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Andrade EHP, Figueiredo LB, Vilela APP, Rosa JCC, Zibaoui HM, Kroon EG. Virological Surveillance of Aedes aegypti Vectors Identifies All Four Dengue Serotypes in a Hyperendemic Region. ECOHEALTH 2022; 19:75-84. [PMID: 35318521 DOI: 10.1007/s10393-022-01583-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/20/2021] [Revised: 01/31/2022] [Accepted: 02/04/2022] [Indexed: 06/14/2023]
Abstract
Dengue virus (DENV) 1-4 is the etiological agent of dengue, the most important viral infection transmitted by Aedes spp mosquitoes to humans. Our goal was to identify the circulating DENV in Aedes aegypti collected in an area of Brazil where all four DENV serotypes had already been detected in humans, understand the epidemiology better, and to test the vector as a virological surveillance tool. Twenty-eight larvae pools and 174 females of Aedes aegypti were screened by reverse transcriptase quantitative polymerase chain reaction and semi-nested PCR assays. PCR products were sequenced, and phylogenetic analyses were performed. Nine larvae pools (32.1%) were positive for DENV, four (44.4%) with DENV-3, and five (55.6%) with more than one serotype. Fifteen females (8.6%) were positive for any DENV serotype. DENV-1 isolates belong to genotype V, DENV-2 to American-Asian genotype, DENV-3 to genotypes I and III, and DENV-4 to genotypes I and II. We demonstrate for the first time the co-circulation of all four DENV serotypes in larvae pools and adult Aedes aegypti in a hyperendemic area. This scenario represents a challenge for disease control and reinforces the importance of virological surveillance in the vector as a tool for predicting circulating DENV serotypes in humans.
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Affiliation(s)
- Elisa Helena Paz Andrade
- Departamento de Tecnologia e Inspeção de Produtos de Origem Animal, Escola de Veterinária, Universidade Federal de Minas Gerais, Belo Horizonte, MG, Brazil
| | - Leandra Barcelos Figueiredo
- Laboratório de Vírus, Departamento de Microbiologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, MG, Brazil
| | | | - Júlio César Câmara Rosa
- Laboratório de Vírus, Departamento de Microbiologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, MG, Brazil
| | | | - Erna Geessien Kroon
- Laboratório de Vírus, Departamento de Microbiologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, MG, Brazil.
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Borkakoty B, Das M, Sarma K, Jakharia A, Das PK, Bhattacharya C, Apum B, Biswas D. Molecular characterisation and phylogenetic analysis of dengue outbreak in Pasighat, Arunachal Pradesh, Northeast India. Indian J Med Microbiol 2018; 36:37-42. [PMID: 29735824 DOI: 10.4103/ijmm.ijmm_17_30] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
Background and Objectives Dengue is one of the most prevalent arboviral diseases in the world with 390 million dengue infections per year. In this study, we report the molecular characterisation of dengue outbreak in Pasighat, Arunachal Pradesh, Northeast India during 2015. Subjects and Methods : A total of 613 dengue-suspected cases were screened for dengue virus by dengue NS1 Ag and anti-dengue IgM antibody depending on the duration of sample collection and onset of symptom. Further, molecular characterisation was done by amplifying the C-PrM region by real-time polymerase chain reaction followed by phylogenetic analysis. Results Molecular characterisation revealed that the dengue outbreak was predominantly due to dengue virus serotype-1 (DENV-1) (90.9%) while DENV-2 was detected in 7.5% of samples. Co-infection of DENV-1 and DENV-2 was detected in one case. Phylogenetic analysis of the DENV-1 strains with the prototype revealed that the DENV-1 strains were grouped within genotype III. Similarly, DENV-2 strains were clustered within genotype IV. The study revealed a change in the predominant serotype in recent years with DENV-3 in 2012 to DENV-1, 2, 3 and 4 in 2014 to DENV-1 in 2015 in the study region. A unique L24M mutation was observed in the DENV-1 strains of Arunachal Pradesh which was absent in all the circulating strains in India except one strain from the state of Kerala in South India. Marked variation within the DENV-2 strains was observed at A102V and I163V in one strain similar to earlier circulating isolates in India. Conclusions The present study reveals a shift in the serotype dominance in the study region. As serotype shifts and secondary infection with a heterologous DENV serotype are frequently associated with disease severity, there is an urgent need for sustained monitoring of the circulating serotypes and enhanced surveillance operations, especially in the monsoon and post-monsoon periods to prevent large-scale, severe dengue outbreaks in this region.
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Affiliation(s)
| | - Mandakini Das
- ICMR- Regional Medical Research Centre, N. E. Region, Dibrugarh, Assam, India
| | - Kishore Sarma
- ICMR- Regional Medical Research Centre, N. E. Region, Dibrugarh, Assam, India
| | - Aniruddha Jakharia
- ICMR- Regional Medical Research Centre, N. E. Region, Dibrugarh, Assam, India
| | - Palash Kumar Das
- ICMR- Regional Medical Research Centre, N. E. Region, Dibrugarh, Assam, India
| | | | - Basumoti Apum
- Department of Microbiology, General Hospital, Pasighat, East Siang, Arunachal Pradesh, India
| | - Dipankar Biswas
- ICMR- Regional Medical Research Centre, N. E. Region, Dibrugarh, Assam, India
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A Multiplex PCR/LDR Assay for Viral Agents of Diarrhea with the Capacity to Genotype Rotavirus. Sci Rep 2018; 8:13215. [PMID: 30181651 PMCID: PMC6123451 DOI: 10.1038/s41598-018-30301-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2018] [Accepted: 07/27/2018] [Indexed: 12/11/2022] Open
Abstract
Rotavirus and noroviruses are major causes of diarrhea. Variable rotavirus vaccination efficacy in Africa and Asia is multifactorial, including the diversity of circulating strains and viral co-infection. We describe a multiplexed assay that detects and genotypes viruses from stool specimens. It includes a one-step reverse transcriptase PCR reaction, a ligase detection reaction (LDR), then hybridization of fluorescent products to micro-beads. In clinical samples it detects rotavirus, caliciviruses (sapovirus and norovirus), mixed infections, and genotypes or genogroups of rotaviruses and noroviruses, respectively. The assay also has the capacity to detect hepatitis A. The assay was validated on reference isolates and 296 stool specimens from the US and Ghana. The assay was 97% sensitive and 100% specific. The genogroup was concordant in 100% of norovirus, and the genotype in 91% and 89% of rotavirus G- and P-types, respectively. Two rare rotavirus strains, G6P[6] and G6P[8], were detected in stool specimens from Ghana. The high-throughput assay is sensitive, specific, and may be of utility in the epidemiological surveillance for rare and emerging viral strains post-rotavirus vaccine implementation.
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Affiliation(s)
- Karen C Carroll
- Division of Medical Microbiology, Department of Pathology, The Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
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Lee H, Nguyen MP, Choi Y, Kim YH. Minimum InDel pattern analysis of the Zika virus. BMC Genomics 2018; 19:535. [PMID: 30005607 PMCID: PMC6045892 DOI: 10.1186/s12864-018-4935-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2018] [Accepted: 07/10/2018] [Indexed: 12/03/2022] Open
Abstract
Background The Zika virus (ZIKV) can cause microcephaly and congenital abnormalities in the foetus. Recent studies have provided insights into the evolution of ZIKV from the current and previous outbreaks, but the types have not been determined. Results We analysed the insertions and deletions (InDels) in 212 ZIKV polyproteins and 5 Dengue virus (DENV) reference sequences. Spearman correlation tests for the minimum InDel (minInDel) patterns were used to assess the type of polyprotein. Using the minInDel frequencies calculated from polyproteins with 11 elements, likelihood estimation was conducted to correct the evolutionary distance. The minInDel-corrected tree topology clearly distinguished between the ZIKV types (I and II) with a unique minInDel character in the E protein. From the 10-year average genetic distance, the African and Asian lineages of ZIKV-II were estimated to have occurred ~ 270 years ago, which is unlikely for ZIKV-I. Conclusions The minInDel pattern analysis showed that the minInDel in the E protein is targetable for the rapid detection and determination of the virus types. Electronic supplementary material The online version of this article (10.1186/s12864-018-4935-z) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Hyeji Lee
- Department of Microbiology, Daegu Catholic University School of Medicine, Daegu, 42472, Republic of Korea
| | - Mai Phuong Nguyen
- Department of Microbiology, Daegu Catholic University School of Medicine, Daegu, 42472, Republic of Korea
| | - Yunhee Choi
- Department of Microbiology, Daegu Catholic University School of Medicine, Daegu, 42472, Republic of Korea
| | - Yong-Hak Kim
- Department of Microbiology, Daegu Catholic University School of Medicine, Daegu, 42472, Republic of Korea.
