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Wu X, Liu G, Chang Y, Zheng M, Liu L, Xia X, Feng Y. Rapid and sensitive detection of chikungunya virus using one-tube, reverse transcription, semi-nested multi-enzyme isothermal rapid amplification, and lateral flow dipstick assays. J Clin Microbiol 2024; 62:e0038324. [PMID: 39140738 PMCID: PMC11389142 DOI: 10.1128/jcm.00383-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2024] [Accepted: 07/02/2024] [Indexed: 08/15/2024] Open
Abstract
Chikungunya fever is an acute infectious disease caused by chikungunya virus (CHIKV), which is transmitted by Aedes mosquitoes. Simple, rapid, and sensitive detection of CHIKV is critical for its prevention and spread. To address this issue, we combined one-tube, reverse transcription semi-nested, multi-enzyme isothermal rapid amplification, and lateral flow dipstick strips assay to detect CHIKV RNA. The study used a 318-bp gene fragment of CHIKV NSP4 as the target of the assay. This method of amplification takes 30 min for two-step amplification at 39°C. The dilution of amplification products was added to the LFD strip with results visible to the naked eye after 10 min. The method has a sensitivity of 1 copy/μL for the detection of CHIKV RNA, which is 100-fold higher than the conventional reverse transcription-multi-enzyme isothermal rapid amplification and 10-fold higher than the reverse transcription quantitative PCR (RT-qPCR) method. In addition, the method demonstrated good specificity and a better detection rate (85.7%, 18 of 21) than RT-qPCR (80.9%, 17 of 21) in clinically confirmed patient plasma samples. Thus, the rapid CHIKV RNA assay developed in this study will be an important tool for the rapid and accurate screening of patients for chikungunya fever. IMPORTANCE This study presents a new one-tube, reverse transcription semi-nested, multi-enzyme isothermal rapid amplification assay combined with lateral flow dipstick strips for the detection of CHIKV. This technique significantly improves sensitivity and outperforms RT-qPCR for the detection of CHIKV, especially in samples with low viral loads. It is also significantly faster than conventional RT-qPCR and does not require special equipment or a standard PCR laboratory. The combination of the isothermal amplification technology developed in this study with point-of-care molecular testing offers the potential for rapid, on-site, low-cost molecular diagnosis of CHIKV.
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Affiliation(s)
- Xinlin Wu
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, Yunnan, China
- Yunnan Kecan Biotechnology Co., Ltd, Kunming, Yunnan, China
| | - Gaowen Liu
- Yunnan Kecan Biotechnology Co., Ltd, Kunming, Yunnan, China
| | - Yingchao Chang
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, Yunnan, China
- Yunnan Kecan Biotechnology Co., Ltd, Kunming, Yunnan, China
| | - Mengyuan Zheng
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, Yunnan, China
| | - Li Liu
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, Yunnan, China
- Yunnan Kecan Biotechnology Co., Ltd, Kunming, Yunnan, China
| | - Xueshan Xia
- Yunnan Provincial Key Laboratory of Public Health and Biosafety, Kunming Medical University, Kunming, Yunnan, China
| | - Yue Feng
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, Yunnan, China
- Yunnan Provincial Key Laboratory of Public Health and Biosafety, Kunming Medical University, Kunming, Yunnan, China
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Muzammil K, Rayyani S, Abbas Sahib A, Gholizadeh O, Naji Sameer H, Jwad Kazem T, Badran Mohammed H, Ghafouri Kalajahi H, Zainul R, Yasamineh S. Recent Advances in Crimean-Congo Hemorrhagic Fever Virus Detection, Treatment, and Vaccination: Overview of Current Status and Challenges. Biol Proced Online 2024; 26:20. [PMID: 38926669 PMCID: PMC11201903 DOI: 10.1186/s12575-024-00244-3] [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: 02/29/2024] [Accepted: 05/16/2024] [Indexed: 06/28/2024] Open
Abstract
Crimean-Congo hemorrhagic fever virus (CCHFV) is a tick-borne virus, and zoonosis, and affects large regions of Asia, Southwestern and Southeastern Europe, and Africa. CCHFV can produce symptoms, including no specific clinical symptoms, mild to severe clinical symptoms, or deadly infections. Virus isolation attempts, antigen-capture enzyme-linked immunosorbent assay (ELISA), and reverse transcription polymerase chain reaction (RT-PCR) are all possible diagnostic tests for CCHFV. Furthermore, an efficient, quick, and cheap technology, including biosensors, must be designed and developed to detect CCHFV. The goal of this article is to offer an overview of modern laboratory tests available as well as other innovative detection methods such as biosensors for CCHFV, as well as the benefits and limits of the assays. Furthermore, confirmed cases of CCHF are managed with symptomatic assistance and general supportive care. This study examined the various treatment modalities, as well as their respective limitations and developments, including immunotherapy and antivirals. Recent biotechnology advancements and the availability of suitable animal models have accelerated the development of CCHF vaccines by a substantial margin. We examined a range of potential vaccines for CCHF in this research, comprising nucleic acid, viral particles, inactivated, and multi-epitope vaccines, as well as the present obstacles and developments in this field. Thus, the purpose of this review is to present a comprehensive summary of the endeavors dedicated to advancing various diagnostic, therapeutic, and preventive strategies for CCHF infection in anticipation of forthcoming hazards.
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Affiliation(s)
- Khursheed Muzammil
- Department of Public Health, College of Applied Medical Sciences, King Khalid University, Khamis Mushait Campus, Abha, 62561, Saudi Arabia
| | - Saba Rayyani
- Medical Faculty, University of Georgi, Tbilisi, Georgia
| | | | | | - Hayder Naji Sameer
- Collage of Pharmacy, National University of Science and Technology, Dhi Qar, 64001, Iraq
| | - Tareq Jwad Kazem
- Scientific Affairs Department, Al-Mustaqbal University, Hillah, Babylon, 51001, Iraq
| | - Haneen Badran Mohammed
- Optics techniques department, health and medical techniques college, Al-Noor University, Mosul, Iraq
| | | | - Rahadian Zainul
- Department of Chemistry, Faculty of Mathematics and Natural Sciences, Universitas Negeri Padang, Padang, Indonesia.
| | - Saman Yasamineh
- Center for Advanced Material Processing, Artificial Intelligence, and Biophysics Informatics (CAMPBIOTICS), Universitas Negeri Padang, Padang, Indonesia.
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Sridhar S, Tonto PB, Lumkong L, Netto EM, Brites C, Wang WK, Herrera BB. Development of RT-RPA-based point-of-care tests for epidemic arthritogenic alphaviruses. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.14.594209. [PMID: 38826256 PMCID: PMC11142058 DOI: 10.1101/2024.05.14.594209] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2024]
Abstract
Chikungunya (CHIKV), o'nyong-nyong (ONNV), and Mayaro (MAYV) viruses are transmitted by mosquitoes and known to cause a debilitating arthritogenic syndrome. These alphaviruses have emerged and re-emerged, leading to outbreaks in tropical and subtropical regions of Asia, South America, and Africa. Despite their prevalence, there persists a critical gap in the availability of sensitive and virus-specific point-of-care (POC) diagnostics. Traditional immunoglobulin-based tests such as enzyme-linked immunosorbent assay (ELISAs) often yield cross-reactive results due to the close genetic relationship between these viruses. Molecular diagnostics such as quantitative polymerase chain reaction (qPCR) offer high sensitivity but are limited by the need for specialized laboratory equipment. Recombinase polymerase amplification (RPA), an isothermal amplification method, is a promising alternative to qPCR, providing rapid results with minimal equipment requirements. Here, we report the development and validation of three virus-specific RPA-based POC tests for CHIKV, ONNV, and MAYV. These tests demonstrated both speed and sensitivity, capable of detecting 10 viral copies within 20 minutes of amplification, without exhibiting cross-reactivity. Furthermore, we evaluated the clinical potential of these tests using serum and tissue samples from CHIKV, ONNV, and MAYV-infected mice, as well as CHIKV-infected human patients. We demonstrate that the RPA amplicons derived from the patient samples can be sequenced, enabling cost-effective molecular epidemiological studies. Our findings highlight the significance of these rapid and specific POC diagnostics in improving the early detection and management of these arboviral infections.
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Soares AP, de Lima Neto DF, Pour SZ, Passos SD, Cunha MDP, Zanotto PMDA. Evaluation of renal markers and liver enzymes in patients infected with the Chikungunya virus. J Med Virol 2023; 95:e29276. [PMID: 38100636 DOI: 10.1002/jmv.29276] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2023] [Revised: 11/03/2023] [Accepted: 11/17/2023] [Indexed: 12/17/2023]
Abstract
Chikungunya virus (CHIKV) is an arbovirus (Togaviridae family, Alphavirus genus) that was first identified in 1953 in Tanzania. In 2014, the Asian and East/Central/South/African (ECSA) genotypes were identified in Brazil, although the genotype that spread the most in the following years across the Brazilian territory was the ECSA. The clinical symptoms associated with the infection caused by CHIKV include mainly fever, myalgia, headache, and arthralgia. In infections caused by other arboviruses (such as the ones caused by Dengue and West Nile viruses), changes in biochemical markers are often observed. This study aims to evaluate the biochemical markers profile of kidney and liver injury in acute patients infected with CHIKV. Two groups of correlations were found between the variables analyzed, namely, one between liver enzymes (r = 0.91), and another for kidney markers (r = 0.54-0.66). A significant elevation in the percentage of altered creatinine in CHIKV-infected patients was observed, followed by uric acid and AST. Altogether, in 8 different comparisons, it was possible to observe statistically significant differences between the levels of the markers when compared to the manifestation of symptoms (presence and absence). These noticeable changes in marker measurements could potentially be connected to the range of clinical symptoms seen in the disease.
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Affiliation(s)
- Anderson Pereira Soares
- Laboratory of Molecular Evolution and Bioinformatics, Department of Microbiology, Biomedical Sciences Institute, University of São Paulo, São Paulo, São Paulo, Brazil
| | - Daniel Ferreira de Lima Neto
- Laboratory of Molecular Evolution and Bioinformatics, Department of Microbiology, Biomedical Sciences Institute, University of São Paulo, São Paulo, São Paulo, Brazil
| | - Shahab Zaki Pour
- Laboratory of Molecular Evolution and Bioinformatics, Department of Microbiology, Biomedical Sciences Institute, University of São Paulo, São Paulo, São Paulo, Brazil
| | - Saulo Duarte Passos
- Department of Pediatrics, Jundiaí School of Medicine, Jundiaí, São Paulo, Brazil
| | - Marielton Dos Passos Cunha
- Laboratory of Molecular Evolution and Bioinformatics, Department of Microbiology, Biomedical Sciences Institute, University of São Paulo, São Paulo, São Paulo, Brazil
| | - Paolo Marinho de Andrade Zanotto
- Laboratory of Molecular Evolution and Bioinformatics, Department of Microbiology, Biomedical Sciences Institute, University of São Paulo, São Paulo, São Paulo, Brazil
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de França Cirilo MV, Pour SZ, de Fatima Benedetti V, Farias JP, Fogaça MMC, da Conceição Simões R, Vidal PO, Birbrair A, de Andrade Zanotto PM, Luiz WB, Amorim JH. Co-circulation of Chikungunya virus, Zika virus, and serotype 1 of Dengue virus in Western Bahia, Brazil. Front Microbiol 2023; 14:1240860. [PMID: 37680530 PMCID: PMC10482036 DOI: 10.3389/fmicb.2023.1240860] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2023] [Accepted: 08/03/2023] [Indexed: 09/09/2023] Open
Abstract
Chikungunya, mayaro, dengue, zika, and yellow fever are mosquito-borne viral diseases caused, respectively, by Chikungunya virus, Mayaro virus (CHIKV and MAYV, respectively: Togaviridae: Alphavirus), Dengue virus, Zika virus, and Yellow fever virus (DENV, ZIKV, and YFV, respectively: Flaviviridae: Flavivirus). These viruses have an important epidemiological impact worldwide, especially in Brazil. Western Bahia is one of the less studied regions in that country regarding the circulation of these pathogens. In this study, we aimed to apply molecular biology assays to better know the mosquito-borne viruses circulating in Barreiras and Luís Eduardo Magalhães, two main cities of Western Bahia. From March to June 2021, we enrolled 98 patients with the clinical diagnosis of dengue. Personal information (gender and age) were retrieved at the moment of enrollment. Serum samples were obtained from volunteers and used in molecular detection of CHIKV, MAYV, DENV, ZIKV, and YFV by reverse transcription followed by real-time polymerase chain reaction as well as in genome sequencing aiming phylogenetic analysis. As the main result, we found that from the 98 patients 45 were infected by CHIKV, 32 were infected by serotype 1 of DENV (DENV-1) and six were infected by ZIKV, while 15 were negative for all arboviruses tested. In addition, phylogenetic analysis revealed that all CHIKV-positive samples were of the East/Central/South African (ECSA) genotype, while all DENV-1-positive samples were of the V genotype. These results clearly show that epidemiological surveillance cannot be based only on clinical evaluations. Laboratory diagnosis is important in arbovirus infection that are prevalent in a particular area. These findings also demonstrate the co-circulation of many arboviruses in Western Bahia in 2021.
