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Fisher R, Lustig Y, Sklan EH, Schwartz E. The Role of NS1 Protein in the Diagnosis of Flavivirus Infections. Viruses 2023; 15:v15020572. [PMID: 36851784 PMCID: PMC9963814 DOI: 10.3390/v15020572] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2023] [Revised: 02/12/2023] [Accepted: 02/17/2023] [Indexed: 02/22/2023] Open
Abstract
Nonstructural protein 1 (NS1) is a glycoprotein among the flavivirus genus. It is found in both membrane-associated and soluble secreted forms, has an essential role in viral replication, and modulates the host immune response. NS1 is secreted from infected cells within hours after viral infection, and thus immunodetection of NS1 can be used for early serum diagnosis of dengue fever infections instead of real-time (RT)-PCR. This method is fast, simple, and affordable, and its availability could provide an easy point-of-care testing solution for developing countries. Early studies show that detecting NS1 in cerebrospinal fluid (CSF) samples is possible and can improve the surveillance of patients with dengue-associated neurological diseases. NS1 can be detected postmortem in tissue specimens. It can also be identified using noninvasive methods in urine, saliva, and dried blood spots, extending the availability and effective detection period. Recently, an enzyme-linked immunosorbent assay (ELISA) assay for detecting antibodies directed against Zika virus NS1 has been developed and used for diagnosing Zika infection. This NS1-based assay was significantly more specific than envelope protein-based assays, suggesting that similar assays might be more specific for other flaviviruses as well. This review summarizes the knowledge on flaviviruses' NS1's potential role in antigen and antibody diagnosis.
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Affiliation(s)
- Ron Fisher
- Department of Otolaryngology/Head & Neck Surgery, Hadassah Hebrew; University Medical Center, Jerusalem 91120, Israel
| | - Yaniv Lustig
- Central Virology Laboratory, Ministry of Health, Sheba Medical Center, Ramat-Gan 52621, Israel
- Sackler Faculty of Medicine, Tel-Aviv University, Tel Aviv 69978, Israel
| | - Ella H. Sklan
- Sackler Faculty of Medicine, Tel-Aviv University, Tel Aviv 69978, Israel
| | - Eli Schwartz
- Sackler Faculty of Medicine, Tel-Aviv University, Tel Aviv 69978, Israel
- The Center of Geographic Medicine and Tropical Diseases, Sheba Medical Center, Ramat-Gan 52621, Israel
- Correspondence:
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Natali EN, Babrak LM, Miho E. Prospective Artificial Intelligence to Dissect the Dengue Immune Response and Discover Therapeutics. Front Immunol 2021; 12:574411. [PMID: 34211454 PMCID: PMC8239437 DOI: 10.3389/fimmu.2021.574411] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2020] [Accepted: 05/17/2021] [Indexed: 01/02/2023] Open
Abstract
Dengue virus (DENV) poses a serious threat to global health as the causative agent of dengue fever. The virus is endemic in more than 128 countries resulting in approximately 390 million infection cases each year. Currently, there is no approved therapeutic for treatment nor a fully efficacious vaccine. The development of therapeutics is confounded and hampered by the complexity of the immune response to DENV, in particular to sequential infection with different DENV serotypes (DENV1-5). Researchers have shown that the DENV envelope (E) antigen is primarily responsible for the interaction and subsequent invasion of host cells for all serotypes and can elicit neutralizing antibodies in humans. The advent of high-throughput sequencing and the rapid advancements in computational analysis of complex data, has provided tools for the deconvolution of the DENV immune response. Several types of complex statistical analyses, machine learning models and complex visualizations can be applied to begin answering questions about the B- and T-cell immune responses to multiple infections, antibody-dependent enhancement, identification of novel therapeutics and advance vaccine research.