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Cloning and Expression of NS3 Gene of Pakistani Isolate Type 2 Dengue Virus. J Vet Res 2018; 62:17-26. [PMID: 29978123 PMCID: PMC5957457 DOI: 10.2478/jvetres-2018-0003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2017] [Accepted: 03/08/2018] [Indexed: 11/20/2022] Open
Abstract
Introduction Dengue is one of the major emerging viral diseases in the world, with dramatic increases in reported cases in the last few decades and annual worldwide occurrence of approximately 390 million infections. It is a highly important mosquito-vectored disease and is a problem in tropical and subtropical areas of the world. The major aim of this study was to clone and express the dengue NS3 gene, in service to its therapeutic importance for the development of stable cell lines. Material and Methods Blood samples from dengue fever (DF) patients were collected and subjected to PCR amplification of the NS3 gene of dengue virus serotype-2 (DENV-2). The NS3 gene was amplified using gene specific primers and cloned in the TA cloning vectors. Results The gene was successfully expressed in mammalian expression vector pcDNA3.1. The current finding was different from a previously reported DENV-2 strain replicon constructed in different cells, in which the whole genetic material of the virus was used instead of an active protease gene, and which gave a low yield of replicon expressing cells. Conclusion Recombinant NS3 could be used to produce an antibody that is possibly helpful for developing a single step diagnostic assay to detect the dengue virus NS3 antigen in sera of dengue patients.
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Antiviral Activity of Thiazolide Derivatives Against Dengue Virus in Huh-7 Cell Line. Jundishapur J Microbiol 2017. [DOI: 10.5812/jjm.62467] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
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Lebani K, Jones ML, Watterson D, Ranzoni A, Traves RJ, Young PR, Mahler SM. Isolation of serotype-specific antibodies against dengue virus non-structural protein 1 using phage display and application in a multiplexed serotyping assay. PLoS One 2017; 12:e0180669. [PMID: 28683141 PMCID: PMC5500353 DOI: 10.1371/journal.pone.0180669] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2017] [Accepted: 06/19/2017] [Indexed: 01/01/2023] Open
Abstract
The multidimensional nature of dengue virus (DENV) infections, which can be caused by four distinct serotypes of the virus, complicates the sensitivity of assays designed for the diagnosis of infection. Different viral markers can be optimally detected at different stages of infection. Of particular clinical importance is the early identification of infection, which is pivotal for disease management and the development of blood screening assays. Non-structural protein 1 (NS1) is an early surrogate marker of infection and its detection in serum coincides with detectable viraemia. The aim of this work was to isolate and characterise serotype-specific monoclonal antibodies that bind to NS1 for each of the four DENV serotypes. This was achieved using phage display and a subtractive biopanning strategy to direct the antibody selection towards serotype-specific epitopes. This antibody isolation strategy has advantages over immunisation techniques where it is difficult to avoid antibody responses to cross-reactive, immunodominant epitopes. Serotype specificity to recombinant antigen for each of the antibodies was confirmed by Enzyme Linked Immunosorbent Assay (ELISA) and Surface Plasmon Resonance. Confirmation of binding to native DENV NS1 was achieved using ELISA and immunofluorescence assay on DENV infected Vero cells. No cross-reactivity with Zika or Kunjin viruses was observed. A previously isolated pan-reactive antibody that binds to an immunodominant epitope was able to pair with each of the serotype-specific antibodies in a sandwich ELISA, indicating that the serotype specific antibodies bind to epitopes which are all spatially distinct from the immunodominant epitope. These antibodies were suitable for use in a multiplexed assay for simultaneous detection and serotyping of DENV NS1 in human serum. This work demonstrates that phage display coupled with novel biopanning strategies is a valuable in vitro methodology for isolation of binders that can discern amongst antigens with high homology for diagnostic applicability.
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Affiliation(s)
- Kebaneilwe Lebani
- Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, Brisbane, Queensland, Australia
| | - Martina L. Jones
- Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, Brisbane, Queensland, Australia
- ARC Training Centre for Biopharmaceutical Innovation, The University of Queensland, Brisbane, Queensland, Australia
- * E-mail:
| | - Daniel Watterson
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Queensland, Australia
- Australian Infectious Diseases Research Centre, The University of Queensland, Brisbane, Queensland, Australia
| | - Andrea Ranzoni
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland, Australia
| | - Renee J. Traves
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Queensland, Australia
| | - Paul R. Young
- ARC Training Centre for Biopharmaceutical Innovation, The University of Queensland, Brisbane, Queensland, Australia
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Queensland, Australia
- Australian Infectious Diseases Research Centre, The University of Queensland, Brisbane, Queensland, Australia
| | - Stephen M. Mahler
- Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, Brisbane, Queensland, Australia
- ARC Training Centre for Biopharmaceutical Innovation, The University of Queensland, Brisbane, Queensland, Australia
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Gibriel AA, Adel O. Advances in ligase chain reaction and ligation-based amplifications for genotyping assays: Detection and applications. MUTATION RESEARCH-REVIEWS IN MUTATION RESEARCH 2017; 773:66-90. [PMID: 28927538 PMCID: PMC7108312 DOI: 10.1016/j.mrrev.2017.05.001] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/06/2016] [Revised: 04/24/2017] [Accepted: 05/01/2017] [Indexed: 02/07/2023]
Abstract
Genetic variants have been reported to cause several genetic diseases. Various genotyping assays have been developed for diagnostic and screening purposes but with certain limitations in sensitivity, specificity, cost effectiveness and/or time savings. Since the discovery of ligase chain reaction (LCR) in the late nineties, it became one of the most favored platforms for detecting these variants and also for genotyping low abundant contaminants. Recent and powerful modifications with the integration of various detection strategies such as electrochemical and magnetic biosensors, nanoparticles (NPs), quantum dots, quartz crystal and leaky surface acoustic surface biosensors, DNAzyme, rolling circle amplification (RCA), strand displacement amplification (SDA), surface enhanced raman scattering (SERS), chemiluminescence and fluorescence resonance energy transfer have been introduced to both LCR and ligation based amplifications to enable high-throughput and inexpensive multiplex genotyping with improved robustness, simplicity, sensitivity and specificity. In this article, classical and up to date modifications in LCR and ligation based amplifications are critically evaluated and compared with emphasis on points of strength and weakness, sensitivity, cost, running time, equipment needed, applications and multiplexing potential. Versatile genotyping applications such as genetic diseases detection, bacterial and viral pathogens detection are also detailed. Ligation based gold NPs biosensor, ligation based RCA and ligation mediated SDA assays enhanced detection limit tremendously with a discrimination power approaching 1.5aM, 2aM and 0.1fM respectively. MLPA (multiplexed ligation dependent probe amplification) and SNPlex assays have been commercialized for multiplex detection of at least 48 SNPs at a time. MOL-PCR (multiplex oligonucleotide ligation) has high-throughput capability with multiplex detection of 50 SNPs/well in a 96 well plate. Ligase detection reaction (LDR) is one of the most widely used LCR versions that have been successfully integrated with several detection strategies with improved sensitivity down to 0.4fM.
