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Silva LDC, Costa LHA, Dos Santos ICDO, de Curcio JS, Barbosa AMDF, Anunciação CE, Silveira-Lacerda EDP. Advancing Chikungunya Diagnosis: A Cost-Effective and Rapid Visual employing Loop-mediated isothermal reaction. Diagn Microbiol Infect Dis 2024; 108:116111. [PMID: 38016385 DOI: 10.1016/j.diagmicrobio.2023.116111] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2023] [Revised: 09/24/2023] [Accepted: 10/14/2023] [Indexed: 11/30/2023]
Abstract
The diagnosis of Chikungunya (CHIKV), along with the simultaneous monitoring of virus circulation in the population or vectors, is essential for global health. Although effective diagnostic methods for CHIKV, such as RT-qPCR, exist, their utilization is constrained by high costs. With the aim of contributing to the field of diagnostics, we have developed a diagnostic assay using isothermal amplification technology with visually interpretable results. This test can detect the virus within a maximum timeframe of 30 minutes. The detection limit of RT-LAMP CHIKV was found to be 66 copies of RNA molecules (Ct ≅ 31.28), and no cross-reactivity with other arboviruses was observed. During test validation, our assay demonstrated a sensitivity of 80.43%, specificity of 100%, and an overall accuracy of 88.89%. By utilizing more cost-effective reagents and equipment compared to RT-qPCR, this test holds the potential for broader application and enhanced accessibility, particularly in point-of-care settings.
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Affiliation(s)
- Lívia do Carmo Silva
- Center for the Study and Research of (Re)Emerging Agents (NUPEREME), Sentinel Unit and International and Travel Medicine Reference Center (USCREMIVI)/, IPTSP/ICB, Federal University of Goiás, Brazil.
| | - Luiz Henrique Alves Costa
- Center for the Study and Research of (Re)Emerging Agents (NUPEREME), Sentinel Unit and International and Travel Medicine Reference Center (USCREMIVI)/, IPTSP/ICB, Federal University of Goiás, Brazil
| | - Isabela Cristina de Oliveira Dos Santos
- Center for the Study and Research of (Re)Emerging Agents (NUPEREME), Sentinel Unit and International and Travel Medicine Reference Center (USCREMIVI)/, IPTSP/ICB, Federal University of Goiás, Brazil
| | - Juliana Santana de Curcio
- Center for the Study and Research of (Re)Emerging Agents (NUPEREME), Sentinel Unit and International and Travel Medicine Reference Center (USCREMIVI)/, IPTSP/ICB, Federal University of Goiás, Brazil
| | - Amanda Munik de Freitas Barbosa
- Center for the Study and Research of (Re)Emerging Agents (NUPEREME), Sentinel Unit and International and Travel Medicine Reference Center (USCREMIVI)/, IPTSP/ICB, Federal University of Goiás, Brazil
| | - Carlos Eduardo Anunciação
- Center for the Study and Research of (Re)Emerging Agents (NUPEREME), Sentinel Unit and International and Travel Medicine Reference Center (USCREMIVI)/, IPTSP/ICB, Federal University of Goiás, Brazil
| | - Elisângela de Paula Silveira-Lacerda
- Center for the Study and Research of (Re)Emerging Agents (NUPEREME), Sentinel Unit and International and Travel Medicine Reference Center (USCREMIVI)/, IPTSP/ICB, Federal University of Goiás, Brazil.
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Stanley SM, Khera HK, Chandrasingh S, George CE, Mishra RK. A comprehensive review of dengue with a focus on emerging solutions for precision and timely detection. Int J Biol Macromol 2024; 254:127613. [PMID: 37875186 DOI: 10.1016/j.ijbiomac.2023.127613] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Revised: 10/19/2023] [Accepted: 10/20/2023] [Indexed: 10/26/2023]
Abstract
Dengue is a global health problem, caused by the dengue virus (DENV), which belongs to the Flaviviridae family of viruses. The transmission of DENV occurs through vectors, Ae. aegypti and Ae. Albopictus mosquitoes, to the human host, classifying it as a vector-borne disease. The disease incidence is increasing at an alarming rate and needs to be tackled to reduce the morbidity and mortality caused by the disease. Environmental and clinical surveillance, detection of the virus, and diagnostics are critical tools to address this issue. In this comprehensive review, we explore various diagnostic techniques and the associated challenges within the context of dengue. While we briefly touch upon dengue's epidemiology, serotypes, and pathogenesis, our primary emphasis remains on diagnostics. We delve into the intricacies of these diagnostic methods, considering both the challenges they entail and the potential they hold in terms of accuracy and accessibility. It's important to note that the review does not extensively cover clinical aspects or regional variations of the disease.
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Affiliation(s)
- Swetha Mariam Stanley
- Tata Institute for Genetics and Society, Bangalore Life Science Cluster (BLiSC), inStem Building, NCBS Campus, GKVK Post, Bellary Road, Bengaluru, India
| | - Harvinder Kour Khera
- Tata Institute for Genetics and Society, Bangalore Life Science Cluster (BLiSC), inStem Building, NCBS Campus, GKVK Post, Bellary Road, Bengaluru, India.
| | | | | | - Rakesh K Mishra
- Tata Institute for Genetics and Society, Bangalore Life Science Cluster (BLiSC), inStem Building, NCBS Campus, GKVK Post, Bellary Road, Bengaluru, India
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3
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Dakhave M, Metkar G, Suryawanshi H. Simultaneous detection and differentiation of dengue and chikungunya viruses for commercial utility. Virusdisease 2023; 34:248-256. [PMID: 37408546 PMCID: PMC10317902 DOI: 10.1007/s13337-023-00822-1] [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: 01/03/2023] [Accepted: 04/10/2023] [Indexed: 07/07/2023] Open
Abstract
The diagnosis of Dengue and Chikungunya infections during acute phase is a priority considering emerging pattern and increasing trends of their infections. The present study describes the commercial development and validation of RT-PCR test for the simultaneous detection of of DEN and CHIK viral RNA in a single tube from human plasma samples. Multistep one step RT-PCR assay was developed and validated for detection and discrimination of DEN and CHIK along with exogenous internal control. The test was evaluated for commercial use using 3 different lots to determine analytical sensitivity, specificity, precision and stability. The external clinical evaluation was performed at NABL accredited lab with known positive and negative Chikungunya and Dengue specimens and comparator assay method. The findings showed that the test could identify CHIK and DEN viral nucleic acid in clinical samples within 80 min, without any cross-reactivity. The analytical detection limit of the test was 1.56 copies/µl for both. The clinical sensitivity and specificity was ≥ 98% and provide a high-throughput and screen up to 90 samples in a single run. It is available in a freeze-dried format and can be used in both the manual and automated platforms. This unique combo test, PathoDetect™ "CHIK DEN Multiplex PCR Kit" enables simultaneous, sensitive, specific detection of DENV and CHIKV and serves as "ready to use" platform for commercial use. It would aid the differential diagnosis as early as day 1 of the infection and facilitate screen-and-treat approach.
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Affiliation(s)
- Minal Dakhave
- R&D Department, Mylab Discovery Solutions Pvt. Ltd., Global Innovation Center, Amar Paradigm, Baner, Pune, Maharashtra 411045 India
| | - Gauri Metkar
- R&D Department, Mylab Discovery Solutions Pvt. Ltd., Global Innovation Center, Amar Paradigm, Baner, Pune, Maharashtra 411045 India
| | - Harshada Suryawanshi
- R&D Department, Mylab Discovery Solutions Pvt. Ltd., Global Innovation Center, Amar Paradigm, Baner, Pune, Maharashtra 411045 India
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4
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Gao Y, Tai W, Wang X, Jiang S, Debnath AK, Du L, Chen S. A gossypol derivative effectively protects against Zika and dengue virus infection without toxicity. BMC Biol 2022; 20:143. [PMID: 35706035 PMCID: PMC9202104 DOI: 10.1186/s12915-022-01344-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2020] [Accepted: 06/07/2022] [Indexed: 11/28/2022] Open
Abstract
Background Zika virus (ZIKV) and dengue virus (DENV) cause microcephaly and dengue hemorrhagic fever, respectively, leading to severe problems. No effective antiviral agents are approved against infections of these flaviviruses, calling for the need to develop potent therapeutics. We previously identified gossypol as an effective inhibitor against ZIKV and DENV infections, but this compound is toxic and not suitable for in vivo treatment. Results In this study, we showed that gossypol derivative ST087010 exhibited potent and broad-spectrum in vitro inhibitory activity against infections of at least ten ZIKV strains isolated from different hosts, time periods, and countries, as well as DENV-1-4 serotypes, and significantly reduced cytotoxicity compared to gossypol. It presented broad-spectrum in vivo protective efficacy, protecting ZIKV-infected Ifnar1−/− mice from lethal challenge, with increased survival and reduced weight loss. Ifnar1−/− mice treated with this gossypol derivative decreased viral titers in various tissues, including the brain and testis, after infection with ZIKV at different human isolates. Moreover, ST087010 potently blocked ZIKV vertical transmission in pregnant Ifnar1−/− mice, preventing ZIKV-caused fetal death, and it was safe for pregnant mice and their pups. It also protected DENV-2-challenged Ifnar1−/− mice against viral replication by reducing the viral titers in the brain, kidney, heart, and sera. Conclusions Overall, our data indicate the potential for further development of this gossypol derivative as an effective and safe broad-spectrum therapeutic agent to treat ZIKV and DENV diseases. Supplementary Information The online version contains supplementary material available at 10.1186/s12915-022-01344-w.
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Affiliation(s)
- Yaning Gao
- Department of Natural Medicines, School of Pharmaceutical Sciences, Peking University, Beijing, 100191, China.,Lindsley F. Kimball Research Institute, New York Blood Center, New York, NY, 10065, USA
| | - Wanbo Tai
- Lindsley F. Kimball Research Institute, New York Blood Center, New York, NY, 10065, USA
| | - Xinyi Wang
- Lindsley F. Kimball Research Institute, New York Blood Center, New York, NY, 10065, USA
| | - Shibo Jiang
- Lindsley F. Kimball Research Institute, New York Blood Center, New York, NY, 10065, USA.,Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), School of Basic Medical Sciences, Fudan University, Shanghai, 200032, China
| | - Asim K Debnath
- Lindsley F. Kimball Research Institute, New York Blood Center, New York, NY, 10065, USA.
| | - Lanying Du
- Lindsley F. Kimball Research Institute, New York Blood Center, New York, NY, 10065, USA.
| | - Shizhong Chen
- Department of Natural Medicines, School of Pharmaceutical Sciences, Peking University, Beijing, 100191, China.