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Affiliation(s)
- Eriberto N. Natali
- Institute of Medical Engineering and Medical Informatics, School of Life Sciences, University of Applied Sciences and Arts Northwestern Switzerland FHNW, Muttenz, Switzerland
| | - Lmar M. Babrak
- Institute of Medical Engineering and Medical Informatics, School of Life Sciences, University of Applied Sciences and Arts Northwestern Switzerland FHNW, Muttenz, Switzerland
| | - Enkelejda Miho
- Institute of Medical Engineering and Medical Informatics, School of Life Sciences, University of Applied Sciences and Arts Northwestern Switzerland FHNW, Muttenz, Switzerland
- SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland
- aiNET GmbH, Basel, Switzerland
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Moran Z, Rodriguez W, Ahmadou D, Soropogui B, Magassouba NF, Kelly-Cirino C, Ben Amor Y. Comparative performance study of three Ebola rapid diagnostic tests in Guinea. BMC Infect Dis 2020; 20:670. [PMID: 32933492 PMCID: PMC7493368 DOI: 10.1186/s12879-020-05339-2] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2019] [Accepted: 08/11/2020] [Indexed: 11/25/2022] Open
Abstract
Background The 2014/15 Ebola outbreak in West Africa resulted in 11,000 deaths and massive strain on local health systems, and the ongoing outbreak in Democratic Republic of Congo has afflicted more than 3000 people. Accurate, rapid Ebola diagnostics suitable for field deployment would enable prompt identification and effective response to future outbreaks, yet remain largely unavailable. The purpose of this study was to assess the accuracy of three novel rapid diagnostic tests (RDTs): an Ebola, an Ebola-Malaria, and a Fever Panel test that includes Ebola, all from a single manufacturer. Methods We evaluated the three RDTs in 109 Ebola-positive and 96 Ebola-negative stored serum samples collected during the outbreak in Guinea in 2014/15, and tested by real-time polymerase chain reaction (RT-PCR). Sensitivity, specificity, and overall percent agreement were calculated for each RDT using RT-PCR as a reference standard, stratified by Ct value ranges. Results All tests performed with high accuracy on samples with low Ct value (high viral load). The Fever Panel test performed with the highest accuracy, with a sensitivity of 89.9% and specificity of 90.6%. The Ebola and Ebola-Malaria tests performed comparably to each other: sensitivity was 77.1 and 78% respectively, and specificity was 91.7% for the Ebola test and 95.8% for the Ebola-Malaria test. Conclusions This study evaluated the accuracy of three novel rapid diagnostic tests for Ebola. The tests may have significant public health relevance, particularly the Fever Panel test, which detects seven pathogens including Ebola. Given limitations to the study resulting from uncertain sample quality, further evaluation is warranted. All tests performed with highest accuracy on samples with low Ct value (high viral load), and the data presented here suggests that these RDTs may be useful for point-of-care diagnosis of cases in the context of an outbreak. Restrictions to their use in non-severe Ebola cases or for longitudinal monitoring, when viral loads are lower, may be appropriate. Highlighting the challenge in developing and evaluating Ebola RDTs, there were concerns regarding sample integrity and reference testing, and there is a need for additional research to validate these assays.
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Affiliation(s)
- Zelda Moran
- Center for Sustainable Development, Earth Institute, Columbia University, 475 Riverside Drive, Suite 1040, New York, NY, 10025, USA
| | | | - Doré Ahmadou
- Laboratoire des Fièvres Hémorragiques en Guinée, Conakry, Guinea
| | - Barré Soropogui
- Laboratoire des Fièvres Hémorragiques en Guinée, Conakry, Guinea
| | | | | | - Yanis Ben Amor
- Center for Sustainable Development, Earth Institute, Columbia University, 475 Riverside Drive, Suite 1040, New York, NY, 10025, USA.
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Reusken CB, Ieven M, Sigfrid L, Eckerle I, Koopmans M. Laboratory preparedness and response with a focus on arboviruses in Europe. Clin Microbiol Infect 2017; 24:221-228. [PMID: 29274465 DOI: 10.1016/j.cmi.2017.12.010] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2017] [Revised: 12/08/2017] [Accepted: 12/12/2017] [Indexed: 12/29/2022]
Abstract
BACKGROUND The global health burden of arboviruses is continuously rising, which results in increasing pressure on local and (inter)national laboratory infrastructures. Timely and accurate diagnosis of cases is one of the main pillars for public health and clinical responses to an arbovirus emergence. AIMS AND SOURCES This narrative review aims to summarize recent advances and to identify needs in laboratory preparedness and response activities, with a focus on viruses transmitted by arthropods in Europe. The review is based on evidence extracted from PubMed searches, Public Health and clinical laboratory experiences from the authors and the authors' opinions substantiated by peer-reviewed scientific literature. CONTENT We illustrate the importance of inter-epidemic laboratory preparedness activities to ensure adequate Public Health and clinical responses. We describe the status of arbovirus endemicity and emergence in Europe thereby highlighting the need for preparedness for these viruses. We discuss the components and pitfalls of an adequate laboratory preparedness and response and the broader context of the current landscape of international research, clinical and laboratory preparedness networks. The complexity of arbovirus laboratory preparedness and response is described. IMPLICATIONS Outbreak preparedness plans need to look beyond national reference laboratories, to include first-line responding onsite hospital laboratories and plans for strengthening of such local capacity and capability as required depending on the nature of the outbreak. In particular, the diagnosis of arbovirus infections is complicated by the existence of geographic overlap of circulation of numerous arboviruses, the overlap in clinical manifestation between many arboviruses and other aetiologies and the existence of cross-reactivity between related arboviruses in serology testing. Inter-epidemic preparedness activities need strong national and international networks addressing these issues. However, the current mushrooming of European preparedness networks requires governance to bring the European preparedness and response to a next level.