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Affiliation(s)
- Abdullah A Gibriel
- Biochemistry & Molecular Biology Department, Faculty of Pharmacy, The British University in Egypt (BUE), Cairo, Egypt; Center for Drug Research & Development (CDRD), Faculty of Pharmacy, The British University in Egypt (BUE), Cairo, Egypt.
| | - Ola Adel
- Biochemistry & Molecular Biology Department, Faculty of Pharmacy, The British University in Egypt (BUE), Cairo, Egypt; Center for Drug Research & Development (CDRD), Faculty of Pharmacy, The British University in Egypt (BUE), Cairo, Egypt
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Lutfullah G, Ahmed J, Khan A, Ihsan H, Ahmad J. Evaluation of Non-Structural Protein-1(NS1) positive patients of 2013 dengue outbreak in Khyber Pakhtunkhwa, Pakistan. Pak J Med Sci 2017; 33:172-176. [PMID: 28367194 PMCID: PMC5368302 DOI: 10.12669/pjms.331.11237] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
Background & Objective: Dengue infection is an arthropod borne disease caused by Dengue virus in humans. Dengue virus infection has more potential to produce severe form of the disease with more severe symptoms. Proper diagnosis of dengue fever is very important for its safe management. The objective of this study was to evaluate the non structural protein-1 (NS1) positive parameter for identification of dengue fever by using ELISA from 2013 dengue outbreak in Khyber Pakhtunkhwa. Methods: It was a cross sectional study conducted among 384 patients tested for dengue admitted to different hospitals of Khyber Pakhtunkhwa April to December 2013 with symptoms related to classical dengue fever. Written informed consent was taken from 100 NS1 positive diagnosed patients, and 3 to 5 ml blood sample was collected for confirmation through ELISA testing. ELISA test for dengue IgG and IgM was performed two time in order to confirm the dengue cases. Data was entered and analyzed by using SPSS version 16. Result: The study performed on 100 NS1 positive samples of patients, admitted to hospitals with symptoms related to classical dengue fever, indicated that after performing the IgM and IgG capture ELISA test only 76 samples were actually found positive for dengue. The rest of the 24 samples were found negative for both IgM and IgG capture ELISAs. The study also revealed that 90.8 % patients had primary dengue infection and 35.5% patients had secondary dengue infection. Most patients were between the age of 10-20 years (26%), among them19.7% were having primary dengue infection. Among 10-20 years of age 50% female patients were false dengue patients. Conclusion: About 24 % NSI protein positive samples were found negative for both IgM and IgG capture ELISAs showed that NS1protein positivity does not confirm actual dengue infection.
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Affiliation(s)
- Ghosia Lutfullah
- Dr. Ghosia Lutfullah, PhD Chemistry. Centre of Biotechnology and Microbiology, University of Peshawar, Peshawar, Pakistan
| | - Jawad Ahmed
- Dr. Jawad Ahmad, PhD Chemistry. Department of Microbiology, Khyber Medical University Peshawar, Peshawar, Pakistan
| | - Aftab Khan
- Mr. Aftab Khan, M. Phil Microbiology. PMRC Research Centre, Khyber Medical College Peshawar, Peshawar, Pakistan
| | - Hina Ihsan
- Miss Hina Ihsan, M. Phil. Centre of Biotechnology and Microbiology, University of Peshawar, Peshawar, Pakistan
| | - Jamshed Ahmad
- Dr. Jamshed Ahmad, PhD Microbiology. Centre of Biotechnology and Microbiology, University of Peshawar, Peshawar, Pakistan
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Tahir ul Q M, Kiran S, Ashfaq UA, Javed MR, Anwar F, Ali MA, Gilani AUH. Discovery of Novel Dengue NS2B/NS3 Protease Inhibitors Using
Pharmacophore Modeling and Molecular Docking Based Virtual
Screening of the ZINC Database. INT J PHARMACOL 2016. [DOI: 10.3923/ijp.2016.621.632] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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Egatz-Gomez A, Wang C, Klacsmann F, Pan Z, Marczak S, Wang Y, Sun G, Senapati S, Chang HC. Future microfluidic and nanofluidic modular platforms for nucleic acid liquid biopsy in precision medicine. BIOMICROFLUIDICS 2016; 10:032902. [PMID: 27190565 PMCID: PMC4859827 DOI: 10.1063/1.4948525] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/08/2016] [Accepted: 04/20/2016] [Indexed: 05/05/2023]
Abstract
Nucleic acid biomarkers have enormous potential in non-invasive diagnostics and disease management. In medical research and in the near future in the clinics, there is a great demand for accurate miRNA, mRNA, and ctDNA identification and profiling. They may lead to screening of early stage cancer that is not detectable by tissue biopsy or imaging. Moreover, because their cost is low and they are non-invasive, they can become a regular screening test during annual checkups or allow a dynamic treatment program that adjusts its drug and dosage frequently. We briefly review a few existing viral and endogenous RNA assays that have been approved by the Federal Drug Administration. These tests are based on the main nucleic acid detection technologies, namely, quantitative reverse transcription polymerase chain reaction (PCR), microarrays, and next-generation sequencing. Several of the challenges that these three technologies still face regarding the quantitative measurement of a panel of nucleic acids are outlined. Finally, we review a cluster of microfluidic technologies from our group with potential for point-of-care nucleic acid quantification without nucleic acid amplification, designed to overcome specific limitations of current technologies. We suggest that integration of these technologies in a modular design can offer a low-cost, robust, and yet sensitive/selective platform for a variety of precision medicine applications.
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Affiliation(s)
- Ana Egatz-Gomez
- Center for Microfluidics and Medical Diagnostics, Department of Chemical and Biomolecular Engineering, University of Notre Dame , Notre Dame, Indiana 46556, USA
| | - Ceming Wang
- Center for Microfluidics and Medical Diagnostics, Department of Chemical and Biomolecular Engineering, University of Notre Dame , Notre Dame, Indiana 46556, USA
| | - Flora Klacsmann
- Center for Microfluidics and Medical Diagnostics, Department of Chemical and Biomolecular Engineering, University of Notre Dame , Notre Dame, Indiana 46556, USA
| | - Zehao Pan
- Center for Microfluidics and Medical Diagnostics, Department of Chemical and Biomolecular Engineering, University of Notre Dame , Notre Dame, Indiana 46556, USA
| | - Steve Marczak
- Center for Microfluidics and Medical Diagnostics, Department of Chemical and Biomolecular Engineering, University of Notre Dame , Notre Dame, Indiana 46556, USA
| | - Yunshan Wang
- Electrical and Computer Engineering, University of Utah , Salt Lake City, Utah 84112, USA
| | - Gongchen Sun
- Center for Microfluidics and Medical Diagnostics, Department of Chemical and Biomolecular Engineering, University of Notre Dame , Notre Dame, Indiana 46556, USA
| | - Satyajyoti Senapati
- Center for Microfluidics and Medical Diagnostics, Department of Chemical and Biomolecular Engineering, University of Notre Dame , Notre Dame, Indiana 46556, USA
| | - Hsueh-Chia Chang
- Center for Microfluidics and Medical Diagnostics, Department of Chemical and Biomolecular Engineering, University of Notre Dame , Notre Dame, Indiana 46556, USA
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Andrade EHP, Figueiredo LB, Vilela APP, Rosa JCC, Oliveira JG, Zibaoui HM, Araújo VEM, Miranda DPJ, Ferreira PCP, Abrahão JS, Kroon EG. Spatial-Temporal Co-Circulation of Dengue Virus 1, 2, 3, and 4 Associated with Coinfection Cases in a Hyperendemic Area of Brazil: A 4-Week Survey. Am J Trop Med Hyg 2016; 94:1080-4. [PMID: 26976882 DOI: 10.4269/ajtmh.15-0892] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2015] [Accepted: 01/26/2016] [Indexed: 11/07/2022] Open
Abstract
Dengue is currently regarded as a major public health problem worldwide. In a hyperendemic region during an outbreak, we detected the co-circulation of all Dengue virus (DENV) serotypes including two different genotypes of DENV-3 and DENV-4, and concurrent infections with up to three serotypes were identified in symptomatic patients. A total of 49 acute phase plasma samples from patients clinically suspected of dengue were collected during the 4 weeks of May 2013. DENV-1-4 was detected by reverse transcriptase semi-nested polymerase chain reaction in 33 samples (67.3%), of which 26 DNA fragments were sequenced. Twenty samples (76.9%) were identified with a single DENV serotype and six (23.1%) with more than one serotype. DENV-3 was the predominant serotype of the outbreak. On the basis of phylogenetic analyses, DENV-1 isolates belong to genotype V, DENV-2 to American-Asian genotype, DENV-3 to genotypes I and III, and DENV-4 to genotypes I and II.