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Affiliation(s)
- Marcus Vinicius de França Cirilo
- Western Bahia Virology Institute, Center of Biological Sciences and Health, Federal University of Western Bahia, Barreiras, Brazil
| | - Shahab Zaki Pour
- Laboratory of Molecular Evolution and Bioinformatics, Department of Microbiology, University of Sao Paulo, Sao Paulo, Brazil
| | - Viviane de Fatima Benedetti
- Laboratory of Molecular Evolution and Bioinformatics, Department of Microbiology, University of Sao Paulo, Sao Paulo, Brazil
| | - Jéssica Pires Farias
- Western Bahia Virology Institute, Center of Biological Sciences and Health, Federal University of Western Bahia, Barreiras, Brazil
| | - Mayanna Moreira Costa Fogaça
- Western Bahia Virology Institute, Center of Biological Sciences and Health, Federal University of Western Bahia, Barreiras, Brazil
| | - Rafael da Conceição Simões
- Laboratory of Biochemistry and Plant Physiology, Center of Biological Sciences and Health, Federal University of Western Bahia, Barreiras, Brazil
| | - Paloma Oliveira Vidal
- Western Bahia Virology Institute, Center of Biological Sciences and Health, Federal University of Western Bahia, Barreiras, Brazil
| | - Alexander Birbrair
- Department of Dermatology, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI, United States
| | | | - Wilson Barros Luiz
- Laboratory of Applied Pathology and Genetics, Department of Biological Sciences, State University of Santa Cruz, Ilhéus, Brazil
| | - Jaime Henrique Amorim
- Western Bahia Virology Institute, Center of Biological Sciences and Health, Federal University of Western Bahia, Barreiras, Brazil
- Laboratory of Molecular Evolution and Bioinformatics, Department of Microbiology, University of Sao Paulo, Sao Paulo, Brazil
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da Silva Duarte G, Jones AD, de Goes Cavalcanti LP, de Melo Rêgo MJB, Ribeiro GS, Boyton RJ, Pereira DB, Croda JHR, Costa FTM, Duarte AP, Consolaro MEL, Stabeli RG, Negrão FJ, Proenca-Modena JL, Villalobos-Salcedo JM, da Rocha Castelar Pinheiro G, de Barros Albuquerque AP, de Almeida Barreto FK, Moreira J, Ferrari IC, Évora PM, da Silva VRS, Lacerda MVG, Altmann DM, Siqueira AM. Multicenter study of the natural history and therapeutic responses of patients with chikungunya, focusing on acute and chronic musculoskeletal manifestations - a study protocol from the clinical and applied research in Chikungunya (REPLICK network). BMC Infect Dis 2023; 23:499. [PMID: 37507666 PMCID: PMC10386654 DOI: 10.1186/s12879-023-08292-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2023] [Accepted: 04/28/2023] [Indexed: 07/30/2023] Open
Abstract
BACKGROUND Chikungunya is associated with high morbidity and the natural history of symptomatic infection has been divided into three phases (acute, post-acute, and chronic) according to the duration of musculoskeletal symptoms. Although this classification has been designed to help guide therapeutic decisions, it does not encompass the complexity of the clinical expression of the disease and does not assist in the evaluation of the prognosis of severity nor chronic disease. Thus, the current challenge is to identify and diagnose musculoskeletal disorders and to provide the optimal treatment in order to prevent perpetuation or progression to a potentially destructive disease course. METHODS The study is the first product of the Clinical and Applied Research Network in Chikungunya (REPLICK). This is a prospective, outpatient department-based, multicenter cohort study in Brazil. Four work packages were defined: i. Clinical research; ii) Translational Science - comprising immunology and virology streams; iii) Epidemiology and Economics; iv) Therapeutic Response and clinical trials design. Scheduled appointments on days 21 (D21) ± 7 after enrollment, D90 ± 15, D120 ± 30, D180 ± 30; D360 ± 30; D720 ± 60, and D1080 ± 60 days. On these visits a panel of blood tests are collected in addition to the clinical report forms to obtain data on socio-demographic, medical history, physical examination and questionnaires devoted to the evaluation of musculoskeletal manifestations and overall health are performed. Participants are asked to consent for their specimens to be maintained in a biobank. Aliquots of blood, serum, saliva, PAXgene, and when clinically indicated to be examined, synovial fluid, are stored at -80° C. The study protocol was submitted and approved to the National IRB and local IRB at each study site. DISCUSSION Standardized and harmonized patient cohorts are needed to provide better estimates of chronic arthralgia development, the clinical spectra of acute and chronic disease and investigation of associated risk factors. This study is the largest evaluation of the long-term sequelae of individuals infected with CHIKV in the Brazilian population focusing on musculoskeletal manifestations, mental health, quality of life, and chronic pain. This information will both define disease burden and costs associated with CHIKV infection, and better inform therapeutic guidelines.
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Affiliation(s)
- Giselle da Silva Duarte
- Laboratório de Pesquisa Clínica Em Doenças Febris Agudas, Instituto Nacional de Infectologia Evandro Chagas, Fundação Oswaldo Cruz, Rio de Janeiro, Brazil
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | - Jose Moreira
- Laboratório de Pesquisa Clínica Em Doenças Febris Agudas, Instituto Nacional de Infectologia Evandro Chagas, Fundação Oswaldo Cruz, Rio de Janeiro, Brazil
| | | | | | | | | | | | - André M Siqueira
- Laboratório de Pesquisa Clínica Em Doenças Febris Agudas, Instituto Nacional de Infectologia Evandro Chagas, Fundação Oswaldo Cruz, Rio de Janeiro, Brazil.
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Rosado LEP, Martelli CMT, Brickley EB, Gomes MBF, de Toledo Lima T, da Costa PSS, de Ávila MP, Viggiano MB, do Amaral WN, de Rezende Feres VC, Fiaccadori FS, de Sene Amancio Zara AL, Ferreira-Lopes A, Turchi MD. Risk of adverse pregnancy and infant outcomes associated with prenatal Zika virus infection: a post-epidemic cohort in Central-West Brazil. Sci Rep 2023; 13:7335. [PMID: 37147405 PMCID: PMC10161159 DOI: 10.1038/s41598-023-33334-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2022] [Accepted: 04/11/2023] [Indexed: 05/07/2023] Open
Abstract
This study aimed to estimate the risks of adverse infant outcomes in the first year of life related to prenatal Zika virus (ZIKV) exposure. A prospective cohort of pregnant women with rash was recruited in Central-West Brazil in a post-epidemic period (January 2017 to April 2019). We evaluated participants' medical histories and performed ZIKV diagnostic testing using molecular (reverse transcription polymerase chain reaction [RT-PCR]) and serologic (immunoglobulin [Ig]M and plaque reduction neutralization tests [PRNT90]) assays. The ZIKV-positive group included both RT-PCR-confirmed cases as well as IgM and/or PRNT90-positive probable cases. Children were evaluated at birth and in the first 12 months of life. Transfontanellar ultrasound, central nervous system computed tomography, eye fundoscopy and retinography were performed. We estimated the absolute risk and 95% confidence interval (95% CI) of adverse infant outcomes among confirmed prenatally ZIKV-exposed children. Among 81 pregnant women with rash, 43 (53.1%) were ZIKV infected. The absolute risk of microcephaly among offspring of ZIKV-infected pregnant women was 7.0% (95% CI: 1.5-19.1), including the two cases of microcephaly detected prenatally and one detected postnatally. In total, 54.5% (95% CI: 39.8-68.7) of children in the ZIKV-exposed group had at least one ophthalmic abnormality, with the most frequent abnormalities being focal pigmentary mottling and chorioretinal atrophy or scarring. Our findings reinforce the importance of long-term monitoring of prenatally ZIKV-exposed children born apparently asymptomatic for Congenital Zika Syndrome.
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Affiliation(s)
- Luiza Emylce Pela Rosado
- Graduate Program in Tropical Medicine and Public Health of the Federal University of Goias, Goiânia, Brazil
- Obstetrics Department, Maternal and Infant Hospital of Goias State, Goiânia, Brazil
| | | | - Elizabeth B Brickley
- Department of Infectious Disease Epidemiology, London School of Hygiene & Tropical Medicine, London, United Kingdom
| | - Maria Barbara Franco Gomes
- Graduate Program in Health Sciences of the Federal University of Goias, Goiânia, Brazil
- Pediatric Department, Maternal and Infant Hospital of Goias State, Goiânia, Brazil
| | - Talita de Toledo Lima
- Graduate Program in Health Sciences of the Federal University of Goias, Goiânia, Brazil
- Reference Center in Ophthalmology of the Federal University of Goias, Goiânia, Brazil
| | | | - Marcos Pereira de Ávila
- Reference Center in Ophthalmology of the Federal University of Goias, Goiânia, Brazil
- Retina and Vitreous Department, School of Medicine, Federal University of Goias, Goiânia, Brazil
| | | | | | | | - Fabiola Souza Fiaccadori
- Virology Department, Institute of Tropical Pathology and Public Health, Federal University of Goias, Goiânia, Brazil
| | | | | | - Marilia Dalva Turchi
- Institute of Tropical Pathology and Public Health, Federal University of Goias, Goiânia, Brazil.
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de Olazarra AS, Wang SX. Advances in point-of-care genetic testing for personalized medicine applications. BIOMICROFLUIDICS 2023; 17:031501. [PMID: 37159750 PMCID: PMC10163839 DOI: 10.1063/5.0143311] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/21/2023] [Accepted: 04/12/2023] [Indexed: 05/11/2023]
Abstract
Breakthroughs within the fields of genomics and bioinformatics have enabled the identification of numerous genetic biomarkers that reflect an individual's disease susceptibility, disease progression, and therapy responsiveness. The personalized medicine paradigm capitalizes on these breakthroughs by utilizing an individual's genetic profile to guide treatment selection, dosing, and preventative care. However, integration of personalized medicine into routine clinical practice has been limited-in part-by a dearth of widely deployable, timely, and cost-effective genetic analysis tools. Fortunately, the last several decades have been characterized by tremendous progress with respect to the development of molecular point-of-care tests (POCTs). Advances in microfluidic technologies, accompanied by improvements and innovations in amplification methods, have opened new doors to health monitoring at the point-of-care. While many of these technologies were developed with rapid infectious disease diagnostics in mind, they are well-suited for deployment as genetic testing platforms for personalized medicine applications. In the coming years, we expect that these innovations in molecular POCT technology will play a critical role in enabling widespread adoption of personalized medicine methods. In this work, we review the current and emerging generations of point-of-care molecular testing platforms and assess their applicability toward accelerating the personalized medicine paradigm.
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Affiliation(s)
- A. S. de Olazarra
- Department of Electrical Engineering, Stanford University, Stanford, California 94305, USA
| | - S. X. Wang
- Author to whom correspondence should be addressed:
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Bartholomeeusen K, Daniel M, LaBeaud DA, Gasque P, Peeling RW, Stephenson KE, Ng LFP, Ariën KK. Chikungunya fever. Nat Rev Dis Primers 2023; 9:17. [PMID: 37024497 PMCID: PMC11126297 DOI: 10.1038/s41572-023-00429-2] [Citation(s) in RCA: 37] [Impact Index Per Article: 37.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 03/10/2023] [Indexed: 04/08/2023]
Abstract
Chikungunya virus is widespread throughout the tropics, where it causes recurrent outbreaks of chikungunya fever. In recent years, outbreaks have afflicted populations in East and Central Africa, South America and Southeast Asia. The virus is transmitted by Aedes aegypti and Aedes albopictus mosquitoes. Chikungunya fever is characterized by severe arthralgia and myalgia that can persist for years and have considerable detrimental effects on health, quality of life and economic productivity. The effects of climate change as well as increased globalization of commerce and travel have led to growth of the habitat of Aedes mosquitoes. As a result, increasing numbers of people will be at risk of chikungunya fever in the coming years. In the absence of specific antiviral treatments and with vaccines still in development, surveillance and vector control are essential to suppress re-emergence and epidemics.
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Affiliation(s)
- Koen Bartholomeeusen
- Virology Unit, Department of Biomedical Sciences, Institute of Tropical Medicine Antwerp, Antwerp, Belgium
| | - Matthieu Daniel
- Unité de Recherche en Pharmaco-Immunologie (UR-EPI), Université et CHU de La Réunion, Saint-Denis, France
- Service de Médecine d'Urgences-SAMU-SMUR, CHU de La Réunion, Saint-Denis, France
| | - Desiree A LaBeaud
- Department of Pediatrics, Division of Infectious Disease, Stanford University School of Medicine, Stanford, CA, USA
| | - Philippe Gasque
- Unité de Recherche en Pharmaco-Immunologie (UR-EPI), Université et CHU de La Réunion, Saint-Denis, France
- Laboratoire d'Immunologie Clinique et Expérimentale Océan Indien LICE-OI, Université de La Réunion, Saint-Denis, France
| | - Rosanna W Peeling
- Clinical Research Department, London School of Hygiene and Tropical Medicine, London, UK
| | - Kathryn E Stephenson
- Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, USA
| | - Lisa F P Ng
- A*STAR Infectious Diseases Labs, Agency for Science, Technology and Research, Singapore, Singapore
- National Institute of Health Research, Health Protection Research Unit in Emerging and Zoonotic Infections, University of Liverpool, Liverpool, UK
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK
| | - Kevin K Ariën
- Virology Unit, Department of Biomedical Sciences, Institute of Tropical Medicine Antwerp, Antwerp, Belgium.