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Affiliation(s)
- C B Reusken
- Department of Viroscience, WHO Collaborating Center for Arboviruses and Viral Haemorrhagic Fever Reference and Research, Erasmus University Medical Centre, Rotterdam, the Netherlands.
| | - M Ieven
- Department of Medical Microbiology, Antwerp University Hospital, Antwerp, Belgium; Vaccine & Infectious Disease Institute (VAXINFECTIO), University of Antwerp, Antwerp, Belgium
| | - L Sigfrid
- Centre for Tropical Medicine and Global Health, Nuffield Dept. of Medicine, University of Oxford, Oxford, UK
| | - I Eckerle
- Institut für Virologie. Universitätsklinikum Bonn, Bonn, Germany
| | - M Koopmans
- Department of Viroscience, WHO Collaborating Center for Arboviruses and Viral Haemorrhagic Fever Reference and Research, Erasmus University Medical Centre, Rotterdam, the Netherlands
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Schmidt M, Geilenkeuser WJ, Sireis W, Seifried E, Hourfar K. Emerging Pathogens - How Safe is Blood? Transfus Med Hemother 2014; 41:10-7. [PMID: 24659943 PMCID: PMC3949612 DOI: 10.1159/000358017] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2013] [Accepted: 12/16/2013] [Indexed: 12/17/2022] Open
Abstract
During the last few decades, blood safety efforts were mainly focused on preventing viral infections. However, humanity's increased mobility and improved migration pathways necessitate a global perspective regarding other transfusion-transmitted pathogens. This review focuses on the general infection risk of blood components for malaria, dengue virus, Trypanosoma cruzi (Chagas disease) and Babesia spp. Approximately 250 million people become infected by Plasmodium spp. per year. Dengue virus affects more than 50 million people annually in more than 100 countries; clinically, it can cause serious diseases, such as dengue haemorrhagic fever and dengue shock syndrome. Chagas disease, which is caused by Trypanosoma cruzi, mainly occurs in South America and infects approximately 10 million people annually. Babesia spp. is a parasitic infection that infects red blood cells; although many infections are asymptomatic, severe clinical disease has been reported, especially in the elderly. Screening assays are available for all considered pathogens but make screening strategies more complex and more expensive. A general pathogen inactivation for all blood components (whole blood) promises to be a long-term, sustainable solution for both known and unknown pathogens. Transfusion medicine therefore eagerly awaits such a system.
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Affiliation(s)
- Michael Schmidt
- Reference Institute for Bioanalytics, Bonn, Goethe University, Frankfurt/M., Germany
| | | | - Walid Sireis
- German Red Cross, Baden-Wuerttemberg – Hessen, Institute of Transfusion Medicine and Immuno-hemotherapy, Goethe University, Frankfurt/M., Germany
| | - Erhard Seifried
- German Red Cross, Baden-Wuerttemberg – Hessen, Institute of Transfusion Medicine and Immuno-hemotherapy, Goethe University, Frankfurt/M., Germany
| | - Kai Hourfar
- German Red Cross, Baden-Wuerttemberg – Hessen, Institute of Transfusion Medicine and Immuno-hemotherapy, Goethe University, Frankfurt/M., Germany
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Sekaran SD, Artsob H. Molecular diagnostics for the detection of human flavivirus infections. ACTA ACUST UNITED AC 2013; 1:521-30. [PMID: 23496358 DOI: 10.1517/17530059.1.4.521] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
Flaviviruses constitute a genus of viruses that are important etiologic agents of human disease, causing clinical disease ranging from fever to severe manifestations, such as encephalitis and hemorrhagic fever. Serology is presently the most frequently used means of diagnosing flavivirus infections. However, other diagnostic tests may be employed, such as molecular detection, virus isolation and antigen-capture procedures. The applicability of the latter three diagnostic procedures can be expected to vary depending upon the infecting flavivirus, as some flaviviruses, such as dengue, display high and long-term viremias, whereas other flaviviruses produce no, or barely detectable, viremias. Molecular diagnostic techniques have been successfully applied to the diagnosis of flavivirus infections and have the advantage of rapidity, sensitivity and specific identification of the infecting virus. However, it is important to ensure that the right detection tools are employed (for example, appropriate primers and probes to detect the specific virus) and that the laboratory maintains a high proficiency in their testing procedures. Some of the studies that have been employed in the diagnosis of flavivirus infections are reviewed in this article. It seems that there is the potential to develop testing algorithms that successfully employ molecular diagnostics alone or in conjunction with other laboratory techniques for the diagnosis of acute human flavivirus infections.
