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Li X, Dang Z, Tang W, Zhang H, Shao J, Jiang R, Zhang X, Huang F. Detection of Parasites in the Field: The Ever-Innovating CRISPR/Cas12a. BIOSENSORS 2024; 14:145. [PMID: 38534252 DOI: 10.3390/bios14030145] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/19/2023] [Revised: 03/11/2024] [Accepted: 03/12/2024] [Indexed: 03/28/2024]
Abstract
The rapid and accurate identification of parasites is crucial for prompt therapeutic intervention in parasitosis and effective epidemiological surveillance. For accurate and effective clinical diagnosis, it is imperative to develop a nucleic-acid-based diagnostic tool that combines the sensitivity and specificity of nucleic acid amplification tests (NAATs) with the speed, cost-effectiveness, and convenience of isothermal amplification methods. A new nucleic acid detection method, utilizing the clustered regularly interspaced short palindromic repeats (CRISPR)-associated (Cas) nuclease, holds promise in point-of-care testing (POCT). CRISPR/Cas12a is presently employed for the detection of Plasmodium falciparum, Toxoplasma gondii, Schistosoma haematobium, and other parasites in blood, urine, or feces. Compared to traditional assays, the CRISPR assay has demonstrated notable advantages, including comparable sensitivity and specificity, simple observation of reaction results, easy and stable transportation conditions, and low equipment dependence. However, a common issue arises as both amplification and cis-cleavage compete in one-pot assays, leading to an extended reaction time. The use of suboptimal crRNA, light-activated crRNA, and spatial separation can potentially weaken or entirely eliminate the competition between amplification and cis-cleavage. This could lead to enhanced sensitivity and reduced reaction times in one-pot assays. Nevertheless, higher costs and complex pre-test genome extraction have hindered the popularization of CRISPR/Cas12a in POCT.
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Affiliation(s)
- Xin Li
- School of Life Science and Engineering, Foshan University, Foshan 528225, China
| | - Zhisheng Dang
- National Institute of Parasitic Diseases, Chinese Center for Diseases Control and Prevention (Chinese Center for Tropical Diseases Research), Key Laboratory of Parasite and Vector Biology, National Health Commission of the People's Republic of China (NHC), World Health Organization (WHO) Collaborating Center for Tropical Diseases, National Center for International Research on Tropical Diseases, Shanghai 200025, China
| | - Wenqiang Tang
- State Key Laboratory of Hulless Barley and Yak Germplasm Resources and Genetic Improvement, Lhasa 850002, China
- Tibet Academy of Agriculture and Animal Husbandry Sciences, Lhasa 850002, China
| | - Haoji Zhang
- School of Life Science and Engineering, Foshan University, Foshan 528225, China
| | - Jianwei Shao
- School of Life Science and Engineering, Foshan University, Foshan 528225, China
| | - Rui Jiang
- College of Animal Science and Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China
| | - Xu Zhang
- School of Life Science and Engineering, Foshan University, Foshan 528225, China
| | - Fuqiang Huang
- School of Life Science and Engineering, Foshan University, Foshan 528225, China
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Ebai R, Kien CA, Fombad FF, Esofi F, Ouam E, Ntuh AN, Amambo GN, Gandjui VNT, Chunda VC, Nietcho F, Nchang LC, Magha C, Cho JF, Esum ME, Enyong PI, Pfarr K, Hoerauf A, Ritter M, Wanji S. Culicoides Species of the Rain Forest Belt of the Littoral Region of Cameroon: Their Incrimination in the Transmission of Mansonella perstans. Pathogens 2024; 13:146. [PMID: 38392884 PMCID: PMC10892414 DOI: 10.3390/pathogens13020146] [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: 11/28/2023] [Revised: 01/05/2024] [Accepted: 01/30/2024] [Indexed: 02/25/2024] Open
Abstract
Biting midges belonging to the genus Culicoides are tiny stout-shaped hematophagous insects and are thought to transmit the filarial nematode Mansonella perstans. Little is known about the Culicoides fauna in the rain forest belt of the Littoral Region of Cameroon. This study was designed to investigate the diversity, abundance and distribution of Culicoides spp. and their role as the purported vector(s) of M. perstans. Overnight light trap collections and human landing catches (HLCs) revealed eight species of Culicoides with C. grahamii being the most abundant species followed by C. milnei. Four anthropophilic species (C. inornatipennis, C. grahamii, C. fulvithorax and C. milnei) were determined by the HLCs with a higher abundance in the 4-6 p.m. collections. The drop trap technique and Mp419 LAMP assay confirmed C. milnei to be the most efficient vector in enabling the development of the microfilarial stage to the infective larval form of M. perstans. The LAMP assay also revealed that natural transmission of this nematode is fostered by C. milnei and C. grahamii in the wild. In conclusion, C. milnei was shown to be the main vector of M. perstans in the rain forest belt of the Littoral Region of Cameroon.
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Affiliation(s)
- Rene Ebai
- Parasite and Vector Research Unit (PAVRU), Department of Microbiology and Parasitology, University of Buea, Buea P.O. Box 63, Cameroon (C.A.K.); (A.N.N.); (V.N.T.G.); (V.C.C.); (C.M.)
- Research Foundation for Tropical Diseases and the Environment (REFOTDE), Buea P.O. Box 63, Cameroon
| | - Chi Anizette Kien
- Parasite and Vector Research Unit (PAVRU), Department of Microbiology and Parasitology, University of Buea, Buea P.O. Box 63, Cameroon (C.A.K.); (A.N.N.); (V.N.T.G.); (V.C.C.); (C.M.)
- Research Foundation for Tropical Diseases and the Environment (REFOTDE), Buea P.O. Box 63, Cameroon
| | - Fanny Fri Fombad
- Parasite and Vector Research Unit (PAVRU), Department of Microbiology and Parasitology, University of Buea, Buea P.O. Box 63, Cameroon (C.A.K.); (A.N.N.); (V.N.T.G.); (V.C.C.); (C.M.)
- Research Foundation for Tropical Diseases and the Environment (REFOTDE), Buea P.O. Box 63, Cameroon
| | - Frederick Esofi
- Parasite and Vector Research Unit (PAVRU), Department of Microbiology and Parasitology, University of Buea, Buea P.O. Box 63, Cameroon (C.A.K.); (A.N.N.); (V.N.T.G.); (V.C.C.); (C.M.)
- Research Foundation for Tropical Diseases and the Environment (REFOTDE), Buea P.O. Box 63, Cameroon
| | - Emmanuel Ouam
- Parasite and Vector Research Unit (PAVRU), Department of Microbiology and Parasitology, University of Buea, Buea P.O. Box 63, Cameroon (C.A.K.); (A.N.N.); (V.N.T.G.); (V.C.C.); (C.M.)
- Research Foundation for Tropical Diseases and the Environment (REFOTDE), Buea P.O. Box 63, Cameroon
| | - Anna Ning Ntuh
- Parasite and Vector Research Unit (PAVRU), Department of Microbiology and Parasitology, University of Buea, Buea P.O. Box 63, Cameroon (C.A.K.); (A.N.N.); (V.N.T.G.); (V.C.C.); (C.M.)
- Research Foundation for Tropical Diseases and the Environment (REFOTDE), Buea P.O. Box 63, Cameroon
| | - Glory Ngongeh Amambo
- Parasite and Vector Research Unit (PAVRU), Department of Microbiology and Parasitology, University of Buea, Buea P.O. Box 63, Cameroon (C.A.K.); (A.N.N.); (V.N.T.G.); (V.C.C.); (C.M.)
- Research Foundation for Tropical Diseases and the Environment (REFOTDE), Buea P.O. Box 63, Cameroon
| | - Victor Narcisse Tchamatchoua Gandjui
- Parasite and Vector Research Unit (PAVRU), Department of Microbiology and Parasitology, University of Buea, Buea P.O. Box 63, Cameroon (C.A.K.); (A.N.N.); (V.N.T.G.); (V.C.C.); (C.M.)
- Research Foundation for Tropical Diseases and the Environment (REFOTDE), Buea P.O. Box 63, Cameroon
| | - Valerine Chawa Chunda
- Parasite and Vector Research Unit (PAVRU), Department of Microbiology and Parasitology, University of Buea, Buea P.O. Box 63, Cameroon (C.A.K.); (A.N.N.); (V.N.T.G.); (V.C.C.); (C.M.)
- Research Foundation for Tropical Diseases and the Environment (REFOTDE), Buea P.O. Box 63, Cameroon
| | - Franck Nietcho
- Research Foundation for Tropical Diseases and the Environment (REFOTDE), Buea P.O. Box 63, Cameroon
| | - Lucy Cho Nchang
- Parasite and Vector Research Unit (PAVRU), Department of Microbiology and Parasitology, University of Buea, Buea P.O. Box 63, Cameroon (C.A.K.); (A.N.N.); (V.N.T.G.); (V.C.C.); (C.M.)
- Research Foundation for Tropical Diseases and the Environment (REFOTDE), Buea P.O. Box 63, Cameroon
| | - Chefor Magha
- Parasite and Vector Research Unit (PAVRU), Department of Microbiology and Parasitology, University of Buea, Buea P.O. Box 63, Cameroon (C.A.K.); (A.N.N.); (V.N.T.G.); (V.C.C.); (C.M.)
- Research Foundation for Tropical Diseases and the Environment (REFOTDE), Buea P.O. Box 63, Cameroon
| | - Jerome Fru Cho
- Parasite and Vector Research Unit (PAVRU), Department of Microbiology and Parasitology, University of Buea, Buea P.O. Box 63, Cameroon (C.A.K.); (A.N.N.); (V.N.T.G.); (V.C.C.); (C.M.)
- Research Foundation for Tropical Diseases and the Environment (REFOTDE), Buea P.O. Box 63, Cameroon
| | - Mathias Eyong Esum
- Parasite and Vector Research Unit (PAVRU), Department of Microbiology and Parasitology, University of Buea, Buea P.O. Box 63, Cameroon (C.A.K.); (A.N.N.); (V.N.T.G.); (V.C.C.); (C.M.)
- Research Foundation for Tropical Diseases and the Environment (REFOTDE), Buea P.O. Box 63, Cameroon
| | - Peter Ivo Enyong
- Parasite and Vector Research Unit (PAVRU), Department of Microbiology and Parasitology, University of Buea, Buea P.O. Box 63, Cameroon (C.A.K.); (A.N.N.); (V.N.T.G.); (V.C.C.); (C.M.)
- Research Foundation for Tropical Diseases and the Environment (REFOTDE), Buea P.O. Box 63, Cameroon
| | - Kenneth Pfarr
- Institute of Medical Microbiology, Immunology and Parasitology (IMMIP), University Hospital Bonn (UKB), 53127 Bonn, Germany (A.H.)
- German Centre for Infection Research (DZIF), Partner Site Bonn-Cologne, 53127 Bonn, Germany
| | - Achim Hoerauf
- Institute of Medical Microbiology, Immunology and Parasitology (IMMIP), University Hospital Bonn (UKB), 53127 Bonn, Germany (A.H.)
- German Centre for Infection Research (DZIF), Partner Site Bonn-Cologne, 53127 Bonn, Germany
- German-West African Centre for Global Health and Pandemic Prevention (G-WAC), Partner Site Bonn, 53127 Bonn, Germany
| | - Manuel Ritter
- Institute of Medical Microbiology, Immunology and Parasitology (IMMIP), University Hospital Bonn (UKB), 53127 Bonn, Germany (A.H.)
