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Applying a pan-flavivirus RT-qPCR assay in Brazilian public health surveillance. Arch Virol 2020; 165:1863-1868. [PMID: 32474687 DOI: 10.1007/s00705-020-04680-w] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2020] [Accepted: 04/24/2020] [Indexed: 10/24/2022]
Abstract
The aim of this study was to improve flavivirus field monitoring in Brazil using a reliable probe-based RT-qPCR assay. Standard flavivirus strains were employed to evaluate the performance of the assay, and its applicability was evaluated using 235 stored pools of Culicidae samples collected between 1993 and 1997 and in 2016. Flavivirus species were identified by sequencing. Sixteen (6.8%) samples tested positive: Ilheus virus, Iguape virus, and Saint Louis encephalitis virus were identified in historical specimens from 1993-1994, while insect-specific flaviviruses were detected in the samples from 2016. This approach was demonstrated to be accurate for flavivirus detection and characterization, and it can be successfully applied for vector surveillance and for monitoring and discovery of insect specific flaviviruses.
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2
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Elizalde M, Cano-Gómez C, Llorente F, Pérez-Ramírez E, Casades-Martí L, Aguilera-Sepúlveda P, Ruiz-Fons F, Jiménez-Clavero MÁ, Fernández-Pinero J. A Duplex Quantitative Real-Time Reverse Transcription-PCR for Simultaneous Detection and Differentiation of Flaviviruses of the Japanese Encephalitis and Ntaya Serocomplexes in Birds. Front Vet Sci 2020; 7:203. [PMID: 32373639 PMCID: PMC7186316 DOI: 10.3389/fvets.2020.00203] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2020] [Accepted: 03/27/2020] [Indexed: 12/14/2022] Open
Abstract
High impact, mosquito-borne flaviviruses such as West Nile virus (WNV), Usutu virus (USUV), Japanese encephalitis virus (JEV), Tembusu virus (TMUV), and Bagaza/Israel turkey meningoencephalomyelitis virus (BAGV/ITV) are emerging in different areas of the world. These viruses belong to the Japanese encephalitis (JE) serocomplex (JEV, WNV, and USUV) and the Ntaya serocomplex (TMUV and BAGV/ITV). Notably, they share transmission route (mosquito bite) and reservoir host type (wild birds), and some of them co-circulate in the same areas, infecting overlapping mosquito and avian population. This may simplify epidemiological surveillance, since it allows the detection of different infections targeting the same population, but also represents a challenge, as the diagnostic tools applied need to detect the whole range of flaviviruses surveyed, and correctly differentiate between these closely related pathogens. To this aim, a duplex real-time RT-PCR (dRRT-PCR) method has been developed for the simultaneous and differential detection of JE and Ntaya flavivirus serocomplexes. The method has been standardized and evaluated by analyzing a panel of 49 flaviviral and non-flaviviral isolates, and clinical samples of different bird species obtained from experimental infections or from the field, proving its value for virus detection in apparently healthy or suspicious animals. This new dRRT-PCR technique is a reliable, specific and highly sensitive tool for rapid detection and differentiation of JE and Ntaya flavivirus groups in either domestic or wild animals. This novel method can be implemented in animal virology diagnostic laboratories as screening tool in routine surveillance and in the event of bird encephalitis emergence.