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Affiliation(s)
- Elisa H P Andrade
- Laboratório de Vírus, Departamento de Microbiologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil; Secretaria de Saúde, Prefeitura Municipal de Contagem, Contagem, Brazil; Laboratório de Imunologia Celular e Molecular, Centro de Pesquisas René Rachou, Fundação Oswaldo Cruz (FIOCRUZ), Belo Horizonte, Brazil; Laboratório de Epidemiologia das Doenças Infecciosas e Parasitárias, Departamento de Parasitologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Leandra B Figueiredo
- Laboratório de Vírus, Departamento de Microbiologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil; Secretaria de Saúde, Prefeitura Municipal de Contagem, Contagem, Brazil; Laboratório de Imunologia Celular e Molecular, Centro de Pesquisas René Rachou, Fundação Oswaldo Cruz (FIOCRUZ), Belo Horizonte, Brazil; Laboratório de Epidemiologia das Doenças Infecciosas e Parasitárias, Departamento de Parasitologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Ana P P Vilela
- Laboratório de Vírus, Departamento de Microbiologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil; Secretaria de Saúde, Prefeitura Municipal de Contagem, Contagem, Brazil; Laboratório de Imunologia Celular e Molecular, Centro de Pesquisas René Rachou, Fundação Oswaldo Cruz (FIOCRUZ), Belo Horizonte, Brazil; Laboratório de Epidemiologia das Doenças Infecciosas e Parasitárias, Departamento de Parasitologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Júlio C C Rosa
- Laboratório de Vírus, Departamento de Microbiologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil; Secretaria de Saúde, Prefeitura Municipal de Contagem, Contagem, Brazil; Laboratório de Imunologia Celular e Molecular, Centro de Pesquisas René Rachou, Fundação Oswaldo Cruz (FIOCRUZ), Belo Horizonte, Brazil; Laboratório de Epidemiologia das Doenças Infecciosas e Parasitárias, Departamento de Parasitologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Jaquelline G Oliveira
- Laboratório de Vírus, Departamento de Microbiologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil; Secretaria de Saúde, Prefeitura Municipal de Contagem, Contagem, Brazil; Laboratório de Imunologia Celular e Molecular, Centro de Pesquisas René Rachou, Fundação Oswaldo Cruz (FIOCRUZ), Belo Horizonte, Brazil; Laboratório de Epidemiologia das Doenças Infecciosas e Parasitárias, Departamento de Parasitologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Hassan M Zibaoui
- Laboratório de Vírus, Departamento de Microbiologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil; Secretaria de Saúde, Prefeitura Municipal de Contagem, Contagem, Brazil; Laboratório de Imunologia Celular e Molecular, Centro de Pesquisas René Rachou, Fundação Oswaldo Cruz (FIOCRUZ), Belo Horizonte, Brazil; Laboratório de Epidemiologia das Doenças Infecciosas e Parasitárias, Departamento de Parasitologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Valdelaine E M Araújo
- Laboratório de Vírus, Departamento de Microbiologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil; Secretaria de Saúde, Prefeitura Municipal de Contagem, Contagem, Brazil; Laboratório de Imunologia Celular e Molecular, Centro de Pesquisas René Rachou, Fundação Oswaldo Cruz (FIOCRUZ), Belo Horizonte, Brazil; Laboratório de Epidemiologia das Doenças Infecciosas e Parasitárias, Departamento de Parasitologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Daniela P J Miranda
- Laboratório de Vírus, Departamento de Microbiologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil; Secretaria de Saúde, Prefeitura Municipal de Contagem, Contagem, Brazil; Laboratório de Imunologia Celular e Molecular, Centro de Pesquisas René Rachou, Fundação Oswaldo Cruz (FIOCRUZ), Belo Horizonte, Brazil; Laboratório de Epidemiologia das Doenças Infecciosas e Parasitárias, Departamento de Parasitologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Paulo C P Ferreira
- Laboratório de Vírus, Departamento de Microbiologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil; Secretaria de Saúde, Prefeitura Municipal de Contagem, Contagem, Brazil; Laboratório de Imunologia Celular e Molecular, Centro de Pesquisas René Rachou, Fundação Oswaldo Cruz (FIOCRUZ), Belo Horizonte, Brazil; Laboratório de Epidemiologia das Doenças Infecciosas e Parasitárias, Departamento de Parasitologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Jonatas S Abrahão
- Laboratório de Vírus, Departamento de Microbiologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil; Secretaria de Saúde, Prefeitura Municipal de Contagem, Contagem, Brazil; Laboratório de Imunologia Celular e Molecular, Centro de Pesquisas René Rachou, Fundação Oswaldo Cruz (FIOCRUZ), Belo Horizonte, Brazil; Laboratório de Epidemiologia das Doenças Infecciosas e Parasitárias, Departamento de Parasitologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Erna G Kroon
- Laboratório de Vírus, Departamento de Microbiologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil; Secretaria de Saúde, Prefeitura Municipal de Contagem, Contagem, Brazil; Laboratório de Imunologia Celular e Molecular, Centro de Pesquisas René Rachou, Fundação Oswaldo Cruz (FIOCRUZ), Belo Horizonte, Brazil; Laboratório de Epidemiologia das Doenças Infecciosas e Parasitárias, Departamento de Parasitologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
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14
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Das S, Rundell MS, Mirza AH, Pingle MR, Shigyo K, Garrison AR, Paragas J, Smith SK, Olson VA, Larone DH, Spitzer ED, Barany F, Golightly LM. A Multiplex PCR/LDR Assay for the Simultaneous Identification of Category A Infectious Pathogens: Agents of Viral Hemorrhagic Fever and Variola Virus. PLoS One 2015; 10:e0138484. [PMID: 26381398 PMCID: PMC4575071 DOI: 10.1371/journal.pone.0138484] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2014] [Accepted: 08/30/2015] [Indexed: 02/04/2023] Open
Abstract
CDC designated category A infectious agents pose a major risk to national security and require special action for public health preparedness. They include viruses that cause viral hemorrhagic fever (VHF) syndrome as well as variola virus, the agent of smallpox. VHF is characterized by hemorrhage and fever with multi-organ failure leading to high morbidity and mortality. Smallpox, a prior scourge, has been eradicated for decades, making it a particularly serious threat if released nefariously in the essentially non-immune world population. Early detection of the causative agents, and the ability to distinguish them from other pathogens, is essential to contain outbreaks, implement proper control measures, and prevent morbidity and mortality. We have developed a multiplex detection assay that uses several species-specific PCR primers to generate amplicons from multiple pathogens; these are then targeted in a ligase detection reaction (LDR). The resultant fluorescently-labeled ligation products are detected on a universal array enabling simultaneous identification of the pathogens. The assay was evaluated on 32 different isolates associated with VHF (ebolavirus, marburgvirus, Crimean Congo hemorrhagic fever virus, Lassa fever virus, Rift Valley fever virus, Dengue virus, and Yellow fever virus) as well as variola virus and vaccinia virus (the agent of smallpox and its vaccine strain, respectively). The assay was able to detect all viruses tested, including 8 sequences representative of different variola virus strains from the CDC repository. It does not cross react with other emerging zoonoses such as monkeypox virus or cowpox virus, or six flaviviruses tested (St. Louis encephalitis virus, Murray Valley encephalitis virus, Powassan virus, Tick-borne encephalitis virus, West Nile virus and Japanese encephalitis virus).