- Department of Biomedical Sciences, University of Antwerp, Antwerp, Belgium.
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10
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Tripathi S, Khatri P, Fatima Z, Pandey RP, Hameed S. A Landscape of CRISPR/Cas Technique for Emerging Viral Disease Diagnostics and Therapeutics: Progress and Prospects. Pathogens 2022; 12:pathogens12010056. [PMID: 36678404 PMCID: PMC9863163 DOI: 10.3390/pathogens12010056] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2022] [Revised: 12/22/2022] [Accepted: 12/25/2022] [Indexed: 12/31/2022] Open
Abstract
Viral diseases have emerged as a serious threat to humanity and as a leading cause of morbidity worldwide. Many viral diagnostic methods and antiviral therapies have been developed over time, but we are still a long way from treating certain infections caused by viruses. Acquired immunodeficiency syndrome (AIDS) is one of the challenges where current medical science advancements fall short. As a result, new diagnostic and treatment options are desperately needed. The CRISPR/Cas9 system has recently been proposed as a potential therapeutic approach for viral disease treatment. CRISPR/Cas9 is a specialised, effective, and adaptive gene-editing technique that can be used to modify, delete, or correct specific DNA sequences. It has evolved into an advanced, configurable nuclease-based single or multiple gene-editing tool with a wide range of applications. It is widely preferred simply because its operational procedures are simple, inexpensive, and extremely efficient. Exploration of infectious virus genomes is required for a comprehensive study of infectious viruses. Herein, we have discussed the historical timeline-based advancement of CRISPR, CRISPR/Cas9 as a gene-editing technology, the structure of CRISPR, and CRISPR as a diagnostic tool for studying emerging viral infections. Additionally, utilizing CRISPR/Cas9 technology to fight viral infections in plants, CRISPR-based diagnostics of viruses, pros, and cons, and bioethical issues of CRISPR/Cas9-based genomic modification are discussed.
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Affiliation(s)
- Shyam Tripathi
- Centre for Drug Design Discovery and Development (C4D), SRM University, Delhi-NCR, Rajiv Gandhi Education City, Sonepat 131029, India
| | - Purnima Khatri
- Centre for Drug Design Discovery and Development (C4D), SRM University, Delhi-NCR, Rajiv Gandhi Education City, Sonepat 131029, India
- Department of Microbiology, SRM University, Delhi-NCR, Rajiv Gandhi Education City, Sonepat 131029, India
| | - Zeeshan Fatima
- Department of Medical Laboratory Sciences, College of Applied Medical Sciences, University of Bisha, Bisha 61922, Saudi Arabia
- Amity Institute of Biotechnology, Amity University Haryana, Gurugram 122413, India
| | - Ramendra Pati Pandey
- Centre for Drug Design Discovery and Development (C4D), SRM University, Delhi-NCR, Rajiv Gandhi Education City, Sonepat 131029, India
- Department of Microbiology, SRM University, Delhi-NCR, Rajiv Gandhi Education City, Sonepat 131029, India
- Correspondence: (R.P.P.); (S.H.)
| | - Saif Hameed
- Amity Institute of Biotechnology, Amity University Haryana, Gurugram 122413, India
- Correspondence: (R.P.P.); (S.H.)
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11
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Abstract
INTRODUCTION Recombinase polymerase amplification (RPA) is a promising and emerging technology for rapidly amplifying target nucleic acid from minimally processed samples and through small portable instruments. RPA is suitable for point-of-care testing (POCT) and on-site field testing, and it is compatible with microfluidic devices. Several detection assays have been developed, but limited research has dug deeper into the chemistry of RPA to understand its kinetics and fix its shortcomings. AREAS COVERED This review provides a detailed introduction of RPA molecular mechanism, kits formats, optimization, application, pros, and cons. Moreover, this critical review discusses the nonspecificity issue of RPA, highlights its consequences, and emphasizes the need for more research to resolve it. This review discusses the reaction kinetics of RPA in relation to target length, product quantity, and sensitivity. This critical review also questions the novelty of recombinase-aided amplification (RAA). In short, this review discusses many aspects of RPA technology that have not been discussed previously and provides a deeper insight and new perspectives of the technology. EXPERT OPINION RPA is an excellent choice for pathogen detection, especially in low-resource settings. It has a potential to replace PCR for all purposes, provided its shortcomings are fixed and its reagent accessibility is improved.
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Affiliation(s)
- Mustafa Ahmad Munawar
- Institute of Biomedicine, School of Medicine, University of Eastern Finland, Kuopio, Finland
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12
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Tamer C, Benkaroun J, Kurucay HN, Albayrak H, Weidmann M. Development of a recombinase polymerase amplification assay for viral haemorrhagic septicemia virus. JOURNAL OF FISH DISEASES 2022; 45:1065-1071. [PMID: 35467756 DOI: 10.1111/jfd.13629] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/14/2022] [Revised: 04/10/2022] [Accepted: 04/13/2022] [Indexed: 06/14/2023]
Abstract
Viral diseases of fish cause significant economic losses in the aquaculture industry. Viral haemorrhagic septicemia virus (VHSV) is one of the most important viral diseases that affects more than 80 fish species. Detection of the disease, especially in the field, is critical to managing disease prevention and control programmes. Recombinase polymerase amplification (RPA) is an isothermal method with a very short amplification period and a single incubation temperature ranging from 37 to 42°C, which is a good alternative to the polymerase chain reaction (PCR). This study aimed to develop an RPA assay as sensitive as a real-time RT-PCR to detect VHSV. For this purpose, primers and probes are designed for the same targeted region of gG of VHSV. The ssRNA standards were prepared to find the detection limits of the assay. Detection limits were found ten-fold differences between real-time RT-PCR and real-time RT-RPA. While the detection limit of the RT-PCR was found as 95.5 viral RNA molecules/reaction in 95% probit value, the detection limit of RT-RPA was found as 943.75 viral RNA molecules/reaction in 95% probit value using ssRNA standards. These results show that RPA is a suitable test for VHSV Ie detection.
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Affiliation(s)
- Cuneyt Tamer
- Department of Virology, Faculty of Veterinary Medicine, Ondokuz Mayıs University, Samsun, Turkey
| | | | - Hanne Nur Kurucay
- Department of Virology, Faculty of Veterinary Medicine, Ondokuz Mayıs University, Samsun, Turkey
| | - Harun Albayrak
- Department of Virology, Faculty of Veterinary Medicine, Ondokuz Mayıs University, Samsun, Turkey
| | - Manfred Weidmann
- Medizinische Hochschule Brandenburg Theodor Fontane, Senftenberg, Germany
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13
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Jang WS, Lim DH, Choe YL, Nam J, Moon KC, Kim C, Choi M, Park I, Park DW, Lim CS. Developing a multiplex loop-mediated isothermal amplification assay (LAMP) to determine severe fever with thrombocytopenia syndrome (SFTS) and scrub typhus. PLoS One 2022; 17:e0262302. [PMID: 35171943 PMCID: PMC8849512 DOI: 10.1371/journal.pone.0262302] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2021] [Accepted: 12/21/2021] [Indexed: 11/19/2022] Open
Abstract
Severe fever with thrombocytopenia syndrome (SFTS) and scrub typhus are endemic zoonotic diseases that pose significant public health threats in East Asia. As these two diseases share common clinical features, as well as overlapping disease regions, it is difficult to differentiate between SFTS and scrub typhus. A multiplex reverse-transcription loop‑mediated isothermal amplification (RT-LAMP) assay was developed to detect large segments and GroES genes for SFTS virus (SFTSV) and Orientia tsutsugamushi (OT). The performance of the RT-LAMP assay was compared and evaluated with those of commercial PowerChek™ SFTSV real-time PCR and LiliF™ TSUTSU nested PCR for 23 SFTS and 12 scrub typhus clinical samples, respectively. The multiplex SFTSV/OT/Internal control (IC) RT-LAMP assay showed comparable sensitivity (91.3%) with that of commercial PowerChek™ SFTSV Real-time PCR (95.6%) and higher sensitivity (91.6%) than that of LiliF™ TSUTSU nested PCR (75%). In addition, the multiplex SFTSV/OT RT-LAMP assay showed 100% specificity and no cross-reactivity for blood from uninfected healthy patients and samples from patients infected with other fever viruses. Thus, the multiplex SFTSV/OT/IC RT-LAMP assay could serve as a useful point-of-care molecular diagnostic test for SFTS and scrub typhus.
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Affiliation(s)
- Woong Sik Jang
- Emergency Medicine, College of Medicine, Korea University Guro Hospital, Seoul, Korea
| | - Da Hye Lim
- Departments of Laboratory Medicine, College of Medicine, Korea University Guro Hospital, Seoul, Korea
| | - Young Lan Choe
- Departments of Laboratory Medicine, College of Medicine, Korea University Guro Hospital, Seoul, Korea
| | - Jeonghun Nam
- Department of Song‐do Bio Engineering, Incheon Jaeneung University, Incheon, Korea
- Artificial Intelligence (AI)‐Bio Research Center, Incheon Jaeneung University, Incheon, Korea
| | - Kyung Chul Moon
- Emergency Medicine, College of Medicine, Korea University Guro Hospital, Seoul, Korea
| | - Chaewon Kim
- Departments of Laboratory Medicine, College of Medicine, Korea University Guro Hospital, Seoul, Korea
| | - Minkyeong Choi
- Departments of Laboratory Medicine, College of Medicine, Korea University Guro Hospital, Seoul, Korea
| | - Insu Park
- Departments of Laboratory Medicine, College of Medicine, Korea University Guro Hospital, Seoul, Korea
| | - Dae Won Park
- Division of Infectious Diseases, Department of Internal Medicine, Korea University Ansan Hospital, Ansan-si, Gyeonggi-do, Republic of Korea
| | - Chae Seung Lim
- Departments of Laboratory Medicine, College of Medicine, Korea University Guro Hospital, Seoul, Korea
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14
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Ding R, Shen Y, Yuan M, Zheng X, Chen S, Duan G. Rapid and facile detection of HBV with CRISPR/Cas13a. NEW J CHEM 2022; 46:19997-20004. [DOI: 10.1039/d2nj02674k] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/03/2024]
Abstract
A rapid point-of-care assay based on CRISPR-Cas13a for HBV was built with a LOD of 1 copy per μL was achieved in 50 min. The lateral flow test strip method can achieve naked-eye results, and the fluorescence readout can achieve real-time detection.
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Affiliation(s)
- Ronghua Ding
- Department of Epidemiology, College of Public Health, Zhengzhou University, No. 100 Kexue Avenue, Zhengzhou 450000, Henan, China
- Jining No. 1 People′s Hospital, Jining 272000, Shandong, China
| | - Yue Shen
- Department of Epidemiology, College of Public Health, Zhengzhou University, No. 100 Kexue Avenue, Zhengzhou 450000, Henan, China
| | - Mingzhu Yuan
- Department of Epidemiology, College of Public Health, Zhengzhou University, No. 100 Kexue Avenue, Zhengzhou 450000, Henan, China
| | - Xue Zheng
- Department of Epidemiology, College of Public Health, Zhengzhou University, No. 100 Kexue Avenue, Zhengzhou 450000, Henan, China
| | - Shuaiyin Chen
- Department of Epidemiology, College of Public Health, Zhengzhou University, No. 100 Kexue Avenue, Zhengzhou 450000, Henan, China
| | - Guangcai Duan
- Department of Epidemiology, College of Public Health, Zhengzhou University, No. 100 Kexue Avenue, Zhengzhou 450000, Henan, China
- Key Laboratory of Molecular Medicine in Henan Province, Zhengzhou University, Zhengzhou 450000, Henan, China
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15
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Reverse transcription recombinase polymerase amplification assay for rapid detection of the cucurbit chlorotic yellows virus. J Virol Methods 2021; 300:114388. [PMID: 34848283 DOI: 10.1016/j.jviromet.2021.114388] [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: 07/31/2021] [Revised: 09/29/2021] [Accepted: 11/26/2021] [Indexed: 11/24/2022]
Abstract
The cucurbit chlorotic yellows virus (CCYV) causes severe economic losses in cucurbit plants. Although it has been widely known in various countries for several years, CCYV is rarely recognized due to the lack of rapid and effective detection methods in the early stage of the disease. Recombinase polymerase amplification (RPA) is a new, efficient, and simple technology for nucleic acid detection. In the present study, reverse transcription (RT)-RPA and quantitative RT-RPA were developed and utilized for fast detection of CCYV in field-collected melon samples. The analysis was performed under constant temperature conditions without the necessity for a thermal cycler in just 20 min. Moreover, the detection limit of RT-RPA for CCYV was determined at 10 pg. In the study, 58 field-collected samples were employed to evaluate the performance of the two assays. The positive rates were established at 72.4 % (42/58) and 75.9 % (44/58) by RT-RPA and qRT-RPA, respectively, and were consistent with the RT-PCR results. The successful application of RPA for the detection of CCYV in field-collected melon samples indicated its potential applicability. Thus, the developed RPA assays provide an alternative for fast, efficient, sensitive, and reliable detection of CCYV in diagnostic laboratories, which lack the precise instrumentation, and fields without appropriate equipment.