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Affiliation(s)
- Shamala Devi Sekaran
- University of Malaya, Department of Medical Microbiology, Faculty of Medicine, 50603 Kuala Lumpur, Malaysia
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Domingo C, Escadafal C, Rumer L, Méndez JA, García P, Sall AA, Teichmann A, Donoso-Mantke O, Niedrig M. First international external quality assessment study on molecular and serological methods for yellow fever diagnosis. PLoS One 2012; 7:e36291. [PMID: 22570700 PMCID: PMC3343050 DOI: 10.1371/journal.pone.0036291] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2011] [Accepted: 03/29/2012] [Indexed: 11/18/2022] Open
Abstract
OBJECTIVE We describe an external quality assurance (EQA) study designed to assess the efficiency and accurateness of molecular and serological methods used by expert laboratories performing YF diagnosis. STUDY DESIGN For molecular diagnosis evaluation, a panel was prepared of 14 human plasma samples containing specific RNA of different YFV strains (YFV-17D, YFV South American strain [Brazil], YFV IvoryC1999 strain), and specificity samples containing other flaviviruses and negative controls. For the serological panel, 13 human plasma samples with anti-YFV-specific antibodies against different strains of YFV (YFV-17D strain, YFV IvoryC1999 strain, and YFV Brazilian strain), as well as specificity and negative controls, were included. RESULTS Thirty-six laboratories from Europe, the Americas, Middle East, and Africa participated in these EQA activities. Only 16% of the analyses reported met all evaluation criteria with optimal performance. Serial dilutions of YFV-17D showed that in general the methodologies reported provided a suitable sensitivity. Failures were mainly due to the inability to detect wild-type strains or the presence of false positives. Performance in the serological diagnosis varied, mainly depending on the methodology used. Anti-YFV IgM detection was not performed in 16% of the reports using IIF or ELISA techniques, although it is preferable for the diagnosis of YFV acute infections. A good sensitivity profile was achieved in general; however, in the detection of IgM antibodies a lack of sensitivity of anti-YFV antibodies against the vaccine strain 17D was observed, and of the anti-YFV IgG antibodies against a West African strain. Neutralization assays showed a very good performance; however, the unexpected presence of false positives underlined the need of improving the running protocols. CONCLUSION This EQA provides information on each laboratory's efficacy of RT-PCR and serological YFV diagnosis techniques. The results indicate the need for improving serological and molecular diagnosis techniques and provide a follow-up of the diagnostic profiles.
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Affiliation(s)
- Cristina Domingo
- Centre for Biological Security, Robert Koch Institute, Berlin, Germany.
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Abstract
Dengue infection is the name of an important arboviral infection that is common in tropical countries. This infection can cause acute febrile illness with possible important serious consequences, hemorrhage and shock. In its most severe subtype – dengue hemorrhagic fever – the fatality rate is very high. In a case of dengue infection, for management to succeed, early diagnosis and prompt treatment is very important. There are many possible investigations with which to diagnose dengue. However, limitations can still be discerned for each method, but the most important consideration is the correctness of the diagnosis. Similar to any kind of laboratory diagnosis, error can be expected in laboratory diagnosis for dengue, and this is an important topic to be considered. In this article, the diagnosis of dengue will be discussed, with special focus on problems to be kept in mind to avoid errors.
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Purcell MK, Getchell RG, McClure CA, Garver KA. Quantitative polymerase chain reaction (PCR) for detection of aquatic animal pathogens in a diagnostic laboratory setting. JOURNAL OF AQUATIC ANIMAL HEALTH 2011; 23:148-161. [PMID: 22216714 DOI: 10.1080/08997659.2011.620217] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
Real-time, or quantitative, polymerase chain reaction (qPCR) is quickly supplanting other molecular methods for detecting the nucleic acids of human and other animal pathogens owing to the speed and robustness of the technology. As the aquatic animal health community moves toward implementing national diagnostic testing schemes, it will need to evaluate how qPCR technology should be employed. This review outlines the basic principles of qPCR technology, considerations for assay development, standards and controls, assay performance, diagnostic validation, implementation in the diagnostic laboratory, and quality assurance and control measures. These factors are fundamental for ensuring the validity of qPCR assay results obtained in the diagnostic laboratory setting.
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Affiliation(s)
- Maureen K Purcell
- U.S. Geological Survey, Western Fisheries Research Center 6505 North East 65th Street, Seattle, Washington 98115, USA.
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Dutra NR, de Paula MB, de Oliveira MD, de Oliveira LL, De Paula SO. The laboratorial diagnosis of dengue: applications and implications. J Glob Infect Dis 2011; 1:38-44. [PMID: 20300385 PMCID: PMC2840934 DOI: 10.4103/0974-777x.52980] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Abstract
The diagnosis of infection by the dengue virus relies, in most cases, on the clinical judgment of the patient, since only a few major centers have clinical laboratories that offer diagnostic tests to confirm the clinical impressions of an infection. At present, routine laboratory diagnosis is done by different kinds of testing. Among them are the methods of serological research, virus isolation, detection of viral antigens, and detection of viral genomes. The continued development of diagnostic tests, which are cheap, sensitive, specific, easy to perform, and capable of giving early diagnosis of the dengue virus infection is still a need. There are also other obstacles that are not specifically related to the technological development of diagnostic methods. For instance, infrastructure of the laboratories, the training of personnel, and the capacity of research of these laboratories are still limited in many parts of Brazil and the world, where dengue is endemic. Clinical laboratories, especially the ones that serve regions with a high incidence of dengue, should be aware of all the diagnostic methods available for routine these days, and choose the one that best suit their working conditions and populations served, in order to save lives.
