1
|
Sinha K, Sharma P, Som Chaudhury S, Das Mukhopadhyay C, Ruidas B. Species detection using probe technology. FOOD TOXICOLOGY AND FORENSICS 2021:313-346. [DOI: 10.1016/b978-0-12-822360-4.00012-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/19/2023]
|
2
|
Rasmussen TB, Boniotti MB, Papetti A, Grasland B, Frossard JP, Dastjerdi A, Hulst M, Hanke D, Pohlmann A, Blome S, van der Poel WHM, Steinbach F, Blanchard Y, Lavazza A, Bøtner A, Belsham GJ. Full-length genome sequences of porcine epidemic diarrhoea virus strain CV777; Use of NGS to analyse genomic and sub-genomic RNAs. PLoS One 2018; 13:e0193682. [PMID: 29494671 PMCID: PMC5832266 DOI: 10.1371/journal.pone.0193682] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2018] [Accepted: 02/15/2018] [Indexed: 11/30/2022] Open
Abstract
Porcine epidemic diarrhoea virus, strain CV777, was initially characterized in 1978 as the causative agent of a disease first identified in the UK in 1971. This coronavirus has been widely distributed among laboratories and has been passaged both within pigs and in cell culture. To determine the variability between different stocks of the PEDV strain CV777, sequencing of the full-length genome (ca. 28kb) has been performed in 6 different laboratories, using different protocols. Not surprisingly, each of the different full genome sequences were distinct from each other and from the reference sequence (Accession number AF353511) but they are >99% identical. Unique and shared differences between sequences were identified. The coding region for the surface-exposed spike protein showed the highest proportion of variability including both point mutations and small deletions. The predicted expression of the ORF3 gene product was more dramatically affected in three different variants of this virus through either loss of the initiation codon or gain of a premature termination codon. The genome of one isolate had a substantially rearranged 5´-terminal sequence. This rearrangement was validated through the analysis of sub-genomic mRNAs from infected cells. It is clearly important to know the features of the specific sample of CV777 being used for experimental studies.
Collapse
Affiliation(s)
- Thomas Bruun Rasmussen
- DTU National Veterinary Institute, Technical University of Denmark, Lindholm, Kalvehave, Denmark
| | - Maria Beatrice Boniotti
- IZSLER, Istituto Zooprofilattico Sperimentale della Lombardia e dell’Emilia Romagna “Bruno Ubertini”, Brescia, Italy
| | - Alice Papetti
- IZSLER, Istituto Zooprofilattico Sperimentale della Lombardia e dell’Emilia Romagna “Bruno Ubertini”, Brescia, Italy
| | - Béatrice Grasland
- ANSES–Laboratory of Ploufragan-Plouzané –BP 53, Ploufragan, France
- Université Bretagne Loire, Rennes, France
| | - Jean-Pierre Frossard
- Animal and Plant Health Agency, Department of Virology, Weybridge, Addlestone, Surrey, United Kingdom
| | - Akbar Dastjerdi
- Animal and Plant Health Agency, Department of Virology, Weybridge, Addlestone, Surrey, United Kingdom
| | - Marcel Hulst
- Wageningen BioVeterinary Research, Department of Virology, Lelystad, The Netherlands
| | - Dennis Hanke
- Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Greifswald—Insel Riems, Germany
| | - Anne Pohlmann
- Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Greifswald—Insel Riems, Germany
| | - Sandra Blome
- Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Greifswald—Insel Riems, Germany
| | | | - Falko Steinbach
- Animal and Plant Health Agency, Department of Virology, Weybridge, Addlestone, Surrey, United Kingdom
| | - Yannick Blanchard
- ANSES–Laboratory of Ploufragan-Plouzané –BP 53, Ploufragan, France
- Université Bretagne Loire, Rennes, France
| | - Antonio Lavazza
- IZSLER, Istituto Zooprofilattico Sperimentale della Lombardia e dell’Emilia Romagna “Bruno Ubertini”, Brescia, Italy
| | - Anette Bøtner
- DTU National Veterinary Institute, Technical University of Denmark, Lindholm, Kalvehave, Denmark
| | - Graham J. Belsham
- DTU National Veterinary Institute, Technical University of Denmark, Lindholm, Kalvehave, Denmark
| |
Collapse
|
3
|
Goecke NB, Hjulsager CK, Kongsted H, Boye M, Rasmussen S, Granberg F, Fischer TK, Midgley SE, Rasmussen LD, Angen Ø, Nielsen JP, Jorsal SE, Larsen LE. No evidence of enteric viral involvement in the new neonatal porcine diarrhoea syndrome in Danish pigs. BMC Vet Res 2017; 13:315. [PMID: 29115952 PMCID: PMC5678564 DOI: 10.1186/s12917-017-1239-5] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2017] [Accepted: 10/30/2017] [Indexed: 12/20/2022] Open
Abstract
