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Luciani L, Combe P, Touret F, Gazin C, Klitting R, Pezzi L, Thirion L, Charrel R, Grard G, de Lamballerie X, Nougairède A. Broad-spectrum dengue virus detection using the commercial RealStar dengue RT-PCR kit 3.0 (Altona) and an in-house combined real-time RT-PCR assay. Heliyon 2024; 10:e31252. [PMID: 38803933 PMCID: PMC11128986 DOI: 10.1016/j.heliyon.2024.e31252] [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: 11/07/2023] [Revised: 05/13/2024] [Accepted: 05/13/2024] [Indexed: 05/29/2024] Open
Abstract
In endemic areas, the genetic diversity among co-circulating dengue virus (DENV) strains is considerable and new, highly divergent strains are identified on a regular basis. It is thus critical to ensure that molecular diagnostic tools effectively detect virus genomes even in case of important genetic variation. Here, we tested both the pan-DENV detection capacity and the limit of detection of two real-time RT-PCR assays: (i) the commercial RealStar Altona 3.0 system and (ii) a laboratory developed test (LDT) combining two RT-PCR systems in a single reaction tube (DenAllDUO). We used a panel of DENV strains representative of the genetic diversity within DENV species, combined with three in vitro transcribed RNAs as surrogates for unavailable strains corresponding to recently discovered strains with substantial genetic divergence: DENV serotype 1 (DENV-1) Brun2014, DENV-2 QML22 and DENV-4 DKE121. Both systems (i) targeted the genome 3' untranslated region, (ii) displayed a broad detection spectrum, encompassing most of DENV species diversity, and (iii) detected the three aforementioned divergent strains. DenAllDUO detected all the strains tested, whereas the RealStar system failed to detect strains from DENV-4 genotype III. Altogether, our findings support the value of these two RT-PCR systems as part of the Dengue diagnostic arsenal.
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Affiliation(s)
- Léa Luciani
- Unité des Virus Émergents (UVE: Aix-Marseille Univ-IRD 190-Inserm 1207), Marseille, France
| | - Pierre Combe
- Unité des Virus Émergents (UVE: Aix-Marseille Univ-IRD 190-Inserm 1207), Marseille, France
| | - Franck Touret
- Unité des Virus Émergents (UVE: Aix-Marseille Univ-IRD 190-Inserm 1207), Marseille, France
| | - Céline Gazin
- Unité des Virus Émergents (UVE: Aix-Marseille Univ-IRD 190-Inserm 1207), Marseille, France
| | - Raphaëlle Klitting
- Unité des Virus Émergents (UVE: Aix-Marseille Univ-IRD 190-Inserm 1207), Marseille, France
- National Reference Center for Arboviruses, National Institute of Health and Medical Research (Inserm) and French Armed Forces Biomedical Research Institute (IRBA), Marseille, France
| | - Laura Pezzi
- Unité des Virus Émergents (UVE: Aix-Marseille Univ-IRD 190-Inserm 1207), Marseille, France
- National Reference Center for Arboviruses, National Institute of Health and Medical Research (Inserm) and French Armed Forces Biomedical Research Institute (IRBA), Marseille, France
| | - Laurence Thirion
- Unité des Virus Émergents (UVE: Aix-Marseille Univ-IRD 190-Inserm 1207), Marseille, France
| | - Rémi Charrel
- Unité des Virus Émergents (UVE: Aix-Marseille Univ-IRD 190-Inserm 1207), Marseille, France
| | - Gilda Grard
- Unité des Virus Émergents (UVE: Aix-Marseille Univ-IRD 190-Inserm 1207), Marseille, France
- National Reference Center for Arboviruses, National Institute of Health and Medical Research (Inserm) and French Armed Forces Biomedical Research Institute (IRBA), Marseille, France
| | - Xavier de Lamballerie
- Unité des Virus Émergents (UVE: Aix-Marseille Univ-IRD 190-Inserm 1207), Marseille, France
- National Reference Center for Arboviruses, National Institute of Health and Medical Research (Inserm) and French Armed Forces Biomedical Research Institute (IRBA), Marseille, France
| | - Antoine Nougairède
- Unité des Virus Émergents (UVE: Aix-Marseille Univ-IRD 190-Inserm 1207), Marseille, France
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2
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Frazer JL, Norton R. Dengue: A review of laboratory diagnostics in the vaccine age. J Med Microbiol 2024; 73. [PMID: 38722305 DOI: 10.1099/jmm.0.001833] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/30/2024] Open
Abstract
Background. Dengue is an important arboviral infection of considerable public health significance. It occurs in a wide global belt within a variety of tropical regions. The timely laboratory diagnosis of Dengue infection is critical to inform both clinical management and an appropriate public health response. Vaccination against Dengue virus is being introduced in some areas.Discussion. Appropriate diagnostic strategies will vary between laboratories depending on the available resources and skills. Diagnostic methods available include viral culture, the serological detection of Dengue-specific antibodies in using enzyme immunoassays (EIAs), microsphere immunoassays, haemagglutination inhibition or in lateral flow point of care tests. The results of antibody tests may be influenced by prior vaccination and exposure to other flaviviruses. The detection of non-structural protein 1 in serum (NS1) has improved the early diagnosis of Dengue and is available in point-of-care assays in addition to EIAs. Direct detection of viral RNA from blood by PCR is more sensitive than NS1 antigen detection but requires molecular skills and resources. An increasing variety of isothermal nucleic acid detection methods are in development. Timing of specimen collection and choice of test is critical to optimize diagnostic accuracy. Metagenomics and the direct detection by sequencing of viral RNA from blood offers the ability to rapidly type isolates for epidemiologic purposes.Conclusion. The impact of vaccination on immune response must be recognized as it will impact test interpretation and diagnostic algorithms.
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Affiliation(s)
| | - Robert Norton
- Pathology Queensland, Townsville QLD, Australia
- Faculty of Medicine, University of Queensland, Brisbane, QLD, Australia
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3
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Yadav PK, Singh S, Paul M, Kumar S, Ponmariappan S, Thavaselvam D. Development of a novel sequence based real-time PCR assay for specific and sensitive detection of Burkholderia pseudomallei in clinical and environmental matrices. Ann Clin Microbiol Antimicrob 2024; 23:30. [PMID: 38600514 PMCID: PMC11007888 DOI: 10.1186/s12941-024-00693-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2023] [Accepted: 03/29/2024] [Indexed: 04/12/2024] Open
Abstract
BACKGROUND Melioidosis, caused by the category B biothreat agent Burkholderia pseudomallei, is a disease with a high mortality rate and requires an immediate culture-independent diagnosis for effective disease management. In this study, we developed a highly sensitive qPCR assay for specific detection of Burkholderia pseudomallei and melioidosis disease diagnosis based on a novel target sequence. METHODS An extensive in-silico analysis was done to identify a novel and highly conserved sequence for developing a qPCR assay. The specificity of the developed assay was analyzed with 65 different bacterial cultures, and the analytical sensitivity of the assay was determined with the purified genomic DNA of B. pseudomallei. The applicability of the assay for B. pseudomallei detection in clinical and environmental matrices was evaluated by spiking B. pseudomallei cells in the blood, urine, soil, and water along with suitable internal controls. RESULTS A novel 85-nucleotide-long sequence was identified using in-silico tools and employed for the development of the highly sensitive and specific quantitative real-time PCR assay S664. The assay S664 was found to be highly specific when evaluated with 65 different bacterial cultures related and non-related to B. pseudomallei. The assay was found to be highly sensitive, with a detection limit of 3 B. pseudomallei genome equivalent copies per qPCR reaction. The detection limit in clinical matrices was found to be 5 × 102 CFU/mL for both human blood and urine. In environmental matrices, the detection limit was found to be 5 × 101 CFU/mL of river water and 2 × 103 CFU/gm of paddy field soil. CONCLUSIONS The findings of the present study suggest that the developed assay S664 along with suitable internal controls has a huge diagnostic potential and can be successfully employed for specific, sensitive, and rapid molecular detection of B. pseudomallei in various clinical and environmental matrices.
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Affiliation(s)
- Pranjal Kumar Yadav
- Biodetector Development Test and Evaluation Division, Defence Research & Development Establishment, Defence Research and Development Organization, Jhansi Road, Gwalior, Madhya Pradesh, 474 002, India
| | - Suchetna Singh
- Biodetector Development Test and Evaluation Division, Defence Research & Development Establishment, Defence Research and Development Organization, Jhansi Road, Gwalior, Madhya Pradesh, 474 002, India
| | - Moumita Paul
- Biodetector Development Test and Evaluation Division, Defence Research & Development Establishment, Defence Research and Development Organization, Jhansi Road, Gwalior, Madhya Pradesh, 474 002, India
| | - Sanjay Kumar
- Biodetector Development Test and Evaluation Division, Defence Research & Development Establishment, Defence Research and Development Organization, Jhansi Road, Gwalior, Madhya Pradesh, 474 002, India.
| | - S Ponmariappan
- Biodetector Development Test and Evaluation Division, Defence Research & Development Establishment, Defence Research and Development Organization, Jhansi Road, Gwalior, Madhya Pradesh, 474 002, India
| | - Duraipandian Thavaselvam
- O/o DGLS, Defence Research and Development Organization, Ministry of Defence, SSPL Campus, Timarpur, New Delhi, 110 054, India.
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Bos S, Graber AL, Cardona-Ospina JA, Duarte EM, Zambrana JV, Ruíz Salinas JA, Mercado-Hernandez R, Singh T, Katzelnick LC, de Silva A, Kuan G, Balmaseda A, Harris E. Protection against symptomatic dengue infection by neutralizing antibodies varies by infection history and infecting serotype. Nat Commun 2024; 15:382. [PMID: 38195666 PMCID: PMC10776616 DOI: 10.1038/s41467-023-44330-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2023] [Accepted: 12/08/2023] [Indexed: 01/11/2024] Open
Abstract
Dengue viruses (DENV1-4) are the most prevalent arboviruses in humans and a major public health concern. Understanding immune mechanisms that modulate DENV infection outcome is critical for vaccine development. Neutralizing antibodies (nAbs) are an essential component of the protective immune response, yet their measurement often relies on a single cellular substrate and partially mature virions, which does not capture the full breadth of neutralizing activity and may lead to biased estimations of nAb potency. Here, we analyze 125 samples collected after one or more DENV infections but prior to subsequent symptomatic or inapparent DENV1, DENV2, or DENV3 infections from a long-standing pediatric cohort study in Nicaragua. By assessing nAb responses using Vero cells with or without DC-SIGN and with mature or partially mature virions, we find that nAb potency and the protective NT50 cutoff are greatly influenced by cell substrate and virion maturation state. Additionally, the correlation between nAb titer and protection from disease depends on prior infection history and infecting serotype. Finally, we uncover variations in nAb composition that contribute to protection from symptomatic infection differently after primary and secondary prior infection. These findings have important implications for identifying antibody correlates of protection for vaccines and natural infections.
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Affiliation(s)
- Sandra Bos
- Division of Infectious Diseases and Vaccinology, School of Public Health, University of California, Berkeley, Berkeley, CA, USA.
| | - Aaron L Graber
- Division of Infectious Diseases and Vaccinology, School of Public Health, University of California, Berkeley, Berkeley, CA, USA
| | - Jaime A Cardona-Ospina
- Division of Infectious Diseases and Vaccinology, School of Public Health, University of California, Berkeley, Berkeley, CA, USA
- Grupo de Investigación Biomedicina, Facultad de Medicina, Institución Universitaria Visión de las Américas, Pereira, Colombia
| | - Elias M Duarte
- Division of Infectious Diseases and Vaccinology, School of Public Health, University of California, Berkeley, Berkeley, CA, USA
| | - Jose Victor Zambrana
- Sustainable Sciences Institute, Managua, Nicaragua
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, MI, USA
| | | | - Reinaldo Mercado-Hernandez
- Division of Infectious Diseases and Vaccinology, School of Public Health, University of California, Berkeley, Berkeley, CA, USA
| | - Tulika Singh
- Division of Infectious Diseases and Vaccinology, School of Public Health, University of California, Berkeley, Berkeley, CA, USA
| | - Leah C Katzelnick
- Viral Epidemiology and Immunity Unit, Laboratory of Infectious Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Aravinda de Silva
- Department of Microbiology and Immunology, University of North Carolina, Chapel Hill, NC, USA
| | - Guillermina Kuan
- Sustainable Sciences Institute, Managua, Nicaragua
- Centro de Salud Sócrates Flores Vivas, Ministerio de Salud, Managua, Nicaragua
| | - Angel Balmaseda
- Sustainable Sciences Institute, Managua, Nicaragua
- Laboratorio Nacional de Virología, Centro Nacional de Diagnóstico y Referencia, Ministerio de Salud, Managua, Nicaragua
| | - Eva Harris
- Division of Infectious Diseases and Vaccinology, School of Public Health, University of California, Berkeley, Berkeley, CA, USA.
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5
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Yadav PK, Paul M, Singh S, Kumar S, Ponmariappan S, Thavaselvam D. Development of a Novel Internally Controlled HrpB1 Gene-Based Real-Time qPCR Assay for Detection of Burkholderia pseudomallei. Mol Diagn Ther 2024; 28:101-112. [PMID: 38085447 DOI: 10.1007/s40291-023-00686-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/09/2023] [Indexed: 01/14/2024]
Abstract
BACKGROUND Melioidosis, caused by category B bioterrorism agent Burkholderia pseudomallei, is a seasonal disease of tropical and subtropical regions with a high mortality rate. An early and culture-independent detection of B. pseudomallei is required for the appropriate disease management and prevention. The present study is designed to identify novel and unique sequences of B. pseudomallei and development of quantitative polymerase chain reaction (qPCR) assay. METHODS A novel B. pseudomallei-specific target sequence was identified by in silico analysis for the qPCR assay development. The specificity of the developed assay was assessed using purified DNA of 65 different bacterial cultures, and the sensitivity was estimated using a cloned target gene. Further, a type III secretion protein HrpB1 (HrpB1) gene-based duplex qPCR assay incorporating suitable extraction and amplification control was developed, and its viability was assessed in different clinical and environmental matrices for the detection of B. pseudomallei. RESULTS In this study, an 80-nucleotide-long B. pseudomallei-specific region within the gene HrpB1 was identified by computational analysis. The developed HrpB1-based qPCR assay was highly specific for B. pseudomallei detection when evaluated with 65 different bacterial cultures. The sensitivity of the qPCR assay with the HrpB1-recombinant plasmid was found to be five copies per qPCR reaction. The assay's detection limit was found to be 5 × 102 CFU/mL for human blood and urine, 5 × 101 CFU/mL in river water, and 2 × 103 CFU/gm in paddy field soil. CONCLUSION The results of the study showed the applicability of a novel HrpB1-based qPCR assay for sensitive and specific detection of B. pseudomallei in diverse clinical and environmental samples.
