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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; 24:473-485. [PMID: 38924448 DOI: 10.1080/14737159.2024.2368591] [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: 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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2
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Xu C, Chen Y, Zhu G, Wu H, Jiang Q, Zhang R, Yu B, Fang L, Wu Z. A Portable, Integrated, Sample-In Result-Out Nucleic Acid Diagnostic Device for Rapid and Sensitive Chikungunya Virus Detection. MICROMACHINES 2024; 15:663. [PMID: 38793236 PMCID: PMC11123350 DOI: 10.3390/mi15050663] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/01/2024] [Revised: 05/09/2024] [Accepted: 05/13/2024] [Indexed: 05/26/2024]
Abstract
Chikungunya virus, a mosquito-borne virus that causes epidemics, is often misdiagnosed due to symptom similarities with other arboviruses. Here, a portable and integrated nucleic acid-based diagnostic device, which combines reverse transcription-loop-mediated isothermal amplification and lateral-flow detection, was developed. The device is simple to use, precise, equipment-free, and highly sensitive, enabling rapid chikungunya virus identification. The result can be obtained by the naked eye within 40 min. The assay can effectively distinguish chikungunya virus from dengue virus, Japanese encephalitis virus, Zika virus, and yellow fever virus with high specificity and sensitivity as low as 598.46 copies mL-1. It has many benefits for the community screening and monitoring of chikungunya virus in resource-limited areas because of its effectiveness and simplicity. The platform has great potential for the rapid nucleic acid detection of other viruses.
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Affiliation(s)
- Changping Xu
- Center for Public Health Research, Medical School of Nanjing University, Nanjing 210093, China
- Zhejiang Provincial Center for Disease Control and Prevention, Hangzhou 310051, China
| | - Yalin Chen
- School of Biomedical Engineering, Med-X Research Institute, Shanghai Jiao Tong University, Shanghai 200030, China
| | - Guiying Zhu
- Shanghai Sci-Tech InnoCenter for Infection & Immunity, Shanghai 200030, China
| | - Huan Wu
- Ustar Biotechnologies (Hangzhou) Ltd., Hangzhou 310051, China
| | - Qi Jiang
- Ustar Biotechnologies (Hangzhou) Ltd., Hangzhou 310051, China
| | - Rui Zhang
- Center for Public Health Research, Medical School of Nanjing University, Nanjing 210093, China
| | - Beibei Yu
- Department of Clinical Laboratory, Sir Run Run Shaw Hospital, Zhejiang University College of Medicine, Hangzhou 310000, China
| | - Lei Fang
- Department of Critical Care Medicine, Sir Run Run Shaw Hospital, Zhejiang University College of Medicine, Hangzhou 310000, China
| | - Zhiwei Wu
- Center for Public Health Research, Medical School of Nanjing University, Nanjing 210093, China
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da Silva SJR, Krokovsky L. Clinical and laboratory diagnosis of Mayaro virus (MAYV): Current status and opportunities for further development. Rev Med Virol 2024; 34:e2528. [PMID: 38497839 DOI: 10.1002/rmv.2528] [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: 01/13/2024] [Revised: 02/06/2024] [Accepted: 03/06/2024] [Indexed: 03/19/2024]
Abstract
The recent outbreaks related to Mayaro virus (MAYV) infection in the Americas have brought this neglected virus as a potential threat to global public health. Given the range of symptoms that can be associated with MAYV infection, it can be challenging to diagnose individuals based on clinical signs, especially in countries with simultaneous circulation of other mosquito-borne viruses, such as dengue virus (DENV) and chikungunya virus (CHIKV). With this challenge in mind, laboratory-based diagnosis assumes a critical role in the introduction of measures to help prevent virus dissemination and to adequately treat patients. In this review, we provide an overview of the clinical features reported in infected patients and currently available laboratory tools that are used for MAYV diagnosis, discussing their advances, advantages, and limitations to apply in the field. Moreover, we explore novel point-of-care (PoC) diagnostic platforms that can provide de-centralised diagnostics for use in areas with limited laboratory infrastructure.
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Affiliation(s)
| | - Larissa Krokovsky
- Department of Entomology, Aggeu Magalhães Institute (IAM), Oswaldo Cruz Foundation (Fiocruz), Recife, Pernambuco, Brazil
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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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Febrer-Sendra B, Fernández-Soto P, García-Bernalt Diego J, Crego-Vicente B, Negredo A, Muñor-Bellido JL, Belhassen-García M, Sánchez-Seco MP, Muro A. A Novel RT-LAMP for the Detection of Different Genotypes of Crimean–Congo Haemorrhagic Fever Virus in Patients from Spain. Int J Mol Sci 2023; 24:ijms24076411. [PMID: 37047384 PMCID: PMC10094476 DOI: 10.3390/ijms24076411] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2023] [Revised: 03/25/2023] [Accepted: 03/27/2023] [Indexed: 03/31/2023] Open
Abstract
Crimean–Congo haemorrhagic fever (CCHF) is a potentially lethal tick-borne viral disease with a wide distribution. In Spain, 12 human cases of CCHF have been confirmed, with four deaths. The diagnosis of CCHF is hampered by the nonspecific symptoms, the high genetic diversity of CCHFV, and the biosafety requirements to manage the virus. RT-qPCR and serological tests are used for diagnosis with limitations. Reverse-transcription loop-mediated isothermal amplification (RT-LAMP) could be an effective alternative in the diagnosis of the disease. However, none of the few RT-LAMP assays developed to date has detected different CCHFV genotypes. Here, we designed a RT-LAMP using a degenerate primer set to compensate for the variability of the CCHFV target sequence. RT-LAMP was performed in colorimetric and real-time tests on RT-qPCR-confirmed CCHF patient samples notified in Spain in 2020 and 2021. Urine from an inpatient was analysed by RT-LAMP for the first time and compared with RT-qPCR. The amplicons obtained by RT-qPCR were sequenced and African III and European V genotypes were identified. RT-LAMP amplified both genotypes and was more sensitive than RT-qPCR in urine samples. We have developed a novel, rapid, specific, and sensitive RT-LAMP test that allows the detection of different CCHFV genotypes in clinical samples. This pan-CCHFV RT-LAMP detected viral RNA for the first time in urine samples. It can be easily performed as a single-tube isothermal colorimetric method on a portable platform in real time and without the need for expensive equipment, thus bringing molecular diagnostics closer to rural or resource-poor areas, where CCHF usually occurs.
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Boora S, Khan A, Sharma V, Kaushik S, Mehta PK, Singh S, Kaushik S. RT-LAMP is a potential future molecular diagnostic tool for influenza A virus. Future Virol 2023. [DOI: 10.2217/fvl-2022-0136] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/17/2023]
Abstract
Aim: Influenza A virus (IAV) causes serious illness and is responsible for significant morbidity and mortality. To diagnose IAV infection in its early stages, a quick, sensitive, precise detection method is needed for effective clinical management. Materials & methods: In-house hydroxylnaphthol blue (HNB)-based RT-LAMP assay for early detection of IAV using the HA gene was compared with RT-PCR/multiplex-RT-PCR. Results: For the reference strains of IAV, (H1N1 (A/Texas/50/2012) and H3N2 (A/Malaysia/2089302/2009)) RT-LAMP and RT-PCR/M-RT-PCR exhibited a limit of detection (LOD) of 10 and 100 fg/ml, respectively. Conclusion: HNB-based RT-LAMP is a rapid, sensitive, cost-effective diagnostic tool, and could be a point-of-care test for IAV patients during outbreaks.
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Affiliation(s)
- Sanjit Boora
- Centre for Biotechnology, Maharshi Dayanand University, Rohtak, Haryana, 124001, India
| | - Anish Khan
- Centre for Biotechnology, Maharshi Dayanand University, Rohtak, Haryana, 124001, India
- Department of Biochemistry, Maharshi Dayanand University, Rohtak, Haryana, 124001, India
| | - Vikrant Sharma
- Centre for Biotechnology, Maharshi Dayanand University, Rohtak, Haryana, 124001, India
- Department of Virology, Postgraduate Institute of Medical Education & Research (PGIMER), Chandigarh, 160012, India
| | - Sulochana Kaushik
- Centre for Biotechnology, Maharshi Dayanand University, Rohtak, Haryana, 124001, India
| | - Promod K Mehta
- Centre for Biotechnology, Maharshi Dayanand University, Rohtak, Haryana, 124001, India
| | - Sandeep Singh
- Department of Biochemistry, Maharshi Dayanand University, Rohtak, Haryana, 124001, India
| | - Samander Kaushik
- Centre for Biotechnology, Maharshi Dayanand University, Rohtak, Haryana, 124001, India
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Hakim MS, Aman AT. Understanding the Biology and Immune Pathogenesis of Chikungunya Virus Infection for Diagnostic and Vaccine Development. Viruses 2022; 15:48. [PMID: 36680088 PMCID: PMC9863735 DOI: 10.3390/v15010048] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2022] [Revised: 12/18/2022] [Accepted: 12/21/2022] [Indexed: 12/28/2022] Open
Abstract
Chikungunya virus, the causative agent of chikungunya fever, is generally characterized by the sudden onset of symptoms, including fever, rash, myalgia, and headache. In some patients, acute chikungunya virus infection progresses to severe and chronic arthralgia that persists for years. Chikungunya infection is more commonly identified in tropical and subtropical regions. However, recent expansions and epidemics in the temperate regions have raised concerns about the future public health impact of chikungunya diseases. Several underlying factors have likely contributed to the recent re-emergence of chikungunya infection, including urbanization, human travel, viral adaptation to mosquito vectors, lack of effective control measures, and the spread of mosquito vectors to new regions. However, the true burden of chikungunya disease is most likely to be underestimated, particularly in developing countries, due to the lack of standard diagnostic assays and clinical manifestations overlapping with those of other endemic viral infections in the regions. Additionally, there have been no chikungunya vaccines available to prevent the infection. Thus, it is important to update our understanding of the immunopathogenesis of chikungunya infection, its clinical manifestations, the diagnosis, and the development of chikungunya vaccines.