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Affiliation(s)
- Maia Elizalde
- Centro de Investigación en Sanidad Animal (CISA), Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), Valdeolmos-Alalpardo, Spain
| | - Cristina Cano-Gómez
- Centro de Investigación en Sanidad Animal (CISA), Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), Valdeolmos-Alalpardo, Spain
| | - Francisco Llorente
- Centro de Investigación en Sanidad Animal (CISA), Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), Valdeolmos-Alalpardo, Spain
| | - Elisa Pérez-Ramírez
- Centro de Investigación en Sanidad Animal (CISA), Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), Valdeolmos-Alalpardo, Spain
| | - Laia Casades-Martí
- Instituto de Investigación de Recursos Cinegéticos IREC (CSIC-UCLM-JCCM), SaBio Group, Ciudad Real, Spain
| | - Pilar Aguilera-Sepúlveda
- Centro de Investigación en Sanidad Animal (CISA), Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), Valdeolmos-Alalpardo, Spain
| | - Francisco Ruiz-Fons
- Instituto de Investigación de Recursos Cinegéticos IREC (CSIC-UCLM-JCCM), SaBio Group, Ciudad Real, Spain
| | - Miguel Ángel Jiménez-Clavero
- Centro de Investigación en Sanidad Animal (CISA), Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), Valdeolmos-Alalpardo, Spain.,Epidemiología y Salud Pública, CIBERESP, Madrid, Spain
| | - Jovita Fernández-Pinero
- Centro de Investigación en Sanidad Animal (CISA), Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), Valdeolmos-Alalpardo, Spain
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3
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Nunes AR, Alves BEB, Pereira HW, Nascimento YM, Morais IC, Fernandes JV, Araújo JM, Lanza DC. Improved reverse transcription-polymerase chain reaction assay for the detection of flaviviruses with semi-nested primers for discrimination between dengue virus serotypes and Zika virus. Mem Inst Oswaldo Cruz 2018. [PMID: 29513820 PMCID: PMC5853760 DOI: 10.1590/0074-02760170393] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
BACKGROUND The genus Flavivirus includes a variety of medically important viruses, including dengue virus (DENV) and Zika virus (ZIKV), which are most prevalent in Brazil. Because the clinical profile of patients affected by different DENV serotypes or ZIKV may be similar, the development of new methods that facilitate a rapid and accurate diagnosis is crucial. OBJECTIVES The current study aimed to develop an improved reverse transcription-polymerase chain reaction (RT-PCR) protocol for universal detection of flaviviruses by using semi-nested primers that discriminate between DENV serotypes and ZIKV. METHODS The bioinformatics workflow adopted for primer design included: (1) alignment of 1,442 flavivirus genome sequences, (2) characterisation of 27 conserved regions, (3) generation of a primer set comprising 77 universal primers, and (4) selection of primer pairs with greatest coverage and specificity. Following primer design, the reaction was validated in vitro. The same approach was applied to the design of primers specific for DENV and ZIKV, using a species-specific sequence database. FINDINGS The new assay amplified an 800-806 nt variable region of the NS5 gene and allowed discrimination of virtually all flavivirus species using reference-sequence comparison. The 800-806 nt fragment was validated as a template for a semi-nested multiplex PCR using five additional primers for the detection of DENV and ZIKV. These primers were designed to generate amplicons of different sizes, allowing differentiation of the four serotypes of DENV, and ZIKV using agarose gel electrophoresis. MAIN CONCLUSIONS The bioinformatics pipeline allowed efficient primer design, making it possible to identify the best targets within the coding region of the NS5 protein. The multiplex system proved effective in differentiation of DENV1-4 and ZIKV on a 2% agarose gel. The possibility of discriminating DENV serotypes and ZIKV in the same reaction provided a faster result consuming less sample. In addition, this simplified approach ensured the reduction of the cost per analysis.
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Affiliation(s)
- Allan Rd Nunes
- Laboratório de Biologia Molecular Aplicada, Departamento de Bioquímica, Universidade Federal do Rio Grande do Norte, Natal, RN, Brasil
| | - Brenda Elen B Alves
- Laboratório de Biologia Molecular de Doenças Infecciosas e Câncer, Departamento de Microbiologia e Parasitologia, Universidade Federal do Rio Grande do Norte, Natal, RN, Brasil
| | - Hannaly Wb Pereira
- Laboratório de Biologia Molecular de Doenças Infecciosas e Câncer, Departamento de Microbiologia e Parasitologia, Universidade Federal do Rio Grande do Norte, Natal, RN, Brasil
| | - Yasmin M Nascimento
- Laboratório de Biologia Molecular de Doenças Infecciosas e Câncer, Departamento de Microbiologia e Parasitologia, Universidade Federal do Rio Grande do Norte, Natal, RN, Brasil
| | - Ingryd C Morais
- Laboratório de Biologia Molecular de Doenças Infecciosas e Câncer, Departamento de Microbiologia e Parasitologia, Universidade Federal do Rio Grande do Norte, Natal, RN, Brasil
| | - José Veríssimo Fernandes
- Laboratório de Biologia Molecular de Doenças Infecciosas e Câncer, Departamento de Microbiologia e Parasitologia, Universidade Federal do Rio Grande do Norte, Natal, RN, Brasil
| | - Josélio Mg Araújo