- German-West African Centre for Global Health and Pandemic Prevention (G-WAC), Partner Site Bonn, 53127 Bonn, Germany
| | - Samuel Wanji
- Parasite and Vector Research Unit (PAVRU), Department of Microbiology and Parasitology, University of Buea, Buea P.O. Box 63, Cameroon (C.A.K.); (A.N.N.); (V.N.T.G.); (V.C.C.); (C.M.)
- Research Foundation for Tropical Diseases and the Environment (REFOTDE), Buea P.O. Box 63, Cameroon
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Portela CS, Mendes de Araújo CP, Moura Sousa P, Gomes Simão CL, Silva de Oliveira JC, Crainey JL. Filarial disease in the Brazilian Amazon and emerging opportunities for treatment and control. CURRENT RESEARCH IN PARASITOLOGY & VECTOR-BORNE DISEASES 2023; 5:100168. [PMID: 38283060 PMCID: PMC10821485 DOI: 10.1016/j.crpvbd.2023.100168] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/04/2023] [Revised: 12/06/2023] [Accepted: 12/15/2023] [Indexed: 01/30/2024]
Abstract
Following the successful eradication of Wuchereria bancrofti, there are now just three species of conventional microfilaremic human filarial parasites endemic to the Brazilian Amazon region: Mansonella ozzardi, Mansonella perstans and Onchocerca volvulus. The zoonotic filarial parasite Dirofilaria immitis is also found in the Amazon region as are several sylvatic filarial parasites, some of which have been recorded causing zoonoses and some of which have never been recorded outside the region. Onchocerca volvulus is only found in the Amazonia onchocerciasis focus in the Brazilian state of Roraima where it affects the people of the Yanomami tribe living around the densely forested Venezuela border region. Mansonella ozzardi is by far the most common filarial parasite in Brazil and has a broad but patchy distribution throughout the western Amazon region. Recorded in the Brazilian states of Acre, Roraima, Matto Grosso, and within almost every municipality of Amazonas state, it is believed that pollution of the urban stream and river systems prevents the development of the simuliid vectors of M. ozzardi and explains the parasite's reduced distribution within urban areas and an absence of recent reports from the state capital Manaus. Decades of WHO-led periodic ivermectin treatment of Yanomami tribe's people have resulted in the partial suppression of O. volvulus transmission in this focus and has also probably affected the transmission of M. ozzardi in the region. Mansonella perstans, O. volvulus and very probably M. ozzardi infections can all be treated and most likely cured with a 4-6-week treatment course of doxycycline. The Brazilian Ministry of Health does not, however, presently recommend any treatment for mansonellosis infections and thus parasitic infections outside the Amazonia focus are typically left untreated. While the long treatment courses required for doxycycline-based mansonellosis therapies preclude their use in control programmes, new fast-acting filarial drug treatments are likely to soon become available for the treatment of both onchocerciasis and mansonellosis in the Amazon region. Filarial disease management in the Brazilian Amazon is thus likely to become dramatically more viable at a time when the public health importance of these diseases is increasingly being recognized.
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Affiliation(s)
- Cleudecir Siqueira Portela
- Instituto Leônidas e Maria Deane, Fundação Oswaldo Cruz Amazônia, Laboratório de Ecologia de Doenças Transmissíveis na Amazônia, Manaus, Amazonas, Brazil
- Programa de Doutorado em Biologia da Interação Patógeno Hospedeiro, Instituto Leônidas e Maria Deane, Manaus, Amazonas, Brazil
| | - Cláudia Patrícia Mendes de Araújo
- Instituto Leônidas e Maria Deane, Fundação Oswaldo Cruz Amazônia, Laboratório de Ecologia de Doenças Transmissíveis na Amazônia, Manaus, Amazonas, Brazil
- Programa de Doutorado em Biologia da Interação Patógeno Hospedeiro, Instituto Leônidas e Maria Deane, Manaus, Amazonas, Brazil
| | - Patrícia Moura Sousa
- Instituto Leônidas e Maria Deane, Fundação Oswaldo Cruz Amazônia, Laboratório de Ecologia de Doenças Transmissíveis na Amazônia, Manaus, Amazonas, Brazil
- Programa de Doutorado em Biologia da Interação Patógeno Hospedeiro, Instituto Leônidas e Maria Deane, Manaus, Amazonas, Brazil
| | - Carla Letícia Gomes Simão
- Instituto Leônidas e Maria Deane, Fundação Oswaldo Cruz Amazônia, Laboratório de Ecologia de Doenças Transmissíveis na Amazônia, Manaus, Amazonas, Brazil
- Programa de Mestrado em Condições de Vida e Situações de Saúde na Amazônia, Instituto Leônidas e Maria Deane, Manaus, Amazonas, Brazil
| | - João Carlos Silva de Oliveira
- Instituto Leônidas e Maria Deane, Fundação Oswaldo Cruz Amazônia, Laboratório de Ecologia de Doenças Transmissíveis na Amazônia, Manaus, Amazonas, Brazil
- Programa de Doutorado em Saúde Pública na Amazônia, Instituto Leônidas e Maria Deane, Fundação Oswaldo Cruz Amazônia, Manaus, Amazonas, Brazil
| | - James Lee Crainey
- Instituto Leônidas e Maria Deane, Fundação Oswaldo Cruz Amazônia, Laboratório de Ecologia de Doenças Transmissíveis na Amazônia, Manaus, Amazonas, Brazil
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CRISPR-Cas12a-assisted elimination of the non-specific signal from non-specific amplification in the Exponential Amplification Reaction. Anal Chim Acta 2023; 1251:340998. [PMID: 36925288 DOI: 10.1016/j.aca.2023.340998] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2023] [Revised: 02/13/2023] [Accepted: 02/21/2023] [Indexed: 02/24/2023]
Abstract
Non-specific amplification is a major problem in nucleic acid amplification resulting in false-positive results, especially for exponential amplification reactions (EXPAR). Although efforts were made to suppress the influence of non-specific amplification, such as chemical blocking of the template's 3'-ends and sequence-independent weakening of template-template interactions, it is still a common problem in many conventional EXPAR reactions. In this study, we propose a novel strategy to eliminate the non-specific signal from non-specific amplification by integrating the CRISPR-Cas12a system into two-templates EXPAR. An EXPAR-Cas12a strategy named EXPCas was developed, where the Cas12a system acted as a filter to filter out non-specific amplificons in EXPAR, suppressing and eliminating the influence of non-specific amplification. As a result, the signal-to-background ratio was improved from 1.3 to 15.4 using this method. With microRNA-21 (miRNA-21) as a target, the detection can be finished in 40 min with a LOD of 103 fM and no non-specific amplification was observed.
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Polatoğlu I, Oncu‐Oner T, Dalman I, Ozdogan S. COVID-19 in early 2023: Structure, replication mechanism, variants of SARS-CoV-2, diagnostic tests, and vaccine & drug development studies. MedComm (Beijing) 2023; 4:e228. [PMID: 37041762 PMCID: PMC10082934 DOI: 10.1002/mco2.228] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2022] [Revised: 01/21/2023] [Accepted: 01/30/2023] [Indexed: 04/13/2023] Open
Abstract
Coronavirus Disease-19 (COVID-19) is an infectious disease caused by severe acute respiratory syndrome-coronaviruses-2 (SARS-CoV-2), a highly pathogenic and transmissible coronavirus. Most cases of COVID-19 have mild to moderate symptoms, including cough, fever, myalgias, and headache. On the other hand, this coronavirus can lead to severe complications and death in some cases. Therefore, vaccination is the most effective tool to prevent and eradicate COVID-19 disease. Also, rapid and effective diagnostic tests are critical in identifying cases of COVID-19. The COVID-19 pandemic has a dynamic structure on the agenda and contains up-to-date developments. This article has comprehensively discussed the most up-to-date pandemic situation since it first appeared. For the first time, not only the structure, replication mechanism, and variants of SARS-CoV-2 (Alpha, Beta, Gamma, Omicron, Delta, Epsilon, Kappa, Mu, Eta, Zeta, Theta, lota, Lambda) but also all the details of the pandemic, such as how it came out, how it spread, current cases, what precautions should be taken, prevention strategies, the vaccines produced, the tests developed, and the drugs used are reviewed in every aspect. Herein, the comparison of diagnostic tests for SARS-CoV-2 in terms of procedure, accuracy, cost, and time has been presented. The mechanism, safety, efficacy, and effectiveness of COVID-19 vaccines against SARS-CoV-2 variants have been evaluated. Drug studies, therapeutic targets, various immunomodulators, and antiviral molecules applied to patients with COVID-19 have been reviewed.
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Affiliation(s)
- Ilker Polatoğlu
- Department of BioengineeringManisa Celal Bayar UniversityYunusemreManisaTurkey
| | - Tulay Oncu‐Oner
- Department of BioengineeringManisa Celal Bayar UniversityYunusemreManisaTurkey
| | - Irem Dalman
- Department of BioengineeringEge UniversityBornovaIzmirTurkey
| | - Senanur Ozdogan
- Department of BioengineeringManisa Celal Bayar UniversityYunusemreManisaTurkey
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Wang G, Wang L, Meng Z, Su X, Jia C, Qiao X, Pan S, Chen Y, Cheng Y, Zhu M. Visual Detection of COVID-19 from Materials Aspect. ADVANCED FIBER MATERIALS 2022; 4:1304-1333. [PMID: 35966612 PMCID: PMC9358106 DOI: 10.1007/s42765-022-00179-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/11/2022] [Accepted: 05/25/2022] [Indexed: 05/25/2023]
Abstract
ABSTRACT In the recent COVID-19 pandemic, World Health Organization emphasized that early detection is an effective strategy to reduce the spread of SARS-CoV-2 viruses. Several diagnostic methods, such as reverse transcription-polymerase chain reaction (RT-PCR) and lateral flow immunoassay (LFIA), have been applied based on the mechanism of specific recognition and binding of the probes to viruses or viral antigens. Although the remarkable progress, these methods still suffer from inadequate cellular materials or errors in the detection and sampling procedure of nasopharyngeal/oropharyngeal swab collection. Therefore, developing accurate, ultrafast, and visualized detection calls for more advanced materials and technology urgently to fight against the epidemic. In this review, we first summarize the current methodologies for SARS-CoV-2 diagnosis. Then, recent representative examples are introduced based on various output signals (e.g., colorimetric, fluorometric, electronic, acoustic). Finally, we discuss the limitations of the methods and provide our perspectives on priorities for future test development.
