available detection kits. Patents protecting inventions in Nipah and Hendra virus detection are also covered. EXPERT OPINION Despite several outbreaks of Nipah and Hendra infections in the past decade, in-depth research into their pathogenesis, Point-of-Care diagnostics, specific therapies, and human vaccines is lacking. A prompt and accurate diagnosis is pivotal for efficient outbreak management, patient treatment, and the adoption of preventative measures. The emergence of rapid point-of-care tests holds promise in enhancing diagnostic capabilities in real-world settings. The patent landscape emphasizes the importance of innovation and collaboration within the legal and business realms.
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Affiliation(s)
- Nancy Sharma
- Infectious Diseases Division, CSIR-Indian Institute of Integrative Medicine (CSIR-IIIM), Jammu, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - Vijay Lakshmi Jamwal
- Microfluidics Design and Bioengineering Lab, Chemical Engineering Department, Indian Institute of Technology Jammu (IIT), Jammu, India
| | - Sakshi Nagial
- Infectious Diseases Division, CSIR-Indian Institute of Integrative Medicine (CSIR-IIIM), Jammu, India
| | - Manish Ranjan
- Department of Microbiology, All India Institute of Medical Sciences Jammu (AIIMS), Jammu, India
| | - Dharitri Rath
- Microfluidics Design and Bioengineering Lab, Chemical Engineering Department, Indian Institute of Technology Jammu (IIT), Jammu, India
| | - Sumit G Gandhi
- Infectious Diseases Division, CSIR-Indian Institute of Integrative Medicine (CSIR-IIIM), Jammu, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
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Silva SJRD, Magalhães JJFD, Matthews Q, Divarzak ALL, Mendes RPG, Santos BNR, Cabral DGDA, Silva JBD, Kohl A, Pardee K, Pena L. Development and field validation of a reverse transcription loop-mediated isothermal amplification assay (RT-LAMP) for the rapid detection of chikungunya virus in patient and mosquito samples. Clin Microbiol Infect 2024; 30:810-815. [PMID: 38460820 PMCID: PMC11161457 DOI: 10.1016/j.cmi.2024.03.004] [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: 09/03/2023] [Revised: 03/02/2024] [Accepted: 03/04/2024] [Indexed: 03/11/2024]
Abstract
OBJECTIVES We aimed to develop a reverse transcription loop-mediated isothermal amplification (RT-LAMP) platform for the rapid detection of chikungunya virus (CHIKV) in both patient and mosquito samples from Brazil. METHODS We optimized an RT-LAMP assay and then evaluated the specificity and sensitivity using visual detection. In comparison with the RT-qPCR reference method, we validated the utility of this assay as a molecular diagnostic test in a reference laboratory for arbovirus diagnostics using 100 serum samples collected from suspected CHIKV cases. RESULTS Our RT-LAMP assay specifically detected CHIKV without cross-reactivity against other arboviruses. The limit of detection of our RT-LAMP was estimated in -1.18 PFU (confidence interval [CI] ranging from -2.08 to 0.45), resulting in a similar analytical sensitivity when directly compared with the reference standard RT-qPCR assay. Then, we demonstrate the ability of our RT-LAMP assay to detect the virus in different human specimens (serum, urine, and saliva), and crude lysate of Aedes aegypti mosquitoes in as little as 20-30 minutes and without a separate RNA isolation step. Lastly, we showed that our RT-LAMP assay could be lyophilized and reactivated by adding water, indicating potential for room-temperature storage. Our RT-LAMP had a clinical sensitivity of 100% (95% CI, 90.97-100.00%), clinical specificity of 96.72% (95% CI, 88.65-99.60%), and overall accuracy of 98.00% (95% CI, 92.96-99.76%). DISCUSSION Taken together, these findings indicate that the RT-LAMP assay reported here solves important practical drawbacks to the deployment of molecular diagnostics in the field and can be used to improve testing capacity, particularly in low- and middle-income countries.
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Affiliation(s)
- Severino Jefferson Ribeiro da Silva
- Laboratory of Virology and Experimental Therapy (Lavite), Department of Virology, Aggeu Magalhães Institute (IAM), Oswaldo Cruz Foundation (Fiocruz), Recife, Pernambuco, Brazil; Leslie Dan Faculty of Pharmacy, University of Toronto, Toronto, ON, Canada.
| | - Jurandy Júnior Ferraz de Magalhães
- Laboratory of Virology and Experimental Therapy (Lavite), Department of Virology, Aggeu Magalhães Institute (IAM), Oswaldo Cruz Foundation (Fiocruz), Recife, Pernambuco, Brazil; Department of Virology, Pernambuco State Central Laboratory (LACEN/PE), Recife, Pernambuco, Brazil; University of Pernambuco (UPE), Serra Talhada Campus, Serra Talhada, Pernambuco, Brazil; Public Health Laboratory of the XI Regional Health, Pernambuco, Brazil
| | - Quinn Matthews
- Leslie Dan Faculty of Pharmacy, University of Toronto, Toronto, ON, Canada
| | | | - Renata Pessôa Germano Mendes
- Laboratory of Virology and Experimental Therapy (Lavite), Department of Virology, Aggeu Magalhães Institute (IAM), Oswaldo Cruz Foundation (Fiocruz), Recife, Pernambuco, Brazil
| | - Bárbara Nazly Rodrigues Santos
- Laboratory of Virology and Experimental Therapy (Lavite), Department of Virology, Aggeu Magalhães Institute (IAM), Oswaldo Cruz Foundation (Fiocruz), Recife, Pernambuco, Brazil
| | | | | | - Alain Kohl
- MRC-University of Glasgow Centre for Virus Research, Glasgow, UK; Department of Vector Biology and Tropical Disease Biology, Liverpool School of Tropical Medicine, Liverpool, UK
| | - Keith Pardee
- Leslie Dan Faculty of Pharmacy, University of Toronto, Toronto, ON, Canada; Department of Mechanical and Industrial Engineering, University of Toronto, Toronto, ON, Canada
| | - Lindomar Pena
- Laboratory of Virology and Experimental Therapy (Lavite), Department of Virology, Aggeu Magalhães Institute (IAM), Oswaldo Cruz Foundation (Fiocruz), Recife, Pernambuco, Brazil.
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Wang Y, Chen J, Yang Z, Wang X, Zhang Y, Chen M, Ming Z, Zhang K, Zhang D, Zheng L. Advances in Nucleic Acid Assays for Infectious Disease: The Role of Microfluidic Technology. Molecules 2024; 29:2417. [PMID: 38893293 PMCID: PMC11173870 DOI: 10.3390/molecules29112417] [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: 04/19/2024] [Revised: 05/16/2024] [Accepted: 05/20/2024] [Indexed: 06/21/2024] Open
Abstract
Within the fields of infectious disease diagnostics, microfluidic-based integrated technology systems have become a vital technology in enhancing the rapidity, accuracy, and portability of pathogen detection. These systems synergize microfluidic techniques with advanced molecular biology methods, including reverse transcription polymerase chain reaction (RT-PCR), loop-mediated isothermal amplification (LAMP), and clustered regularly interspaced short palindromic repeats (CRISPR), have been successfully used to identify a diverse array of pathogens, including COVID-19, Ebola, Zika, and dengue fever. This review outlines the advances in pathogen detection, attributing them to the integration of microfluidic technology with traditional molecular biology methods and smartphone- and paper-based diagnostic assays. The cutting-edge diagnostic technologies are of critical importance for disease prevention and epidemic surveillance. Looking ahead, research is expected to focus on increasing detection sensitivity, streamlining testing processes, reducing costs, and enhancing the capability for remote data sharing. These improvements aim to achieve broader coverage and quicker response mechanisms, thereby constructing a more robust defense for global public health security.
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Affiliation(s)
- Yiran Wang
- Engineering Research Center of Optical Instrument and System, The Ministry of Education, Shanghai Key Laboratory of Modern Optical System, University of Shanghai for Science and Technology, Shanghai 200093, China
| | - Jingwei Chen
- Engineering Research Center of Optical Instrument and System, The Ministry of Education, Shanghai Key Laboratory of Modern Optical System, University of Shanghai for Science and Technology, Shanghai 200093, China
| | - Zhijin Yang
- Engineering Research Center of Optical Instrument and System, The Ministry of Education, Shanghai Key Laboratory of Modern Optical System, University of Shanghai for Science and Technology, Shanghai 200093, China
| | - Xuanyu Wang
- Engineering Research Center of Optical Instrument and System, The Ministry of Education, Shanghai Key Laboratory of Modern Optical System, University of Shanghai for Science and Technology, Shanghai 200093, China
| | - Yule Zhang
- Engineering Research Center of Optical Instrument and System, The Ministry of Education, Shanghai Key Laboratory of Modern Optical System, University of Shanghai for Science and Technology, Shanghai 200093, China
| | - Mengya Chen
- Engineering Research Center of Optical Instrument and System, The Ministry of Education, Shanghai Key Laboratory of Modern Optical System, University of Shanghai for Science and Technology, Shanghai 200093, China
| | - Zizhen Ming
- Shanghai Institute of Immunology, Department of Immunology and Microbiology, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Kaihuan Zhang
- 2020 X-Lab, Shanghai Institute of Microsystem and Information Technology, Chinese Academy of Sciences, Shanghai 200050, China
| | - Dawei Zhang
- Engineering Research Center of Optical Instrument and System, The Ministry of Education, Shanghai Key Laboratory of Modern Optical System, University of Shanghai for Science and Technology, Shanghai 200093, China
- Shanghai Engineering Research Center of Environmental Biosafety Instruments and Equipment, University of Shanghai for Science and Technology, Shanghai 200093, China
- Shanghai Institute of Intelligent Science and Technology, Tongji University, Shanghai 200092, China
| | - Lulu Zheng
- Engineering Research Center of Optical Instrument and System, The Ministry of Education, Shanghai Key Laboratory of Modern Optical System, University of Shanghai for Science and Technology, Shanghai 200093, China
- Shanghai Engineering Research Center of Environmental Biosafety Instruments and Equipment, University of Shanghai for Science and Technology, Shanghai 200093, China
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Sen S, Bhowmik P, Tiwari S, Peleg Y, Bandyopadhyay B. Versatility of reverse transcriptase loop-mediated isothermal amplification (RT-LAMP) from diagnosis of early pathological infection to mutation detection in organisms. Mol Biol Rep 2024; 51:211. [PMID: 38270670 DOI: 10.1007/s11033-023-09110-z] [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: 07/23/2023] [Accepted: 12/05/2023] [Indexed: 01/26/2024]
Abstract
Loop-mediated isothermal amplification (LAMP) is a rapid, state-of-the-art DNA amplification technology, used primarily for the quick diagnosis and early identification of microbial infection, caused by pathogens such as virus, bacteria and malaria. A target DNA can be amplified within 30 min using the LAMP reaction, taking place at a steady temperature. The LAMP method uses four or six primers to bind eight regions of a target DNA and has a very high specificity. The devices used for conducting LAMP are usually simple since the LAMP method is an isothermal process. When LAMP is coupled with Reverse Transcription (RT), it allows direct detection of RNA in a sample. This greatly enhances the efficiency of diagnosis of RNA viruses in a sample. Recently, the rampant spread of COVID-19 demanded such a rapid, simple, and cost-effective Point of Care Test (PoCT) for the accurate diagnosis of this pandemic. Loop-mediated isothermal amplification (LAMP) assays are not only used for the detection of microbial pathogens, but there are various other applications such as detection of genetic mutations in food and various organisms. In this review, various implementations of RT-LAMP techniques would be discussed.
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Affiliation(s)
- Srishti Sen
- School of Bioscience, Engineering and Technology, VIT Bhopal University, Bhopal, Madhya Pradesh, India
| | - Priyanka Bhowmik
- Department of Biological Sciences, School of Life Science and Biotechnology, Adamas University, Kolkata, India
| | - Shubhangi Tiwari
- School of Bioscience, Engineering and Technology, VIT Bhopal University, Bhopal, Madhya Pradesh, India
| | - Yoav Peleg
- Structural Proteomics Unit (SPU), Life Sciences Core Facilities (LSCF), Weizmann Institute of Science, Rehovot, Israel
| | - Boudhayan Bandyopadhyay
- Department of Biotechnology, School of Life Science and Biotechnology, Adamas University, Kolkata, India.
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Silva SJRD, Kohl A, Pena L, Pardee K. Clinical and laboratory diagnosis of monkeypox (mpox): Current status and future directions. iScience 2023; 26:106759. [PMID: 37206155 PMCID: PMC10183700 DOI: 10.1016/j.isci.2023.106759] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/21/2023] Open
Abstract
The emergence and rapid spread of the monkeypox virus (MPXV) to non-endemic countries has brought this once obscure pathogen to the forefront of global public health. Given the range of conditions that cause similar skin lesions, and because the clinical manifestation may often be atypical in the current mpox outbreak, it can be challenging to diagnose patients based on clinical signs and symptoms. With this perspective in mind, laboratory-based diagnosis assumes a critical role for the clinical management, along with the implementation of countermeasures. Here, we review the clinical features reported in mpox patients, the available laboratory tests for mpox diagnosis, and discuss the principles, advances, advantages, and drawbacks of each assay. We also highlight the diagnostic platforms with the potential to guide ongoing clinical response, particularly those that increase diagnostic capacity in low- and middle-income countries. With the outlook of this evolving research area, we hope to provide a resource to the community and inspire more research and the development of diagnostic alternatives with applications to this and future public health crises.