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Affiliation(s)
- Mohamad S. Hakim
- Department of Microbiology, Faculty of Medicine, Public Health, and Nursing, Universitas Gadjah Mada, Yogyakarta 55281, Indonesia
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9
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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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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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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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12
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JEV-nanobarcode and colorimetric reverse transcription loop-mediated isothermal amplification (cRT-LAMP). Mikrochim Acta 2021; 188:333. [PMID: 34498149 DOI: 10.1007/s00604-021-04986-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2021] [Accepted: 08/11/2021] [Indexed: 10/20/2022]
Abstract
Nucleic acid amplification tests (NAATs) are powerful tools for the Japanese encephalitis virus (JEV). We demonstrated highly sensitive, specific, and rapid detection of JEV by colorimetric reverse-transcription loop-mediated isothermal amplification (cRT-LAMP). Under optimized conditions, the RT-LAMP assay results showed that the limit of detection was approximately equivalent to 1 RNA genome copy/μL with an assay time of 30 min. The assay was highly specific to JEV when tested with other mosquito-borne virus panels (Zika virus and dengue virus types 2-4). The ability to detect JEV directly from crude human sample matrices (serum and urine) demonstrated the suitability of our JEV RT-LAMP for widespread clinical application. The JEV RT-LAMP provides combination of rapid colorimetric determination of true-positive JEV RT-LAMP amplicons with our recently developed JEV-nanobarcodes, measured at absorbance wavelenght of 530 (A530) and 650 (A650), which have a limit of detection of 23.3 ng/μL. The AuNP:polyA10-JEV RT-LAMP nanobarcodes exhibited superior capability for stabilizing the true-positive JEV RT-LAMP amplicons against salt-induced AuNP aggregation, which improved the evaluation of true/false positive signals in the assay. These advances enable to expand the use of RT-LAMP for point-of-care tests, which will greatly bolster JEV clinical programs. The JEV RT-LAMP nanobarcode assay targeting the envelope (E) gene and MgSO4 induced AuNP aggregation, indicated by an instant pink-to-violet colorimetric read-out.
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Ganguli A, Mostafa A, Berger J, Lim J, Araud E, Baek J, Stewart de Ramirez SA, Baltaji A, Roth K, Aamir M, Aedma S, Mady M, Mahajan P, Sathe S, Johnson M, White K, Kumar J, Valera E, Bashir R. Reverse Transcription Loop-Mediated Isothermal Amplification Assay for Ultrasensitive Detection of SARS-CoV-2 in Saliva and Viral Transport Medium Clinical Samples. Anal Chem 2021; 93:7797-7807. [PMID: 34033472 DOI: 10.1021/acs.analchem.0c05170] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
The COVID-19 pandemic has underscored the shortcomings in the deployment of state-of-the-art diagnostics platforms. Although several polymerase chain reaction (PCR)-based techniques have been rapidly developed to meet the growing testing needs, such techniques often need samples collected through a swab, the use of RNA extraction kits, and expensive thermocyclers in order to successfully perform the test. Isothermal amplification-based approaches have also been recently demonstrated for rapid severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) detection by minimizing sample preparation while also reducing the instrumentation and reaction complexity. In addition, there are limited reports of saliva as the sample source, and some of these indicate inferior sensitivity when comparing reverse transcription loop-mediated isothermal amplification (RT-LAMP) with PCR-based techniques. In this paper, we demonstrate an improved sensitivity assay from saliva using a two-step RT-LAMP assay, where a short 10 min RT step is performed with only B3 and backward inner primers before the final reaction. We show that while the one-step RT-LAMP demonstrates satisfactory results, the optimized two-step approach allows detection of only few molecules per reaction and performs significantly better than the one-step RT-LAMP and conventional two-step RT-LAMP approaches with all primers included in the RT step. We show control measurements with RT-PCR, and importantly, we demonstrate RNA extraction-free RT-LAMP-based assays for detection of SARS-CoV-2 from viral transport media and saliva clinical samples.
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Affiliation(s)
- Anurup Ganguli
- Department of Bioengineering, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801-3028, United States.,Nick Holonyak Jr. Micro and Nanotechnology Laboratory, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801-3028, United States
| | - Ariana Mostafa
- Department of Bioengineering, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801-3028, United States.,Nick Holonyak Jr. Micro and Nanotechnology Laboratory, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801-3028, United States
| | - Jacob Berger
- Department of Bioengineering, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801-3028, United States.,Nick Holonyak Jr. Micro and Nanotechnology Laboratory, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801-3028, United States
| | - Jongwon Lim
- Department of Bioengineering, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801-3028, United States.,Nick Holonyak Jr. Micro and Nanotechnology Laboratory, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801-3028, United States
| | - Elbashir Araud
- Nick Holonyak Jr. Micro and Nanotechnology Laboratory, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801-3028, United States
| | - Janice Baek
- Department of Bioengineering, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801-3028, United States.,Department of Materials Science and Engineering, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801-3028, United States
| | - Sarah A Stewart de Ramirez
- Emergency Medicine, University of Illinois College of Medicine at Peoria & OSF Healthcare, Peoria, Illinois 61603-3200, United States
| | - Ali Baltaji
- Carle Foundation Hospital, Urbana, Illinois 61801-2500, United States
| | - Kelly Roth
- Carle Foundation Hospital, Urbana, Illinois 61801-2500, United States
| | - Muhammad Aamir
- Carle Foundation Hospital, Urbana, Illinois 61801-2500, United States
| | - Surya Aedma
- Carle Foundation Hospital, Urbana, Illinois 61801-2500, United States
| | - Mohamed Mady
- Carle Foundation Hospital, Urbana, Illinois 61801-2500, United States
| | - Pranav Mahajan
- Carle Foundation Hospital, Urbana, Illinois 61801-2500, United States
| | - Sanjivani Sathe
- Carle Foundation Hospital, Urbana, Illinois 61801-2500, United States
| | - Mark Johnson
- Carle Foundation Hospital, Urbana, Illinois 61801-2500, United States.,Carle Illinois College of Medicine, Urbana, Illinois 61820, United States
| | - Karen White
- Carle Foundation Hospital, Urbana, Illinois 61801-2500, United States.,Carle Illinois College of Medicine, Urbana, Illinois 61820, United States
| | - James Kumar
- Carle Foundation Hospital, Urbana, Illinois 61801-2500, United States.,Carle Illinois College of Medicine, Urbana, Illinois 61820, United States
| | - Enrique Valera
- Department of Bioengineering, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801-3028, United States.,Nick Holonyak Jr. Micro and Nanotechnology Laboratory, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801-3028, United States
| | - Rashid Bashir
- Department of Bioengineering, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801-3028, United States.,Nick Holonyak Jr. Micro and Nanotechnology Laboratory, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801-3028, United States.,Department of Materials Science and Engineering, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801-3028, United States.,Carle Illinois College of Medicine, Urbana, Illinois 61820, United States
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14
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Huang X, Tang G, Ismail N, Wang X. Developing RT-LAMP Assays for Detection of SARS-CoV-2 in Saliva. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2021. [PMID: 33948614 DOI: 10.1101/2021.04.25.21256085] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
The coronavirus disease 2019 (COVID-19) caused by SARS-CoV-2 has killed millions of people worldwide. The current crisis has created an unprecedented demand for rapid test of SARS-CoV-2 infection. Reverse transcription loop-mediated isothermal amplification (RT-LAMP) is a fast and convenient method to amplify and identify the transcripts of a targeted pathogen. However, the sensitivity and specificity of RT-LAMP were generally regarded as inferior when compared with the gold standard RT-qPCR. To address this issue, we combined bioinformatic and experimental analyses to improve the assay performance for COVID-19 diagnosis. First, we developed an improved algorithm to design LAMP primers targeting the nucleocapsid (N), membrane (M), and spike (S) genes of SARS-CoV-2. Next, we rigorously validated these new assays for their efficacy and specificity. Further, we demonstrated that multiplexed RT-LAMP assays could directly detect as low as a few copies of SARS-CoV-2 RNA in saliva, without the need of RNA isolation. Importantly, further testing using saliva samples from COVID-19 patients indicated that the new RT-LAMP assays were in total agreement in sensitivity and specificity with standard RT-qPCR. In summary, our new LAMP primer design algorithm along with the validated assays provide a fast and reliable method for the diagnosis of COVID-19 cases.
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15
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Abstract
Molecular detection of Zika virus (ZIKV) is a key element of outbreak management. Multiple PCR and isothermal ZIKV assays targeting different ZIKV sequences have been published. In this study, we compared a qRT-PCR, 2 RT-LAMP assays (based on different primer design approaches), and an RT-RPA for the detection of African and Asian/American lineages of ZIKV isolates from human, mosquito, and monkey. Results showed that RT-LAMP detected 100% of samples with a time threshold (Tt) of 18.01 ± 11.71 min while qRT-PCR detected 88.88% of samples with a Tt of 58.30 ± 16.58 min and RT-RPA 50% of samples with a Tt of 3.70 ± 0.44 min.