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Affiliation(s)
- Gang Wang
- State Key Laboratory for Modification of Chemical Fibers and Polymer Materials, College of Materials Science and Engineering, Donghua University, Shanghai, 201620 China
| | - Le Wang
- State Key Laboratory for Modification of Chemical Fibers and Polymer Materials, College of Materials Science and Engineering, Donghua University, Shanghai, 201620 China
| | - Zheyi Meng
- State Key Laboratory for Modification of Chemical Fibers and Polymer Materials, College of Materials Science and Engineering, Donghua University, Shanghai, 201620 China
| | - Xiaolong Su
- State Key Laboratory for Modification of Chemical Fibers and Polymer Materials, College of Materials Science and Engineering, Donghua University, Shanghai, 201620 China
| | - Chao Jia
- State Key Laboratory for Modification of Chemical Fibers and Polymer Materials, College of Materials Science and Engineering, Donghua University, Shanghai, 201620 China
| | - Xiaolan Qiao
- State Key Laboratory for Modification of Chemical Fibers and Polymer Materials, College of Materials Science and Engineering, Donghua University, Shanghai, 201620 China
| | - Shaowu Pan
- State Key Laboratory for Modification of Chemical Fibers and Polymer Materials, College of Materials Science and Engineering, Donghua University, Shanghai, 201620 China
| | - Yinjun Chen
- State Key Laboratory for Modification of Chemical Fibers and Polymer Materials, College of Materials Science and Engineering, Donghua University, Shanghai, 201620 China
| | - Yanhua Cheng
- State Key Laboratory for Modification of Chemical Fibers and Polymer Materials, College of Materials Science and Engineering, Donghua University, Shanghai, 201620 China
| | - Meifang Zhu
- State Key Laboratory for Modification of Chemical Fibers and Polymer Materials, College of Materials Science and Engineering, Donghua University, Shanghai, 201620 China
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7
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Loop mediated isothermal amplification for detection of foodborne parasites: A journey from lab to lab-on-a-chip. Food Control 2022. [DOI: 10.1016/j.foodcont.2022.109251] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
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8
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Ta-Tang TH, Febrer-Sendra B, Berzosa P, Rubio JM, Romay-Barja M, Ncogo P, Agudo D, Herrador Z, Fernández-Soto P, Muro A, Benito A. Comparison of three PCR-based methods to detect Loa loa and Mansonella perstans in long-term frozen storage dried blood spots. Trop Med Int Health 2022; 27:686-695. [PMID: 35653502 DOI: 10.1111/tmi.13786] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
OBJECTIVES Loa loa and Mansonella perstans are two very common filarial species in Africa. Although microscopy is the traditional diagnostic method for human filariasis, several polymerase chain reaction (PCR) methods have emerged as an alternative approach for identifying filarial parasites. The aim of this study is to compare three molecular methods and decide which is the most suitable for diagnosing human loiasis and mansonellosis in non-endemic regions using dried blood spot (DBS) as a medium for sample collection and storage. METHODS A total of 100 DBS samples, with their corresponding thin and thick blood smears, were selected for this study. Microscopy was used as the reference method to diagnose and calculate the microfilaraemia. Filarial DNA was extracted using the saponin/Chelex method and the DNA isolated was assayed by Filaria-real time-PCR, filaria-nested PCR, and cytochrome oxidase I PCR. All PCR products were subsequently purified and sequenced. The statistical values for each molecular test were calculated and compared. RESULTS Overall, 64 samples were identified as negative by all tests and a further 36 samples were positive by at least one of the methods used. The sensitivity and specificity were similar for the different molecular methods, all of which demonstrated good agreement with microscopy. CONCLUSIONS Based on this study, and from a practical point of view (single and short amplification round), the optimal technique for diagnosing filarial infection in non-endemic regions is filaria-real time-PCR, which presents high sensitivity and specificity and is also able to detect a wide range of human filariae.
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Affiliation(s)
- Thuy-Huong Ta-Tang
- Malaria and Neglected Tropical Diseases Laboratory, National Centre of Tropical Medicine, Institute of Health Carlos III, Biomedical Research Networking Center of Infectious Diseases, Madrid, Spain.,Cooperative Research Network in Tropical Diseases, Madrid, Spain
| | - Begoña Febrer-Sendra
- Cooperative Research Network in Tropical Diseases, Madrid, Spain.,Infectious and Tropical Diseases Research Group (e-INTRO), Biomedical Research Institute of Salamanca-Research Centre for Tropical Diseases at the University of Salamanca, Faculty of Pharmacy, University of Salamanca, Salamanca, Spain
| | - Pedro Berzosa
- Malaria and Neglected Tropical Diseases Laboratory, National Centre of Tropical Medicine, Institute of Health Carlos III, Biomedical Research Networking Center of Infectious Diseases, Madrid, Spain.,Cooperative Research Network in Tropical Diseases, Madrid, Spain
| | - José Miguel Rubio
- Cooperative Research Network in Tropical Diseases, Madrid, Spain.,Malaria and Emerging Parasitic Diseases Laboratory, National Microbiology Center, Institute of Health Carlos III, Madrid, Spain
| | - María Romay-Barja
- Malaria and Neglected Tropical Diseases Laboratory, National Centre of Tropical Medicine, Institute of Health Carlos III, Biomedical Research Networking Center of Infectious Diseases, Madrid, Spain.,Cooperative Research Network in Tropical Diseases, Madrid, Spain
| | - Policarpo Ncogo
- Ministry of Health, Malabo, Equatorial Guinea.,Fundación Estatal, Salud, Infancia y Bienestar Social, Madrid, Spain
| | - Diego Agudo
- Facultad de Ciencias Biológicas, Universidad Complutense de Madrid, Madrid, Spain
| | - Zaida Herrador
- Malaria and Neglected Tropical Diseases Laboratory, National Centre of Tropical Medicine, Institute of Health Carlos III, Biomedical Research Networking Center of Infectious Diseases, Madrid, Spain.,Cooperative Research Network in Tropical Diseases, Madrid, Spain
| | - Pedro Fernández-Soto
- Cooperative Research Network in Tropical Diseases, Madrid, Spain.,Infectious and Tropical Diseases Research Group (e-INTRO), Biomedical Research Institute of Salamanca-Research Centre for Tropical Diseases at the University of Salamanca, Faculty of Pharmacy, University of Salamanca, Salamanca, Spain
| | - Antonio Muro
- Cooperative Research Network in Tropical Diseases, Madrid, Spain.,Infectious and Tropical Diseases Research Group (e-INTRO), Biomedical Research Institute of Salamanca-Research Centre for Tropical Diseases at the University of Salamanca, Faculty of Pharmacy, University of Salamanca, Salamanca, Spain
| | - Agustín Benito
- Malaria and Neglected Tropical Diseases Laboratory, National Centre of Tropical Medicine, Institute of Health Carlos III, Biomedical Research Networking Center of Infectious Diseases, Madrid, Spain.,Cooperative Research Network in Tropical Diseases, Madrid, Spain
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9
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Colorimetric and Real-Time Loop-Mediated Isothermal Amplification (LAMP) for Detection of Loa loa DNA in Human Blood Samples. Diagnostics (Basel) 2022; 12:diagnostics12051079. [PMID: 35626235 PMCID: PMC9139441 DOI: 10.3390/diagnostics12051079] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2022] [Revised: 04/22/2022] [Accepted: 04/23/2022] [Indexed: 02/04/2023] Open
Abstract
Loiasis, caused by the filarial nematode Loa loa, is endemic in Central and West Africa. Loa loa has been associated with severe adverse reactions in high Loa-infected individuals receiving ivermectin during mass drug administration programs for the control of onchocerciasis and lymphatic filariasis. Diagnosis of loiasis still depends on microscopy in blood samples, but this is not effective for large-scale surveys. New diagnostics methods for loiasis are urgently needed. Previously, we developed a colorimetric high-sensitive and species-specific LAMP for Loa loa DNA detection. Here, we evaluate it in a set of 100 field-collected clinical samples stored as dried blood spots. In addition, Loa loa-LAMP was also evaluated in real-time testing and compared with microscopy and a specific PCR/nested PCR. A simple saponin/Chelex-based method was used to extract DNA. Colorimetric and real-time LAMP assays detected more samples with microscopy-confirmed Loa loa and Loa loa/Mansonella perstans mixed infections than PCR/nested-PCR. Samples with the highest Loa loa microfilariae counts were amplified faster in real-time LAMP assays. Our Loa loa-LAMP could be a promising molecular tool for the easy, rapid and accurate screening of patients for loiasis in endemic areas with low-resource settings. The real-time testing (feasible in a handheld device) could be very useful to rule out high-microfilariae loads in infected patients.
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10
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Yoboue CA, Hosch S, Donfack OT, Guirou EA, Nlavo BM, Ayekaba MO, Guerra C, Phiri WP, Garcia GA, Schindler T, Daubenberger CA. Characterising co-infections with Plasmodium spp., Mansonella perstans or Loa loa in asymptomatic children, adults and elderly people living on Bioko Island using nucleic acids extracted from malaria rapid diagnostic tests. PLoS Negl Trop Dis 2022; 16:e0009798. [PMID: 35100277 PMCID: PMC8830708 DOI: 10.1371/journal.pntd.0009798] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2021] [Revised: 02/10/2022] [Accepted: 01/10/2022] [Indexed: 11/18/2022] Open
Abstract
Background Regular and comprehensive epidemiological surveys of the filarial nematodes Mansonella perstans and Loa loa in children, adolescents and adults living across Bioko Island, Equatorial Guinea are lacking. We aimed to demonstrate that blood retained on malaria rapid diagnostic tests, commonly deployed for malaria surveys, could be used as a source of nucleic acids for molecular based detection of M. perstans and L. loa. We wanted to determine the positivity rate and distribution of filarial nematodes across different age groups and geographical areas as well as to understand level of co-infections with malaria in an asymptomatic population. Methodology M. perstans, L. loa and Plasmodium spp. parasites were monitored by qPCR in a cross-sectional study using DNA extracted from a subset malaria rapid diagnostic tests (mRDTs) collected during the annual malaria indicator survey conducted on Bioko Island in 2018. Principal findings We identified DNA specific for the two filarial nematodes investigated among 8.2% (263) of the 3214 RDTs screened. Positivity rates of M. perstans and L. loa were 6.6% and 1.5%, respectively. M. perstans infection were more prominent in male (10.5%) compared to female (3.9%) survey participants. M. perstans parasite density and positivity rate was higher among older people and the population living in rural areas. The socio-economic status of participants strongly influenced the infection rate with people belonging to the lowest socio-economic quintile more than 3 and 5 times more likely to be L. loa and M. perstans infected, respectively. No increased risk of being co-infected with Plasmodium spp. parasites was observed among the different age groups. Conclusions/Significance We found otherwise asymptomatic individuals were infected with M. perstans and L. loa. Our study demonstrates that employing mRDTs probed with blood for malaria testing represents a promising, future tool to preserve and ship NAs at room temperature to laboratories for molecular, high-throughput diagnosis and genotyping of blood-dwelling nematode filarial infections. Using this approach, asymptomatic populations can be reached and surveyed for infectious diseases beyond malaria. Mansonella perstans and Loa loa are filarial nematodes that infect millions of people living in less developed areas, predominantly in sub-Saharan Africa. Both parasites are neglected among other filarial nematodes because both are regarded as causing mainly asymptomatic infections. The aim of this study was to explore the feasibility of using malaria rapid diagnostic tests (mRDTs) deployed during malaria surveys as a convenient sampling strategy for molecular surveillance of blood-dwelling filarial nematode infections. Our findings demonstrate the potential of mRDTs as a source of parasite DNA beyond malaria, providing an opportunity to expand current knowledge on the distribution and populations mostly affected by M. perstans and L. loa infections to Equatorial Guinea, located in Central-West Africa.