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Affiliation(s)
- Nina Rocha Dutra
- Laboratory of Molecular Immunovirology, Department of General Biology, Federal University of Viçosa, Viçosa, Minas Gerais, Brazil
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Garver KA, Hawley LM, McClure CA, Schroeder T, Aldous S, Doig F, Snow M, Edes S, Baynes C, Richard J. Development and validation of a reverse transcription quantitative PCR for universal detection of viral hemorrhagic septicemia virus. DISEASES OF AQUATIC ORGANISMS 2011; 95:97-112. [PMID: 21848118 DOI: 10.3354/dao02344] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
Viral hemorrhagic septicemia virus (VHSV) infects over 70 fish species inhabiting marine, brackish or freshwater environments throughout the Northern Hemisphere. Over its geographic range, 4 VHSV genotypes and multiple subtypes exist. Here, we describe the development and validation of a rapid, sensitive and specific real-time reverse transcription quantitative PCR assay (RT-qPCR) that amplifies sequence from representative isolates of all VHSV genotypes (I, II, III and IV). The pan-specific VHSV RT-qPCR assay reliably detects 100 copies of VHSV nucleoprotein RNA without cross-reacting with infectious hematopoietic necrosis virus, spring viremia of carp virus or aquatic birnavirus. Test performance characteristics evaluated on experimentally infected Atlantic salmon Salmo salar L. revealed a diagnostic sensitivity (DSe) > or = 93% and specificity (DSp) = 100%. The repeatability and reproducibility of the procedure was exceptionally high, with 93% agreement among test results within and between 2 laboratories. Furthermore, proficiency testing demonstrated the VHSV RT-qPCR assay to be easily transferred to and performed by a total of 9 technicians representing 4 laboratories in 2 countries. The assay performed equivalent to the traditional detection method of virus isolation via cell culture with the advantage of faster turnaround times and high throughput capacity, further suggesting the suitability of the use of this VHSV RT-qPCR in a diagnostic setting.
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Affiliation(s)
- Kyle A Garver
- Fisheries & Oceans Canada, Pacific Biological Station, Nanaimo, British Columbia, V9T 6N7, Canada.
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Domingo C, Niedrig M, Teichmann A, Kaiser M, Rumer L, Jarman RG, Donoso-Mantke O. 2nd International external quality control assessment for the molecular diagnosis of dengue infections. PLoS Negl Trop Dis 2010; 4. [PMID: 20957194 PMCID: PMC2950135 DOI: 10.1371/journal.pntd.0000833] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2010] [Accepted: 09/01/2010] [Indexed: 11/24/2022] Open
Abstract
Background Currently dengue viruses (DENV) pose an increasing threat to over 2.5 billion people in over 100 tropical and sub-tropical countries worldwide. International air travel is facilitating rapid global movement of DENV, increasing the risk of severe dengue epidemics by introducing different serotypes. Accurate diagnosis is critical for early initiation of preventive measures. Different reverse transcriptase PCR (RT-PCR) methods are available, which should be evaluated and standardized. Epidemiological and laboratory-based surveillance is required to monitor and guide dengue prevention and control programmes, i.e., by mosquito control or possible vaccination (as soon as an effective and safe vaccine becomes available). Objective The purpose of the external quality assurance (EQA) study described is to assess the efficiency and accuracy of dengue molecular diagnosis methods applied by expert laboratories. Study Design A panel of 12 human plasma samples was distributed and tested for DENV-specific RNA. The panel comprised 9 samples spiked with different DENV serotypes (DENV-1 to DENV-4), including 10-fold dilution series of DENV-1 and DENV-3. Two specificity controls consisted of a sample with a pool of 4 other flaviviruses and a sample with chikungunya virus. A negative control sample was also included. Results Thirty-seven laboratories (from Europe, Middle East Asia, Asia, the Americas/Caribbean, and Africa) participated in this EQA study, and reports including 46 sets of results were returned. Performance among laboratories varied according to methodologies used. Only 5 (10.9%) data sets met all criteria with optimal performance, and 4 (8.7%) with acceptable performance, while 37 (80.4%) reported results showed the need for improvement regarding accomplishment of dengue molecular diagnosis. Failures were mainly due to lack of sensitivity and the presence of false positives. Conclusions The EQA provides information on each laboratory's efficacy of RT-PCR techniques for dengue diagnosis and indicates for most laboratories an urgent need to improve sensitivity and specificity. Dengue viruses (DENV) are the most widespread arthropod-borne viruses which have shown an unexpected geographic expansion, as well as an increase in the number and severity of outbreaks in the last decades. In this context, the accurate diagnosis and reliable surveillance of dengue infections are essential. The laboratory diagnosis of dengue relies on the use of several methods detecting markers of DENV infection present in patient serum. Molecular diagnosis methods are usually rapid, sensitive, and simple when correctly standardized. Moreover, PCR-based diagnosis techniques are able to readily detect DENV during the acute phase of the disease and may assume an important role in dengue diagnosis and surveillance. Different reverse transcriptase PCR (RT-PCR) methods have been developed and are currently available and should be standardized in each laboratory to maintain high quality performance. In this work an External quality assessment (EQA) activity has been carried out to evaluate the accuracy and quality of laboratory data for the molecular diagnosis and surveillance of dengue, which involved worldwide dengue reference laboratories. In conclusion, RT-PCR techniques for dengue diagnosis applied by the participating laboratories demonstrated the need of further improvement in most laboratories.