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16
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Joshi S, Sharma V, Ramesh V, Singh R, Salotra P. Development of a novel loop-mediated isothermal amplification assay for rapid detection of Mycobacterium leprae in clinical samples. Indian J Dermatol Venereol Leprol 2021; 87:491-497. [PMID: 34219438 DOI: 10.25259/ijdvl_248_19] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2019] [Accepted: 02/01/2020] [Indexed: 11/04/2022]
Abstract
BACKGROUND Sensitive and definitive diagnostic tests are required for timely treatment of leprosy and to control its transmission. AIM In the present study, we report the development of loop-mediated isothermal amplification assay using six primers targeting the RLEP gene sequence uniquely present in Mycobacterium leprae. METHODS Tissue punch samples (n = 50) and slit aspirates (n = 50) from confirmed cases of leprosy (M. leprae positive by quantitative polymerase chain reaction), reporting at the Department of Dermatology, Safdarjung Hospital, New Delhi, were analyzed using newly developed closed tube loop-mediated isothermal amplification assay. The sensitivity and specificity; positive predictive value, negative predictive value and accuracy were calculated using MedCalc statistical software. RESULTS The loop-mediated isothermal amplification assay specifically amplified M. leprae genomic DNA with an analytical sensitivity of 100 fg. About 47 Out of the 50 quantitative polymerase chain reactions confirmed M. leprae positive tissue samples, 47 were positive by loop-mediated isothermal amplification assay (sensitivity 94%; 95% confidence interval 83.5%-98.8%) while only 31/50 were positive by histopathology (sensitivity 62%; 95% confidence interval 47.2%-75.4%) . Using slit aspirate samples of these 50 patients, 42 were positive by both quantitative polymerase chain reaction and loop-mediated isothermal amplification assay (sensitivity 84%; 95% confidence interval 70.9%-92.8%) while only 23/50 (sensitivity 46%; 95% confidence interval 31.8%-60.7%) were positive by microscopy. LIMITATIONS In the present study, the leprosy patient cohort was not uniform, as it comprised a lower number of paucibacillary cases (22%) compared to multibacillary (78%) cases. CONCLUSION Loop-mediated isothermal amplification assay established here provides a rapid and accurate diagnostic test for leprosy in terms of sensitivity and specificity. The assay is simple to perform in comparison with other molecular techniques (polymerase chain reaction/quantitative polymerase chain reaction) and has potential for field applicability.
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Affiliation(s)
- Shweta Joshi
- Molecular Parasitology Lab, ICMR-National Institute of Pathology, New Delhi, India
| | - Vanila Sharma
- Molecular Parasitology Lab, ICMR-National Institute of Pathology, New Delhi, India
| | - V Ramesh
- Department of Dermatology, Safdarjung Hospital, New Delhi, India
| | - Ruchi Singh
- Molecular Parasitology Lab, ICMR-National Institute of Pathology, New Delhi, India
| | - Poonam Salotra
- Molecular Parasitology Lab, ICMR-National Institute of Pathology, New Delhi, India
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17
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Hin S, Lopez-Jimena B, Bakheit M, Klein V, Stack S, Fall C, Sall A, Enan K, Mustafa M, Gillies L, Rusu V, Goethel S, Paust N, Zengerle R, Frischmann S, Weidmann M, Mitsakakis K. Fully automated point-of-care differential diagnosis of acute febrile illness. PLoS Negl Trop Dis 2021; 15:e0009177. [PMID: 33630852 PMCID: PMC7906357 DOI: 10.1371/journal.pntd.0009177] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2020] [Accepted: 01/26/2021] [Indexed: 12/13/2022] Open
Abstract
Background In this work, a platform was developed and tested to allow to detect a variety of candidate viral, bacterial and parasitic pathogens, for acute fever of unknown origin. The platform is based on a centrifugal microfluidic cartridge, the LabDisk (“FeverDisk” for the specific application), which integrates all necessary reagents for sample-to-answer analysis and is processed by a compact, point-of-care compatible device. Methodology/Principal findings A sample volume of 200 μL per FeverDisk was used. In situ extraction with pre-stored reagents was achieved by bind-wash-elute chemistry and magnetic particles. Enzymes for the loop-mediated isothermal amplification (LAMP) were pre-stored in lyopellet form providing stability and independence from the cold chain. The total time to result from sample inlet to read out was 2 h. The proof-of-principle was demonstrated in three small-scale feasibility studies: in Dakar, Senegal and Khartoum, Sudan we tested biobanked samples using 29 and 9 disks, respectively; in Reinfeld, Germany we tested spiked samples and analyzed the limit of detection using three bacteria simultaneously spiked in whole blood using 15 disks. Overall during the three studies, the FeverDisk detected dengue virus (different serotypes), chikungunya virus, Plasmodium falciparum, Salmonella enterica Typhi, Salmonella enterica Paratyphi A and Streptococcus pneumoniae. Conclusions/Significance The FeverDisk proved to be universally applicable as it successfully detected all different types of pathogens as single or co-infections, while it also managed to define the serotype of un-serotyped dengue samples. Thirty-eight FeverDisks at the two African sites provided 59 assay results, out of which 51 (86.4%) were confirmed with reference assay results. The results provide a promising outlook for future implementation of the platform in larger prospective clinical studies for defining its clinical sensitivity and specificity. The technology aims to provide multi-target diagnosis of the origins of fever, which will help fight lethal diseases and the incessant rise of antimicrobial resistance. Infectious diseases in tropical regions may have a variety of viral, bacterial or parasitic origins and a patient may suffer from several diseases simultaneously, each presenting with acute fever as a clinical symptom. This makes it difficult to determine the origin of the pathogen causing the disease(s). In addition to the endemic infectious diseases, outbreaks of epidemics frequently complicate diagnostic demands. Accurate diagnosis for proper patient management requires the utilization of highly sensitive and specific, rapid, easy-to-use diagnostic tools compatible with point-of-care settings. We describe the use of a disk-shaped microfluidic platform, the “FeverDisk”, for differential diagnosis of acute fever. Our FeverDisk platform demonstrated its capability to detect bacteria, viruses and parasites that are typical of tropical single and co-infections from biobanked samples within only 2 hours and in very good agreement with reference method results. This, in combination with its easy-to-use and point-of-care compatible nature, render our platform a promising candidate for detection of tropical diseases and precise identification of the cause of acute fever, in endemic and epidemic settings. Future work will involve extensive clinical characterization of the platform in prospective studies.
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Affiliation(s)
- Sebastian Hin
- Laboratory for MEMS Applications, IMTEK – Department of Microsystems Engineering, University of Freiburg, Freiburg, Germany
| | - Benjamin Lopez-Jimena
- Institute of Aquaculture, University of Stirling, Scotland, United Kingdom
- Mast Group Ltd, Mast House, Bootle, Liverpool, United Kingdom
| | | | - Vanessa Klein
- Laboratory for MEMS Applications, IMTEK – Department of Microsystems Engineering, University of Freiburg, Freiburg, Germany
| | - Seamus Stack
- Mast Group Ltd, Mast House, Bootle, Liverpool, United Kingdom
| | - Cheikh Fall
- Arbovirus and viral haemorrhagic fever unit, Institut Pasteur de Dakar, Dakar, Senegal
| | - Amadou Sall
- Arbovirus and viral haemorrhagic fever unit, Institut Pasteur de Dakar, Dakar, Senegal
| | - Khalid Enan
- Department of Virology, Central Laboratory-The Ministry of Higher Education and Scientific Research, Khartoum, Sudan
| | - Mohamed Mustafa
- Department of Virology, Central Laboratory-The Ministry of Higher Education and Scientific Research, Khartoum, Sudan
| | - Liz Gillies
- Mast Group Ltd, Mast House, Bootle, Liverpool, United Kingdom
| | - Viorel Rusu
- MagnaMedics Diagnostics BV, Geleen, The Netherlands
| | - Sven Goethel
- MagnaMedics Diagnostics BV, Geleen, The Netherlands
| | - Nils Paust
- Laboratory for MEMS Applications, IMTEK – Department of Microsystems Engineering, University of Freiburg, Freiburg, Germany
- Hahn-Schickard, Freiburg, Germany
| | - Roland Zengerle
- Laboratory for MEMS Applications, IMTEK – Department of Microsystems Engineering, University of Freiburg, Freiburg, Germany
- Hahn-Schickard, Freiburg, Germany
| | | | - Manfred Weidmann
- Institute of Aquaculture, University of Stirling, Scotland, United Kingdom
| | - Konstantinos Mitsakakis
- Laboratory for MEMS Applications, IMTEK – Department of Microsystems Engineering, University of Freiburg, Freiburg, Germany
- Hahn-Schickard, Freiburg, Germany
- * E-mail:
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18
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Moehling TJ, Choi G, Dugan LC, Salit M, Meagher RJ. LAMP Diagnostics at the Point-of-Care: Emerging Trends and Perspectives for the Developer Community. Expert Rev Mol Diagn 2021; 21:43-61. [PMID: 33474990 DOI: 10.1080/14737159.2021.1873769] [Citation(s) in RCA: 89] [Impact Index Per Article: 29.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Introduction: Over the past decade, loop-mediated isothermal amplification (LAMP) technology has played an important role in molecular diagnostics. Amongst numerous nucleic acid amplification assays, LAMP stands out in terms of sample-to-answer time, sensitivity, specificity, cost, robustness, and accessibility, making it ideal for field-deployable diagnostics in resource-limited regions.Areas covered: In this review, we outline the front-end LAMP design practices for point-of-care (POC) applications, including sample handling and various signal readout methodologies. Next, we explore existing LAMP technologies that have been validated with clinical samples in the field. We summarize recent work that utilizes reverse transcription (RT) LAMP to rapidly detect SARS-CoV-2 as an alternative to standard PCR protocols. Finally, we describe challenges in translating LAMP from the benchtop to the field and opportunities for future LAMP assay development and performance reporting.Expert opinion: Despite the popularity of LAMP in the academic research community and a recent surge in interest in LAMP due to the COVID-19 pandemic, there are numerous areas for improvement in the fundamental understanding of LAMP, which are needed to elevate the field of LAMP assay development and characterization.