BACKGROUND The aim of this study was to investigate whether the syndrome New Neonatal Porcine Diarrhoea Syndrome (NNPDS) is associated with a viral aetiology. Four well-managed herds experiencing neonatal diarrhoea and suspected to be affected by NNPDS were included in a case-control set up. A total of 989 piglets were clinically examined on a daily basis. Samples from diarrhoeic and non-diarrhoeic piglets at the age of three to seven days were selected for extensive virological examination using specific real time polymerase chain reactions (qPCRs) and general virus detection methods. RESULTS A total of 91.7% of the animals tested positive by reverse transcription qPCR (RT-qPCR) for porcine kobuvirus 1 (PKV-1) while 9% and 3% were found to be positive for rotavirus A and porcine teschovirus (PTV), respectively. The overall prevalence of porcine astrovirus (PAstV) was 75% with 69.8% of the PAstV positive pigs infected with PAstV type 3. No animals tested positive for rotavirus C, coronavirus (TGEV, PEDV and PRCV), sapovirus, enterovirus, parechovirus, saffoldvirus, cosavirus, klassevirus or porcine circovirus type 2 (PCV2). Microarray analyses performed on a total of 18 animals were all negative, as were eight animals examined by Transmission Electron Microscopy (TEM). Using Next Generation de novo sequencing (de novo NGS) on pools of samples from case animals within all herds, PKV-1 was detected in four herds and rotavirus A, rotavirus C and PTV were detected in one herd each. CONCLUSIONS Our detailed analyses of piglets from NNPDS-affected herds demonstrated that viruses did not pose a significant contribution to NNPDS. However, further investigations are needed to investigate if a systemic virus infection plays a role in the pathogenesis of NNPDS.
Collapse
Affiliation(s)
- N B Goecke
- National Veterinary Institute, Technical University of Denmark, Kemitorvet, Lyngby, DK-2800, Denmark.
| | - C K Hjulsager
- National Veterinary Institute, Technical University of Denmark, Kemitorvet, Lyngby, DK-2800, Denmark
| | - H Kongsted
- Pig Research Centre, Danish Agriculture and Food Council, Vinkelvej 13, DK-8620, Kjellerup, Denmark
| | - M Boye
- National Veterinary Institute, Technical University of Denmark, Kemitorvet, Lyngby, DK-2800, Denmark.,Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Gronnegaardsvej 15, DK-1870, Frederiksberg, Denmark
| | - S Rasmussen
- National Veterinary Institute, Technical University of Denmark, Kemitorvet, Lyngby, DK-2800, Denmark
| | - F Granberg
- Department of Biomedical Sciences and Veterinary Public Health (BVF), Swedish University of Agricultural Sciences (SLU), Uppsala, Sweden
| | - T K Fischer
- Statens Serum Institut (SSI), Artillerivej 5, Copenhagen S, DK-2300, Denmark
| | - S E Midgley
- Statens Serum Institut (SSI), Artillerivej 5, Copenhagen S, DK-2300, Denmark
| | - L D Rasmussen
- Statens Serum Institut (SSI), Artillerivej 5, Copenhagen S, DK-2300, Denmark.,National Veterinary Institute, Technical University of Denmark, Lindholm, Kalvehave, DK-4771, Denmark
| | - Ø Angen
- National Veterinary Institute, Technical University of Denmark, Kemitorvet, Lyngby, DK-2800, Denmark.,Statens Serum Institut (SSI), Artillerivej 5, Copenhagen S, DK-2300, Denmark
| | - J P Nielsen
- Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Gronnegaardsvej 15, DK-1870, Frederiksberg, Denmark
| | - S E Jorsal
- National Veterinary Institute, Technical University of Denmark, Kemitorvet, Lyngby, DK-2800, Denmark
| | - L E Larsen
- National Veterinary Institute, Technical University of Denmark, Kemitorvet, Lyngby, DK-2800, Denmark
| |
Collapse
|
4
|
Giles T, Yon L, de Bree F, Bossers A, Hannant D, Barrow P, Abu-Median AB. Development of a DNA-based microarray for the detection of zoonotic pathogens in rodent species. Mol Cell Probes 2015; 29:427-437. [PMID: 26188129 PMCID: PMC7127396 DOI: 10.1016/j.mcp.2015.07.005] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2015] [Revised: 07/14/2015] [Accepted: 07/14/2015] [Indexed: 11/30/2022]
Abstract
The demand for diagnostic tools that allow simultaneous screening of samples for multiple pathogens is increasing because they overcome the limitations of other methods, which can only screen for a single or a few pathogens at a time. Microarrays offer the advantages of being capable to test a large number of samples simultaneously, screening for multiple pathogen types per sample and having comparable sensitivity to existing methods such as PCR. Array design is often considered the most important process in any microarray experiment and can be the deciding factor in the success of a study. There are currently no microarrays for simultaneous detection of rodent-borne pathogens. The aim of this report is to explicate the design, development and