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Affiliation(s)
- Charlene Aya Yoboue
- Department of Medical Parasitology and Infection Biology, Swiss Tropical and Public Health Institute, Basel, Switzerland
- University of Basel, Basel, Switzerland
- Centre Suisse de Recherches Scientifiques en Côte d’Ivoire, Abidjan, Côte d’Ivoire
| | - Salome Hosch
- Department of Medical Parasitology and Infection Biology, Swiss Tropical and Public Health Institute, Basel, Switzerland
- University of Basel, Basel, Switzerland
| | | | - Etienne A. Guirou
- Department of Medical Parasitology and Infection Biology, Swiss Tropical and Public Health Institute, Basel, Switzerland
- University of Basel, Basel, Switzerland
| | | | | | - Carlos Guerra
- Medical Care Development International, Malabo, Equatorial Guinea
| | - Wonder P. Phiri
- Medical Care Development International, Malabo, Equatorial Guinea
| | | | - Tobias Schindler
- Department of Medical Parasitology and Infection Biology, Swiss Tropical and Public Health Institute, Basel, Switzerland
- University of Basel, Basel, Switzerland
- * E-mail: (TS); (CAD)
| | - Claudia A. Daubenberger
- Department of Medical Parasitology and Infection Biology, Swiss Tropical and Public Health Institute, Basel, Switzerland
- University of Basel, Basel, Switzerland
- * E-mail: (TS); (CAD)
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11
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Sciuto EL, Leonardi AA, Calabrese G, Luca GD, Coniglio MA, Irrera A, Conoci S. Nucleic Acids Analytical Methods for Viral Infection Diagnosis: State-of-the-Art and Future Perspectives. Biomolecules 2021; 11:1585. [PMID: 34827583 PMCID: PMC8615992 DOI: 10.3390/biom11111585] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2021] [Revised: 10/23/2021] [Accepted: 10/25/2021] [Indexed: 11/25/2022] Open
Abstract
The analysis of viral nucleic acids (NA), DNA or RNA, is a crucial issue in the diagnosis of infections and the treatment and prevention of related human diseases. Conventional nucleic acid tests (NATs) require multistep approaches starting from the purification of the pathogen genetic material in biological samples to the end of its detection, basically performed by the consolidated polymerase chain reaction (PCR), by the use of specialized instruments and dedicated laboratories. However, since the current NATs are too constraining and time and cost consuming, the research is evolving towards more integrated, decentralized, user-friendly, and low-cost methods. These will allow the implementation of massive diagnoses addressing the growing demand of fast and accurate viral analysis facing such global alerts as the pandemic of coronavirus disease of the recent period. Silicon-based technology and microfluidics, in this sense, brought an important step up, leading to the introduction of the genetic point-of-care (PoC) systems. This review goes through the evolution of the analytical methods for the viral NA diagnosis of infection diseases, highlighting both advantages and drawbacks of the innovative emerging technologies versus the conventional approaches.
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Affiliation(s)
- Emanuele Luigi Sciuto
- Azienda Ospedaliero, Universitaria Policlinico “G. Rodolico-San Marco”, Via Santa Sofia 78, 95123 Catania, Italy
| | - Antonio Alessio Leonardi
- CNR-IPCF, Istituto per i Processi Chimico-Fisici, Viale F. Stagno D’Alcontres 37, 98158 Messina, Italy; (A.A.L.); (A.I.)
- Department of Chemical, Biological, Pharmaceutical and Environmental Sciences, University of Messina, Viale Ferdinando Stagno d’Alcontres 5, 98166 Messina, Italy; (G.C.); (G.D.L.)
| | - Giovanna Calabrese
- Department of Chemical, Biological, Pharmaceutical and Environmental Sciences, University of Messina, Viale Ferdinando Stagno d’Alcontres 5, 98166 Messina, Italy; (G.C.); (G.D.L.)
| | - Giovanna De Luca
- Department of Chemical, Biological, Pharmaceutical and Environmental Sciences, University of Messina, Viale Ferdinando Stagno d’Alcontres 5, 98166 Messina, Italy; (G.C.); (G.D.L.)
| | - Maria Anna Coniglio
- Department of Medical and Surgical Sciences and Advanced Technologies “G.F. Ingrassia”, University of Catania, Via Sofia 87, 95123 Catania, Italy;
| | - Alessia Irrera
- CNR-IPCF, Istituto per i Processi Chimico-Fisici, Viale F. Stagno D’Alcontres 37, 98158 Messina, Italy; (A.A.L.); (A.I.)
- Department of Chemical, Biological, Pharmaceutical and Environmental Sciences, University of Messina, Viale Ferdinando Stagno d’Alcontres 5, 98166 Messina, Italy; (G.C.); (G.D.L.)
| | - Sabrina Conoci
- CNR-IPCF, Istituto per i Processi Chimico-Fisici, Viale F. Stagno D’Alcontres 37, 98158 Messina, Italy; (A.A.L.); (A.I.)
- Department of Chemical, Biological, Pharmaceutical and Environmental Sciences, University of Messina, Viale Ferdinando Stagno d’Alcontres 5, 98166 Messina, Italy; (G.C.); (G.D.L.)
- Istituto per la Microelettronica e Microsistemi, Consiglio Nazionale delle Ricerche (CNR-IMM), Ottava Strada n.5, 95121 Catania, Italy
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12
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Ta-Tang TH, Luz SLB, Crainey JL, Rubio JM. An Overview of the Management of Mansonellosis. Res Rep Trop Med 2021; 12:93-105. [PMID: 34079424 PMCID: PMC8163967 DOI: 10.2147/rrtm.s274684] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2021] [Accepted: 04/30/2021] [Indexed: 02/02/2023] Open
Abstract
Mansonellosis is caused by three filarial parasite species from the genus Mansonella that commonly produce chronic human microfilaraemias: M. ozzardi, M. perstans and M. streptocerca. The disease is widespread in Africa, the Caribbean and South and Central America, and although it is typically asymptomatic it has been associated with mild pathologies including leg-chills, joint-pains, headaches, fevers, and corneal lesions. No robust mansonellosis disease burden estimates have yet been made and the impact the disease has on blood bank stocks and the monitoring of other filarial diseases is not thought to be of sufficient public health importance to justify dedicated disease management interventions. Mansonellosis´s Ceratopogonidae and Simuliidae vectors are not targeted by other control programmes and because of their small size and out-door biting habits are unlikely to be affected by interventions targeting other disease vectors like mosquitoes. The ivermectin and mebendazole-based mass drug administration (iMDA and mMDA) treatment regimens deployed by the WHO´s Elimination of Neglected Tropical Diseases (ESPEN) programme and its forerunners have, however, likely impacted significantly on the mansonellosis disease burden, principally by reducing the transmission of M. streptocerca in Africa. The increasingly popular plan of using iMDA to control malaria could also affect M. ozzardi parasite prevalence and transmission in Latin America in the future. However, a potentially far greater mansonellosis disease burden impact is likely to come from short-course curative anti-Wolbachia therapeutics, which are presently being developed for onchocerciasis and lymphatic filariasis treatment. Even if the WHO´s ESPEN programme does not choose to deploy these drugs in MDA interventions, they have the potential to dramatically increase the financial and logistical feasibility of effective mansonellosis management. There is, thus, now a fresh and urgent need to better characterise the disease burden and eco-epidemiology of mansonellosis so that effective management programmes can be designed, advocated for and implemented.
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Affiliation(s)
- Thuy-Huong Ta-Tang
- Malaria and NTDs Laboratory, National Centre of Tropical Medicine, Instituto de Salud Carlos III, Madrid, Spain
| | - Sergio L B Luz
- Laboratório de Ecologia de Doenças Transmissíveis na Amazônia, Instituto Leônidas e Maria Deane, Fundação Oswaldo Cruz, Manaus, Amazonas State, Brazil
| | - James L Crainey
- Laboratório de Ecologia de Doenças Transmissíveis na Amazônia, Instituto Leônidas e Maria Deane, Fundação Oswaldo Cruz, Manaus, Amazonas State, Brazil
| | - José M Rubio
- Malaria & Emerging Parasitic Diseases Laboratory, National Microbiology Center, Instituto de Salud Carlos III, Madrid, Spain
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13
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Yao L, Zhu W, Shi J, Xu T, Qu G, Zhou W, Yu XF, Zhang X, Jiang G. Detection of coronavirus in environmental surveillance and risk monitoring for pandemic control. Chem Soc Rev 2021; 50:3656-3676. [PMID: 33710177 DOI: 10.1039/d0cs00595a] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
The novel human infectious coronaviruses (CoVs) responsible for severe respiratory syndromes have raised concerns owing to the global public health emergencies they have caused repeatedly over the past two decades. However, the ongoing coronavirus disease 2019 (COVID-19) pandemic induced by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has received unprecedented attention internationally. Monitoring pathogenic CoVs in environmental compartments has been proposed as a promising strategy in preventing the environmental spread and tracing of infectious diseases, but a lack of reliable and efficient detection techniques is still a significant challenge. Moreover, the lack of information regarding the monitoring methodology may pose a barrier to primary researchers. Here, we provide a systematic introduction focused on the detection of CoVs in various environmental matrices, comprehensively involving methods and techniques of sampling, pretreatment, and analysis. Furthermore, the review addresses the challenges and potential improvements in virus detection techniques for environmental surveillance.
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Affiliation(s)
- Linlin Yao
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, P. R. China.
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14
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Ta-Tang TH, Berzosa P, Rubio JM, Romay-Barja M, Ncogo P, Agudo D, Herrador Z, Cerrada-Gálvez L, Benito A. Evaluation of LAMP for the diagnosis of Loa loa infection in dried blood spots compared to PCR-based assays and microscopy. Mem Inst Oswaldo Cruz 2021; 116:e210210. [PMID: 35170676 PMCID: PMC8843042 DOI: 10.1590/0074-02760210210] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2021] [Accepted: 12/14/2021] [Indexed: 11/25/2022] Open
Abstract
BACKGROUND Loa loa is a filarial species found exclusively in West and Central Africa. Microscopy is the traditional diagnosis method for human loiasis. Several molecular methods have developed as an alternative approach for identification of L. loa filarial parasites. OBJECTIVES The aim of this study was to evaluate a Loa-Loop-mediated isothermal amplification (LAMP) assay to diagnose loiasis disease on dried blood spots (DBS) samples, compared to microscopy, filaria-real time-polymerase chain reaction (PCR) and nested-Loa PCR. METHODS A total of 100 DBS samples and 100 blood smears were used for this study. DNA was extracted using saponin/Chelex method. DNA isolated was assayed by a Loa-LAMP assay in parallel to microscopy, filaria-real time PCR and nested-Loa PCR. The sensitivities and specificities of Loa-LAMP assay was computed comparing to each one of the reference methods. FINDINGS Loa-LAMP’s sensitivity was more than 90% and specificity was nearly 100% when compared to molecular methods. On the other hand, sensitivity was decreased a bit when Loa-LAMP faced microscopy, but keeping the other statistical values high. MAIN CONCLUSIONS Loa-LAMP is an appropriate method for loiasis diagnosis in endemic areas. Though, it has disadvantages like the reagents’ high price at the moment and not to be able to detect more filarial species at once.