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16
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Cantera JL, White HN, Forrest MS, Stringer OW, Belizario VY, Storey HL, de Hostos EL, de los Santos T. Sensitive and semiquantitative detection of soil-transmitted helminth infection in stool using a recombinase polymerase amplification-based assay. PLoS Negl Trop Dis 2021; 15:e0009782. [PMID: 34516554 PMCID: PMC8459997 DOI: 10.1371/journal.pntd.0009782] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2020] [Revised: 09/23/2021] [Accepted: 09/01/2021] [Indexed: 01/03/2023] Open
Abstract
Background Soil-transmitted helminths (STHs) are parasitic nematodes that inhabit the human intestine. They affect more than 1.5 billion people worldwide, causing physical and cognitive impairment in children. The global strategy to control STH infection includes periodic mass drug administration (MDA) based on the results of diagnostic testing among populations at risk, but the current microscopy method for detecting infection has diminished sensitivity as the intensity of infection decreases. Thus, improved diagnostic tools are needed to support decision-making for STH control programs. Methodology We developed a nucleic acid amplification test based on recombinase polymerase amplification (RPA) technology to detect STH in stool. We designed primers and probes for each of the four STH species, optimized the assay, and then verified its performance using clinical stool samples. Principal findings Each RPA assay was as sensitive as a real-time polymerase chain reaction (PCR) assay in detecting copies of cloned target DNA sequences. The RPA assay amplified the target in DNA extracted from human stool samples that were positive for STH based on the Kato-Katz method, with no cross-reactivity of the non-target genomic DNA. When tested with clinical stool samples from patients with infections of light, moderate, and heavy intensity, the RPA assays demonstrated performance comparable to that of real-time PCR, with better results than Kato-Katz. This new rapid, sensitive and field-deployable method for detecting STH infections can help STH control programs achieve their goals. Conclusions Semi-quantitation of target by RPA assay is possible and is comparable to real-time PCR. With proper instrumentation, RPA assays can provide robust, semi-quantification of STH DNA targets as an alternative field-deployable indicator to counts of helminth eggs for assessing infection intensity. More than 1.5 billion people are infected with parasitic intestinal worms called soil-transmitted helminths. Infection is transmitted by helminth eggs in human feces, which contaminate soil in areas with poor sanitation. Adverse health effects include physical and cognitive impairment in children. A key strategy to control infection is periodic mass drug administration for populations with a high prevalence of disease based on the results of diagnostic testing. The current microscopy method for detecting infection, however, has limited ability to detect disease as the intensity of infection decreases with repeated mass drug administration. To address limitations of current diagnostic methods, we developed a novel technique to diagnose infections, including those at very low levels of intensity, by detecting helminth DNA in stool samples. Our initial studies suggest that the new diagnostic technique reliably detects the presence of intestinal worms, even at low intensities of infection, and may be more useful than currently available diagnostic tools for guiding the use of periodic mass drug administration to eliminate disease in low-resource settings.
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Affiliation(s)
| | | | | | | | - Vicente Y. Belizario
- Department of Parasitology, College of Public Health, University of the Philippines, Ermita, Manila, Philippines
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17
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Mori A, Pomari E, Deiana M, Perandin F, Caldrer S, Formenti F, Mistretta M, Orza P, Ragusa A, Piubelli C. Molecular techniques for the genomic viral RNA detection of West Nile, Dengue, Zika and Chikungunya arboviruses: a narrative review. Expert Rev Mol Diagn 2021; 21:591-612. [PMID: 33910444 DOI: 10.1080/14737159.2021.1924059] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Introduction: Molecular technology has played an important role in arboviruses diagnostics. PCR-based methods stand out in terms of sensitivity, specificity, cost, robustness, and accessibility, and especially the isothermal amplification (IA) method is ideal for field-adaptable diagnostics in resource-limited settings (RLS).Areas covered: In this review, we provide an overview of the various molecular methods for West Nile, Zika, Dengue and Chikungunya. We summarize literature works reporting the assessment and use of in house and commercial assays. We describe limitations and challenges in the usage of methods and opportunities for novel approaches such as NNext-GenerationSequencing (NGS).Expert opinion: The rapidity and accuracy of differential diagnosis is essential for a successful clinical management, particularly in co-circulation area of arboviruses. Several commercial diagnostic molecular assays are available, but many are not affordable by RLS and not usable as Point-of-care/Point-of-need (POC/PON) such as RReal-TimeRT-PCR, Array-based methods and NGS. In contrast, the IA-based system fits better for POC/PON but it is still not ideal for the multiplexing detection system. Improvement in the characterization and validation of current molecular assays is needed to optimize their translation to the point of care.
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Affiliation(s)
- Antonio Mori
- Department of Infectious-Tropical Diseases and Microbiology, IRCCS Sacro Cuore Don Calabria Hospital, Verona, Italy.,Department of Diagnostics and Public Health, University of Verona, Verona, Italy
| | - Elena Pomari
- Department of Infectious-Tropical Diseases and Microbiology, IRCCS Sacro Cuore Don Calabria Hospital, Verona, Italy
| | - Michela Deiana
- Department of Infectious-Tropical Diseases and Microbiology, IRCCS Sacro Cuore Don Calabria Hospital, Verona, Italy
| | - Francesca Perandin
- Department of Infectious-Tropical Diseases and Microbiology, IRCCS Sacro Cuore Don Calabria Hospital, Verona, Italy
| | - Sara Caldrer
- Department of Infectious-Tropical Diseases and Microbiology, IRCCS Sacro Cuore Don Calabria Hospital, Verona, Italy
| | - Fabio Formenti
- Department of Infectious-Tropical Diseases and Microbiology, IRCCS Sacro Cuore Don Calabria Hospital, Verona, Italy
| | - Manuela Mistretta
- Department of Infectious-Tropical Diseases and Microbiology, IRCCS Sacro Cuore Don Calabria Hospital, Verona, Italy
| | - Pierantonio Orza
- Department of Infectious-Tropical Diseases and Microbiology, IRCCS Sacro Cuore Don Calabria Hospital, Verona, Italy
| | - Andrea Ragusa
- Department of Infectious-Tropical Diseases and Microbiology, IRCCS Sacro Cuore Don Calabria Hospital, Verona, Italy
| | - Chiara Piubelli
- Department of Infectious-Tropical Diseases and Microbiology, IRCCS Sacro Cuore Don Calabria Hospital, Verona, Italy
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18
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Abstract
Despite numerous viral outbreaks in the last decade, including a devastating global pandemic, diagnostic and therapeutic technologies remain severely lacking. CRISPR-Cas systems have the potential to address these critical needs in the response against infectious disease. Initially discovered as the bacterial adaptive immune system, these systems provide a unique opportunity to create programmable, sequence-specific technologies for detection of viral nucleic acids and inhibition of viral replication. This review summarizes how CRISPR-Cas systems-in particular the recently discovered DNA-targeting Cas12 and RNA-targeting Cas13, both possessing a unique trans-cleavage activity-are being harnessed for viral diagnostics and therapies. We further highlight the numerous technologies whose development has accelerated in response to the COVID-19 pandemic.
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Affiliation(s)
- Catherine A. Freije
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA 02142, USA,Ph.D. Program in Virology, Harvard Medical School, Boston, MA 02115, USA,Corresponding author
| | - Pardis C. Sabeti
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA 02142, USA,Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA,Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA,Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA,Massachusetts Consortium on Pathogen Readiness, Boston, MA 02115, USA,Corresponding author
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19
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Tomar PS, Kumar S, Patel S, Kumar JS. Development and Evaluation of Real-Time Reverse Transcription Recombinase Polymerase Amplification Assay for Rapid and Sensitive Detection of West Nile Virus in Human Clinical Samples. Front Cell Infect Microbiol 2021; 10:619071. [PMID: 33708642 PMCID: PMC7940365 DOI: 10.3389/fcimb.2020.619071] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2020] [Accepted: 12/31/2020] [Indexed: 11/17/2022] Open
Abstract
West Nile virus (WNV) causes West Nile fever and encephalitis worldwide. Currently, there are no effective drugs or vaccines available in the market to treat WNV infection in humans. Hence, it is of paramount importance to detect WNV early for the success of the disease control programs and timely clinical management in endemic areas. In the present paper, we report the development of real-time reverse transcription recombinase polymerase amplification (RT-RPA) assay for rapid and real-time detection of WNV targeting the envelope (env) gene of the virus. The RPA reaction was performed successfully at 39°C for 15 min in a real-time thermal cycler. The sensitivity of this assay was found similar to that of the quantitative real-time RT PCR (RT-qPCR) assay, which could detect 10 copies of the gene. The efficacy of the assay was evaluated with a panel of 110 WN suspected human samples showing the signs of retinitis, febrile illness and acute posterior uveitis. In comparison with RT-qPCR, RT-RPA showed a specificity of 100% (CI, 95.07–100%) and sensitivity of 96.15% (CI, 80.36–99.90%) with a negative (NPV) and positive predictive value (PPV) of 98.65 and 100%, respectively. The level of agreement between RT-RPA and reference RT-qPCR assay was shown to be very high. The turnaround time of real-time RPA assay is about 10-20 times faster than the RT-qPCR, which confirms its utility in the rapid and sensitive diagnosis of WNV infection. To the best of our knowledge, this is the first report which deals with the development of real-time RT-RPA assay for simple, rapid, sensitive, and specific detection of WNV in human clinical samples. The present RT-RPA assay proves to be a powerful tool that can be used for the rapid diagnosis of a large number of patient samples in endemic settings.
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Affiliation(s)
- Priyanka Singh Tomar
- Division of Virology, Defence Research and Development Establishment, Gwalior, India
| | - Sanjay Kumar
- Division of BDTE, Defence Research and Development Establishment, Gwalior, India
| | - Sapan Patel
- School of Studies in Botany, Jiwaji University, Gwalior, India
| | - Jyoti S Kumar
- Division of Virology, Defence Research and Development Establishment, Gwalior, India
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20
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El Wahed AA, Patel P, Maier M, Pietsch C, Rüster D, Böhlken-Fascher S, Kissenkötter J, Behrmann O, Frimpong M, Diagne MM, Faye M, Dia N, Shalaby MA, Amer H, Elgamal M, Zaki A, Ismail G, Kaiser M, Corman VM, Niedrig M, Landt O, Faye O, Sall AA, Hufert FT, Truyen U, Liebert UG, Weidmann M. Suitcase Lab for Rapid Detection of SARS-CoV-2 Based on Recombinase Polymerase Amplification Assay. Anal Chem 2021; 93:2627-2634. [PMID: 33471510 PMCID: PMC7839158 DOI: 10.1021/acs.analchem.0c04779] [Citation(s) in RCA: 45] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2020] [Accepted: 01/11/2021] [Indexed: 12/30/2022]
Abstract
In March 2020, the SARS-CoV-2 virus outbreak was declared as a world pandemic by the World Health Organization (WHO). The only measures for controlling the outbreak are testing and isolation of infected cases. Molecular real-time polymerase chain reaction (PCR) assays are very sensitive but require highly equipped laboratories and well-trained personnel. In this study, a rapid point-of-need detection method was developed to detect the RNA-dependent RNA polymerase (RdRP), envelope protein (E), and nucleocapsid protein (N) genes of SARS-CoV-2 based on the reverse transcription recombinase polymerase amplification (RT-RPA) assay. RdRP, E, and N RT-RPA assays required approximately 15 min to amplify 2, 15, and 15 RNA molecules of molecular standard/reaction, respectively. RdRP and E RT-RPA assays detected SARS-CoV-1 and 2 genomic RNA, whereas the N RT-RPA assay identified only SARS-CoV-2 RNA. All established assays did not cross-react with nucleic acids of other respiratory pathogens. The RT-RPA assay's clinical sensitivity and specificity in comparison to real-time RT-PCR (n = 36) were 94 and 100% for RdRP; 65 and 77% for E; and 83 and 94% for the N RT-RPA assay. The assays were deployed to the field, where the RdRP RT-RPA assays confirmed to produce the most accurate results in three different laboratories in Africa (n = 89). The RPA assays were run in a mobile suitcase laboratory to facilitate the deployment at point of need. The assays can contribute to speed up the control measures as well as assist in the detection of COVID-19 cases in low-resource settings.