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Affiliation(s)
- Sanchita Das
- Department of Medicine, Division of Infectious Diseases, Weill Medical College of Cornell University, New York, New York, United States of America
| | - Mark S. Rundell
- Department of Microbiology and Immunology, Weill Medical College of Cornell University, New York, New York, United States of America
| | - Aashiq H. Mirza
- Department of Microbiology and Immunology, Weill Medical College of Cornell University, New York, New York, United States of America
| | - Maneesh R. Pingle
- Department of Microbiology and Immunology, Weill Medical College of Cornell University, New York, New York, United States of America
| | - Kristi Shigyo
- Department of Medicine, Division of Infectious Diseases, Weill Medical College of Cornell University, New York, New York, United States of America
| | - Aura R. Garrison
- United States Army Medical Research Institute of Infectious Diseases, Frederick, Maryland, United States of America
| | - Jason Paragas
- Integrated Research Facility, Division of Clinical Research, NIAID, NIH, Fort Detrick, Maryland, United States of America
| | - Scott K. Smith
- Poxvirus Team, Poxvirus and Rabies Branch, Division of High Consequence Pathogens and Pathology, National Center of Emerging Zoonotic and Infectious Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, United States of America
| | - Victoria A. Olson
- Poxvirus Team, Poxvirus and Rabies Branch, Division of High Consequence Pathogens and Pathology, National Center of Emerging Zoonotic and Infectious Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, United States of America
| | - Davise H. Larone
- Department of Microbiology and Immunology, Weill Medical College of Cornell University, New York, New York, United States of America
- Department of Pathology and Laboratory Medicine, Weill Medical College of Cornell University, New York, NY, United States of America
| | - Eric D. Spitzer
- Department of Pathology, Stony Brook University Medical Center, Stony Brook, New York, United States of America
| | - Francis Barany
- Department of Microbiology and Immunology, Weill Medical College of Cornell University, New York, New York, United States of America
| | - Linnie M. Golightly
- Department of Medicine, Division of Infectious Diseases, Weill Medical College of Cornell University, New York, New York, United States of America
- Department of Microbiology and Immunology, Weill Medical College of Cornell University, New York, New York, United States of America
- * E-mail:
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15
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Ranzoni A, den Hamer A, Karoli T, Buechler J, Cooper MA. Improved Immunoassay Sensitivity in Serum as a Result of Polymer-Entrapped Quantum Dots: ‘Papaya Particles’. Anal Chem 2015; 87:6150-7. [DOI: 10.1021/acs.analchem.5b00762] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Affiliation(s)
- Andrea Ranzoni
- Institute
for Molecular Bioscience, The University of Queensland, St. Lucia, Brisbane, 4072, Australia
| | - Anniek den Hamer
- Institute
for Molecular Bioscience, The University of Queensland, St. Lucia, Brisbane, 4072, Australia
| | - Tomislav Karoli
- Institute
for Molecular Bioscience, The University of Queensland, St. Lucia, Brisbane, 4072, Australia
| | - Joseph Buechler
- ALERE Inc., 9975 Summers Ridge Road, San Diego, California 92121, United States
| | - Matthew. A. Cooper
- Institute
for Molecular Bioscience, The University of Queensland, St. Lucia, Brisbane, 4072, Australia
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Kim JH, Chong CK, Sinniah M, Sinnadurai J, Song HO, Park H. Clinical diagnosis of early dengue infection by novel one-step multiplex real-time RT-PCR targeting NS1 gene. J Clin Virol 2015; 65:11-9. [PMID: 25766980 DOI: 10.1016/j.jcv.2015.01.018] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2014] [Revised: 01/16/2015] [Accepted: 01/24/2015] [Indexed: 11/18/2022]
Abstract
BACKGROUND Dengue is a mosquito-borne disease that causes a public health problem in tropical and subtropical countries. Current immunological diagnostics based on IgM and/or nonstructural protein 1 (NS1) antigen are limited for acute dengue infection due to low sensitivity and accuracy. OBJECTIVES This study aimed to develop a one-step multiplex real-time RT-PCR assay showing higher sensitivity and accuracy than previous approaches. STUDY DESIGN Serotype-specific primers and probes were designed through the multiple alignment of NS1 gene. The linearity and limit of detection (LOD) of the assay were determined. The assay was clinically validated with an evaluation panel that was immunologically tested by WHO and Malaysian specimens. RESULTS The LOD of the assay was 3.0 log10 RNA copies for DENV-1, 2.0 for DENV-3, and 1.0 for DENV-2 and DENV-4. The assay showed 95.2% sensitivity (20/21) in an evaluation panel, whereas NS1 antigen- and anti-dengue IgM-based immunological assays exhibited 0% and 23.8-47.6% sensitivities, respectively. The assay showed 100% sensitivity both in NS1 antigen- and anti-dengue IgM-positive Malaysian specimens (26/26). The assay provided the information of viral loads and serotype with discrimination of heterotypic mixed infection. CONCLUSIONS The assay could be clinically applied to early dengue diagnosis, especially during the first 5 days of illness and approximately 14 days after infection showing an anti-dengue IgM-positive response.
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Affiliation(s)
- Je-Hyoung Kim
- Zoonosis Research Center, Department of Infection Biology, Wonkwang University School of Medicine, Iksan, Jeonbuk, Republic of Korea
| | - Chom-Kyu Chong
- Department of Biochemistry, Division of Life Science, Chungbuk National University, Cheongju, Chungbuk, Republic of Korea
| | - Mangalam Sinniah
- Hospital Kuala Lumpur, Jalan Pahang, Kuala Lumpur 50586 Malaysia
| | | | - Hyun-Ok Song
- Zoonosis Research Center, Department of Infection Biology, Wonkwang University School of Medicine, Iksan, Jeonbuk, Republic of Korea.
| | - Hyun Park
- Zoonosis Research Center, Department of Infection Biology, Wonkwang University School of Medicine, Iksan, Jeonbuk, Republic of Korea.
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Alm E, Lesko B, Lindegren G, Ahlm C, Söderholm S, Falk KI, Lagerqvist N. Universal single-probe RT-PCR assay for diagnosis of dengue virus infections. PLoS Negl Trop Dis 2014; 8:e3416. [PMID: 25522325 PMCID: PMC4270494 DOI: 10.1371/journal.pntd.0003416] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2014] [Accepted: 11/13/2014] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND Dengue is a mosquito-borne viral disease that has become more prevalent in the last few decades. Most patients are viremic when they present with symptoms, and early diagnosis of dengue is important in preventing severe clinical complications associated with this disease and also represents a key factor in differential diagnosis. Here, we designed and validated a hydrolysis-probe-based one-step real-time RT-PCR assay that targets the genomes of dengue virus serotypes 1-4. METHODOLOGY/PRINCIPAL FINDINGS The primers and probe used in our RT-PCR assay were designed to target the 3' untranslated region of all complete genome sequences of dengue virus available in GenBank (n = 3,305). Performance of the assay was evaluated using in vitro transcribed RNA, laboratory-adapted virus strains, external control panels, and clinical specimens. The linear dynamic range was found to be 104-1011 GCE/mL, and the detection limit was between 6.0×102 and 1.1×103 GCE/mL depending on target sequence. The assay did not cross-react with human RNA, nor did it produce false-positive results for other human pathogenic flaviviruses or clinically important etiological agents of febrile illnesses. We used clinical serum samples obtained from returning travelers with dengue-compatible symptomatology (n = 163) to evaluate the diagnostic relevance of our assay, and laboratory diagnosis performed by the RT-PCR assay had 100% positive agreement with diagnosis performed by NS1 antigen detection. In a retrospective evaluation including 60 archived serum samples collected from confirmed dengue cases 1-9 days after disease onset, the RT-PCR assay detected viral RNA up to 9 days after appearance of symptoms. CONCLUSIONS/SIGNIFICANCE The validation of the RT-PCR assay presented here indicates that this technique can be a reliable diagnostic tool, and hence we suggest that it be introduced as the method of choice during the first 5 days of dengue symptoms.
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Affiliation(s)
- Erik Alm
- Department of Microbiology, Public Health Agency of Sweden, Solna, Sweden
| | - Birgitta Lesko
- Department of Microbiology, Public Health Agency of Sweden, Solna, Sweden
- Department of Laboratory Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Gunnel Lindegren
- Department of Microbiology, Public Health Agency of Sweden, Solna, Sweden
| | - Clas Ahlm
- Department of Clinical Microbiology, Umeå University, Umeå, Sweden
| | - Sandra Söderholm
- Department of Microbiology, Public Health Agency of Sweden, Solna, Sweden
| | - Kerstin I. Falk
- Department of Microbiology, Public Health Agency of Sweden, Solna, Sweden
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Nina Lagerqvist
- Department of Microbiology, Public Health Agency of Sweden, Solna, Sweden
- Department of Medicine, Karolinska Institutet, Karolinska University Hospital Huddinge, Stockholm, Sweden
- * E-mail:
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18
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Discovery and design of cyclic peptides as dengue virus inhibitors through structure-based molecular docking. ASIAN PAC J TROP MED 2014; 7:513-6. [PMID: 25063278 DOI: 10.1016/s1995-7645(14)60085-7] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2014] [Revised: 05/15/2014] [Accepted: 06/15/2014] [Indexed: 11/23/2022] Open
Abstract
OBJECTIVE To find potential peptide inhibitors against the NS2B/NS3 protease of DENV which in turn, can inhibit the viral replication inside host cell. METHODS Cyclic peptides were designed having combination of positively charged amino acids using ChemSketch software and were converted to 3D structures. DENV NS3 protein structure was retrieved from Protein Data Bank (PDB) using PDB Id: 2FOM. DENV NS3 and cylic peptides were docked using MOE software after structural optimization. RESULTS Through molecular docking it was revealed that most of the peptides bound deeply in the binding pocket of DENV NS2B/NS3 protease an had interactions with catalytic triad. Peptide 2 successfully blocked the catalytic triad of NS2B/NS3 protease. Peptide 1, 4 and 6 also had potential interactions with active residues of the NS2B/NS3 protease while all other peptides were in close contact with the active sites of NS2B/NS3 protease thus, these peptides can serve as a potential drug candidate to stop viral replication. CONCLUSIONS Thus, it can be concluded from the study that these peptides could serve as important inhibitors to inhibit the viral replication and need further in-vitro investigations to confirm their efficacy.