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Affiliation(s)
- Taylor J Moehling
- Sandia National Laboratories, Biotechnology & Bioengineering Dept., Livermore, CA, USA
| | - Gihoon Choi
- Sandia National Laboratories, Biotechnology & Bioengineering Dept., Livermore, CA, USA
| | - Lawrence C Dugan
- Lawrence Livermore National Laboratory, Biosciences & Biotechnology Div., Livermore, CA, USA
| | - Marc Salit
- Joint Initiative for Metrology in Biology, SLAC National Accelerator Lab and Departments of Bioengineering and Pathology, Stanford University, Stanford, CA, USA
| | - Robert J Meagher
- Sandia National Laboratories, Biotechnology & Bioengineering Dept., Livermore, CA, USA
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19
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Prasannakumar MK, Parivallal PB, Pramesh D, Mahesh HB, Raj E. LAMP-based foldable microdevice platform for the rapid detection of Magnaporthe oryzae and Sarocladium oryzae in rice seed. Sci Rep 2021; 11:178. [PMID: 33420312 PMCID: PMC7794292 DOI: 10.1038/s41598-020-80644-z] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2020] [Accepted: 12/24/2020] [Indexed: 11/11/2022] Open
Abstract
Rice blast (caused by Magnaporthe oryzae) and sheath rot diseases (caused by Sarocladium oryzae) are the most predominant seed-borne pathogens of rice. The detection of both pathogens in rice seed is essential to avoid production losses. In the present study, a microdevice platform was designed, which works on the principles of loop-mediated isothermal amplification (LAMP) to detect M. oryzae and S. oryzae in rice seeds. Initially, a LAMP, polymerase chain reaction (PCR), quantitative PCR (qPCR), and helicase dependent amplification (HDA) assays were developed with primers, specifically targeting M. oryzae and S. oryzae genome. The LAMP assay was highly efficient and could detect the presence of M. oryzae and S. oryzae genome at a concentration down to 100 fg within 20 min at 60 °C. Further, the sensitivity of the LAMP, HDA, PCR, and qPCR assays were compared wherein; the LAMP assay was highly sensitive up to 100 fg of template DNA. Using the optimized LAMP assay conditions, a portable foldable microdevice platform was developed to detect M. oryzae and S. oryzae in rice seeds. The foldable microdevice assay was similar to that of conventional LAMP assay with respect to its sensitivity (up to 100 fg), rapidity (30 min), and specificity. This platform could serve as a prototype for developing on-field diagnostic kits to be used at the point of care centers for the rapid diagnosis of M. oryzae and S. oryzae in rice seeds. This is the first study to report a LAMP-based foldable microdevice platform to detect any plant pathogens.
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Affiliation(s)
- M K Prasannakumar
- Department of Plant Pathology, University of Agricultural Sciences, Bangalore, India.
| | - P Buela Parivallal
- Department of Plant Pathology, University of Agricultural Sciences, Bangalore, India
| | - Devanna Pramesh
- Rice Pathology Laboratory, All India Coordinated Rice Improvement Programme, University of Agricultural Sciences, Raichur, India.
| | - H B Mahesh
- Department of Genetics and Plant Breeding, College of Agriculture, V.C. Farm, Mandya, India
| | - Edwin Raj
- Plant Pathology Division, ICAR - National Research Center for Banana, Thayanur, India
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20
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Prasannakumar MK, Parivallal BP, Manjunatha C, Pramesh D, Narayan KS, Venkatesh G, Banakar SN, Mahesh HB, Vemanna RS, Rangaswamy KT. Rapid genotyping of bacterial leaf blight resistant genes of rice using loop-mediated isothermal amplification assay. Mol Biol Rep 2021; 48:467-474. [PMID: 33394228 DOI: 10.1007/s11033-020-06077-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2020] [Accepted: 12/10/2020] [Indexed: 01/15/2023]
Abstract
The use of resistant (R) genes is the most effective strategy to manage bacterial leaf blight (BLB) disease of rice. Several attempts were made to incorporate R genes into susceptible rice cultivars using marker-assisted backcross breeding (MABB). However, MABB relies exclusively on PCR for foreground selection of R genes, which requires expensive equipment for thermo-cycling and visualization of results; hence, it is limited to sophisticated research facilities. Isothermal nucleic acid amplification techniques such as loop-mediated isothermal amplification (LAMP) assay do not require thermo-cycling during the assay. Therefore, it will be the best alternative to PCR-based genotyping. In this study, we have developed a LAMP assay for the specific and sensitive genotyping of seven BLB resistance (R) genes viz., Xa1, Xa3, Xa4, Xa7, Xa10, Xa11, and Xa21 in rice. Gene-specific primers were designed for the LAMP assay. The LAMP assay was optimized for time, temperature, and template DNA concentration. For effective detection, incubation at 60 °C for 30 min was optimum for all seven R genes. A DNA intercalating dye ethidium bromide and a calorimetric dye hydroxynaphthol blue was used for result visualization. Further, sensitivity assay revealed that the LAMP assay could detect R genes at 100 fg of template DNA compared to 1 ng and 10 pg, respectively, in conventional PCR and q-PCR assays. The LAMP assay developed in this study provides a simple, specific, sensitive, robust, and cost-effective method for foreground selection of R genes in the resistance breeding programs of resource-poor laboratory.
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Affiliation(s)
- M K Prasannakumar
- Department of Plant Pathology, University of Agricultural Sciences, Bangalore, India.
| | - Buela P Parivallal
- Department of Plant Pathology, University of Agricultural Sciences, Bangalore, India
| | - Chennappa Manjunatha
- ICAR-Indian Agricultural Research Institute, Regional Station Wellington, Nilgiris, Tamil Nadu, India
| | - Devanna Pramesh
- Rice Pathology Laboratory, All India Coordinated Rice Improvement Programme, Gangavathi, University of Agricultural Sciences, Raichur, Karnataka, India.
| | - Karthik S Narayan
- Centre for Advanced Studies in Botany, University of Madras, Guindy Campus, Chennai, India
| | - Gopal Venkatesh
- Centre for Advanced Studies in Botany, University of Madras, Guindy Campus, Chennai, India
| | - Sahana N Banakar
- Department of Plant Pathology, University of Agricultural Sciences, Bangalore, India
| | - H B Mahesh
- Department of Genetics and Plant Breeding, University of Agricultural Sciences, Bangalore, Karnataka, India
| | - Ramu S Vemanna
- Department of Biotechnology, Regional Centre for Biotechnology, Gurgaon, Haryana, India
| | - K T Rangaswamy
- Department of Plant Pathology, University of Agricultural Sciences, Bangalore, India
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21
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Srivastava S, Upadhyay DJ, Srivastava A. Next-Generation Molecular Diagnostics Development by CRISPR/Cas Tool: Rapid Detection and Surveillance of Viral Disease Outbreaks. Front Mol Biosci 2020; 7:582499. [PMID: 33425987 PMCID: PMC7785713 DOI: 10.3389/fmolb.2020.582499] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2020] [Accepted: 11/04/2020] [Indexed: 12/26/2022] Open
Abstract
Virus disease spreads effortlessly mechanically or through minute insect vectors that are extremely challenging to avoid. Emergence and reemergence of new viruses such as severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), H1N1 influenza virus, avian influenza virus, dengue virus, Citrus tristeza virus, and Tomato yellow leaf curl virus have paralyzed the economy of many countries. The cure for major viral diseases is not feasible; however, early detection and surveillance of the disease can obstruct their spread. Therefore, advances in the field of virus diagnosis and the development of new point-of-care testing kits become necessary globally. Clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated protein (Cas) is an emerging technology for gene editing and diagnostics development. Several rapid nucleic acid diagnostic kits have been developed and validated using Cas9, Cas12, and Cas13 proteins. This review summarizes the CRISPR/Cas-based next-generation molecular diagnostic techniques and portability of devices for field-based utilization.