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Affiliation(s)
- Pranjal Kumar Yadav
- Biodetector Development Test and Evaluation Division, Defence Research & Development Establishment, Defence Research and Development Organization, Jhansi Road, Gwalior, Madhya Pradesh, 474 002, India
| | - Moumita Paul
- Biodetector Development Test and Evaluation Division, Defence Research & Development Establishment, Defence Research and Development Organization, Jhansi Road, Gwalior, Madhya Pradesh, 474 002, India
| | - Suchetna Singh
- Biodetector Development Test and Evaluation Division, Defence Research & Development Establishment, Defence Research and Development Organization, Jhansi Road, Gwalior, Madhya Pradesh, 474 002, India
| | - Sanjay Kumar
- Biodetector Development Test and Evaluation Division, Defence Research & Development Establishment, Defence Research and Development Organization, Jhansi Road, Gwalior, Madhya Pradesh, 474 002, India.
| | - S Ponmariappan
- Biodetector Development Test and Evaluation Division, Defence Research & Development Establishment, Defence Research and Development Organization, Jhansi Road, Gwalior, Madhya Pradesh, 474 002, India
| | - Duraipandian Thavaselvam
- O/o Director General Life Science (DGLS), Defence Research and Development Organization, Ministry of Defence, SSPL Campus, Timarpur, New Delhi, 110 054, India.
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6
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Bos S, Graber AL, Cardona-Ospina JA, Duarte EM, Zambrana JV, Ruíz Salinas JA, Mercado-Hernandez R, Singh T, Katzelnick LC, de Silva A, Kuan G, Balmaseda A, Harris E. The association of neutralizing antibodies with protection against symptomatic dengue virus infection varies by serotype, prior infection history, and assay condition. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2023:2023.06.20.23291522. [PMID: 37502957 PMCID: PMC10371115 DOI: 10.1101/2023.06.20.23291522] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/29/2023]
Abstract
The four dengue virus serotypes (DENV1-4) are the most prevalent arboviruses in humans and a major public health concern worldwide. Understanding immune mechanisms that modulate DENV infection outcome is critical for epidemic preparedness and development of a safe and effective vaccine. Neutralizing antibodies (nAbs) are an essential component of the protective response, yet their measurement often relies on a single cellular substrate and partially mature virions, which do not capture the full breadth of neutralizing activity and may lead to biased estimations of nAb potency. Here, we investigated the characteristics of nAbs associated with protection against dengue cases using samples collected after one or more DENV infections but prior to subsequent symptomatic or inapparent DENV1, DENV2, or DENV3 infections from a long- standing pediatric cohort study in Nicaragua. By assessing nAb responses using Vero cells with or without the attachment factor DC-SIGN and with mature or partially mature virions, we found that nAb potency and the protective NT 50 cutoff were greatly influenced by cell substrate and virion maturation state. Additionally, the correlation between nAb titer and protection from disease depended on an individual's prior infection history and the subsequent infecting DENV serotype. Finally, we uncovered variations in nAbs composition that contributed to protection from symptomatic DENV infection differently after primary and secondary prior infection. These findings have important implications for identifying antibody correlates of protection in the context of vaccines and natural infections.
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7
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Dakhave M, Metkar G, Suryawanshi H. Simultaneous detection and differentiation of dengue and chikungunya viruses for commercial utility. Virusdisease 2023; 34:248-256. [PMID: 37408546 PMCID: PMC10317902 DOI: 10.1007/s13337-023-00822-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2023] [Accepted: 04/10/2023] [Indexed: 07/07/2023] Open
Abstract
The diagnosis of Dengue and Chikungunya infections during acute phase is a priority considering emerging pattern and increasing trends of their infections. The present study describes the commercial development and validation of RT-PCR test for the simultaneous detection of of DEN and CHIK viral RNA in a single tube from human plasma samples. Multistep one step RT-PCR assay was developed and validated for detection and discrimination of DEN and CHIK along with exogenous internal control. The test was evaluated for commercial use using 3 different lots to determine analytical sensitivity, specificity, precision and stability. The external clinical evaluation was performed at NABL accredited lab with known positive and negative Chikungunya and Dengue specimens and comparator assay method. The findings showed that the test could identify CHIK and DEN viral nucleic acid in clinical samples within 80 min, without any cross-reactivity. The analytical detection limit of the test was 1.56 copies/µl for both. The clinical sensitivity and specificity was ≥ 98% and provide a high-throughput and screen up to 90 samples in a single run. It is available in a freeze-dried format and can be used in both the manual and automated platforms. This unique combo test, PathoDetect™ "CHIK DEN Multiplex PCR Kit" enables simultaneous, sensitive, specific detection of DENV and CHIKV and serves as "ready to use" platform for commercial use. It would aid the differential diagnosis as early as day 1 of the infection and facilitate screen-and-treat approach.
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Affiliation(s)
- Minal Dakhave
- R&D Department, Mylab Discovery Solutions Pvt. Ltd., Global Innovation Center, Amar Paradigm, Baner, Pune, Maharashtra 411045 India
| | - Gauri Metkar
- R&D Department, Mylab Discovery Solutions Pvt. Ltd., Global Innovation Center, Amar Paradigm, Baner, Pune, Maharashtra 411045 India
| | - Harshada Suryawanshi
- R&D Department, Mylab Discovery Solutions Pvt. Ltd., Global Innovation Center, Amar Paradigm, Baner, Pune, Maharashtra 411045 India
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8
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Tamura T, Zhang J, Madan V, Biswas A, Schwoerer MP, Cafiero TR, Heller BL, Wang W, Ploss A. Generation and characterization of genetically and antigenically diverse infectious clones of dengue virus serotypes 1-4. Emerg Microbes Infect 2022; 11:227-239. [PMID: 34931940 PMCID: PMC8745371 DOI: 10.1080/22221751.2021.2021808] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Dengue is caused by four genetically distinct viral serotypes, dengue virus (DENV) 1-4. Following transmission by Aedes mosquitoes, DENV can cause a broad spectrum of clinically apparent disease ranging from febrile illness to dengue hemorrhagic fever and dengue shock syndrome. Progress in the understanding of different dengue serotypes and their impacts on specific host-virus interactions has been hampered by the scarcity of tools that adequately reflect their antigenic and genetic diversity. To bridge this gap, we created and characterized infectious clones of DENV1-4 originating from South America, Africa, and Southeast Asia. Analysis of whole viral genome sequences of five DENV isolates from each of the four serotypes confirmed their broad genetic and antigenic diversity. Using a modified circular polymerase extension reaction (CPER), we generated de novo viruses from these isolates. The resultant clones replicated robustly in human and insect cells at levels similar to those of the parental strains. To investigate in vivo properties of these genetically diverse isolates, representative viruses from each DENV serotype were administered to NOD Rag1-/-, IL2rgnull Flk2-/- (NRGF) mice, engrafted with components of a human immune system. All DENV strains tested resulted in viremia in humanized mice and induced cellular and IgM immune responses. Collectively, we describe here a workflow for rapidly generating de novo infectious clones of DENV - and conceivably other RNA viruses. The infectious clones described here are a valuable resource for reverse genetic studies and for characterizing host responses to DENV in vitro and in vivo.
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Affiliation(s)
- Tomokazu Tamura
- Department of Molecular Biology, Princeton University, Princeton, NJ, USA
| | - Jiayu Zhang
- Department of Molecular Biology, Princeton University, Princeton, NJ, USA
| | - Vrinda Madan
- Department of Molecular Biology, Princeton University, Princeton, NJ, USA
| | - Abhishek Biswas
- Department of Molecular Biology, Princeton University, Princeton, NJ, USA.,Research Computing, Office of Information Technology, Princeton University, Princeton, NJ, USA
| | | | - Thomas R Cafiero
- Department of Molecular Biology, Princeton University, Princeton, NJ, USA
| | - Brigitte L Heller
- Department of Molecular Biology, Princeton University, Princeton, NJ, USA
| | - Wei Wang
- Carl Icahn Laboratory, Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, USA
| | - Alexander Ploss
- Department of Molecular Biology, Princeton University, Princeton, NJ, USA
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Xu Z, Peng Y, Yang M, Li X, Wang J, Zou R, Liang J, Fang S, Liu Y, Yang Y. Simultaneous detection of Zika, Chikungunya, Dengue, Yellow fever, West Nile and Japanese encephalitis viruses by a two-tube multiplex real-time RT-PCR assay. J Med Virol 2022; 94:2528-2536. [PMID: 35146775 DOI: 10.1002/jmv.27658] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2021] [Revised: 02/04/2022] [Accepted: 02/08/2022] [Indexed: 11/07/2022]
Abstract
Due to the concurrent prevalence and increasing risk of co-infection of the clinically important Arboviruses, timely and accurate differential diagnosis is important for clinical management and the epidemiological investigation. A two-tube multiplex real-time RT-PCR assay for the simultaneous detection of Zika virus (ZIKV), Chikungunya virus (CHIKV), Dengue virus (DENV), Yellow fever virus (YFV), West Nile virus (WNV) and Japanese encephalitis virus (JEV) was developed and optimized with high specificity and sensitivity. The detection limit for all the 6 viruses could reach as low as 5 genome equivalent copies and 2.8 × 10-3 TCID50 for ZIKV, YFV, CHIKV and 2.8 × 10-2 TCID50 for JEV per reaction, with high accuracy and precision (R2 > 0.99). Coefficient of variation (CV) of intra-assay and inter-assay for our qRT-PCR assay was low, and the obtained positive rates ad Ct values of this assay were comparable with singleplex commercial kits. Moreover, the multiplex qRT-PCR assay was able to detect possible co-infections without competitive inhibition of target viral genomes. In conclusion, our rapid, sensitive, cost effective multiplex qRT-PCR will be of great use for the differential diagnosis in clinical setting and epidemiological investigation during surveillance. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Zhixiang Xu
- Shenzhen Key Laboratory of Pathogen and Immunity, National Clinical Research Center for Infectious Disease, State Key Discipline of Infectious Disease, Shenzhen Third People's Hospital, Second Hospital Affiliated to Southern University of Science and Technology, Shenzhen, Guangdong, 518100, China.,Savid Medical School, University of Chinese Academy of Sciences, Beijing, 101408, China
| | - Yun Peng
- Shenzhen Key Laboratory of Pathogen and Immunity, National Clinical Research Center for Infectious Disease, State Key Discipline of Infectious Disease, Shenzhen Third People's Hospital, Second Hospital Affiliated to Southern University of Science and Technology, Shenzhen, Guangdong, 518100, China
| | - Minghui Yang
- Shenzhen Key Laboratory of Pathogen and Immunity, National Clinical Research Center for Infectious Disease, State Key Discipline of Infectious Disease, Shenzhen Third People's Hospital, Second Hospital Affiliated to Southern University of Science and Technology, Shenzhen, Guangdong, 518100, China.,Shenzhen Center for Disease Control and Prevention, Shenzhen, China
| | - Xiaohe Li
- Shenzhen Key Laboratory of Pathogen and Immunity, National Clinical Research Center for Infectious Disease, State Key Discipline of Infectious Disease, Shenzhen Third People's Hospital, Second Hospital Affiliated to Southern University of Science and Technology, Shenzhen, Guangdong, 518100, China
| | - Jun Wang
- Shenzhen Key Laboratory of Pathogen and Immunity, National Clinical Research Center for Infectious Disease, State Key Discipline of Infectious Disease, Shenzhen Third People's Hospital, Second Hospital Affiliated to Southern University of Science and Technology, Shenzhen, Guangdong, 518100, China
| | - Rongrong Zou
- Shenzhen Key Laboratory of Pathogen and Immunity, National Clinical Research Center for Infectious Disease, State Key Discipline of Infectious Disease, Shenzhen Third People's Hospital, Second Hospital Affiliated to Southern University of Science and Technology, Shenzhen, Guangdong, 518100, China
| | - Jinhu Liang
- Shenzhen Key Laboratory of Pathogen and Immunity, National Clinical Research Center for Infectious Disease, State Key Discipline of Infectious Disease, Shenzhen Third People's Hospital, Second Hospital Affiliated to Southern University of Science and Technology, Shenzhen, Guangdong, 518100, China
| | - Shisong Fang
- Shenzhen Center for Disease Control and Prevention, Shenzhen, China
| | - Yingxia Liu
- Shenzhen Key Laboratory of Pathogen and Immunity, National Clinical Research Center for Infectious Disease, State Key Discipline of Infectious Disease, Shenzhen Third People's Hospital, Second Hospital Affiliated to Southern University of Science and Technology, Shenzhen, Guangdong, 518100, China.,Savid Medical School, University of Chinese Academy of Sciences, Beijing, 101408, China
| | - Yang Yang
- Shenzhen Key Laboratory of Pathogen and Immunity, National Clinical Research Center for Infectious Disease, State Key Discipline of Infectious Disease, Shenzhen Third People's Hospital, Second Hospital Affiliated to Southern University of Science and Technology, Shenzhen, Guangdong, 518100, China
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10
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Basawarajappa SG, Rangaiah A, Venugopal SJ, Varun CN, Nagaraj V, Padukone S, Shankar SM. Clinical and Molecular facets of Dengue Virus infection from Bengaluru, South India. Nepal J Epidemiol 2021; 11:1053-1062. [PMID: 34733567 PMCID: PMC8560139 DOI: 10.3126/nje.v11i3.37712] [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: 06/11/2021] [Revised: 09/01/2021] [Accepted: 09/20/2021] [Indexed: 11/30/2022] Open
Abstract
Background Dengue virus (DENV) continues to be an epidemic with high mortality rates. The clinical features, especially in the early phase of infection, are nonspecific and there is no single marker that can be reliably deployed for diagnostics. Further, serotype and genotype diversity is not clearly understood. This study was conceived to understand the performance characteristics of various diagnostic markers; serotype and genotype distribution is thus a vital requirement. Methods A subset of blood samples was obtained for all the clinically suspected Dengue cases during the period January to December 2017. The samples were tested for IgM and IgG antibodies and NS1 antigen by both ELISA and rapid tests. Real-time PCR, Conventional PCR and sequencing was performed based on the serology results. Correlation of the data with demographic and clinical details was used to analyze the performance characteristics of various tests. Results Clinical signs and symptoms could not predict dengue positivity due to lack of specific symptoms. The performance of IgM rapid test was found to be lower than the ELISA method (53.5% agreement). The NS1 rapid and NS1 ELISA tests were comparable (89.2% agreement). Majority of the infections were caused due to DEN-2 serotype and phylogenetic analysis revealed all the sequenced DEN-2 serotypes belong to Genotype IV. Three sequences were deposited into NCBI GenBank (GenBank accession number MW583116, MW579054 and MW579053). Conclusion Our comprehensive data suggests that NS1 ELISA and PCR are best used in the early phase of dengue infection (< 5 days post-onset of fever), whereas IgM antibody detection is reliable only in the late phase. We also highlight the unreliable performance of rapid tests.