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Affiliation(s)
- Thuy-Huong Ta-Tang
- National Centre of Tropical Medicine, Spain; Cooperative Research Network on Tropical Diseases, Spain
| | - Pedro Berzosa
- National Centre of Tropical Medicine, Spain; Cooperative Research Network on Tropical Diseases, Spain
| | - José Miguel Rubio
- National Microbiology Centre, Spain; Cooperative Research Network on Tropical Diseases, Spain
| | - María Romay-Barja
- National Centre of Tropical Medicine, Spain; Cooperative Research Network on Tropical Diseases, Spain
| | - Policarpo Ncogo
- Ministry of Health, Equatorial Guinea; Fundación Estatal, Spain
| | | | - Zaida Herrador
- National Centre of Tropical Medicine, Spain; Cooperative Research Network on Tropical Diseases, Spain
| | | | - Agustín Benito
- National Centre of Tropical Medicine, Spain; Cooperative Research Network on Tropical Diseases, Spain
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15
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Zulch MF, Pilotte N, Grant JR, Minetti C, Reimer LJ, Williams SA. Selection and exploitation of prevalent, tandemly repeated genomic targets for improved real-time PCR-based detection of Wuchereria bancrofti and Plasmodium falciparum in mosquitoes. PLoS One 2020; 15:e0232325. [PMID: 32357154 PMCID: PMC7194414 DOI: 10.1371/journal.pone.0232325] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2020] [Accepted: 04/12/2020] [Indexed: 11/18/2022] Open
Abstract
BACKGROUND Optimization of polymerase chain reaction (PCR)-based diagnostics requires the careful selection of molecular targets that are both highly repetitive and pathogen-specific. Advances in both next-generation sequencing (NGS) technologies and bioinformatics-based analysis tools are facilitating this selection process, informing target choices and reducing labor. Once developed, such assays provide disease control and elimination programs with an additional set of tools capable of evaluating and monitoring intervention successes. The importance of such tools is heightened as intervention efforts approach their endpoints, as accurate and complete information is an essential component of the informed decision-making process. As global efforts for the control and elimination of both lymphatic filariasis and malaria continue to make significant gains, the benefits of diagnostics with improved analytical and clinical/field-based sensitivities and specificities will become increasingly apparent. METHODOLOGY/PRINCIPAL FINDINGS Coupling Illumina-based NGS with informatics approaches, we have successfully identified the tandemly repeated elements in both the Wuchereria bancrofti and Plasmodium falciparum genomes of putatively greatest copy number. Utilizing these sequences as quantitative real-time PCR (qPCR)-based targets, we have developed assays capable of exploiting the most abundant tandem repeats for both organisms. For the detection of P. falciparum, analysis and development resulted in an assay with improved analytical and field-based sensitivity vs. an established ribosomal sequence-targeting assay. Surprisingly, analysis of the W. bancrofti genome predicted a ribosomal sequence to be the genome's most abundant tandem repeat. While resulting cycle quantification values comparing a qPCR assay targeting this ribosomal sequence and a commonly targeted repetitive DNA sequence from the literature supported our finding that this ribosomal sequence was the most prevalent tandemly repeated target in the W. bancrofti genome, the resulting assay did not significantly improve detection sensitivity in conjunction with field sample testing. CONCLUSIONS/SIGNIFICANCE Examination of pathogen genomes facilitates the development of PCR-based diagnostics targeting the most abundant and specific genomic elements. While in some instances currently available tools may deliver equal or superior performance, systematic analysis of potential targets provides confidence that the selected assays represent the most advantageous options available and that informed assay selection is occurring in the context of a particular study's objectives.
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Affiliation(s)
- Michael F Zulch
- Department of Biological Sciences, Smith College, Northampton, Massachusetts, United States of America
| | - Nils Pilotte
- Department of Biological Sciences, Smith College, Northampton, Massachusetts, United States of America.,Molecular and Cellular Biology Program, University of Massachusetts, Amherst, Massachusetts, United States of America
| | - Jessica R Grant
- Department of Biological Sciences, Smith College, Northampton, Massachusetts, United States of America
| | - Corrado Minetti
- Department of Vector Biology, Liverpool School of Tropical Medicine, Liverpool, United Kingdom
| | - Lisa J Reimer
- Department of Vector Biology, Liverpool School of Tropical Medicine, Liverpool, United Kingdom
| | - Steven A Williams
- Department of Biological Sciences, Smith College, Northampton, Massachusetts, United States of America.,Molecular and Cellular Biology Program, University of Massachusetts, Amherst, Massachusetts, United States of America
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16
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Hedtke SM, Kuesel AC, Crawford KE, Graves PM, Boussinesq M, Lau CL, Boakye DA, Grant WN. Genomic Epidemiology in Filarial Nematodes: Transforming the Basis for Elimination Program Decisions. Front Genet 2020; 10:1282. [PMID: 31998356 PMCID: PMC6964045 DOI: 10.3389/fgene.2019.01282] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2019] [Accepted: 11/21/2019] [Indexed: 11/25/2022] Open
Abstract
Onchocerciasis and lymphatic filariasis are targeted for elimination, primarily using mass drug administration at the country and community levels. Elimination of transmission is the onchocerciasis target and global elimination as a public health problem is the end point for lymphatic filariasis. Where program duration, treatment coverage, and compliance are sufficiently high, elimination is achievable for both parasites within defined geographic areas. However, transmission has re-emerged after apparent elimination in some areas, and in others has continued despite years of mass drug treatment. A critical question is whether this re-emergence and/or persistence of transmission is due to persistence of local parasites-i.e., the result of insufficient duration or drug coverage, poor parasite response to the drugs, or inadequate methods of assessment and/or criteria for determining when to stop treatment-or due to re-introduction of parasites via human or vector movement from another endemic area. We review recent genetics-based research exploring these questions in Onchocerca volvulus, the filarial nematode that causes onchocerciasis, and Wuchereria bancrofti, the major pathogen for lymphatic filariasis. We focus in particular on the combination of genomic epidemiology and genome-wide associations to delineate transmission zones and distinguish between local and introduced parasites as the source of resurgence or continuing transmission, and to identify genetic markers associated with parasite response to chemotherapy. Our ultimate goal is to assist elimination efforts by developing easy-to-use tools that incorporate genetic information about transmission and drug response for more effective mass drug distribution, surveillance strategies, and decisions on when to stop interventions to improve sustainability of elimination.
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Affiliation(s)
- Shannon M. Hedtke
- Department of Physiology, Anatomy and Microbiology, La Trobe University, Bundoora, VIC, Australia
| | - Annette C. Kuesel
- Unicef/UNDP/World Bank/World Health Organization Special Programme for Research and Training in Tropical Diseases (TDR), World Health Organization, Geneva, Switzerland
| | - Katie E. Crawford
- Department of Physiology, Anatomy and Microbiology, La Trobe University, Bundoora, VIC, Australia
| | - Patricia M. Graves
- College of Public Health, Medical and Veterinary Sciences, James Cook University, Cairns, QLD, Australia
| | - Michel Boussinesq
- Unité Mixte Internationale 233 "TransVIHMI", Institut de Recherche pour le Développement (IRD), INSERM U1175, University of Montpellier, Montpellier, France
| | - Colleen L. Lau
- Department of Global Health, Research School of Population Health, Australian National University, Acton, ACT, Australia
| | - Daniel A. Boakye
- Parasitology Department, Noguchi Memorial Institute for Medical Research, Accra, Ghana
| | - Warwick N. Grant
- Department of Physiology, Anatomy and Microbiology, La Trobe University, Bundoora, VIC, Australia
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17
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In Silico Identification of Novel Biomarkers and Development of New Rapid Diagnostic Tests for the Filarial Parasites Mansonella perstans and Mansonella ozzardi. Sci Rep 2019; 9:10275. [PMID: 31311985 PMCID: PMC6635353 DOI: 10.1038/s41598-019-46550-9] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2019] [Accepted: 06/29/2019] [Indexed: 02/02/2023] Open
Abstract
Mansonelliasis is a widespread yet neglected tropical infection of humans in Africa and South America caused by the filarial nematodes, Mansonella perstans, M. ozzardi, M. rodhaini and M. streptocerca. Clinical symptoms are non-distinct and diagnosis mainly relies on the detection of microfilariae in skin or blood. Species-specific DNA repeat sequences have been used as highly sensitive biomarkers for filarial nematodes. We have developed a bioinformatic pipeline to mine Illumina reads obtained from sequencing M. perstans and M. ozzardi genomic DNA for new repeat biomarker candidates which were used to develop loop-mediated isothermal amplification (LAMP) diagnostic tests. The M. perstans assay based on the Mp419 repeat has a limit of detection of 0.1 pg, equivalent of 1/1000th of a microfilaria, while the M. ozzardi assay based on the Mo2 repeat can detect as little as 0.01 pg. Both LAMP tests possess remarkable species-specificity as they did not amplify non-target DNAs from closely related filarial species, human or vectors. We show that both assays perform successfully on infected human samples. Additionally, we demonstrate the suitability of Mp419 to detect M. perstans infection in Culicoides midges. These new tools are field deployable and suitable for the surveillance of these understudied filarial infections.
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18
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Deng MH, Zhong LY, Kamolnetr O, Limpanont Y, Lv ZY. Detection of helminths by loop-mediated isothermal amplification assay: a review of updated technology and future outlook. Infect Dis Poverty 2019; 8:20. [PMID: 30905322 PMCID: PMC6432754 DOI: 10.1186/s40249-019-0530-z] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2018] [Accepted: 03/07/2019] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND Helminths are endemic in more than half of the world's countries, raising serious public health concerns. Accurate diagnosis of helminth infection is crucial to control strategies. Traditional parasitological methods, serological tests and PCR-based assays are the major means of the diagnosis of helminth infection, but they are time-consuming and/or expensive, and sometimes provide inaccurate results. Loop mediated isothermal amplification (LAMP) assay, a sensitive, simple and rapid method was therefore developed for detection of helminths. This study aims to discuss the current status of application of LAMP on helminths detection and to make a comprehensive evaluation about this updated technology and its future outlook by comparing with several other diagnostic methods. MAIN BODY This review summarizes LAMP assay applied for helminth detection and helminthiasis surveillance. The basic principle of LAMP is introduced to help better understand its characteristics and each reported assay is assessed mainly based on its detection sensitivity, specificity and limitations, in comparison with other common diagnostic tests. Moreover, we discuss the limitations of the assays so as to clarify some potential ways of improvement. CONCLUSIONS Here, we summarize and discuss the advantages, disadvantages and promising future of LAMP in heliminth detection, which is expected to help update current knowledge and future perspectives of LAMP in highly sensitive and specific diagnosis and surveillance of helminthiasis and other parasitic diseases, and can contribute to the elimination of the diseases from endemic areas.