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Affiliation(s)
- Sonal Srivastava
- Amity Institute of Virology and Immunology, Amity University Uttar Pradesh, Noida, India
| | | | - Ashish Srivastava
- Amity Institute of Virology and Immunology, Amity University Uttar Pradesh, Noida, India
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22
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VectorDisk: A Microfluidic Platform Integrating Diagnostic Markers for Evidence-Based Mosquito Control. Processes (Basel) 2020. [DOI: 10.3390/pr8121677] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Effective mosquito monitoring relies on the accurate identification and characterization of the target population. Since this process requires specialist knowledge and equipment that is not widely available, automated field-deployable systems are highly desirable. We present a centrifugal microfluidic cartridge, the VectorDisk, which integrates TaqMan PCR assays in two feasibility studies, aiming to assess multiplexing capability, specificity, and reproducibility in detecting disk-integrated vector-related assays. In the first study, pools of 10 mosquitoes were used as samples. We tested 18 disks with 27 DNA and RNA assays each, using a combination of multiple microfluidic chambers and detection wavelengths (geometric and color multiplexing) to identify mosquito and malaria parasite species as well as insecticide resistance mechanisms. In the second study, purified nucleic acids served as samples to test arboviral and malaria infective mosquito assays. Nine disks were tested with 14 assays each. No false positive results were detected on any of the disks. The coefficient of variation in reproducibility tests was <10%. The modular nature of the platform, the easy adaptation of the primer/probe panels, the cold chain independence, the rapid (2–3 h) analysis, and the assay multiplexing capacity are key features, rendering the VectorDisk a potential candidate for automated vector analysis.
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23
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Han Q, Zhang S, Liu D, Yan F, Wang H, Huang P, Bi J, Jin H, Feng N, Cao Z, Gao Y, Chi H, Yang S, Zhao Y, Xia X. Development of a Visible Reverse Transcription-Loop-Mediated Isothermal Amplification Assay for the Detection of Rift Valley Fever Virus. Front Microbiol 2020; 11:590732. [PMID: 33281787 PMCID: PMC7691480 DOI: 10.3389/fmicb.2020.590732] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2020] [Accepted: 10/28/2020] [Indexed: 12/14/2022] Open
Abstract
Rift Valley fever (RVF) is a severe infectious disease, which can through mosquito bites, direct contact and aerosol transmission infect sheep, goats, people, camels, cattle, buffaloes, and so on. In this paper, a conserved region of the S RNA segment of Rift Valley fever virus (RVFV) ZH501 strain was used as target sequence. The RVFV RT-LAMP-VF assay was successfully established combined reverse transcription-loop-mediated isothermal amplification with a vertical flow visualization strip. The detection limit is up to 1.94 × 100 copies/μl of synthesized RVFV-RNA. RNA extracted from cell culture of an inactivated RVFV-BJ01 strain was also used as templates, and the detection limit is 1.83 × 103 copies/μl. In addition, there was no cross-reactivity with other viruses that can cause similar fever symptoms. The RVFV-LAMP-VF assay exhibited very high levels of diagnostic sensitivity, which had 100-fold more sensitive than RVFV real-time RT-PCR assay. Accordingly, the RVFV RT-LAMP-VF assay developed in this study is suitable for the rapid and sensitive diagnosis of RVFV without specialized equipment and can rapidly complete detection within 60 min, and the results are visible by vertical flow visualization strip within 5 min.
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Affiliation(s)
- Qiuxue Han
- Institute of Laboratory Animal Science, Chinese Academy of Medical Sciences (CAMS) and Comparative Medicine Center, Peking Union Medical College (PUMC), Beijing, China.,Key Laboratory of Jilin Province for Zoonosis Prevention and Control, Institute of Military Veterinary Medicine, Academy of Military Medical Sciences, Changchun, China
| | - Shengnan Zhang
- Key Laboratory of Jilin Province for Zoonosis Prevention and Control, Institute of Military Veterinary Medicine, Academy of Military Medical Sciences, Changchun, China
| | - Dongping Liu
- The Nanjing Unicorn Academy of Innovation, Institute Pasteur of Shanghai, Chinese Academy of Sciences, Nanjing, China
| | - Feihu Yan
- Key Laboratory of Jilin Province for Zoonosis Prevention and Control, Institute of Military Veterinary Medicine, Academy of Military Medical Sciences, Changchun, China.,Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Disease and Zoonoses, Yangzhou University, Yangzhou, China
| | - Hualei Wang
- College of Veterinary Medicine, Jilin University, Changchun, China
| | - Pei Huang
- Key Laboratory of Jilin Province for Zoonosis Prevention and Control, Institute of Military Veterinary Medicine, Academy of Military Medical Sciences, Changchun, China.,Animal Science and Technology College, Jilin Agricultural University, Changchun, China
| | - Jinhao Bi
- Key Laboratory of Jilin Province for Zoonosis Prevention and Control, Institute of Military Veterinary Medicine, Academy of Military Medical Sciences, Changchun, China.,Animal Science and Technology College, Jilin Agricultural University, Changchun, China
| | - Hongli Jin
- Key Laboratory of Jilin Province for Zoonosis Prevention and Control, Institute of Military Veterinary Medicine, Academy of Military Medical Sciences, Changchun, China.,College of Veterinary Medicine, Jilin University, Changchun, China
| | - Na Feng
- Key Laboratory of Jilin Province for Zoonosis Prevention and Control, Institute of Military Veterinary Medicine, Academy of Military Medical Sciences, Changchun, China
| | - Zengguo Cao
- Key Laboratory of Jilin Province for Zoonosis Prevention and Control, Institute of Military Veterinary Medicine, Academy of Military Medical Sciences, Changchun, China.,College of Veterinary Medicine, Jilin University, Changchun, China
| | - Yuwei Gao
- Key Laboratory of Jilin Province for Zoonosis Prevention and Control, Institute of Military Veterinary Medicine, Academy of Military Medical Sciences, Changchun, China.,Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Disease and Zoonoses, Yangzhou University, Yangzhou, China
| | - Hang Chi
- Key Laboratory of Jilin Province for Zoonosis Prevention and Control, Institute of Military Veterinary Medicine, Academy of Military Medical Sciences, Changchun, China.,Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Disease and Zoonoses, Yangzhou University, Yangzhou, China
| | - Songtao Yang
- Key Laboratory of Jilin Province for Zoonosis Prevention and Control, Institute of Military Veterinary Medicine, Academy of Military Medical Sciences, Changchun, China.,Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Disease and Zoonoses, Yangzhou University, Yangzhou, China
| | - Yongkun Zhao
- Key Laboratory of Jilin Province for Zoonosis Prevention and Control, Institute of Military Veterinary Medicine, Academy of Military Medical Sciences, Changchun, China.,Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Disease and Zoonoses, Yangzhou University, Yangzhou, China
| | - Xianzhu Xia
- Institute of Laboratory Animal Science, Chinese Academy of Medical Sciences (CAMS) and Comparative Medicine Center, Peking Union Medical College (PUMC), Beijing, China.,Key Laboratory of Jilin Province for Zoonosis Prevention and Control, Institute of Military Veterinary Medicine, Academy of Military Medical Sciences, Changchun, China.,Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Disease and Zoonoses, Yangzhou University, Yangzhou, China
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24
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Reddy A, Bosch I, Salcedo N, Herrera BB, de Puig H, Narváez CF, Caicedo-Borrero DM, Lorenzana I, Parham L, García K, Mercado M, Turca AMR, Villar-Centeno LA, Gélvez-Ramírez M, Ríos NAG, Hiley M, García D, Diamond MS, Gehrke L. Development and Validation of a Rapid Lateral Flow E1/E2-Antigen Test and ELISA in Patients Infected with Emerging Asian Strain of Chikungunya Virus in the Americas. Viruses 2020; 12:E971. [PMID: 32882998 PMCID: PMC7552019 DOI: 10.3390/v12090971] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2020] [Revised: 08/28/2020] [Accepted: 08/30/2020] [Indexed: 12/17/2022] Open
Abstract
Since its 2013 emergence in the Americas, Chikungunya virus (CHIKV) has posed a serious threat to public health. Early and accurate diagnosis of the disease, though currently lacking in clinics, is integral to enable timely care and epidemiological response. We developed a dual detection system: a CHIKV antigen E1/E2-based enzyme-linked immunosorbent assay (ELISA) and a lateral flow test using high-affinity anti-CHIKV antibodies. The ELISA was validated with 100 PCR-tested acute Chikungunya fever samples from Honduras. The assay had an overall sensitivity and specificity of 51% and 96.67%, respectively, with accuracy reaching 95.45% sensitivity and 92.03% specificity at a cycle threshold (Ct) cutoff of 22. As the Ct value decreased from 35 to 22, the ELISA sensitivity increased. We then developed and validated two lateral flow tests using independent antibody pairs. The sensitivity and specificity reached 100% for both lateral flow tests using 39 samples from Colombia and Honduras at Ct cutoffs of 20 and 27, respectively. For both lateral flow tests, sensitivity decreased as the Ct increased after 27. Because CHIKV E1/E2 are exposed in the virion surfaces in serum during the acute infection phase, these sensitive and specific assays demonstrate opportunities for early detection of this emerging human pathogen.