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Affiliation(s)
- Shantala Gowdara Basawarajappa
- Department of Microbiology, Bangalore Medical College and Research Institute, Bengaluru, Karnataka, India.,State Level VRDL, Department of Microbiology, Bangalore Medical College and Research Institute, Bengaluru, Karnataka, India
| | - Ambica Rangaiah
- Department of Microbiology, Bangalore Medical College and Research Institute, Bengaluru, Karnataka, India.,State Level VRDL, Department of Microbiology, Bangalore Medical College and Research Institute, Bengaluru, Karnataka, India
| | - Shwetha Jinnahalli Venugopal
- Department of Microbiology, Bangalore Medical College and Research Institute, Bengaluru, Karnataka, India.,State Level VRDL, Department of Microbiology, Bangalore Medical College and Research Institute, Bengaluru, Karnataka, India
| | - Chakrakodi N Varun
- State Level VRDL, Department of Microbiology, Bangalore Medical College and Research Institute, Bengaluru, Karnataka, India
| | - Vijay Nagaraj
- Institute of Animal Health and Veterinary Biologicals, Hebbal, Bengaluru-560024
| | - Shashiraja Padukone
- State Level VRDL, Department of Microbiology, Bangalore Medical College and Research Institute, Bengaluru, Karnataka, India
| | - Sathyanarayan Muthur Shankar
- Department of Microbiology, Bangalore Medical College and Research Institute, Bengaluru, Karnataka, India.,State Level VRDL, Department of Microbiology, Bangalore Medical College and Research Institute, Bengaluru, Karnataka, India
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11
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Evaluation of Two Serological Assays for Diagnosing Zika Virus Infection. Diagnostics (Basel) 2021; 11:diagnostics11091696. [PMID: 34574037 PMCID: PMC8469165 DOI: 10.3390/diagnostics11091696] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2021] [Revised: 09/09/2021] [Accepted: 09/13/2021] [Indexed: 11/17/2022] Open
Abstract
Zika virus (ZIKV) emerged and spread rapidly in South American countries during 2015. Efforts to diagnose ZIKV infection using serological tools were challenging in dengue-endemic areas because of antigenic similarities between both viruses. Here, we assessed the performance of an in-house developed IgM antibody capture enzyme-linked immunosorbent assay (MAC-ELISA) and the plaque reduction neutralization test (PRNT) to diagnose ZIKV infection. Acute and convalescent paired serum samples from 51 patients who presented with clinical symptoms suggestive of an arbovirus illness in dengue-endemic areas of Honduras, Venezuela, Colombia and Peru were used in the assessment. Samples were tested for ZIKV, dengue and chikungunya virus using a variety of laboratory techniques. The results for the ZIKV-RNA screening and seroconversion detected by the microneutralization test were used to construct a composite reference standard. The overall sensitivity and specificity for the MAC-ELISA were 93.5% and 100.0%, respectively. Contrastingly, the overall sensitivity and specificity for the PRNT were 96.8% and 95.0%, respectively. Restricting the analysis according to IgM or neutralizing antibodies against dengue, the performances of both serological assays were adequate. The findings of this study reveal that the MAC-ELISA and PRNT would provide initial reliable laboratory diagnostic assays for ZIKV infection in dengue-endemic areas.
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12
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Belaunzarán-Zamudio PF, Rincón León HA, Caballero Sosa S, Ruiz E, Nájera Cancino JG, de La Rosa PR, Guerrero Almeida MDL, Powers JH, Beigel JH, Hunsberger S, Trujillo K, Ramos P, Arteaga-Cabello FJ, López-Roblero A, Valdés-Salgado R, Arroyo-Figueroa H, Becerril E, Ruiz-Palacios G. Different epidemiological profiles in patients with Zika and dengue infection in Tapachula, Chiapas in Mexico (2016-2018): an observational, prospective cohort study. BMC Infect Dis 2021; 21:881. [PMID: 34454432 PMCID: PMC8397877 DOI: 10.1186/s12879-021-06520-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2020] [Accepted: 08/02/2021] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The introduction of Zika and chikungunya to dengue hyperendemic regions increased interest in better understanding characteristics of these infections. We conducted a cohort study in Mexico to evaluate the natural history of Zika infection. We describe here the frequency of Zika, chikungunya and dengue virus infections immediately after Zika introduction in Mexico, and baseline characteristics of participants for each type of infection. METHODS Prospective, observational cohort evaluating the natural history of Zika virus infection in the Mexico-Guatemala border area. Patients with fever, rash or both, meeting the modified criteria of PAHO for probable Zika cases were enrolled (June 2016-July 2018) and followed-up for 6 months. We collected data on sociodemographic, environmental exposure, clinical and laboratory characteristics. Diagnosis was established based on viral RNA identification in serum and urine samples using RT-PCR for Zika, chikungunya, and dengue. We describe the baseline sociodemographic and environmental exposure characteristics of participants according to diagnosis, and the frequency of these infections over a two-year period immediately after Zika introduction in Mexico. RESULTS We enrolled 427 participants. Most patients (n = 307, 65.7%) had an acute illness episode with no identified pathogen (UIE), 37 (8%) Zika, 82 (17.6%) dengue, and 1 (0.2%) chikungunya. In 2016 Zika predominated, declined in 2017 and disappeared in 2018; while dengue increased after 2017. Patients with dengue were more likely to be men, younger, and with lower education than those with Zika and UIE. They also reported closer contact with water sources, and with other people diagnosed with dengue. Participants with Zika reported sexual exposure more frequently than people with dengue and UIE. Zika was more likely to be identified in urine while dengue was more likely found in blood in the first seven days of symptoms; but PCR results for both were similar at day 7-14 after symptom onset. CONCLUSIONS During the first 2 years of Zika introduction to this dengue hyper-endemic region, frequency of Zika peaked and fell over a two-year period; while dengue progressively increased with a predominance in 2018. Different epidemiologic patterns between Zika, dengue and UIE were observed. Trial registration Clinical.Trials.gov (NCT02831699).
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Affiliation(s)
- Pablo F Belaunzarán-Zamudio
- Departamento de Infectología, Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubirán, Mexico City, Mexico.
- National Institute of Allergy and Infectious Diseases, Bethesda, MD, USA.
| | | | - Sandra Caballero Sosa
- Clínica Hospital Dr. Roberto Nettel Flores, Instituto de Seguridad y Servicios Sociales de los Trabajadores del Estado, Tapachula, Chiapas, Mexico
| | - Emilia Ruiz
- Hospital General de Tapachula, Tapachula, Chiapas, Mexico
| | | | | | | | - John H Powers
- Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - John H Beigel
- National Institute of Allergy and Infectious Diseases, Bethesda, MD, USA
| | - Sally Hunsberger
- National Institute of Allergy and Infectious Diseases, Bethesda, MD, USA
| | - Karina Trujillo
- Hospital Regional de Alta Especialidad Ciudad Salud, Tapachula, Chiapas, Mexico
| | - Pilar Ramos
- Departamento de Infectología, Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubirán, Mexico City, Mexico
| | - Fernando J Arteaga-Cabello
- Departamento de Infectología, Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubirán, Mexico City, Mexico
| | | | | | - Hugo Arroyo-Figueroa
- Mexican Emerging Infectious Diseases Clinical Research Network (La Red), Mexico City, Mexico
| | - Eli Becerril
- Mexican Emerging Infectious Diseases Clinical Research Network (La Red), Mexico City, Mexico
| | - Guillermo Ruiz-Palacios
- Departamento de Infectología, Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubirán, Mexico City, Mexico
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13
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Belaunzarán-Zamudio PF, Ortega-Villa AM, Mimenza-Alvarado AJ, Guerra-De-Blas PDC, Aguilar-Navarro SG, Sepúlveda-Delgado J, Hunsberger S, Salgado RV, Ramos-Castañeda J, Rincón León HA, Rodríguez de La Rosa P, Nájera Cancino JG, Beigel J, Caballero Sosa S, Ruiz Hernández E, Powers JH, Ruiz-Palacios GM, Lane C. Comparison of the Impact of Zika and Dengue Virus Infection, and Other Acute Illnesses of Unidentified Origin on Cognitive Functions in a Prospective Cohort in Chiapas Mexico. Front Neurol 2021; 12:631801. [PMID: 33828518 PMCID: PMC8019918 DOI: 10.3389/fneur.2021.631801] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2020] [Accepted: 02/22/2021] [Indexed: 02/03/2023] Open
Abstract
Zika has been associated with a variety of severe neurologic manifestations including meningitis and encephalitis. We hypothesized that it may also cause mild to subclinical neurocognitive alterations during acute infection or over the long term. In this observational cohort study, we explored whether Zika cause subclinical or mild neurocognitive alterations, estimate its frequency and duration, and compare it to other acute illnesses in a cohort of people with suspected Zika infection, in the region of Tapachula in Chiapas, Mexico during 2016-2018. We enrolled patients who were at least 12 years old with suspected Zika virus infection and followed them up for 6 months. During each visit participants underwent a complete clinical exam, including a screening test for neurocognitive dysfunction (Montreal Cognitive Assessment score). We enrolled 406 patients [37 with Zika, 73 with dengue and 296 with other acute illnesses of unidentified origin (AIUO)]. We observed a mild and transient impact over cognitive functions in patients with Zika, dengue and with other AIUO. The probability of having an abnormal MoCA score (<26 points) was significantly higher in patients with Zika and AIUO than in those with dengue. Patients with Zika and AIUO had lower memory scores than patients with dengue (Zika vs. Dengue: -0.378, 95% CI-0.678 to -0.078; p = 0.014: Zika vs. AIUO 0.264, 95% CI 0.059, 0.469; p = 0.012). The low memory performance in patients with Zika and AIUO accounts for most of the differences in the overall MoCA score when compared with patients with dengue. Our results show a decrease in cognitive function during acute illness and provides no evidence to support the hypothesis that Zika might cause neurocognitive alterations longer than the period of acute infection or different to other infectious diseases. While effects on memory or perhaps other cognitive functions over the long term are possible, larger studies using more refined tools for neurocognitive functioning assessment are needed to identify these. Trial Registration: NCT02831699.
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Affiliation(s)
- Pablo F. Belaunzarán-Zamudio
- Departamento de Infectología, Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubirán, Mexico City, Mexico
- National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, United States
| | - Ana M. Ortega-Villa
- Biostatistics Research Branch, Division of Clinical Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, United States
| | - Alberto J. Mimenza-Alvarado
- Department of Geriatric Medicine, Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubirán, Mexico City, Mexico
- Geriatrics & Neurology Fellowship, Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubirán, Mexico City, Mexico
| | | | - Sara G. Aguilar-Navarro
- Department of Geriatric Medicine, Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubirán, Mexico City, Mexico
| | - Jesús Sepúlveda-Delgado
- Directorate of Research, Hospital Regional de Alta Especialidad Ciudad Salud, Tapachula & Medical Science Research, Hospital General de Zona 1, Instituto Mexicano del Seguro Social, Mexico City, Mexico
| | - Sally Hunsberger
- Biostatistics Research Branch, Division of Clinical Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, United States
| | | | - José Ramos-Castañeda
- Departamento de Infectología, Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubirán, Mexico City, Mexico
- Departamento de Inmunidad, Instituto Nacional de Salud Pública, Cuernavaca, Mexico
| | | | | | - José Gabriel Nájera Cancino
- Directorate of Research, Hospital Regional de Alta Especialidad Ciudad Salud, Tapachula & Medical Science Research, Hospital General de Zona 1, Instituto Mexicano del Seguro Social, Mexico City, Mexico
| | - John Beigel
- National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, United States
| | - Sandra Caballero Sosa
- Clínica Hospital Dr. Roberto Nettel Flores, Instituto de Seguridad y Servicios Sociales de los Trabajadores del Estado, Tapachula, Mexico
| | | | - John H. Powers
- Clinical Research Directorate, Frederick National Laboratory for Cancer Research, Frederick, MD, United States
| | - Guillermo M. Ruiz-Palacios
- Departamento de Infectología, Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubirán, Mexico City, Mexico
| | - Clifford Lane
- National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, United States
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14
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Wozniak A, Cerda A, Ibarra-Henríquez C, Sebastian V, Armijo G, Lamig L, Miranda C, Lagos M, Solari S, Guzmán AM, Quiroga T, Hitschfeld S, Riveras E, Ferrés M, Gutiérrez RA, García P. A simple RNA preparation method for SARS-CoV-2 detection by RT-qPCR. Sci Rep 2020; 10:16608. [PMID: 33024174 PMCID: PMC7538882 DOI: 10.1038/s41598-020-73616-w] [Citation(s) in RCA: 52] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2020] [Accepted: 09/16/2020] [Indexed: 12/25/2022] Open
Abstract
The technique RT-qPCR for viral RNA detection is the current worldwide strategy used for early detection of the novel coronavirus SARS-CoV-2. RNA extraction is a key pre-analytical step in RT-qPCR, often achieved using commercial kits. However, the magnitude of the COVID-19 pandemic is causing disruptions to the global supply chains used by many diagnostic laboratories to procure the commercial kits required for RNA extraction. Shortage in these essential reagents is even more acute in developing countries with no means to produce kits locally. We sought to find an alternative procedure to replace commercial kits using common reagents found in molecular biology laboratories. Here we report a method for RNA extraction that takes about 40 min to complete ten samples, and is not more laborious than current commercial RNA extraction kits. We demonstrate that this method can be used to process nasopharyngeal swab samples and yields RT-qPCR results comparable to those obtained with commercial kits. Most importantly, this procedure can be easily implemented in any molecular diagnostic laboratory. Frequent testing is crucial for individual patient management as well as for public health decision making in this pandemic. Implementation of this method could maintain crucial testing going despite commercial kit shortages.