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5
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Evaluation of reverse transcription-loop-mediated isothermal amplification for rapid detection of SARS-CoV-2. Sci Rep 2021; 11:24234. [PMID: 34930933 PMCID: PMC8688429 DOI: 10.1038/s41598-021-03623-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2021] [Accepted: 10/14/2021] [Indexed: 12/23/2022] Open
Abstract
The main strategy for response and control of COVID-19 demands the use of rapid, accurate diagnostic tests aimed at the first point of health care. During the emergency, an increase in asymptomatic and symptomatic cases results in a great demand for molecular tests, which is promoting the development and application of rapid diagnostic technologies. In this study, we describe the development and evaluation of RT-LAMP to detect SARS-CoV-2 based on three genes (ORF1ab, M and N genes) in monoplex and triplex format. RT-LAMP assays were compared with the gold standard method RT-qPCR. The triplex format (RdRp, M and N genes) allowed obtaining comparable results with de RT-qPCR (RdRp and E genes), presented a sensitivity of 98.9% and a specificity of 97.9%, opening the opportunity to apply this method to detect SARS-CoV-2 at primary health-care centers.
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6
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Taguchi array optimization of the reverse transcription loop-mediated isothermal amplification (RT-LAMP) assay for sensitive and rapid detection of dengue virus serotype 2. Biotechnol Lett 2021; 43:2149-2160. [PMID: 34533679 DOI: 10.1007/s10529-021-03175-1] [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: 05/19/2021] [Accepted: 08/26/2021] [Indexed: 10/20/2022]
Abstract
OBJECTIVES Serotype 2 of dengue virus (DENV-2) is the most prevalent cause of dengue fevers. In this study, the C-prM gene was used for specific detection of DENV-2 by RT-LAMP assay. The RT-LAMP assay was optimized using the Taguchi design of experiments. RESULTS The efficiency of the assay in such optimal conditions resulted in 100% sensitivity, 100% specificity, and 100% overall accuracy for detection of 4 copies/μL of the genome of DENV-2. In addition, the detection of 2 copies/μL of the genome of DENV-2 was feasible, although the sensitivity was 50%. Considering the importance of the specific detection of the dengue virus serotypes, the cost-effective RT-LAMP approach can be used for rapid, specific, and sensitive detection of DENV-2. CONCLUSION RT-LAMP, as a cost-effective method, was optimized using Taguchi array approach for specific and rapid detection of DENV-2. Such methods can facilitate the diagnosis procedure in remote regions.
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7
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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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Saechue B, Kamiyama N, Wang Y, Fukuda C, Watanabe K, Soga Y, Goto M, Dewayani A, Ariki S, Hirose H, Ozaka S, Sachi N, Hidano S, Faisal K, Chowdhury R, Anik Ashfaq Khan M, Hossain F, Ghosh P, Shirin T, Mondal D, Murakami K, Kobayashi T. Development of a portable reverse transcription loop-mediated isothermal amplification system to detect the E1 region of Chikungunya virus in a cost-effective manner. Genes Cells 2020; 25:615-625. [PMID: 32562326 DOI: 10.1111/gtc.12797] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2019] [Revised: 06/01/2020] [Accepted: 06/10/2020] [Indexed: 12/11/2022]
Abstract
Chikungunya fever is a mosquito-borne disease cause of persistent arthralgia. The current diagnosis of Chikungunya virus (CHIKV) relies on a conventional reverse transcription polymerase chain reaction assay. Reverse transcription loop-mediated isothermal amplification (RT-LAMP) is a rapid and simple tool used for DNA-based diagnosis of a variety of infectious diseases. In this study, we established an RT-LAMP system to recognize CHIKV by targeting the envelope protein 1 (E1) gene that could also detect CHIKV at a concentration of 8 PFU without incorrectly detecting other mosquito-borne viruses. The system also amplified the E1 genome in the serum of CHIKV-infected mice with high sensitivity and specificity. Moreover, we established a dry RT-LAMP system that can be transported without a cold chain, which detected the virus genome in CHIKV-infected patient samples with high accuracy. Thus, the dry RT-LAMP system has great potential to be applied as a novel CHIKV screening kit in endemic areas.
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Affiliation(s)
- Benjawan Saechue
- Department of Infectious Disease Control, Faculty of Medicine, Oita University, Oita, Japan
| | - Naganori Kamiyama
- Department of Infectious Disease Control, Faculty of Medicine, Oita University, Oita, Japan
| | - Yinan Wang
- Department of Infectious Disease Control, Faculty of Medicine, Oita University, Oita, Japan
| | - Chiaki Fukuda
- Department of Infectious Disease Control, Faculty of Medicine, Oita University, Oita, Japan
| | - Kei Watanabe
- Department of Infectious Disease Control, Faculty of Medicine, Oita University, Oita, Japan
| | - Yasuhiro Soga
- Department of Infectious Disease Control, Faculty of Medicine, Oita University, Oita, Japan
| | - Mizuki Goto
- Department of Infectious Disease Control, Faculty of Medicine, Oita University, Oita, Japan
| | - Astri Dewayani
- Department of Infectious Disease Control, Faculty of Medicine, Oita University, Oita, Japan
| | - Shimpei Ariki
- Department of Infectious Disease Control, Faculty of Medicine, Oita University, Oita, Japan
| | - Haruna Hirose
- Department of Infectious Disease Control, Faculty of Medicine, Oita University, Oita, Japan
| | - Sotaro Ozaka
- Department of Infectious Disease Control, Faculty of Medicine, Oita University, Oita, Japan
| | - Nozomi Sachi
- Department of Infectious Disease Control, Faculty of Medicine, Oita University, Oita, Japan
| | - Shinya Hidano
- Department of Infectious Disease Control, Faculty of Medicine, Oita University, Oita, Japan
| | - Khaledul Faisal
- Nutrition and Clinical Services Division, International Centre for Diarrhoeal Disease Research, Bangladesh (icddr, b), Dhaka, Bangladesh
| | - Rajashree Chowdhury
- Nutrition and Clinical Services Division, International Centre for Diarrhoeal Disease Research, Bangladesh (icddr, b), Dhaka, Bangladesh
| | - Md Anik Ashfaq Khan
- Nutrition and Clinical Services Division, International Centre for Diarrhoeal Disease Research, Bangladesh (icddr, b), Dhaka, Bangladesh
| | - Faria Hossain
- Nutrition and Clinical Services Division, International Centre for Diarrhoeal Disease Research, Bangladesh (icddr, b), Dhaka, Bangladesh
| | - Prakash Ghosh
- Nutrition and Clinical Services Division, International Centre for Diarrhoeal Disease Research, Bangladesh (icddr, b), Dhaka, Bangladesh
| | - Tahmina Shirin
- Department of Virology, Institute of Epidemiology Disease Control and Research (IEDCR), Dhaka, Bangladesh
| | - Dinesh Mondal
- Nutrition and Clinical Services Division, International Centre for Diarrhoeal Disease Research, Bangladesh (icddr, b), Dhaka, Bangladesh
| | - Kazunari Murakami
- Department of Gastroenterology, Faculty of Medicine, Oita University, Oita, Japan
| | - Takashi Kobayashi
- Department of Infectious Disease Control, Faculty of Medicine, Oita University, Oita, Japan
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9
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Dunbar S, Das S. Amplification chemistries in clinical virology. J Clin Virol 2019; 115:18-31. [PMID: 30953805 PMCID: PMC7106405 DOI: 10.1016/j.jcv.2019.03.015] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2018] [Revised: 02/19/2019] [Accepted: 03/25/2019] [Indexed: 01/04/2023]
Abstract
Molecular diagnostic methods have evolved and matured considerably over the last several decades and are constantly being evaluated and adopted by clinical laboratories for the identification of infectious pathogens. Advancement in other technologies such as fluorescence, electronics, instrumentation, automation, and sensors have made the overall diagnostic process more accurate, sensitive, and rapid. Nucleic acid based detection procedures, which rely on the fundamental principles of DNA replication have emerged as a popular and standard diagnostic method, and several commercial assays are currently available based on different nucleic acid amplification techniques. This review focuses on the major amplification chemistries that are used for developing commercial assays and discusses their application in the clinical virology laboratory.
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10
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Lee JL, Loe MWC, Lee RCH, Chu JJH. Antiviral activity of pinocembrin against Zika virus replication. Antiviral Res 2019; 167:13-24. [PMID: 30959074 DOI: 10.1016/j.antiviral.2019.04.003] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2018] [Revised: 03/25/2019] [Accepted: 04/01/2019] [Indexed: 12/22/2022]
Abstract
Zika virus (ZIKV) is a mosquito-borne virus that has garnered a lot of attention in recent years, due to the explosive epidemic from 2014 to 2016. Since its introduction in the Americas in late 2014, ZIKV has spread at an unprecedented rate and scale throughout the world and infected millions of people. Its infection has also been associated with severe neurological disorders like Guillain-Barré syndrome and microcephaly in fetuses. Despite these, there is currently no approved antiviral against ZIKV. In this study, an immunofluorescence-based high throughput screen was conducted on a library of 483 flavonoid derivatives to identify potential anti-ZIKV compounds. Flavonoids, which are natural polyphenolic compounds found in plants, represent an attractive source of antivirals due to their abundance in food and expected low toxicity. From the primary screen, three hits were selected for validation by cell viability and viral plaque reduction assays. Pinocembrin, a flavanone found in honey, tea and red wine, was chosen for downstream studies as it exhibited the strongest inhibition of ZIKV infection in human placental JEG-3 cells (IC50 = 17.4 μM). Time-course studies revealed that pinocembrin acts on post-entry process(es) of the ZIKV replication cycle. Furthermore, pinocembrin inhibits viral RNA production and envelope protein synthesis based on quantitative reverse transcription-PCR (qRT-PCR) and Western blot analyses. This study has demonstrated for the first time the in vitro anti-ZIKV activity of pinocembrin.