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Affiliation(s)
- Ankita Reddy
- E25Bio, Cambridge, MA 02139, USA
- Institute for Medical Engineering & Science, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Irene Bosch
- E25Bio, Cambridge, MA 02139, USA
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
- Department of Medicine, Mount Sinai School of Medicine, New York, NY 10029, USA
| | | | - Bobby Brooke Herrera
- E25Bio, Cambridge, MA 02139, USA
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA
| | - Helena de Puig
- Institute for Medical Engineering & Science, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Wyss Institute for Biologically Inspired Engineering, Harvard Medical School, Boston, MA 02115, USA
| | - Carlos F Narváez
- Programa de Medicina, Facultad de Salud, Universidad Surcolombiana, Neiva, Huila, Colombia
| | - Diana María Caicedo-Borrero
- Departamento de Salud Pública y Epidemiología de la Pontificia Universidad, Javeriana Cali y Escuela de Salud Pública de la Universidad del Valle, Cali, Colombia
| | - Ivette Lorenzana
- Instituto de Investigación en Microbiología, Universidad Nacional Autónoma de Honduras, Tegucigalpa, Honduras
| | - Leda Parham
- Instituto de Investigación en Microbiología, Universidad Nacional Autónoma de Honduras, Tegucigalpa, Honduras
| | - Kimberly García
- Instituto de Investigación en Microbiología, Universidad Nacional Autónoma de Honduras, Tegucigalpa, Honduras
| | - Marcela Mercado
- Dirección de Investigación en Salud Pública, Instituto Nacional de Salud, Bogotá, Colombia
| | - Angélica María Rico Turca
- Laboratorio de Virología, Dirección de Redes en Salud Pública, Instituto Nacional de Salud, Bogotá, Colombia
| | - Luis A Villar-Centeno
- Departments of Escuela de Medicina, Universidad Industrial de Santander and AEDES Network, Bucaramanga, Santander, Colombia
| | - Margarita Gélvez-Ramírez
- Departments of Escuela de Medicina, Universidad Industrial de Santander and AEDES Network, Bucaramanga, Santander, Colombia
| | - Natalia Andrea Gómez Ríos
- Departments of Escuela de Medicina, Universidad Industrial de Santander and AEDES Network, Bucaramanga, Santander, Colombia
| | - Megan Hiley
- Institute for Medical Engineering & Science, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Dawlyn García
- Institute for Medical Engineering & Science, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Michael S Diamond
- Departments of Medicine, Molecular Microbiology, Pathology & Immunology, Washington University School of Medicine, Saint Louis, MO 63110, USA
| | - Lee Gehrke
- E25Bio, Cambridge, MA 02139, USA
- Institute for Medical Engineering & Science, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Department of Microbiology and Immunobiology, Harvard Medical School, Boston, MA 02115, USA
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25
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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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26
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Saechue B, Kamiyama N, Wang Y, Fukuda C, Watanabe K, Soga Y, Goto M, Dewayani A, Ariki S, Hirose H, Ozaka S, Sachi N, Hidano S, Faisal K, Chowdhury R, Anik Ashfaq Khan M, Hossain F, Ghosh P, Shirin T, Mondal D, Murakami K, Kobayashi T. Development of a portable reverse transcription loop-mediated isothermal amplification system to detect the E1 region of Chikungunya virus in a cost-effective manner. Genes Cells 2020; 25:615-625. [PMID: 32562326 DOI: 10.1111/gtc.12797] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2019] [Revised: 06/01/2020] [Accepted: 06/10/2020] [Indexed: 12/11/2022]
Abstract
Chikungunya fever is a mosquito-borne disease cause of persistent arthralgia. The current diagnosis of Chikungunya virus (CHIKV) relies on a conventional reverse transcription polymerase chain reaction assay. Reverse transcription loop-mediated isothermal amplification (RT-LAMP) is a rapid and simple tool used for DNA-based diagnosis of a variety of infectious diseases. In this study, we established an RT-LAMP system to recognize CHIKV by targeting the envelope protein 1 (E1) gene that could also detect CHIKV at a concentration of 8 PFU without incorrectly detecting other mosquito-borne viruses. The system also amplified the E1 genome in the serum of CHIKV-infected mice with high sensitivity and specificity. Moreover, we established a dry RT-LAMP system that can be transported without a cold chain, which detected the virus genome in CHIKV-infected patient samples with high accuracy. Thus, the dry RT-LAMP system has great potential to be applied as a novel CHIKV screening kit in endemic areas.
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Affiliation(s)
- Benjawan Saechue
- Department of Infectious Disease Control, Faculty of Medicine, Oita University, Oita, Japan
| | - Naganori Kamiyama
- Department of Infectious Disease Control, Faculty of Medicine, Oita University, Oita, Japan
| | - Yinan Wang
- Department of Infectious Disease Control, Faculty of Medicine, Oita University, Oita, Japan
| | - Chiaki Fukuda
- Department of Infectious Disease Control, Faculty of Medicine, Oita University, Oita, Japan
| | - Kei Watanabe
- Department of Infectious Disease Control, Faculty of Medicine, Oita University, Oita, Japan
| | - Yasuhiro Soga
- Department of Infectious Disease Control, Faculty of Medicine, Oita University, Oita, Japan
| | - Mizuki Goto
- Department of Infectious Disease Control, Faculty of Medicine, Oita University, Oita, Japan
| | - Astri Dewayani
- Department of Infectious Disease Control, Faculty of Medicine, Oita University, Oita, Japan
| | - Shimpei Ariki
- Department of Infectious Disease Control, Faculty of Medicine, Oita University, Oita, Japan
| | - Haruna Hirose
- Department of Infectious Disease Control, Faculty of Medicine, Oita University, Oita, Japan
| | - Sotaro Ozaka
- Department of Infectious Disease Control, Faculty of Medicine, Oita University, Oita, Japan
| | - Nozomi Sachi
- Department of Infectious Disease Control, Faculty of Medicine, Oita University, Oita, Japan
| | - Shinya Hidano
- Department of Infectious Disease Control, Faculty of Medicine, Oita University, Oita, Japan
| | - Khaledul Faisal
- Nutrition and Clinical Services Division, International Centre for Diarrhoeal Disease Research, Bangladesh (icddr, b), Dhaka, Bangladesh
| | - Rajashree Chowdhury
- Nutrition and Clinical Services Division, International Centre for Diarrhoeal Disease Research, Bangladesh (icddr, b), Dhaka, Bangladesh
| | - Md Anik Ashfaq Khan
- Nutrition and Clinical Services Division, International Centre for Diarrhoeal Disease Research, Bangladesh (icddr, b), Dhaka, Bangladesh
| | - Faria Hossain
- Nutrition and Clinical Services Division, International Centre for Diarrhoeal Disease Research, Bangladesh (icddr, b), Dhaka, Bangladesh
| | - Prakash Ghosh
- Nutrition and Clinical Services Division, International Centre for Diarrhoeal Disease Research, Bangladesh (icddr, b), Dhaka, Bangladesh
| | - Tahmina Shirin
- Department of Virology, Institute of Epidemiology Disease Control and Research (IEDCR), Dhaka, Bangladesh
| | - Dinesh Mondal
- Nutrition and Clinical Services Division, International Centre for Diarrhoeal Disease Research, Bangladesh (icddr, b), Dhaka, Bangladesh
| | - Kazunari Murakami
- Department of Gastroenterology, Faculty of Medicine, Oita University, Oita, Japan
| | - Takashi Kobayashi
- Department of Infectious Disease Control, Faculty of Medicine, Oita University, Oita, Japan
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27
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Artika IM, Wiyatno A, Ma'roef CN. Pathogenic viruses: Molecular detection and characterization. INFECTION GENETICS AND EVOLUTION 2020; 81:104215. [PMID: 32006706 PMCID: PMC7106233 DOI: 10.1016/j.meegid.2020.104215] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/15/2019] [Revised: 01/23/2020] [Accepted: 01/28/2020] [Indexed: 12/14/2022]
Abstract
Pathogenic viruses are viruses that can infect and replicate within human cells and cause diseases. The continuous emergence and re-emergence of pathogenic viruses has become a major threat to public health. Whenever pathogenic viruses emerge, their rapid detection is critical to enable implementation of specific control measures and the limitation of virus spread. Further molecular characterization to better understand these viruses is required for the development of diagnostic tests and countermeasures. Advances in molecular biology techniques have revolutionized the procedures for detection and characterization of pathogenic viruses. The development of PCR-based techniques together with DNA sequencing technology, have provided highly sensitive and specific methods to determine virus circulation. Pathogenic viruses potentially having global catastrophic consequences may emerge in regions where capacity for their detection and characterization is limited. Development of a local capacity to rapidly identify new viruses is therefore critical. This article reviews the molecular biology of pathogenic viruses and the basic principles of molecular techniques commonly used for their detection and characterization. The principles of good laboratory practices for handling pathogenic viruses are also discussed. This review aims at providing researchers and laboratory personnel with an overview of the molecular biology of pathogenic viruses and the principles of molecular techniques and good laboratory practices commonly implemented for their detection and characterization. The continous emergence and re-emergence of pathogenic viruses has become a major threat to public health. PCR-based techniques together with DNA sequencing technology have provided highly sensitive and specific methods to determine virus circulation. Southeast Asia is considered to be vulnerable to potential outbreaks of pathogenic viruses. A number of pathogenic viruses have been reported to circulate in this region. The 2019 novel coronavirus has also been identified in Southeast Asia. Development of local capacity to rapidly identify new viruses is very important.