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Affiliation(s)
- Aniela Wozniak
- Department Clinical Laboratories, School of Medicine, Pontificia Universidad Católica de Chile, Av. Vicuña Mackenna 4686, Santiago, Chile
| | - Ariel Cerda
- Department Molecular Genetics and Microbiology, School of Biological Sciences, Pontificia Universidad Católica de Chile, Av. Libertador Bernardo O`Higgins 340, Santiago, Chile
| | - Catalina Ibarra-Henríquez
- Department Molecular Genetics and Microbiology, School of Biological Sciences, Pontificia Universidad Católica de Chile, Av. Libertador Bernardo O`Higgins 340, Santiago, Chile
| | - Valentina Sebastian
- Laboratorio de Microbiología. Servicio de Laboratorios Clínicos. Red de Salud UC-CHRISTUS, Santiago, Chile
| | - Grace Armijo
- Department Molecular Genetics and Microbiology, School of Biological Sciences, Pontificia Universidad Católica de Chile, Av. Libertador Bernardo O`Higgins 340, Santiago, Chile
| | - Liliana Lamig
- Department Molecular Genetics and Microbiology, School of Biological Sciences, Pontificia Universidad Católica de Chile, Av. Libertador Bernardo O`Higgins 340, Santiago, Chile
| | - Carolina Miranda
- Laboratorio de Microbiología. Servicio de Laboratorios Clínicos. Red de Salud UC-CHRISTUS, Santiago, Chile
| | - Marcela Lagos
- Department Clinical Laboratories, School of Medicine, Pontificia Universidad Católica de Chile, Av. Vicuña Mackenna 4686, Santiago, Chile
| | - Sandra Solari
- Department Clinical Laboratories, School of Medicine, Pontificia Universidad Católica de Chile, Av. Vicuña Mackenna 4686, Santiago, Chile
| | - Ana María Guzmán
- Department Clinical Laboratories, School of Medicine, Pontificia Universidad Católica de Chile, Av. Vicuña Mackenna 4686, Santiago, Chile
| | - Teresa Quiroga
- Department Clinical Laboratories, School of Medicine, Pontificia Universidad Católica de Chile, Av. Vicuña Mackenna 4686, Santiago, Chile
| | - Susan Hitschfeld
- Department Molecular Genetics and Microbiology, School of Biological Sciences, Pontificia Universidad Católica de Chile, Av. Libertador Bernardo O`Higgins 340, Santiago, Chile
| | - Eleodoro Riveras
- Department Molecular Genetics and Microbiology, School of Biological Sciences, Pontificia Universidad Católica de Chile, Av. Libertador Bernardo O`Higgins 340, Santiago, Chile
| | - Marcela Ferrés
- Department Clinical Laboratories, School of Medicine, Pontificia Universidad Católica de Chile, Av. Vicuña Mackenna 4686, Santiago, Chile
- Departamento Enfermedades Infecciosas e Inmunología Pediátrica, Escuela Medicina, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Rodrigo A Gutiérrez
- Department Molecular Genetics and Microbiology, School of Biological Sciences, Pontificia Universidad Católica de Chile, Av. Libertador Bernardo O`Higgins 340, Santiago, Chile.
| | - Patricia García
- Department Clinical Laboratories, School of Medicine, Pontificia Universidad Católica de Chile, Av. Vicuña Mackenna 4686, Santiago, Chile.
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15
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Cantero C, Cardozo F, Waggoner JJ, Pinsky BA, Espínola A, Infanzón B, Acosta ME, Aria L, Arévalo de Guillén Y, Cuevas T, Rojas V, Segovia C, Centurión A, Rojas A. Implementation of a Multiplex rRT-PCR for Zika, Chikungunya, and Dengue Viruses: Improving Arboviral Detection in an Endemic Region. Am J Trop Med Hyg 2020; 102:625-628. [PMID: 31933462 DOI: 10.4269/ajtmh.19-0707] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Arboviral diagnosis has been complicated throughout the tropical and subtropical Americas by the recent co-circulation of Zika virus (ZIKV), chikungunya virus (CHIKV), and dengue virus (DENV). The aim of this study was to implement a multiplex real-time RT-PCR (rRT-PCR) for ZIKV, CHIKV, and DENV in Paraguay to test patients who were clinically suspected of having dengue. We tested 110 sera from patients who presented to the Hospital de Clínicas in 2016 and had testing for DENV nonstructural protein 1 (NS1; 40 positive and 70 negative). Using a composite reference standard, we confirmed 51 dengue cases (46.4%): 38/40 NS1 positive and 13/70 NS1 negative. Chikungunya virus and ZIKV were detected in one sample each, both were DENV NS1 negative. The NS1 test demonstrated good agreement with rRT-PCR for DENV. However, multiplex rRT-PCR identified a subset of dengue cases and additional arboviral infections that would not be detected if NS1 assays are relied upon for diagnosis.
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Affiliation(s)
- César Cantero
- Departamento de Producción, Instituto de Investigaciones en Ciencias de la Salud, Universidad Nacional de Asunción, Asunción, Paraguay
| | - Fátima Cardozo
- Departamento de Salud Pública, Instituto de Investigaciones en Ciencias de la Salud, Universidad Nacional de Asunción, Asunción, Paraguay
| | - Jesse J Waggoner
- Department of Global Health, Rollins School of Public Health, Atlanta, Georgia.,Division of Infectious Diseases, Department of Medicine, Emory University, Atlanta, Georgia
| | - Benjamin A Pinsky
- Division of Infectious Diseases and Geographic Medicine, Department of Medicine, Stanford University School of Medicine, Palo Alto, California.,Department of Pathology, Stanford University School of Medicine, Palo Alto, California
| | - Anibal Espínola
- Departamento de Patología, Instituto de Investigaciones en Ciencias de la Salud, Universidad Nacional de Asunción, Asunción, Paraguay
| | - Belén Infanzón
- Departamento de Producción, Instituto de Investigaciones en Ciencias de la Salud, Universidad Nacional de Asunción, Asunción, Paraguay
| | - María Eugenia Acosta
- Departamento de Producción, Instituto de Investigaciones en Ciencias de la Salud, Universidad Nacional de Asunción, Asunción, Paraguay
| | - Laura Aria
- Departamento de Producción, Instituto de Investigaciones en Ciencias de la Salud, Universidad Nacional de Asunción, Asunción, Paraguay
| | - Yvalena Arévalo de Guillén
- Departamento de Producción, Instituto de Investigaciones en Ciencias de la Salud, Universidad Nacional de Asunción, Asunción, Paraguay
| | - Teresa Cuevas
- Facultad de Ciencias Médicas, Hospital de Clínicas, Universidad Nacional de Asunción, Asunción, Paraguay
| | - Vicenta Rojas
- Facultad de Ciencias Médicas, Hospital de Clínicas, Universidad Nacional de Asunción, Asunción, Paraguay
| | - Clotilde Segovia
- Facultad de Ciencias Médicas, Hospital de Clínicas, Universidad Nacional de Asunción, Asunción, Paraguay
| | - Ana Centurión
- Facultad de Ciencias Médicas, Hospital de Clínicas, Universidad Nacional de Asunción, Asunción, Paraguay
| | - Alejandra Rojas
- Departamento de Producción, Instituto de Investigaciones en Ciencias de la Salud, Universidad Nacional de Asunción, Asunción, Paraguay
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16
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Waggoner JJ, Katzelnick LC, Burger-Calderon R, Gallini J, Moore RH, Kuan G, Balmaseda A, Pinsky BA, Harris E. Antibody-Dependent Enhancement of Severe Disease Is Mediated by Serum Viral Load in Pediatric Dengue Virus Infections. J Infect Dis 2020; 221:1846-1854. [PMID: 32236481 PMCID: PMC7213574 DOI: 10.1093/infdis/jiz618] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2019] [Accepted: 11/19/2019] [Indexed: 01/09/2023] Open
Abstract
BACKGROUND Low preexisting anti-dengue virus (DENV) antibody levels are associated with elevated disease severity. While antibody-dependent enhancement of dengue is thought to be driven by viral load, this has not been conclusively shown. We evaluated the association between preinfection anti-DENV antibody titers, viral load, and disease severity among 133 dengue cases in a Nicaraguan pediatric cohort study. METHODS Viral load was quantified in acute-phase serum by real-time reverse transcription polymerase chain reaction and analyzed in relation to preinfection antibody titer (measured by inhibition enzyme-linked immunosorbent assay) and dengue severity, categorized using 3 definitions. RESULTS Higher viral load was significantly associated with dengue severity; for each increase of 1.0 log10 copies/mL, the odds of severe dengue increased approximately 50%, regardless of severity definition. Viral load at presentation and the odds of severe disease were highest among patients with low to intermediate preinfection antibody titers and lowest among those with the highest antibody titers. We showed the effect of preinfection antibody titer on disease severity was mediated by viral load for each of 3 dengue severity outcomes. CONCLUSIONS This study demonstrates the association between preinfection anti-DENV antibody titer, serum viral load, and disease severity, and provides evidence for the mechanism of antibody-dependent enhancement in dengue cases.
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Affiliation(s)
- Jesse J Waggoner
- Department of Medicine, Emory University, Atlanta, Georgia, USA
- Department of Global Health, Rollins School of Public Health, Atlanta, Georgia, USA
| | - Leah C Katzelnick
- Division of Infectious Diseases and Vaccinology, School of Public Health, University of California Berkeley, Berkeley, California, USA
| | | | - Julia Gallini
- Biostatistics Collaboration Core, Department of Biostatistics and Bioinformatics, Emory University, Atlanta, Georgia, USA
| | - Renee H Moore
- Biostatistics Collaboration Core, Department of Biostatistics and Bioinformatics, Emory University, Atlanta, Georgia, USA
| | - Guillermina Kuan
- Centro de Salud Sócrates Flores Vivas, Ministry of Health, Managua, Nicaragua
| | - Angel Balmaseda
- Sustainable Sciences Institute, Managua, Nicaragua
- Laboratorio Nacional de Virología, Centro Nacional de Diagnóstico y Referencia, Ministry of Health, Managua, Nicaragua
| | - Benjamin A Pinsky
- Department of Pathology, Stanford University School of Medicine, Stanford, California, USA
- Department of Medicine, Division of Infectious Diseases, Stanford University School of Medicine, Stanford, California, USA
| | - Eva Harris
- Division of Infectious Diseases and Vaccinology, School of Public Health, University of California Berkeley, Berkeley, California, USA
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17
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Gouel-Cheron A, Lumbard K, Hunsberger S, Arteaga-Cabello FJ, Beigel J, Belaunzarán-Zamudio PF, Caballero-Sosa S, Escobedo-López K, Ibarra-González V, Nájera-Cancino JG, Rincón-León HA, Ruiz-Hernández E, Sepúlveda-Delgado J, Trujillo-Murillo K, Ruiz-Palacios G. Serial real-time RT-PCR and serology measurements substantially improve Zika and Dengue virus infection classification in a co-circulation area. Antiviral Res 2019; 172:104638. [PMID: 31672665 PMCID: PMC6901092 DOI: 10.1016/j.antiviral.2019.104638] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2019] [Revised: 09/04/2019] [Accepted: 10/20/2019] [Indexed: 11/17/2022]
Abstract
BACKGROUND Real-time RT-PCR (Reverse Transcriptase Polymerase Chain Reaction) is considered the gold standard for Zika virus (ZIKV) infection diagnosis, despite its low sensitivity. Diagnosis using recommended serologic cutoffs in co-circulating Flaviviruses areas maybe inadequate due to in-vitro cross-reactivities of Flaviviruses-specific antibodies. We evaluated Zika diagnosis in symptomatic patients using serial RT-PCR and develop a classification model using serial Dengue virus (DENV) and ZIKV serologies. METHODS A prospective longitudinal multicentric study in Southern Mexico (NCT02831699) enrolled symptomatic and non-symptomatic participants. In the classification model, true positives were symptomatic (using a modified World Health Organization/Pan American Health Organization definition) with RT-PCR positive for ZIKV or DENV. True negatives were non-symptomatic with negative RT-PCR. Serial serology measurements were used to predict disease status. RESULTS Analyzing ZIKV and DENV RT-PCR at 3 timepoints between days 3 and 13 of symptom onset detected 25% more cases than a single RT-PCR analysis between day 0 and 6. When considering sensitivity and specificity together, the serial serology model predicted all categories of disease and negatives better than manufactures cutoffs. Their cutoffs optimized sensitivity or specificity but not both. CONCLUSIONS We demonstrated the importance of serial RT-PCR and antibody measurements to diagnose arbovirus infection in symptomatic patients living in regions with co-circulating flaviviruses.
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Affiliation(s)
- Aurelie Gouel-Cheron
- Biostatistics Research Branch, National Institute of Allergy and Infectious Diseases, National Institute of Health, Rockville, MD, USA; Département d'Anesthésie et Réanimation Chirurgicale, Groupe Hospitalier Bichat Claude Bernard, Université de Paris, Assistance Publique Hôpitaux de Paris, Paris, France; Unit of Antibodies in Therapy and Pathology, Pasteur Institut, UMR 1222 INSERM, Paris, France.
| | - Keith Lumbard
- Biostatistics Research Branch, National Institute of Allergy and Infectious Diseases, National Institute of Health, Rockville, MD, USA.
| | - Sally Hunsberger
- Biostatistics Research Branch, National Institute of Allergy and Infectious Diseases, National Institute of Health, Rockville, MD, USA.
| | - Fernando J Arteaga-Cabello
- Departamento de Infectología, Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubirán, Mexico City, Mexico.
| | - John Beigel
- National Institute of Allergy and Infectious Diseases, Bethesda, MD, USA.
| | - Pablo F Belaunzarán-Zamudio
- Departamento de Infectología, Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubirán, Mexico City, Mexico.
| | - Sandra Caballero-Sosa
- Clínica Hospital Dr. Roberto Nettel Flores, Instituto de Seguridad y Servicios Sociales de los Trabajadores del Estado, Tapachula, Chiapas, Mexico.
| | - Kenia Escobedo-López
- Departamento de Infectología, Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubirán, Mexico City, Mexico.
| | - Violeta Ibarra-González
- Departamento de Infectología, Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubirán, Mexico City, Mexico.
| | | | | | | | | | | | - Guillermo Ruiz-Palacios
- Departamento de Infectología, Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubirán, Mexico City, Mexico.