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Affiliation(s)
- Ahmed Abd El Wahed
- Institute
of Animal Hygiene and Veterinary Public Health, University of Leipzig, 04103 Leipzig, Germany
- Division
of Microbiology and Animal Hygiene, Georg-August-University, 37077 Goettingen, Germany
| | - Pranav Patel
- Expert
Molecular Diagnostics, 82256Fürstenfeldbruck, Germany
| | - Melanie Maier
- Institute
of Medical Microbiology and VirologyLeipzig
University Hospital, 04103 Leipzig, Germany
| | - Corinna Pietsch
- Institute
of Medical Microbiology and VirologyLeipzig
University Hospital, 04103 Leipzig, Germany
| | - Dana Rüster
- Institute
of Animal Hygiene and Veterinary Public Health, University of Leipzig, 04103 Leipzig, Germany
| | - Susanne Böhlken-Fascher
- Division
of Microbiology and Animal Hygiene, Georg-August-University, 37077 Goettingen, Germany
| | - Jonas Kissenkötter
- Division
of Microbiology and Animal Hygiene, Georg-August-University, 37077 Goettingen, Germany
| | - Ole Behrmann
- Institute
of Microbiology & Virology, Brandenburg Medical School, 01968 Senftenberg, Germany
| | - Michael Frimpong
- Kumasi Centre
for Collaborative Research in Tropical Medicine, Department of Molecular
Medicine, Kwame Nkrumah University of Science and Technology, Kumasi, Ghana
| | | | - Martin Faye
- Virology
Department, Institute Pasteur de Dakar, BP 220, Dakar, Senegal
| | - Ndongo Dia
- Virology
Department, Institute Pasteur de Dakar, BP 220, Dakar, Senegal
| | - Mohamed A. Shalaby
- Virology
Department, Faculty of Veterinary Medicine, Cairo University, 12211 Giza, Egypt
| | - Haitham Amer
- Virology
Department, Faculty of Veterinary Medicine, Cairo University, 12211 Giza, Egypt
| | - Mahmoud Elgamal
- Virology
Department, Faculty of Veterinary Medicine, Cairo University, 12211 Giza, Egypt
| | - Ali Zaki
- Department
of Medical Microbiology and Immunology, Faculty of Medicine, Ain Shams University, 11591 Cairo, Egypt
| | - Ghada Ismail
- Department
of Clinical Pathology, Faculty of Medicine, Ain Shams University, 11591 Cairo, Egypt
| | - Marco Kaiser
- GenExpress Gesellschaft für Proteindesign, 12103 Berlin, Germany
| | - Victor M. Corman
- Charité−Universitätsmedizin
Berlin, Institute
of Virology, Berlin, Germany
- German Centre for Infection Research (DZIF), 10117 Berlin, Germany
| | | | | | - Ousmane Faye
- Virology
Department, Institute Pasteur de Dakar, BP 220, Dakar, Senegal
| | - Amadou A. Sall
- Virology
Department, Institute Pasteur de Dakar, BP 220, Dakar, Senegal
| | - Frank T. Hufert
- Institute
of Microbiology & Virology, Brandenburg Medical School, 01968 Senftenberg, Germany
| | - Uwe Truyen
- Institute
of Animal Hygiene and Veterinary Public Health, University of Leipzig, 04103 Leipzig, Germany
| | - Uwe G. Liebert
- Institute
of Medical Microbiology and VirologyLeipzig
University Hospital, 04103 Leipzig, Germany
| | - Manfred Weidmann
- Institute
of Microbiology & Virology, Brandenburg Medical School, 01968 Senftenberg, Germany
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21
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RPA-PCR couple: an approach to expedite plant diagnostics and overcome PCR inhibitors. Biotechniques 2020; 69:270-280. [PMID: 32815734 DOI: 10.2144/btn-2020-0065] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
DNA extraction can be lengthy and sometimes ends up with amplification inhibitors. We present the potential of recombinase polymerase amplification (RPA) to replace plant DNA extraction. In our rapid 'RPA-PCR couple' concept, RPA is tuned to slower reaction kinetics to promote amplification of long targets. RPA primers amplify target and some flanking regions directly from simple plant macerates. Then PCR primers exponentially amplify the target directly from the RPA reaction. We present the coupling of RPA with conventional, TaqMan and SYBR Green PCR assays. We applied the concept to strawberry Phytophthora pathogens and the Phytophthora identification marker atp9-nad9. We found RPA-PCR couple specific, sensitive and reliable. The approach may also benefit other difficult samples such as food, feces and ancient samples.
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22
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Kissenkötter J, Böhlken-Fascher S, Forrest MS, Piepenburg O, Czerny CP, Abd El Wahed A. Recombinase polymerase amplification assays for the identification of pork and horsemeat. Food Chem 2020; 322:126759. [DOI: 10.1016/j.foodchem.2020.126759] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2019] [Revised: 09/30/2019] [Accepted: 04/05/2020] [Indexed: 12/19/2022]
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Zou Y, Mason MG, Botella JR. Evaluation and improvement of isothermal amplification methods for point-of-need plant disease diagnostics. PLoS One 2020; 15:e0235216. [PMID: 32598374 PMCID: PMC7323990 DOI: 10.1371/journal.pone.0235216] [Citation(s) in RCA: 49] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2020] [Accepted: 06/10/2020] [Indexed: 01/01/2023] Open
Abstract
A number of isothermal DNA amplification technologies claim to be ideal for point-of-need (PON) applications as they enable reactions to be performed using a single-temperature heat source (e.g. water bath). Thus, we examined several isothermal amplification methods focusing on simplicity, cost, sensitivity and reproducibility to identify the most suitable method(s) for low resource PON applications. A number of methods were found unsuitable as they either involved multiple temperature incubations, were relatively expensive or required relatively large amounts target DNA for amplification. Among the methods examined, loop-mediated isothermal amplification (LAMP) and recombinase polymerase amplification (RPA) were found to be the most suitable for PON applications as they are both single step methods that provide highly sensitive and reproducible amplifications. The speed of LAMP reactions was greatly enhanced, up to 76%, with the addition of loop primers while the presence of swarm primers and the sequestration of free magnesium ions with nucleotides also enhanced the amplification speed. In contrast, we were unable to enhance RPA's performance from the original published literature. While both RPA and LAMP have some drawbacks, either isothermal technology can reliably be used for on-site diagnostics with minimal equipment.
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Affiliation(s)
- Yiping Zou
- School of Agriculture and Food Sciences, The University of Queensland, Brisbane, QLD, Australia
| | - Michael Glenn Mason
- School of Agriculture and Food Sciences, The University of Queensland, Brisbane, QLD, Australia
| | - Jose Ramon Botella
- School of Agriculture and Food Sciences, The University of Queensland, Brisbane, QLD, Australia
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Dieng I, Hedible BG, Diagne MM, El Wahed AA, Diagne CT, Fall C, Richard V, Vray M, Weidmann M, Faye O, Sall AA, Faye O. Mobile Laboratory Reveals the Circulation of Dengue Virus Serotype I of Asian Origin in Medina Gounass (Guediawaye), Senegal. Diagnostics (Basel) 2020; 10:diagnostics10060408. [PMID: 32560073 PMCID: PMC7345902 DOI: 10.3390/diagnostics10060408] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2020] [Revised: 06/09/2020] [Accepted: 06/11/2020] [Indexed: 01/09/2023] Open
Abstract
With the growing success of controlling malaria in Sub-Saharan Africa, the incidence of fever due to malaria is in decline, whereas the proportion of patients with non-malaria febrile illness (NMFI) is increasing. Clinical diagnosis of NMFI is hampered by unspecific symptoms, but early diagnosis is a key factor for both better patient care and disease control. The aim of this study was to determine the arboviral aetiologies of NMFI in low resource settings, using a mobile laboratory based on recombinase polymerase amplification (RPA) assays. The panel of tests for this study was expanded to five arboviruses: dengue virus (DENV), zika virus (ZIKV), yellow fever virus (YFV), chikungunya virus (CHIKV), and rift valley fever virus (RVFV). One hundred and four children aged between one month and 115 months were enrolled and screened. Three of the 104 blood samples of children <10 years presented at an outpatient clinic tested positive for DENV. The results were confirmed by RT-PCR, partial sequencing, and non-structural protein 1 (NS1) antigen capture by ELISA (Biorad, France). Phylogenetic analysis of the derived DENV-1 sequences clustered them with sequences of DENV-1 isolated from Guangzhou, China, in 2014. In conclusion, this mobile setup proved reliable for the rapid identification of the causative agent of NMFI, with results consistent with those obtained in the reference laboratory’s settings.
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Affiliation(s)
- Idrissa Dieng
- Arboviruses and Hemorrhagic Fever Viruses Unit, Virology Department, Institut Pasteur de Dakar, BP220 Dakar, Senegal; (I.D.); (M.M.D.); (C.T.D.); (C.F.); (A.A.S.)
| | - Boris Gildas Hedible
- Epidemiology Unit, Institut Pasteur de Dakar, BP220 Dakar, Senegal; (B.G.H.); (V.R.); (M.V.)
| | - Moussa Moïse Diagne
- Arboviruses and Hemorrhagic Fever Viruses Unit, Virology Department, Institut Pasteur de Dakar, BP220 Dakar, Senegal; (I.D.); (M.M.D.); (C.T.D.); (C.F.); (A.A.S.)
| | - Ahmed Abd El Wahed
- Microbiology and Animal Hygiene, University of Goettingen, D-33077 Goettingen, Germany;
| | - Cheikh Tidiane Diagne
- Arboviruses and Hemorrhagic Fever Viruses Unit, Virology Department, Institut Pasteur de Dakar, BP220 Dakar, Senegal; (I.D.); (M.M.D.); (C.T.D.); (C.F.); (A.A.S.)
| | - Cheikh Fall
- Arboviruses and Hemorrhagic Fever Viruses Unit, Virology Department, Institut Pasteur de Dakar, BP220 Dakar, Senegal; (I.D.); (M.M.D.); (C.T.D.); (C.F.); (A.A.S.)
| | - Vicent Richard
- Epidemiology Unit, Institut Pasteur de Dakar, BP220 Dakar, Senegal; (B.G.H.); (V.R.); (M.V.)
| | - Muriel Vray
- Epidemiology Unit, Institut Pasteur de Dakar, BP220 Dakar, Senegal; (B.G.H.); (V.R.); (M.V.)
| | - Manfred Weidmann
- Institute of Aquaculture, University of Stirling, Scotland FK9 4LA, UK;
| | - Ousmane Faye
- Arboviruses and Hemorrhagic Fever Viruses Unit, Virology Department, Institut Pasteur de Dakar, BP220 Dakar, Senegal; (I.D.); (M.M.D.); (C.T.D.); (C.F.); (A.A.S.)
- Correspondence: (O.F.); (O.F.)
| | - Amadou Alpha Sall
- Arboviruses and Hemorrhagic Fever Viruses Unit, Virology Department, Institut Pasteur de Dakar, BP220 Dakar, Senegal; (I.D.); (M.M.D.); (C.T.D.); (C.F.); (A.A.S.)
| | - Oumar Faye
- Arboviruses and Hemorrhagic Fever Viruses Unit, Virology Department, Institut Pasteur de Dakar, BP220 Dakar, Senegal; (I.D.); (M.M.D.); (C.T.D.); (C.F.); (A.A.S.)
- Correspondence: (O.F.); (O.F.)
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Development and evaluation of a rapid detection assay for severe fever with thrombocytopenia syndrome virus based on reverse-transcription recombinase polymerase amplification. Mol Cell Probes 2020; 52:101580. [PMID: 32330556 PMCID: PMC7172814 DOI: 10.1016/j.mcp.2020.101580] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2020] [Revised: 04/06/2020] [Accepted: 04/18/2020] [Indexed: 12/03/2022]
Abstract
Rapid detection of severe fever with thrombocytopenia syndrome virus (SFTSV) is crucial for its control and surveillance. In this study, a rapid isothermal real-time reverse-transcription recombinase polymerase amplification (RT-RPA) assay was developed for the detection of SFTSV. The detection limit at 95% probability was 241 copies per reaction. A test of 120 serum samples of suspected severe fever with thrombocytopenia syndrome (SFTS) patients revealed that the sensitivity and specificity of the RT-RPA assay was approximately 96.00% (95%CI: 80.46%–99.79%) and 98.95% (95% CI: 94.28%–99.95%), respectively; the kappa value was 0.9495 (P<0.001). The Bland-Altman analysis showed that 87.50% of the different data points were located within the 95% limits of agreement, indicating a good correlation between the results from RT-RPA assays and those of RT-qPCR assays. In conclusion, the rapid and efficient RT-RPA assay can be a promising candidate for point-of-care detection method of SFTSV. A RT-RPA assay was developed to detect SFTSV RNA isothermally. The assay can rapidly produce a result in 15 min at 39 °C. The detection limit of the assay is 241 RNA sequences. The results of RT-RPA compare well with RT-qPCR. The RT-RPA assay may be used for field detection of SFTSV in resource-limited settings.
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Broeders S, Garlant L, Fraiture MA, Vandermassen E, Suin V, Vanhomwegen J, Dupont-Rouzeyrol M, Rousset D, Van Gucht S, Roosens N. A new multiplex RT-qPCR method for the simultaneous detection and discrimination of Zika and chikungunya viruses. Int J Infect Dis 2020; 92:160-170. [PMID: 31884173 PMCID: PMC7129992 DOI: 10.1016/j.ijid.2019.12.028] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2019] [Revised: 12/11/2019] [Accepted: 12/20/2019] [Indexed: 12/19/2022] Open
Abstract
OBJECTIVE The re-emergence and spread of tropical viruses to new areas has raised a wave of concern worldwide. In order to treat patients at an early stage and prevent the diffusion of an outbreak, early diagnosis, and therefore fast and adequate detection, is needed. To this end, a multiplex reverse transcription real-time polymerase chain reaction TaqMan method was designed to detect Zika (ZIKV) and chikungunya (CHIKV) viruses simultaneously. METHODS Two methods targeting different genome segments were selected from the literature for each virus. These were adapted for high genome coverage and combined in a four-plex assay that was thoroughly validated in-house. The SCREENED tool was used to evaluate the sequence coverage of the method. RESULTS The full validation approach showed that the new four-plex method allows the specific and sensitive identification and discrimination of ZIKV and CHIKV in routine samples. The combination of two targets per virus allowing almost 100% coverage of about 500 genomes is shown for the first time. CONCLUSIONS PCR is a reliable user-friendly technique that can be applied in remote areas. Such multiplex methods enable early and efficient diagnosis, leading to rapid treatment and effective confinement in outbreak cases. They may also serve as an aid for surveillance, and the full validation permits easy method-transfer allowing worldwide harmonization.