- Laboratório de Biologia Molecular de Doenças Infecciosas e Câncer, Departamento de Microbiologia e Parasitologia, Universidade Federal do Rio Grande do Norte, Natal, RN, Brasil
| | - Daniel Cf Lanza
- Laboratório de Biologia Molecular Aplicada, Departamento de Bioquímica, Universidade Federal do Rio Grande do Norte, Natal, RN, Brasil
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4
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Al-Saeed MS, El-Kafrawy SA, Farraj SA, Al-Subhi TL, Othman NA, Alsultan A, Ben Helaby HG, Alshawdari MM, Hassan AM, Charrel RN, Azhar EI, Hashem AM. Phylogenetic characterization of circulating Dengue and Alkhumra Hemorrhagic Fever viruses in western Saudi Arabia and lack of evidence of Zika virus in the region: A retrospective study, 2010-2015. J Med Virol 2017; 89:1339-1346. [PMID: 28198548 PMCID: PMC7167144 DOI: 10.1002/jmv.24785] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2016] [Revised: 01/05/2017] [Accepted: 01/24/2017] [Indexed: 11/27/2022]
Abstract
Flaviviruses represent a global public health concern. They consist of ∼70 viruses with almost half of them causing human diseases with unspecified febrile illnesses. Cities in western Saudi Arabia are endemic for viruses (DENV) with sporadic infections due to Alkhumra hemorrhagic fever virus (AHFV). They also represent a major destination for travelers coming for annual religious pilgrimages (Hajj and Umrah) from all over the world. However, whether other flaviviruses are circulating is not known because of the limited number of surveillance studies. Here, we retrospectively screened 690 samples for flaviviruses in samples from patients with unexplained febrile illnesses between 2010 and 2015 in western Saudi Arabia using a pan‐flaviviruses RT‐PCR assay. Despite Zika virus RNA was not detected, this study confirms circulation and/or sporadic spread of DENV‐2, DENV‐3, and AHFV, higher prevalence of DENV‐2, and a role for visitors from DENV endemic countries in DENV importation into the Kingdom. Further analysis also showed very low genetic diversity of AHFV confirming its slow microevolution. Accordingly, continuous and prospective surveillance for flaviviruses using such assay are warranted in Saudi Arabia which receives millions of Muslims annually to implement effective control measures in light of the global widespread and outbreaks of several flaviviruses.
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Affiliation(s)
- Moneerah S Al-Saeed
- Special Infectious Agents Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Sherif A El-Kafrawy
- Special Infectious Agents Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Suha A Farraj
- Special Infectious Agents Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Tagreed L Al-Subhi
- Special Infectious Agents Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Norah A Othman
- Special Infectious Agents Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Arwa Alsultan
- Special Infectious Agents Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Huda G Ben Helaby
- Special Infectious Agents Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Mustafa M Alshawdari
- Special Infectious Agents Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Ahmed M Hassan
- Special Infectious Agents Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Remi N Charrel
- Special Infectious Agents Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah, Saudi Arabia.,UMR "Emergence des Pathologies Virales" (EPV: Aix-Marseille university-IRD 190-Inserm 1207-EHESP), Marseille, France.,Institut hospitalo-universitaire Méditerranée infection, APHM Public Hospitals of Marseille, Marseille, France
| | - Esam I Azhar
- Special Infectious Agents Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah, Saudi Arabia.,Faculty of Applied Medical Sciences, Department of Medical Laboratory Technology, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Anwar M Hashem
- Special Infectious Agents Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah, Saudi Arabia.,Faculty of Medicine, Department of Medical Microbiology and Parasitology, King Abdulaziz University, Jeddah, Saudi Arabia
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5
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David S, Abraham AM. Epidemiological and clinical aspects on West Nile virus, a globally emerging pathogen. Infect Dis (Lond) 2016; 48:571-86. [PMID: 27207312 DOI: 10.3109/23744235.2016.1164890] [Citation(s) in RCA: 56] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
BACKGROUND Since the isolation of West Nile virus (WNV) in 1937, in Uganda, it has spread globally, causing significant morbidity and mortality. While birds serve as amplifier hosts, mosquitoes of the Culex genus function as vectors. Humans and horses are dead end hosts. The clinical manifestations of West Nile infection in humans range from asymptomatic illness to West Nile encephalitis. METHODS The laboratory offers an array of tests, the preferred method being detection of RNA and serum IgM for WNV, which, if detected, confirms the clinical diagnosis. Although no definitive antiviral therapy and vaccine are available for humans, many approaches are being studied. STUDY This article will review the current literature of the natural cycle, geographical distribution, virology, replication cycle, molecular epidemiology, pathogenesis, laboratory diagnosis, clinical manifestations, blood donor screening for WNV, treatment, prevention and vaccines.