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Rojas A, Cardozo F, Cantero C, Stittleburg V, López S, Bernal C, Gimenez Acosta FE, Mendoza L, Pinsky BA, Arévalo de Guillén I, Páez M, Waggoner J. Characterization of dengue cases among patients with an acute illness, Central Department, Paraguay. PeerJ 2019; 7:e7852. [PMID: 31616598 PMCID: PMC6790102 DOI: 10.7717/peerj.7852] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2019] [Accepted: 09/08/2019] [Indexed: 01/01/2023] Open
Abstract
BACKGROUND In 2018, Paraguay experienced a large dengue virus (DENV) outbreak. The primary objective of this study was to characterize dengue cases in the Central Department, where the majority of cases occur, and identify factors associated with DENV infection. METHODS Patients were enrolled from January-May 2018 if they presented with a suspected arboviral illness. Acute-phase specimens (≤8 days after symptom onset) were tested using rRT-PCR, a rapid diagnostic test for DENV nonstructural protein 1 (NS1) and anti-DENV IgM and IgG, and ELISA for IgG against NS1 from Zika virus (ZIKV). RESULTS A total of 231 patients were enrolled (95.2% adults) at two sites: emergency care and an outpatient clinical site. Patients included 119 (51.5%) dengue cases confirmed by rRT-PCR (n = 115, 96.6%) and/or the detection of NS1 and anti-DENV IgM (n = 4, 3.4%). DENV-1 was the predominant serotype (109/115, 94.8%). Epidemiologically, dengue cases and non-dengue cases were similar, though dengue cases were less likely to reside in a house/apartment or report a previous dengue case. Clinical and laboratory findings associated with dengue included red eyes, absence of sore throat, leucopenia and thrombocytopenia. At an emergency care site, 26% of dengue cases (26/100) required hospitalization. In univariate analysis, hospitalization was associated with increased viral load, anti-DENV IgG, and thrombocytopenia. Among dengue cases that tested positive for IgG against ZIKV NS1, the odds of DENV NS1 detection in the acute phase were decreased 10-fold (OR 0.1, 0.0-0.3). CONCLUSIONS Findings from a predominantly adult population demonstrate clinical and laboratory factors associated with DENV infections and the potential severity of dengue in this group. The combination of viral load and specific IgG antibodies warrant further study as a prognostic to identify patients at risk for severe disease.
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Affiliation(s)
- Alejandra Rojas
- Departamento de Producción, Instituto de Investigaciones en Ciencias de la Salud, Universidad Nacional de Asunción, San Lorenzo, Paraguay
| | - Fátima Cardozo
- Departamento de Salud Pública, Instituto de Investigaciones en Ciencias de la Salud, Universidad Nacional de Asunción, San Lorenzo, Paraguay
| | - César Cantero
- Departamento de Producción, Instituto de Investigaciones en Ciencias de la Salud, Universidad Nacional de Asunción, San Lorenzo, Paraguay
| | - Victoria Stittleburg
- Department of Medicine, Division of Infectious Diseases, Emory University, Atlanta, GA, United States of America
| | - Sanny López
- Departamento de Producción, Instituto de Investigaciones en Ciencias de la Salud, Universidad Nacional de Asunción, San Lorenzo, Paraguay
| | - Cynthia Bernal
- Departamento de Producción, Instituto de Investigaciones en Ciencias de la Salud, Universidad Nacional de Asunción, San Lorenzo, Paraguay
| | | | - Laura Mendoza
- Departamento de Salud Pública, Instituto de Investigaciones en Ciencias de la Salud, Universidad Nacional de Asunción, San Lorenzo, Paraguay
| | - Benjamin A. Pinsky
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, United States of America
- Department of Medicine, Division of Infectious Diseases and Geographic Medicine, Stanford University School of Medicine, Stanford, CA, United States of America
| | - Ivalena Arévalo de Guillén
- Departamento de Producción, Instituto de Investigaciones en Ciencias de la Salud, Universidad Nacional de Asunción, San Lorenzo, Paraguay
| | - Malvina Páez
- Departamento de Salud Pública, Instituto de Investigaciones en Ciencias de la Salud, Universidad Nacional de Asunción, San Lorenzo, Paraguay
| | - Jesse Waggoner
- Department of Medicine, Division of Infectious Diseases, Emory University, Atlanta, GA, United States of America
- Rollins School of Public Health, Department of Global Health, Emory University, Atlanta, GA, United States of America
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19
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Ravichandran S, Hahn M, Belaunzarán-Zamudio PF, Ramos-Castañeda J, Nájera-Cancino G, Caballero-Sosa S, Navarro-Fuentes KR, Ruiz-Palacios G, Golding H, Beigel JH, Khurana S. Differential human antibody repertoires following Zika infection and the implications for serodiagnostics and disease outcome. Nat Commun 2019; 10:1943. [PMID: 31028263 PMCID: PMC6486612 DOI: 10.1038/s41467-019-09914-3] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2018] [Accepted: 04/08/2019] [Indexed: 12/21/2022] Open
Abstract
Zika virus (ZIKV) outbreak in Americas led to extensive efforts to develop vaccines and ZIKV-specific diagnostics. In the current study, we use whole genome phage display library spanning the entire ZIKV genome (ZIKV-GFPDL) for in-depth immune profiling of IgG and IgM antibody repertoires in serum and urine longitudinal samples from individuals acutely infected with ZIKV. We observe a very diverse IgM immune repertoire encompassing the entire ZIKV polyprotein on day 0 in both serum and urine. ZIKV-specific IgG antibodies increase 10-fold between day 0 and day 7 in serum, but not in urine; these are highly focused on prM/E, NS1 and NS2B. Differential antibody affinity maturation is observed against ZIKV structural E protein compared with nonstructural protein NS1. Serum antibody affinity to ZIKV-E protein inversely correlates with ZIKV disease symptoms. Our study provides insight into unlinked evolution of immune response to ZIKV infection and identified unique targets for ZIKV serodiagnostics.
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Affiliation(s)
- Supriya Ravichandran
- Division of Viral Products, Center for Biologics Evaluation and Research (CBER), FDA, Silver Spring, MD, 20993, USA
| | - Megan Hahn
- Division of Viral Products, Center for Biologics Evaluation and Research (CBER), FDA, Silver Spring, MD, 20993, USA
| | - Pablo F Belaunzarán-Zamudio
- Departamento de Infectología, Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubirán, Mexico City, 14080, Mexico
| | | | | | - Sandra Caballero-Sosa
- Instituto de Seguridad y Servicios Sociales de los Trabajadores del Estado, Tapachula, 30740, Chiapas, Mexico
| | | | - Guillermo Ruiz-Palacios
- Comisión Coordinadora de los Institutos Nacionales de Salud y Hospitales de Alta Especialidad, Ministry of Health, Mexico City, 14080, Mexico
| | - Hana Golding
- Division of Viral Products, Center for Biologics Evaluation and Research (CBER), FDA, Silver Spring, MD, 20993, USA
| | - John H Beigel
- Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, MD, 21701, USA
- National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, 20852, USA
| | - Surender Khurana
- Division of Viral Products, Center for Biologics Evaluation and Research (CBER), FDA, Silver Spring, MD, 20993, USA.
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20
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Rojas A, Diagne CT, Stittleburg VD, Mohamed-Hadley A, de Guillén YA, Balmaseda A, Faye O, Faye O, Sall AA, Harris E, Pinsky BA, Waggoner JJ. Internally Controlled, Multiplex Real-Time Reverse Transcription PCR for Dengue Virus and Yellow Fever Virus Detection. Am J Trop Med Hyg 2018; 98:1833-1836. [PMID: 29611509 DOI: 10.4269/ajtmh.18-0024] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022] Open
Abstract
The differential diagnosis of dengue virus (DENV) and yellow fever virus (YFV) infections in endemic areas is complicated by nonspecific early clinical manifestations. In this study, we describe an internally controlled, multiplex real-time reverse transcription polymerase chain reaction (rRT-PCR) for the detection of DENV and YFV. The DENV-YFV assay demonstrated specific detection and had a dynamic range of 2.0-8.0 log10 copies/μL of eluate for each DENV serotype and YFV. Clinical performance was similar to a published pan-DENV assay: 48/48 acute-phase samples from dengue cases were detected in both assays. For YFV detection, mock samples were prepared with nine geographically diverse YFV isolates over a range of concentrations. The DENV-YFV assay detected 62/65 replicates, whereas 54/65 were detected using a reference YFV rRT-PCR. Given the reemergence of DENV and YFV in areas around the world, the DENV-YFV assay should be a useful tool to narrow the differential diagnosis and provide early case detection.
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Affiliation(s)
- Alejandra Rojas
- Departamento de Producción, Instituto de Investigaciones en Ciencias de la Salud, Universidad Nacional de Asunción, Asunción, Paraguay
| | | | - Victoria D Stittleburg
- Division of Infectious Diseases, Department of Medicine, Emory University School of Medicine, Atlanta, Georgia
| | - Alisha Mohamed-Hadley
- Department of Pathology, Stanford University School of Medicine, Stanford, California
| | - Yvalena Arévalo de Guillén
- Departamento de Producción, Instituto de Investigaciones en Ciencias de la Salud, Universidad Nacional de Asunción, Asunción, Paraguay
| | - Angel Balmaseda
- Sustainable Sciences Institute, Managua, Nicaragua.,Laboratorio Nacional de Virología, Centro Nacional de Diagnóstico y Referencia, Ministry of Health, Managua, Nicaragua
| | - Oumar Faye
- Institut Pasteur de Dakar, Dakar, Sénégal
| | | | | | - Eva Harris
- Division of Infectious Diseases and Vaccinology, School of Public Health, University of California, Berkeley, Berkeley, California.,Sustainable Sciences Institute, Managua, Nicaragua
| | - Benjamin A Pinsky
- Division of Infectious Diseases and Geographic Medicine, Department of Medicine, Stanford University School of Medicine, Stanford, California.,Department of Pathology, Stanford University School of Medicine, Stanford, California
| | - Jesse J Waggoner
- Division of Infectious Diseases, Department of Medicine, Emory University School of Medicine, Atlanta, Georgia.,Department of Global Health, Rollins School of Public Health, Atlanta, Georgia
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21
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Balmaseda A, Zambrana JV, Collado D, García N, Saborío S, Elizondo D, Mercado JC, Gonzalez K, Cerpas C, Nuñez A, Corti D, Waggoner JJ, Kuan G, Burger-Calderon R, Harris E. Comparison of Four Serological Methods and Two Reverse Transcription-PCR Assays for Diagnosis and Surveillance of Zika Virus Infection. J Clin Microbiol 2018; 56:e01785-17. [PMID: 29305550 PMCID: PMC5824050 DOI: 10.1128/jcm.01785-17] [Citation(s) in RCA: 49] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2017] [Accepted: 12/22/2017] [Indexed: 11/20/2022] Open
Abstract
Zika virus (ZIKV) is a mosquito-borne flavivirus that is responsible for recent explosive epidemics in the Americas. Notably, ZIKV infection during pregnancy has been found to cause congenital birth defects, including microcephaly, and ZIKV has been associated with Guillain-Barré syndrome in adults. Diagnosis and surveillance of Zika in the Americas have been challenging due to similar clinical manifestations and extensive antibody cross-reactivity with endemic flaviviral diseases, such as dengue. We evaluated four serological and two reverse transcription-PCR (RT-PCR) methods in acute-phase (mean day, 1.8), early-convalescent-phase (mean day, 16.7), and late-convalescent-phase (mean, ~7 months) samples from the same individuals in a long-term pediatric cohort study in Nicaragua. Well-characterized samples from 301 cases of Zika, dengue, or non-Zika, nondengue febrile illnesses were tested. Compared to a composite reference, an in-house IgM antibody capture enzyme-linked immunosorbent assay (MAC-ELISA) and the NIAID-Biodefense and Emerging Infections (BEI) MAC-ELISA measuring IgM yielded sensitivities of 94.5% and 70.1% and specificities of 85.6% and 82.8%, respectively. The NS1 blockade-of-binding ELISA measuring anti-ZIKV NS1 antibody levels yielded sensitivities of 85.0% and 96.5% and specificities of 91.4% and 92.6% at early and late convalescence, respectively. An inhibition ELISA detecting total anti-ZIKV antibodies had sensitivity and specificity values of 68.3% and 58.3% for diagnosis and 94.0% and 98.6% for measuring annual infection incidence. Finally, the ZCD and Trioplex real-time RT-PCR assays detecting Zika, chikungunya, and dengue viruses both yielded a sensitivity of 96.1% and specificity of 100%. Together, these assays resolve the urgent need for diagnostic and surveillance tools for countries affected by Zika virus infections.
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Affiliation(s)
- Angel Balmaseda
- Laboratorio Nacional de Virología, Centro Nacional de Diagnóstico y Referencia, Ministry of Health, Managua, Nicaragua
- Sustainable Sciences Institute, Managua, Nicaragua
| | | | | | - Nadezna García
- Laboratorio Nacional de Virología, Centro Nacional de Diagnóstico y Referencia, Ministry of Health, Managua, Nicaragua
- Sustainable Sciences Institute, Managua, Nicaragua
| | - Saira Saborío
- Laboratorio Nacional de Virología, Centro Nacional de Diagnóstico y Referencia, Ministry of Health, Managua, Nicaragua
- Sustainable Sciences Institute, Managua, Nicaragua
| | | | - Juan Carlos Mercado
- Laboratorio Nacional de Virología, Centro Nacional de Diagnóstico y Referencia, Ministry of Health, Managua, Nicaragua
- Sustainable Sciences Institute, Managua, Nicaragua
| | - Karla Gonzalez
- Laboratorio Nacional de Virología, Centro Nacional de Diagnóstico y Referencia, Ministry of Health, Managua, Nicaragua
- Sustainable Sciences Institute, Managua, Nicaragua
| | - Cristhiam Cerpas
- Laboratorio Nacional de Virología, Centro Nacional de Diagnóstico y Referencia, Ministry of Health, Managua, Nicaragua
- Sustainable Sciences Institute, Managua, Nicaragua
| | - Andrea Nuñez
- Laboratorio Nacional de Virología, Centro Nacional de Diagnóstico y Referencia, Ministry of Health, Managua, Nicaragua
- Sustainable Sciences Institute, Managua, Nicaragua
| | - Davide Corti
- Humabs Biomed SA, subsidiary of Vir Biotechnology, Inc., Bellinzona, Switzerland
| | - Jesse J Waggoner
- Department of Medicine, Division of Infectious Diseases, Emory University, Atlanta, Georgia, USA
| | - Guillermina Kuan
- Sustainable Sciences Institute, Managua, Nicaragua
- Health Center Sócrates Flores Vivas, Ministry of Health, Managua, Nicaragua
| | - Raquel Burger-Calderon
- Sustainable Sciences Institute, Managua, Nicaragua
- Division of Infectious Diseases and Vaccinology, School of Public Health, University of California, Berkeley, Berkeley, California, USA
| | - Eva Harris
- Sustainable Sciences Institute, Managua, Nicaragua
- Division of Infectious Diseases and Vaccinology, School of Public Health, University of California, Berkeley, Berkeley, California, USA
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22
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Tang S, Hemyari P, Canchola JA, Duncan J. Dual composite reference standards (dCRS) in molecular diagnostic research: A new approach to reduce bias in the presence of Imperfect reference. J Biopharm Stat 2018; 28:951-965. [PMID: 29355450 DOI: 10.1080/10543406.2018.1428613] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
A main challenge in molecular diagnostic research is to accurately evaluate the performance of a new nucleic acid amplification test when the reference standard is imperfect. Several approaches, such as discrepant analysis, composite reference standard (CRS) method, or latent class analysis (LCA), are commonly applied for this purpose by combining multiple imperfect (reference) test results. In discrepant analysis or LCA, test results from the new assay are often involved in the construction of a new pseudo-reference standard, which results in the potential risk of overestimating the parameters of interest. On the contrary, the CRS methods only combine the results of reference tests, which is more preferable in practice. In this article, we study the properties of two extreme CRS methods, i.e., combining multiple reference test results by the "any positive" rule or by the "all-positive" rule, and propose a new approach "dual composite reference standards (dCRS)" based on these two extreme methods to reduce the biases of the estimates. Simulations are performed for various scenarios and the proposed approach is applied to two real datasets. The results demonstrate that our approach outperforms other commonly used approaches and therefore is recommended for future applications.