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Affiliation(s)
- Miao-Han Deng
- Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, 510080 China
- Key Laboratory of Tropical Disease Control (Sun Yat-sen University), Ministry of Education, Guangzhou, 510080 China
| | - Lan-Yi Zhong
- Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, 510080 China
- Key Laboratory of Tropical Disease Control (Sun Yat-sen University), Ministry of Education, Guangzhou, 510080 China
| | - Okanurak Kamolnetr
- Faculty of Tropical Medicine, Mahidol University, Bangkok, 10400 Thailand
| | - Yanin Limpanont
- Faculty of Tropical Medicine, Mahidol University, Bangkok, 10400 Thailand
| | - Zhi-Yue Lv
- Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, 510080 China
- Key Laboratory of Tropical Disease Control (Sun Yat-sen University), Ministry of Education, Guangzhou, 510080 China
- Provincial Engineering Technology Research Center for Biological Vector Control, Guangzhou, 510080 China
- Fifth Affiliated Hospital, Sun Yat-sen University, Guangzhou, 519000 China
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Khatri V, Amdare N, Chauhan N, Togre N, Reddy MV, Hoti SL, Kalyanasundaram R. Epidemiological screening and xenomonitoring for human lymphatic filariasis infection in select districts in the states of Maharashtra and Karnataka, India. Parasitol Res 2019; 118:1045-1050. [PMID: 30666407 PMCID: PMC6401222 DOI: 10.1007/s00436-019-06205-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2018] [Accepted: 01/04/2019] [Indexed: 10/27/2022]
Abstract
Lymphatic filariasis (LF) is a mosquito-transmitted tropical neglected parasitic infection that currently affects over 120 million people around the world and another 856 million people are at risk of acquiring the infection. Mass Drug Administration (MDA) spearheaded by the World Health Organization is the only current strategy to control this infection in endemic areas. In this study, we performed an epidemiological survey in select regions in the southern parts of India to determine the current status of LF infection in subjects. Night blood samples were collected from 916 subjects after proper consent and were screened for the presence of circulating microfilariae of Wuchereria bancrofti in their peripheral blood. Our results showed the presence of 51 (5.56%) cases of human LF infection in the surveyed areas including new cases for LF, which were not recorded previously. Given the presence of new cases of LF infections, we trapped mosquitoes from these regions and screened for the presence of W. bancrofti L3 specific Ssp1 DNA repeat sequences by PCR. Our results confirmed the presence of LF infection in the mosquitoes collected from six out of nine districts that we surveyed. These findings confirm active transmission of LF infection in all of the areas that we surveyed, despite several years of MDA treatment. The findings in this study suggest potential reemergence of LF infection in most of the areas we surveyed and warrants for a more stringent strategy for controlling LF in these endemic areas.
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Affiliation(s)
- Vishal Khatri
- Department of Biomedical Sciences, University of Illinois College of Medicine, Rockford, IL, USA
| | - Nitin Amdare
- Albert Einstein College of Medicine, Montefiore Medical Center, Bronx, NY, USA
| | - Nikhil Chauhan
- Department of Biomedical Sciences, University of Illinois College of Medicine, Rockford, IL, USA
| | - Namdev Togre
- Department of Biochemistry, Mahatma Gandhi Institute of Medical Sciences, Sevagram, India
| | - Maryada V Reddy
- Department of Biochemistry, Mahatma Gandhi Institute of Medical Sciences, Sevagram, India
| | - Subhash L Hoti
- Regional Medical Research Centre, Indian Council of Medical Research, Belgaum, India
| | - Ramaswamy Kalyanasundaram
- Department of Biomedical Sciences, University of Illinois College of Medicine, Rockford, IL, USA.
- Department of Biomedical Sciences, University of Illinois College of Medicine, 1601 Parkview Avenue, Rockford, IL, 61107, USA.
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20
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Keroack CD, Williams KM, Fessler M, DeAngelis KE, Tsekitsidou E, Tozloski JM, Williams SA. A novel quantitative real-time PCR diagnostic assay for seal heartworm ( Acanthocheilonema spirocauda) provides evidence for possible infection in the grey seal ( Halichoerus grypus). Int J Parasitol Parasites Wildl 2018; 7:147-154. [PMID: 29988808 PMCID: PMC6031957 DOI: 10.1016/j.ijppaw.2018.04.001] [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: 01/22/2018] [Revised: 03/29/2018] [Accepted: 04/05/2018] [Indexed: 11/15/2022]
Abstract
The distinct evolutionary pressures faced by Pinnipeds have likely resulted in strong coevolutionary ties to their parasites (Leidenberger et al., 2007). This study focuses on the phocid seal filarial heartworm species Acanthocheilonema spirocauda. A. spirocauda is known to infect a variety of phocid seals, but does not appear to be restricted to a single host species (Measures et al., 1997; Leidenberger et al., 2007; Lehnert et al., 2015). However, to date, seal heartworm has never been reported in grey seals (Halichoerus grypus) (Measures et al., 1997; Leidenberger et al., 2007; Lehnert et al., 2015). The proposed vector for seal heartworm is Echinophthirius horridus, the seal louse. Seal lice are known to parasitize a wide array of phocid seal species, including the grey seal. With the advent of climate change, disease burden is expected to increase across terrestrial and marine mammals (Harvell et al., 2002). Accordingly, increased prevalence of seal heartworm has recently been reported in harbor seals (Phoca vitulina) (Lehnert et al., 2015). Thus, the need for improved, rapid, and cost-effective diagnostics is urgent. Here we present the first A. spirocauda-specific rapid diagnostic test (a quantitative real-time PCR assay), based on a highly repetitive genomic DNA repeat identified using whole genome sequencing and subsequent bioinformatic analysis. The presence of an insect vector provides the opportunity to develop a multifunctional diagnostic tool that can be used not only to detect the parasite directly from blood or tissue specimens, but also as a molecular xenomonitoring (XM) tool that can be used to assess the epidemiological profile of the parasite by screening the arthropod vector. Using this assay, we provide evidence for the first reported case of seal heartworm in a grey seal.
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21
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Kelly-Hope LA, Blundell HJ, Macfarlane CL, Molyneux DH. Innovative Surveillance Strategies to Support the Elimination of Filariasis in Africa. Trends Parasitol 2018; 34:694-711. [PMID: 29958813 DOI: 10.1016/j.pt.2018.05.004] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2018] [Revised: 05/18/2018] [Accepted: 05/30/2018] [Indexed: 01/18/2023]
Abstract
Lymphatic filariasis (LF) and onchocerciasis are two neglected tropical diseases (NTDs) of public health significance targeted for global elimination. The World Health Organization (WHO) African Region is a priority region, with the highest collective burden of LF and onchocerciasis globally. Coendemic loiasis further complicates elimination due to the risk of adverse events associated with ivermectin treatment. A public health framework focusing on health-related data, systematic collection of data, and analysis and interpretation of data is used to highlight the range of innovative surveillance strategies required for filariasis elimination. The most recent and significant developments include: rapid point-of-care test (POCT) diagnostics; clinical assessment tools; new WHO guidelines; open-access online data portals; mHealth platforms; large-scale prevalence maps; and the optimisation of mathematical models.
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Affiliation(s)
- Louise A Kelly-Hope
- Department of Parasitology, Liverpool School of Tropical Medicine, Liverpool, UK.
| | - Harriet J Blundell
- Department of Parasitology, Liverpool School of Tropical Medicine, Liverpool, UK
| | - Cara L Macfarlane
- Department of Parasitology, Liverpool School of Tropical Medicine, Liverpool, UK
| | - David H Molyneux
- Department of Parasitology, Liverpool School of Tropical Medicine, Liverpool, UK
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22
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Gonzalez-Moa MJ, Van Dorst B, Lagatie O, Verheyen A, Stuyver L, Biamonte MA. Proof-of-Concept Rapid Diagnostic Test for Onchocerciasis: Exploring Peptide Biomarkers and the Use of Gold Nanoshells as Reporter Nanoparticles. ACS Infect Dis 2018; 4:912-917. [PMID: 29547260 DOI: 10.1021/acsinfecdis.8b00031] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Three O. volvulus immunogenic peptide sequences recently discovered by peptide microarray were adapted to a lateral flow assay (LFA). The LFA employs gold nanoshells as novel high-contrast reporter nanoparticles and detects a serological response against the 3 peptides, found in OvOC9384, OvOC198, and OvOC5528, respectively. When tested on 118 sera from O. volvulus infected patients and 208 control sera, the LFA was 90%, 63%, and 98% sensitive for each peptide, respectively, and 99-100% specific vs samples from healthy volunteers. Samples of other filarial infections cross-reacted by 7-24%. The sensitivity, specificity, and cross-reactivity values matched those obtained by ELISA with the same sample set. While the exact choice of peptide(s) will require fine-tuning, this work establishes that O. volvulus peptides identified by peptide microarray can be translated into an antibody-based LFA and that gold nanoshells provide the same sensitivity, specificity, and cross-reactivity as the corresponding ELISA assays.
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Affiliation(s)
- Maria J. Gonzalez-Moa
- Drugs & Diagnostics for Tropical Diseases, 4898 Ronson Ct., Suite C, San Diego, California 92111, United States
| | - Bieke Van Dorst
- Janssen Diagnostics, Turnhoutseweg 30, B-2340 Beerse, Belgium
| | - Ole Lagatie
- Janssen Diagnostics, Turnhoutseweg 30, B-2340 Beerse, Belgium
| | - Ann Verheyen
- Janssen Diagnostics, Turnhoutseweg 30, B-2340 Beerse, Belgium
| | - Lieven Stuyver
- Janssen Diagnostics, Turnhoutseweg 30, B-2340 Beerse, Belgium
| | - Marco A. Biamonte
- Drugs & Diagnostics for Tropical Diseases, 4898 Ronson Ct., Suite C, San Diego, California 92111, United States
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23
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Abstract
Mansonellosis is a filarial disease caused by three species of filarial (nematode) parasites (Mansonella perstans, Mansonella streptocerca, and Mansonella ozzardi) that use humans as their main definitive hosts. These parasites are transmitted from person to person by bloodsucking females from two families of flies (Diptera). Biting midges (Ceratopogonidae) transmit all three species of Mansonella, but blackflies (Simuliidae) are also known to play a role in the transmission of M. ozzardi in parts of Latin America. M. perstans and M. streptocerca are endemic in western, eastern, and central Africa, and M. perstans is also present in the neotropical region from equatorial Brazil to the Caribbean coast. M. ozzardi has a patchy distribution in Latin America and the Caribbean. Mansonellosis infections are thought to have little pathogenicity and to be almost always asymptomatic, but occasionally causing itching, joint pains, enlarged lymph glands, and vague abdominal symptoms. In Brazil, M. ozzardi infections are also associated with corneal lesions. Diagnosis is usually performed by detecting microfilariae in peripheral blood or skin without any periodicity. There is no standard treatment at present for mansonellosis. The combination therapy of diethylcarbamazine plus mebendazole for M. perstans microfilaremia is presently one of the most widely used, but the use of ivermectin has also been proven to be very effective against microfilariae. Recently, doxycycline has shown excellent efficacy and safety when used as an antimicrobial against endosymbiotic Wolbachia bacteria harbored by some strains of M. perstans and M. ozzardi. Diethylcarbamazine and ivermectin have been used effectively to treat M. streptocerca infection. There are at present no estimates of the disease burden caused by mansonellosis, and thus its importance to many global health professionals and policy makers is presently limited to how it can interfere with diagnostic tools used in modern filarial disease control and elimination programs aimed at other species of filariae.