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Affiliation(s)
- Sylvia Broeders
- Sciensano, Transversal Activities in Applied Genomics, J. Wytsmanstraat 14, 1050 Brussels, Belgium.
| | - Linda Garlant
- Sciensano, Transversal Activities in Applied Genomics, J. Wytsmanstraat 14, 1050 Brussels, Belgium.
| | - Marie-Alice Fraiture
- Sciensano, Transversal Activities in Applied Genomics, J. Wytsmanstraat 14, 1050 Brussels, Belgium.
| | - Els Vandermassen
- Sciensano, Transversal Activities in Applied Genomics, J. Wytsmanstraat 14, 1050 Brussels, Belgium.
| | - Vanessa Suin
- Sciensano, Viral Diseases, J. Wytsmanstraat 14, 1050 Brussels, Belgium.
| | - Jessica Vanhomwegen
- Institut Pasteur France, Cellule d'Intervention Biologique d'Urgence (CIBU), 25-28 rue du docteur Roux, 75724 Paris Cedex 15, France.
| | - Myrielle Dupont-Rouzeyrol
- Institut Pasteur de Nouvelle-Calédonie, URE Dengue et Arboviroses, 11 ave P. Doumer, BP 61, 98845 Nouméa Cedex, New Caledonia.
| | - Dominique Rousset
- Institut Pasteur de la Guyane, Laboratoire de Virologie, 23 avenue Pasteur - BP 6010, 97306 Cayenne Cedex, Guyana.
| | - Steven Van Gucht
- Sciensano, Viral Diseases, J. Wytsmanstraat 14, 1050 Brussels, Belgium.
| | - Nancy Roosens
- Sciensano, Transversal Activities in Applied Genomics, J. Wytsmanstraat 14, 1050 Brussels, Belgium.
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Weidmann M, Faye O, Faye O, Abd El Wahed A, Patel P, Batejat C, Manugerra JC, Adjami A, Niedrig M, Hufert FT, Sall AA. Development of Mobile Laboratory for Viral Hemorrhagic Fever Detection in Africa. J Infect Dis 2019; 218:1622-1630. [PMID: 29917112 PMCID: PMC6173574 DOI: 10.1093/infdis/jiy362] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2018] [Accepted: 06/12/2018] [Indexed: 11/22/2022] Open
Abstract
Background A mobile laboratory transportable on commercial flights was developed to enable local response to viral hemorrhagic fever outbreaks. Methods The development progressed from use of mobile real-time reverse-transcription polymerase chain reaction to mobile real-time recombinase polymerase amplification. In this study, we describe various stages of the mobile laboratory development. Results A brief overview of mobile laboratory deployments, which culminated in the first on-site detection of Ebola virus disease (EVD) in March 2014, and their successful use in a campaign to roll back EVD cases in Conakry in the West Africa Ebola virus outbreak are described. Conclusions The developed mobile laboratory successfully enabled local teams to perform rapid disgnostic testing for viral hemorrhagic fever.
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Affiliation(s)
- Manfred Weidmann
- Institute of Aquaculture, University of Stirling, Scotland, United Kingdom
- Correspondence: M. Weidmann, Dr. rer. nat., University of Stirling, Institute of Aquaculture, Stirling FK9 4LA, Scotland, United Kingdom ()
| | - Ousmane Faye
- Arbovirus Unit, Pasteur Institute, Dakar, Senegal
| | - Oumar Faye
- Arbovirus Unit, Pasteur Institute, Dakar, Senegal
| | - Ahmed Abd El Wahed
- Unit of Infection Models, German Primate Center, Goettingen, Germany
- Division of Microbiology and Animal Hygiene, University of Goettingen, Germany
| | | | - Christophe Batejat
- Laboratory for Urgent Response to Biological Threats (CIBU), Environment and Infectious Risks Unit, Institut Pasteur, Paris, France
| | - Jean Claude Manugerra
- Laboratory for Urgent Response to Biological Threats (CIBU), Environment and Infectious Risks Unit, Institut Pasteur, Paris, France
| | - Aimee Adjami
- Multi Disease Surveillance Centre WHO, Ougadougou, Burkina Faso
| | | | - Frank T Hufert
- Institute of Microbiology and Virology, Brandenburg Medical School Fontane (and Member of the Faculty of Environment and Natural Sciences of B-TU Senftenberg site), Senftenberg, Brandenburg, Germany
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Davi SD, Kissenkötter J, Faye M, Böhlken-Fascher S, Stahl-Hennig C, Faye O, Faye O, Sall AA, Weidmann M, Ademowo OG, Hufert FT, Czerny CP, Abd El Wahed A. Recombinase polymerase amplification assay for rapid detection of Monkeypox virus. Diagn Microbiol Infect Dis 2019; 95:41-45. [PMID: 31126795 PMCID: PMC9629024 DOI: 10.1016/j.diagmicrobio.2019.03.015] [Citation(s) in RCA: 68] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2018] [Revised: 03/04/2019] [Accepted: 03/28/2019] [Indexed: 12/17/2022]
Abstract
In this study, a rapid method for the detection of Central and West Africa clades of Monkeypox virus (MPXV) using recombinase polymerase amplification (RPA) assay targeting the G2R gene was developed. MPXV, an Orthopoxvirus, is a zoonotic dsDNA virus, which is listed as a biothreat agent. RPA was operated at a single constant temperature of 42°C and produced results within 3 to 10 minutes. The MPXV-RPA-assay was highly sensitive with a limit of detection of 16 DNA molecules/μl. The clinical performance of the MPXV-RPA-assay was tested using 47 sera and whole blood samples from humans collected during the recent MPXV outbreak in Nigeria as well as 48 plasma samples from monkeys some of which were experimentally infected with MPXV. The specificity of the MPXV-RPA-assay was 100% (50/50), while the sensitivity was 95% (43/45). This new MPXV-RPA-assay is fast and can be easily utilised at low resource settings using a solar powered mobile suitcase laboratory.
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Affiliation(s)
- Saskia Dede Davi
- Institute of Microbiology and Virology, Brandenburg Medical School Theodor Fontane, Senftenberg, Germany
| | - Jonas Kissenkötter
- Department of Animal Sciences, Microbiology and Animal Hygiene, Georg-August-University of Goettingen, Goettingen, Germany
| | | | - Susanne Böhlken-Fascher
- Department of Animal Sciences, Microbiology and Animal Hygiene, Georg-August-University of Goettingen, Goettingen, Germany
| | | | - Oumar Faye
- Institute Pasteur de Dakar, Dakar, Senegal
| | | | | | - Manfred Weidmann
- Institute of Aquaculture, University of Stirling, Stirling, Scotland, United Kingdom
| | - Olusegun George Ademowo
- Institute for Advanced Medical Research and Training, College of Medicine, University of Ibadan, Ibadan, Nigeria
| | - Frank T Hufert
- Institute of Microbiology and Virology, Brandenburg Medical School Theodor Fontane, Senftenberg, Germany
| | - Claus-Peter Czerny
- Department of Animal Sciences, Microbiology and Animal Hygiene, Georg-August-University of Goettingen, Goettingen, Germany
| | - Ahmed Abd El Wahed
- Department of Animal Sciences, Microbiology and Animal Hygiene, Georg-August-University of Goettingen, Goettingen, Germany.
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Coertse J, Weyer J, Nel LH, Markotter W. Reverse transcription recombinase polymerase amplification assay for rapid detection of canine associated rabies virus in Africa. PLoS One 2019; 14:e0219292. [PMID: 31276479 PMCID: PMC6611627 DOI: 10.1371/journal.pone.0219292] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2019] [Accepted: 06/20/2019] [Indexed: 12/22/2022] Open
Abstract
Rabies is a neglected disease mostly affecting the developing world. Accurate and reliable diagnostic and surveillance data forms the foundation for the formulation and monitoring of control strategies. Although various sensitive and specific tests are available for detection of rabies virus, implementation of these tests in low-resource settings are challenging and remains limited. In this study, we describe the developed of a reverse transcription recombinase polymerase amplification assay for the detection of rabies virus. The analytical sensitivity of this assay was determined to be 562 RNA copies and was performed in 20 minutes. The diagnostic sensitivity of the RT-RPA was 100% for detection of rabies virus in field samples. In conclusion, the RT-RPA assay allowed for very quick and sensitive detection of rabies virus and could be adapted for use in low-source settings.
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Affiliation(s)
- Jessica Coertse
- Centre for Viral Zoonoses, Department of Medical Virology, Faculty of Health Sciences, University of Pretoria, Pretoria, South Africa
| | - Jacqueline Weyer
- Centre for Viral Zoonoses, Department of Medical Virology, Faculty of Health Sciences, University of Pretoria, Pretoria, South Africa
- The Centre for Emerging Zoonotic and Parasitic Diseases, National Institute for Communicable Diseases, a Division of the National Health Laboratory Services, Sandringham, South Africa
| | - Louis H. Nel
- Centre for Viral Zoonoses, Department of Biochemistry, Genetics and Microbiology, Faculty of Natural and Agricultural Sciences, University of Pretoria, Pretoria, South Africa
| | - Wanda Markotter
- Centre for Viral Zoonoses, Department of Medical Virology, Faculty of Health Sciences, University of Pretoria, Pretoria, South Africa
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Jung L, Hogan ME, Sun Y, Liang BM, Hayward JA. Rapid authentication of pharmaceuticals via DNA tagging and field detection. PLoS One 2019; 14:e0218314. [PMID: 31194827 PMCID: PMC6564018 DOI: 10.1371/journal.pone.0218314] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2018] [Accepted: 05/26/2019] [Indexed: 11/23/2022] Open
Abstract
A small PCR-generated DNA fragment was introduced into a pharmaceutical grade ink as a molecular taggant, and the DNA tagged ink was delivered onto the surface of capsules by standard high-speed offset printing. The amount of DNA in the ink on each capsule is roughly 10−12 fold lower than that allowed as safe by the United States Food and Drug Administration (FDA) and the WHO with regards to acceptable limits of residual DNA. The printed ink on the capsule surface was sampled by swabbing, followed by direct analysis of the DNA-swab complex, without subsequent DNA purification. It was shown that DNA recovered from the ink by swabbing was suitable for PCR-CE analysis—a widely used method in forensic science and was also suitable for qPCR and isothermal DNA amplification, when coupled with portable devices similar to those used for environmental sampling and food safety testing. The data set a precedent: A small DNA fragment could be introduced as an excipient into a pharmaceutical application, and thereafter tracked through the pharmaceutical supply chain via forensic DNA authentication.
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Affiliation(s)
- Lawrence Jung
- Applied DNA Sciences, Inc. Stony Brook, New York, United States of America
- * E-mail: (MEH); (LJ)
| | - Michael E. Hogan
- Applied DNA Sciences, Inc. Stony Brook, New York, United States of America
- * E-mail: (MEH); (LJ)
| | - Yuhua Sun
- Applied DNA Sciences, Inc. Stony Brook, New York, United States of America
| | | | - James A. Hayward
- Applied DNA Sciences, Inc. Stony Brook, New York, United States of America
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Abstract
Chikungunya virus (CHIKV) is an alphavirus that is primarily transmitted by Aedes species mosquitoes. Though reports of an illness consistent with chikungunya date back over 200 years, CHIKV only gained worldwide attention during a massive pandemic that began in East Africa in 2004. Chikungunya, the clinical illness caused by CHIKV, is characterized by a rapid onset of high fever and debilitating joint pain, though in practice, etiologic confirmation of CHIKV requires the availability and use of specific laboratory diagnostics. Similar to infections caused by other arboviruses, CHIKV infections are most commonly detected with a combination of molecular and serological methods, though cell culture and antigen detection are reported. This review provides an overview of available CHIKV diagnostics and highlights aspects of basic virology and epidemiology that pertain to viral detection. Although the number of chikungunya cases has decreased since 2014, CHIKV has become endemic in countries across the tropics and will continue to cause sporadic outbreaks in naive individuals. Consistent access to accurate diagnostics is needed to detect individual cases and initiate timely responses to new outbreaks.