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Affiliation(s)
- Shoba David
- a Department of Clinical Virology , Christian Medical College , Vellore , Tamil Nadu , India
| | - Asha Mary Abraham
- a Department of Clinical Virology , Christian Medical College , Vellore , Tamil Nadu , India
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6
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Ergunay K, Tkachev S, Kozlova I, Růžek D. A Review of Methods for Detecting Tick-Borne Encephalitis Virus Infection in Tick, Animal, and Human Specimens. Vector Borne Zoonotic Dis 2016; 16:4-12. [DOI: 10.1089/vbz.2015.1896] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Affiliation(s)
- Koray Ergunay
- Hacettepe University, Faculty of Medicine, Department of Medical Microbiology, Virology Unit, Sihhiye Ankara, Turkey
| | - Sergey Tkachev
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - Irina Kozlova
- FSSFE Scientific Centre of Family Health and Human Reproduction Problems, Siberian Branch of the Russian Academy of Medical Sciences, Irkutsk, Russia
| | - Daniel Růžek
- Veterinary Research Institute, Brno, Czech Republic
- Institute of Parasitology, Biology Centre of the Czech Academy of Sciences, and Faculty of Science, University of South Bohemia, České Budějovice, Czech Republic
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7
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Shirafuji H, Yazaki R, Shuto Y, Yanase T, Kato T, Ishikura Y, Sakaguchi Z, Suzuki M, Yamakawa M. Broad-range detection of arboviruses belonging to Simbu serogroup lineage 1 and specific detection of Akabane, Aino and Peaton viruses by newly developed multiple TaqMan assays. J Virol Methods 2015; 225:9-15. [PMID: 26341063 DOI: 10.1016/j.jviromet.2015.08.021] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2015] [Revised: 08/30/2015] [Accepted: 08/30/2015] [Indexed: 12/22/2022]
Abstract
TaqMan assays were developed for the broad-range detection of arboviruses belonging to Simbu serogroup lineage 1 in the genus Orthobunyavirus and also for the specific detection of three viruses in the lineage, Akabane, Aino and Peaton viruses (AKAV, AINOV and PEAV, respectively). A primer and probe set was designed for the broad-range detection of Simbu serogroup lineage 1 (Pan-Simbu1 set) mainly targeting AKAV, AINOV, PEAV, Sathuperi and Shamonda viruses (SATV and SHAV), and the forward and reverse primers of the Pan-Simbu1 set were also used for the specific detection of AKAV with another probe (AKAV-specific set). In addition, two more primer and probe sets were designed for AINOV- and PEAV-specific detection, respectively (AINOV- and PEAV-specific sets). All of the four primer and probe sets successfully detected targeted viruses, and thus broad-range and specific detection of all the targeted viruses can be achieved by using two multiplex assays and a single assay in a dual (two-color) assay format when another primer and probe set for a bovine β-actin control is also used. The assays had an analytical sensitivity of 10 copies/tube for AKAV, at least 100 copies/tube for AINOV, 100 copies/tube for PEAV, one copy/tube for SATV and at least 10 copies/tube for SHAV, respectively. Diagnostic sensitivity of the assays was tested with field-collected bovine samples, and the results suggested that the sensitivity was higher than that of a conventional RT-PCR. These data indicate that the newly developed TaqMan assays will be useful tools for the diagnosis and screening of field-collected samples for infections of AKAV and several other arboviruses belonging to the Simbu serogroup lineage 1.