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Affiliation(s)
| | - Alain Kohl
- MRC-University of Glasgow Centre for Virus Research, Glasgow G61 1QH, UK
| | - Lindomar Pena
- Department of Virology, Aggeu Magalhães Institute (IAM), Oswaldo Cruz Foundation (Fiocruz), 50670-420 Recife, Pernambuco, Brazil
| | - Keith Pardee
- Department of Pharmaceutical Sciences, Leslie Dan Faculty of Pharmacy, University of Toronto, Toronto ON M5S 3M2, Canada
- Department of Mechanical and Industrial Engineering, University of Toronto, Toronto ON M5S 3G8, Canada
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Simon DS, Yew CW, Kumar VS. Multiplexed Reverse Transcription Loop-Mediated Isothermal Amplification Coupled with a Nucleic Acid-Based Lateral Flow Dipstick as a Rapid Diagnostic Method to Detect SARS-CoV-2. Microorganisms 2023; 11:1233. [PMID: 37317207 PMCID: PMC10223058 DOI: 10.3390/microorganisms11051233] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2023] [Revised: 04/30/2023] [Accepted: 05/03/2023] [Indexed: 06/16/2023] Open
Abstract
Due to the high reproduction rate of COVID-19, it is important to identify and isolate infected patients at the early stages of infection. The limitations of current diagnostic methods are speed, cost, and accuracy. Furthermore, new viral variants have emerged with higher rates of infectivity and mortality, many with mutations at various primer binding sites, which may evade detection via conventional PCR kits. Therefore, a rapid method that is sensitive, specific, and cost-effective is needed for a point-of-care molecular test. Accordingly, we developed a rapid molecular SARS-CoV-2 detection kit with high specificity and sensitivity, RT-PCR, taking advantage of the loop-mediated isothermal amplification (LAMP) technique. Four sets of six primers were designed based on conserved regions of the SARS-CoV-2 genome: two outer, two inner and two loop primers. Using the optimized protocol, SARS-CoV-2 genes were detected as quickly as 10 min but were most sensitive at 30 min, detecting as little as 100 copies of template DNA. We then coupled the RT-LAMP with a lateral flow dipstick (LFD) for multiplex detection. The LFD could detect two genic amplifications on a single strip, making it suitable for multiplexed detection. The development of a multiplexed RT-LAMP-LFD reaction on crude VTM samples would be suitable for the point-of-care diagnosis of COVID-19 in diagnostic laboratories as well as in private homes.
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Affiliation(s)
| | | | - Vijay Subbiah Kumar
- Biotechnology Research Institute, Universiti Malaysia Sabah, Kota Kinabalu 88400, Malaysia; (D.S.S.); (C.-W.Y.)
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Dias BDP, Barbosa CC, Ferreira CS, Mayra Soares Alves Dos Santos S, Arrieta OAP, Malta WC, Gomes MLMD, Alves E Silva M, Fonseca JDM, Borges LP, Silva BDM. Challenges in Direct Detection of Flaviviruses: A Review. Pathogens 2023; 12:pathogens12050643. [PMID: 37242313 DOI: 10.3390/pathogens12050643] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2023] [Revised: 04/18/2023] [Accepted: 04/20/2023] [Indexed: 05/28/2023] Open
Abstract
Arthropods transmit arboviruses via mosquito and tick bites to humans and other animals. The genus flavivirus, which causes diseases, sequelae, and thousands of deaths, mainly in developing and underdeveloped countries, is among the arboviruses of interest to public health. Given the importance of early and accurate diagnosis, this review analyzes the methods of direct detection of flaviviruses, such as reverse transcription loop-mediated isothermal amplification, microfluidics, localized surface plasmon resonance, and surface-enhanced Raman scattering, and presents the advantages, disadvantages, and detection limits identified in studies reported in the literature for each methodology. Among the different methods available, it is essential to balance four fundamental indicators to determine the ideal test: good sensitivity, high specificity, low false positive rate, and rapid results. Among the methods analyzed, reverse transcription loop-mediated isothermal amplification stands out, owing to result availability within a few minutes, with good sensitivity and specificity; in addition, it is the best-characterized methodology.
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Affiliation(s)
- Bruna de Paula Dias
- Department of Biological Sciences, Federal University of Ouro Preto, Ouro Preto 35400-000, Brazil
| | - Camila Cavadas Barbosa
- Department of Biological Sciences, Federal University of Ouro Preto, Ouro Preto 35400-000, Brazil
| | - Cyntia Silva Ferreira
- Department of Biological Sciences, Federal University of Ouro Preto, Ouro Preto 35400-000, Brazil
| | | | | | | | | | - Mariela Alves E Silva
- Department of Biological Sciences, Federal University of Ouro Preto, Ouro Preto 35400-000, Brazil
| | - Júlia de Matos Fonseca
- Department of Biological Sciences, Federal University of Ouro Preto, Ouro Preto 35400-000, Brazil
| | - Lysandro Pinto Borges
- Department of Pharmacy, Federal University of Sergipe, São Cristóvão 9100-000, Brazil
| | - Breno de Mello Silva
- Department of Biological Sciences, Federal University of Ouro Preto, Ouro Preto 35400-000, Brazil
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Tavakoli-Koopaei R, Javadi-Zarnaghi F, Aboutalebian S, Mirhendi H. Malachite Green-Based Detection of SARS-CoV-2 by One-Step Reverse Transcription Loop-Mediated Isothermal Amplification. IRANIAN JOURNAL OF SCIENCE 2023. [PMCID: PMC9898859 DOI: 10.1007/s40995-022-01392-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/09/2023]
Abstract
The pandemic of severe acute respiratory syndrome 2 (SARS-CoV-2) revealed the necessity of diagnosis of the infected people to prevent the prevalence infection cycle. Many commercial pathogen diagnosis methods are based on the detection of genomic materials. Isothermal amplification methods such as loop-mediated-isothermal amplification (LAMP) are the method of choice in these cases. Reverse transcription steps are efficiently coupled to LAMP for the detection of pathogens with genomic RNAs such as SARS-CoV-2. Many detection systems for LAMP include fluorescent readout systems. Although such systems result in desirable limits of detection, the need for special instrumentation is the main dispute of such systems to become real point of care assays. In contrast, colorimetric detection methods would reduce costs and improve the applicability of the system. In this study one-step reverse transcription-LAMP reaction was established that enables visual detection of the SARS-CoV-2 genome. Nasopharyngeal RNA samples were first validated by reverse transcription quantitative polymerase chain reaction and then subjected to RT-LAMP. To lower the cost associated with the readout system equipment, malachite green (MG) was used. The color change of MG to blue allowed visual detection of the virus. Firstly, experiments were set up as two-step RT-LAMP reaction to identify the best primer sets. In addition, MG concentration was optimized with the significant colorimetric signal for the positive samples. Next, a one-step colorimetric method was developed for the detection of SARS-CoV-2 based on MG color shift in 2 h.
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Affiliation(s)
- Reyhaneh Tavakoli-Koopaei
- grid.411750.60000 0001 0454 365XDepartment of Cell and Molecular Biology & Microbiology, Faculty of Biological Science and Technology, University of Isfahan, Isfahan, Iran
| | - Fatemeh Javadi-Zarnaghi
- grid.411750.60000 0001 0454 365XDepartment of Cell and Molecular Biology & Microbiology, Faculty of Biological Science and Technology, University of Isfahan, Isfahan, Iran
| | - Shima Aboutalebian
- grid.411036.10000 0001 1498 685XDepartment of Medical Parasitology and Mycology, School of Medicine, Research Core Facilities Laboratory, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Hossein Mirhendi
- grid.411036.10000 0001 1498 685XDepartment of Medical Parasitology and Mycology, School of Medicine, Research Core Facilities Laboratory, Isfahan University of Medical Sciences, Isfahan, Iran
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Dahiya N, Yadav M, Singh H, Jakhar R, Sehrawat N. ZIKV: Epidemiology, infection mechanism and current therapeutics. FRONTIERS IN TROPICAL DISEASES 2023. [DOI: 10.3389/fitd.2022.1059283] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023] Open
Abstract
The Zika virus (ZIKV) is a vector-borne flavivirus that has been detected in 87 countries worldwide. Outbreaks of ZIKV infection have been reported from various places around the world and the disease has been declared a public health emergency of international concern. ZIKV has two modes of transmission: vector and non-vector. The ability of ZIKV to vertically transmit in its competent vectors, such as Aedes aegypti and Aedes albopictus, helps it to cope with adverse conditions, and this could be the reason for the major outbreaks that occur from time to time. ZIKV outbreaks are a global threat and, therefore, there is a need for safe and effective drugs and vaccines to fight the virus. In more than 80% of cases, ZIKV infection is asymptomatic and leads to complications, such as microcephaly in newborns and Guillain–Barré syndrome (GBS) in adults. Drugs such as sofosbuvir, chloroquine, and suramin have been found to be effective against ZIKV infections, but further evaluation of their safety in pregnant women is needed. Although temoporfin can be given to pregnant women, it needs to be tested further for side effects. Many vaccine types based on protein, vector, DNA, and mRNA have been formulated. Some vaccines, such as mRNA-1325 and VRC-ZKADNA090-00-VP, have reached Phase II clinical trials. Some new techniques should be used for formulating and testing the efficacy of vaccines. Although there have been no recent outbreaks of ZIKV infection, several studies have shown continuous circulation of ZIKV in mosquito vectors, and there is a risk of re-emergence of ZIKV in the near future. Therefore, vaccines and drugs for ZIKV should be tested further, and safe and effective therapeutic techniques should be licensed for use during outbreaks.
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Siriyasatien P, Wacharapluesadee S, Kraivichian K, Suwanbamrung C, Sutthanont N, Cantos-Barreda A, Phumee A. Development and evaluation of a visible reverse transcription-loop-mediated isothermal amplification (RT-LAMP) for the detection of Asian lineage ZIKV in field-caught mosquitoes. Acta Trop 2022; 236:106691. [PMID: 36103950 DOI: 10.1016/j.actatropica.2022.106691] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2022] [Revised: 09/09/2022] [Accepted: 09/10/2022] [Indexed: 11/01/2022]
Abstract
The Zika virus (ZIKV) infection is an emerging and re-emerging arbovirus infection that is transmitted to humans through the bite of infected mosquitoes. Early detection of ZIKV in mosquitoes is one of the prerequisite approaches for tracking the spread of the virus. Therefore, this study aims to develop and validate a visual reverse transcription-loop-mediated isothermal amplification (RT-LAMP) method called ZIKV-RT-LAMP, for detecting ZIKV in field collected mosquito samples from Thailand. A single-tube ZIKV-RT-LAMP assay was developed to detect Asian lineage ZIKV RNA. The detection limit and cross-reactivity of ZIKV were investigated. The hemi-nested RT-PCR (hn-RT-PCR) and the colorimetric LAMP kit (cLAMP kit) were performed as reference assays. The detection limit of the ZIKV-RT-LAMP assay was 10-6 ffu/ml or pfu/ml, making it highly specific and 100 times more sensitive than the hn-RT-PCR and cLAMP kits. The ZIKV-RT-LAMP assay detected the Asian lineage of ZIKV RNA without cross-reactivity with other arthropod-borne viruses. The sensitivity and specificity of the ZIKV-RT-LAMP assay were 92.31% and 100%, respectively. The ZIKV-RT-LAMP is a simple, rapid, and inexpensive method for detecting ZIKV in field-caught mosquitos. In the future, extensive surveys of field-caught mosquito populations should be conducted. Early detection of ZIKV in field-caught mosquitoes provides for prompt and effective implementation of mosquito control strategies in endemic areas.
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Affiliation(s)
- Padet Siriyasatien
- Center of Excellence in Vector Biology and Vector Borne Diseases, Department of Parasitology, Faculty of Medicine, Chulalongkorn University, Bangkok 10330, Thailand; Department of Parasitology, Faculty of Medicine, Chulalongkorn University, Bangkok 10330, Thailand
| | - Supaporn Wacharapluesadee
- Thai Red Cross Emerging Infectious Diseases Clinical Centre, King Chulalongkorn Memorial Hospital, Faculty of Medicine, Chulalongkorn University, Bangkok 10330, Thailand
| | - Kanyarat Kraivichian
- Department of Parasitology, Faculty of Medicine, Chulalongkorn University, Bangkok 10330, Thailand
| | - Charuai Suwanbamrung
- School of Public Health, Walailak University, Nakhon Si Thammarat, Thailand; Excellent Center for Dengue and Community Public Health (EC for DACH), Walailak University, Nakhon Si Thammarat 80160, Thailand
| | - Nataya Sutthanont
- Department of Medical Entomology, Faculty of Tropical Medicine, Mahidol University Bangkok 10400, Thailand
| | - Ana Cantos-Barreda
- Department of Biochemistry and Molecular Biology-A, Faculty of Veterinary Medicine, Regional Campus of International Excellence "Campus Mare Nostrum", University of Murcia, Espinardo, Murcia 30100, Spain
| | - Atchara Phumee
- Excellent Center for Dengue and Community Public Health (EC for DACH), Walailak University, Nakhon Si Thammarat 80160, Thailand; Department of Medical Technology, School of Allied Health Sciences, Walailak University, Nakhon Si Thammarat 80160, Thailand.
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da Silva SJR, do Nascimento JCF, Germano Mendes RP, Guarines KM, Targino Alves da Silva C, da Silva PG, de Magalhães JJF, Vigar JRJ, Silva-Júnior A, Kohl A, Pardee K, Pena L. Two Years into the COVID-19 Pandemic: Lessons Learned. ACS Infect Dis 2022; 8:1758-1814. [PMID: 35940589 PMCID: PMC9380879 DOI: 10.1021/acsinfecdis.2c00204] [Citation(s) in RCA: 32] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is a highly transmissible and virulent human-infecting coronavirus that emerged in late December 2019 in Wuhan, China, causing a respiratory disease called coronavirus disease 2019 (COVID-19), which has massively impacted global public health and caused widespread disruption to daily life. The crisis caused by COVID-19 has mobilized scientists and public health authorities across the world to rapidly improve our knowledge about this devastating disease, shedding light on its management and control, and spawned the development of new countermeasures. Here we provide an overview of the state of the art of knowledge gained in the last 2 years about the virus and COVID-19, including its origin and natural reservoir hosts, viral etiology, epidemiology, modes of transmission, clinical manifestations, pathophysiology, diagnosis, treatment, prevention, emerging variants, and vaccines, highlighting important differences from previously known highly pathogenic coronaviruses. We also discuss selected key discoveries from each topic and underline the gaps of knowledge for future investigations.