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Affiliation(s)
- Jia Le Lee
- Laboratory of Molecular RNA Virology and Antiviral Strategies, Department of Microbiology, Yong Loo Lin School of Medicine, National University Health System, National University of Singapore, Singapore
| | - Marcus Wing Choy Loe
- Laboratory of Molecular RNA Virology and Antiviral Strategies, Department of Microbiology, Yong Loo Lin School of Medicine, National University Health System, National University of Singapore, Singapore
| | - Regina Ching Hua Lee
- Laboratory of Molecular RNA Virology and Antiviral Strategies, Department of Microbiology, Yong Loo Lin School of Medicine, National University Health System, National University of Singapore, Singapore
| | - Justin Jang Hann Chu
- Laboratory of Molecular RNA Virology and Antiviral Strategies, Department of Microbiology, Yong Loo Lin School of Medicine, National University Health System, National University of Singapore, Singapore; Institute of Molecular and Cell Biology, Agency for Science, Technology and Research (A*STAR), Singapore.
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11
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GloPID-R report on Chikungunya, O'nyong-nyong and Mayaro virus, part I: Biological diagnostics. Antiviral Res 2019; 166:66-81. [PMID: 30905821 DOI: 10.1016/j.antiviral.2019.03.009] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2019] [Accepted: 03/17/2019] [Indexed: 11/20/2022]
Abstract
The GloPID-R (Global Research Collaboration for Infectious Disease Preparedness) Chikungunya (CHIKV), O'nyong-nyong (ONNV) and Mayaro virus (MAYV) Working Group is investigating the natural history, epidemiology and medical management of infection by these viruses, to identify knowledge gaps and to propose recommendations for direct future investigations and rectification measures. Here, we present the first report dedicated to diagnostic aspects of CHIKV, ONNV and MAYV. Regarding diagnosis of the disease at the acute phase, molecular assays previously described for the three viruses require further evaluation, standardized protocols and the availability of international standards representing the genetic diversity of the viruses. Detection of specific IgM would benefit from further investigations to clarify the extent of cross-reactivity among the three viruses, the sensitivity of the assays, and the possible interfering role of cryoglobulinaemia. Implementation of reference panels and external quality assessments for both molecular and serological assays is necessary. Regarding sero-epidemiological studies, there is no reported high-throughput assay that can distinguish among these different viruses in areas of potential co-circulation. New specific tools and/or improved standardized protocols are needed to enable large-scale epidemiological studies of public health relevance to be performed. Considering the high risk of future CHIKV, MAYV and ONNV outbreaks, the Working Group recommends that a major investigation should be initiated to fill the existing diagnostic gaps.
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12
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Oliveira DBL, Durigon GS, Mendes ÉA, Ladner JT, Andreata-Santos R, Araujo DB, Botosso VF, Paola ND, Neto DFL, Cunha MP, Braconi CT, Alves RPS, Jesus MR, Pereira LR, Melo SR, Mesquita FS, Silveira VB, Thomazelli LM, Favoretto SR, Almonfrey FB, Abdulkader RCRM, Gabrili JM, Tambourgi DV, Oliveira SF, Prieto K, Wiley MR, Ferreira LCS, Silva MV, Palacios GF, Zanotto PMA, Durigon EL. Persistence and Intra-Host Genetic Evolution of Zika Virus Infection in Symptomatic Adults: A Special View in the Male Reproductive System. Viruses 2018; 10:v10110615. [PMID: 30405055 PMCID: PMC6267439 DOI: 10.3390/v10110615] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2018] [Revised: 10/04/2018] [Accepted: 10/20/2018] [Indexed: 01/27/2023] Open
Abstract
We followed the presence of Zika virus (ZIKV) in four healthy adults (two men and two women), for periods ranging from 78 to 298 days post symptom onset. The patients were evaluated regarding the presence of the virus in different body fluids (blood, saliva, urine and semen), development of immune responses (including antibodies, cytokines and chemokines), and virus genetic variation within samples collected from semen and urine during the infection course. The analysis was focused primarily on the two male patients who shed the virus for up to 158 days after the initial symptoms. ZIKV particles were detected in the spermatozoa cytoplasm and flagella, in immature sperm cells and could also be isolated from semen in cell culture, confirming that the virus is able to preserve integrity and infectivity during replication in the male reproductive system (MRS). Despite the damage caused by ZIKV infection within the MRS, our data showed that ZIKV infection did not result in infertility at least in one of the male patients. This patient was able to conceive a child after the infection. We also detected alterations in the male genital cytokine milieu, which could play an important role in the replication and transmission of the virus which could considerably increase the risk of ZIKV sexual spread. In addition, full genome ZIKV sequences were obtained from several samples (mainly semen), which allowed us to monitor the evolution of the virus within a patient during the infection course. We observed genetic changes over time in consensus sequences and lower frequency intra-host single nucleotide variants (iSNV), that suggested independent compartmentalization of ZIKV populations in the reproductive and urinary systems. Altogether, the present observations confirm the risks associated with the long-term replication and shedding of ZIKV in the MRS and help to elucidate patterns of intra-host genetic evolution during long term replication of the virus.
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Affiliation(s)
- Danielle B L Oliveira
- Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, SP 05508-000, Brazil.
| | - Giuliana S Durigon
- Medical School Clinic Hospital, University of São Paulo, São Paulo, SP 05403-000, Brazil.
| | - Érica A Mendes
- Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, SP 05508-000, Brazil.
| | - Jason T Ladner
- Center for Genome Sciences, US Army Medical Research Institute of Infectious Diseases, Frederick, MD 21702, USA.
- The Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ 86011-4073, USA.
| | - Robert Andreata-Santos
- Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, SP 05508-000, Brazil.
| | - Danielle B Araujo
- Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, SP 05508-000, Brazil.
| | - Viviane F Botosso
- Virology Laboratory, Butantan Institute, São Paulo, SP 05503-900, Brazil.
| | - Nicholas D Paola
- Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, SP 05508-000, Brazil.
| | - Daniel F L Neto
- Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, SP 05508-000, Brazil.
| | - Marielton P Cunha
- Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, SP 05508-000, Brazil.
| | - Carla T Braconi
- Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, SP 05508-000, Brazil.
| | - Rúbens P S Alves
- Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, SP 05508-000, Brazil.
| | - Monica R Jesus
- Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, SP 05508-000, Brazil.
| | - Lennon R Pereira
- Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, SP 05508-000, Brazil.
| | - Stella R Melo
- Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, SP 05508-000, Brazil.
| | - Flávio S Mesquita
- Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, SP 05508-000, Brazil.
| | - Vanessa B Silveira
- Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, SP 05508-000, Brazil.
| | - Luciano M Thomazelli
- Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, SP 05508-000, Brazil.
| | | | - Franciane B Almonfrey
- Medical School Clinic Hospital, University of São Paulo, São Paulo, SP 05403-000, Brazil.
| | | | - Joel M Gabrili
- Virology Laboratory, Butantan Institute, São Paulo, SP 05503-900, Brazil.
- Immunochemistry Laboratory, Butantan Institute, São Paulo, SP 05503-900, Brazil.
| | - Denise V Tambourgi
- Virology Laboratory, Butantan Institute, São Paulo, SP 05503-900, Brazil.
| | - Sérgio F Oliveira
- Department of Cellular and Developmental Biology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, SP 05508-000, Brazil.
| | - Karla Prieto
- Center for Genome Sciences, US Army Medical Research Institute of Infectious Diseases, Frederick, MD 21702, USA.
- Department of Environmental, Agricultural and Occupational Health, University of Nebraska Medical Center, Omaha, NE 68198-4388, USA.
| | - Michael R Wiley
- Center for Genome Sciences, US Army Medical Research Institute of Infectious Diseases, Frederick, MD 21702, USA.
- Department of Environmental, Agricultural and Occupational Health, University of Nebraska Medical Center, Omaha, NE 68198-4388, USA.
| | - Luís C S Ferreira
- Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, SP 05508-000, Brazil.
| | - Marcos V Silva
- Institute of Infectology Emílio Ribas e Pontifícia Universidade Católica (PUC-SP), São Paulo, SP 01246-900, Brazil.
| | - Gustavo F Palacios
- Center for Genome Sciences, US Army Medical Research Institute of Infectious Diseases, Frederick, MD 21702, USA.
| | - Paolo M A Zanotto
- Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, SP 05508-000, Brazil.
| | - Edison L Durigon
- Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, SP 05508-000, Brazil.
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13
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Yang Z, Liu W, Liang H, Wen R, Zhang Y. Development and evaluation of LAMP, CPA and IMSA methods for rapid detection of the AML1/ETO fusion gene in acute myeloid leukemia. Exp Ther Med 2018; 16:3353-3362. [PMID: 30233681 PMCID: PMC6143909 DOI: 10.3892/etm.2018.6617] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2018] [Accepted: 06/29/2018] [Indexed: 12/15/2022] Open
Abstract
The objective of the present study was to determine whether the loop-mediated isothermal amplification (LAMP), cross-priming amplification (CPA), and/or isothermal multiple-self-matching-initiated amplification (IMSA) methods can provide rapid detection of the runt related transcription factor 1/runt related transcription factor 1 translocation partner 1 (AML1/ETO) fusion gene in acute myeloid leukemia (AML). According to the sequence of the AML1/ETO fusion gene available in GenBank and the principles of the LAMP, CPA and IMSA methods, specific primers were designed to bind a conserved region of the AML1/ETO gene in each assay. Following optimization of the conditions for the LAMP, CPA and IMSA assays, the specificity and sensitivity of the assays were examined and compared. In addition, 41 clinical samples were assayed using the three methods. It was observed that a ladder-like pattern of DNA products was produced in AML1/ETO-positive samples in all three assays, whereas no DNA product was generated with the controls. The detection limit of the LAMP and CPA assays was 50 copies/tube, and for the IMSA assay was 10 copies/tube. This sensitivity was consistent, and improved in the latter case, compared with that of the reverse transcription-polymerase chain reaction (RT-PCR) assay. Furthermore, the detection rate for bone marrow or peripheral blood samples was 9.76%, and the agreement among the LAMP, CPA, IMSA and RT-PCR methods was 100%. Therefore, the LAMP, CPA and IMSA methods optimized in the present study provided rapid detection of the AML1/ETO fusion gene for an initial clinical diagnosis of AML. In addition, the LAMP, CPA and IMSA assays are straightforward to perform and do not require specialized instruments. Therefore, these three isothermal methods may be used to perform field tests or assays at resource-limited hospitals.