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Qamar MTU, Mumtaz A, Naseem R, Ali A, Fatima T, Jabbar T, Ahmad Z, Ashfaq UA. Molecular Docking Based Screening of Plant Flavonoids as Dengue NS1 Inhibitors. Bioinformation 2014; 10:460-5. [PMID: 25187688 PMCID: PMC4135296 DOI: 10.6026/97320630010460] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2014] [Accepted: 07/01/2014] [Indexed: 12/15/2022] Open
Abstract
Dengue infection has turned into a serious health concern globally due to its high morbidity rate and a high possibility of increase
in its mortality rate on the account of unavailability of any proper treatment for severe dengue infection. The situation demands an
urgent development of efficient and practicable treatment to deal with Dengue virus (DENV). Flavonoids, a class of
phytochemicals present in medicinal plants, possess anti-viral activity and can be strong drug candidates against viruses. NS1
glycoprotein of Dengue virus is involved in its RNA replication and can be a strong target for screening of drugs against this virus.
Current study focuses on the identification of flavonoids which can block Asn-130 glycosylation site of Dengue virus NS1 to inhibit
viral replication as glycosylation of NS1 is required for its biological functioning. Molecular docking approach was used in this
study and the results revealed that flavonoids have strong potential interactions with active site of NS1. Six flavonoids
(Deoxycalyxin A; 3,5,7,3',4'-pentahydroxyflavonol-3-O-beta-D-galactopyranoside; (3R)-3',8-Dihydroxyvestitol; Sanggenon O;
Epigallocatechin gallate; Chamaejasmin) blocked the Asn-130 glycosylation site of NS1 and could be able to inhibit the viral
replication. It can be concluded from this study that these flavonoids could serve as antiviral drugs for dengue infections. Further
in-vitro analyses are required to confirm their efficacy and to evaluate their drug potency.
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Affiliation(s)
- Muhammad Tahir Ul Qamar
- Department of Bioinformatics and Biotechnology, Government College University Faisalabad (GCUF), 38000, Punjab, Pakistan
| | - Arooj Mumtaz
- Department of Bioinformatics and Biotechnology, Government College University Faisalabad (GCUF), 38000, Punjab, Pakistan
| | - Rabbia Naseem
- Department of Bioinformatics and Biotechnology, Government College University Faisalabad (GCUF), 38000, Punjab, Pakistan
| | - Amna Ali
- Department of Bioinformatics and Biotechnology, Government College University Faisalabad (GCUF), 38000, Punjab, Pakistan
| | - Tabeer Fatima
- Department of Bioinformatics and Biotechnology, Government College University Faisalabad (GCUF), 38000, Punjab, Pakistan
| | - Tehreem Jabbar
- Department of Bioinformatics and Biotechnology, Government College University Faisalabad (GCUF), 38000, Punjab, Pakistan
| | - Zubair Ahmad
- Department of Bioinformatics and Biotechnology, Government College University Faisalabad (GCUF), 38000, Punjab, Pakistan
| | - Usman Ali Ashfaq
- Department of Bioinformatics and Biotechnology, Government College University Faisalabad (GCUF), 38000, Punjab, Pakistan
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20
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Qamar TU, Mumtaz A, Ashfaq UA, Azhar S, Fatima T, Hassan M, Hussain SS, Akram W, Idrees S. Computer Aided Screening of Phytochemicals from Garcinia against the Dengue NS2B/NS3 Protease. Bioinformation 2014; 10:115-8. [PMID: 24748749 PMCID: PMC3974236 DOI: 10.6026/97320630010115] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2013] [Accepted: 01/31/2014] [Indexed: 11/23/2022] Open
Abstract
Dengue virus NS2/NS3 protease because of its ability to cleave viral proteins is considered as an attractive target to screen antiviral agents. Medicinal plants contain a variety of phytochemicals that can be used as drug against different diseases and infections. Therefore, this study was designed to uncover possible phytochemical of different classes (Aromatic, Carbohydrates, Lignin, Saponins, Steroids, Tannins, Terpenoids, Xanthones) that could be used as inhibitors against the NS2B/NS3 protease of DENV. With the help of molecular docking, Garcinia phytochemicals found to be bound deeply inside the active site of DENV NS2B/NS3 protease among all tested phytochemicals and had interactions with catalytic triad (His51, Asp75, Ser135). Thus, it can be concluded from the study that these Gracinia phytochemicals could serve as important inhibitors to inhibit the viral replication inside the host cell. Further in-vitro investigations require confirming their efficacy.
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Affiliation(s)
- Tahir ul Qamar
- Department of Bioinformatics and Biotechnology, Government College University Faisalabad (GCUF), 38000, Pakistan; Tahir ul Qamar
| | - Arooj Mumtaz
- Department of Bioinformatics and Biotechnology, Government College University Faisalabad (GCUF), 38000, Pakistan; Tahir ul Qamar
| | - Usman Ali Ashfaq
- Department of Bioinformatics and Biotechnology, Government College University Faisalabad (GCUF), 38000, Pakistan; Tahir ul Qamar
| | - Samia Azhar
- Department of Bioinformatics and Biotechnology, Government College University Faisalabad (GCUF), 38000, Pakistan; Tahir ul Qamar
| | - Tabeer Fatima
- Department of Bioinformatics and Biotechnology, Government College University Faisalabad (GCUF), 38000, Pakistan; Tahir ul Qamar
| | - Muhammad Hassan
- Department of Bioinformatics and Biotechnology, Government College University Faisalabad (GCUF), 38000, Pakistan; Tahir ul Qamar
| | - Syed Sajid Hussain
- Department of Bioinformatics and Biotechnology, Government College University Faisalabad (GCUF), 38000, Pakistan; Tahir ul Qamar
| | - Waheed Akram
- Department of Bioinformatics and Biotechnology, Government College University Faisalabad (GCUF), 38000, Pakistan; Tahir ul Qamar
| | - Sobia Idrees
- Department of Bioinformatics and Biotechnology, Government College University Faisalabad (GCUF), 38000, Pakistan; Tahir ul Qamar
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De La Cruz Hernández SI, Flores-Aguilar H, González-Mateos S, López-Martínez I, Ortiz-Navarrete V, Ludert JE, Del Angel RM. Viral load in patients infected with dengue is modulated by the presence of anti-dengue IgM antibodies. J Clin Virol 2013; 58:258-61. [DOI: 10.1016/j.jcv.2013.06.016] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2013] [Revised: 06/06/2013] [Accepted: 06/10/2013] [Indexed: 11/16/2022]
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22
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Waggoner JJ, Abeynayake J, Sahoo MK, Gresh L, Tellez Y, Gonzalez K, Ballesteros G, Pierro AM, Gaibani P, Guo FP, Sambri V, Balmaseda A, Karunaratne K, Harris E, Pinsky BA. Single-reaction, multiplex, real-time rt-PCR for the detection, quantitation, and serotyping of dengue viruses. PLoS Negl Trop Dis 2013; 7:e2116. [PMID: 23638191 PMCID: PMC3630127 DOI: 10.1371/journal.pntd.0002116] [Citation(s) in RCA: 76] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2012] [Accepted: 01/31/2013] [Indexed: 12/17/2022] Open
Abstract
Background Dengue fever results from infection with one or more of four different serotypes of dengue virus (DENV). Despite the widespread nature of this infection, available molecular diagnostics have significant limitations. The aim of this study was to develop a multiplex, real-time, reverse transcriptase-PCR (rRT-PCR) for the detection, quantitation, and serotyping of dengue viruses in a single reaction. Methodology/Principal Findings An rRT-PCR assay targeting the 5′ untranslated region and capsid gene of the DENV genome was designed using molecular beacons to provide serotype specificity. Using reference DENV strains, the assay was linear from 7.0 to 1.0 log10 cDNA equivalents/µL for each serotype. The lower limit of detection using genomic RNA was 0.3, 13.8, 0.8, and 12.4 cDNA equivalents/µL for serotypes 1–4, respectively, which was 6- to 275-fold more analytically sensitive than a widely used hemi-nested RT-PCR. Using samples from Nicaragua collected within the first five days of illness, the multiplex rRT-PCR was positive in 100% (69/69) of specimens that were positive by the hemi-nested assay, with full serotype agreement. Furthermore, the multiplex rRT-PCR detected DENV RNA in 97.2% (35/36) of specimens from Sri Lanka positive for anti-DENV IgM antibodies compared to just 44.4% (16/36) by the hemi-nested RT-PCR. No amplification was observed in 80 clinical samples sent for routine quantitative hepatitis C virus testing or when genomic RNA from other flaviviruses was tested. Conclusions/Significance This single-reaction, quantitative, multiplex rRT-PCR for DENV serotyping demonstrates superior analytical and clinical performance, as well as simpler workflow compared to the hemi-nested RT-PCR reference. In particular, this multiplex rRT-PCR detects viral RNA and provides serotype information in specimens collected more than five days after fever onset and from patients who had already developed anti-DENV IgM antibodies. The implementation of this assay in dengue-endemic areas has the potential to improve both dengue diagnosis and epidemiologic surveillance. Dengue, or break-bone fever, is the most common mosquito-borne viral disease of humans with over half the world's population at risk for infection. Dengue has a wide spectrum of clinical manifestations, from self-limited febrile illness to fatal hypovolemic shock, and because of this, dengue is difficult to distinguish from many other infections based on clinical characteristics alone. Diagnostic testing is therefore critical to accurately identify dengue virus (DENV)-infected patients and also rule out dengue in patients with undifferentiated fever. Unfortunately, current diagnostics for early DENV detection consist of point-of-care or laboratory-based antigen tests that lack sensitivity or molecular assays that are laborious to perform or lack the test characteristics necessary for routine use. To address these limitations, we developed a single-reaction, multiplex, real-time RT-PCR for the detection, quantitation, and serotyping of dengue viruses from patient serum or plasma. We demonstrate that this diagnostic test is more analytically sensitive than a commonly used reference molecular assay, and is able to detect viral RNA and provide serotype information in specimens collected more than 5 days after fever onset and from patients who had already developed anti-DENV IgM antibodies. This unique combination of sensitivity and serotyping capability in a simple, single-reaction format represents a step forward in dengue diagnostics.