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Affiliation(s)
- Hiroaki Shirafuji
- Kyushu Research Station, National Institute of Animal Health (NIAH), National Agriculture and Food Research Organization (NARO), Japan.
| | - Ryu Yazaki
- Kusu Livestock Hygiene Service Center, Oita Prefectural Government, Japan
| | - Yozo Shuto
- Oita Livestock Hygiene Service Center, Oita Prefectural Government, Japan
| | - Tohru Yanase
- Kyushu Research Station, National Institute of Animal Health (NIAH), National Agriculture and Food Research Organization (NARO), Japan
| | - Tomoko Kato
- Kyushu Research Station, National Institute of Animal Health (NIAH), National Agriculture and Food Research Organization (NARO), Japan
| | - Youji Ishikura
- Domestic Livestock Disease Identification Office, Food Safety Promotion Division, Shimane Prefectural Government, Japan
| | - Zenjiro Sakaguchi
- Kagoshima Central Livestock Hygiene Service Center, Kagoshima Prefectural Government, Japan
| | - Moemi Suzuki
- Okinawa Prefectural Institute of Animal Health, Okinawa Prefectural Government, Japan
| | - Makoto Yamakawa
- Viral Disease and Epidemiology Research Division, NIAH, NARO, Japan
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8
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Venter M, Zaayman D, van Niekerk S, Stivaktas V, Goolab S, Weyer J, Paweska JT, Swanepoel R. Macroarray assay for differential diagnosis of meningoencephalitis in southern Africa. J Clin Virol 2014; 60:50-6. [DOI: 10.1016/j.jcv.2014.02.001] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2013] [Revised: 01/30/2014] [Accepted: 02/01/2014] [Indexed: 11/26/2022]
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9
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Dhama K, Pawaiya R, Chakrabort S, Tiwari R, Verma A. Powassan virus (POWV) Infection in Animals and Humans: A Review. ACTA ACUST UNITED AC 2014. [DOI: 10.3923/ajava.2014.177.189] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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10
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Rasool V, Rasool S, Mushtaq S. Viral encephalitis and its management through advanced molecular diagnostic methods: a review. Clin Pediatr (Phila) 2014; 53:118-20. [PMID: 23737611 DOI: 10.1177/0009922813490229] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Affiliation(s)
- Vamiq Rasool
- 1G.B. Pant Hospital, Government Medical College, Srinagar, Kashmir, India
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11
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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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12
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Armstrong PM, Prince N, Andreadis TG. Development of a multi-target TaqMan assay to detect eastern equine encephalitis virus variants in mosquitoes. Vector Borne Zoonotic Dis 2012; 12:872-6. [PMID: 22835151 DOI: 10.1089/vbz.2012.1008] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
Abstract
Disease outbreaks caused by eastern equine encephalitis virus (EEEV; Togaviridae, Alphavirus) may be prevented by implementing effective surveillance and intervention strategies directed against the mosquito vector. Methods for EEEV detection in mosquitoes include a real-time reverse transcriptase PCR technique (TaqMan assay), but we report its failure to detect variants isolated in Connecticut in 2011, due to a single base-pair mismatch in the probe-binding site. To improve the molecular detection of EEEV, we developed a multi-target TaqMan assay by adding a second primer/probe set to provide redundant targets for EEEV detection. The multi-target TaqMan assay had similar performance characteristics to the conventional assay, but also detected newly-evolving strains of EEEV. The approach described here increases the reliability of the TaqMan assay by creating back-up targets for virus detection without sacrificing sensitivity or specificity.
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Affiliation(s)
- Philip M Armstrong
- Center for Vector Biology and Zoonotic Diseases, The Connecticut Agricultural Experiment Station, New Haven, Connecticut 06504, USA.
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13
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De Filette M, Ulbert S, Diamond M, Sanders NN. Recent progress in West Nile virus diagnosis and vaccination. Vet Res 2012; 43:16. [PMID: 22380523 PMCID: PMC3311072 DOI: 10.1186/1297-9716-43-16] [Citation(s) in RCA: 97] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2011] [Accepted: 03/01/2012] [Indexed: 01/22/2023] Open
Abstract
West Nile virus (WNV) is a positive-stranded RNA virus belonging to the Flaviviridae family, a large family with 3 main genera (flavivirus, hepacivirus and pestivirus). Among these viruses, there are several globally relevant human pathogens including the mosquito-borne dengue virus (DENV), yellow fever virus (YFV), Japanese encephalitis virus (JEV) and West Nile virus (WNV), as well as tick-borne viruses such as tick-borne encephalitis virus (TBEV). Since the mid-1990s, outbreaks of WN fever and encephalitis have occurred throughout the world and WNV is now endemic in Africa, Asia, Australia, the Middle East, Europe and the Unites States. This review describes the molecular virology, epidemiology, pathogenesis, and highlights recent progress regarding diagnosis and vaccination against WNV infections.