evaluation of a microarray platform for use as a screening tool that combines ease of use and rapid identification of a number of rodent-borne pathogens of zoonotic importance. Nucleic acid was amplified by multiplex biotinylation PCR prior to hybridisation onto microarrays. The array sensitivity was comparable to standard PCR, though less sensitive than real-time PCR. The array presented here is a prototype microarray identification system for zoonotic pathogens that can infect rodent species. We have developed a microarray to detect zoonotic pathogens in rodent species. The design stage of a microarray experiment is crucial for a successful experiment. We examined the difference between amplification methods prior to hybridisation.
Collapse
Affiliation(s)
- Timothy Giles
- University of Nottingham, Nottingham, United Kingdom.
| | - Lisa Yon
- University of Nottingham, Nottingham, United Kingdom.
| | | | | | | | - Paul Barrow
- University of Nottingham, Nottingham, United Kingdom.
| | | |
Collapse
|
5
|
Ribosomal RNA depletion or exclusion has negligible effect on the detection of viruses in a pan viral microarray. J Virol Methods 2014; 207:163-8. [PMID: 25034125 PMCID: PMC7119560 DOI: 10.1016/j.jviromet.2014.07.012] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2014] [Revised: 07/06/2014] [Accepted: 07/08/2014] [Indexed: 01/23/2023]
Abstract
Ribosomal RNA depletion protocols were assessed to improve microarray performance. The outcome was compared with random amplification protocol. Ribosomal RNA depletion had little effect on the microarray performance.
Pan viral DNA microarrays, which can detect known, novel and multiple viral infections, are major laboratory assets contributing to the control of infectious diseases. The large quantity of ribosomal RNA (rRNA) found in tissue samples is thought to be a major factor contributing to the comparatively lower sensitivity of detecting RNA viruses, as a sequence-independent PCR is used to amplify unknown samples for microarray analysis. This study aimed to determine whether depletion or exclusion of rRNA can improve microarray detection and simplify its analysis. Therefore, two different rRNA depletion and exclusion protocols, RiboMinus™ technology and non-rRNA binding hexanucleotides, were applied to the microarray sample processing and the outcome was compared with those of the sequence-independent amplification protocol. This study concludes that the two procedures, described to deplete or exclude rRNA, have negligible effect on the microarrays detection and analysis and might only in combination with further techniques result in a significant enhancement of sensitivity. Currently, existing protocols of random amplification and background adjustment are pertinent for the purpose of sample processing for microarray analysis.
Collapse
|
6
|
Schock A, Gurrala R, Fuller H, Foyle L, Dauber M, Martelli F, Scholes S, Roberts L, Steinbach F, Dastjerdi A. Investigation into an outbreak of encephalomyelitis caused by a neuroinvasive porcine sapelovirus in the United Kingdom. Vet Microbiol 2014; 172:381-9. [PMID: 24984944 DOI: 10.1016/j.vetmic.2014.06.001] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2013] [Revised: 06/01/2014] [Accepted: 06/03/2014] [Indexed: 01/12/2023]
Abstract
An outbreak of neurological disease in grower pigs characterised by ataxia and paraparesis was investigated in this study. The outbreak occurred 3-4 weeks post weaning in grower pigs which displayed signs of spinal cord damage progressing to recumbency. Pathology in the affected spinal cords and to a lesser extent in the brainstem was characterised by pronounced inflammation and neuronophagia in the grey matter. Molecular investigation using a pan-virus microarray identified a virus related to porcine sapelovirus (PSV) in the spinal cord of the two affected pigs examined. Analysis of 802 nucleotides of the virus polymerase gene showed the highest homology with those of viruses in the genus Sapelovirus of Picornaviridae. This PSV, strain G5, shared 91-93%, 67-69% and 63% nucleotide homology with porcine, simian and avian sapeloviruses, respectively. The nucleotide homology to other members of the Picornaviridae ranged from 41% to 62%. Furthermore, viral antigen was detected and co-localised in the spinal cord lesions of affected animals by an antibody known to react with PSV. In conclusion, clinical and laboratory observations of the diseased pigs in this outbreak are consistent with PSV-G5 being the causative agent. To the best of the authors' knowledge, this is the first unequivocal report of polioencephalomyelitis in pigs by a neuroinvasive PSV in the United Kingdom.