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Affiliation(s)
- Zhigang Yang
- Department of Hematology and Rheumatology, Affiliated Central People's Hospital of Zhanjiang of Guangdong Medical University, Zhanjiang, Guangdong 524045, P.R. China.,Laboratory of Hematology, Guangdong Medical University, Zhanjiang, Guangdong 524023, P.R. China
| | - Wenxin Liu
- Department of Hematology, Affiliated Hospital of Guangdong Medical University, Zhanjiang, Guangdong 524001, P.R. China
| | - Haiyan Liang
- Department of Hematology, Jiangmen Central Hospital Affiliated Jiangmen Hospital of Sun Yat-Sen University, Jiangmen, Guangdong 529030, P.R. China
| | - Ruiting Wen
- Department of Hematopoietic Stem Cell Transplantation, The 307th Hospital of The People's Liberation Army, Beijing 100071, P.R. China
| | - Yuming Zhang
- Department of Hematology, Affiliated Hospital of Guangdong Medical University, Zhanjiang, Guangdong 524001, P.R. China
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14
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Lopez-Jimena B, Bekaert M, Bakheit M, Frischmann S, Patel P, Simon-Loriere E, Lambrechts L, Duong V, Dussart P, Harold G, Fall C, Faye O, Sall AA, Weidmann M. Development and validation of four one-step real-time RT-LAMP assays for specific detection of each dengue virus serotype. PLoS Negl Trop Dis 2018; 12:e0006381. [PMID: 29813062 PMCID: PMC5973574 DOI: 10.1371/journal.pntd.0006381] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2016] [Accepted: 03/12/2018] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND 4 one-step, real-time, reverse transcription loop-mediated isothermal amplification (RT-LAMP) assays were developed for the detection of dengue virus (DENV) serotypes by considering 2,056 full genome DENV sequences. DENV1 and DENV2 RT-LAMP assays were validated with 31 blood and 11 serum samples from Tanzania, Senegal, Sudan and Mauritania. DENV3 and DENV4 RT-LAMP assays were validated with 25 serum samples from Cambodia. METHODOLOGY/PRINCIPAL FINDINGS 4 final reaction primer mixes were obtained by using a combination of Principal Component Analysis of the full DENV genome sequences, and LAMP primer design based on sequence alignments using the LAVA software. These mixes contained 14 (DENV1), 12 (DENV2), 8 (DENV3) and 3 (DENV4) LAMP primer sets. The assays were evaluated with an External Quality Assessment panel from Quality Control for Molecular Diagnostics. The assays were serotype-specific and did not cross-detect with other flaviviruses. The limits of detection, with 95% probability, were 22 (DENV1), 542 (DENV2), 197 (DENV3) and 641 (DENV4) RNA molecules, and 100% reproducibility in the assays was obtained with up to 102 (DENV1) and 103 RNA molecules (DENV2, DENV3 and DENV4). Validation of the DENV2 assay with blood samples from Tanzania resulted in 23 samples detected by RT-LAMP, demonstrating that the assay is 100% specific and 95.8% sensitive (positive predictive value of 100% and a negative predictive value of 85.7%). All serum samples from Senegal, Sudan and Mauritania were detected and 3 untyped as DENV1. The sensitivity of RT-LAMP for DENV4 samples from Cambodia did not quite match qRT-PCR. CONCLUSIONS/SIGNIFICANCE We have shown a novel approach to design LAMP primers that makes use of fast growing sequence databases. The DENV1 and DENV2 assays were validated with viral RNA extracted clinical samples, showing very good performance parameters.
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Affiliation(s)
- Benjamin Lopez-Jimena
- Institute of Aquaculture, University of Stirling, Stirling, Scotland, United Kingdom
| | - Michaël Bekaert
- Institute of Aquaculture, University of Stirling, Stirling, Scotland, United Kingdom
| | | | | | - Pranav Patel
- Robert Koch Institute, Centre for biological security 1 (ZBS1), Berlin, Germany
| | - Etienne Simon-Loriere
- Functional Genetics of Infectious Diseases Unit, Department of Genomes and Genetics, Institut Pasteur, Paris, France
- Centre National de la Recherche Scientifique, Unité de Recherche Associée, Paris, France
| | - Louis Lambrechts
- Centre National de la Recherche Scientifique, Unité de Recherche Associée, Paris, France
- Insect-Virus Interactions Group, Department of Genomes and Genetics, Institut Pasteur, Paris, France
| | - Veasna Duong
- Virology Unit, Institut Pasteur du Cambodge, Institut Pasteur International Network, Phnom Penh, Cambodia
| | - Philippe Dussart
- Virology Unit, Institut Pasteur du Cambodge, Institut Pasteur International Network, Phnom Penh, Cambodia
| | - Graham Harold
- Institute of Aquaculture, University of Stirling, Stirling, Scotland, United Kingdom
| | - Cheikh Fall
- Arbovirus and viral haemorrhagic fever unit, Institut Pasteur de Dakar, Institut Pasteur International Network, Dakar, Senegal
| | - Oumar Faye
- Arbovirus and viral haemorrhagic fever unit, Institut Pasteur de Dakar, Institut Pasteur International Network, Dakar, Senegal
| | - Amadou Alpha Sall
- Arbovirus and viral haemorrhagic fever unit, Institut Pasteur de Dakar, Institut Pasteur International Network, Dakar, Senegal
| | - Manfred Weidmann
- Institute of Aquaculture, University of Stirling, Stirling, Scotland, United Kingdom
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15
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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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16
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Abstract
The four serotypes of dengue virus (DENV) cause one of the most important and rapidly emerging mosquito-borne viral diseases in humans. Of the currently available diagnostic tests for dengue, the reverse transcription-PCR (RT-PCR) assay is the most sensitive and specific, and so it is commonly used as the gold standard. However, the requirement of a sophisticated and expensive thermal cycler makes it very difficult to use as a point-of-care diagnostic test in resource-limited regions where dengue is endemic. Tsai et al. (J Clin Microbiol 56:e01865-17, 2018, https://doi.org/10.1128/JCM.01865-17) report the analytical and clinical performances of a reverse transcription-insulated isothermal PCR (RT-iiPCR) assay with a portable nucleic acid analyzer for rapid detection of the four DENV serotypes; its reproducibility and complete agreement on clinical samples with the multiplex RT-PCR assay developed by the Centers for Disease Control and Prevention suggest that the dengue RT-iiPCR is a potential point-of-care test. Compared with other DENV RNA detection methods, the unique isothermal PCR design of RT-iiPCR, together with further improvements, would represent a promising new type of field-deployable diagnostic test for dengue.
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17
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Sharma V, Chaudhry D, Kaushik S. Evaluation of clinical applicability of reverse transcription-loop-mediated isothermal amplification assay for detection and subtyping of Influenza A viruses. J Virol Methods 2018; 253:18-25. [PMID: 29253497 PMCID: PMC7113880 DOI: 10.1016/j.jviromet.2017.12.005] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2017] [Revised: 11/03/2017] [Accepted: 12/15/2017] [Indexed: 12/20/2022]
Abstract
BACKGROUND Influenza A viruses (IAVs) have always remain a serious concern for the global economy and public health. A rapid, specific and sensitive detection method is always needed to control the influenza in its early stages by timely intervention of therapy and early clinical management. OBJECTIVES To develop RT-LAMP assays for detection of influenza A viruses, their further subtyping into seasonal (H1N1, H3N2) and novel pandemic H1N1 viruses and to evaluate clinical applicability of optimized RT-LAMP assays on patients' samples. STUDY DESIGN In this study, we optimized RT-LAMP assay to detect IAVs by using primers against matrix gene and subtyping of IAVs was done by using primers against hemagglutinin gene. Optimized RT-LAMP assays were applied on clinical samples from patients having influenza like illness and results were compared with conventional one-step RT-PCR and real-time RT-PCR. RESULTS RT-LAMP assays successfully detected and differentiated IAVs into H1N1, H3N2 and pdm09/H1N1 subtypes. One hundred and sixty seven clinical swab samples from influenza suspected patients were taken and tested with RT-LAMP assay, detecting 30 (17.9%) samples positive for Influenza A virus. Out of 30 samples, 21, 7 and 2 were found positive for pdm09/H1N1, H3N2 and seasonal H1 respectively. Conventional one-step RT-PCR detected a total of 27 (16.2%) samples for influenza A and further subtyping showed 20 and 7 samples positive for pdm09/H1N1 and H3N2 virus respectively whereas none was found positive for seasonal H1N1. RT-LAMP assay demonstrated higher sensitivity (93.8%) than conventional RT-PCR (84.4%) for influenza A viruses detection in clinical samples. CONCLUSIONS RT-LAMP assay is rapid, sensitive, specific and cost effective method for detection of influenza A viruses than conventional one-step RT-PCR and it can serve as a good alternate for diagnosis and surveillance studies during influenza outbreaks in resource-limited setups of developing countries.
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Affiliation(s)
- Vikrant Sharma
- Centre for Biotechnology, Maharshi Dayanand University, Rohtak, Haryana, India.
| | - Dhruva Chaudhry
- Pulmonary and Critical Care Medicine, Post Graduate Institute of Medical Sciences, Rohtak, Haryana, India.
| | - Samander Kaushik
- Centre for Biotechnology, Maharshi Dayanand University, Rohtak, Haryana, India.
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18
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Xiao Y, Xie Y, Xu M, Liu S, Jiang C, Zhao F, Zeng T, Liu Z, Yu J, Wu Y. Development and Evaluation of a Loop-Mediated Isothermal Amplification Assay for the Detection of Treponema pallidum DNA in the Peripheral Blood of Secondary Syphilis Patients. Am J Trop Med Hyg 2017; 97:1673-1678. [PMID: 29016285 DOI: 10.4269/ajtmh.17-0051] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
Abstract
Secondary syphilis (SS) has always been puzzling for the clinicians because of the similarity of the appearance of skin rashes with other dermatoses. Serological assays are useful, but less sensitive at an early stage of SS or when patients are immunodeficient. Therefore, there is an urgent need to develop a rapid and effective tool for the diagnosis of SS, which may play an important role in the control of epidemic syphilis outbreaks. In this study, we evaluated a loop-mediated isothermal amplification (LAMP) assay, targeting gene encoding the basic membrane protein of Treponema pallidum, to detect the presence of circulating T. pallidum DNA in the blood of SS patients. The specificity of LAMP was validated using three strains of Spirochaetales and six common clinical bacteria. The clinical applicability of LAMP assay was assessed using 642 blood samples from clinically suspected SS patients and 80 samples from healthy blood donors, showing a sensitivity of 82.1% and a specificity of 100.0% in the diagnosis of SS. Thus, our results indicate that the LAMP can be used as a supplementary method for the diagnosis of SS.