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Affiliation(s)
- Jesse J. Waggoner
- Department of Medicine, Division of Infectious Diseases and Geographic Medicine, Stanford University School of Medicine, Stanford, California, United States of America
| | - Janaki Abeynayake
- Department of Pathology, Stanford University School of Medicine, Stanford, California, United States of America
| | - Malaya K. Sahoo
- Department of Pathology, Stanford University School of Medicine, Stanford, California, United States of America
| | - Lionel Gresh
- Sustainable Sciences Institute, Managua, Nicaragua
| | - Yolanda Tellez
- National Virology Laboratory, Centro Nacional de Diagnóstico y Referencia, Ministry of Health, Managua, Nicaragua
| | - Karla Gonzalez
- National Virology Laboratory, Centro Nacional de Diagnóstico y Referencia, Ministry of Health, Managua, Nicaragua
| | - Gabriela Ballesteros
- National Virology Laboratory, Centro Nacional de Diagnóstico y Referencia, Ministry of Health, Managua, Nicaragua
| | - Anna M. Pierro
- Clinical Microbiology Unit, Regional Reference Centre for Microbiological Emergencies – CRREM, St. Orsola-Malpighi University Hospital, Bologna, Italy
| | - Paolo Gaibani
- Clinical Microbiology Unit, Regional Reference Centre for Microbiological Emergencies – CRREM, St. Orsola-Malpighi University Hospital, Bologna, Italy
| | - Frances P. Guo
- Department of Pathology, Stanford University School of Medicine, Stanford, California, United States of America
| | - Vittorio Sambri
- Clinical Microbiology Unit, Regional Reference Centre for Microbiological Emergencies – CRREM, St. Orsola-Malpighi University Hospital, Bologna, Italy
| | - Angel Balmaseda
- National Virology Laboratory, Centro Nacional de Diagnóstico y Referencia, Ministry of Health, Managua, Nicaragua
| | - Kumudu Karunaratne
- Department of Medical Microbiology, Lady Ridgeway Hospital, Colombo, Sri Lanka
| | - Eva Harris
- Division of Infectious Diseases and Vaccinology, School of Public Health, University of California, Berkeley, California, United States of America
| | - Benjamin A. Pinsky
- Department of Medicine, Division of Infectious Diseases and Geographic Medicine, Stanford University School of Medicine, Stanford, California, United States of America
- Department of Pathology, Stanford University School of Medicine, Stanford, California, United States of America
- * E-mail:
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23
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Wei Y, Wong LP, Toh CS. Fuel Cell Virus Sensor Using Virus Capture within Antibody-Coated Nanochannels. Anal Chem 2013; 85:1350-7. [DOI: 10.1021/ac302942y] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Yanyan Wei
- Division
of Chemistry and Biological Chemistry, School
of Physical and Mathematical Sciences, Nanyang Technological University, 21 Nanyang Link, Singapore 637371
| | - Lai Peng Wong
- Division
of Chemistry and Biological Chemistry, School
of Physical and Mathematical Sciences, Nanyang Technological University, 21 Nanyang Link, Singapore 637371
| | - Chee-Seng Toh
- Division
of Chemistry and Biological Chemistry, School
of Physical and Mathematical Sciences, Nanyang Technological University, 21 Nanyang Link, Singapore 637371
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24
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Chen YY, Lin JW, Fan YC, Chiou SS. Detection and differentiation of genotype I and III Japanese encephalitis virus in mosquitoes by multiplex reverse transcriptase-polymerase chain reaction. Transbound Emerg Dis 2012; 61:37-43. [PMID: 23157736 DOI: 10.1111/j.1865-1682.2012.01369.x] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2012] [Indexed: 11/29/2022]
Abstract
Japanese encephalitis (JE) is a disease that threatens both human and animal populations in Asian countries, and the causative agent of JE, Japanese encephalitis virus (JEV), has recently changed from genotype III (GIII) to genotype I (GI). However, a test for the rapid differentiation of GI and GIII JEV is still unavailable, especially one that can be used for mosquito-based surveillance. We have designed GI- and GIII-specific primer sets for the rapid detection and differentiation of GI and GIII JEV by multiplex reverse transcriptase-polymerase chain reaction (multiplex RT-PCR). The GI-specific and GIII-specific primer sets were able to specifically amplify the target gene from GI and GIII JEV, respectively. The limitations of detection were 0.00225 and 0.225 pfu for the GI-specific and GIII-specific primers, respectively. Using a mixture of GI-specific and GIII-specific primers, the multiplex RT-PCR was able to specifically detect and differentiate GI and GIII JEV. The multiplex RT-PCR was able to successfully differentiate GI and GIII virus in JEV-infected mosquitoes. Thus, a sensitive and specific multiplex RT-PCR system for the rapid detection and differentiation of GI and GIII JEV has been developed, and this test is likely to be valuable when carrying out mosquito-based JEV surveillance.
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Affiliation(s)
- Y Y Chen
- Graduate Institute of Microbiology and Public Health, College of Veterinary Medicine, National Chung Hsing University, Taichung, Taiwan
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25
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Ortiz A, Capitan Z, Mendoza Y, Cisneros J, Moreno B, Zaldivar Y, Garcia M, Smith RE, Motta J, Pascale JM. Simple, specific molecular typing of dengue virus isolates using one-step RT-PCR and restriction fragment length polymorphism. J Virol Methods 2012; 185:129-35. [PMID: 22766181 DOI: 10.1016/j.jviromet.2012.06.016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2011] [Revised: 06/03/2012] [Accepted: 06/12/2012] [Indexed: 11/26/2022]
Abstract
A one-step RT-PCR and one-enzyme RFLP was used to detect and distinguish among flaviviruses, including the four serotypes of dengue and the St. Louis Encephalitis, West Nile and Yellow Fever viruses in cultured virus samples or acute-phase human serum. Using a previously described RT-PCR, but novel RFLP procedure, results are obtained in 24 h with basic PCR and electrophoresis equipment. There is 95% agreement between RT-PCR/RFLP results and those achieved by indirect immunofluorescence assays, and 100% agreement between RT-PCR/RFLP results and gene sequencing. This method is more rapid than tests of cytopathic effect based on virus isolation in tissue culture, and simpler than real-time PCR. It does not require specialized equipment, radioisotopes or computer analysis and is a method that can be applied widely in the developing world. It allows for prompt determination of whether a flavivirus is the cause of illness in a febrile patient, rapid identification of dengue serotypes in circulation, and improved patient management in cases where prior dengue exposure make dengue hemorrhagic fever or dengue shock syndrome a risk.
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Affiliation(s)
- Alma Ortiz
- Gorgas Memorial Institute for Health Studies, Panama City, Panama.