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Affiliation(s)
- Severino Jefferson Ribeiro da Silva
- Laboratory of Virology and Experimental Therapy (LAVITE), Department of Virology, Aggeu Magalhães Institute (IAM), Oswaldo Cruz Foundation (Fiocruz), 50670-420 Recife, Pernambuco, Brazil.,Department of Pharmaceutical Sciences, Leslie Dan Faculty of Pharmacy, University of Toronto, Toronto, ON M5S 3M2, Canada
| | - Jessica Catarine Frutuoso do Nascimento
- Laboratory of Virology and Experimental Therapy (LAVITE), Department of Virology, Aggeu Magalhães Institute (IAM), Oswaldo Cruz Foundation (Fiocruz), 50670-420 Recife, Pernambuco, Brazil
| | - Renata Pessôa Germano Mendes
- Laboratory of Virology and Experimental Therapy (LAVITE), Department of Virology, Aggeu Magalhães Institute (IAM), Oswaldo Cruz Foundation (Fiocruz), 50670-420 Recife, Pernambuco, Brazil
| | - Klarissa Miranda Guarines
- Laboratory of Virology and Experimental Therapy (LAVITE), Department of Virology, Aggeu Magalhães Institute (IAM), Oswaldo Cruz Foundation (Fiocruz), 50670-420 Recife, Pernambuco, Brazil
| | - Caroline Targino Alves da Silva
- Laboratory of Virology and Experimental Therapy (LAVITE), Department of Virology, Aggeu Magalhães Institute (IAM), Oswaldo Cruz Foundation (Fiocruz), 50670-420 Recife, Pernambuco, Brazil
| | - Poliana Gomes da Silva
- Laboratory of Virology and Experimental Therapy (LAVITE), Department of Virology, Aggeu Magalhães Institute (IAM), Oswaldo Cruz Foundation (Fiocruz), 50670-420 Recife, Pernambuco, Brazil
| | - Jurandy Júnior Ferraz de Magalhães
- Laboratory of Virology and Experimental Therapy (LAVITE), Department of Virology, Aggeu Magalhães Institute (IAM), Oswaldo Cruz Foundation (Fiocruz), 50670-420 Recife, Pernambuco, Brazil.,Department of Virology, Pernambuco State Central Laboratory (LACEN/PE), 52171-011 Recife, Pernambuco, Brazil.,University of Pernambuco (UPE), Serra Talhada Campus, 56909-335 Serra Talhada, Pernambuco, Brazil.,Public Health Laboratory of the XI Regional Health, 56912-160 Serra Talhada, Pernambuco, Brazil
| | - Justin R J Vigar
- Department of Pharmaceutical Sciences, Leslie Dan Faculty of Pharmacy, University of Toronto, Toronto, ON M5S 3M2, Canada
| | - Abelardo Silva-Júnior
- Institute of Biological and Health Sciences, Federal University of Alagoas (UFAL), 57072-900 Maceió, Alagoas, Brazil
| | - Alain Kohl
- MRC-University of Glasgow Centre for Virus Research, Glasgow G61 1QH, United Kingdom
| | - Keith Pardee
- Department of Pharmaceutical Sciences, Leslie Dan Faculty of Pharmacy, University of Toronto, Toronto, ON M5S 3M2, Canada.,Department of Mechanical and Industrial Engineering, University of Toronto, Toronto, ON M5S 3G8, Canada
| | - Lindomar Pena
- Laboratory of Virology and Experimental Therapy (LAVITE), Department of Virology, Aggeu Magalhães Institute (IAM), Oswaldo Cruz Foundation (Fiocruz), 50670-420 Recife, Pernambuco, Brazil
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12
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de Vries EM, Cogan NOI, Gubala AJ, Mee PT, O'Riley KJ, Rodoni BC, Lynch SE. Rapid, in-field deployable, avian influenza virus haemagglutinin characterisation tool using MinION technology. Sci Rep 2022; 12:11886. [PMID: 35831457 PMCID: PMC9279447 DOI: 10.1038/s41598-022-16048-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2021] [Accepted: 07/04/2022] [Indexed: 11/29/2022] Open
Abstract
Outbreaks of avian influenza virus (AIV) from wild waterfowl into the poultry industry is of upmost significance and is an ongoing and constant threat to the industry. Accurate surveillance of AIV in wild waterfowl is critical in understanding viral diversity in the natural reservoir. Current surveillance methods for AIV involve collection of samples and transportation to a laboratory for molecular diagnostics. Processing of samples using this approach takes more than three days and may limit testing locations to those with practical access to laboratories. In potential outbreak situations, response times are critical, and delays have implications in terms of the spread of the virus that leads to increased economic cost. This study used nanopore sequencing technology for in-field sequencing and subtype characterisation of AIV strains collected from wild bird faeces and poultry. A custom in-field virus screening and sequencing protocol, including a targeted offline bioinformatic pipeline, was developed to accurately subtype AIV. Due to the lack of optimal diagnostic MinION packages for Australian AIV strains the bioinformatic pipeline was specifically targeted to confidently subtype local strains. The method presented eliminates the transportation of samples, dependence on internet access and delivers critical diagnostic information in a timely manner.
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Affiliation(s)
- Ellen M de Vries
- Agriculture Victoria, AgriBio, Centre for AgriBioscience, Bundoora, VIC, 3083, Australia. .,School of Applied Systems Biology, La Trobe University, Bundoora, VIC, 3083, Australia.
| | - Noel O I Cogan
- Agriculture Victoria, AgriBio, Centre for AgriBioscience, Bundoora, VIC, 3083, Australia.,School of Applied Systems Biology, La Trobe University, Bundoora, VIC, 3083, Australia
| | - Aneta J Gubala
- Land Division, Defence Science & Technology Group, Fishermans Bend, VIC, 3207, Australia
| | - Peter T Mee
- Agriculture Victoria, AgriBio, Centre for AgriBioscience, Bundoora, VIC, 3083, Australia
| | - Kim J O'Riley
- Agriculture Victoria, AgriBio, Centre for AgriBioscience, Bundoora, VIC, 3083, Australia
| | - Brendan C Rodoni
- Agriculture Victoria, AgriBio, Centre for AgriBioscience, Bundoora, VIC, 3083, Australia.,School of Applied Systems Biology, La Trobe University, Bundoora, VIC, 3083, Australia
| | - Stacey E Lynch
- Agriculture Victoria, AgriBio, Centre for AgriBioscience, Bundoora, VIC, 3083, Australia
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13
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Development of a Rapid Gold Nanoparticle-Based Lateral Flow Immunoassay for the Detection of Dengue Virus. BIOSENSORS 2022; 12:bios12070495. [PMID: 35884298 PMCID: PMC9313084 DOI: 10.3390/bios12070495] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Revised: 06/29/2022] [Accepted: 07/04/2022] [Indexed: 11/16/2022]
Abstract
Flavivirus detection in humans and mosquito reservoirs has been an important issue since it can cause a variety of illnesses and could represent a health problem in geographical zones where the vector is endemic. In this work, we designed and characterized a biosensor based on gold nanoparticles (AuNPs) and antibody 4G2 for the detection of dengue virus (DENV) in vitro, obtaining different conjugates (with different antibody concentrations). The AuNP–4G2 conjugates at concentrations of 1, 3, and 6 µg/mL presented an increase in the average hydrodynamic diameter compared to the naked AuNPs. Also, as part of the characterization, differences in the UV-Vis absorbance spectrum and electrophoretic migration were observed between the conjugated AuNPs (with BSA or antibody) and naked AuNPs. Additionally, we used this biosensor (AuNP–4G2 conjugate with 3 µg/mL antibody) in the assembly of a competitive lateral flow assay (LFA) for the development of an alternative test to detect the flavivirus envelope protein in isolated DENV samples as a future tool for dengue detection (and other flaviviruses) in the mosquito vector (Aedesaegypti) for the identification of epidemic risk regions. Functionality tests were performed using Dengue virus 2 isolated solution (TCID50/mL = 4.58 × 103) as a positive sample and PBS buffer as a negative control. The results showed that it is possible to detect Dengue virus in vitro with this gold nanoparticle-based lateral flow assay with an estimated detection limit of 5.12 × 102 PFU. We suggest that this biosensor could be used as an additional detection tool by coupling it to different point-of-care tests (POCT) for the easy detection of other flaviviruses.
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14
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Clementino M, Cavalcante KF, Viana VAF, Silva DDO, Damasceno CR, Fernandes de Souza J, Gondim RNDG, Jorge DMDM, Magalhães LMVC, Arruda ÉAGD, Neto RDJP, Medeiros MS, Santos AAD, Magalhães PJC, Mello LP, Arruda E, Lima AÂM, Havt A. Detection of SARS-CoV-2 in Different Human Biofluids Using the Loop-Mediated Isothermal Amplification Assay: A Prospective Diagnostic Study in Fortaleza, Brazil. J Med Virol 2022; 94:4170-4180. [PMID: 35535440 PMCID: PMC9348339 DOI: 10.1002/jmv.27842] [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: 03/26/2022] [Revised: 04/21/2022] [Accepted: 05/05/2022] [Indexed: 11/19/2022]
Abstract
We adopted the reverse‐transcriptase‐loop‐mediated isothermal amplification (RT‐LAMP) to detect severe acute respiratory syndrome coronavirus 2 (SARS‐Cov‐2) in patient samples. Two primer sets for genes N and Orf1ab were designed to detect SARS‐CoV‐2, and one primer set was designed to detect the human gene Actin. We collected prospective 138 nasopharyngeal swabs, 70 oropharyngeal swabs, 69 salivae, and 68 mouth saline wash samples from patients suspected to have severe acute respiratory syndrome (SARS) caused by SARS‐CoV‐2 to test the RT‐LAMP in comparison with the gold standard technique reverse‐transcription quantitative polymerase chain reaction (RT‐qPCR). The accuracy of diagnosis using both primers, N5 and Orf9, was evaluated. Sensitivity and specificity for diagnosis were 96% (95% confidence interval [CI]: 87–99) and 85% (95% CI: 76–91) in 138 samples, respectively. Accurate diagnosis results were obtained only in nasopharyngeal swabs processed via extraction kit. Accurate and rapid diagnosis could aid coronavirus disease 2019 (COVID‐19) pandemic management by identifying, isolating, and treating patients rapidly.
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Affiliation(s)
- Marco Clementino
- INCT-Biomedicina no Semiárido Brasileiro, Faculdade de Medicina, Universidade Federal do Ceará, Fortaleza, CE, Brazil
| | | | | | - Dayara de Oliveira Silva
- INCT-Biomedicina no Semiárido Brasileiro, Faculdade de Medicina, Universidade Federal do Ceará, Fortaleza, CE, Brazil
| | - Caroline Rebouças Damasceno
- INCT-Biomedicina no Semiárido Brasileiro, Faculdade de Medicina, Universidade Federal do Ceará, Fortaleza, CE, Brazil
| | - Jessica Fernandes de Souza
- INCT-Biomedicina no Semiárido Brasileiro, Faculdade de Medicina, Universidade Federal do Ceará, Fortaleza, CE, Brazil
| | | | - Daniel Macedo de Melo Jorge
- Departamento de Biologia Celular e Molecular, Faculdade de Medicina, Universidade do Estado de S. Paulo, Ribeirão Preto, SP, Brazil
| | | | | | - Roberto da Justa Pires Neto
- Hospital S. José de Doenças Infecciosas e Transmissíveis, Secretaria de Saúde do Ceará, Fortaleza, CE, Brazil
| | - Melissa Soares Medeiros
- Hospital S. José de Doenças Infecciosas e Transmissíveis, Secretaria de Saúde do Ceará, Fortaleza, CE, Brazil
| | - Armênio Aguiar Dos Santos
- INCT-Biomedicina no Semiárido Brasileiro, Faculdade de Medicina, Universidade Federal do Ceará, Fortaleza, CE, Brazil
| | - Pedro Jorge Caldas Magalhães
- INCT-Biomedicina no Semiárido Brasileiro, Faculdade de Medicina, Universidade Federal do Ceará, Fortaleza, CE, Brazil
| | - Liana Perdigão Mello
- Secretaria de Vigilância em Saúde e Laboratórios Central de Saúde Pública, Secretaria de Saúde do Ceará
| | - Eurico Arruda
- Departamento de Biologia Celular e Molecular, Faculdade de Medicina, Universidade do Estado de S. Paulo, Ribeirão Preto, SP, Brazil.,Rede Vírus, Ministério da Ciência, Tecnologia, Inovações e Comunicações-MCTIC, Brasília, DF, Brazil
| | - Aldo Ângelo Moreira Lima
- INCT-Biomedicina no Semiárido Brasileiro, Faculdade de Medicina, Universidade Federal do Ceará, Fortaleza, CE, Brazil.,Rede Vírus, Ministério da Ciência, Tecnologia, Inovações e Comunicações-MCTIC, Brasília, DF, Brazil
| | - Alexandre Havt
- INCT-Biomedicina no Semiárido Brasileiro, Faculdade de Medicina, Universidade Federal do Ceará, Fortaleza, CE, Brazil
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15
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Narahari T, Dahmer J, Sklavounos A, Kim T, Satkauskas M, Clotea I, Ho M, Lamanna J, Dixon C, Rackus DG, Silva SJRD, Pena L, Pardee K, Wheeler AR. Portable sample processing for molecular assays: application to Zika virus diagnostics. LAB ON A CHIP 2022; 22:1748-1763. [PMID: 35357372 DOI: 10.1039/d1lc01068a] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
This paper introduces a digital microfluidic (DMF) platform for portable, automated, and integrated Zika viral RNA extraction and amplification. The platform features reconfigurable DMF cartridges offering a closed, humidified environment for sample processing at elevated temperatures, as well as programmable control instrumentation with a novel thermal cycling unit regulated using a proportional integral derivative (PID) feedback loop. The system operates on 12 V DC power, which can be supplied by rechargeable battery packs for remote testing. The DMF system was optimized for an RNA processing pipeline consisting of the following steps: 1) magnetic-bead based RNA extraction from lysed plasma samples, 2) RNA clean-up, and 3) integrated, isothermal amplification of Zika RNA. The DMF pipeline was coupled to a paper-based, colorimetric cell-free protein expression assay for amplified Zika RNA mediated by toehold switch-based sensors. Blinded laboratory evaluation of Zika RNA spiked in human plasma yielded a sensitivity and specificity of 100% and 75% respectively. The platform was then transported to Recife, Brazil for evaluation with infectious Zika viruses, which were detected at the 100 PFU mL-1 level from a 5 μL sample (equivalent to an RT-qPCR cycle threshold value of 32.0), demonstrating its potential as a sample processing platform for miniaturized diagnostic testing.
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Affiliation(s)
- Tanya Narahari
- Department of Chemistry, University of Toronto, 80 St. George Street, Toronto, Ontario, M5S 3H6, Canada.