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Affiliation(s)
- Yongjian Xiao
- Institute of Pathogenic Biology Institute, Medical College, University of South China, Hengyang, China.,Hunan Province Cooperative Innovation Center for Molecular Targeted New Drug Study, Hengyang, China.,Department of Clinical Laboratory, The Second Affiliated Hospital of University of South China, Hengyang, China.,Hunan Provincial Key Laboratory for Special Pathogen Prevention and Control, Hengyang, China
| | - Yafeng Xie
- Hunan Province Cooperative Innovation Center for Molecular Targeted New Drug Study, Hengyang, China.,Hunan Provincial Key Laboratory for Special Pathogen Prevention and Control, Hengyang, China.,Institute of Pathogenic Biology Institute, Medical College, University of South China, Hengyang, China.,Department of Clinical Laboratory, The Second Affiliated Hospital of University of South China, Hengyang, China
| | - Man Xu
- Hunan Provincial Key Laboratory for Special Pathogen Prevention and Control, Hengyang, China.,Hunan Province Cooperative Innovation Center for Molecular Targeted New Drug Study, Hengyang, China.,Institute of Pathogenic Biology Institute, Medical College, University of South China, Hengyang, China
| | - Shuangquan Liu
- Department of Clinical Laboratory, The First Affiliated Hospital of University of South China, Hengyang, China
| | - Chuanhao Jiang
- Hunan Provincial Key Laboratory for Special Pathogen Prevention and Control, Hengyang, China.,Hunan Province Cooperative Innovation Center for Molecular Targeted New Drug Study, Hengyang, China.,Institute of Pathogenic Biology Institute, Medical College, University of South China, Hengyang, China
| | - Feijun Zhao
- Hunan Provincial Key Laboratory for Special Pathogen Prevention and Control, Hengyang, China.,Hunan Province Cooperative Innovation Center for Molecular Targeted New Drug Study, Hengyang, China.,Institute of Pathogenic Biology Institute, Medical College, University of South China, Hengyang, China
| | - Tiebing Zeng
- Hunan Provincial Key Laboratory for Special Pathogen Prevention and Control, Hengyang, China.,Hunan Province Cooperative Innovation Center for Molecular Targeted New Drug Study, Hengyang, China.,Institute of Pathogenic Biology Institute, Medical College, University of South China, Hengyang, China
| | - Zhuoran Liu
- Department of Clinical Laboratory, The Second Affiliated Hospital of University of South China, Hengyang, China
| | - Jian Yu
- Department of Experimental Zoology, Medical College, University of South China, Hengyang, China
| | - Yimou Wu
- Hunan Provincial Key Laboratory for Special Pathogen Prevention and Control, Hengyang, China.,Institute of Pathogenic Biology Institute, Medical College, University of South China, Hengyang, China.,Hunan Province Cooperative Innovation Center for Molecular Targeted New Drug Study, Hengyang, China
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19
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Robinson ML, Manabe YC. Reducing Uncertainty for Acute Febrile Illness in Resource-Limited Settings: The Current Diagnostic Landscape. Am J Trop Med Hyg 2017; 96:1285-1295. [PMID: 28719277 DOI: 10.4269/ajtmh.16-0667] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
AbstractDiagnosing the cause of acute febrile illness in resource-limited settings is important-to give the correct antimicrobials to patients who need them, to prevent unnecessary antimicrobial use, to detect emerging infectious diseases early, and to guide vaccine deployment. A variety of approaches are yielding more rapid and accurate tests that can detect more pathogens in a wider variety of settings. After decades of slow progress in diagnostics for acute febrile illness in resource-limited settings, a wave of converging advancements will enable clinicians in resource-limited settings to reduce uncertainty for the diagnosis of acute febrile illness.
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Affiliation(s)
- Matthew L Robinson
- Division of Infectious Disease, Department of Medicine, Johns Hopkins School of Medicine, Baltimore, Maryland
| | - Yukari C Manabe
- Division of Infectious Disease, Department of Medicine, Johns Hopkins School of Medicine, Baltimore, Maryland
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20
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Chotiwan N, Brewster CD, Magalhaes T, Weger-Lucarelli J, Duggal NK, Rückert C, Nguyen C, Garcia Luna SM, Fauver JR, Andre B, Gray M, Black WC, Kading RC, Ebel GD, Kuan G, Balmaseda A, Jaenisch T, Marques ETA, Brault AC, Harris E, Foy BD, Quackenbush SL, Perera R, Rovnak J. Rapid and specific detection of Asian- and African-lineage Zika viruses. Sci Transl Med 2017; 9:eaag0538. [PMID: 28469032 PMCID: PMC5654541 DOI: 10.1126/scitranslmed.aag0538] [Citation(s) in RCA: 78] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2016] [Revised: 08/12/2016] [Accepted: 02/15/2017] [Indexed: 01/23/2023]
Abstract
Understanding the dynamics of Zika virus transmission and formulating rational strategies for its control require precise diagnostic tools that are also appropriate for resource-poor environments. We have developed a rapid and sensitive loop-mediated isothermal amplification (LAMP) assay that distinguishes Zika viruses of Asian and African lineages. The assay does not detect chikungunya virus or flaviviruses such as dengue, yellow fever, or West Nile viruses. The assay conditions allowed direct detection of Zika virus RNA in cultured infected cells; in mosquitoes; in virus-spiked samples of human blood, plasma, saliva, urine, and semen; and in infected patient serum, plasma, and semen samples without the need for RNA isolation or reverse transcription. The assay offers rapid, specific, sensitive, and inexpensive detection of the Asian-lineage Zika virus strain that is currently circulating in the Western hemisphere, and can also detect the African-lineage Zika virus strain using separate, specific primers.
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Affiliation(s)
- Nunya Chotiwan
- Department of Microbiology, Immunology and Pathology, College of Veterinary Medicine and Biomedical Sciences, Colorado State University, Fort Collins, CO 80523, USA
- Arthropod-borne Infectious Disease Laboratories, College of Veterinary Medicine and Biomedical Sciences, Colorado State University, Fort Collins, CO 80523, USA
| | - Connie D Brewster
- Department of Microbiology, Immunology and Pathology, College of Veterinary Medicine and Biomedical Sciences, Colorado State University, Fort Collins, CO 80523, USA
| | - Tereza Magalhaes
- Arthropod-borne Infectious Disease Laboratories, College of Veterinary Medicine and Biomedical Sciences, Colorado State University, Fort Collins, CO 80523, USA
- Laboratory of Virology and Experimental Therapeutics, Centro de Pesquisas Aggeu Magalhaes, Fundacao Oswaldo Cruz, Recife-PE, Brazil
| | - James Weger-Lucarelli
- Department of Microbiology, Immunology and Pathology, College of Veterinary Medicine and Biomedical Sciences, Colorado State University, Fort Collins, CO 80523, USA
- Arthropod-borne Infectious Disease Laboratories, College of Veterinary Medicine and Biomedical Sciences, Colorado State University, Fort Collins, CO 80523, USA
| | - Nisha K Duggal
- Division of Vector-Borne Diseases, Centers for Disease Control and Prevention, Fort Collins, CO 80521, USA
| | - Claudia Rückert
- Department of Microbiology, Immunology and Pathology, College of Veterinary Medicine and Biomedical Sciences, Colorado State University, Fort Collins, CO 80523, USA
- Arthropod-borne Infectious Disease Laboratories, College of Veterinary Medicine and Biomedical Sciences, Colorado State University, Fort Collins, CO 80523, USA
| | - Chilinh Nguyen
- Department of Microbiology, Immunology and Pathology, College of Veterinary Medicine and Biomedical Sciences, Colorado State University, Fort Collins, CO 80523, USA
- Arthropod-borne Infectious Disease Laboratories, College of Veterinary Medicine and Biomedical Sciences, Colorado State University, Fort Collins, CO 80523, USA
| | - Selene M Garcia Luna
- Department of Microbiology, Immunology and Pathology, College of Veterinary Medicine and Biomedical Sciences, Colorado State University, Fort Collins, CO 80523, USA
- Arthropod-borne Infectious Disease Laboratories, College of Veterinary Medicine and Biomedical Sciences, Colorado State University, Fort Collins, CO 80523, USA
| | - Joseph R Fauver
- Department of Microbiology, Immunology and Pathology, College of Veterinary Medicine and Biomedical Sciences, Colorado State University, Fort Collins, CO 80523, USA
- Arthropod-borne Infectious Disease Laboratories, College of Veterinary Medicine and Biomedical Sciences, Colorado State University, Fort Collins, CO 80523, USA
| | - Barb Andre
- Department of Microbiology, Immunology and Pathology, College of Veterinary Medicine and Biomedical Sciences, Colorado State University, Fort Collins, CO 80523, USA
| | - Meg Gray
- Department of Microbiology, Immunology and Pathology, College of Veterinary Medicine and Biomedical Sciences, Colorado State University, Fort Collins, CO 80523, USA
- Arthropod-borne Infectious Disease Laboratories, College of Veterinary Medicine and Biomedical Sciences, Colorado State University, Fort Collins, CO 80523, USA
| | - William C Black
- Department of Microbiology, Immunology and Pathology, College of Veterinary Medicine and Biomedical Sciences, Colorado State University, Fort Collins, CO 80523, USA
- Arthropod-borne Infectious Disease Laboratories, College of Veterinary Medicine and Biomedical Sciences, Colorado State University, Fort Collins, CO 80523, USA
| | - Rebekah C Kading
- Department of Microbiology, Immunology and Pathology, College of Veterinary Medicine and Biomedical Sciences, Colorado State University, Fort Collins, CO 80523, USA
- Arthropod-borne Infectious Disease Laboratories, College of Veterinary Medicine and Biomedical Sciences, Colorado State University, Fort Collins, CO 80523, USA
| | - Gregory D Ebel
- Department of Microbiology, Immunology and Pathology, College of Veterinary Medicine and Biomedical Sciences, Colorado State University, Fort Collins, CO 80523, USA
- Arthropod-borne Infectious Disease Laboratories, College of Veterinary Medicine and Biomedical Sciences, Colorado State University, Fort Collins, CO 80523, USA
| | - Guillermina Kuan
- Centro de Salud Sócrates Flores Vivas, Ministry of Health, Managua, Nicaragua
| | - Angel Balmaseda
- Laboratorio Nacional de Virología, Centro Nacional de Diagnóstico y Referencia, Ministry of Health, Managua, Nicaragua
| | - Thomas Jaenisch
- Section Clinical Tropical Medicine, Department for Infectious Diseases, Heidelberg University Hospital, Heidelberg, Germany
- German Centre for Infection Research (DZIF), partner site Heidelberg, Heidelberg, Germany
| | - Ernesto T A Marques
- Laboratory of Virology and Experimental Therapeutics, Centro de Pesquisas Aggeu Magalhaes, Fundacao Oswaldo Cruz, Recife-PE, Brazil
- Center for Vaccine Research, School of Public Health, University of Pittsburgh, Pittsburgh, PA 15261, USA
| | - Aaron C Brault
- Division of Vector-Borne Diseases, Centers for Disease Control and Prevention, Fort Collins, CO 80521, USA
| | - Eva Harris
- Division of Infectious Diseases and Vaccinology, School of Public Health, University of California, Berkeley, Berkeley, CA 94720-7360, USA
| | - Brian D Foy
- Department of Microbiology, Immunology and Pathology, College of Veterinary Medicine and Biomedical Sciences, Colorado State University, Fort Collins, CO 80523, USA
- Arthropod-borne Infectious Disease Laboratories, College of Veterinary Medicine and Biomedical Sciences, Colorado State University, Fort Collins, CO 80523, USA
| | - Sandra L Quackenbush
- Department of Microbiology, Immunology and Pathology, College of Veterinary Medicine and Biomedical Sciences, Colorado State University, Fort Collins, CO 80523, USA
| | - Rushika Perera
- Department of Microbiology, Immunology and Pathology, College of Veterinary Medicine and Biomedical Sciences, Colorado State University, Fort Collins, CO 80523, USA
- Arthropod-borne Infectious Disease Laboratories, College of Veterinary Medicine and Biomedical Sciences, Colorado State University, Fort Collins, CO 80523, USA
| | - Joel Rovnak
- Department of Microbiology, Immunology and Pathology, College of Veterinary Medicine and Biomedical Sciences, Colorado State University, Fort Collins, CO 80523, USA.