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Affiliation(s)
- Shaowu Tang
- a Roche Molecular Systems, Inc ., Biometrics, Pleasanton , California , USA
| | - Parichehr Hemyari
- a Roche Molecular Systems, Inc ., Biometrics, Pleasanton , California , USA
| | - Jesse A Canchola
- a Roche Molecular Systems, Inc ., Biometrics, Pleasanton , California , USA
| | - John Duncan
- a Roche Molecular Systems, Inc ., Biometrics, Pleasanton , California , USA
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Preparation of MS2-based nanoparticles as control and standard materials for the molecular detection of dengue virus serotypes. Virus Res 2017; 233:42-50. [PMID: 28288812 DOI: 10.1016/j.virusres.2017.02.011] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2016] [Revised: 02/14/2017] [Accepted: 02/23/2017] [Indexed: 11/20/2022]
Abstract
To quantify dengue virus (DENV) and evaluate the performance of clinical laboratories using quantitative real-time polymerase chain reaction (qRT-PCR) assays, we constructed high-efficiency expression systems to produce DENV-1 to 4 nanoparticles and assessed their suitability as standard and control materials in 20 laboratories across China. Targeted gene sequences of DENV-1 to 4 were synthesized and inserted into pACYC-Duet 1-MS2 recombinant plasmids to generate corresponding nanoparticle expression systems. After collection, verification, and quantification by digital PCR (dPCR), DENV-1 to 4 nanoparticles were prepared as control and standard materials. Five positive and three negative samples of each DENV serotype in every panel were used for assessing the performance of the participating laboratories across China, as well as standard materials for the quantitative detection of DENV using qRT-PCR assays. The accuracy, sensitivity, and specificity of qRT-PCR used by the 20 evaluated laboratories were 89.6 (569/635), 85.1 (336/395), and 97.1% (233/240), respectively. Overall, sixteen (80.0%) laboratories were qualified in detecting DENV, among which five (25.0%) were designated as "competent", eleven (55.0%) were defined as "acceptable", and four (20%) were considered to be "improvable". The results generated from the DENV standard samples were significantly positively correlated with those generated by dPCR (r2=0.8698, P<0.001). In summary, DENV nanoparticles could potentially be used as controls for improving the performance of laboratories and as standards for the quantitative detection of DENV.
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Sekaran SD, Soe HJ. Issues in contemporary and potential future molecular diagnostics for dengue. Expert Rev Mol Diagn 2016; 17:217-223. [PMID: 28004604 DOI: 10.1080/14737159.2017.1275963] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
INTRODUCTION Dengue has been the most common arbovirus infection worldwide with 2.5 billion people living in over 100 endemic tropical and subtropical regions. Due to the high number of asymptomatic cases and the signs and symptoms being rather unspecific, dengue cases are often under-reported and might influence dengue surveillance programs. Therefore, a rapid, easy to use, inexpensive, and highly sensitive and specific diagnostic tool is essential for early and accurate diagnosis to ease the clinical management of patients as well as for the development of new interventions. Areas covered: This report discusses the contemporary dengue diagnostic tool, mainly from the aspect of molecular diagnosis where an overview of several nuclei acid amplification tests has been included. Potential molecular diagnostic tools such as biosensor and microarray are also discussed in this report. Expert commentary: Rapidness and accuracy in terms of sensitivity and specificity is imperative in dengue diagnosis for both clinical management and surveillance of dengue to ensure early treatment and corrective control measures can be carried out. In the next five years it is expected that there will be newer tests developed using not only the lateral flow techniques but more specifically biosensors and nanotechnology. These new technologies will have to be validated with the appropriate number and category of samples and to address the issue of cross-reactivity.
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Affiliation(s)
- Shamala Devi Sekaran
- a Department of Medical Microbiology, Faculty of Medicine , University of Malaya , Kuala Lumpur , Malaysia
| | - Hui Jen Soe
- a Department of Medical Microbiology, Faculty of Medicine , University of Malaya , Kuala Lumpur , Malaysia
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Tsai HP, Tsai YY, Lin IT, Kuo PH, Chang KC, Chen JC, Ko WC, Wang JR. Validation and Application of a Commercial Quantitative Real-Time Reverse Transcriptase-PCR Assay in Investigation of a Large Dengue Virus Outbreak in Southern Taiwan. PLoS Negl Trop Dis 2016; 10:e0005036. [PMID: 27732593 PMCID: PMC5061319 DOI: 10.1371/journal.pntd.0005036] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2016] [Accepted: 09/13/2016] [Indexed: 11/30/2022] Open
Abstract
Background Accurate, rapid, and early diagnosis of dengue virus (DENV) infections is essential for optimal clinical care. Here, we evaluated the efficacy of the quantitative real-time PCR (qRT-PCR)-LightMix dengue virus EC kit for DENV detection using samples from a dengue outbreak in Taiwan in 2015. Methods Sera from patients with suspected DENV infection were analyzed and compared using the LightMix kit, a Dengue NS1 Ag + Ab Combo kit for detection of NS1 antigen and DENV-specific IgM and IgG antibodies, and an “in-house” qualitative DENV-specific RT-PCR assay. Results A total of 8,989, 8,954, and 1581 samples were subjected to NS1 antigen detection, IgM and IgG detection, and LightMix assays, respectively. The LightMix assay yielded a linear curve for viral loads (VL) between 102 and 106 copies/reaction, and the minimum detection limits for DENV serotype 1 (DENV1) and DENV2, DENV3, and DENV4 were 1, 10, and 100 focus forming units (FFU)/mL, respectively. There was 88.9% concordance between the results obtained using the NS1 antigen combo kit and by LightMix analysis, and the diagnostic sensitivity and specificity of the two methods were 89.4 and 100%, and 84.7 and 100%, respectively. Notably, fatal cases were attributed to DENV2 infection, and 79.5% (27/34) of these cases occurred in patients ≥ 71 years of age. Among these older patients, 82.3% (14/17) were NS1/IgM/IgG (+/-/-), exhibiting VLs between 106–109 copies/mL, which was markedly higher than the rate observed in the other age groups. Conclusions The LightMix assay was effective for early diagnosis of DENV infection. Our data indicate that high VLs during primary infection in elderly patients may be a positive predictor for severe illness, and may contribute to high mortality rates. The LightMix dengue virus EC qRT-PCR assay is effective for early diagnosis of DENV infection. High viral loads during primary infection in elderly patients may comprise a positive predictor for severe illness, and may contribute to high mortality rates.
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Affiliation(s)
- Huey-Pin Tsai
- Department of Pathology, National Cheng Kung University Hospital, Tainan, Taiwan
- Medical Laboratory Science and Biotechnology, National Cheng Kung University, Tainan, Taiwan
| | - You-Yuan Tsai
- Department of Pathology, National Cheng Kung University Hospital, Tainan, Taiwan
| | - I-Ting Lin
- Department of Pathology, National Cheng Kung University Hospital, Tainan, Taiwan
| | - Pin-Hwa Kuo
- Department of Pathology, National Cheng Kung University Hospital, Tainan, Taiwan
| | - Kung-Chao Chang
- Department of Pathology, National Cheng Kung University Hospital, Tainan, Taiwan
| | - Jung-Chin Chen
- Department of Pathology, National Cheng Kung University Hospital, Tainan, Taiwan
| | - Wen-Chien Ko
- Department of Internal Medicine, National Cheng Kung University Hospital, Tainan, Taiwan
| | - Jen-Ren Wang
- Department of Pathology, National Cheng Kung University Hospital, Tainan, Taiwan
- Medical Laboratory Science and Biotechnology, National Cheng Kung University, Tainan, Taiwan
- Center of Infectious Disease and Signaling Research, National Cheng Kung University, Tainan, Taiwan
- National Institute of Infectious Diseases and Vaccinology, National Health Research Institutes, Tainan, Taiwan
- * E-mail:
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Waggoner JJ, Gresh L, Mohamed-Hadley A, Ballesteros G, Davila MJV, Tellez Y, Sahoo MK, Balmaseda A, Harris E, Pinsky BA. Single-Reaction Multiplex Reverse Transcription PCR for Detection of Zika, Chikungunya, and Dengue Viruses. Emerg Infect Dis 2016; 22:1295-7. [PMID: 27184629 PMCID: PMC4918162 DOI: 10.3201/eid2207.160326] [Citation(s) in RCA: 124] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
Clinical manifestations of Zika virus, chikungunya virus, and dengue virus infections can be similar. To improve virus detection, streamline molecular workflow, and decrease test costs, we developed and evaluated a multiplex real-time reverse transcription PCR for these viruses.
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Waggoner JJ, Ballesteros G, Gresh L, Mohamed-Hadley A, Tellez Y, Sahoo MK, Abeynayake J, Balmaseda A, Harris E, Pinsky BA. Clinical evaluation of a single-reaction real-time RT-PCR for pan-dengue and chikungunya virus detection. J Clin Virol 2016; 78:57-61. [PMID: 26991052 PMCID: PMC4836994 DOI: 10.1016/j.jcv.2016.01.007] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2015] [Revised: 01/07/2016] [Accepted: 01/08/2016] [Indexed: 11/28/2022]
Abstract
BACKGROUND Dengue virus (DENV) and chikungunya virus (CHIKV) now co-circulate throughout tropical regions of the world, with billions of people living at risk of infection. The differentiation of these infections is important for epidemiologic surveillance as well as clinical care, though widely-used molecular diagnostics for DENV and CHIKV require the performance of two to four separate PCR reactions for detection. OBJECTIVES In the current study, we sought to develop and evaluate a single-reaction, multiplex real-time RT-PCR (rRT-PCR) for the detection and differentiation of DENV and CHIKV (the pan-DENV-CHIKV rRT-PCR). STUDY DESIGN From an alignment of all available CHIKV complete genome sequences in GenBank, a new CHIKV rRT-PCR was designed for use in multiplex with a previously described assay for pan-DENV detection. Analytical evaluation was performed in accordance with published recommendations, and the pan-DENV-CHIKV rRT-PCR was clinically compared to reference molecular diagnostics for DENV and CHIKV using 182 serum samples from suspected cases in Managua, Nicaragua. RESULTS The pan-DENV-CHIKV rRT-PCR had a dynamic range extending from 7.0 to 2.0 log10copies/μL for each DENV serotype and CHIKV, and the lower limits of 95% detection were 7.9-37.4copies/μL. The pan-DENV-CHIKV rRT-PCR detected DENV in 81 patients compared to 75 using a reference, hemi-nested DENV RT-PCR, and it demonstrated perfect agreement with a reference CHIKV rRT-PCR (54 positive samples). CONCLUSIONS The single-reaction, multiplex format of the pan-DENV-CHIKV rRT-PCR, combined with sensitive detection of both viruses, has the potential to improve detection while decreasing testing costs and streamlining molecular workflow.
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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, CA, USA
| | - Gabriela Ballesteros
- National Virology Laboratory, Centro Nacional de Diagnóstico y Referencia, Ministry of Health, Managua, Nicaragua
| | - Lionel Gresh
- Sustainable Sciences Institute, Managua, Nicaragua
| | | | - Yolanda Tellez
- National Virology Laboratory, Centro Nacional de Diagnóstico y Referencia, Ministry of Health, Managua, Nicaragua
| | - Malaya K Sahoo
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - Janaki Abeynayake
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - Angel Balmaseda
- National Virology Laboratory, Centro Nacional de Diagnóstico y Referencia, Ministry of Health, Managua, Nicaragua
| | - Eva Harris
- Division of Infectious Diseases and Vaccinology, School of Public Health, University of California, Berkeley, CA, USA
| | - Benjamin A Pinsky
- Department of Medicine, Division of Infectious Diseases and Geographic Medicine, Stanford University School of Medicine, Stanford, CA, USA; Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA.
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Development and Validation of a Quantitative, One-Step, Multiplex, Real-Time Reverse Transcriptase PCR Assay for Detection of Dengue and Chikungunya Viruses. J Clin Microbiol 2016; 54:1766-1773. [PMID: 27098955 DOI: 10.1128/jcm.00299-16] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2016] [Accepted: 04/12/2016] [Indexed: 11/20/2022] Open
Abstract
Dengue virus (DENV) and chikungunya virus (CHIKV) are important human pathogens with common transmission vectors and similar clinical presentations. Patient care may be impacted by the misdiagnosis of DENV and CHIKV in areas where both viruses cocirculate. In this study, we have developed and validated a one-step multiplex reverse transcriptase PCR (RT-PCR) to simultaneously detect, quantify, and differentiate between four DENV serotypes (pan-DENV) and chikungunya virus. The assay uses TaqMan technology, employing two forward primers, three reverse primers, and four fluorophore-labeled probes in a single-reaction format. Coextracted and coamplified RNA was used as an internal control (IC), and in vitro-transcribed DENV and CHIKV RNAs were used to generate standard curves for absolute quantification. The diagnostic 95% limits of detection (LOD) within the linear range were 50 and 60 RNA copies/reaction for DENV (serotypes 1 to 4) and CHIKV, respectively. Our assay was able to detect 53 different strains of DENV, representing four serotypes, and six strains of CHIKV. No cross-reactivity was observed with related flaviviruses and alphaviruses, To evaluate diagnostic sensitivity and specificity, 89 clinical samples positive or negative for DENV (serotypes 1 to 4) and CHIKV by the standard virus isolation method were tested in our assay. The multiplex RT-PCR assay showed 95% sensitivity and 100% specificity for DENV and 100% sensitivity and specificity for CHIKV. With an assay turnaround time of less than 2 h, including extraction of RNA, the multiplex quantitative RT-PCR assay provides rapid diagnosis for the differential detection of two clinically indistinguishable diseases, whose geographical occurrence is increasingly overlapping.