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Affiliation(s)
- Marina De Filette
- Laboratory of Gene Therapy, Faculty of Veterinary Sciences, Ghent University, Heidestraat 19, 9820 Merelbeke, Belgium.
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14
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Rapid molecular detection methods for arboviruses of livestock of importance to northern Europe. J Biomed Biotechnol 2011; 2012:719402. [PMID: 22219660 PMCID: PMC3246798 DOI: 10.1155/2012/719402] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2011] [Revised: 10/14/2011] [Accepted: 10/25/2011] [Indexed: 11/18/2022] Open
Abstract
Arthropod-borne viruses (arboviruses) have been responsible for some of the most explosive epidemics of emerging infectious diseases over the past decade. Their impact on both human and livestock populations has been dramatic. The early detection either through surveillance or diagnosis of virus will be a critical feature in responding and resolving the emergence of such epidemics in the future. Although some of the most important emerging arboviruses are human pathogens, this paper aims to highlight those diseases that primarily affect livestock, although many are zoonotic and some occasionally cause human mortality. This paper also highlights the molecular detection methods specific to each virus and identifies those emerging diseases for which a rapid detection methods are not yet developed.
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15
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Abstract
The genus Flavivirus includes major pathogens such as dengue, yellow fever, Japanese encephalitis, West Nile and tick-borne encephalitis viruses. Molecular amplification assays for the diagnosis of flaviviruses have been developed in the last decades. These assays were formerly based on reverse transcriptase PCR, while in recent years the real-time reverse transcriptase PCR format has taken a predominant role. In this article, we focus on the more recent developments for the molecular diagnosis of flaviviruses, with special attention to those based on new methodologies such as nucleic acid sequence-based amplification or loop-mediated isothermal amplification techniques. These new approaches may provide a good profile of sensitivity and specificity and offer a real chance to implement flavivirus molecular diagnosis in clinical and point-of-care settings.
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Affiliation(s)
| | - Pranav Patel
- Robert Koch-Institut, Center for Biological Security 1, Highly Pathogenic Viruses, Nordufer 20, 13353 Berlin, Germany
| | - Sonja Linke
- Robert Koch-Institut, Center for Biological Security 1, Highly Pathogenic Viruses, Nordufer 20, 13353 Berlin, Germany
| | - Katharina Achazi
- Robert Koch-Institut, Center for Biological Security 1, Highly Pathogenic Viruses, Nordufer 20, 13353 Berlin, Germany
| | - Matthias Niedrig
- Robert Koch-Institut, Center for Biological Security 1, Highly Pathogenic Viruses, Nordufer 20, 13353 Berlin, Germany
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16
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Johnson N, Wakeley PR, Mansfield KL, McCracken F, Haxton B, Phipps LP, Fooks AR. Assessment of a novel real-time pan-flavivirus RT-polymerase chain reaction. Vector Borne Zoonotic Dis 2011; 10:665-71. [PMID: 20854019 DOI: 10.1089/vbz.2009.0210] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Outbreaks of West Nile virus (WNV) have occurred intermittently in regions around the Mediterranean coast, and the virus may have become established in Northern Italy and Romania, with reported intermittent outbreaks in Spain, Hungary, and France. WNV has also spread rapidly throughout the Americas since its introduction into New York in 1999. This capacity to emerge in new geographical locations and to spread rapidly together with the current increase in incidence of other flaviviruses such as tick-borne encephalitis virus, dengue virus, and Usutu virus has prompted us to design a novel pan-flavivirus RT-polymerase chain reaction for the purpose of surveillance for a range of flaviviruses. The assay utilizes degenerate primers targeting the flavivirus NS5 gene (RNA-dependent RNA polymerase) and detects a range of flaviviruses, including WNV. A small panel of WNV bird samples obtained from the United States has been shown to be detected using this assay. The amplicon generated is of sufficient size to provide sequence data to confirm the identity of the virus detected and undertake limited phylogenetic analysis. Testing using this assay has shown its ability to detect a range of tick-borne flaviviruses, particularly louping ill virus that is endemic in areas of the United Kingdom. The assay has been used to survey 160 bird samples and 1000 mosquito samples from the United Kingdom and found no evidence for WNV.