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21
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Patel P, Abd El Wahed A, Faye O, Prüger P, Kaiser M, Thaloengsok S, Ubol S, Sakuntabhai A, Leparc-Goffart I, Hufert FT, Sall AA, Weidmann M, Niedrig M. A Field-Deployable Reverse Transcription Recombinase Polymerase Amplification Assay for Rapid Detection of the Chikungunya Virus. PLoS Negl Trop Dis 2016; 10:e0004953. [PMID: 27685649 PMCID: PMC5042537 DOI: 10.1371/journal.pntd.0004953] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2016] [Accepted: 08/03/2016] [Indexed: 01/02/2023] Open
Abstract
Background Chikungunya virus (CHIKV) is a mosquito-borne virus currently transmitted in about 60 countries. CHIKV causes acute flu-like symptoms and in many cases prolonged musculoskeletal and joint pain. Detection of the infection is mostly done using RT-RCR or ELISA, which are not suitable for point-of-care diagnosis. Methodology/Principal Findings In this study, a reverse transcription recombinase polymerase amplification (RT-RPA) assay for the detection of the CHIKV was developed. The assay sensitivity, specificity, and cross-reactivity were tested. CHIKV RT-RPA assay detected down to 80 genome copies/reaction in a maximum of 15 minutes. It successfully identified 18 isolates representing the three CHIKV genotypes. No cross-reactivity was detected to other alphaviruses and arboviruses except O'nyong'nyong virus, which could be differentiated by a modified RPA primer pair. Seventy-eight samples were screened both by RT-RPA and real-time RT-PCR. The diagnostic sensitivity and specificity of the CHIKV RT-RPA assay were determined at 100%. Conclusions/Significance The developed RT-RPA assay represents a promising method for the molecular detection of CHIKV at point of need. CHIKV is transmitted to humans via mosquitos. CHIKV induces clinical signs similar to Influenza, Dengue, and Zika viruses. We have developed a molecular assay for the detection of CHIKV genome based on isothermal„recombinase polymerase amplification (RPA) assay”performed at 42°C. The result was obtained in maximum of 15 minutes, which is 4–6 times faster than the current molecular diagnostic techniques. Our CHIKV RPA assay is rapid and sensitive, as well as easy to use at the point of need.
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Affiliation(s)
- Pranav Patel
- Centre for Biological Threats and Special Pathogens, Robert Koch Institute, Berlin, Germany
| | - Ahmed Abd El Wahed
- Division of Microbiology and Animal Hygiene, Georg-August-University, Goettingen, Germany
| | - Oumar Faye
- Arbovirus Unit, Pasteur Institute, Dakar, Senegal
| | - Pauline Prüger
- Centre for Biological Threats and Special Pathogens, Robert Koch Institute, Berlin, Germany
| | - Marco Kaiser
- GenExpress Gesellschaft für Proteindesign, Berlin, Germany
| | - Sasikanya Thaloengsok
- Department of Microbiology, Faculty of Science, Mahidol University, Bangkok, Thailand
| | - Sukathida Ubol
- Department of Microbiology, Faculty of Science, Mahidol University, Bangkok, Thailand
| | - Anavaj Sakuntabhai
- Functional Genetics of Infectious Diseases Unit, Institute Pasteur, Paris, France
| | | | - Frank T. Hufert
- Institute of Microbiology & Virology, Brandenburg Medical School Fontane, Senftenberg, Germany
| | | | - Manfred Weidmann
- Institute of Aquaculture, University of Stirling, Stirling, Scotland, United Kingdom
| | - Matthias Niedrig
- Centre for Biological Threats and Special Pathogens, Robert Koch Institute, Berlin, Germany
- * E-mail:
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22
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Chen H, Parimelalagan M, Lai YL, Lee KS, Koay ESC, Hapuarachchi HC, Ng LC, Ho PS, Chu JJH. Development and Evaluation of a SYBR Green-Based Real-Time Multiplex RT-PCR Assay for Simultaneous Detection and Serotyping of Dengue and Chikungunya Viruses. J Mol Diagn 2016; 17:722-8. [PMID: 26455921 PMCID: PMC7106138 DOI: 10.1016/j.jmoldx.2015.06.008] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2015] [Revised: 05/27/2015] [Accepted: 06/17/2015] [Indexed: 01/14/2023] Open
Abstract
Chikungunya virus (CHIKV) and dengue virus (DENV) have emerged as the two most important arbovirus diseases of global health significance. Similar clinical manifestations, transmission vectors, geographical distribution, and seasonal correlation often result in misdiagnosis of chikungunya infections as dengue cases and vice versa. In this study, we developed a rapid and accurate laboratory confirmative method to simultaneously detect, quantify, and differentiate DENV serotypes 1, 2, 3, and 4 and CHIKV. This SYBR Green I–based one-step multiplex real-time RT-PCR assay is highly sensitive and specific for CHIKV and DENV. Melting temperature analysis of PCR amplicons was used to serotype DENV and to differentiate from CHIKV. The detection limit of the assay was 20, 10, 50, 5, and 10 RNA copies/reaction for DENV-1, DENV-2, DENV-3, DENV-4, and CHIKV, respectively. Our assay did not cross-react with a panel of viruses that included other flaviviruses, alphaviruses, influenza viruses, human enteroviruses, and human coronaviruses. The feasibility of using this assay for clinical diagnosis was evaluated in DENV- and CHIKV-positive patient sera. Accordingly, the assay sensitivity for DENV-1, DENV-2, DENV-3, DENV-4, and CHIKV was 89.66%, 96.67%, 96.67%, 94.12%, and 95.74%, respectively, with 100% specificity. These findings confirmed the potential of our assay to be used as a rapid test for simultaneous detection and serotyping of DENV and CHIKV in clinical samples.
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Affiliation(s)
- Huixin Chen
- Laboratory of Molecular RNA Virology and Antiviral Strategies, Department of Microbiology, National University Health System, National University of Singapore, Singapore
| | | | - Yee Ling Lai
- Environmental Health Institute, National Environment Agency, Singapore
| | - Kim Sung Lee
- Environmental Health Institute, National Environment Agency, Singapore
| | - Evelyn Siew-Chuan Koay
- Departments of Laboratory Medicine and Pathology, Molecular Diagnosis Centre, Yong Loo Lin School of Medicine, National University Health System, National University of Singapore, Singapore
| | | | - Lee Ching Ng
- Environmental Health Institute, National Environment Agency, Singapore
| | - Phui San Ho
- School of Applied Science, Republic Polytechnic, Singapore.
| | - Justin Jang Hann Chu
- Laboratory of Molecular RNA Virology and Antiviral Strategies, Department of Microbiology, National University Health System, National University of Singapore, Singapore.
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23
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Duncan R, Kourout M, Grigorenko E, Fisher C, Dong M. Advances in multiplex nucleic acid diagnostics for blood-borne pathogens: promises and pitfalls. Expert Rev Mol Diagn 2015; 16:83-95. [PMID: 26581018 DOI: 10.1586/14737159.2016.1112272] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
The large number of blood-borne viruses, bacteria and parasites currently of concern, as well as many newly emerging pathogens, presents a daunting challenge to protection of the safety of blood for transfusion and diagnosing infectious diseases. Focusing on nucleic acid diagnostic tests, multiplex devices are coming into use with many more in various developmental stages that promise to offer solutions to the clinical need. The characteristics, advantages and disadvantages of platforms in clinical use and at the research and development stage are examined here. The presence of multiple assays and associated reagents operating simultaneously on one platform, implementation in traditional clinical laboratories and regulatory review will present special challenges. Fortunately, clinical laboratories have made dramatic technical progress in the last two decades and regulatory agencies have publicly expressed support for development of multiplex devices.