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Affiliation(s)
| | | | | | | | | | - Richard G. Jarman
- United States Army Medical Component of the Armed Forces Research Institute of the Medical Sciences (USAMC-AFRIMS), Bangkok, Thailand
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Huhtamo E, Hasu E, Uzcátegui NY, Erra E, Nikkari S, Kantele A, Vapalahti O, Piiparinen H. Early diagnosis of dengue in travelers: comparison of a novel real-time RT-PCR, NS1 antigen detection and serology. J Clin Virol 2009; 47:49-53. [PMID: 19963435 DOI: 10.1016/j.jcv.2009.11.001] [Citation(s) in RCA: 85] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2009] [Accepted: 11/04/2009] [Indexed: 11/15/2022]
Abstract
BACKGROUND The increased traveling to dengue endemic regions and the numerous epidemics have led to a rise in imported dengue. The laboratory diagnosis of acute dengue requires several types of tests and often paired samples are needed for obtaining reliable results. Although several diagnostic methods are available, proper comparative data on their performance are lacking. OBJECTIVES To compare the performance of novel methods including a novel pan-DENV real-time RT-PCR and a commercially available NS1 capture-EIA in regard to IgM detection for optimizing the early diagnosis of DENV in travelers. STUDY DESIGN A panel of 99 selected early phase serum samples of dengue patients was studied by real-time RT-PCR, NS1 antigen ELISA, IgM-EIA, IgG-IFA and cell culture virus isolation. RESULTS The novel real-time RT-PCR was shown specific and sensitive for detection of DENV-1-4 RNA and suitable for diagnostic use. The diagnostic rate using combination of RNA and IgM detection was 99% and using NS1 and IgM detection 95.9%. The results of RNA and NS1 antigen detection disagreed in 15.5% of samples that had only RNA or NS1 antigen detected. CONCLUSIONS The diagnostic rates of early samples are higher when either RNA or NS1 antigen detection is combined with IgM detection. Besides the differences in the RNA and NS1 detection assays, the observed discrepancy of results could suggest individual variation or differences in timing of these markers in patient serum.
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Affiliation(s)
- Eili Huhtamo
- Department of Virology, Haartman Institute, Faculty of Medicine, University of Helsinki, PO Box 21, Haartmaninkatu 3, FI-00014 University of Helsinki, Finland.
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Bustin SA, Benes V, Garson JA, Hellemans J, Huggett J, Kubista M, Mueller R, Nolan T, Pfaffl MW, Shipley GL, Vandesompele J, Wittwer CT. The MIQE guidelines: minimum information for publication of quantitative real-time PCR experiments. Clin Chem 2009; 55:611-22. [PMID: 19246619 DOI: 10.1373/clinchem.2008.112797] [Citation(s) in RCA: 10526] [Impact Index Per Article: 701.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
BACKGROUND Currently, a lack of consensus exists on how best to perform and interpret quantitative real-time PCR (qPCR) experiments. The problem is exacerbated by a lack of sufficient experimental detail in many publications, which impedes a reader's ability to evaluate critically the quality of the results presented or to repeat the experiments. CONTENT The Minimum Information for Publication of Quantitative Real-Time PCR Experiments (MIQE) guidelines target the reliability of results to help ensure the integrity of the scientific literature, promote consistency between laboratories, and increase experimental transparency. MIQE is a set of guidelines that describe the minimum information necessary for evaluating qPCR experiments. Included is a checklist to accompany the initial submission of a manuscript to the publisher. By providing all relevant experimental conditions and assay characteristics, reviewers can assess the validity of the protocols used. Full disclosure of all reagents, sequences, and analysis methods is necessary to enable other investigators to reproduce results. MIQE details should be published either in abbreviated form or as an online supplement. SUMMARY Following these guidelines will encourage better experimental practice, allowing more reliable and unequivocal interpretation of qPCR results.