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Affiliation(s)
- I Made Artika
- Biosafety Level 3 Unit, Eijkman Institute for Molecular Biology, Jalan Diponegoro 69, Jakarta 10430, Indonesia; Department of Biochemistry, Faculty of Mathematics and Natural Sciences, Bogor Agricultural University, Darmaga Campus, Bogor 16680, Indonesia.
| | - Ageng Wiyatno
- Emerging Virus Research Unit, Eijkman Institute for Molecular Biology, Jalan Diponegoro 69, Jakarta 10430, Indonesia
| | - Chairin Nisa Ma'roef
- Emerging Virus Research Unit, Eijkman Institute for Molecular Biology, Jalan Diponegoro 69, Jakarta 10430, Indonesia
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28
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Lopez-Jimena B, Bakheit M, Bekaert M, Harold G, Frischmann S, Fall C, Diagne CT, Faye O, Faye O, Sall AA, Weidmann M. Development and Validation of Real-Time RT-LAMP Assays for the Specific Detection of Zika Virus. Methods Mol Biol 2020; 2142:147-164. [PMID: 32367366 DOI: 10.1007/978-1-0716-0581-3_13] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Two one-step real-time reverse transcription loop-mediated isothermal amplification (RT-LAMP) assays for the detection of Zika virus (ZIKV) were developed, based on two different primer design approaches: (1) open source, based on a combination of sequence diversity clustering (phylogeny and principal component analysis) and LAVA algorithm, using 45 whole genome ZIKV sequences retrieved from the National Center for Biotechnology Information (NCBI) database; (2) standard software for LAMP primer design (Primer Explorer V4), using 59 sequences of the ZIKV 3' UTR. The assays were firstly evaluated with External Quality Assessment panels from INSTAND e.V. (Germany) and EVD-LabNet (The Netherlands) including 4 and 12 unknown samples, respectively, and secondly, with 9 human, mosquito, and monkey ZIKV isolates from Africa (Senegal, Ivory Coast, and Uganda) and America (Brazil). The limit of detection as determined by probit analysis was 181 molecules for both RT-LAMP assays, and 100% reproducibility in the assays was obtained for 103 molecules (4/8 repetitions were positive for 102 molecules). Both assays were specific, amplifying only ZIKV RNA and not cross-detecting other arboviruses included in this study.
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Affiliation(s)
- Benjamin Lopez-Jimena
- Institute of Aquaculture, University of Stirling, Scotland, UK.
- Centre for Diagnostics Development, LifeArc, Scotland, UK.
| | | | - Michaël Bekaert
- Institute of Aquaculture, University of Stirling, Scotland, UK
| | - Graham Harold
- Institute of Aquaculture, University of Stirling, Scotland, UK
| | | | - Cheikh Fall
- Arbovirus and Viral Haemorrhagic Fever Unit, Institut Pasteur de Dakar, Dakar, Senegal
| | - Cheikh Tidiane Diagne
- Arbovirus and Viral Haemorrhagic Fever Unit, Institut Pasteur de Dakar, Dakar, Senegal
| | - Oumar Faye
- Arbovirus and Viral Haemorrhagic Fever Unit, Institut Pasteur de Dakar, Dakar, Senegal
| | - Ousmane Faye
- Arbovirus and Viral Haemorrhagic Fever Unit, Institut Pasteur de Dakar, Dakar, Senegal
| | - Amadou Alpha Sall
- Arbovirus and Viral Haemorrhagic Fever Unit, Institut Pasteur de Dakar, Dakar, Senegal
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29
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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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30
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Development of a reverse transcription-loop-mediated isothermal amplification assay for the detection of parrot bornavirus 4. J Virol Methods 2019; 275:113749. [PMID: 31622637 DOI: 10.1016/j.jviromet.2019.113749] [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: 07/23/2019] [Revised: 09/21/2019] [Accepted: 10/08/2019] [Indexed: 10/25/2022]
Abstract
Avian bornavirus (ABV) is the causative agent of proventricular dilatation disease, which is fatal in psittacine birds. ABVs have spread worldwide, and outbreaks have led to mass deaths of captive birds in commercial and breeding facilities. The segregation of infected birds is a countermeasure to prevent ABV spread in aviaries. However, this approach requires a highly sensitive detection method for the screening of infected birds before virus transmission. In this study, we developed a reverse transcription-loop-mediated isothermal amplification (RT-LAMP) assay for the diagnosis of parrot bornavirus 4 (PaBV-4), a dominant ABV genotype. Using this assay, we successfully detected PaBV-4 RNA in cell cultures, brain tissues, and feces. We also developed methods for simple RNA extraction and visual detection without electrophoresis. The sensitivity of the newly established RT-LAMP assay was 100-fold higher than that of the real-time PCR (RT-qPCR) assay. Accordingly, the RT-LAMP assay developed in this study is suitable for the rapid and sensitive diagnosis of PaBV-4 without specialized equipment and will contribute to virus control in aviaries.
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31
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Li H, Li K, Bi Z, Gu J, Song D, Lei D, Luo S, Huang D, Wu Q, Ding Z, Wang L, Ye Y, Tang Y. Development of a reverse transcription-loop-mediated isothermal amplification (RT-LAMP) assay for the detection of porcine pegivirus. J Virol Methods 2019; 270:59-65. [PMID: 31022411 PMCID: PMC7113777 DOI: 10.1016/j.jviromet.2019.04.019] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2019] [Revised: 04/20/2019] [Accepted: 04/21/2019] [Indexed: 02/07/2023]
Abstract
A simple and accurate reverse transcription-loop-mediated isothermal amplification (RT-LAMP) assay was developed and evaluated for the detection of porcine pegivirus (PPgV). The specific RT-LAMP primers targeting the conserved regions of NS5A genes were designed and used to detect PPgV. The optimal reaction parameter for RT-LAMP assay was 63℃ for 60 min. The detection limit of the RT-LAMP assay was 10 copies of PPgV genome, which was 100 times more sensitive than that of the conventional RT-PCR and comparable to nested RT-PCR and quantitative RT-PCR (qRT-PCR). There was no cross amplification with other related RNA viruses. In the clinical evaluation, the RT-LAMP assay exhibited a similar sensitivity with nested RT-PCR and qRT-PCR. The results indicated that RT-LAMP assay developed in this study could be a highly specific, sensitive, and cost-effective alternative for a rapid detection of PPgV in field settings.
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Affiliation(s)
- Hao Li
- Department of Preventive Veterinary Medicine, College of Animal Science and Technology, Jiangxi Agricultural University, Nanchang, Jiangxi, 330045, China; Key Laboratory for Animal Health of Jiangxi Province, Nanchang, Jiangxi, 330045, China
| | - Kai Li
- Department of Preventive Veterinary Medicine, College of Animal Science and Technology, Jiangxi Agricultural University, Nanchang, Jiangxi, 330045, China; Key Laboratory for Animal Health of Jiangxi Province, Nanchang, Jiangxi, 330045, China
| | - Zhen Bi
- Department of Preventive Veterinary Medicine, College of Animal Science and Technology, Jiangxi Agricultural University, Nanchang, Jiangxi, 330045, China; Key Laboratory for Animal Health of Jiangxi Province, Nanchang, Jiangxi, 330045, China
| | - Jun Gu
- Department of Preventive Veterinary Medicine, College of Animal Science and Technology, Jiangxi Agricultural University, Nanchang, Jiangxi, 330045, China; Key Laboratory for Animal Health of Jiangxi Province, Nanchang, Jiangxi, 330045, China
| | - Deping Song
- Department of Preventive Veterinary Medicine, College of Animal Science and Technology, Jiangxi Agricultural University, Nanchang, Jiangxi, 330045, China; Key Laboratory for Animal Health of Jiangxi Province, Nanchang, Jiangxi, 330045, China
| | - Dan Lei
- Department of Preventive Veterinary Medicine, College of Animal Science and Technology, Jiangxi Agricultural University, Nanchang, Jiangxi, 330045, China; Key Laboratory for Animal Health of Jiangxi Province, Nanchang, Jiangxi, 330045, China
| | - Suoxian Luo
- Department of Preventive Veterinary Medicine, College of Animal Science and Technology, Jiangxi Agricultural University, Nanchang, Jiangxi, 330045, China; Key Laboratory for Animal Health of Jiangxi Province, Nanchang, Jiangxi, 330045, China
| | - Dongyan Huang
- Department of Preventive Veterinary Medicine, College of Animal Science and Technology, Jiangxi Agricultural University, Nanchang, Jiangxi, 330045, China; Key Laboratory for Animal Health of Jiangxi Province, Nanchang, Jiangxi, 330045, China
| | - Qiong Wu
- Department of Preventive Veterinary Medicine, College of Animal Science and Technology, Jiangxi Agricultural University, Nanchang, Jiangxi, 330045, China; Key Laboratory for Animal Health of Jiangxi Province, Nanchang, Jiangxi, 330045, China
| | - Zhen Ding
- Department of Preventive Veterinary Medicine, College of Animal Science and Technology, Jiangxi Agricultural University, Nanchang, Jiangxi, 330045, China; Key Laboratory for Animal Health of Jiangxi Province, Nanchang, Jiangxi, 330045, China
| | - Leyi Wang
- Department of Veterinary Clinical Medicine and the Veterinary Diagnostic Laboratory, College of Veterinary Medicine, University of Illinois, Urbana, IL, 61802, USA
| | - Yu Ye
- Department of Preventive Veterinary Medicine, College of Animal Science and Technology, Jiangxi Agricultural University, Nanchang, Jiangxi, 330045, China; Key Laboratory for Animal Health of Jiangxi Province, Nanchang, Jiangxi, 330045, China.
| | - Yuxin Tang
- Department of Preventive Veterinary Medicine, College of Animal Science and Technology, Jiangxi Agricultural University, Nanchang, Jiangxi, 330045, China; Key Laboratory for Animal Health of Jiangxi Province, Nanchang, Jiangxi, 330045, China.