Collapse
Affiliation(s)
- Alex Schock
- Mammalian Pathology, Animal Health and Veterinary Laboratories Agency Lasswade, Pentlands Science Park, Bush Loan, Penicuik, Midlothian EH26 0PZ, United Kingdom
| | - Rajesh Gurrala
- Division of Microbial Sciences, Faculty of Health and Medical Sciences, University of Surrey, Guildford, Surrey GU2 7XH, United Kingdom; Virology Department, Animal Health and Veterinary Laboratories Agency, New Haw, Addlestone, Surrey KT15 3NB, United Kingdom
| | - Harriet Fuller
- Marches Veterinary Group, Ryelands Road, Leominster, Herefordshire HR6 8PN, United Kingdom
| | - Leo Foyle
- College of Public Health, Medical and Veterinary Sciences, James Cook University, Solander Road, Townsville 4811, QLD, Australia
| | - Malte Dauber
- Institute of Diagnostic Virology Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Südufer 10, D-17493 Greifswald-Insel Riems, Germany
| | - Francesca Martelli
- Bacteriology Department, Animal Health and Veterinary Laboratories Agency, New Haw, Addlestone, Surrey KT15 3NB, United Kingdom
| | - Sandra Scholes
- Mammalian Pathology, Animal Health and Veterinary Laboratories Agency Lasswade, Pentlands Science Park, Bush Loan, Penicuik, Midlothian EH26 0PZ, United Kingdom
| | - Lisa Roberts
- Faculty of Health and Medical Sciences, University of Surrey, Guildford, Surrey GU2 7XH, United Kingdom
| | - Falko Steinbach
- Virology Department, Animal Health and Veterinary Laboratories Agency, New Haw, Addlestone, Surrey KT15 3NB, United Kingdom
| | - Akbar Dastjerdi
- Virology Department, Animal Health and Veterinary Laboratories Agency, New Haw, Addlestone, Surrey KT15 3NB, United Kingdom.
| |
Collapse
|
7
|
Polar Bear Encephalitis: Establishment of a Comprehensive Next-generation Pathogen Analysis Pipeline for Captive and Free-living Wildlife. J Comp Pathol 2014; 150:474-88. [DOI: 10.1016/j.jcpa.2013.12.005] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2013] [Revised: 10/17/2013] [Accepted: 12/10/2013] [Indexed: 11/19/2022]
|
8
|
Molecular diagnostics for the detection of Bokeloh bat lyssavirus in a bat from Bavaria, Germany. Virus Res 2013; 177:201-4. [PMID: 23932899 DOI: 10.1016/j.virusres.2013.07.021] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2013] [Revised: 07/30/2013] [Accepted: 07/30/2013] [Indexed: 11/22/2022]
Abstract
A brain sample of a Natterer's bat tested positive for rabies with classical virological techniques. Molecular techniques confirmed the presence of Bokeloh bat lyssavirus (BBLV) in Germany for the second time. Sequence analysis revealed a close genetic relationship to the initial German BBLV case. Using a TaqMan RT-PCR specific for BBLV viral RNA was detected in various other organs albeit with differences in the relative viral load.