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Hunsperger EA, Muñoz-Jordán J, Beltran M, Colón C, Carrión J, Vazquez J, Acosta LN, Medina-Izquierdo JF, Horiuchi K, Biggerstaff BJ, Margolis HS. Performance of Dengue Diagnostic Tests in a Single-Specimen Diagnostic Algorithm. J Infect Dis 2016; 214:836-44. [PMID: 26984143 DOI: 10.1093/infdis/jiw103] [Citation(s) in RCA: 58] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2015] [Accepted: 01/25/2016] [Indexed: 11/13/2022] Open
Abstract
BACKGROUND Anti-dengue virus (DENV) immunoglobulin M (IgM) seroconversion has been the reference standard for dengue diagnosis. However, paired specimens are rarely obtained, and the interval for this testing negates its usefulness in guiding clinical case management. The presence of DENV viremia and appearance of IgM during the febrile phase of dengue provides the framework for dengue laboratory diagnosis by using a single serum specimen. METHODS Archived paired serum specimens (n = 1234) from patients with laboratory-confirmed dengue from 2005 through 2011 were used to determine the diagnostic performance of real-time reverse transcription polymerase chain reaction (RT-PCR), for detection of DENV serotypes 1-4, and enzyme-linked immunosorbent assays (ELISAs), for detection of DENV nonstructural protein 1 (NS1) antigen and anti-DENV IgM. RESULTS During 1-3 days after illness onset, real-time RT-PCR and NS1 antigen testing detected 82%-69% and 90%-84% of cases, respectively, as viremia levels declined, while anti-DENV IgM ELISA detected 5%-41% of cases as antibody appeared. Over the 10-day period of the febrile phase of dengue, the cumulative effect of using these 3 types of tests in a diagnostic algorithm confirmed ≥90% of dengue cases. CONCLUSIONS The use of molecular or NS1 antigen tests to detect DENV and one to detect anti-DENV IgM in a single serum specimen collected during the first 10 days of illness accurately identified ≥90% of dengue primary and secondary cases.
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Affiliation(s)
- Elizabeth A Hunsperger
- Dengue Branch, Division of Vector-Borne Diseases, Centers for Diseases Control and Prevention (CDC), San Juan, Puerto Rico
| | - Jorge Muñoz-Jordán
- Dengue Branch, Division of Vector-Borne Diseases, Centers for Diseases Control and Prevention (CDC), San Juan, Puerto Rico
| | - Manuela Beltran
- Dengue Branch, Division of Vector-Borne Diseases, Centers for Diseases Control and Prevention (CDC), San Juan, Puerto Rico
| | - Candimar Colón
- Dengue Branch, Division of Vector-Borne Diseases, Centers for Diseases Control and Prevention (CDC), San Juan, Puerto Rico
| | - Jessica Carrión
- Dengue Branch, Division of Vector-Borne Diseases, Centers for Diseases Control and Prevention (CDC), San Juan, Puerto Rico
| | - Jesus Vazquez
- Dengue Branch, Division of Vector-Borne Diseases, Centers for Diseases Control and Prevention (CDC), San Juan, Puerto Rico
| | - Luz Nereida Acosta
- Dengue Branch, Division of Vector-Borne Diseases, Centers for Diseases Control and Prevention (CDC), San Juan, Puerto Rico
| | - Juan F Medina-Izquierdo
- Dengue Branch, Division of Vector-Borne Diseases, Centers for Diseases Control and Prevention (CDC), San Juan, Puerto Rico
| | - Kalanthe Horiuchi
- Office of the Director, Division of Vector-Borne Diseases, CDC, Fort Collins, Colorado
| | - Brad J Biggerstaff
- Office of the Director, Division of Vector-Borne Diseases, CDC, Fort Collins, Colorado
| | - Harold S Margolis
- Dengue Branch, Division of Vector-Borne Diseases, Centers for Diseases Control and Prevention (CDC), San Juan, Puerto Rico
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Waggoner JJ, Balmaseda A, Gresh L, Sahoo MK, Montoya M, Wang C, Abeynayake J, Kuan G, Pinsky BA, Harris E. Homotypic Dengue Virus Reinfections in Nicaraguan Children. J Infect Dis 2016; 214:986-93. [PMID: 26984144 DOI: 10.1093/infdis/jiw099] [Citation(s) in RCA: 90] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2015] [Accepted: 02/01/2016] [Indexed: 11/14/2022] Open
Abstract
BACKGROUND Infection with any of the 4 related dengue virus serotypes (DENV-1-4) is thought to result in lifelong immunity to homotypic reinfection (ie, reinfection with the same serotype). METHODS Archived serum samples collected as part of an ongoing pediatric dengue cohort study in Nicaragua were tested for DENV by real-time reverse transcription polymerase chain reaction. Samples were collected from 2892 children who presented with an acute febrile illness clinically attributed to a non-DENV cause (hereafter, "C cases"). Test results were added to a database of previously identified symptomatic dengue cases in the cohort to identify repeat infections. RESULTS Four patients with homotypic DENV reinfections were identified and confirmed among 29 repeat DENV infections (13.8%) with serotype confirmation. Homotypic reinfections with DENV-1, DENV-2, and DENV-3 occurred 325-621 days after the initial infection. Each patient experienced 1 symptomatic dengue case and 1 DENV-positive C case, and 2 patients presented with symptomatic dengue during their second infection. These DENV-positive C cases did not elicit long-lived humoral immune responses, despite viremia levels of up to 6.44 log10 copies per mL of serum. CONCLUSIONS We describe the first set of virologically confirmed homotypic DENV reinfections. Such cases challenge the current understanding of DENV immunity and have important implications for modeling DENV transmission.
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Affiliation(s)
- Jesse J Waggoner
- Division of Infectious Diseases and Geographic Medicine, Department of Medicine
| | - Angel Balmaseda
- National Virology Laboratory, Centro Nacional de Diagnóstico y Referencia
| | - Lionel Gresh
- Sustainable Sciences Institute, Managua, Nicaragua
| | - Malaya K Sahoo
- Department of Pathology, Stanford University School of Medicine
| | - Magelda Montoya
- Division of Infectious Diseases and Vaccinology, School of Public Health, University of California, Berkeley
| | - Chunling Wang
- Division of Infectious Diseases and Vaccinology, School of Public Health, University of California, Berkeley
| | | | | | - Benjamin A Pinsky
- Division of Infectious Diseases and Geographic Medicine, Department of Medicine Department of Pathology, Stanford University School of Medicine
| | - Eva Harris
- Division of Infectious Diseases and Vaccinology, School of Public Health, University of California, Berkeley
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Alm E, Lindegren G, Falk KI, Lagerqvist N. One-step real-time RT-PCR assays for serotyping dengue virus in clinical samples. BMC Infect Dis 2015; 15:493. [PMID: 26527283 PMCID: PMC4630907 DOI: 10.1186/s12879-015-1226-z] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2015] [Accepted: 10/19/2015] [Indexed: 01/07/2023] Open
Abstract
Background Dengue is one of the leading causes of morbidity in tropical and subtropical regions and infection with any of the four dengue virus serotypes (DENV1-4) result in a wide range of clinical manifestations. Given the geographic expansion of DENV1-4, assays for serotyping are needed to be able to perform surveillance and epidemiological studies. In this study, we describe the design and validation of one-step real-time serotype-specific DENV RT-PCR assays. Methods The DENV1, DENV2, DENV3, and DENV4 RT-PCR assays were designed using all available whole genome DENV sequences in the NCBI nucleotide collection. Because of the high mutation rates of RNA viruses, the assays were performed in singleplex format to enable quick modifications to the primer and probe sequences when new genetic variants emerge. The analytical performance of the RT-PCR assays were evaluated using in vitro transcribed RNA and their specificity was determined by testing 24 DENV isolates, external DENV control panels and RNA preparation of non-DENV flaviviruses and non-dengue clinical samples. Additionally, the clinical performance of the serotype-specific DENV RT-PCR were compared to that of the CDC DENV-1-4 RT-PCR using 85 clinical samples collected from patients presenting with acute dengue. Results The RT-PCR assays were found to be specific for their respective serotype and did not cross-react with other flaviviruses or human mRNA. All assays had a linear dynamic range of 102 to 106 copies/reaction with detection limits between 12 and 44 copies/reaction. When testing sera from 85 confirmed acute dengue cases, the serotype-specific DENV RT-PCR assays had 100 % positive agreement with the FDA-approved CDC DENV-1-4 RT-PCR assay performed in a singleplex format. Additionally 15 samples that tested negative in the CDC DENV-1-4- RT-PCR assay were found positive using the serotype-specific DENV RT-PCR assays. Conclusions Our results suggest that these RT-PCR assays are useful alternatives to existing methods for serotyping DENV in clinical sera. Electronic supplementary material The online version of this article (doi:10.1186/s12879-015-1226-z) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Erik Alm
- Department of Microbiology, The Public Health Agency of Sweden, SE-171 82, Solna, Sweden.
| | - Gunnel Lindegren
- Department of Microbiology, The Public Health Agency of Sweden, SE-171 82, Solna, Sweden.
| | - Kerstin Ingrid Falk
- Department of Microbiology, The Public Health Agency of Sweden, SE-171 82, Solna, Sweden. .,Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, SE-171 77, Stockholm, Sweden.
| | - Nina Lagerqvist
- Department of Microbiology, The Public Health Agency of Sweden, SE-171 82, Solna, Sweden.
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Paul AM, Fan Z, Sinha SS, Shi Y, Le L, Bai F, Ray PC. Bio-Conjugated Gold Nanoparticle Based SERS Probe for Ultrasensitive Identification of Mosquito-Borne Viruses Using Raman Fingerprinting. THE JOURNAL OF PHYSICAL CHEMISTRY. C, NANOMATERIALS AND INTERFACES 2015; 119:23669-23775. [PMID: 27441043 PMCID: PMC4948854 DOI: 10.1021/acs.jpcc.5b07387] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
Dengue virus (DENV) and West Nile virus (WNV) are two well-documented mosquito-borne flaviviruses that cause significant health problems worldwide. Driven by this need, we have developed a bio-conjugated gold nanoparticle (AuNP)-based surface enhanced Raman spectroscopy (SERS) probe for the detection of both DENV and WNV. Reported data demonstrate anti-flavivirus 4G2 antibody conjugated gold nanoparticle (GNP) SERS probe can be used as a Raman fingerprint for the ultrasensitive detection of DENV and WNV selectively. Experimental data show that due to the plasmon coupling in nano-assembly, antibody conjugated GNP- based SERS is able to detect as low as 10 plaque-forming units (PFU)/ml of DENV-2 and WNV, which is comparable with the sensitivity of quantitative PCR-based assays. Selectivity of our probe was demonstrated using another mosquito-borne chikungunya virus (CHIKV) as a negative control. Experimental data demonstrate a huge enhancement of SERS intensity is mainly due to the strong electric field enhancement, which has been confirmed by the finite-difference time-domain (FDTD) simulation. Reported FDTD simulation data indicate the SERS enhancement factor can be more than 104 times, due to the assembled structure. Reported results suggest that bio-conjugated AuNP-4G2 based SERS probes have great potential to be used to screen viral particles in clinical and research-based laboratories.
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Affiliation(s)
- Amber M. Paul
- Department of Biological Sciences, University of Southern Mississippi, Hattiesburg, MS 39406, USA
| | - Zhen Fan
- Department of Chemistry and Biochemistry, Jackson State University, Jackson, MS, USA
| | - Sudarson S. Sinha
- Department of Chemistry and Biochemistry, Jackson State University, Jackson, MS, USA
| | - Yongliang Shi
- Department of Chemistry and Biochemistry, Jackson State University, Jackson, MS, USA
| | - Linda Le
- Department of Biological Sciences, University of Southern Mississippi, Hattiesburg, MS 39406, USA
| | - Fengwei Bai
- Department of Biological Sciences, University of Southern Mississippi, Hattiesburg, MS 39406, USA
- ; Fax: 16012665797
| | - Paresh C. Ray
- Department of Chemistry and Biochemistry, Jackson State University, Jackson, MS, USA
- ; Fax: +16019793674
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Inconclusive reverse transcription-PCR assay comparison for dengue virus detection and serotyping. J Clin Microbiol 2015; 52:1800. [PMID: 24744402 DOI: 10.1128/jcm.03420-13] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
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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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Sensitive real-time PCR detection of pathogenic Leptospira spp. and a comparison of nucleic acid amplification methods for the diagnosis of leptospirosis. PLoS One 2014; 9:e112356. [PMID: 25379890 PMCID: PMC4224423 DOI: 10.1371/journal.pone.0112356] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2014] [Accepted: 10/03/2014] [Indexed: 02/06/2023] Open
Abstract
Background Bacteria of the genus Leptospira, the causative agents of leptospirosis, are categorized into pathogenic and non-pathogenic species. However, the benefit of using a clinical diagnostic that is specific for pathogenic species remains unclear. In this study, we present the development of a real-time PCR (rtPCR) for the detection of pathogenic Leptospira (the pathogenic rtPCR), and we perform a comparison of the pathogenic rtPCR with a published assay that detects all Leptospira species [the undifferentiated febrile illness (UFI) assay] and a reference 16S Leptospira rtPCR, which was originally designed to detect pathogenic species. Methodology/Principal Findings For the pathogenic rtPCR, a new hydrolysis probe was designed for use with primers from the UFI assay, which targets the 16S gene. The pathogenic rtPCR detected Leptospira DNA in 37/37 cultured isolates from 5 pathogenic and one intermediate species. Two strains of the non-pathogenic L. biflexa produced no signal. Clinical samples from 65 patients with suspected leptospirosis were then tested using the pathogenic rtPCR and a reference Leptospira 16S rtPCR. All 65 samples had tested positive for Leptospira using the UFI assay; 62 (95.4%) samples tested positive using the pathogenic rtPCR (p = 0.24). Only 24 (36.9%) samples tested positive in the reference 16S rtPCR (p<0.0001 for comparison with the pathogenic rtPCR and UFI assays). Amplicon sequencing confirmed the detection of pathogenic Leptospira species in 49/50 cases, including 3 cases that were only detected using the UFI assay. Conclusions/Significance The pathogenic rtPCR displayed similar sensitivity to the UFI assay when testing clinical specimens with no difference in specificity. Both assays proved significantly more sensitive than a real-time molecular test used for comparison. Future studies are needed to investigate the clinical and epidemiologic significance of more sensitive Leptospira detection using these tests.