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, 160 College Street, Toronto, Ontario, M5S 3E1, Canada
| | - Joshua Dahmer
- Department of Chemistry, University of Toronto, 80 St. George Street, Toronto, Ontario, M5S 3H6, Canada.
| | - Alexandros Sklavounos
- Department of Chemistry, University of Toronto, 80 St. George Street, Toronto, Ontario, M5S 3H6, Canada.
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, 160 College Street, Toronto, Ontario, M5S 3E1, Canada
| | - Taehyeong Kim
- Department of Chemistry, University of Toronto, 80 St. George Street, Toronto, Ontario, M5S 3H6, Canada.
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, 160 College Street, Toronto, Ontario, M5S 3E1, Canada
| | - Monika Satkauskas
- Department of Chemistry, University of Toronto, 80 St. George Street, Toronto, Ontario, M5S 3H6, Canada.
| | - Ioana Clotea
- Department of Chemistry, University of Toronto, 80 St. George Street, Toronto, Ontario, M5S 3H6, Canada.
| | - Man Ho
- Department of Chemistry, University of Toronto, 80 St. George Street, Toronto, Ontario, M5S 3H6, Canada.
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, 160 College Street, Toronto, Ontario, M5S 3E1, Canada
| | - Julian Lamanna
- Department of Chemistry, University of Toronto, 80 St. George Street, Toronto, Ontario, M5S 3H6, Canada.
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, 160 College Street, Toronto, Ontario, M5S 3E1, Canada
| | - Christopher Dixon
- Department of Chemistry, University of Toronto, 80 St. George Street, Toronto, Ontario, M5S 3H6, Canada.
| | - Darius G Rackus
- Department of Chemistry, University of Toronto, 80 St. George Street, Toronto, Ontario, M5S 3H6, Canada.
- Leslie Dan Faculty of Pharmacy, University of Toronto, 144 College Street, Toronto, Ontario, M5S 3M2, Canada
| | - Severino Jefferson Ribeiro da Silva
- Department of Virology, Aggeu Magalhães Institute (IAM), Oswaldo Cruz Institute (FIOCRUZ Pernambuco), Av. Professor Moraes Rego, s/n - Cidade Universitária, Recife, PE, CEP 50.740-465, Brazil
| | - Lindomar Pena
- Department of Virology, Aggeu Magalhães Institute (IAM), Oswaldo Cruz Institute (FIOCRUZ Pernambuco), Av. Professor Moraes Rego, s/n - Cidade Universitária, Recife, PE, CEP 50.740-465, Brazil
| | - Keith Pardee
- Leslie Dan Faculty of Pharmacy, University of Toronto, 144 College Street, Toronto, Ontario, M5S 3M2, Canada
- Department of Mechanical and Industrial Engineering, University of Toronto, Toronto, Ontario, M5S 3G8 Canada
| | - Aaron R Wheeler
- Department of Chemistry, University of Toronto, 80 St. George Street, Toronto, Ontario, M5S 3H6, Canada.
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, 160 College Street, Toronto, Ontario, M5S 3E1, Canada
- Institute for Biomedical Engineering, University of Toronto, 164 College Street, Toronto, Ontario, M5S 3G9, Canada
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16
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Krokovsky L, Paiva MHS, Guedes DRD, Barbosa RMR, de Oliveira ALS, Anastácio DB, Pontes CR, Ayres CFJ. Arbovirus Surveillance in Field-Collected Mosquitoes From Pernambuco-Brazil, During the Triple Dengue, Zika and Chikungunya Outbreak of 2015-2017. FRONTIERS IN TROPICAL DISEASES 2022. [DOI: 10.3389/fitd.2022.875031] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
The (re) emergence of arboviruses around the world is a public health concern once severe outbreaks are usually associated with these infections. The co-circulation of Dengue (DENV), Zika (ZIKV) and Chikungunya (CHIKV) viruses in the past few years has caused a unique epidemic situation in Brazil. The northeast region of the country was the most affected by clinical complications from such arboviruses’ infections, including neurological disorders caused by ZIKV. In this particular region, Aedes mosquitoes are the main vectors of DENV, ZIKV and CHIKV, with Culex quinquefasciatus also considered as a potential vector of ZIKV. Therefore, virological surveillance in mosquitoes contributes to understanding the epidemiological profile of these diseases. Here, we report the circulation of DENV, ZIKV and CHIKV in Aedes spp. and Cx. quinquefasciatus female mosquitoes collected in areas with a high arbovirus circulation in humans in the Metropolitan Region of Recife, Pernambuco, Brazil, during the triple-epidemics of 2015-17. All the field-caught mosquitoes were sent to the laboratory for arbovirus screening after RNA extraction and RT-PCR/RT-qPCR. A total of 6,227 females were evaluated and, as a result, DENV, ZIKV and CHIKV were identified in Ae. aegypti, Ae. taeniorhynchus and Cx. quinquefasciatus mosquito pools. In addition, DENV and ZIKV were isolated in C6/36 cells. In conclusion, it is important to highlight that arbovirus surveillance performed in mosquitoes from DENV-ZIKV-CHIKV hotspots areas can serve as an early-warning system to target vector control actions more efficiently in each studied area.
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17
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Karlikow M, da Silva SJR, Guo Y, Cicek S, Krokovsky L, Homme P, Xiong Y, Xu T, Calderón-Peláez MA, Camacho-Ortega S, Ma D, de Magalhães JJF, Souza BNRF, de Albuquerque Cabral DG, Jaenes K, Sutyrina P, Ferrante T, Benitez AD, Nipaz V, Ponce P, Rackus DG, Collins JJ, Paiva M, Castellanos JE, Cevallos V, Green AA, Ayres C, Pena L, Pardee K. Field validation of the performance of paper-based tests for the detection of the Zika and chikungunya viruses in serum samples. Nat Biomed Eng 2022; 6:246-256. [PMID: 35256758 PMCID: PMC8940623 DOI: 10.1038/s41551-022-00850-0] [Citation(s) in RCA: 27] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2021] [Accepted: 01/24/2022] [Indexed: 12/11/2022]
Abstract
AbstractIn low-resource settings, resilience to infectious disease outbreaks can be hindered by limited access to diagnostic tests. Here we report the results of double-blinded studies of the performance of paper-based diagnostic tests for the Zika and chikungunya viruses in a field setting in Latin America. The tests involved a cell-free expression system relying on isothermal amplification and toehold-switch reactions, a purpose-built portable reader and onboard software for computer vision-enabled image analysis. In patients suspected of infection, the accuracies and sensitivities of the tests for the Zika and chikungunya viruses were, respectively, 98.5% (95% confidence interval, 96.2–99.6%, 268 serum samples) and 98.5% (95% confidence interval, 91.7–100%, 65 serum samples) and approximately 2 aM and 5 fM (both concentrations are within clinically relevant ranges). The analytical specificities and sensitivities of the tests for cultured samples of the viruses were equivalent to those of the real-time quantitative PCR. Cell-free synthetic biology tools and companion hardware can provide de-centralized, high-capacity and low-cost diagnostics for use in low-resource settings.
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18
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Maddison MD, Li Z, Miley KM, Poole CB, Carlow CKS, Unnasch TR. Development and Validation of a Colorimetric Reverse Transcriptase Loop-Mediated Isothermal Amplification Assay for Detection of Eastern Equine Encephalitis Virus in Mosquitoes. JOURNAL OF THE AMERICAN MOSQUITO CONTROL ASSOCIATION 2022; 38:7-18. [PMID: 35276729 DOI: 10.2987/21-7047] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Eastern equine encephalitis virus (EEEV) is a highly pathogenic alphavirus that causes periodic outbreaks in the eastern USA. Mosquito abatement programs are faced with various challenges with surveillance and control of EEEV and other mosquito-borne illnesses. Environmental sampling of mosquito populations can be technically complex. Here we report the identification of biomarkers, development and validation of a colorimetric reverse transcription loop-mediated isothermal amplification (RT-LAMP) assay for the detection of EEEV. Positive samples are easily visualized by a color change from pink to yellow. The assay was validated using EEEV from viral culture, experimentally spiked mosquito pools, and previously tested mosquito pools. The RT-LAMP assay detected viral titers down to approximately 10% of what would be present in a single infectious mosquito, based upon EEEV viral titers determined by previous competency studies. The RT-LAMP assay efficiently detected EEEV in combined aliquots from previously homogenized pools of mosquitoes, allowing up to 250 individual mosquitoes to be tested in a single reaction. No false positive results were obtained from RNA prepared from negative mosquito pools acquired from known and potential EEEV vectors. The colorimetric RT-LAMP assay is highly accurate, technically simple, and does not require sophisticated equipment, making it a cost-effective alternative to real time reverse transcriptase-polymerase chain reaction (RT-PCR) for vector surveillance.
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19
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Burkhalter KL, O'Keefe M, Holbert-Watson Z, Green T, Savage HM, Markowski DM. Laboratory and Field Evaluations of a Commercially Available Real-Time Loop-Mediated Isothermal Amplification Assay for the Detection of West Nile Virus in Mosquito Pools. JOURNAL OF THE AMERICAN MOSQUITO CONTROL ASSOCIATION 2021; 37:256-262. [PMID: 34817603 DOI: 10.2987/21-7033] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Although the specific cDNA amplification mechanisms of reverse-transcriptase polymerase chain reaction (RT-PCR) and RT loop-mediated isothermal amplification (RT-LAMP) are very different, both molecular assays serve as options to detect arboviral RNA in mosquito pools. Like RT-PCR, RT-LAMP uses a reverse transcription step to synthesize complementary DNA (cDNA) from an RNA template and then uses target-specific primers to amplify cDNA to detectable levels in a single-tube reaction. Using laboratory-generated West Nile virus (WNV) samples and field-collected mosquito pools, we evaluated the sensitivity and specificity of a commercially available WNV real-time RT-LAMP assay (Pro-AmpRT™ WNV; Pro-Lab Diagnostics, Inc., Round Rock, Texas) and compared the results to a validated real-time RT-PCR assay. Laboratory generated virus stock samples containing ≥ 2.3 log10 plaque-forming units (PFU)/ml and intrathoracically inoculated mosquitoes containing ≥ 2.4 log10 PFU/ml produced positive results in the Pro-AmpRT WNV assay. Of field-collected pools that were WNV positive by real-time RT-PCR, 74.5% (70 of 94) were also positive by the Pro-AmpRT WNV assay, resulting in an overall Cohen's kappa agreement of 79.4% between the 2 tests. The Pro-AmpRT WNV assay shows promise as a suitable virus screening tool for vector surveillance programs provided agencies are aware of its characteristics and limitations.
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20
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Alcántara R, Peñaranda K, Mendoza-Rojas G, Nakamoto JA, Martins-Luna J, del Valle-Mendoza J, Adaui V, Milón P. Unlocking SARS-CoV-2 detection in low- and middle-income countries. CELL REPORTS METHODS 2021; 1:100093. [PMID: 34697612 PMCID: PMC8529268 DOI: 10.1016/j.crmeth.2021.100093] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/09/2021] [Revised: 07/31/2021] [Accepted: 09/20/2021] [Indexed: 12/12/2022]
Abstract
Low- and middle-income countries (LMICs) are significantly affected by SARS-CoV-2, partially due to their limited capacity for local production and implementation of molecular testing. Here, we provide detailed methods and validation of a molecular toolkit that can be readily produced and deployed using laboratory equipment available in LMICs. Our results show that lab-scale production of enzymes and nucleic acids can supply over 50,000 tests per production batch. The optimized one-step RT-PCR coupled to CRISPR-Cas12a-mediated detection showed a limit of detection of 102 ge/μL in a turnaround time of 2 h. The clinical validation indicated an overall sensitivity of 80%-88%, while for middle and high viral load samples (Cq ≤ 31) the sensitivity was 92%-100%. The specificity was 96%-100% regardless of viral load. Furthermore, we show that the toolkit can be used with the mobile laboratory Bento Lab, potentially enabling LMICs to implement detection services in unattended remote regions.
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Affiliation(s)
- Roberto Alcántara
- Centre for Research and Innovation, Health Sciences Faculty, Universidad Peruana de Ciencias Aplicadas (UPC), Lima 15023, Peru
| | - Katherin Peñaranda
- Centre for Research and Innovation, Health Sciences Faculty, Universidad Peruana de Ciencias Aplicadas (UPC), Lima 15023, Peru
| | - Gabriel Mendoza-Rojas
- Centre for Research and Innovation, Health Sciences Faculty, Universidad Peruana de Ciencias Aplicadas (UPC), Lima 15023, Peru
| | - Jose A. Nakamoto
- Centre for Research and Innovation, Health Sciences Faculty, Universidad Peruana de Ciencias Aplicadas (UPC), Lima 15023, Peru
| | - Johanna Martins-Luna
- Centre for Research and Innovation, Health Sciences Faculty, Universidad Peruana de Ciencias Aplicadas (UPC), Lima 15023, Peru
- Laboratorio de Biología Molecular, Instituto de Investigación Nutricional, Lima, Peru
| | - Juana del Valle-Mendoza
- Centre for Research and Innovation, Health Sciences Faculty, Universidad Peruana de Ciencias Aplicadas (UPC), Lima 15023, Peru
- Laboratorio de Biología Molecular, Instituto de Investigación Nutricional, Lima, Peru
| | - Vanessa Adaui
- Centre for Research and Innovation, Health Sciences Faculty, Universidad Peruana de Ciencias Aplicadas (UPC), Lima 15023, Peru
| | - Pohl Milón
- Centre for Research and Innovation, Health Sciences Faculty, Universidad Peruana de Ciencias Aplicadas (UPC), Lima 15023, Peru
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21
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Alves PA, de Oliveira EG, Franco-Luiz APM, Almeida LT, Gonçalves AB, Borges IA, Rocha FDS, Rocha RP, Bezerra MF, Miranda P, Capanema FD, Martins HR, Weber G, Teixeira SMR, Wallau GL, do Monte-Neto RL. Optimization and Clinical Validation of Colorimetric Reverse Transcription Loop-Mediated Isothermal Amplification, a Fast, Highly Sensitive and Specific COVID-19 Molecular Diagnostic Tool That Is Robust to Detect SARS-CoV-2 Variants of Concern. Front Microbiol 2021; 12:713713. [PMID: 34867841 PMCID: PMC8637279 DOI: 10.3389/fmicb.2021.713713] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2021] [Accepted: 09/28/2021] [Indexed: 12/23/2022] Open
Abstract
The coronavirus disease 2019 (COVID-19) pandemic unfolded due to the widespread severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) transmission reinforced the urgent need for affordable molecular diagnostic alternative methods for massive testing screening. We present the clinical validation of a pH-dependent colorimetric reverse transcription loop-mediated isothermal amplification (RT-LAMP) for SARS-CoV-2 detection. The method revealed a limit of detection of 19.3 ± 2.7 viral genomic copies/μL when using RNA extracted samples obtained from nasopharyngeal swabs collected in guanidine-containing viral transport medium. Typical RT-LAMP reactions were performed at 65°C for 30 min. When compared to reverse transcriptase-quantitative polymerase chain reaction (RT-qPCR), up to cycle-threshold (Ct) value 32, RT-LAMP presented 98% [95% confidence interval (CI) = 95.3-99.5%] sensitivity and 100% (95% CI = 94.5-100%) specificity for SARS-CoV-2 RNA detection targeting E and N genes. No cross-reactivity was detected when testing other non-SARS-CoV virus, confirming high specificity. The test is compatible with primary RNA extraction-free samples. We also demonstrated that colorimetric RT-LAMP can detect SARS-CoV-2 variants of concern and variants of interest, such as variants occurring in Brazil named gamma (P.1), zeta (P.2), delta (B.1.617.2), B.1.1.374, and B.1.1.371. The method meets point-of-care requirements and can be deployed in the field for high-throughput COVID-19 testing campaigns, especially in countries where COVID-19 testing efforts are far from ideal to tackle the pandemics. Although RT-qPCR is considered the gold standard for SARS-CoV-2 RNA detection, it requires expensive equipment, infrastructure, and highly trained personnel. In contrast, RT-LAMP emerges as an affordable, inexpensive, and simple alternative for SARS-CoV-2 molecular detection that can be applied to massive COVID-19 testing campaigns and save lives.