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Abstract
Viruses, which are the most abundant biological entities on the planet, have been regarded as the "dark matter" of biology in the sense that despite their ubiquity and frequent presence in large numbers, their detection and analysis are not always straightforward. The majority of them are very small (falling under the limit of 0.5 μm), and collectively, they are extraordinarily diverse. In fact, the majority of the genetic diversity on the planet is found in the so-called virosphere, or the world of viruses. Furthermore, the most frequent viral agents of disease in humans display an RNA genome, and frequently evolve very fast, due to the fact that most of their polymerases are devoid of proofreading activity. Therefore, their detection, genetic characterization, and epidemiological surveillance are rather challenging. This review (part of the Curated Collection on Advances in Molecular Epidemiology of Infectious Diseases) describes many of the methods that, throughout the last few decades, have been used for viral detection and analysis. Despite the challenge of having to deal with high genetic diversity, the majority of these methods still depend on the amplification of viral genomic sequences, using sequence-specific or sequence-independent approaches, exploring thermal profiles or a single nucleic acid amplification temperature. Furthermore, viral populations, and especially those with RNA genomes, are not usually genetically uniform but encompass swarms of genetically related, though distinct, viral genomes known as viral quasispecies. Therefore, sequence analysis of viral amplicons needs to take this fact into consideration, as it constitutes a potential analytic problem. Possible technical approaches to deal with it are also described here. *This article is part of a curated collection.
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Dengue and Chikungunya Infections in Children : Guest Editor: Bhim S. Pandhi. Indian J Pediatr 2019; 86:287-295. [PMID: 30511272 DOI: 10.1007/s12098-018-2794-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/06/2018] [Accepted: 09/07/2018] [Indexed: 12/15/2022]
Abstract
Dengue and Chikungunya are two important mosquito-borne acute febrile illnesses in children. With increased urbanization and newer strains of chikungunya virus with improved transmission with Aedes albopictus, the at-risk population for these infections has greatly increased. Dengue fever has been classified by WHO as dengue with/ without warning signs and severe dengue. Severe dengue is associated with hemorrhagic manifestations, hypovolemia and hypotension secondary to third space loss due to capillary leak or severe end organ dysfunction. NS1 antigen detection and dengue polymerase chain reaction, [polymerase chain reaction (PCR during first 5 d)] and IgM for dengue (6th day of fever onwards) are commonly utilized diagnostic tests. Appropriate fluid therapy with timely tapering of intravenous fluid rate with hematocrit, treatment of hemorrhagic manifestations and clinical monitoring are the mainstay of dengue treatment. Chikungunya has less severe course with shorter febrile phase with prominent and persistent joint symptoms. PCR and IgM against chikungunya are appropriate investigations. Treatment is supportive for chikungunya infection with appropriate joint pain relief.
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Nelson MM, Waldron CL, Bracht JR. Rapid molecular detection of macrolide resistance. BMC Infect Dis 2019; 19:144. [PMID: 30755177 PMCID: PMC6373131 DOI: 10.1186/s12879-019-3762-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2018] [Accepted: 01/30/2019] [Indexed: 12/23/2022] Open
Abstract
BACKGROUND Emerging antimicrobial resistance is a significant threat to human health. However, methods for rapidly diagnosing antimicrobial resistance generally require multi-day culture-based assays. Macrolide efflux gene A, mef(A), provides resistance against erythromycin and azithromycin and is known to be laterally transferred among a wide range of bacterial species. METHODS We use Recombinase Polymerase Assay (RPA) to detect the antimicrobial resistance gene mef(A) from raw lysates without nucleic acid purification. To validate these results we performed broth dilution assays to assess antimicrobial resistance to erythromycin and ampicillin (a negative control). RESULTS We validate the detection of mef(A) in raw lysates of Streptococcus pyogenes, S. pneumoniae, S. salivarius, and Enterococcus faecium bacterial lysates within 7-10 min of assay time. We show that detection of mef(A) accurately predicts real antimicrobial resistance assessed by traditional culture methods, and that the assay is robust to high levels of spiked-in non-specific nucleic acid contaminant. The assay was unaffected by single-nucleotide polymorphisms within divergent mef(A) gene sequences, strengthening its utility as a robust diagnostic tool. CONCLUSIONS This finding opens the door to implementation of rapid genomic diagnostics in a clinical setting, while providing researchers a rapid, cost-effective tool to track antibiotic resistance in both pathogens and commensal strains.
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Affiliation(s)
- Megan M. Nelson
- Department of Biology, American University, Washington, DC 20016 USA
| | | | - John R. Bracht
- Department of Biology, American University, Washington, DC 20016 USA
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35
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Li J, Macdonald J, von Stetten F. Review: a comprehensive summary of a decade development of the recombinase polymerase amplification. Analyst 2019; 144:31-67. [DOI: 10.1039/c8an01621f] [Citation(s) in RCA: 240] [Impact Index Per Article: 48.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
RPA is a versatile complement or replacement of PCR, and now is stepping into practice.
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Affiliation(s)
- Jia Li
- Laboratory for MEMS Applications
- IMTEK – Department of Microsystems Engineering
- University of Freiburg
- 79110 Freiburg
- Germany
| | - Joanne Macdonald
- Inflammation and Healing Research Cluster
- Genecology Research Centre
- School of Science and Engineering
- University of the Sunshine Coast
- Australia
| | - Felix von Stetten
- Laboratory for MEMS Applications
- IMTEK – Department of Microsystems Engineering
- University of Freiburg
- 79110 Freiburg
- Germany
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Abstract
Chikungunya (CHIK) is an arboviral infection caused by the chikungunya virus. An unusual feature of CHIK is its long periods of quiescence followed by an epidemic of devastating severity that can involve millions of people. Manifestations of CHIK range from a mild self-limiting febrile illness with arthralgia and rash to crippling acute and lingering debilitating arthritis. In about 10–60% of patients, musculoskeletal symptoms may persist for up to 3–5 years. Management is mainly symptomatic, with analgesics, antipyretics and non-steroidal anti-inflammatory agents. Ecological changes together with alterations in the viral genome facilitate the development of newer variants with greater pathogenicity, a matter of great concern. The social and economic burdens to a society as a result of CHIK epidemics have generated a considerable interest in the scientific community to decipher the reasons underlying myriad manifestations and to develop management strategies for tackling the menace of CHIK across the globe.
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Sensitive and Specific Recombinase Polymerase Amplification Assays for Fast Screening, Detection, and Identification of Bacillus anthracis in a Field Setting. Appl Environ Microbiol 2018; 84:AEM.00506-18. [PMID: 29602786 PMCID: PMC5960963 DOI: 10.1128/aem.00506-18] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2018] [Accepted: 03/26/2018] [Indexed: 01/02/2023] Open
Abstract
Four isothermal recombinase polymerase amplification (RPA) assays were developed for fast in-field identification of Bacillus anthracis The RPA assays targeted three specific sequences (i.e., the BA_5345 chromosomal marker, the lethal factor lef [from pXO1], and the capsule-biosynthesis-related capA [from pXO2]) and a conserved sequence in the adenylate cyclase gene (adk) for the Bacillus cereus group. B. anthracis-specific RPA assays were tested first with purified genomic DNAs (n = 60), including 11 representatives of B. anthracis, and then with soil (n = 8) and white powder (n = 8) samples spiked with inactivated B. anthracis spores and/or other biological agents. The RPA assays were also tested in another laboratory facility, which blindly provided DNA and lysate samples (n = 30, including 20 B. anthracis strains). RPA assays displayed 100% specificity and sensitivity. The hands-off turnaround times at 42°C ranged from 5 to 6 min for 102 genomic copies. The analytical sensitivity of each RPA assay was ∼10 molecules per reaction. In addition, the BA_5345 and adk RPA assays were assessed under field conditions with a series of surface swabs (n = 13, including 11 swabs contaminated with B. thuringiensis spores) that were blindly brought to the field laboratory by a chemical, biological, radiological, and nuclear (CBRN) sampling team. None of the 13 samples, except the control, tested positive for B. anthracis, and all samples that had been harvested from spore-contaminated surfaces tested positive with the adk RPA assay. All three B. anthracis-specific RPA assays proved suitable for rapid and reliable identification of B. anthracis and therefore could easily be used by first responders under field conditions to quickly discriminate between a deliberate release of B. anthracis spores and a hoax attack involving white powder.IMPORTANCE In recent decades, particularly following the 11 September 2001 and Amerithrax attacks, the world has experienced attempts to sow panic and chaos in society through thousands of white-powder copycats using household powders to mimic real bioterrorism attacks. In such circumstances, field-deployable detection methods are particularly needed to screen samples collected from the scene. The aim is to test the samples directly using a fast and reliable assay for detection of the presence of B. anthracis While this would not preclude further confirmatory tests from being performed in reference laboratories, it would bring useful, timely, and relevant information to local crisis managers and help them make appropriate decisions without having to wait for quantitative PCR results (with turnaround times of a few hours) or phenotypic identification and sequencing (with turnaround times of a few days). In the current investigation, we developed a set of isothermal RPA assays for the rapid screening and identification of B. anthracis in powders and soil samples, with the purpose of discriminating a deliberate release of B. anthracis spores from a hoax attack involving white powder; this would also apply to dispersion by spraying of aerosolized forms of B. anthracis Further work is now ongoing to confirm the first observations and validate the on-site use of these assays by first responders.
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Lopez-Jimena B, Wehner S, Harold G, Bakheit M, Frischmann S, Bekaert M, Faye O, Sall AA, Weidmann M. Development of a single-tube one-step RT-LAMP assay to detect the Chikungunya virus genome. PLoS Negl Trop Dis 2018; 12:e0006448. [PMID: 29813065 PMCID: PMC5973553 DOI: 10.1371/journal.pntd.0006448] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2016] [Accepted: 04/12/2018] [Indexed: 12/17/2022] Open
Abstract
BACKGROUND A single-tube one-step real-time reverse transcription loop-mediated isothermal amplification (RT-LAMP) assay for rapid detection of chikungunya virus (CHIKV) targeting the conserved 6K-E1 target region was developed. The assay was validated with sera collected from a CHIKV outbreak in Senegal in 2015. METHODOLOGY/PRINCIPAL FINDINGS A novel design approach by combining Principal Component Analysis and phylogenetic analysis of 110 available CHIKV sequences and the LAMP oligonucleotide design software LAVA was used. The assay was evaluated with an External Quality Assessment panel from the European Network for Diagnostics of "Imported" Viral Diseases and was shown to be sensitive and specific and did not cross-detect other arboviruses. The limit of detection as determined by probit analysis, was 163 molecules, and 100% reproducibility in the assays was obtained for 103 molecules (7/8 repetitions were positive for 102 molecules). The assay was validated using 35 RNA samples extracted from sera, and results were compared with those obtained by quantitative RT-PCR carried out at the Institut Pasteur Dakar, demonstrating that the RT-LAMP is 100% sensitive and 80% specific, with a positive predictive value of 97% and negative predictive value of 100%. CONCLUSIONS/SIGNIFICANCE The RT-LAMP appeared to show superior performance with material stored for months compared to qRT-PCR and can be therefore recommended for use in infrastructures with poor settings.
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Affiliation(s)
- Benjamin Lopez-Jimena
- Institute of Aquaculture, School of Natural Sciences, University of Stirling, Stirling, Scotland, United Kingdom
| | - Stefanie Wehner
- Institute of Aquaculture, School of Natural Sciences, University of Stirling, Stirling, Scotland, United Kingdom
| | - Graham Harold
- Institute of Aquaculture, School of Natural Sciences, University of Stirling, Stirling, Scotland, United Kingdom
| | | | | | - Michaël Bekaert
- Institute of Aquaculture, School of Natural Sciences, University of Stirling, Stirling, Scotland, United Kingdom
| | - Oumar 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
| | - Manfred Weidmann
- Institute of Aquaculture, School of Natural Sciences, University of Stirling, Stirling, Scotland, United Kingdom
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Development of a pan-rickettsial molecular diagnostic test based on recombinase polymerase amplification assay. Anal Biochem 2018; 544:29-33. [DOI: 10.1016/j.ab.2017.12.018] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2017] [Revised: 12/11/2017] [Accepted: 12/12/2017] [Indexed: 01/15/2023]
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Affiliation(s)
- Shefali Khanna Sharma
- Unit of Clinical Immunology and Rheumatology; Department of Internal Medicine; Postgraduate Institute of Medical Education and Research; Chandigarh India
| | - Sanjay Jain
- Unit of Clinical Immunology and Rheumatology; Department of Internal Medicine; Postgraduate Institute of Medical Education and Research; Chandigarh India
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Higgins O, Clancy E, Forrest MS, Piepenburg O, Cormican M, Boo TW, O'Sullivan N, McGuinness C, Cafferty D, Cunney R, Smith TJ. Duplex recombinase polymerase amplification assays incorporating competitive internal controls for bacterial meningitis detection. Anal Biochem 2018; 546:10-16. [PMID: 29378166 DOI: 10.1016/j.ab.2018.01.016] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2017] [Revised: 01/16/2018] [Accepted: 01/18/2018] [Indexed: 10/18/2022]
Abstract
Recombinase polymerase amplification (RPA) is an isothermal nucleic acid amplification technology that provides rapid and robust infectious disease pathogen detection, ideal for point-of-care (POC) diagnostics in disease-prevalent low-resource countries. We have developed and evaluated three duplex RPA assays incorporating competitive internal controls for the detection of leading bacterial meningitis pathogens. Streptococcus pneumoniae, Neisseria meningitidis and Haemophilus influenzae singleplex RPA assays were initially developed and evaluated, demonstrating 100% specificity with limits of detection of 4.1, 8.5 and 3.9 genome copies per reaction, respectively. Each assay was further developed into internally controlled duplex RPA assays via the incorporation of internal amplification control templates. Clinical performance of each internally controlled duplex RPA assay was evaluated by testing 64 archived PCR-positive clinical samples. Compared to real-time PCR, all duplex RPA assays demonstrated 100% diagnostic specificity, with diagnostic sensitivities of 100%, 86.3% and 100% for the S. pneumoniae, N. meningitidis and H. influenzae assays, respectively. This study details the first report of internally controlled duplex RPA assays for the detection of bacterial meningitis pathogens: S. pneumoniae, N. meningitidis and H. influenzae. We have successfully demonstrated the clinical diagnostic utility of each duplex RPA assay, introducing effective diagnostic technology for POC bacterial meningitis identification in disease-prevalent developing countries.