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Affiliation(s)
- Thuy-Huong Ta-Tang
- Malaria and Emerging Parasitic Diseases Laboratory, National Microbiology Center, Instituto de Salud Carlos III, Majadahonda, Spain,
| | - James L Crainey
- Laboratory of Infectious Disease Ecology in the Amazon, Oswaldo Cruz Foundation, Instituto Leônidas e Maria Deane, Manaus, Brazil
| | - Rory J Post
- School of Natural Sciences and Psychology, John Moores University, Liverpool
- Department of Disease Control, Faculty of Infectious Tropical Diseases, London School of Hygiene and Tropical Medicine, London, UK
| | - Sergio Lb Luz
- Laboratory of Infectious Disease Ecology in the Amazon, Oswaldo Cruz Foundation, Instituto Leônidas e Maria Deane, Manaus, Brazil
| | - José M Rubio
- Malaria and Emerging Parasitic Diseases Laboratory, National Microbiology Center, Instituto de Salud Carlos III, Majadahonda, Spain,
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24
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Targeting Human Onchocerciasis: Recent Advances Beyond Ivermectin. ANNUAL REPORTS IN MEDICINAL CHEMISTRY 2018. [DOI: 10.1016/bs.armc.2018.08.001] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
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25
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Bennuru S, O'Connell EM, Drame PM, Nutman TB. Mining Filarial Genomes for Diagnostic and Therapeutic Targets. Trends Parasitol 2017; 34:80-90. [PMID: 29031509 DOI: 10.1016/j.pt.2017.09.003] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2017] [Revised: 09/12/2017] [Accepted: 09/20/2017] [Indexed: 02/04/2023]
Abstract
Filarial infections of humans cause some of the most important neglected tropical diseases. The global efforts for eliminating filarial infections by mass drug administration programs may require additional tools (safe macrofilaricidal drugs, vaccines, and diagnostic biomarkers). The accurate and sensitive detection of viable parasites is essential for diagnosis and for surveillance programs. Current community-wide treatment modalities do not kill the adult filarial worms effectively; hence, there is a need to identify and develop safe macrofilaricidal drugs. High-throughput sequencing, mass spectroscopy methods and advances in computational biology have greatly accelerated the discovery process. Here, we describe post-genomic developments toward the identification of diagnostic biomarkers and drug targets for the filarial infection of humans.
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Affiliation(s)
- Sasisekhar Bennuru
- Laboratory of Parasitic Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA.
| | - Elise M O'Connell
- Laboratory of Parasitic Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Papa M Drame
- Laboratory of Parasitic Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Thomas B Nutman
- Laboratory of Parasitic Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
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26
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Quintana JF, Babayan SA, Buck AH. Small RNAs and extracellular vesicles in filarial nematodes: From nematode development to diagnostics. Parasite Immunol 2017; 39. [PMID: 27748953 DOI: 10.1111/pim.12395] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2016] [Revised: 10/08/2016] [Accepted: 10/12/2016] [Indexed: 02/06/2023]
Abstract
Parasitic nematodes have evolved sophisticated mechanisms to communicate with their hosts in order to survive and successfully establish an infection. The transfer of RNA within extracellular vesicles (EVs) has recently been described as a mechanism that could contribute to this communication in filarial nematodes. It has been shown that these EVs are loaded with several types of RNAs, including microRNAs, leading to the hypothesis that parasites could actively use these molecules to manipulate host gene expression and to the exciting prospect that these pathways could result in new diagnostic and therapeutic strategies. Here, we review the literature on the diverse RNAi pathways that operate in nematodes and more specifically our current knowledge of extracellular RNA (exRNA) and EVs derived from filarial nematodes in vitro and within their hosts. We further detail some of the issues and questions related to the capacity of RNA-mediated communication to function in parasite-host interactions and the ability of exRNA to enable us to distinguish and detect different nematode parasites in their hosts.
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Affiliation(s)
- J F Quintana
- Institute of Immunology and Infection Research and Centre for Immunity, Infection & Evolution, School of Biological Sciences, University of Edinburgh, Edinburgh, UK
| | - S A Babayan
- Institute of Biodiversity Animal Health and Comparative Medicine, University of Glasgow, Glasgow, UK
| | - A H Buck
- Institute of Immunology and Infection Research and Centre for Immunity, Infection & Evolution, School of Biological Sciences, University of Edinburgh, Edinburgh, UK
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27
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Pilotte N, Unnasch TR, Williams SA. The Current Status of Molecular Xenomonitoring for Lymphatic Filariasis and Onchocerciasis. Trends Parasitol 2017; 33:788-798. [PMID: 28756911 DOI: 10.1016/j.pt.2017.06.008] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2017] [Revised: 06/19/2017] [Accepted: 06/21/2017] [Indexed: 10/19/2022]
Abstract
The capacity of vector insect surveillance to provide estimates of pathogen prevalence and transmission potential has long been recognized within the global communities tasked with eliminating lymphatic filariasis (LF), the underlying cause of elephantiasis and hydrocele, and onchocerciasis (river blindness). Initially restricted to the practice of dissection, the potential of vector monitoring has grown due to the advent of molecular methods capable of increasing the sensitivity and throughput of testing. However, despite such advancement, operational research gaps remain. If insufficiently addressed, these gaps will reduce the utility of molecular xenomonitoring (MX) for onchocerciasis as elimination efforts expand into Africa. Similarly, such shortcomings will limit the programmatic usefulness of MX for LF, resulting in this technique's significant underutilization.
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Affiliation(s)
- Nils Pilotte
- Department of Biological Sciences, Smith College, Northampton, MA, USA; Molecular and Cellular Biology Program, University of Massachusetts, Amherst, MA, USA; These authors contributed equally to this work
| | - Thomas R Unnasch
- Department of Global Health, University of South Florida, Tampa, FL, USA; These authors contributed equally to this work
| | - Steven A Williams
- Department of Biological Sciences, Smith College, Northampton, MA, USA; Molecular and Cellular Biology Program, University of Massachusetts, Amherst, MA, USA.
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28
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Affiliation(s)
- Sara Lustigman
- Molecular Parasitology, New York Blood Center, New York, NY, United States of America
- * E-mail:
| | - Alexandra Grote
- Center for Genomics and Systems Biology, Department of Biology, New York University, New York, NY, United States of America
| | - Elodie Ghedin
- Center for Genomics and Systems Biology, Department of Biology, New York University, New York, NY, United States of America
- College of Global Public Health, New York University, New York, NY, United States of America
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29
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Poole CB, Li Z, Alhassan A, Guelig D, Diesburg S, Tanner NA, Zhang Y, Evans TC, LaBarre P, Wanji S, Burton RA, Carlow CKS. Colorimetric tests for diagnosis of filarial infection and vector surveillance using non-instrumented nucleic acid loop-mediated isothermal amplification (NINA-LAMP). PLoS One 2017; 12:e0169011. [PMID: 28199317 PMCID: PMC5310896 DOI: 10.1371/journal.pone.0169011] [Citation(s) in RCA: 62] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2016] [Accepted: 11/19/2016] [Indexed: 11/26/2022] Open
Abstract
Accurate detection of filarial parasites in humans is essential for the implementation and evaluation of mass drug administration programs to control onchocerciasis and lymphatic filariasis. Determining the infection levels in vector populations is also important for assessing transmission, deciding when drug treatments may be terminated and for monitoring recrudescence. Immunological methods to detect infection in humans are available, however, cross-reactivity issues have been reported. Nucleic acid-based molecular assays offer high levels of specificity and sensitivity, and can be used to detect infection in both humans and vectors. In this study we developed loop-mediated isothermal amplification (LAMP) tests to detect three different filarial DNAs in human and insect samples using pH sensitive dyes for enhanced visual detection of amplification. Furthermore, reactions were performed in a portable, non-instrumented nucleic acid amplification (NINA) device that provides a stable heat source for LAMP. The efficacy of several strand displacing DNA polymerases were evaluated in combination with neutral red or phenol red dyes. Colorimetric NINA-LAMP assays targeting Brugia Hha I repeat, Onchocerca volvulus GST1a and Wuchereria bancrofti LDR each exhibit species-specificity and are also highly sensitive, detecting DNA equivalent to 1/10-1/5000th of one microfilaria. Reaction times varied depending on whether a single copy gene (70 minutes, O. volvulus) or repetitive DNA (40 min, B. malayi and W. bancrofti) was employed as a biomarker. The NINA heater can be used to detect multiple infections simultaneously. The accuracy, simplicity and versatility of the technology suggests that colorimetric NINA-LAMP assays are ideally suited for monitoring the success of filariasis control programs.
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Affiliation(s)
| | - Zhiru Li
- New England Biolabs, Ipswich, MA United States of America
| | - Andy Alhassan
- New England Biolabs, Ipswich, MA United States of America
| | - Dylan Guelig
- PATH, Seattle, Washington, United States of America
| | | | | | - Yinhua Zhang
- New England Biolabs, Ipswich, MA United States of America
| | | | - Paul LaBarre
- PATH, Seattle, Washington, United States of America
| | - Samuel Wanji
- Research Foundation in Tropical Diseases and Environment, Buea, Cameroon
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30
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Hernández-González A, Moya L, Perteguer MJ, Herrador Z, Nguema R, Nguema J, Aparicio P, Benito A, Gárate T. Evaluation of onchocerciasis seroprevalence in Bioko Island (Equatorial Guinea) after years of disease control programmes. Parasit Vectors 2016; 9:509. [PMID: 27645887 PMCID: PMC5028998 DOI: 10.1186/s13071-016-1779-8] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2016] [Accepted: 08/29/2016] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Onchocerciasis or "river blindness" is a chronic parasitic disease caused by the filarial worm Onchocerca volvulus, transmitted through infected blackflies (Simulium spp.). Bioko Island (Equatorial Guinea) used to show a high endemicity for onchocerciasis. During the last years, the disease control programmes using different larvicides and ivermectin administration have considerably reduced the prevalence and intensity of infection. Based on this new epidemiological scenario, in the present work we aimed to assess the impact of the strategies applied against onchocerciasis in Bioko Island by an evaluation of IgG4 antibodies specific for recombinant Ov-16 in ELISA. METHODS A cross-sectional study was conducted in Bioko Island from mid-January to mid-February, 2014. Twenty communities were randomly selected from rural and urban settings. A total of 140 households were chosen. In every selected household, all individuals aged 5 years and above were recruited; 544 study participants agreed to be part of this work. No previous data on onchocerciasis seroprevalence in the selected communities were available. Blood samples were collected and used in an "ELISA in-house" prepared with recombinant Ov-16, expressed and further purified. IgG4 antibodies specific for recombinant Ov-16 were evaluated by ELISA in all of the participants. RESULTS Based on the Ov-16 ELISA, the onchocerciasis seroprevalence was 7.9 %, mainly concentrated in rural settings; samples from community Catedral Ela Nguema (# 16) were missed during the field work. Among the rural setups, communities Inasa Maule (# 7), Ruiché (# 20) and Barrios Adyacentes Riaba (# 14), had the highest seropositivity percentages (29.2, 26.9 and 23.8 %, respectively). With respect to the urban settings, we did not find any positive case in communities Manzana Casa Bola (# 3), Colas Sesgas (# 6), Getesa (# 8), Moka Bioko (# 9), Impecsa (# 10), Baney Zona Baja (# 12) and Santo Tomás de Aquino (# 1). No onchocerciasis seropositive samples were found in 10-year-old individuals or younger. The IgG4 positive titles increased in older participants. CONCLUSIONS A significant decline in onchocerciasis prevalence was observed in Bioko Island after years of disease-vector control and CDTI strategy. The seroprevalence increased with age, mainly in rural settings that could be due to previous exposure of population to the filarial parasite, eliminated by the control programmes introduced against onchocerciasis. A new Ov-16 serological evaluation with a larger sample size of children below 10 years of age is required to demonstrate the interruption of transmission of O. volvulus in the human population of Bioko Island (Equatorial Guinea) according to the WHO criteria.