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Affiliation(s)
- Pedro A. Alves
- Instituto René Rachou, Fundação Oswaldo Cruz, Belo Horizonte, Brazil
- Centro de Tecnologia em Vacinas, UFMG/Fiocruz, Belo Horizonte, Brazil
| | | | | | | | | | - Iara A. Borges
- Instituto René Rachou, Fundação Oswaldo Cruz, Belo Horizonte, Brazil
| | | | - Raissa P. Rocha
- Centro de Tecnologia em Vacinas, UFMG/Fiocruz, Belo Horizonte, Brazil
| | - Matheus F. Bezerra
- Departamento de Microbiologia, Instituto Aggeu Magalhães, Fundação Oswaldo Cruz, Recife, Brazil
| | - Pâmella Miranda
- Departamento de Física, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Flávio D. Capanema
- Núcleo de Inovação Tecnológica, Fundação Hospitalar do Estado de Minas Gerais, Belo Horizonte, Brazil
| | - Henrique R. Martins
- Visuri Equipamentos e Serviços, Belo Horizonte, Brazil
- Departamento de Engenharia Elétrica, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Gerald Weber
- Departamento de Física, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | | | - Gabriel Luz Wallau
- Departamento de Entomologia e Núcleo de Bioinformática, Instituto Aggeu Magalhães, Fundação Oswaldo Cruz, Recife, Brazil
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22
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Jamwal VL, Kumar N, Bhat R, Jamwal PS, Singh K, Dogra S, Kulkarni A, Bhadra B, Shukla MR, Saran S, Dasgupta S, Vishwakarma RA, Gandhi SG. Optimization and validation of RT-LAMP assay for diagnosis of SARS-CoV2 including the globally dominant Delta variant. Virol J 2021; 18:178. [PMID: 34461941 PMCID: PMC8404189 DOI: 10.1186/s12985-021-01642-9] [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: 03/17/2021] [Accepted: 08/12/2021] [Indexed: 01/12/2023] Open
Abstract
Background Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2), the causative agent of COVID-19 pandemic, has infected more than 179 million people worldwide. Testing of infected individuals is crucial for identification and isolation, thereby preventing further spread of the disease. Presently, Taqman™ Reverse Transcription Real Time PCR is considered gold standard, and is the most common technique used for molecular testing of COVID-19, though it requires sophisticated equipments, expertise and is also relatively expensive. Objective Development and optimization of an alternate molecular testing method for the diagnosis of COVID-19, through a two step Reverse Transcription Loop-mediated isothermal AMPlification (RT-LAMP). Results Primers for LAMP were carefully designed for discrimination from other closely related human pathogenic coronaviruses. Care was also taken that primer binding sites are present in conserved regions of SARS-CoV2. Our analysis shows that the primer binding sites are well conserved in all the variants of concern (VOC) and variants of interest (VOI), notified by World Health Organization (WHO). These lineages include B.1.1.7, B.1.351, P.1, B.1.617.2, B.1.427/B.1.429, P.2, B.1.525, P.3, B.1.526 and B.1.617.1. Various DNA polymerases with strand displacement activity were evaluated and conditions were optimized for LAMP amplification and visualization. Different LAMP primer sets were also evaluated using synthetic templates as well as patient samples. Conclusion In a double blind study, the RT-LAMP assay was validated on more than 150 patient samples at two different sites. The RT-LAMP assay appeared to be 89.2% accurate when compared to the Taqman™ rt-RT-PCR assay. Supplementary Information The online version contains supplementary material available at 10.1186/s12985-021-01642-9.
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Affiliation(s)
- Vijay Lakshmi Jamwal
- CSIR-Indian Institute of Integrative Medicine, Canal Road, Jammu, 180001, India.,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Natish Kumar
- CSIR-Indian Institute of Integrative Medicine, Canal Road, Jammu, 180001, India
| | - Rahul Bhat
- CSIR-Indian Institute of Integrative Medicine, Canal Road, Jammu, 180001, India.,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Piyush Singh Jamwal
- CSIR-Indian Institute of Integrative Medicine, Canal Road, Jammu, 180001, India
| | - Kaurab Singh
- Higher Education Department, Union Territory of Jammu and Kashmir, Jammu, India
| | - Sandeep Dogra
- Department of Microbiology, Government Medical College, Jammu, 180001, India
| | - Abhishek Kulkarni
- A2O - Biology, Reliance Technology Group, Reliance Industries Limited, RCP, Navi Mumbai, 400701, India
| | - Bhaskar Bhadra
- A2O - Biology, Reliance Technology Group, Reliance Industries Limited, RCP, Navi Mumbai, 400701, India
| | - Manish R Shukla
- A2O - Biology, Reliance Technology Group, Reliance Industries Limited, RCP, Navi Mumbai, 400701, India
| | - Saurabh Saran
- CSIR-Indian Institute of Integrative Medicine, Canal Road, Jammu, 180001, India.,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Santanu Dasgupta
- A2O - Biology, Reliance Technology Group, Reliance Industries Limited, RCP, Navi Mumbai, 400701, India
| | - Ram A Vishwakarma
- CSIR-Indian Institute of Integrative Medicine, Canal Road, Jammu, 180001, India
| | - Sumit G Gandhi
- CSIR-Indian Institute of Integrative Medicine, Canal Road, Jammu, 180001, India. .,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India.
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23
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Development of a Loop-mediated isothermal amplification (LAMP) technique for specific and early detection of Mycobacterium leprae in clinical samples. Sci Rep 2021; 11:9859. [PMID: 33972644 PMCID: PMC8110778 DOI: 10.1038/s41598-021-89304-2] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2020] [Accepted: 03/19/2021] [Indexed: 11/26/2022] Open
Abstract
Leprosy, a progressive, mutilating and highly stigmatized disease caused by Mycobacterium leprae (ML), continues to prevail in the developing world. This is due to the absence of rapid, specific and sensitive diagnostic tools for its early detection since the disease gets notified only with the advent of physical scarring in patients. This study reports the development of a Loop-mediated isothermal amplification (LAMP) technique for fast, sensitive and specific amplification of 16S rRNA gene of ML DNA for early detection of leprosy in resource-limited areas. Various parameters were optimized to obtain robust and reliable amplification of ML DNA. Blind clinical validation studies were performed which showed that this technique had complete concurrence with conventional techniques. Total absence of amplification of negative control DNA confirmed the specificity of this test. Various visual detection methods viz. colorimetric, turbidity differentiation and bridge flocculation were standardized to establish easy-to-read and rapid diagnosis. This technique eliminates the lack of accuracy and sensitivity in skin smear tests in patients and the requirement for expensive lab equipments and trained technicians. The technique holds promise for further expansion and has the potential to cater to the unmet needs of society for a cheap, highly-sensitive and robust rapid diagnosis of ML.
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24
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Gist of Zika Virus pathogenesis. Virology 2021; 560:86-95. [PMID: 34051478 DOI: 10.1016/j.virol.2021.04.008] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2021] [Revised: 04/03/2021] [Accepted: 04/28/2021] [Indexed: 12/29/2022]
Abstract
Zika virus (ZIKV) is a mosquito-borne neurotropic flavivirus. ZIKV infection may lead to microcephaly in developing fetus and Guillain-Barré Syndrome (GBS) like symptoms in adults. ZIKV was first reported in humans in 1952 from Uganda and the United Republic of Tanzania. Later, ZIKV outbreak was reported in 2007 from the Yap Island. ZIKV re-emerged as major outbreak in the year 2013 from French Polynesia followed by second outbreak in the year 2015 from Brazil. ZIKV crosses the blood-tissue barriers to enter immune-privileged organs. Clinical manifestations in ZIKV disease includes rash, fever, conjunctivitis, muscle and joint pain, headache, transverse myelitis, meningoencephalitis, Acute Disseminated Encephalomyelitis (ADEM). The understanding of the molecular mechanism of ZIKV pathogenesis is very important to develop potential diagnostic and therapeutic interventions for ZIKV infected patients.
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25
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Cassedy A, Parle-McDermott A, O’Kennedy R. Virus Detection: A Review of the Current and Emerging Molecular and Immunological Methods. Front Mol Biosci 2021; 8:637559. [PMID: 33959631 PMCID: PMC8093571 DOI: 10.3389/fmolb.2021.637559] [Citation(s) in RCA: 55] [Impact Index Per Article: 18.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2020] [Accepted: 02/01/2021] [Indexed: 12/14/2022] Open
Abstract
Viruses are ubiquitous in the environment. While many impart no deleterious effects on their hosts, several are major pathogens. This risk of pathogenicity, alongside the fact that many viruses can rapidly mutate highlights the need for suitable, rapid diagnostic measures. This review provides a critical analysis of widely used methods and examines their advantages and limitations. Currently, nucleic-acid detection and immunoassay methods are among the most popular means for quickly identifying viral infection directly from source. Nucleic acid-based detection generally offers high sensitivity, but can be time-consuming, costly, and require trained staff. The use of isothermal-based amplification systems for detection could aid in the reduction of results turnaround and equipment-associated costs, making them appealing for point-of-use applications, or when high volume/fast turnaround testing is required. Alternatively, immunoassays offer robustness and reduced costs. Furthermore, some immunoassay formats, such as those using lateral-flow technology, can generate results very rapidly. However, immunoassays typically cannot achieve comparable sensitivity to nucleic acid-based detection methods. Alongside these methods, the application of next-generation sequencing can provide highly specific results. In addition, the ability to sequence large numbers of viral genomes would provide researchers with enhanced information and assist in tracing infections.
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Affiliation(s)
- A. Cassedy
- School of Biotechnology, Dublin City University, Dublin, Ireland
| | | | - R. O’Kennedy
- School of Biotechnology, Dublin City University, Dublin, Ireland
- Hamad Bin Khalifa University, Doha, Qatar
- Qatar Foundation, Doha, Qatar
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26
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Point-of-care bulk testing for SARS-CoV-2 by combining hybridization capture with improved colorimetric LAMP. Nat Commun 2021; 12:1467. [PMID: 33674580 PMCID: PMC7935920 DOI: 10.1038/s41467-021-21627-0] [Citation(s) in RCA: 64] [Impact Index Per Article: 21.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2020] [Accepted: 02/01/2021] [Indexed: 01/12/2023] Open
Abstract
Efforts to contain the spread of SARS-CoV-2 have spurred the need for reliable, rapid, and cost-effective diagnostic methods which can be applied to large numbers of people. However, current standard protocols for the detection of viral nucleic acids while sensitive, require a high level of automation and sophisticated laboratory equipment to achieve throughputs that allow whole communities to be tested on a regular basis. Here we present Cap-iLAMP (capture and improved loop-mediated isothermal amplification) which combines a hybridization capture-based RNA extraction of gargle lavage samples with an improved colorimetric RT-LAMP assay and smartphone-based color scoring. Cap-iLAMP is compatible with point-of-care testing and enables the detection of SARS-CoV-2 positive samples in less than one hour. In contrast to direct addition of the sample to improved LAMP (iLAMP), Cap-iLAMP prevents false positives and allows single positive samples to be detected in pools of 25 negative samples, reducing the reagent cost per test to ~1 Euro per individual. Current SARS-CoV-2 diagnostic methods are sensitive yet poorly suited to testing whole communities on a regular basis. Here the authors present Cap-iLAMP that tests gargle lavage samples with an improved colorimetric RT-LAMP.
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27
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da Silva SJR, Pardee K, Balasuriya UBR, Pena L. Development and validation of a one-step reverse transcription loop-mediated isothermal amplification (RT-LAMP) for rapid detection of ZIKV in patient samples from Brazil. Sci Rep 2021; 11:4111. [PMID: 33602985 PMCID: PMC7893177 DOI: 10.1038/s41598-021-83371-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2020] [Accepted: 01/18/2021] [Indexed: 01/03/2023] Open
Abstract
We have previously developed and validated a one-step assay based on reverse transcription loop-mediated isothermal amplification (RT-LAMP) for rapid detection of the Zika virus (ZIKV) from mosquito samples. Patient diagnosis of ZIKV is currently carried out in centralized laboratories using the reverse transcription-quantitative polymerase chain reaction (RT-qPCR), which, while the gold standard molecular method, has several drawbacks for use in remote and low-resource settings, such as high cost and the need of specialized equipment. Point-of-care (POC) diagnostic platforms have the potential to overcome these limitations, especially in low-resource countries where ZIKV is endemic. With this in mind, here we optimized and validated our RT-LAMP assay for rapid detection of ZIKV from patient samples. We found that the assay detected ZIKV from diverse sample types (serum, urine, saliva, and semen) in as little as 20 min, without RNA extraction. The RT-LAMP assay was highly specific and up to 100 times more sensitive than RT-qPCR. We then validated the assay using 100 patient serum samples collected from suspected cases of arbovirus infection in the state of Pernambuco, which was at the epicenter of the last Zika epidemic. Analysis of the results, in comparison to RT-qPCR, found that the ZIKV RT-LAMP assay provided sensitivity of 100%, specificity of 93.75%, and an overall accuracy of 95.00%. Taken together, the RT-LAMP assay provides a straightforward and inexpensive alternative for the diagnosis of ZIKV from patients and has the potential to increase diagnostic capacity in ZIKV-affected areas, particularly in low and middle-income countries.