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Affiliation(s)
- Owen Higgins
- Molecular Diagnostics Research Group, School of Natural Sciences and National Centre for Biomedical Engineering Science, National University of Ireland, Galway, Ireland.
| | - Eoin Clancy
- Molecular Diagnostics Research Group, School of Natural Sciences and National Centre for Biomedical Engineering Science, National University of Ireland, Galway, Ireland
| | | | | | - Martin Cormican
- School of Medicine, Galway University Hospital, National University of Ireland, Galway, Ireland
| | - Teck Wee Boo
- School of Medicine, Galway University Hospital, National University of Ireland, Galway, Ireland
| | - Nicola O'Sullivan
- Irish Meningitis and Sepsis Reference Laboratory, Temple Street Children's University Hospital, Temple Street, Dublin, Ireland
| | - Claire McGuinness
- Irish Meningitis and Sepsis Reference Laboratory, Temple Street Children's University Hospital, Temple Street, Dublin, Ireland
| | - Deirdre Cafferty
- Irish Meningitis and Sepsis Reference Laboratory, Temple Street Children's University Hospital, Temple Street, Dublin, Ireland
| | - Robert Cunney
- Irish Meningitis and Sepsis Reference Laboratory, Temple Street Children's University Hospital, Temple Street, Dublin, Ireland
| | - Terry J Smith
- Molecular Diagnostics Research Group, School of Natural Sciences and National Centre for Biomedical Engineering Science, National University of Ireland, Galway, Ireland
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Cunha MDP, Santos CAD, Neto DFDL, Schanoski AS, Pour SZ, Passos SD, Souza MSFD, Costa DD, Zanotto PMDA. Outbreak of chikungunya virus in a vulnerable population of Sergipe, Brazil-A molecular and serological survey. J Clin Virol 2017; 97:44-49. [PMID: 29100064 DOI: 10.1016/j.jcv.2017.10.015] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2017] [Revised: 10/03/2017] [Accepted: 10/24/2017] [Indexed: 11/15/2022]
Abstract
BACKGROUND Chikungunya virus (CHIKV) is a re-emerging arbovirus that is causing outbreaks in several countries of the Americas. The virus was introduced in Brazil in 2014, and since then, several Brazilian states have notified autochthonous cases. OBJECTIVES Provide additional evidence on a CHIKV outbreak and an outline of the laboratory and clinical profile of symptomatic patients in Sergipe, Brazil. STUDY DESIGN In February 2016, we collected 142 serum samples from symptomatic patients for arboviruses in Sergipe, Brazil. All samples were submitted to qRT-PCR for the emerging arboviruses circulating in Brazil - ZIKV, CHIKV, and DENV - and later submitted to the immunoenzymatic assay. RNA positive samples were randomly selected and sequenced for characterization of the genotype involved in the outbreak. RESULTS Our study had 75.35% (107/142) positivity for CHIKV infection, with all age groups and genera being equally infected. The virus was identified in 11 of the 13 cities studied in that state, including the ECSA genotype. Importantly, fever was the only statistically significant symptoms for CHIKV infection (p<0.05), while asthenia was significantly associated with symptomatic patients that were CHIKV-negative (p<0.05). CONCLUSIONS Our findings support the importance of fever as a clinical marker and contribute to molecular and serological surveillance data, which may help in the understanding of CHIKV circulation, emergence and clinical description.
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Affiliation(s)
- Marielton Dos Passos Cunha
- Laboratory of Molecular Evolution and Bioinformatics, Department of Microbiology, Biomedical Sciences Institute, University of São Paulo, São Paulo, Brazil
| | - Cliomar Alves Dos Santos
- Health Foundation Parreiras Horta (FSPH), Central Laboratory of Public Health (LACEN/SE), State Secretary for Health, Sergipe, Brazil
| | - Daniel Ferreira de Lima Neto
- Laboratory of Molecular Evolution and Bioinformatics, Department of Microbiology, Biomedical Sciences Institute, University of São Paulo, São Paulo, Brazil
| | | | - Shahab Zaki Pour
- Laboratory of Molecular Evolution and Bioinformatics, Department of Microbiology, Biomedical Sciences Institute, University of São Paulo, São Paulo, Brazil
| | | | | | - Danuza Duarte Costa
- Health Foundation Parreiras Horta (FSPH), Central Laboratory of Public Health (LACEN/SE), State Secretary for Health, Sergipe, Brazil
| | - Paolo Marinho de Andrade Zanotto
- Laboratory of Molecular Evolution and Bioinformatics, Department of Microbiology, Biomedical Sciences Institute, University of São Paulo, São Paulo, Brazil.
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Abstract
Recombinase polymerase amplification (RPA) is a highly sensitive and selective isothermal amplification technique, operating at 37-42°C, with minimal sample preparation and capable of amplifying as low as 1-10 DNA target copies in less than 20 min. It has been used to amplify diverse targets, including RNA, miRNA, ssDNA and dsDNA from a wide variety of organisms and samples. An ever increasing number of publications detailing the use of RPA are appearing and amplification has been carried out in solution phase, solid phase as well as in a bridge amplification format. Furthermore, RPA has been successfully integrated with different detection strategies, from end-point lateral flow strips to real-time fluorescent detection amongst others. This review focuses on the different methodologies and advances related to RPA technology, as well as highlighting some of the advantages and drawbacks of the technique.
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Affiliation(s)
- Ivan Magriñá Lobato
- INTERFIBIO Consolidated Research Group, Departament d'Enginyeria Química, Universitat Rovira i Virgili, Països Catalans, 26, 43007, Tarragona, Spain
| | - Ciara K O'Sullivan
- INTERFIBIO Consolidated Research Group, Departament d'Enginyeria Química, Universitat Rovira i Virgili, Països Catalans, 26, 43007, Tarragona, Spain.,Institució Catalana de Recerca i Estudis Avançats, Passeig Lluís Companys, 23, 08010 Barcelona, Spain
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Ullerich L, Campbell S, Krieg-Schneider F, Bürsgens F, Stehr J. Ultra-fast PCR technologies for point-of-care testing. ACTA ACUST UNITED AC 2017. [DOI: 10.1515/labmed-2017-0093] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
AbstractThis contribution presents exemplary approaches on how to improve the most time-limiting part of polymerase chain reactions, the heating and cooling steps. A new technology, Laser PCR
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Abstract
Chikungunya virus (CHIKV) has been involved in epidemics in African and Asian subcontinents and, of late, has transcended to affect the Americas. Aedes aegypti and Aedes albopictus are the major vectors for CHIKV infection, which results in dissemination of virus to various vital organs. Entry of virus into these tissues causes infiltration of innate immune cells, monocytes, macrophages, neutrophils, natural killer cells, and adaptive immune cells. Macrophages bearing the replicating virus, in turn, secrete pro-inflammatory cytokines IL-1β, TNF-α, and IL-17. Together, this pro-inflammatory milieu induces osteoclastogenesis, bone loss, and erosion. CHIKV is characterized by fever, headache, myalgia, rash, and symmetric polyarthritis, which is generally self-limiting. In a subset of cases, however, musculoskeletal symptoms may persist for up to 3-5 years. Viral culture and isolation from blood cells of infected patients are the gold standards for diagnosis of CHIKV. In routine practice, however, assays for anti-CHIKV IgM antibodies are used for diagnosis, as elevated levels in blood of infected patients are noted from 10 days following infection for up to 3-6 months. Early diagnosis of CHIKV is possible by nucleic acid detection techniques. Treatment of acute CHIKV is mainly symptomatic, with analgesics, non-steroidal anti-inflammatory agents (NSAIDs), and low-dose steroids. No vaccines or anti-viral medicines have been approved for clinical therapy in CHIKV as yet. Hydroxychloroquine and methotrexate have been used in chronic CHIKV infection with variable success.
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Costa-da-Silva AL, Ioshino RS, Petersen V, Lima AF, Cunha MDP, Wiley MR, Ladner JT, Prieto K, Palacios G, Costa DD, Suesdek L, Zanotto PMDA, Capurro ML. First report of naturally infected Aedes aegypti with chikungunya virus genotype ECSA in the Americas. PLoS Negl Trop Dis 2017; 11:e0005630. [PMID: 28614394 PMCID: PMC5470658 DOI: 10.1371/journal.pntd.0005630] [Citation(s) in RCA: 52] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2016] [Accepted: 05/09/2017] [Indexed: 01/08/2023] Open
Abstract
BACKGROUND The worldwide expansion of new emergent arboviruses such as Chikungunya and Zika reinforces the importance in understanding the role of mosquito species in spreading these pathogens in affected regions. This knowledge is essential for developing effective programs based on species specificity to avoid the establishment of endemic transmission cycles sustained by the identified local vectors. Although the first autochthonous transmission of Chikungunya virus was described in 2014 in the north of Brazil, the main outbreaks were reported in 2015 and 2016 in the northeast of Brazil. METHODOLOGY/PRINCIPAL FINDINGS During 5 days of February 2016, we collected mosquitoes in homes of 6 neighborhoods of Aracaju city, the capital of Sergipe state. Four mosquito species were identified but Culex quinquefasciatus and Aedes aegypti were the most abundant. Field-caught mosquitoes were tested for Chikungunya (CHIKV), Zika (ZIKV) and Dengue viruses (DENV) by qRT-PCR and one CHIKV-infected Ae. aegypti female was detected. The complete sequence of CHIKV genome was obtained from this sample and phylogenetic analysis revealed that this isolate belongs to the East-Central-South-African (ECSA) genotype. CONCLUSIONS Our study describes the first identification of a naturally CHIKV-infected Ae. aegypti in Brazil and the first report of a CHIKV from ECSA genotype identified in this species in the Americas. These findings support the notion of Ae. aegypti being a vector involved in CHIKV outbreaks in northeast of Brazil.
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Affiliation(s)
- André Luis Costa-da-Silva
- Departamento de Parasitologia, Instituto de Ciências Biomédicas, Universidade de São Paulo, São Paulo, SP, Brasil
- Instituto Nacional de Ciência e Tecnologia em Entomologia Molecular, INCT-EM, Rio de Janeiro, Rio de Janeiro, Brazil
| | - Rafaella Sayuri Ioshino
- Departamento de Parasitologia, Instituto de Ciências Biomédicas, Universidade de São Paulo, São Paulo, SP, Brasil
- Instituto Nacional de Ciência e Tecnologia em Entomologia Molecular, INCT-EM, Rio de Janeiro, Rio de Janeiro, Brazil
| | - Vivian Petersen
- Departamento de Parasitologia, Instituto de Ciências Biomédicas, Universidade de São Paulo, São Paulo, SP, Brasil
- Laboratório de Parasitologia, Instituto Butantan, São Paulo, Brazil
| | | | | | - Michael R. Wiley
- Center for Genome Sciences, United States Army Medical Research Institute of Infectious Diseases, Frederick, Maryland, United States of America
| | - Jason T. Ladner
- Center for Genome Sciences, United States Army Medical Research Institute of Infectious Diseases, Frederick, Maryland, United States of America
| | - Karla Prieto
- Center for Genome Sciences, United States Army Medical Research Institute of Infectious Diseases, Frederick, Maryland, United States of America
| | - Gustavo Palacios
- Center for Genome Sciences, United States Army Medical Research Institute of Infectious Diseases, Frederick, Maryland, United States of America
| | | | - Lincoln Suesdek
- Laboratório de Parasitologia, Instituto Butantan, São Paulo, Brazil
- Programa de Pós-graduação do Instituto de Medicina Tropical, Universidade de São Paulo, SP, Brasil
| | | | - Margareth Lara Capurro
- Departamento de Parasitologia, Instituto de Ciências Biomédicas, Universidade de São Paulo, São Paulo, SP, Brasil
- Instituto Nacional de Ciência e Tecnologia em Entomologia Molecular, INCT-EM, Rio de Janeiro, Rio de Janeiro, Brazil
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Abstract
Background: Currently the detection of Zika virus (ZIKV) in patient samples is done by real-time RT-PCR. Samples collected from rural area are sent to highly equipped laboratories for screening. A rapid point-of-care test is needed to detect the virus, especially at low resource settings. Methodology/Principal Findings: In this report, we describe the development of a reverse transcription isothermal recombinase polymerase amplification (RT-RPA) assay for the identification of ZIKV. RT-RPA assay was portable, sensitive (21 RNA molecules), and rapid (3-15 minutes). No cross-reactivity was detected to other flaviviruses, alphaviruses and arboviruses. Compared to real-time RT-PCR, the diagnostic sensitivity was 92%, while the specificity was 100%. Conclusions/Significance: The developed assay is a promising platform for rapid point of need detection of ZIKV in low resource settings and elsewhere (e.g. during mass gathering).
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