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Affiliation(s)
- Nicholas Johnson
- Rabies and Wildlife Zoonoses Group, Veterinary Laboratories Agency, Addlestone, United Kingdom.
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Monini M, Falcone E, Busani L, Romi R, Ruggeri FM. West nile virus: characteristics of an african virus adapting to the third millennium world. Open Virol J 2010; 4:42-51. [PMID: 20517488 DOI: 10.2174/1874357901004020042] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2009] [Revised: 12/16/2009] [Accepted: 12/17/2009] [Indexed: 12/13/2022] Open
Abstract
The emergence and spread of West Nile Virus (WNV) from North through South America during the last decade, and the recent outbreaks of disease in both humans and horses in Europe suggest that the epidemiology of this infection is evolving. WNV is now considered among the emerging threats for both human and veterinary public health in areas like Europe where it was previously regarded to as an exotic agent. Further knowledge has built up from studies investigating the characteristics of the virus and its genome evolution capacity, the adaptation to new avian host species, the changes in vector competence and biology, and the host-pathogen interactions, including the immune response. Also, the new needs for preparedness to future major outbursts of disease have stimulated research on virus detection and characterization, filling the gaps in both specialized diagnostic technology and the need for field rapid assays. This review will present an overview of WNV virology, remarking the impact of virus diversity and evolution on theoretical and practical aspects involved in both risk definition, detection and control of infection.
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Affiliation(s)
- Marina Monini
- Dipartimento di Sanità Pubblica Veterinaria e Sicurezza Alimentare
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Simultaneous detection of enterovirus 70 and coxsackievirus A24 variant by multiplex real-time RT-PCR using an internal control. J Virol Methods 2009; 159:23-8. [DOI: 10.1016/j.jviromet.2009.02.022] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2008] [Revised: 02/17/2009] [Accepted: 02/17/2009] [Indexed: 11/19/2022]
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19
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Rapid and accurate in vitro assays for detection of West Nile virus in blood and tissues. Transfus Med Rev 2009; 23:146-54. [PMID: 19304115 DOI: 10.1016/j.tmrv.2008.12.008] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
West Nile virus (WNV) is a mosquito-borne single-stranded RNA virus, which has relatively recently emerged as a blood transfusion and organ transplantation transmissible pathogen. Low levels of WNV (viremia) are found in asymptomatic blood transfusion or cell/tissue donors with an infection, which poses a health threat to recipients. Since the introduction of nucleic acid testing (NAT) in 2003, many changes have occurred in the field of WNV detection and diagnosis. This review will focus on the recent progress in the in vitro assays for rapid and accurate detection of WNV in blood and tissues.
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Dos Santos HWG, Poloni TRRS, Souza KP, Muller VDM, Tremeschin F, Nali LC, Fantinatti LR, Amarilla AA, Castro HLA, Nunes MR, Casseb SM, Vasconcelos PF, Badra SJ, Figueiredo LTM, Aquino VH. A simple one-step real-time RT-PCR for diagnosis of dengue virus infection. J Med Virol 2008; 80:1426-33. [PMID: 18551599 DOI: 10.1002/jmv.21203] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Dengue is the most important arbovirus disease in tropical and sub-tropical countries, and can be caused by infection with any of the four-dengue virus (DENV) serotypes. Infection with DENV can lead to a broad clinical spectrum, ranging from sub-clinical infection or an influenza-like disease known as dengue fever (DF) to a severe, sometimes fatal, disease characterized by hemorrhage and plasma leakage that can lead to shock, known as dengue hemorrhagic fever/dengue shock syndrome (DHF/DSS). The diagnosis of dengue is routinely accomplished by serologic assays, such as IgM and IgG ELISAs, as well as HI tests, analyzing serum samples obtained from patients with at least 7 days of symptoms onset. These tests cannot be used for diagnosis during the early symptomatic phase. In addition, antibodies against dengue are broad reactive with other flaviviruses. Therefore, a specific diagnostic method for acute DENV infection is of great interest. In that sense, the real-time RT-PCR has become an important tool that can be used for early and specific detection of dengue virus genome in human serum samples. This study describes a simple, specific, and sensitive real-time RT-PCR for early diagnosis of dengue virus infection.