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Affiliation(s)
- Severino Jefferson Ribeiro da Silva
- Department of Virology, Aggeu Magalhães Institute (IAM), Oswaldo Cruz Foundation (Fiocruz), Avenida Professor Moraes Rego, Recife, Pernambuco, 50670-420, Brazil
| | - Keith Pardee
- Leslie Dan Faculty of Pharmacy, University of Toronto, Toronto, ON, M5S 3M2, Canada
| | - Udeni B R Balasuriya
- Louisiana Animal Disease Diagnostic Laboratory and Department of Pathobiological Sciences, School of Veterinary Medicine, Louisiana State University, Baton Rouge, LA, USA
| | - Lindomar Pena
- Department of Virology, Aggeu Magalhães Institute (IAM), Oswaldo Cruz Foundation (Fiocruz), Avenida Professor Moraes Rego, Recife, Pernambuco, 50670-420, Brazil.
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28
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Chan SK, Du P, Ignacio C, Mehta S, Newton IG, Steinmetz NF. Virus-Like Particles as Positive Controls for COVID-19 RT-LAMP Diagnostic Assays. Biomacromolecules 2021; 22:1231-1243. [PMID: 33539086 DOI: 10.1021/acs.biomac.0c01727] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Reverse transcription loop-mediated isothermal amplification (RT-LAMP) is a rapid and inexpensive isothermal alternative to the current gold standard reverse transcription quantitative polymerase chain reaction (RT-qPCR) for the detection of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). However, unlike RT-qPCR, there are no consensus detection regions or optimal RT-LAMP methods, and most protocols do not include internal controls to ensure reliability. Naked RNAs, plasmids, or even RNA from infectious COVID-19 patients have been used as external positive controls for RT-LAMP assays, but such reagents lack the stability required for full-process control. To overcome the lack of proper internal and external positive controls and the instability of the detection RNA, we developed virus-like particles (VLPs) using bacteriophage Qβ and plant virus cowpea chlorotic mottle virus (CCMV) for the encapsidation of target RNA, namely a so-called SARS-CoV-2 LAMP detection module (SLDM). The target RNA is a truncated segment of the SARS-CoV-2 nucleocapsid (N) gene and human RNase P gene (internal control) as positive controls for RT-qPCR and RT-LAMP. Target RNAs stably encapsidated in Qβ and CCMV VLPs were previously shown to function as full-process controls in RT-qPCR assays, and here we show that SLDMs can fulfill the same function for RT-LAMP and swab-to-test (direct RT-LAMP with heat lysis) assays. The SLDM was validated in a clinical setting, highlighting the promise of VLPs as positive controls for molecular assays.
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Machado BAS, Hodel KVS, Barbosa-Júnior VG, Soares MBP, Badaró R. The Main Molecular and Serological Methods for Diagnosing COVID-19: An Overview Based on the Literature. Viruses 2020; 13:E40. [PMID: 33383888 PMCID: PMC7823618 DOI: 10.3390/v13010040] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2020] [Revised: 12/18/2020] [Accepted: 12/24/2020] [Indexed: 02/07/2023] Open
Abstract
Diagnostic tests have been considered as the main alternative for the control of coronavirus disease (COVID-19), caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), as a correct diagnosis allows for decision making when facing the disease, particularly as there is a lack of effective therapeutic protocols and vaccines. Thus, in this review, we summarized the main diagnostic approaches currently available for the diagnosis of SARS-CoV-2 infection in humans based on studies available in article databases. The tests can be organized into two main categories: nucleic acid-based tests, recommended for the initial detection of the virus, and serological tests, recommended for assessing the disease progression. The studies have shown that the performance of diagnostic methods depends on different factors, such as the type of samples and the characteristics of each assay. It was identified that the positivity of the tests is mainly related to the onset of symptoms. We also observed that point-of-care diagnoses are considered as one of the main trends in this area, due to the low-cost and simplicity of the assay; however, the analytical performance must be critically analyzed. Thus, the COVID-19 pandemic has highlighted the critical role of diagnostic technologies in the control of infectious diseases.
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Affiliation(s)
- Bruna Aparecida Souza Machado
- SENAI Institute of Innovation (ISI) in Health Advanced Systems (CIMATEC ISI SAS), University Center SENAI/CIMATEC, Salvador 41650-010, Bahia, Brazil; (K.V.S.H.); (V.G.B.-J.); (M.B.P.S.); (R.B.)
| | - Katharine Valéria Saraiva Hodel
- SENAI Institute of Innovation (ISI) in Health Advanced Systems (CIMATEC ISI SAS), University Center SENAI/CIMATEC, Salvador 41650-010, Bahia, Brazil; (K.V.S.H.); (V.G.B.-J.); (M.B.P.S.); (R.B.)
| | - Valdir Gomes Barbosa-Júnior
- SENAI Institute of Innovation (ISI) in Health Advanced Systems (CIMATEC ISI SAS), University Center SENAI/CIMATEC, Salvador 41650-010, Bahia, Brazil; (K.V.S.H.); (V.G.B.-J.); (M.B.P.S.); (R.B.)
| | - Milena Botelho Pereira Soares
- SENAI Institute of Innovation (ISI) in Health Advanced Systems (CIMATEC ISI SAS), University Center SENAI/CIMATEC, Salvador 41650-010, Bahia, Brazil; (K.V.S.H.); (V.G.B.-J.); (M.B.P.S.); (R.B.)
- Gonçalo Moniz Institute, Oswaldo Cruz Foundation (IGM-FIOCRUZ/BA), Salvador 40296-710, Bahia, Brazil
| | - Roberto Badaró
- SENAI Institute of Innovation (ISI) in Health Advanced Systems (CIMATEC ISI SAS), University Center SENAI/CIMATEC, Salvador 41650-010, Bahia, Brazil; (K.V.S.H.); (V.G.B.-J.); (M.B.P.S.); (R.B.)
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Pilchová V, Seinige D, Hennig-Pauka I, Büttner K, Abdulmawjood A, Kehrenberg C. Development and Validation of a Loop-Mediated Isothermal Amplification (LAMP) Assay for Rapid Detection of Glaesserella ( Haemophilus) parasuis. Microorganisms 2020; 9:E41. [PMID: 33375599 PMCID: PMC7823361 DOI: 10.3390/microorganisms9010041] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2020] [Revised: 12/19/2020] [Accepted: 12/21/2020] [Indexed: 11/16/2022] Open
Abstract
Glaesserella parasuis is a fastidious pathogen that colonizes the respiratory tract of pigs and can lead to considerable economic losses in pig production. Therefore, a rapid detection assay for the pathogen, preferably applicable in the field, is important. In the current study, we developed a new and improved detection method using loop-mediated isothermal amplification (LAMP). This assay, which targets the infB gene, was tested on a collection of 60 field isolates of G. parasuis comprising 14 different serovars. In addition, 63 isolates from seven different closely related species of the family Pasteurellaceae, including A. indolicus, A. porcinus, and A. minor, and a species frequently found in the respiratory tract of pigs were used for exclusivity experiments. This assay showed an analytical specificity of 100% (both inclusivity and exclusivity) and an analytical sensitivity of 10 fg/µL. In further steps, 36 clinical samples were tested with the LAMP assay. An agreement of 77.1 (95% CI: 59.9, 89.6) and 91.4% (95% CI: 75.9, 98.2) to the culture-based and PCR results was achieved. The mean limit of detection for the spiked bronchoalveolar lavage fluid was 2.58 × 102 CFU/mL. A colorimetric assay with visual detection by the naked eye was tested to provide an alternative method in the field and showed the same sensitivity as the fluorescence-based LAMP assay. Overall, the optimized LAMP assay represents a fast and reliable method and is suitable for detecting G. parasuis in the laboratory environment or in the field.
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Affiliation(s)
- Veronika Pilchová
- Research Center for Emerging Infections and Zoonoses, University of Veterinary Medicine Hannover, Foundation, 30559 Hannover, Germany;
| | - Diana Seinige
- Lower Saxony State Office for Consumer Protection and Food Safety, 26203 Wardenburg, Germany;
| | - Isabel Hennig-Pauka
- Field Station for Epidemiology in Bakum, University of Veterinary Medicine Hannover, Foundation, 30559 Hannover, Germany;
| | - Kathrin Büttner
- Unit for Bioinformatics and Data Processing, Justus-Liebig-University Giessen, 35392 Giessen, Germany;
| | - Amir Abdulmawjood
- Institute of Food Quality and Food Safety, University of Veterinary Medicine Hannover, Foundation, 30173 Hannover, Germany;
| | - Corinna Kehrenberg
- Institute for Veterinary Food Science, Justus-Liebig-University Giessen, 35392 Giessen, Germany
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32
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Aonuma H, Iizuka-Shiota I, Hoshina T, Tajima S, Kato F, Hori S, Saijo M, Kanuka H. Detection and discrimination of multiple strains of Zika virus by reverse transcription-loop-mediated isothermal amplification. Trop Med Health 2020; 48:87. [PMID: 33100882 PMCID: PMC7576873 DOI: 10.1186/s41182-020-00274-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2020] [Accepted: 10/12/2020] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Monitoring both invasion of Zika virus disease into free countries and circulation in endemic countries is essential to avoid a global pandemic. However, the difficulty lies in detecting Zika virus due to the large variety of mutations in its genomic sequence. To develop a rapid and simple method with high accuracy, reverse transcription-loop-mediated isothermal amplification (RT-LAMP) was adopted for the detection of Zika virus strains derived from several countries. RESULTS Common primers for RT-LAMP were designed based on the genomic sequences of two standard Zika strains: African lineage, MR-766, and Asian lineage, PRVABC59. RT-LAMP reactions using a screened primer set, targeting the NS3 region, detected both Zika virus strains. The minimum detectable quantity was 3 × 10-2 ng of virus RNA. Measurable lag of reaction times among strains was observed. The RT-LAMP method amplified the target virus sequence from the urine and serum of a patient with a travel history in the Caribbean Islands and also provided a prediction about which lineage of Zika virus strain was present. CONCLUSIONS The RT-LAMP method using a well-optimized primer set demonstrated high specificity and sensitivity for the detection of Zika virus strains with a variety in genomic RNA sequences. In combination with the simplicity of LAMP reaction in isothermal conditions, the optimized primer set established in this study may facilitate rapid and accurate diagnosis of Zika fever patients with virus strain information.
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Affiliation(s)
- Hiroka Aonuma
- Department of Tropical Medicine, The Jikei University School of Medicine, Tokyo, Japan
- Center for Medical Entomology, The Jikei University School of Medicine, Tokyo, Japan
| | - Itoe Iizuka-Shiota
- Department of Tropical Medicine, The Jikei University School of Medicine, Tokyo, Japan
- Center for Medical Entomology, The Jikei University School of Medicine, Tokyo, Japan
- Present Address: Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, USA
| | - Tokio Hoshina
- Department of Tropical Medicine, The Jikei University School of Medicine, Tokyo, Japan
- Department of Infectious Diseases and Infection Control, The Jikei University School of Medicine, Tokyo, Japan
| | - Shigeru Tajima
- Department of Virology 1, National Institute of Infectious Diseases, Tokyo, Japan
| | - Fumihiro Kato
- Department of Virology 1, National Institute of Infectious Diseases, Tokyo, Japan
| | - Seiji Hori
- Department of Infectious Diseases and Infection Control, The Jikei University School of Medicine, Tokyo, Japan
| | - Masayuki Saijo
- Department of Virology 1, National Institute of Infectious Diseases, Tokyo, Japan
| | - Hirotaka Kanuka
- Department of Tropical Medicine, The Jikei University School of Medicine, Tokyo, Japan
- Center for Medical Entomology, The Jikei University School of Medicine, Tokyo, Japan
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Nath P, Kabir A, Khoubafarin Doust S, Kreais ZJ, Ray A. Detection of Bacterial and Viral Pathogens Using Photonic Point-of-Care Devices. Diagnostics (Basel) 2020; 10:diagnostics10100841. [PMID: 33086578 PMCID: PMC7603237 DOI: 10.3390/diagnostics10100841] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2020] [Revised: 10/05/2020] [Accepted: 10/15/2020] [Indexed: 12/15/2022] Open
Abstract
Infectious diseases caused by bacteria and viruses are highly contagious and can easily be transmitted via air, water, body fluids, etc. Throughout human civilization, there have been several pandemic outbreaks, such as the Plague, Spanish Flu, Swine-Flu, and, recently, COVID-19, amongst many others. Early diagnosis not only increases the chance of quick recovery but also helps prevent the spread of infections. Conventional diagnostic techniques can provide reliable results but have several drawbacks, including costly devices, lengthy wait time, and requirement of trained professionals to operate the devices, making them inaccessible in low-resource settings. Thus, a significant effort has been directed towards point-of-care (POC) devices that enable rapid diagnosis of bacterial and viral infections. A majority of the POC devices are based on plasmonics and/or microfluidics-based platforms integrated with mobile readers and imaging systems. These techniques have been shown to provide rapid, sensitive detection of pathogens. The advantages of POC devices include low-cost, rapid results, and portability, which enables on-site testing anywhere across the globe. Here we aim to review the recent advances in novel POC technologies in detecting bacteria and viruses that led to a breakthrough in the modern healthcare industry.