Collapse
|
9
|
Grubaugh ND, Petz LN, Melanson VR, McMenamy SS, Turell MJ, Long LS, Pisarcik SE, Kengluecha A, Jaichapor B, O'Guinn ML, Lee JS. Evaluation of a field-portable DNA microarray platform and nucleic acid amplification strategies for the detection of arboviruses, arthropods, and bloodmeals. Am J Trop Med Hyg 2012; 88:245-53. [PMID: 23249687 DOI: 10.4269/ajtmh.2012.12-0048] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022] Open
Abstract
Highly multiplexed assays, such as microarrays, can benefit arbovirus surveillance by allowing researchers to screen for hundreds of targets at once. We evaluated amplification strategies and the practicality of a portable DNA microarray platform to analyze virus-infected mosquitoes. The prototype microarray design used here targeted the non-structural protein 5, ribosomal RNA, and cytochrome b genes for the detection of flaviviruses, mosquitoes, and bloodmeals, respectively. We identified 13 of 14 flaviviruses from virus inoculated mosquitoes and cultured cells. Additionally, we differentiated between four mosquito genera and eight whole blood samples. The microarray platform was field evaluated in Thailand and successfully identified flaviviruses (Culex flavivirus, dengue-3, and Japanese encephalitis viruses), differentiated between mosquito genera (Aedes, Armigeres, Culex, and Mansonia), and detected mammalian bloodmeals (human and dog). We showed that the microarray platform and amplification strategies described here can be used to discern specific information on a wide variety of viruses and their vectors.
Collapse
Affiliation(s)
- Nathan D Grubaugh
- Virology Division, United States Army Medical Research Institute of Infectious Diseases, Fort Detrick, Frederick, MD 21702, USA.
| | | | | | | | | | | | | | | | | | | | | |
Collapse
|
10
|
Mahgoub HA, Bailey M, Kaiser P. An overview of infectious bursal disease. Arch Virol 2012; 157:2047-57. [PMID: 22707044 DOI: 10.1007/s00705-012-1377-9] [Citation(s) in RCA: 110] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2012] [Accepted: 05/08/2012] [Indexed: 11/27/2022]
Abstract
Infectious bursal disease (IBD) is a viral immunosuppressive disease of chickens attacking mainly an important lymphoid organ in birds [the bursa of Fabricius (BF)]. The emergence of new variant strains of the causative agent [infectious bursal disease virus (IBDV)] has made it more urgent to develop new vaccination strategies against IBD. One of these strategies is the use of recombinant vaccines (DNA and viral-vectored vaccines). Several studies have investigated the host immune response towards IBDV. This review will present a detailed background on the disease and its causative agent, accompanied by a summary of the most recent findings regarding the host immune response to IBDV infection and the use of recombinant vaccines against IBD.
Collapse
|
11
|
Barlow AM, Schock A, Bradshaw J, Mullineaux E, Dastjerdi A, Everest DJ, McGowan S, Steinbach F, Cowen S. Parvovirus enteritis in Eurasian badgers (Meles meles
). Vet Rec 2012; 170:416. [DOI: 10.1136/vr.100680] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
Affiliation(s)
| | | | | | | | - A. Dastjerdi
- Virology Department; AHVLA - Weybridge; New Haw Addlestone Surrey KT15 3NB UK
| | - D. J. Everest
- Specialist Scientific Services Department; AHVLA - Weybridge; Addlestone KT15 3NB UK
| | - S. McGowan
- Virology Department; AHVLA - Weybridge; New Haw Addlestone Surrey KT15 3NB UK
| | - F. Steinbach
- Virology Department; AHVLA - Weybridge; New Haw Addlestone Surrey KT15 3NB UK
| | | |
Collapse
|
12
|
Differentiation of the seven major lyssavirus species by oligonucleotide microarray. J Clin Microbiol 2011; 50:619-25. [PMID: 22189108 DOI: 10.1128/jcm.00848-11] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
An oligonucleotide microarray, LyssaChip, has been developed and verified as a highly specific diagnostic tool for differentiation of the 7 major lyssavirus species. As with conventional typing microarray methods, the LyssaChip relies on sequence differences in the 371-nucleotide region coding for the nucleoprotein. This region was amplified using nested reverse transcription-PCR primers that bind to the 7 major lyssaviruses. The LyssaChip includes 57 pairs of species typing and corresponding control oligonucleotide probes (oligoprobes) immobilized on glass slides, and it can analyze 12 samples on a single slide within 8 h. Analysis of 111 clinical brain specimens (65 from animals with suspected rabies submitted to the laboratory and 46 of butchered dog brain tissues collected from restaurants) showed that the chip method was 100% sensitive and highly consistent with the "gold standard," a fluorescent antibody test (FAT). The chip method could detect rabies virus in highly decayed brain tissues, whereas the FAT did not, and therefore the chip test may be more applicable to highly decayed brain tissues than the FAT. LyssaChip may provide a convenient and inexpensive alternative for diagnosis and differentiation of rabies and rabies-related diseases.