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Affiliation(s)
- Robert Duncan
- a Center for Biologics Evaluation and Research , US FDA , Silver Spring , MD , USA
| | - Moussa Kourout
- a Center for Biologics Evaluation and Research , US FDA , Silver Spring , MD , USA
| | | | - Carolyn Fisher
- a Center for Biologics Evaluation and Research , US FDA , Silver Spring , MD , USA
| | - Ming Dong
- a Center for Biologics Evaluation and Research , US FDA , Silver Spring , MD , USA
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24
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Hu SF, Li M, Zhong LL, Lu SM, Liu ZX, Pu JY, Wen JS, Huang X. Development of reverse-transcription loop-mediated isothermal amplification assay for rapid detection and differentiation of dengue virus serotypes 1-4. BMC Microbiol 2015; 15:265. [PMID: 26572227 PMCID: PMC4647581 DOI: 10.1186/s12866-015-0595-1] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2015] [Accepted: 10/30/2015] [Indexed: 12/03/2022] Open
Abstract
Background Dengue virus (DENV), the most widely prevalent arbovirus, continues to be a threat to human health in the tropics and subtropics. Early and rapid detection of DENV infection during the acute phase of illness is crucial for proper clinical patient management and preventing the spread of infection. The aim of the current study was to develop a specific, sensitive, and robust reverse transcriptase loop-mediated isothermal amplification (RT-LAMP) assay for detection and differentiation of DENV1-4 serotypes. Results The method detection primers, which were designed to target the different DENV serotypes, were identified by inspection of multiple sequence alignments of the non-structural protein (NS) 2A of DENV1, NS4B of DENV2, NS4A of DENV3 and the 3′ untranslated region of the NS protein of DENV4. No cross-reactions of the four serotypes were observed during the tests. The detection limits of the DENV1-4-specific RT-LAMP assays were approximately 10-copy templates per reaction. The RT-LAMP assays were ten-fold more sensitive than RT-PCR or real-time PCR. The diagnostic rate was 100 % for clinical strains of DENV, and 98.9 % of the DENV-infected patients whose samples were tested were detected by RT-LAMP. Importantly, no false-positives were detected with the new equipment and methodology that was used to avoid aerosol contamination of the samples. Conclusion The RT-LAMP method used in our study is specific, sensitive, and suitable for further investigation as a useful alternative to the current methods used for clinical diagnosis of DENV1-4, especially in hospitals and laboratories that lack sophisticated diagnostic systems.
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Affiliation(s)
- Sheng-feng Hu
- Program of Immunology, Institute of Human Virology, Affiliated Guangzhou Women and Children's Medical Center, Zhongshan School of Medicine, Sun Yat-sen University, 74 Zhongshan 2nd Road, Guangzhou, 510080, China. .,Key Laboratory of Tropical Diseases Control (Sun Yat-sen University), Ministry of Education, Guangzhou, 510080, China.
| | - Miao Li
- Program of Immunology, Institute of Human Virology, Affiliated Guangzhou Women and Children's Medical Center, Zhongshan School of Medicine, Sun Yat-sen University, 74 Zhongshan 2nd Road, Guangzhou, 510080, China. .,Key Laboratory of Tropical Diseases Control (Sun Yat-sen University), Ministry of Education, Guangzhou, 510080, China.
| | - Lan-lan Zhong
- Program of Immunology, Institute of Human Virology, Affiliated Guangzhou Women and Children's Medical Center, Zhongshan School of Medicine, Sun Yat-sen University, 74 Zhongshan 2nd Road, Guangzhou, 510080, China. .,Key Laboratory of Tropical Diseases Control (Sun Yat-sen University), Ministry of Education, Guangzhou, 510080, China.
| | - Shi-miao Lu
- Program of Immunology, Institute of Human Virology, Affiliated Guangzhou Women and Children's Medical Center, Zhongshan School of Medicine, Sun Yat-sen University, 74 Zhongshan 2nd Road, Guangzhou, 510080, China. .,Key Laboratory of Tropical Diseases Control (Sun Yat-sen University), Ministry of Education, Guangzhou, 510080, China.
| | - Ze-xia Liu
- Program of Immunology, Institute of Human Virology, Affiliated Guangzhou Women and Children's Medical Center, Zhongshan School of Medicine, Sun Yat-sen University, 74 Zhongshan 2nd Road, Guangzhou, 510080, China. .,Key Laboratory of Tropical Diseases Control (Sun Yat-sen University), Ministry of Education, Guangzhou, 510080, China.
| | - Jie-ying Pu
- Program of Immunology, Institute of Human Virology, Affiliated Guangzhou Women and Children's Medical Center, Zhongshan School of Medicine, Sun Yat-sen University, 74 Zhongshan 2nd Road, Guangzhou, 510080, China. .,Key Laboratory of Tropical Diseases Control (Sun Yat-sen University), Ministry of Education, Guangzhou, 510080, China.
| | - Jin-sheng Wen
- Department of microbiology and immunology, Wenzhou, Medical University, Wenzhou, China.
| | - Xi Huang
- Program of Immunology, Institute of Human Virology, Affiliated Guangzhou Women and Children's Medical Center, Zhongshan School of Medicine, Sun Yat-sen University, 74 Zhongshan 2nd Road, Guangzhou, 510080, China. .,Key Laboratory of Tropical Diseases Control (Sun Yat-sen University), Ministry of Education, Guangzhou, 510080, China. .,Department of microbiology and immunology, Wenzhou, Medical University, Wenzhou, China.
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25
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Nunes MRT, Vianez JL, Nunes KNB, da Silva SP, Lima CPS, Guzman H, Martins LC, Carvalho VL, Tesh RB, Vasconcelos PFC. Analysis of a Reverse Transcription Loop-mediated Isothermal Amplification (RT-LAMP) for yellow fever diagnostic. J Virol Methods 2015; 226:40-51. [PMID: 26459206 DOI: 10.1016/j.jviromet.2015.10.003] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2015] [Revised: 10/06/2015] [Accepted: 10/07/2015] [Indexed: 12/23/2022]
Abstract
Yellow Fever virus (YFV) is an important human pathogen in tropical areas of Africa and South America. Although an efficient vaccine is available and has been used since the early 1940s, sylvatic YFV transmission still occurs in forested areas where anthropogenic actions are present, such as mineral extraction, rearing livestock and agriculture, and ecological tourism. In this context, two distinct techniques based on the RT-PCR derived method have been previously developed, however both methods are expensive due to the use of thermo cyclers and labeled probes. We developed isothermal genome amplification, which is a rapid, sensitive, specific and low cost molecular approach for YFV genome detection. This assay used a set of degenerate primers designed for the NS1 gene and was able to amplify, within 30 min in isothermal conditions, the YFV 17D vaccine strain derived from an African wild prototype strain (Asibi), as well as field strains from Brazil, other endemic countries from South and Central America, and the Caribbean. The generic RT-LAMP assay could be helpful for YFV surveillance in field and rapid response during outbreaks in endemic areas.
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Affiliation(s)
- Marcio R T Nunes
- Center for Technological Innovation, Evandro Chagas Institute, Brazilian Ministry of Health, Ananindeua, Pará, Brazil.
| | - João Lídio Vianez
- Center for Technological Innovation, Evandro Chagas Institute, Brazilian Ministry of Health, Ananindeua, Pará, Brazil
| | - Keley N B Nunes
- Center for Technological Innovation, Evandro Chagas Institute, Brazilian Ministry of Health, Ananindeua, Pará, Brazil
| | - Sandro Patroca da Silva
- Center for Technological Innovation, Evandro Chagas Institute, Brazilian Ministry of Health, Ananindeua, Pará, Brazil
| | - Clayton P S Lima
- Center for Technological Innovation, Evandro Chagas Institute, Brazilian Ministry of Health, Ananindeua, Pará, Brazil
| | - Hilda Guzman
- Department of Pathology, University of Texas Medical Branch, Galveston, TX, USA
| | - Lívia C Martins
- Department of Arbovirology and Hemorrhagic Fevers, Evandro Chagas Institute, Brazilian Ministry of Health, Ananindeua, Pará, Brazil
| | - Valéria L Carvalho
- Department of Arbovirology and Hemorrhagic Fevers, Evandro Chagas Institute, Brazilian Ministry of Health, Ananindeua, Pará, Brazil
| | - Robert B Tesh
- Department of Pathology, University of Texas Medical Branch, Galveston, TX, USA
| | - Pedro F C Vasconcelos
- Department of Arbovirology and Hemorrhagic Fevers, Evandro Chagas Institute, Brazilian Ministry of Health, Ananindeua, Pará, Brazil; Department of Pathology, University of Para State, Belem, Brazil
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26
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Diagnostic Options and Challenges for Dengue and Chikungunya Viruses. BIOMED RESEARCH INTERNATIONAL 2015; 2015:834371. [PMID: 26509163 PMCID: PMC4609775 DOI: 10.1155/2015/834371] [Citation(s) in RCA: 58] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 03/10/2015] [Revised: 06/23/2015] [Accepted: 06/25/2015] [Indexed: 01/16/2023]
Abstract
Dengue virus (DENV) and Chikungunya virus (CHIKV) are arboviruses that share the same Aedes mosquito vectors and thus overlap in their endemic areas. These two viruses also cause similar clinical presentations, especially in the initial stages of infection, with neither virus possessing any specific distinguishing clinical features. Because the outcomes and management strategies for these two viruses are vastly different, early and accurate diagnosis is imperative. Diagnosis is also important for surveillance, outbreak control, and research related to vaccine and drug development. Available diagnostic tests are aimed at detection of the virus, its antigenic components, or the host immune antibody response. In this review, we describe the recent progress and continued challenges related to the diagnosis of DENV and CHIKV infections.