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Affiliation(s)
- Ana Hernández-González
- Helminth Unit, Parasitology Department, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Crtra. Majadahonda-Pozuelo, km 2.2, 28220, Majadahonda, Madrid, Spain.,Network Biomedical Research on Tropical Diseases (RICET), Madrid, Spain
| | - Laura Moya
- National Centre for Tropical Medicine, Instituto de Salud Carlos III, C/ Sinesio Delgado, 4, 28029, Madrid, Spain.,Jimenez Diaz Foundation University Hospital, Avda. Reyes Católicos, 2, 28040, Madrid, Spain
| | - María J Perteguer
- Helminth Unit, Parasitology Department, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Crtra. Majadahonda-Pozuelo, km 2.2, 28220, Majadahonda, Madrid, Spain.,Network Biomedical Research on Tropical Diseases (RICET), Madrid, Spain
| | - Zaida Herrador
- National Centre for Tropical Medicine, Instituto de Salud Carlos III, C/ Sinesio Delgado, 4, 28029, Madrid, Spain.,Network Biomedical Research on Tropical Diseases (RICET), Madrid, Spain
| | - Rufino Nguema
- Network Biomedical Research on Tropical Diseases (RICET), Madrid, Spain.,National Program for Control of Onchocerciasis and other Filariasis, Ministry of Health, Malabo, Equatorial Guinea
| | - Justino Nguema
- Network Biomedical Research on Tropical Diseases (RICET), Madrid, Spain.,National Program for Control of Onchocerciasis and other Filariasis, Ministry of Health, Malabo, Equatorial Guinea
| | - Pilar Aparicio
- National Centre for Tropical Medicine, Instituto de Salud Carlos III, C/ Sinesio Delgado, 4, 28029, Madrid, Spain.,Network Biomedical Research on Tropical Diseases (RICET), Madrid, Spain
| | - Agustín Benito
- National Centre for Tropical Medicine, Instituto de Salud Carlos III, C/ Sinesio Delgado, 4, 28029, Madrid, Spain.,Network Biomedical Research on Tropical Diseases (RICET), Madrid, Spain
| | - Teresa Gárate
- Helminth Unit, Parasitology Department, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Crtra. Majadahonda-Pozuelo, km 2.2, 28220, Majadahonda, Madrid, Spain. .,Network Biomedical Research on Tropical Diseases (RICET), Madrid, Spain.
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31
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Alhassan A, Osei-Atweneboana MY, Kyeremeh KF, Poole CB, Li Z, Tettevi E, Tanner NA, Carlow CKS. Comparison of a new visual isothermal nucleic acid amplification test with PCR and skin snip analysis for diagnosis of onchocerciasis in humans. Mol Biochem Parasitol 2016; 210:10-12. [PMID: 27473357 DOI: 10.1016/j.molbiopara.2016.07.006] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2016] [Revised: 07/21/2016] [Accepted: 07/22/2016] [Indexed: 10/21/2022]
Abstract
Accurate, simple and affordable diagnostics are needed to detect Onchocerca volvulus infection in humans. A newly developed colorimetric loop-mediated isothermal amplification (LAMP) assay was compared to PCR and skin snip analysis for diagnosis of onchocerciasis. The robustness and simplicity of the assay indicates that it may be a useful field tool for surveillance in endemic countries.
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Affiliation(s)
| | | | - Kwadwo F Kyeremeh
- University of Ghana, Noguchi Memorial Institute for Medical Research, Accra, Ghana
| | | | - Zhiru Li
- New England Biolabs, Ipswich, MA, USA
| | - Edward Tettevi
- Council for Scientific and Industrial Research, Water Research Institute, Accra, Ghana
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32
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Improved PCR-Based Detection of Soil Transmitted Helminth Infections Using a Next-Generation Sequencing Approach to Assay Design. PLoS Negl Trop Dis 2016; 10:e0004578. [PMID: 27027771 PMCID: PMC4814118 DOI: 10.1371/journal.pntd.0004578] [Citation(s) in RCA: 95] [Impact Index Per Article: 11.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2015] [Accepted: 03/04/2016] [Indexed: 12/31/2022] Open
Abstract
BACKGROUND The soil transmitted helminths are a group of parasitic worms responsible for extensive morbidity in many of the world's most economically depressed locations. With growing emphasis on disease mapping and eradication, the availability of accurate and cost-effective diagnostic measures is of paramount importance to global control and elimination efforts. While real-time PCR-based molecular detection assays have shown great promise, to date, these assays have utilized sub-optimal targets. By performing next-generation sequencing-based repeat analyses, we have identified high copy-number, non-coding DNA sequences from a series of soil transmitted pathogens. We have used these repetitive DNA elements as targets in the development of novel, multi-parallel, PCR-based diagnostic assays. METHODOLOGY/PRINCIPAL FINDINGS Utilizing next-generation sequencing and the Galaxy-based RepeatExplorer web server, we performed repeat DNA analysis on five species of soil transmitted helminths (Necator americanus, Ancylostoma duodenale, Trichuris trichiura, Ascaris lumbricoides, and Strongyloides stercoralis). Employing high copy-number, non-coding repeat DNA sequences as targets, novel real-time PCR assays were designed, and assays were tested against established molecular detection methods. Each assay provided consistent detection of genomic DNA at quantities of 2 fg or less, demonstrated species-specificity, and showed an improved limit of detection over the existing, proven PCR-based assay. CONCLUSIONS/SIGNIFICANCE The utilization of next-generation sequencing-based repeat DNA analysis methodologies for the identification of molecular diagnostic targets has the ability to improve assay species-specificity and limits of detection. By exploiting such high copy-number repeat sequences, the assays described here will facilitate soil transmitted helminth diagnostic efforts. We recommend similar analyses when designing PCR-based diagnostic tests for the detection of other eukaryotic pathogens.
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Weerakoon KG, McManus DP. Cell-Free DNA as a Diagnostic Tool for Human Parasitic Infections. Trends Parasitol 2016; 32:378-391. [PMID: 26847654 DOI: 10.1016/j.pt.2016.01.006] [Citation(s) in RCA: 97] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2015] [Revised: 12/28/2015] [Accepted: 01/11/2016] [Indexed: 12/18/2022]
Abstract
Parasites often cause devastating diseases and represent a significant public health and economic burden. More accurate and convenient diagnostic tools are needed in support of parasite control programmes in endemic regions, and for rapid point-of-care diagnosis in nonendemic areas. The detection of cell-free DNA (cfDNA) is a relatively new concept that is being applied in the current armamentarium of diagnostics. Here, we review the application of cfDNA detection with nucleic acid amplification tests for the diagnosis and evaluation of different human parasitic infections and highlight the significant benefits of the approach using non-invasive clinical samples.
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Affiliation(s)
- Kosala G Weerakoon
- Molecular Parasitology Laboratory, QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia; School of Public Health, University of Queensland, Brisbane, QLD, Australia; Department of Parasitology, Faculty of Medicine and Allied Sciences, Rajarata University of Sri Lanka, Saliyapura, Sri Lanka.
| | - Donald P McManus
- Molecular Parasitology Laboratory, QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia.
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Historic accounts of Mansonella parasitaemias in the South Pacific and their relevance to lymphatic filariasis elimination efforts today. ASIAN PAC J TROP MED 2016; 9:205-10. [PMID: 26972389 DOI: 10.1016/j.apjtm.2016.01.040] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2015] [Revised: 12/20/2015] [Accepted: 12/30/2015] [Indexed: 11/21/2022] Open
Abstract
There are two species of filarial parasites with sheathless microfilariae known to commonly cause parasitaemias in humans: Mansonella perstans and Mansonella ozzardi. In most contemporary accounts of the distribution of these parasites, neither is usually considered to occur anywhere in the Eastern Hemisphere. However, Sir Patrick Manson, who first described both parasite species, recorded the existence of sheathless sharp-tailed Mansonella ozzardi-like parasites occurring in the blood of natives from New Guinea in each and every version of his manual for tropical disease that he wrote before his death in 1922. Manson's reports were based on his own identifications and were made from at least two independent blood sample collections that were taken from the island. Pacific region Mansonella perstans parasitaemias were also later (in 1923) reported to occur in New Guinea and once before this (in 1905) in Fiji. Although Mansonella-parasitaemias are generally regarded as benign, they are thought to be of public health importance because they can affect the epidemiological monitoring of other filarial diseases. In this article, we reviewed the historic literature concerning Pacific-origin Mansonella-parasitaemias in an attempt to explain how, despite repeated reports of Pacific-region Mansonella-parasitaemias, by as early as the 1970s, the WHO had arrived at the present-day view that Wuchereria bancrofti is the only cause of filarial parasitaemias in Papua New Guinea. We have also evaluated the evidence supporting the contemporary existence of Pacific-area parasitaemia-causing Mansonella parasites and assessed the relevance such parasites could have for present-day lymphatic filariasis elimination efforts in the region.
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Poole CB, Ettwiller L, Tanner NA, Evans TC, Wanji S, Carlow CKS. Genome Filtering for New DNA Biomarkers of Loa loa Infection Suitable for Loop-Mediated Isothermal Amplification. PLoS One 2015; 10:e0139286. [PMID: 26414073 PMCID: PMC4586141 DOI: 10.1371/journal.pone.0139286] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2015] [Accepted: 09/09/2015] [Indexed: 11/18/2022] Open
Abstract
Loa loa infections have emerged as a serious public health problem in patients co-infected with Onchocerca volvulus or Wuchereria bancrofti because of severe adverse neurological reactions after treatment with ivermectin. Accurate diagnostic tests are needed for careful mapping in regions where mass drug administration is underway. Loop-mediated isothermal amplification (LAMP) has become a widely adopted screening method because of its operational simplicity, rapidity and versatility of visual detection readout options. Here, we present a multi-step bioinformatic pipeline to generate diagnostic candidates suitable for LAMP and experimentally validate this approach using one of the identified candidates to develop a species-specific LAMP assay for L. loa. The pipeline identified ~140 new L. loa specific DNA repeat families as putative biomarkers of infection. The consensus sequence of one family, repeat family 4 (RF4), was compiled from ~ 350 sequences dispersed throughout the L. loa genome and maps to a L. loa-specific region of the long terminal repeats found at the boundaries of Bel/Pao retrotransposons. PCR and LAMP primer sets targeting RF4 specifically amplified L. loa but not W. bancrofti, O. volvulus, Brugia malayi, human or mosquito DNA. RF4 LAMP detects the DNA equivalent of one microfilaria (100 pg) in 25-30 minutes and as little as 0.060 pg of L. loa DNA (~1/1600th of a microfilaria) purified from spiked blood samples in approximately 50 minutes. In summary, we have successfully employed a bioinformatic approach to mine the L. loa genome for species-specific repeat families that can serve as new DNA biomarkers for LAMP. The RF4 LAMP assay shows promise as a field tool for the implementation and management of mass drug administration programs and warrants further testing on clinical samples as the next stage in development towards this goal.
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Affiliation(s)
| | | | - Nathan A. Tanner
- New England Biolabs, Ipswich, Massachusetts, United States of America
| | - Thomas C. Evans
- New England Biolabs, Ipswich, Massachusetts, United States of America
| | - Samuel Wanji
- Research Foundation in Tropical Diseases and Environment, Buea, Cameroon
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