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Waggoner JJ, Sahadeo NSD, Brown A, Mohamed-Hadley A, Hadley D, Carrington L, Carrington CVF, Pinsky BA. Improved serotype-specific dengue virus detection in Trinidad and Tobago using a multiplex, real-time RT-PCR. Diagn Microbiol Infect Dis 2014; 81:105-6. [PMID: 25533614 DOI: 10.1016/j.diagmicrobio.2014.10.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2014] [Revised: 08/24/2014] [Accepted: 10/01/2014] [Indexed: 12/29/2022]
Abstract
Dengue virus (DENV) transmission occurs throughout the Caribbean, though laboratory confirmation and epidemiologic surveillance are limited by the availability of serotype-specific molecular diagnostics. In this study, we show that a serotype-specific DENV multiplex, real-time reverse transcriptase-PCR (RT-PCR) detected DENV RNA in significantly more samples (82/182) than a reference hemi-nested RT-PCR (57/182; P=0.01).
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Affiliation(s)
- Jesse J Waggoner
- Department of Medicine, Division of Infectious Diseases, Stanford University School of Medicine, Stanford, CA, USA
| | - Nikita S D Sahadeo
- Department of Pre-Clinical Studies, Faculty of Medical Sciences, The University of the West Indies, St. Augustine, Trinidad and Tobago
| | - Arianne Brown
- Trinidad Public Health Laboratory, Port of Spain, Trinidad and Tobago
| | | | - Dexter Hadley
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - Leslie Carrington
- Trinidad Public Health Laboratory, Port of Spain, Trinidad and Tobago
| | - Christine V F Carrington
- Department of Pre-Clinical Studies, Faculty of Medical Sciences, The University of the West Indies, St. Augustine, Trinidad and Tobago
| | - Benjamin A Pinsky
- Department of Medicine, Division of Infectious Diseases, Stanford University School of Medicine, Stanford, CA, USA; Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA.
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Najioullah F, Viron F, Césaire R. Evaluation of four commercial real-time RT-PCR kits for the detection of dengue viruses in clinical samples. Virol J 2014; 11:164. [PMID: 25219286 PMCID: PMC4177702 DOI: 10.1186/1743-422x-11-164] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2013] [Accepted: 09/03/2014] [Indexed: 11/17/2022] Open
Abstract
Background Dengue is the most frequent arthropod-borne viral disease worldwide. Because dengue manifestations are similar to those of many other febrile syndromes, the availability of dengue-specific laboratory tests is useful for the differential diagnosis. Timely and accurate diagnosis of dengue virus (DENV) infection is important for appropriate management of complications, pathophysiological studies, epidemiological investigations and optimization of vector-control measures. Several “in-house” reverse transcriptase-polymerase chain reaction (RT-PCR) methods have been developed to detect, type and/or quantify DENV. Standardized dengue RT-PCR kits with internal controls have been recently introduced, but need clinical evaluation. We assessed the performances of 4 commercial DENV real-time RT-PCR kits. Findings The 4 kits were evaluated using a panel of 162 samples positive with an existing in-place hemi-nested RT-PCR used for routine DENV-infection diagnosis in patients with acute-febrile disease. The panel included 46 DENV-1, 37 DENV-2, 33 DENV-3, and 46 DENV-4. Also, 70 negative serum specimens were used to determine specificity. Geno-Sen’s Dengue 1–4 Real-Time RT-PCR kit was the only assay to provide quantification using standards, but lacked sensitivity for DENV-4 detection. The SimplexaTM Dengue RT-PCR assay, with 151 (93.2% [95% confidence interval, 89.3–97.1]) positive samples, had significantly higher sensitivity than the other 3 kits; in a complementary evaluation of 111 consecutive patients’ samples, its performance and genotyping agreed with the hemi-nested gold-standard assay. Conclusions The SimplexaTM Dengue RT-PCR’s good performance to detect and genotype DENV1–4 requires further evaluation in multicenter and prospective studies, particularly in settings of clinical diagnosis during dengue outbreaks.
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Affiliation(s)
- Fatiha Najioullah
- Laboratoire de Virologie, Centre Hospitalier Universitaire de Fort-de-France, and EA 4537, Université des Antilles et de la Guyane, Martinique, France.
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Sasmono RT, Aryati A, Wardhani P, Yohan B, Trimarsanto H, Fahri S, Setianingsih TY, Meutiawati F. Performance of Simplexa dengue molecular assay compared to conventional and SYBR green RT-PCR for detection of dengue infection in Indonesia. PLoS One 2014; 9:e103815. [PMID: 25102066 PMCID: PMC4125142 DOI: 10.1371/journal.pone.0103815] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2013] [Accepted: 07/05/2014] [Indexed: 11/18/2022] Open
Abstract
Diagnostic tests based on detection of dengue virus (DENV) genome are available with varying sensitivities and specificities. The Simplexa Dengue assay (Focus Diagnostics) is a newly developed real-time RT-PCR method designed to detect and serotype DENV simultaneously. To assess the performance of the Simplexa Dengue assay, we performed comparison with conventional RT-PCR and SYBR Green real-time RT-PCR on patients sera isolated from eight cities across Indonesia, a dengue endemic country. A total of 184 sera that were confirmed using NS1 and/or IgM and IgG ELISA were examined. Using conventional and SYBR Green real-time RT-PCR, we detected DENV in 53 (28.8%) and 81 (44.0%) out of 184 sera, respectively. When the Simplexa Dengue assay was employed, the detection rate was increased to 76.6% (141 out of 184 samples). When tested in 40 sera that were confirmed by virus isolation as the gold standard, the conventional RT-PCR yielded 95% sensitivity while the sensitivity of SYBR Green real-time RT-PCR and Simplexa Dengue assay reached 97.5% and 100%, respectively. The specificities of all methods were 100% when tested in 43 non-dengue illness and 20 healthy human samples. Altogether, our data showed the higher detection rate of Simplexa Dengue compared to conventional and SYBR Green real-time RT-PCR in field/surveillance setting. In conclusion, Simplexa Dengue offers rapid and accurate detection and typing of dengue infection and is suitable for both routine diagnostic and surveillance.
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Affiliation(s)
| | - Aryati Aryati
- Clinical Pathology Department, School of Medicine and Institute of Tropical Disease, Airlangga University, Surabaya, Indonesia
| | - Puspa Wardhani
- Clinical Pathology Department, School of Medicine and Institute of Tropical Disease, Airlangga University, Surabaya, Indonesia
| | | | - Hidayat Trimarsanto
- Eijkman Institute for Molecular Biology, Jakarta, Indonesia; Agency for the Assessment and Application of Technology, Jakarta, Indonesia
| | - Sukmal Fahri
- Health Polytechnic, Jambi Provincial Health Office, Kotabaru, Jambi, Indonesia and Graduate School in Medicine, Diponegoro University, Semarang, Indonesia
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Karataylı E, Altunoğlu YÇ, Karataylı SC, Yurdaydın C, Bozdayı AM. Free circulating nucleic acids in plasma and serum as a novel approach to the use of internal controls in real time PCR based detection. J Virol Methods 2014; 207:133-7. [PMID: 25034126 DOI: 10.1016/j.jviromet.2014.07.008] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2014] [Revised: 06/30/2014] [Accepted: 07/04/2014] [Indexed: 01/05/2023]
Abstract
Internal controls (ICs), are the main components of any real-time PCR based amplification methods, which are co-purified and co-amplified with the actual target. The existence of free circulating nucleic acids in plasma and serum (CNAPS) has been known for many years. The aim of this study was to verify whether CNAPS can be used as ICs in real-time PCR based detection and quantification of DNA or RNA targets in plasma and serum samples. Glyceraldehyde-3-phosphate dehydrogenase (GAPDH) as a housekeeping gene, was chosen at random as CNAPS to serve as an intrinsic internal control in two different real-time PCR based quantification models in plasma and serum. Viral loads of hepatitis B virus (HBV) DNA and hepatitis delta virus (HDV) RNA were quantified as actual targets in parallel to GAPDH as IC in a total of 519 serum or plasma samples including 21 healthy controls, 202 positive chronic hepatitis delta patients, 37 chronic hepatitis C patients, 168 chronic hepatitis B patients, 52 patients with hepatocellular carcinoma, and 39 patients with non-alcoholic steatohepatitis/non-alcoholic fatty liver disease. GAPDH levels did not show significant variance in different patient groups and yielded positive signals in all 519 patients with persistent cycle threshold (CT) values 27.85±1.57 (mean±standard deviation (SD)). Reproducibility of the GAPDH amplification in HDV RNA and HBV DNA quantifications was shown with a SD value of CT ranging from 0.42 to 2.14 (mean SD; 1.18) and 0.24 to 1.75 (mean SD; 1.03), respectively. In conclusion, the freely circulating nucleic acids can clearly be used as internal controls for real-time PCR based detection and quantification of any RNA and mainly DNA targets (pathogens) in serum or plasma and this simply excludes the compulsory external addition of any IC molecules into the reaction.
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Affiliation(s)
| | | | | | - Cihan Yurdaydın
- Ankara University, Institute of Hepatology, Ankara, Turkey; Ankara University, School of Medicine, Department of Gastroenterology, Ankara, Turkey
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Waggoner JJ, Abeynayake J, Balassiano I, Lefterova M, Sahoo MK, Liu Y, Vital-Brazil JM, Gresh L, Balmaseda A, Harris E, Banaei N, Pinsky BA. Multiplex nucleic acid amplification test for diagnosis of dengue fever, malaria, and leptospirosis. J Clin Microbiol 2014; 52:2011-8. [PMID: 24671788 PMCID: PMC4042768 DOI: 10.1128/jcm.00341-14] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2014] [Accepted: 03/21/2014] [Indexed: 01/24/2023] Open
Abstract
Dengue, leptospirosis, and malaria are among the most common etiologies of systemic undifferentiated febrile illness (UFI) among travelers to the developing world, and these pathogens all have the potential to cause life-threatening illness in returned travelers. The current study describes the development of an internally controlled multiplex nucleic acid amplification test for the detection of dengue virus (DENV) and Leptospira and Plasmodium species, with a specific callout for Plasmodium falciparum (referred to as the UFI assay). During analytical evaluation, the UFI assay displayed a wide dynamic range and a sensitive limit of detection for each target, including all four DENV serotypes. In a clinical evaluation including 210 previously tested samples, the sensitivities of the UFI assay were 98% for DENV (58/59 samples detected) and 100% for Leptospira and malaria (65/65 and 20/20 samples, respectively). Malaria samples included all five Plasmodium species known to cause human disease. The specificity of the UFI assay was 100% when evaluated with a panel of 66 negative clinical samples. Furthermore, no amplification was observed when extracted nucleic acids from related pathogens were tested. Compared with whole-blood samples, the UFI assay remained positive for Plasmodium in 11 plasma samples from patients with malaria (parasitemia levels of 0.0037 to 3.4%). The syndrome-based design of the UFI assay, combined with the sensitivities of the component tests, represents a significant improvement over the individual diagnostic tests available for these pathogens.
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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, USA
| | - Janaki Abeynayake
- Department of Pathology, Stanford University School of Medicine, Stanford, California, USA
| | - Ilana Balassiano
- Laboratório de Zoonoses Bacterianas, Centro de Referência Nacional para Leptospirose, Coleção de Leptospira, WHO/PAHO Centro Colaborador para Leptospirose, Instituto Oswaldo Cruz, Rio de Janeiro, Brazil
| | - Martina Lefterova
- Department of Pathology, Stanford University School of Medicine, Stanford, California, USA
| | - Malaya K Sahoo
- Department of Pathology, Stanford University School of Medicine, Stanford, California, USA
| | - Yuanyuan Liu
- Department of Pathology, Stanford University School of Medicine, Stanford, California, USA
| | - Juliana Magalhães Vital-Brazil
- Laboratório de Zoonoses Bacterianas, Centro de Referência Nacional para Leptospirose, Coleção de Leptospira, WHO/PAHO Centro Colaborador para Leptospirose, Instituto Oswaldo Cruz, Rio de Janeiro, Brazil
| | - Lionel Gresh
- Sustainable Sciences Institute, Managua, Nicaragua
| | - Angel Balmaseda
- National Virology Laboratory, Centro Nacional de Diagnóstico y Referencia, Ministry of Health, Managua, Nicaragua
| | - Eva Harris
- Division of Infectious Diseases and Vaccinology, School of Public Health, University of California, Berkeley, California, USA
| | - Niaz Banaei
- Department of Medicine, Division of Infectious Diseases and Geographic Medicine, Stanford University School of Medicine, Stanford, California, USA Department of Pathology, Stanford University School of Medicine, Stanford, California, USA
| | - Benjamin A Pinsky
- Department of Medicine, Division of Infectious Diseases and Geographic Medicine, Stanford University School of Medicine, Stanford, California, USA Department of Pathology, Stanford University School of Medicine, Stanford, California, USA
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Abstract
Dengue viruses cause mild disease in the majority of infected individuals. In most cases, the disease is characterised by fever, headache, pain behind the eyes, muscle ache, joint pains, vomiting and diarrhoea. In a low percentage of patients, bleeding and loss of plasma (haemorrhage and plasma leakage) may occur. The hyper-permeability syndrome results in plasma leakage and, if the compensatory mechanisms of the body fail to control the plasma leakage or if medical intervention is late, shock may set in. Profound shock will subsequently lead to acidic blood (metabolic acidosis) and development of disseminated intravascular coagulation (DIC). During DIC multiple micro thromboses occur, leading to organ failure. The mechanisms governing pathogenesis of these forms of severe disease are not clear. High amounts of virus in the blood are believed to cause vascular fragility which, together with infection of endothelial cells and high levels of cytokines and other soluble mediators, may result in bleeding. In the absence of a correlation between the amount of virus in the blood and disease severity, it is likely that response to infection is an important cause of disease. The aberrant immune response to infection is believed to result in a cytokine storm, defined as an imbalance between cytokines driving an inflammation (pro-inflammatory) and those silencing an inflammation (anti-inflammatory). Several lines of evidence indicate that displacement of viral genotype and host genetic background are key factors driving the production of a cytokine storm. Several cytokines are known to induce apoptosis, a form of cell suicide (cause of haemorrhage), and/or affect adherens junctions (cause permeability) in vitro. Whether these cytokines may have such effects in vivo remains to be established.
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Comparison of the FDA-approved CDC DENV-1-4 real-time reverse transcription-PCR with a laboratory-developed assay for dengue virus detection and serotyping. J Clin Microbiol 2013; 51:3418-20. [PMID: 23903549 DOI: 10.1128/jcm.01359-13] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023] Open
Abstract
Dengue virus (DENV) is the agent of the most common vector-borne disease worldwide. Using 199 clinical samples collected from Nicaragua and Sri Lanka, a laboratory-developed DENV multiplex real-time reverse transcription-PCR (rRT-PCR) proved more clinically sensitive than the FDA-approved CDC assay for DENV serotypes 1 to 4 when measured against a composite reference standard, with sensitivities of 97.4% versus 87.1%, respectively.
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