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Javalkote VS, Kancharla N, Bhadra B, Shukla M, Soni B, Goodin M, Bandyopadhyay A, Dasgupta S. CRISPR-based assays for rapid detection of SARS-CoV-2. Methods 2020; 203:594-603. [PMID: 33045362 PMCID: PMC7546951 DOI: 10.1016/j.ymeth.2020.10.003] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2020] [Revised: 09/16/2020] [Accepted: 10/06/2020] [Indexed: 12/18/2022] Open
Abstract
COVID-19 pandemic posed an unprecedented threat to global public health and economies. There is no effective treatment of the disease, hence, scaling up testing for rapid diagnosis of SARS-CoV-2 infected patients and quarantine them from healthy individuals is one the best strategies to curb the pandemic. Establishing globally accepted easy-to-access diagnostic tests is extremely important to understanding the epidemiology of the present pandemic. While nucleic acid based tests are considered to be more sensitive with respect to serological tests but present gold standard qRT-PCR-based assays possess limitations such as low sample throughput, requirement for sophisticated reagents and instrumentation. To overcome these shortcomings, recent efforts of incorporating LAMP-based isothermal detection, and minimizing the number of reagents required are on rise. CRISPR based novel techniques, when merge with isothermal and allied technologies, promises to provide sensitive and rapid detection of SARS-CoV-2 nucleic acids. Here, we discuss and present compilation of state-of-the-art detection techniques for COVID-19 using CRISPR technology which has tremendous potential to transform diagnostics and epidemiology.
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Affiliation(s)
- Vivek S Javalkote
- Reliance Industries Ltd, R&D-Synthetic Biology group, Reliance Corporate park, Navi Mumbai, India
| | - Nagesh Kancharla
- Reliance Industries Ltd, R&D-Synthetic Biology group, Reliance Corporate park, Navi Mumbai, India
| | - Bhaskar Bhadra
- Reliance Industries Ltd, R&D-Synthetic Biology group, Reliance Corporate park, Navi Mumbai, India
| | - Manish Shukla
- Reliance Industries Ltd, R&D-Synthetic Biology group, Reliance Corporate park, Navi Mumbai, India
| | - Badrish Soni
- Reliance Industries Ltd, R&D-Synthetic Biology group, Reliance Corporate park, Navi Mumbai, India
| | - Michael Goodin
- Department of Plant Pathology, University of Kentucky, Lexington, KY, 40546, USA
| | - Anindya Bandyopadhyay
- Reliance Industries Ltd, R&D-Synthetic Biology group, Reliance Corporate park, Navi Mumbai, India.
| | - Santanu Dasgupta
- Reliance Industries Ltd, R&D-Synthetic Biology group, Reliance Corporate park, Navi Mumbai, India.
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da Silva SJR, Silva CTAD, Guarines KM, Mendes RPG, Pardee K, Kohl A, Pena L. Clinical and Laboratory Diagnosis of SARS-CoV-2, the Virus Causing COVID-19. ACS Infect Dis 2020; 6:2319-2336. [PMID: 32786280 PMCID: PMC7441751 DOI: 10.1021/acsinfecdis.0c00274] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2020] [Indexed: 01/08/2023]
Abstract
In December 2019, a novel beta (β) coronavirus eventually named SARS-CoV-2 emerged in Wuhan, Hubei province, China, causing an outbreak of severe and even fatal pneumonia in humans. The virus has spread very rapidly to many countries across the world, resulting in the World Health Organization (WHO) to declare a pandemic on March 11, 2020. Clinically, the diagnosis of this unprecedented illness, called coronavirus disease-2019 (COVID-19), becomes difficult because it shares many symptoms with other respiratory pathogens, including influenza and parainfluenza viruses. Therefore, laboratory diagnosis is crucial for the clinical management of patients and the implementation of disease control strategies to contain SARS-CoV-2 at clinical and population level. Here, we summarize the main clinical and imaging findings of COVID-19 patients and discuss the advances, features, advantages, and limitations of different laboratory methods used for SARS-CoV-2 diagnosis.
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Affiliation(s)
| | - Caroline Targino Alves da Silva
- Department of Virology, Aggeu
Magalhães Institute (IAM), Oswaldo Cruz Foundation (Fiocruz),
50670-420, Recife, Pernambuco, Brazil
| | - Klarissa Miranda Guarines
- Department of Virology, Aggeu
Magalhães Institute (IAM), Oswaldo Cruz Foundation (Fiocruz),
50670-420, Recife, Pernambuco, Brazil
| | - Renata Pessôa Germano Mendes
- Department of Virology, Aggeu
Magalhães Institute (IAM), Oswaldo Cruz Foundation (Fiocruz),
50670-420, Recife, Pernambuco, Brazil
| | - Keith Pardee
- Leslie Dan Faculty of Pharmacy,
University of Toronto, Toronto, ON M5S 3M2,
Canada
| | - Alain Kohl
- MRC-University of Glasgow Centre for Virus
Research, Glasgow, Scotland G61 1QH, U.K.
| | - Lindomar Pena
- Department of Virology, Aggeu
Magalhães Institute (IAM), Oswaldo Cruz Foundation (Fiocruz),
50670-420, Recife, Pernambuco, Brazil
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Qin Z, Peng R, Baravik IK, Liu X. Fighting COVID-19: Integrated Micro- and Nanosystems for Viral Infection Diagnostics. MATTER 2020; 3:628-651. [PMID: 32838297 PMCID: PMC7346839 DOI: 10.1016/j.matt.2020.06.015] [Citation(s) in RCA: 57] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2023]
Abstract
The pandemic of coronavirus disease 2019 (COVID-19) highlights the importance of rapid and sensitive diagnostics of viral infection that enables the efficient tracing of cases and the implementation of public health measures for disease containment. The immediate actions from both academia and industry have led to the development of many COVID-19 diagnostic systems that have secured fast-track regulatory approvals and have been serving our healthcare frontlines since the early stage of the pandemic. On diagnostic technologies, many of these clinically validated systems have significantly benefited from the recent advances in micro- and nanotechnologies in terms of platform design, analytical method, and system integration and miniaturization. The continued development of new diagnostic platforms integrating micro- and nanocomponents will address some of the shortcomings we have witnessed in the existing COVID-19 diagnostic systems. This Perspective reviews the previous and ongoing research efforts on developing integrated micro- and nanosystems for nucleic acid-based virus detection, and highlights promising technologies that could provide better solutions for the diagnosis of COVID-19 and other viral infectious diseases. With the summary and outlook of this rapidly evolving research field, we hope to inspire more research and development activities to better prepare our society for future public health crises.
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Affiliation(s)
- Zhen Qin
- Department of Mechanical and Industrial Engineering, University of Toronto, Toronto, ON M5S 3G8, Canada
| | - Ran Peng
- Department of Mechanical and Industrial Engineering, University of Toronto, Toronto, ON M5S 3G8, Canada
| | - Ilina Kolker Baravik
- Department of Mechanical and Industrial Engineering, University of Toronto, Toronto, ON M5S 3G8, Canada
| | - Xinyu Liu
- Department of Mechanical and Industrial Engineering, University of Toronto, Toronto, ON M5S 3G8, Canada
- Institute of Biomaterials and Biomedical Engineering, University of Toronto, Toronto, ON M5S 3G9, Canada
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Lee JYH, Best N, McAuley J, Porter JL, Seemann T, Schultz MB, Sait M, Orlando N, Mercoulia K, Ballard SA, Druce J, Tran T, Catton MG, Pryor MJ, Cui HL, Luttick A, McDonald S, Greenhalgh A, Kwong JC, Sherry NL, Graham M, Hoang T, Herisse M, Pidot SJ, Williamson DA, Howden BP, Monk IR, Stinear TP. Validation of a single-step, single-tube reverse transcription loop-mediated isothermal amplification assay for rapid detection of SARS-CoV-2 RNA. J Med Microbiol 2020; 69:1169-1178. [PMID: 32755529 PMCID: PMC7656183 DOI: 10.1099/jmm.0.001238] [Citation(s) in RCA: 50] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2020] [Accepted: 07/10/2020] [Indexed: 12/21/2022] Open
Abstract
Introduction. The SARS-CoV-2 pandemic of 2020 has resulted in unparalleled requirements for RNA extraction kits and enzymes required for virus detection, leading to global shortages. This has necessitated the exploration of alternative diagnostic options to alleviate supply chain issues.Aim. To establish and validate a reverse transcription loop-mediated isothermal amplification (RT- LAMP) assay for the detection of SARS-CoV-2 from nasopharyngeal swabs.Methodology. We used a commercial RT-LAMP mastermix from OptiGene in combination with a primer set designed to detect the CDC N1 region of the SARS-CoV-2 nucleocapsid (N) gene. A single-tube, single-step fluorescence assay was implemented whereby 1 µl of universal transport medium (UTM) directly from a nasopharyngeal swab could be used as template, bypassing the requirement for RNA purification. Amplification and detection could be conducted in any thermocycler capable of holding 65 °C for 30 min and measure fluorescence in the FAM channel at 1 min intervals.Results. Assay evaluation by assessment of 157 clinical specimens previously screened by E-gene RT-qPCR revealed assay sensitivity and specificity of 87 and 100%, respectively. Results were fast, with an average time-to-positive (Tp) for 93 clinical samples of 14 min (sd±7 min). Using dilutions of SARS-CoV-2 virus spiked into UTM, we also evaluated assay performance against FDA guidelines for implementation of emergency-use diagnostics and established a limit-of-detection of 54 Tissue Culture Infectious Dose 50 per ml (TCID50 ml-1), with satisfactory assay sensitivity and specificity. A comparison of 20 clinical specimens between four laboratories showed excellent interlaboratory concordance; performing equally well on three different, commonly used thermocyclers, pointing to the robustness of the assay.Conclusion. With a simplified workflow, The N1 gene Single Tube Optigene LAMP assay (N1-STOP-LAMP) is a powerful, scalable option for specific and rapid detection of SARS-CoV-2 and an additional resource in the diagnostic armamentarium against COVID-19.
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Affiliation(s)
- Jean Y. H. Lee
- Department of Microbiology and Immunology, University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
- Department of Infectious Diseases, Monash Health, Clayton, Victoria, Australia
| | - Nickala Best
- GenWorks Pty Ltd, Thebarton, South Australia, Australia
| | - Julie McAuley
- Department of Microbiology and Immunology, University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
| | - Jessica L. Porter
- Department of Microbiology and Immunology, University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
| | - Torsten Seemann
- Department of Microbiology and Immunology, University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
- Microbiological Diagnostic Unit Public Health Laboratory, University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
| | - Mark B. Schultz
- Microbiological Diagnostic Unit Public Health Laboratory, University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
| | - Michelle Sait
- Microbiological Diagnostic Unit Public Health Laboratory, University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
| | - Nicole Orlando
- Microbiological Diagnostic Unit Public Health Laboratory, University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
| | - Karolina Mercoulia
- Microbiological Diagnostic Unit Public Health Laboratory, University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
| | - Susan A. Ballard
- Microbiological Diagnostic Unit Public Health Laboratory, University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
| | - Julian Druce
- Victorian Infectious Diseases Reference Laboratory, Melbourne Health at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
| | - Thomas Tran
- Victorian Infectious Diseases Reference Laboratory, Melbourne Health at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
| | - Mike G. Catton
- Victorian Infectious Diseases Reference Laboratory, Melbourne Health at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
| | | | | | | | - Sean McDonald
- GenWorks Pty Ltd, Thebarton, South Australia, Australia
| | | | - Jason C. Kwong
- Department of Microbiology and Immunology, University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
- Department of Infectious Diseases, Austin Health, Heidelberg, Victoria, Australia
| | - Norelle L. Sherry
- Microbiological Diagnostic Unit Public Health Laboratory, University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
- Department of Infectious Diseases, Austin Health, Heidelberg, Victoria, Australia
| | - Maryza Graham
- Department of Microbiology, Monash Health, Clayton, Victoria, Australia
| | - Tuyet Hoang
- Department of Microbiology and Immunology, University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
- Microbiological Diagnostic Unit Public Health Laboratory, University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
| | - Marion Herisse
- Department of Microbiology and Immunology, University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
| | - Sacha J. Pidot
- Department of Microbiology and Immunology, University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
| | - Deborah A. Williamson
- Department of Microbiology and Immunology, University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
- Microbiological Diagnostic Unit Public Health Laboratory, University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
- Melbourne Health, Melbourne, Victoria, Australia
| | - Benjamin P. Howden
- Department of Microbiology and Immunology, University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
- Microbiological Diagnostic Unit Public Health Laboratory, University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
- Department of Infectious Diseases, Austin Health, Heidelberg, Victoria, Australia
| | - Ian R. Monk
- Department of Microbiology and Immunology, University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
| | - Timothy P. Stinear
- Department of Microbiology and Immunology, University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
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Seok Y, Batule BS, Kim MG. Lab-on-paper for all-in-one molecular diagnostics (LAMDA) of zika, dengue, and chikungunya virus from human serum. Biosens Bioelectron 2020; 165:112400. [PMID: 32729520 DOI: 10.1016/j.bios.2020.112400] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2020] [Revised: 06/13/2020] [Accepted: 06/17/2020] [Indexed: 01/23/2023]
Abstract
Several tropical fever viruses transmitted by mosquitoes including zika, dengue, and chikungunya, are becoming a serious problem in global public health. Simple diagnostic tools in early stages are strongly required to monitor and prevent these diseases. Paper diagnostic platforms can provide a solution for these needs, with integration of fluidic control techniques and isothermal amplification methods. Here, we demonstrate a Lab-on-paper for all-in-one molecular diagnostics of zika, dengue, and chikungunya virus from human serum. The entire process of nucleic acid testing that involves sampling, extraction, amplification, and detection is simply operated on a single paper chip. Based on the engineered structure of paper materials and dried chemicals on the all-in-one chip, serum samples containing the target virus RNA were simply added by automatic flow from distilled water injection. Target RNA molecules were concentrated on the binding pad with chitosan and then transported to reaction pads following a pH increase for specific reverse transcription loop-mediated isothermal amplification with fluorescence signal generation. Three targets, zika virus, dengue virus, and chikungunya virus, in human serum were simultaneously detected on the all-in-one paper chip within 60 min at 65 °C. The all-in-one paper chip can be used as a real-time quantitative assay for 5-5000 copies of zika virus RNA. This all-in-one device was successfully used with 5 clinical specimens of zika and dengue virus from real patients. We believe that the proposed all-in-one paper chip can provide a portable, low-cost, user-friendly, sensitive, and specific NAT platform with great potential in point-of-care diagnostics.