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Affiliation(s)
- Stephen A Bustin
- Centre for Academic Surgery, Institute of Cell and Molecular Science, Barts and the London School of Medicine and Dentistry, London, UK.
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Pan-dengue virus detection by PCR for travelers returning from the tropics. J Clin Microbiol 2008; 46:3104-6. [PMID: 18650359 DOI: 10.1128/jcm.01294-08] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
We performed dengue virus (DENV) serology and quantitative real-time pan-DENV reverse transcription-PCR (RT-PCR) on 186 sera of 171 patients returning from the tropics. DENV loads significantly decreased with increasing times of disease and were higher in immunoglobulin M-negative samples. In the first week of disease, pan-DENV RT-PCR is the test of choice.
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Hapugoda MD, Batra G, Abeyewickreme W, Swaminathan S, Khanna N. Single antigen detects both immunoglobulin M (IgM) and IgG antibodies elicited by all four dengue virus serotypes. CLINICAL AND VACCINE IMMUNOLOGY : CVI 2007; 14:1505-14. [PMID: 17898184 PMCID: PMC2168164 DOI: 10.1128/cvi.00145-07] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
The resurgence of dengue (DEN) virus infections in the last few decades coupled with the lack of a preventive vaccine and specific antiviral drugs has jointly contributed to making this a significant global public health problem. Currently, symptomatic supportive treatment and fluid replacement therapy are the only means available to minimize DEN-induced mortality. As the clinical symptoms associated with DEN virus infections are indistinguishable from those of many other viral, bacterial, and parasitic infections, specific diagnostic tests assume critical importance in the unequivocal identification of DEN virus infections. We have designed a novel chimeric antigen based on envelope domain III (EDIII), a critical antigenic region of the major structural protein of DEN viruses. We fused EDIIIs corresponding to each of the four DEN virus serotypes using pentaglycyl linkers, overexpressed the resultant tetravalent chimeric protein in Escherichia coli, and affinity purified it in high yields, obtaining approximately 30 mg protein of >95% purity per liter of culture. We show that this tetravalent antigen could specifically recognize anti-DEN virus antibodies of both the immunoglobulin M (IgM) and IgG classes. Using a large panel of IgM antibody capture-enzyme-linked immunosorbent assay- and hemagglutination inhibition-confirmed DEN virus-infected and uninfected patient sera (n = 289), we demonstrate that this tetravalent antigen can function as a diagnostic tool of high sensitivity and specificity.
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Affiliation(s)
- Menaka D Hapugoda
- Recombinant Gene Products Group, International Centre for Genetic Engineering and Biotechnology, P.O. Box 10504, Aruna Asaf Ali Marg, New Delhi 110067, India
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Donoso Mantke O, Aberle SW, Avsic-Zupanc T, Labuda M, Niedrig M. Quality control assessment for the PCR diagnosis of tick-borne encephalitis virus infections. J Clin Virol 2007; 38:73-7. [PMID: 17070730 DOI: 10.1016/j.jcv.2006.09.001] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2006] [Revised: 09/01/2006] [Accepted: 09/07/2006] [Indexed: 12/24/2022]
Abstract
BACKGROUND Reverse transcriptase-polymerase chain reaction (RT-PCR) is an efficient method for the early detection of tick-borne encephalitis virus (TBEV) RNA in blood and serum samples taken prior to the appearance of antibodies. Improved diagnostics are critical for optimally detecting and managing TBE infections and quality control measures are therefore essential. OBJECTIVE To assess the diagnostic quality of laboratories by performing an external quality assurance (EQA) programme for the molecular detection of TBE infections. STUDY DESIGN A panel of 12 prepared human plasma samples were distributed and tested for the presence of TBEV-specific RNA. The panel comprised eight samples spiked with different TBEV strains of European, Siberian and Far Eastern subtypes, and included a 10-fold dilution series. Two specificity controls consisted of a sample with Louping ill virus (LIV) and a sample with a pool of four other flaviviruses, and two negative control samples were further included. RESULTS Twenty-three laboratories from 16 European and 2 non-European countries participated in this EQA programme. Only two participants correctly identified all samples. Nine laboratories correctly identified 75.0-91.7% of the samples; seven laboratories correctly identified 54.5-66.7% and five laboratories correctly identified < or =50%. CONCLUSIONS The EQA programme provides information on the quality of the RT-PCR methods used by the participating laboratories and indicates that most of these need to improve sensitivity and specificity of their molecular assays for TBEV.
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Affiliation(s)
- Oliver Donoso Mantke
- Robert Koch-Institut, Centre for Biological Safety, Division of Highly Pathogenic Viruses (ZBS-1), Nordufer 20, D-13353 Berlin, Germany.