Collapse
|
13
|
Comparative detection of rabies RNA by NASBA, real-time PCR and conventional PCR. J Virol Methods 2011; 175:278-82. [PMID: 21600930 DOI: 10.1016/j.jviromet.2011.05.007] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2010] [Revised: 04/20/2011] [Accepted: 05/04/2011] [Indexed: 11/20/2022]
Abstract
Five methods for the RNA detection of rabies virus were directly compared in this study. These included conventional nucleic acid sequence-based amplification with electrochemiluminescence (NASBA-ECL) assay, reverse transcription (RT)-heminested (hn) polymerase chain reaction (PCR) and TaqMan real-time RT-PCR using protocols as described previously. The first two methods have been routinely utilised for ante-mortem diagnosis of human rabies in Thailand and other rabies-endemic Asian and African countries. In addition, two real-time NASBA assays based on the use of a NucliSens EasyQ analyser (NASBA-Beacon-EQ) and LightCycler real-time PCR machine (NASBA-Beacon-LC) were studied in parallel. All methods target the N gene, whereas the L gene is used for RT-hnPCR. Using serial dilutions of purified RNA from rabies-infected dog brain tissue to assess sensitivity, all five methods had comparable degrees of sensitivities of detection. However, both real-time NASBA assays had slightly lower sensitivities by 10-fold than the other three assays. This finding was also true (except for TaqMan real-time RT-PCR due to a mismatch between the target and probe sequences) when laboratory-adapted (challenge virus standard-11) virus was used in the assays. Testing on previously NASBA-ECL positive clinical samples from 10 rabies patients (saliva [6] and brain [4]) and 10 rabies-infected dog brain tissues, similar results were obtained among the five methods; real-time NASBA assays yielded false-negative results on 2 saliva samples. None of the assays showed positive results on cerebrospinal fluid specimens of 10 patients without rabies encephalitis. Due to the unavailability of the NASBA-ECL assay, the results show that TaqMan real-time RT-PCR and RT-hnPCR can be useful for ante- and post-mortem diagnosis of rabies.
Collapse
|
14
|
De Benedictis P, De Battisti C, Dacheux L, Marciano S, Ormelli S, Salomoni A, Caenazzo ST, Lepelletier A, Bourhy H, Capua I, Cattoli G. Lyssavirus detection and typing using pyrosequencing. J Clin Microbiol 2011; 49:1932-8. [PMID: 21389152 PMCID: PMC3122702 DOI: 10.1128/jcm.02015-10] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2010] [Accepted: 02/24/2011] [Indexed: 10/18/2022] Open
Abstract
Rabies is a fatal zoonosis caused by a nonsegmented negative-strand RNA virus, namely, rabies virus (RABV). Apart from RABV, at least 10 additional species are known as rabies-related lyssaviruses (RRVs), and some of them are responsible for occasional spillovers into humans. More lyssaviruses have also been detected recently in different bat ecosystems, thanks to the application of molecular diagnostic methods. Due to the variety of the members of the genus Lyssavirus, there is the necessity to develop a reliable molecular assay for rabies diagnosis able to detect and differentiate among the existing rabies and rabies-related viruses. In the present study, a pyrosequencing protocol targeting the 3' terminus of the nucleoprotein (N) gene was applied for the rapid characterization of lyssaviruses. Correct identification of species was achieved for each sample tested. Results from the pyrosequencing assay were also confirmed by those obtained using the Sanger sequencing method. A pan-lyssavirus one-step reverse transcription (RT)-PCR was developed within the framework of the pyrosequencing procedure. The sensitivity (Se) of the one-step RT-PCR assay was determined by using in vitro-transcribed RNA and serial dilutions of titrated viruses. The assay demonstrated high analytical and relative specificity (Sp) (98.94%) and sensitivity (99.71%). To date, this is the first case in which pyrosequencing has been applied for lyssavirus identification using a cheaper diagnostic approach than the one for all the other protocols for rapid typing that we are acquainted with. Results from this study indicate that this procedure is suitable for lyssavirus detection in samples of both human and animal origin.