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Affiliation(s)
- Harryson Wings Godoy Dos Santos
- Departamento de Análises Clínicas, Toxicológicas e Bromatológicas, Faculdade de Ciências Farmacêuticas, USP, Ribeirão Preto, SP, Brazil
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21
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Yang M, Cheng A, Wang M, Xing H. Development and application of a one-step real-time Taqman RT-PCR assay for detection of Duck hepatitis virus type1. J Virol Methods 2008; 153:55-60. [PMID: 18611411 DOI: 10.1016/j.jviromet.2008.06.012] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2008] [Revised: 06/05/2008] [Accepted: 06/09/2008] [Indexed: 12/25/2022]
Abstract
A one-step real-time RT-PCR assay (rRT-PCR) was developed for efficient detection of Duck hepatitis virus type1 (DHV-1). A pair of specific primers was designed against the conserved region in the 3D gene that encodes the RNA dependent RNA polymerase with a single conserved TaqMan probe. The detection limit of this assay was 10 viral genomic copies per reaction and it was highly specific to DHV-1. The rRT-PCR assay was used to determine the distribution and concentration of DHV-1 virulent strain in duck embryos as well as the DHV-1 attenuated vaccine strain in chicken embryos. The results revealed that the copy numbers of DHV-1 reached a peak in duck embryos and chicken embryos at 28-40h, 44-56h postinoculation respectively. The comparative tests for ducklings infected artificially and clinical samples between neutralization test and rRT-PCR showed that the positive results of infected samples were the same, while the rRT-PCR method was more sensitive than neutralization test for detection of clinical samples. The rapid, sensitive and specific rRT-PCR assay will be a powerful tool for detection of suspected cases of DHV-1, distribution pattern of DHV-1 in vivo and molecular epidemiological screening.
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Affiliation(s)
- Miao Yang
- Avian Disease Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Ya'an 625014, China
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Blow JA, Mores CN, Dyer J, Dohm DJ. Viral nucleic acid stabilization by RNA extraction reagent. J Virol Methods 2008; 150:41-4. [PMID: 18387678 DOI: 10.1016/j.jviromet.2008.02.003] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2008] [Revised: 01/29/2008] [Accepted: 02/04/2008] [Indexed: 11/18/2022]
Abstract
In the collection of field materials to test for the presence of arboviruses, samples must be appropriately maintained to detect arboviral nucleic acids. In austere field conditions this is often difficult to achieve because, during routine specimen processing, storage, and shipping viral RNA degradation could result in detection failure. RNA extraction reagents, while used commonly for their intended purpose of stabilizing RNA during the extraction process, have not been assessed fully for their potential to stabilize RNA before extraction. The potential for virus stabilization at varying temperatures and periods of time remains unknown. Accordingly, the ability of buffer AVL (Qiagen, Valencia, CA), an RNA extraction reagent, to stabilize viral suspensions of dengue, Venezuelan equine encephalitis and Rift Valley fever viruses was evaluated. The ability of buffer AVL to stabilize each viral suspension was examined at 32, 20, 4, and -20 degrees C. RNA in samples placed in buffer AVL was stable for at least 48h at 32 degrees C and refrigerating samples prolonged stabilization. Additionally, placing the sample/buffer AVL mixture at either 4 or -20 degrees C stabilized samples for at least 35 days. When combined with the ability of buffer AVL to inactivate viral samples, this provides the ability to collect and handle potentially infectious samples in a safe way that also provides sample stabilization.
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Affiliation(s)
- Jamie A Blow
- Virology Division, United States Army Medical Research Institute of Infectious Diseases, 1425 Porter Street, Fort Detrick, MD 21702, USA
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Liu Z, Teng Y, Liu H, Jiang Y, Xie X, Li H, Lv J, Gao L, He J, Shi X, Tian F, Yang J, Xie C. Simultaneous detection of three fish rhabdoviruses using multiplex real-time quantitative RT-PCR assay. J Virol Methods 2008; 149:103-9. [DOI: 10.1016/j.jviromet.2007.12.017] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2007] [Revised: 12/01/2007] [Accepted: 12/20/2007] [Indexed: 11/25/2022]
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