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Affiliation(s)
- Youngung Seok
- Department of Mechanical Engineering and Applied Mechanics, School of Engineering and Applied Science, University of Pennsylvania, 233 Towne Building, 220 S. 33rd Street, Philadelphia, PA, 19104, USA
| | - Bhagwan S Batule
- Department of Chemistry, School of Physics and Chemistry, Gwangju Institute of Science and Technology (GIST), 123 Cheomdan-gwagiro, Gwangju, 500-712, Republic of Korea; Boditech Med Inc., 43, Geodudanji 1-gil, Dongnae-myeon, Chuncheon-si, Gangwon-do, 24398, Republic of Korea
| | - Min-Gon Kim
- Department of Chemistry, School of Physics and Chemistry, Gwangju Institute of Science and Technology (GIST), 123 Cheomdan-gwagiro, Gwangju, 500-712, Republic of Korea.
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Santos VSV, Limongi JE, Pereira BB. Association of low concentrations of pyriproxyfen and spinosad as an environment-friendly strategy to rationalize Aedes aegypti control programs. CHEMOSPHERE 2020; 247:125795. [PMID: 31927181 DOI: 10.1016/j.chemosphere.2019.125795] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/25/2019] [Revised: 12/28/2019] [Accepted: 12/29/2019] [Indexed: 06/10/2023]
Abstract
The association of low concentrations of pyriproxyfen and Spinosad, a naturally-occurring insecticide, was evaluated as an environment-friendly strategy to rationalize Aedes aegypti control programs by reducing larvicide consumption, saving financial costs and increasing residual effect against mosquitoes development. Firstly, the ecotoxicological parameters of the mixture was performed on non-target species Daphnia magna and the results confirmed that the low concentrations used in this larvicide mixture were not able to alter the reproductive parameters of chronically exposed microcrustaceans. In contrast, the mixture altered the behavior and development of Aedes aegypti, effectively inhibiting the emergence of adult insects for a long period. The results confirm the hypothesis that even at very low concentrations, the combination of the Spinosad and Pyriproxyfen larvicides offers an opportunity for Aedes aegypti public control programs to be more efficient.
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Affiliation(s)
- Vanessa Santana Vieira Santos
- Federal University of Uberlândia, Institute of Biotechnology, Umuarama Campus, Avenida Pará, 1720, 38.400-902, Uberlândia, Minas Gerais, Brazil
| | - Jean Ezequiel Limongi
- Federal University of Uberlandia, Institute of Geography, Laboratory of Macroecology and Environmental Health, Santa Monica Campus, Avenida João Naves de Ávila, 2121, 38.408-100, Uberlândia, Minas Gerais, Brazil
| | - Boscolli Barbosa Pereira
- Federal University of Uberlândia, Institute of Biotechnology, Umuarama Campus, Avenida Pará, 1720, 38.400-902, Uberlândia, Minas Gerais, Brazil; Federal University of Uberlandia, Institute of Geography, Laboratory of Macroecology and Environmental Health, Santa Monica Campus, Avenida João Naves de Ávila, 2121, 38.408-100, Uberlândia, Minas Gerais, Brazil.
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Qiao N, Dai H, Liu J, Zhu X, Li J, Zhang D, Liu Y. Detection of melon necrotic spot virus by one-step reverse transcription loop-mediated isothermal amplification assay. PLoS One 2020; 15:e0230023. [PMID: 32134962 PMCID: PMC7058275 DOI: 10.1371/journal.pone.0230023] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2019] [Accepted: 02/19/2020] [Indexed: 12/16/2022] Open
Abstract
Melon necrotic spot virus (MNSV) can cause significant economic losses due to decreased quality in cucurbit crops. The current study is the first to use reverse transcription loop-mediated isothermal amplification (RT-LAMP) for detection of MNSV. A set of four LAMP primers was designed based on the coat protein gene sequence of MNSV, and a RT-LAMP reaction was successfully performed for 1 h at 62°C. The results of RT-LAMP showed high specificity for MNSV and no cross-reaction with other viruses. Compared to traditional reverse transcription-PCR (RT-PCR), the RT-LAMP assay was 103-fold more sensitive in detecting MNSV. Due to its sensitivity, speed and visual assessment, RT-LAMP is appropriate for detecting MNSV in the laboratory.
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Affiliation(s)
- Ning Qiao
- College of Plant Protection, Shandong Agricultural University, Taian, Shandong, China
- Facility Horticulture Laboratory of Universities in Shandong, Weifang University of Science and Technology, Shouguang, Shandong, China
| | - Huijie Dai
- Facility Horticulture Laboratory of Universities in Shandong, Weifang University of Science and Technology, Shouguang, Shandong, China
| | - Jie Liu
- Facility Horticulture Laboratory of Universities in Shandong, Weifang University of Science and Technology, Shouguang, Shandong, China
| | - Xiaoping Zhu
- College of Plant Protection, Shandong Agricultural University, Taian, Shandong, China
- * E-mail:
| | - Jintang Li
- Facility Horticulture Laboratory of Universities in Shandong, Weifang University of Science and Technology, Shouguang, Shandong, China
| | - Dezhen Zhang
- Facility Horticulture Laboratory of Universities in Shandong, Weifang University of Science and Technology, Shouguang, Shandong, China
| | - Yongguang Liu
- Facility Horticulture Laboratory of Universities in Shandong, Weifang University of Science and Technology, Shouguang, Shandong, China
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A LAMP-based colorimetric assay to expedite field surveillance of the invasive mosquito species Aedes aegypti and Aedes albopictus. PLoS Negl Trop Dis 2020; 14:e0008130. [PMID: 32130209 PMCID: PMC7055815 DOI: 10.1371/journal.pntd.0008130] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2019] [Accepted: 02/10/2020] [Indexed: 01/24/2023] Open
Abstract
BACKGROUND Yellow fever, dengue, chikungunya and Zika viruses are responsible for considerable morbidity and mortality in humans. Aedes aegypti and Aedes albopictus are the most important mosquito vectors involved in their transmission. Accurate identification of these species is essential for the implementation of control programs to limit arbovirus transmission, during suspected detections at ports of first entry, to delimit incursions or during presence/absence surveillance programs in regions vulnerable to invasion. We developed and evaluated simple and rapid colorimetric isothermal tests to detect these two mosquito species based on loop-mediated isothermal amplification (LAMP) targeting the ribosomal RNA internal transcribed spacer 1 (ITS1). METHODOLOGY/PRINCIPAL FINDINGS Samples were prepared by homogenizing and heating at 99 oC for 10 min before an aliquot was added to the LAMP reaction. After 40 min incubation at 65 oC, a colour change indicated a positive result. The tests were 100% sensitive and species-specific, and demonstrated a limit of detection comparable with PCR-based detection (TaqMan chemistry). The LAMP assays were able to detect target species for various life stages tested (adult, 1st instar larva, 4th instar larva and pupa), and body components, such as legs, wings and pupal exuviae. Importantly, the LAMP assays could detect Ae. aegypti DNA in mosquitoes stored in Biogents Sentinel traps deployed in the field for 14 d. A single 1st instar Ae. aegypti larva could also be detected in a pool of 1,000 non-target 1st instar Aedes notoscriptus, thus expediting processing of ovitrap collections obtained during presence/absence surveys. A simple syringe-sponge protocol facilitated the concentration and collection of larvae from the ovitrap water post-hatch. CONCLUSIONS/SIGNIFICANCE We describe the development of LAMP assays for species identification and demonstrate their direct application for surveillance in different field contexts. The LAMP assays described herein are useful adjuncts to laboratory diagnostic testing or could be employed as standalone tests. Their speed, ease-of-use, low cost and need for minimal equipment and training make the LAMP assays ideal for adoption in low-resource settings without the need to access diagnostic laboratory services.
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da Silva SJR, Pardee K, Pena L. Loop-Mediated Isothermal Amplification (LAMP) for the Diagnosis of Zika Virus: A Review. Viruses 2019; 12:v12010019. [PMID: 31877989 PMCID: PMC7019470 DOI: 10.3390/v12010019] [Citation(s) in RCA: 64] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2019] [Revised: 11/30/2019] [Accepted: 12/04/2019] [Indexed: 12/17/2022] Open
Abstract
The recent outbreak of Zika virus (ZIKV) in the Americas and its devastating developmental and neurological manifestations has prompted the development of field-based diagnostics that are rapid, reliable, handheld, specific, sensitive, and inexpensive. The gold standard molecular method for lab-based diagnosis of ZIKV, from either patient samples or insect vectors, is reverse transcription-quantitative polymerase chain reaction (RT-qPCR). The method, however, is costly and requires lab-based equipment and expertise, which severely limits its use as a point-of-care (POC) tool in resource-poor settings. Moreover, given the lack of antivirals or approved vaccines for ZIKV infection, a POC diagnostic test is urgently needed for the early detection of new outbreaks and to adequately manage patients. Loop-mediated isothermal amplification (LAMP) is a compelling alternative to RT-qPCR for ZIKV and other arboviruses. This low-cost molecular system can be freeze-dried for distribution and exhibits high specificity, sensitivity, and efficiency. A growing body of evidence suggests that LAMP assays can provide greater accessibility to much-needed diagnostics for ZIKV infections, especially in developing countries where the ZIKV is now endemic. This review summarizes the different LAMP methods that have been developed for the virus and summarizes their features, advantages, and limitations.
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Affiliation(s)
| | - Keith Pardee
- Leslie Dan Faculty of Pharmacy, University of Toronto, Toronto, ON M5S 3M2, Canada;
| | - Lindomar Pena
- Department of Virology, Aggeu Magalhaes Institute (IAM), Oswaldo Cruz Foundation (Fiocruz), 50670-420 Recife, Brazil;
- Correspondence: ; Tel.: +55-81-2123-7849
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Rajko-Nenow P, Flannery J, Arnold H, Howson ELA, Darpel K, Stedman A, Corla A, Batten C. A rapid RT-LAMP assay for the detection of all four lineages of Peste des Petits Ruminants Virus. J Virol Methods 2019; 274:113730. [PMID: 31513860 PMCID: PMC6859475 DOI: 10.1016/j.jviromet.2019.113730] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2019] [Revised: 09/05/2019] [Accepted: 09/07/2019] [Indexed: 12/13/2022]
Abstract
Peste des petits ruminants (PPR) is a viral disease of small ruminants that is caused by the PPR virus (PPRV) and is a significant burden on subsistence farmers across the developing world. Loop-mediated isothermal amplification (LAMP) provides cost-effective, rapid, specific and sensitive detection of nucleic acid and has been demonstrated to have field application for a range of viruses. We describe the development of a novel PPRV RT-LAMP assay utilising carefully-selected primers (targeting the N-gene) allowing for the detection of all known PPRV lineages in < 20 min. The assay was evaluated in comparison with a "gold standard" real-time RT-PCR assay using more than 200 samples, comprising samples from recent PPRV outbreaks, experimentally-infected goats, well-characterised cell culture isolates and samples collected from uninfected animals. The RT-LAMP assay demonstrated 100% diagnostic specificity and greater than 97% diagnostic sensitivity in comparison with the real-time RT-PCR assay. The limit of detection was between 0.3 and 0.8 log10 TCID50 ml-1 equating to a CT value of 31.52 to 33.48. In experimentally-infected animals, the RT-LAMP could detect PPRV as early as 4 days post infection (dpi) - before clinical signs were observed at 7 dpi. The RT-LAMP assay can support the global PPR eradication campaign.
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Affiliation(s)
| | - John Flannery
- The Pirbright Institute, Ash Road, Pirbright, Woking, Surrey, GU24 0NF, UK
| | - Hannah Arnold
- The Pirbright Institute, Ash Road, Pirbright, Woking, Surrey, GU24 0NF, UK
| | - Emma L A Howson
- The Pirbright Institute, Ash Road, Pirbright, Woking, Surrey, GU24 0NF, UK
| | - Karin Darpel
- The Pirbright Institute, Ash Road, Pirbright, Woking, Surrey, GU24 0NF, UK
| | - Anna Stedman
- The Pirbright Institute, Ash Road, Pirbright, Woking, Surrey, GU24 0NF, UK
| | - Amanda Corla
- The Pirbright Institute, Ash Road, Pirbright, Woking, Surrey, GU24 0NF, UK
| | - Carrie Batten
- The Pirbright Institute, Ash Road, Pirbright, Woking, Surrey, GU24 0NF, UK
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Vontas J, Mavridis K. Vector population monitoring tools for insecticide resistance management: Myth or fact? PESTICIDE BIOCHEMISTRY AND PHYSIOLOGY 2019; 161:54-60. [PMID: 31685197 DOI: 10.1016/j.pestbp.2019.08.005] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/24/2019] [Revised: 08/10/2019] [Accepted: 08/21/2019] [Indexed: 06/10/2023]
Abstract
Insecticide resistance is a large and growing problem for the control of mosquito disease vectors. The World Health Organization (WHO) established the Global Plan for Insecticide Resistance Management (GPIRM) in 2012. In that context, both classical and molecular tools, as well as entomological databases and decision support platforms have been developed and used for IRM. Despite major advances in the molecular elucidation of resistance mechanisms and the development of diagnostic tools, their impact on disease control programs has been limited. In most cases diagnostic tools provide a retrospective examination of changes imposed by insecticides rather than a prospective analysis to guide vector control strategies. The uncertainty of the predictive value of markers, the assay robustness and the common misconceptions in resistance diagnosis terminology are continuing challenges in monitoring vector resistance. Furthermore, an often logistics, as opposed to systematic scientific evidence, based approach to decision for the use of the very few alternative chemicals in vector control, has reduced the value of resistance monitoring in practice. The current deployment of new insecticidal active ingredients should necessitate the application of companion diagnostics (CDx) and the development of modern ways for interpretation and management of the data by trained programme managers. This will establish their real value for use in decision-making, in line with evidence based choice of chemicals in agriculture and medical applications.
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Affiliation(s)
- John Vontas
- Institute of Molecular Biology & Biotechnology, Foundation for Research & Technology Hellas, 100 N. Plastira Street, GR-700 13 Heraklion, Crete, Greece; Laboratory of Pesticide Science, Department of Crop Science, Agricultural University of Athens, Greece.
| | - Konstantinos Mavridis
- Institute of Molecular Biology & Biotechnology, Foundation for Research & Technology Hellas, 100 N. Plastira Street, GR-700 13 Heraklion, Crete, Greece
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