Collapse
Affiliation(s)
- Paola De Benedictis
- OIE and National Collaborating Centre for Diseases at the Animal-Human Interface, Istituto Zooprofilattico Sperimentale delle Venezie, Viale dell'Università 10, 35020 Legnaro, Padova, Italy.
| | | | | | | | | | | | | | | | | | | | | |
Collapse
|
15
|
Dacheux L, Wacharapluesadee S, Hemachudha T, Meslin FX, Buchy P, Reynes JM, Bourhy H. More accurate insight into the incidence of human rabies in developing countries through validated laboratory techniques. PLoS Negl Trop Dis 2010; 4:e765. [PMID: 21152054 PMCID: PMC2994914 DOI: 10.1371/journal.pntd.0000765] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022] Open
Affiliation(s)
- Laurent Dacheux
- Institut Pasteur, Dynamics and Host Adaptation Unit, National Reference Centre for Rabies, WHO Collaborative Centre for Reference and Research on Rabies, Paris, France.
| | | | | | | | | | | | | |
Collapse
|
16
|
Wacharapluesadee S, Hemachudha T. Ante- and post-mortem diagnosis of rabies using nucleic acid-amplification tests. Expert Rev Mol Diagn 2010; 10:207-18. [PMID: 20214539 DOI: 10.1586/erm.09.85] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Sensitivity, specificity and short turn-around time nucleic acid-amplification tests (NATs) have been steadily improving. NATs have been employed in the diagnosis of rabies to distinct different strains, as well as to identify new lyssaviruses. NATs have advantages over traditional methods, such as the direct fluorescence antibody test. They can be applied to fluid samples and brain tissue that is substantially decomposed. NATs can be used as an alternative method for confirmation or exclusion of the diagnosis in a suspected rabies patient. Real-time PCR methods are more favored than conventional reverse-transcription PCR methods by several laboratories. Second-round PCR, either nested or heminested, has been used for ante-mortem diagnosis to detect low levels of RNA. This review the details obstacles in making a diagnosis, how to properly utilize NATs (sample preparation, nucleic amplification techniques, amplification targets and primer design); and interprets the results obtained in recent studies.
Collapse
Affiliation(s)
- Supaporn Wacharapluesadee
- WHO Collaborating Centre for Research and Training on Viral Zoonoses, Faculty of Medicine, Chulalongkorn University and King Chulalongkorn Memorial Hospital, Thai Red Cross Society, Bangkok, Thailand, 10330.
| | | |
Collapse
|
17
|
Willoughby K, Gilray J, Maley M, Dastjerdi A, Steinbach F, Banks M, Scholes S, Howie F, Holliman A, Baird P, McKillen J. Lack of evidence for circovirus involvement in bovine neonatal pancytopenia. Vet Rec 2010; 166:436-7. [PMID: 20364016 DOI: 10.1136/vr.c1685] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
|
18
|
Leski TA, Malanoski AP, Stenger DA, Lin B. Target amplification for broad spectrum microbial diagnostics and detection. Future Microbiol 2010; 5:191-203. [DOI: 10.2217/fmb.09.126] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Microarrays are massively parallel detection platforms that were first used extensively for gene expression studies, but have also been successfully applied to microbial detection in a number of diverse fields requiring broad-range microbial identification. This technology has enabled researchers to gain an insight into the microbial diversity of environmental samples, facilitated discovery of a number of new pathogens and enabled studies of multipathogen infections. In contrast to gene expression studies, the concentrations of targets in analyzed samples for microbial detection are usually much lower, and require the use of nucleic acid amplification techniques. The rapid advancement of manufacturing technologies has increased the content of the microarrays; thus, the required amplification is a challenging problem. The constant parallel improvements in both microarray and sample amplification techniques in the near future may lead to a radical progression in medical diagnostics and systems for efficient detection of microorganisms in the environment.
Collapse
Affiliation(s)
- Tomasz A Leski
- Center for Bio/Molecular Science & Engineering, Code 6900, Naval Research Laboratory, Washington, DC, USA and Nova Research Inc., 1900 Elkin Street, Suite 230, Alexandria, VA, USA
| | - Anthony P Malanoski
- Center for Bio/Molecular Science & Engineering, Code 6900, Naval Research Laboratory, Washington, DC, USA
| | - David A Stenger
- Center for Bio/Molecular Science & Engineering, Code 6900, Naval Research Laboratory, Washington, DC, USA
| | - Baochuan Lin
- Center for Bio/Molecular Science & Engineering, Code 6900, Naval Research Laboratory, Washington, DC, USA
| |
Collapse
|