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Zhang B, Salieb-Beugelaar GB, Nigo MM, Weidmann M, Hunziker P. Diagnosing dengue virus infection: rapid tests and the role of micro/nanotechnologies. NANOMEDICINE-NANOTECHNOLOGY BIOLOGY AND MEDICINE 2015; 11:1745-61. [PMID: 26093055 DOI: 10.1016/j.nano.2015.05.009] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/24/2015] [Revised: 05/15/2015] [Accepted: 05/25/2015] [Indexed: 12/18/2022]
Abstract
UNLABELLED Due to the progressive spread of the dengue virus and a rising incidence of dengue disease, its rapid diagnosis is important for developing countries and of increasing relevance for countries in temperate climates. Recent advances in bioelectronics, micro- and nanofabrication technologies have led to new miniaturized point-of-care devices and analytical platforms suited for rapid detection of infections. Starting from the available tests for dengue diagnosis, this review examines emerging rapid, micro/nanotechnologies-based tools, including label-free biosensor methods, microarray and microfluidic platforms, which hold significant potential, but still need further development and evaluation. The epidemiological and clinical setting as key determinants for selecting the best analytical strategy in patients presenting with fever is then discussed. This review is aimed at the clinicians and microbiologists to deepen understanding and enhance application of dengue diagnostics, and also serves as knowledge base for researchers and test developers to overcome the challenges posed by this disease. FROM THE CLINICAL EDITOR Dengue disease remains a significant problem in many developing countries. Unfortunately rapid diagnosis with easy and low cost tests for this disease is currently still not realized. In this comprehensive review, the authors highlighted recent advances in nanotechnology which would enable development in this field, which would result in beneficial outcomes to the population.
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Affiliation(s)
- Bei Zhang
- Nanomedicine Research Laboratory, Medical Intensive Care Clinic, University Hospital Basel, Basel, Switzerland.
| | - Georgette B Salieb-Beugelaar
- Nanomedicine Research Laboratory, Medical Intensive Care Clinic, University Hospital Basel, Basel, Switzerland; CLINAM-European Foundation for Clinical Nanomedicine, Basel, Switzerland.
| | - Maurice Mutro Nigo
- Nanomedicine Research Laboratory, Medical Intensive Care Clinic, University Hospital Basel, Basel, Switzerland; Institut Supérieur des Techniques Médicales-NYANKUNDE, Bunia, Congo.
| | | | - Patrick Hunziker
- Nanomedicine Research Laboratory, Medical Intensive Care Clinic, University Hospital Basel, Basel, Switzerland; CLINAM-European Foundation for Clinical Nanomedicine, Basel, Switzerland.
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Neeraja M, Lakshmi V, Lavanya V, Priyanka EN, Parida MM, Dash PK, Sharma S, Rao PVL, Reddy G. Rapid detection and differentiation of dengue virus serotypes by NS1 specific reverse transcription loop-mediated isothermal amplification (RT-LAMP) assay in patients presenting to a tertiary care hospital in Hyderabad, India. J Virol Methods 2014; 211:22-31. [PMID: 25455901 PMCID: PMC7119600 DOI: 10.1016/j.jviromet.2014.10.005] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2014] [Revised: 10/04/2014] [Accepted: 10/10/2014] [Indexed: 11/24/2022]
Abstract
This research article highlights the development of an improved, inexpensive, faster, sensitive and specific RT-LAMP assay for detection and serotyping of DENV, targeting NS1 region using Genie II fluorometer. RT-LAMP or CDC Real time assay when used in combination with NS1 antigen and anti Dengue IgG and IgM Elisa increased the diagnostic coverage of febrile patients to 96%. Tm values and anneal curves displayed at the end of the reaction eliminates the need for gel electrophoresis or turbidity detection and allows for a closed-tube system thus reducing the cost of the assay.
Early and rapid detection of dengue virus (DENV) infection during the acute phase of illness is crucial for proper patient management and prevention of the spread of the infection. In the present study, the standardization and validation of a one step, four tube reverse transcription loop-mediated isothermal amplification assay (RT-LAMP) for rapid detection and serotyping of the DENV targeting NS1 gene using the Genie® II flourometer was carried out. The performance of the RT-LAMP was compared to RT-PCR, CDC 1-4 Real time PCR and the NS1 antigen ELISA, IgM and IgG anti DENV antibodies. Acute DENV infection was confirmed in 250/300 patients suspected clinically of DENV infection. RT- LAMP and CDC 1-4 Real time PCR assay was positive in 148/250 patients, while 92/250 patients were positive for anti- Dengue IgM and IgG antibodies. The RT-LAMP assay and the CDC real-time RT-PCR assay showed high concordance (k = 1.0). The detection rate of acute DENV infection improved to 96% (240/250) when the results of RT-LAMP were combined with NS1 Ag, IgM and IgG ELISA. The RT-LAMP had a detection limit of 100 copies for DEN-1 and DEN-2, 10 copies for DEN-3 and DEN-4 compared to 1000 copies for DEN-1 and DEN-2, 100 copies for DEN-3 and DEN-4 by the conventional RT-PCR. The assay showed 100% specificity. The RT-LAMP assay developed in this study has potential use for early clinical diagnosis, serotyping and surveillance of DENV infection in endemic countries such as India.
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Affiliation(s)
- M Neeraja
- Dept. of Microbiology, Nizam's Institute of Medical Sciences, Punjagutta, Hyderabad 500082, Andhra Pradesh, India.
| | - V Lakshmi
- Dept. of Microbiology, Nizam's Institute of Medical Sciences, Punjagutta, Hyderabad 500082, Andhra Pradesh, India.
| | - Vanjari Lavanya
- Dept. of Microbiology, Nizam's Institute of Medical Sciences, Punjagutta, Hyderabad 500082, Andhra Pradesh, India.
| | - E N Priyanka
- Dept. of Microbiology, Nizam's Institute of Medical Sciences, Punjagutta, Hyderabad 500082, Andhra Pradesh, India.
| | - M M Parida
- Department of Virology, Defense R&D Establishment, DRDE, DRDO, Ministry of Defence, Jhansi Road, Gwalior 474002, Madhya Pradesh, India.
| | - P K Dash
- Department of Virology, Defense R&D Establishment, DRDE, DRDO, Ministry of Defence, Jhansi Road, Gwalior 474002, Madhya Pradesh, India.
| | - Shashi Sharma
- Department of Virology, Defense R&D Establishment, DRDE, DRDO, Ministry of Defence, Jhansi Road, Gwalior 474002, Madhya Pradesh, India.
| | | | - Gopal Reddy
- Dept. of Microbiology, Osmania University, Hyderabad 500007, Andhra Pradesh, India.
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Woźniakowski G, Samorek-Salamonowicz E. First survey of the occurrence of duck enteritis virus (DEV) in free-ranging Polish water birds. Arch Virol 2013; 159:1439-44. [DOI: 10.1007/s00705-013-1936-8] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2013] [Accepted: 10/27/2013] [Indexed: 11/28/2022]
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Chikungunya emergency in China: microevolution and genetic analysis for a local outbreak. Virus Genes 2013; 48:15-22. [DOI: 10.1007/s11262-013-0991-2] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2013] [Accepted: 10/03/2013] [Indexed: 12/29/2022]
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Teoh BT, Sam SS, Tan KK, Johari J, Danlami MB, Hooi PS, Md-Esa R, AbuBakar S. Detection of dengue viruses using reverse transcription-loop-mediated isothermal amplification. BMC Infect Dis 2013; 13:387. [PMID: 23964963 PMCID: PMC3846474 DOI: 10.1186/1471-2334-13-387] [Citation(s) in RCA: 69] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2013] [Accepted: 08/16/2013] [Indexed: 11/15/2022] Open
Abstract
Background Early and rapid detection of dengue virus (DENV) infection during the febrile period is crucial for proper patient management and prevention of disease spread. An easy to perform and highly sensitive method is needed for routine implementation especially in the resource-limited rural healthcare settings where dengue is endemic. Methods A single-tube reverse transcription-loop-mediated isothermal amplification (RT-LAMP) assay with a set of nine primers was developed for the detection of all four DENV serotypes and their different genotypes. The sensitivity and specificity of the RT-LAMP were evaluated. The clinical applicability of RT-LAMP assay for detection of DENV RNA was assessed in a total of 305 sera of clinically-suspected dengue patients. The test results of RT-LAMP were statistically compared to those of quantitative reverse transcription-polymerase chain reaction (qRT-PCR), IgM- and IgG-capture enzyme-linked immunosorbent assays (ELISA). Results Acute DENV infection was confirmed in 171 samples (n = 305); 43.3% (74/171) and 46.8% (80/171) of the samples were positive for DENV using RT-LAMP and qRT-PCR, respectively. The combination of RT-LAMP with the dengue IgM and IgG ELISA increased detection of acute DENV infection to 97.7% (167/171), in comparison to only 70.8% (121/171) when dengue IgM and IgG ELISA alone were used. The RT-LAMP assays showed high concordance (κ = 0.939) with the qRT-PCR. The RT-LAMP assay detected up to 10 copies of virus RNA within an hour but 100% reproducibility (12/12) was achieved with 100 copies. There was no cross reactivity of RT-LAMP with other closely related arboviruses. Conclusion The RT-LAMP assay developed in this study is sensitive, specific and simple to perform. The assay improved the detection of dengue when used in combination with serological methods.
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Affiliation(s)
- Boon-Teong Teoh
- Tropical Infectious Diseases Research and Education Centre (TIDREC), Department of Medical Microbiology, Faculty of Medicine, University of Malaya, Kuala Lumpur 50603, Malaysia.
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Mori Y, Kanda H, Notomi T. Loop-mediated isothermal amplification (LAMP): recent progress in research and development. J Infect Chemother 2013; 19:404-11. [PMID: 23539453 PMCID: PMC7088141 DOI: 10.1007/s10156-013-0590-0] [Citation(s) in RCA: 171] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2013] [Indexed: 11/21/2022]
Abstract
Loop-mediated isothermal amplification (LAMP) is an established technology that continues to attract the attention of researchers in many fields. Research and development efforts on LAMP technology in recent years have focused on two major areas; first, the study of its clinical application as an approved in vitro diagnostics tool in Japan and certain other countries; and second, research aimed at further simplifying the LAMP test process. This review provides an overview of the status of LAMP on these two topics by summarizing research work conducted, in the main, after our previous review article.
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Affiliation(s)
- Yasuyoshi Mori
- Eiken Chemical Co., Ltd, 1381-3 Shimoishigami, Ohtawara, Tochigi, Japan.
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