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Chao DY, Davis BS, Chang GJJ. Development of multiplex real-time reverse transcriptase PCR assays for detecting eight medically important flaviviruses in mosquitoes. J Clin Microbiol 2006; 45:584-9. [PMID: 17108075 PMCID: PMC1829073 DOI: 10.1128/jcm.00842-06] [Citation(s) in RCA: 96] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
A multiplex real-time reverse transcriptase PCR has been developed for the rapid detection and identification of eight medically important flaviviruses from laboratory-reared, virus-infected mosquito pools. The method used involves the gene-specific amplification of yellow fever virus (YFV), Japanese encephalitis virus (JEV), West Nile virus (WNV), St. Louis encephalitis virus (SLEV), and dengue virus (DENV) serotypes 1 to 4 (DENV-1 to DENV-4, respectively) by use of the flavivirus consensus amplimers located at the RNA-dependent RNA polymerase domain of nonstructural protein 5. Virus-specific amplicons were detected by four newly characterized TaqMan fluorogenic probes (probes specific for YFV, JEV, WNV, and SLEV) and four previously published probes specific for DENV-1 to -4 (L. J. Chien, T. L. Liao, P. Y. Shu, J. H. Huang, D. J. Gubler, and G. J. Chang, J. Clin. Microbiol. 44:1295-1304, 2006). This assay had a specificity of 100% and various sensitivities of at least 3.5 PFU/ml for YFV, 2.0 PFU/ml for JEV, 10.0 PFU/ml for WNV, and 10.0 PFU/ml for SLEV. Additionally, we have developed an in vitro transcription system to generate RNase-resistant RNA templates for each of these eight viruses. These templates can be incorporated into the assay as RNA copy number controls and/or as external controls for RNA-spiked mosquito pools for quality assurance purposes. Although further study with mosquitoes collected in the field is needed, the incorporation of this assay into mosquito surveillance could be used as an early-warning system for the detection of medically important flaviviruses, particularly when the cocirculation of multiple viruses in the same region is suspected.
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Affiliation(s)
- Day-Yu Chao
- Arboviral Diseases Branch, Division of Vector-Borne Infectious Diseases, Centers for Disease Control and Prevention, 3150 Rampart Road, Fort Collins, CO 80521, USA
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Grobusch MP, Niedrig M, Göbels K, Klipstein-Grobusch K, Teichmann D. Evaluation of the use of RT-PCR for the early diagnosis of dengue fever. Clin Microbiol Infect 2006; 12:395-7. [PMID: 16524419 DOI: 10.1111/j.1469-0691.2006.01353.x] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
RT-PCR was used to diagnose dengue virus infections confirmed serologically in 26 returning travellers. RT-PCR was positive for three (75%) of four samples taken on or before day 3 of the illness, for 15 (78.9%) of 19 samples taken between days 4 and 7, and for none of three samples tested on or after day 8 (p 0.0337). When applied early, RT-PCR seems to be a useful tool for the diagnosis of dengue fever.
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Affiliation(s)
- M P Grobusch
- Medical Clinic, Department of Infectious Diseases, Charité/Campus Virchow Hospital, Humboldt University, Germany.
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AnandaRao R, Swaminathan S, Fernando S, Jana AM, Khanna N. A custom-designed recombinant multiepitope protein as a dengue diagnostic reagent. Protein Expr Purif 2005; 41:136-47. [PMID: 15802231 DOI: 10.1016/j.pep.2005.01.009] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2004] [Revised: 01/10/2005] [Indexed: 11/16/2022]
Abstract
Currently, dengue fever is the most important re-emerging mosquito-borne viral disease, with the major proportion of the target population residing in the developing countries of the world. In endemic areas, potentially fatal secondary dengue infections, characterized by high anti-dengue IgG antibody titers, are most common. Most currently available commercial dengue diagnostic kits rely on the use of whole virus antigens and are consequently associated with false positives due to serologic cross-reactivity, high cost of antigen production, and biohazard risk. This has prompted the need to develop an alternate antigen to replace the whole virus antigen in diagnostic tests. We have designed and expressed a novel recombinant protein antigen by assembling key immunodominant linear IgG-specific dengue virus epitopes, chosen on the basis of pepscan analysis, phage display, and computer predictions. The recombinant dengue multiepitope protein was expressed to high levels in Escherichia coli, purified in a single step, yielding >25 mg pure protein per liter culture. We developed an in-house enzyme-linked immunosorbent assay (ELISA) to detect anti-dengue antibodies in a panel of 20 patient sera using the purified recombinant dengue multiepitope protein as the capture antigen. The ELISA results were in excellent agreement with those obtained using a commercially available diagnostic test, Dengue Duo rapid strip test from PanBio, Australia. The high epitope density, careful choice of epitopes, and the use of E. coli system for expression, coupled to simple purification, jointly have the potential to lead to the development of an inexpensive diagnostic test with a high degree of sensitivity and specificity.
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Affiliation(s)
- Ravulapalli AnandaRao
- International Centre for Genetic Engineering and Biotechnology, New Delhi-110067, India
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