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Seck MC, Badiane AS, Thwing J, Moss D, Fall FB, Gomis JF, Deme AB, Diongue K, Sy M, Mbaye A, Ndiaye T, Gaye A, Ndiaye YD, Diallo MA, Ndiaye D, Rogier E. Serological Data Shows Low Levels of Chikungunya Exposure in Senegalese Nomadic Pastoralists. Pathogens 2019; 8:pathogens8030113. [PMID: 31357631 PMCID: PMC6789836 DOI: 10.3390/pathogens8030113] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2019] [Revised: 07/18/2019] [Accepted: 07/21/2019] [Indexed: 12/28/2022] Open
Abstract
The chikungunya virus (CHIKV) is spread by Aedes aegypti and Ae. albopictus mosquitos worldwide; infection can lead to disease including joint pain, fever, and rash, with some convalescent persons experiencing chronic symptoms. Historically, CHIKV transmission has occurred in Africa and Asia, but recent outbreaks have taken place in Europe, Indonesia, and the Americas. From September to October 2014, a survey was undertaken with nomadic pastoralists residing in the northeast departments of Senegal. Blood dried on filter paper (dried blood spots; DBS) were collected from 1465 participants of all ages, and assayed for Immunoglobulin G (IgG) antibodies against CHIKV E1 antigen by a bead-based multiplex assay. The overall seroprevalence of all participants to CHIKV E1 was 2.7%, with no persons under 10 years of age found to be antibody positive. Above 10 years of age, clear increases of seroprevalence and IgG levels were observed with increasing age; 7.6% of participants older than 50 years were found to be positive for anti-CHIKV IgG. Reported net ownership, net usage, and gender were all non-significant explanatory variables of seropositivity. These data show a low-level historical exposure of this pastoralist population to CHIKV, with no evidence of recent CHIKV transmission in the past decade.
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Affiliation(s)
- Mame Cheikh Seck
- Department of Parasitology, Faculty of Medicine and Pharmacy, Cheikh Anta Diop University, Dakar 12500, Senegal.
| | - Aida Sadikh Badiane
- Department of Parasitology, Faculty of Medicine and Pharmacy, Cheikh Anta Diop University, Dakar 12500, Senegal
| | - Julie Thwing
- Malaria Branch, Division of Parasitic Diseases and Malaria, Centers for Disease Control and Prevention, Atlanta, GA 30333, USA
- President's Malaria Initiative, Atlanta, GA 30303, USA
| | - Delynn Moss
- Division of Foodborne, Waterborne, and Environmental Diseases, National Center for Emerging and Zoonotic Infectious Diseases, Centers for Disease Control and Prevention, Atlanta, GA 30333, USA
| | - Fatou Ba Fall
- Senegal National Malaria Control Program, Dakar 999066, Senegal
| | - Jules Francois Gomis
- Department of Parasitology, Faculty of Medicine and Pharmacy, Cheikh Anta Diop University, Dakar 12500, Senegal
| | - Awa Bineta Deme
- Department of Parasitology, Faculty of Medicine and Pharmacy, Cheikh Anta Diop University, Dakar 12500, Senegal
| | - Khadim Diongue
- Department of Parasitology, Faculty of Medicine and Pharmacy, Cheikh Anta Diop University, Dakar 12500, Senegal
| | - Mohamed Sy
- Department of Parasitology, Faculty of Medicine and Pharmacy, Cheikh Anta Diop University, Dakar 12500, Senegal
| | - Aminata Mbaye
- Department of Parasitology, Faculty of Medicine and Pharmacy, Cheikh Anta Diop University, Dakar 12500, Senegal
| | - Tolla Ndiaye
- Department of Parasitology, Faculty of Medicine and Pharmacy, Cheikh Anta Diop University, Dakar 12500, Senegal
| | - Aminata Gaye
- Department of Parasitology, Faculty of Medicine and Pharmacy, Cheikh Anta Diop University, Dakar 12500, Senegal
| | - Yaye Die Ndiaye
- Department of Parasitology, Faculty of Medicine and Pharmacy, Cheikh Anta Diop University, Dakar 12500, Senegal
| | - Mamadou Alpha Diallo
- Department of Parasitology, Faculty of Medicine and Pharmacy, Cheikh Anta Diop University, Dakar 12500, Senegal
| | - Daouda Ndiaye
- Department of Parasitology, Faculty of Medicine and Pharmacy, Cheikh Anta Diop University, Dakar 12500, Senegal
| | - Eric Rogier
- Malaria Branch, Division of Parasitic Diseases and Malaria, Centers for Disease Control and Prevention, Atlanta, GA 30333, USA.
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Field diagnosis and genotyping of chikungunya virus using a dried reverse transcription loop-mediated isothermal amplification (LAMP) assay and MinION sequencing. PLoS Negl Trop Dis 2019; 13:e0007480. [PMID: 31158221 PMCID: PMC6564047 DOI: 10.1371/journal.pntd.0007480] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2019] [Revised: 06/13/2019] [Accepted: 05/20/2019] [Indexed: 12/17/2022] Open
Abstract
Detection and sequencing of chikungunya virus (CHIKV) genome was performed using a combination of a modified reverse transcription loop-mediated isothermal amplification (RT-LAMP) method and a MinION sequencer. We developed the protocol for drying all the reagents for the RT-LAMP in a single reaction tube. Using this system, the CHIKV genome was effectively amplified under isothermal conditions, and used as a template for MinION sequencing with a laptop computer. Our in-house RT-LAMP method and MinION sequencing system were also validated with RNAs and serum samples from recent outbreaks of CHIKV patients in Brazil. The obtained sequence data confirmed the CHIKV outbreaks and identified the genotype. In summary, our established inexpensive on-site genome detection and sequencing system is applicable for both diagnosis of CHIKV infected patients and genotyping of the CHIKV virus in future outbreak in remote areas. Chikungunya virus has re-emerged as an important pathogen causing several outbreaks in the world. As the clinical symptoms of chikungunya is similar to other mosquito-borne febrile diseases, the definitive diagnosis of the disease is based on the detection of viral genome from the patient blood. Loop-mediated isothermal amplification (LAMP) is a method that rapidly amplify nucleic acids under isothermal condition. In the present work, a simple dried format LAMP test for chikungunya diagnosis was developed which can be directly amplified from human blood. Combining with the portable sequencer MinION sequencing system, a method to identify the viral genotype was also established. The developed on-site diagnosis and genotyping system is easy to perform, sensitive, and rapid. Therefore, it offers great promise as a routine simple tool for diagnosis and disease management of chikungunya.
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Liu H, Li LX, Bu YP, Liu Y, Sun XT, Shi N, Deng XY, Lu RG, Hu B, Jin NY, Yan XJ. Rapid Visual Detection of Getah Virus Using a Loop-Mediated Isothermal Amplification Method. Vector Borne Zoonotic Dis 2019; 19:741-746. [PMID: 30964395 DOI: 10.1089/vbz.2018.2434] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
Getah virus (GETV) is a mosquito-borne alphavirus that is considered to be an emerging pathogen. To date, reverse transcription loop-mediated isothermal amplification (RT-LAMP) has not been used to detect GETV. Therefore, we describe a novel, fast, and sensitive LAMP method to detect GETV. Amplification of GETV RNA can be obtained within 50 min at 65°C. This RT-LAMP method was verified to be highly specific for GETV, with no cross detection of other viruses. The assay was 103 and 101 times more sensitive than RT-PCR and RT-qPCR, respectively, for the detection of GETV RNA. This novel RT-LAMP method provides a practical and economical alternative for detecting GETV in mosquitoes and serum samples that can be used even in the field.
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Affiliation(s)
- Hao Liu
- School of Life Sciences and Engineering, Foshan University, Foshan, China
| | - Li-Xia Li
- Forestry Department of Jilin Province, Jilin Wildlife Rescue and Rehabilitation Center, Changchun, China
| | - Ya-Ping Bu
- Engineering Research Center of Chinese Ministry of Education for Edible and Medicinal Fungi, Jilin Agricultural University, Changchun, China
| | - Yu Liu
- Engineering Research Center of Chinese Ministry of Education for Edible and Medicinal Fungi, Jilin Agricultural University, Changchun, China
| | - Xiu-Tao Sun
- Honghe Animal Disease Prevention and Control Center, Mengzi, China
| | - Ning Shi
- Institute of Special Economic Animal and Plant Sciences, Chinese Academy of Agricultural Sciences, Changchun, China
| | - Xiao-Yu Deng
- Institute of Special Economic Animal and Plant Sciences, Chinese Academy of Agricultural Sciences, Changchun, China
| | - Rong-Guang Lu
- Institute of Special Economic Animal and Plant Sciences, Chinese Academy of Agricultural Sciences, Changchun, China
| | - Bo Hu
- Institute of Special Economic Animal and Plant Sciences, Chinese Academy of Agricultural Sciences, Changchun, China
| | - Ning-Yi Jin
- Military Veterinary Institute, Academy of Military Medical Sciences, Changchun, China
| | - Xi-Jun Yan
- Institute of Special Economic Animal and Plant Sciences, Chinese Academy of Agricultural Sciences, Changchun, China
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