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26
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Wang H, Chen HW, Hupert ML, Chen PC, Datta P, Pittman TL, Goettert J, Murphy MC, Williams D, Barany F, Soper SA. Fully Integrated Thermoplastic Genosensor for the Highly Sensitive Detection and Identification of Multi-Drug-Resistant Tuberculosis. Angew Chem Int Ed Engl 2012. [DOI: 10.1002/ange.201200732] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
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27
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Wang H, Chen HW, Hupert ML, Chen PC, Datta P, Pittman TL, Goettert J, Murphy MC, Williams D, Barany F, Soper SA. Fully integrated thermoplastic genosensor for the highly sensitive detection and identification of multi-drug-resistant tuberculosis. Angew Chem Int Ed Engl 2012; 51:4349-53. [PMID: 22431490 DOI: 10.1002/anie.201200732] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2012] [Indexed: 11/08/2022]
Affiliation(s)
- Hong Wang
- Department of Chemistry and Mechanical Engineering, Louisiana State University, USA
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28
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Hasib L, Dilcher M, Hufert F, Meyer-König U, Weidmann M. Development of a flow-through [corrected] microarray based reverse transcriptase multiplex ligation-dependent probe amplification assay for the detection of European Bunyaviruses. [corrected]. Mol Biotechnol 2012; 49:176-86. [PMID: 21390485 PMCID: PMC3172416 DOI: 10.1007/s12033-011-9389-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
It is suspected that apart from tick-borne encephalitis virus several additional European Arboviruses such as the sandfly borne Toscana virus, sandfly fever Sicilian virus and sandfly fever Naples virus, mosquito-borne Tahyna virus, Inkoo virus, Batai virus and tick-borne Uukuniemi virus cause aseptic meningo-encephalitis or febrile disease in Europe. Currently, the microarray technology is developing rapidly and there are many efforts to apply it to infectious diseases diagnostics. In order to arrive at an assay system useful for high throughput analysis of samples from aseptic meningo-encephalitis cases the authors developed a combined multiplex ligation-dependent probe amplification and flow-through microarray assay for the detection of European Bunyaviruses. These results show that this combined assay indeed is highly sensitive, and specific for the accurate detection of multiple viruses.
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Affiliation(s)
- Lekbira Hasib
- Department of Virology, University Medical Center Göttingen, Kreuzbergring 57 37075, Göttingen, Germany.
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29
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Jiang Y, Guo Y, Wang P, Dong Q, Opriessnig T, Cheng J, Xu H, Ding X, Guo J. A novel diagnostic platform based on multiplex ligase detection–PCR and microarray for simultaneous detection of swine viruses. J Virol Methods 2011; 178:171-8. [DOI: 10.1016/j.jviromet.2011.09.008] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2010] [Revised: 08/30/2011] [Accepted: 09/12/2011] [Indexed: 10/17/2022]
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30
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Fatima Z, Idrees M, Bajwa MA, Tahir Z, Ullah O, Zia MQ, Hussain A, Akram M, Khubaib B, Afzal S, Munir S, Saleem S, Rauff B, Badar S, Naudhani M, Butt S, Aftab M, Ali L, Ali M. Serotype and genotype analysis of dengue virus by sequencing followed by phylogenetic analysis using samples from three mini outbreaks-2007-2009 in Pakistan. BMC Microbiol 2011; 11:200. [PMID: 21906394 PMCID: PMC3180347 DOI: 10.1186/1471-2180-11-200] [Citation(s) in RCA: 62] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2011] [Accepted: 09/10/2011] [Indexed: 11/24/2022] Open
Abstract
Background Since the first reported outbreak of dengue hemorrhagic fever in Pakistan, several mini outbreaks have erupted in the region. Dengue virus serotype 3 (DEN-3) was first documented in 2005 outbreak in Karachi. Reports show that serotype 3 is prevalent in Lahore since 2008. Serotype 2 (DEN-2) is the major circulating serotype in Pakistan as it is documented since 1994. We have conducted a detailed study of three outbreaks of dengue virus infection that occurred in years 2007, 2008 and 2009 in Lahore by using molecular techniques such as PCR and nucleotide sequencing of the C-prM gene junction of Dengue virus. Results Through the analysis of 114 serum samples collected over the period of three years (2007-2009), total 20 patients were found to be infected with dengue virus. In year 2007, four were positive for serotype 2 and one sample was positive for serotype DEN-3. In 2008, five samples had concurrent infection with serotypes DEN-2 and DEN-3 while three samples were infected only with serotype DEN-2. In year 2009, one sample had concurrent infection with serotypes DEN-2 and DEN-3 while six were positive for serotype DEN-2 only. Conclusions Our study showed that serotype DEN-2 was dominant in positive samples of dengue virus infection collected during the period of three years (2007-2009). The other serotype present was serotype DEN-3. Genotypes of serotype DEN-2 and serotype DEN-3 were subtype IV and subtype III, respectively.
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Affiliation(s)
- Zareen Fatima
- Division of Molecular Virology, CEMB University of the Punjab, 87-West Canal Bank Road, Thokar Niaz Baig, Lahore-53700, Pakistan
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Abstract
The genus Flavivirus includes major pathogens such as dengue, yellow fever, Japanese encephalitis, West Nile and tick-borne encephalitis viruses. Molecular amplification assays for the diagnosis of flaviviruses have been developed in the last decades. These assays were formerly based on reverse transcriptase PCR, while in recent years the real-time reverse transcriptase PCR format has taken a predominant role. In this article, we focus on the more recent developments for the molecular diagnosis of flaviviruses, with special attention to those based on new methodologies such as nucleic acid sequence-based amplification or loop-mediated isothermal amplification techniques. These new approaches may provide a good profile of sensitivity and specificity and offer a real chance to implement flavivirus molecular diagnosis in clinical and point-of-care settings.
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Affiliation(s)
| | - Pranav Patel
- Robert Koch-Institut, Center for Biological Security 1, Highly Pathogenic Viruses, Nordufer 20, 13353 Berlin, Germany
| | - Sonja Linke
- Robert Koch-Institut, Center for Biological Security 1, Highly Pathogenic Viruses, Nordufer 20, 13353 Berlin, Germany
| | - Katharina Achazi
- Robert Koch-Institut, Center for Biological Security 1, Highly Pathogenic Viruses, Nordufer 20, 13353 Berlin, Germany
| | - Matthias Niedrig
- Robert Koch-Institut, Center for Biological Security 1, Highly Pathogenic Viruses, Nordufer 20, 13353 Berlin, Germany
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33
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Shin GW, Hwang HS, Chung B, Jung GY. Recent developments in CE-based detection methods for food-borne pathogens. Electrophoresis 2010; 31:2137-53. [DOI: 10.1002/elps.200900682] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
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Pingle M, Rundell M, Das S, Golightly LM, Barany F. PCR/LDR/universal array platforms for the diagnosis of infectious disease. Methods Mol Biol 2010; 632:141-57. [PMID: 20217576 DOI: 10.1007/978-1-60761-663-4_9] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Infectious diseases account for between 14 and 17 million deaths worldwide each year. Accurate and rapid diagnosis of bacterial, fungal, viral, and parasitic infections is therefore essential to reduce the morbidity and mortality associated with these diseases. Classical microbiological and serological methods have long served as the gold standard for diagnosis but are increasingly being replaced by molecular diagnostic methods that demonstrate increased sensitivity and specificity and provide an identification of the etiologic agent in a shorter period of time. PCR/LDR coupled with universal array detection provides a highly sensitive and specific platform for the detection and identification of bacterial and viral infections.
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Affiliation(s)
- Maneesh Pingle
- Department of Microbiology, Weill Medical College, Cornell University, New York, NY, USA.
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35
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Multiplex PCR-ligation detection reaction assay for simultaneous detection of drug resistance and toxin genes from Staphylococcus aureus, Enterococcus faecalis, and Enterococcus faecium. J Clin Microbiol 2009; 48:277-80. [PMID: 19864481 DOI: 10.1128/jcm.01411-09] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
A multiplex PCR-ligation detection reaction (PCR-LDR) assay was developed for rapid detection of methicillin, tetracycline, and vancomycin resistance, as well as toxic shock toxin and Panton-Valentine leukocidin. The assay was tested on 470 positive blood culture bottles containing Staphylococcus aureus or enterococci. PCR-LDR exhibited a sensitivity and specificity of > or = 98% for all components except tetracycline resistance, which had a sensitivity of 94.7%. Rapid and sensitive detection of antimicrobial resistance and virulence genes could help guide therapy and appropriate infection control measures.
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