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Hassan KE, Ahrens AK, Ali A, El-Kady MF, Hafez HM, Mettenleiter TC, Beer M, Harder T. Improved Subtyping of Avian Influenza Viruses Using an RT-qPCR-Based Low Density Array: 'Riems Influenza a Typing Array', Version 2 (RITA-2). Viruses 2022; 14:415. [PMID: 35216008 PMCID: PMC8879595 DOI: 10.3390/v14020415] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2021] [Revised: 02/08/2022] [Accepted: 02/15/2022] [Indexed: 12/10/2022] Open
Abstract
Avian influenza virus (AIV) variants emerge frequently, which challenges rapid diagnosis. Appropriate diagnosis reaching the sub- and pathotype level is the basis of combatting notifiable AIV infections. Real-time RT-PCR (RT-qPCR) has become a standard diagnostic tool. Here, a total of 24 arrayed RT-qPCRs is introduced for full subtyping of 16 hemagglutinin and nine neuraminidase subtypes of AIV. This array, designated Riems Influenza A Typing Array version 2 (RITA-2), represents an updated and economized version of the RITA-1 array previously published by Hoffmann et al. RITA-2 provides improved integration of assays (24 instead of 32 parallel reactions) and reduced assay volume (12.5 µL). The technique also adds RT-qPCRs to detect Newcastle Disease (NDV) and Infectious Bronchitis viruses (IBV). In addition, it maximizes inclusivity (all sequences within one subtype) and exclusivity (no intersubtypic cross-reactions) as shown in validation runs using a panel of 428 AIV reference isolates, 15 reference samples each of NDV and IBV, and 122 clinical samples. The open format of RITA-2 is particularly tailored to subtyping influenza A virus of avian hosts and Eurasian geographic origin. Decoupling and re-arranging selected RT-qPCRs to detect specific AIV variants causing epizootic outbreaks with a temporal and/or geographic restriction is possible.
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Affiliation(s)
- Kareem E. Hassan
- Institute of Diagnostic Virology, Friedrich-Loeffler-Institut, 17493 Greifswald-Insel Riems, Germany; (K.E.H.); (A.K.A.); (M.B.)
- Department of Poultry Diseases, Faculty of Veterinary Medicine, Beni-Suef University, Beni-Suef 62511, Egypt; (A.A.); (M.F.E.-K.)
| | - Ann Kathrin Ahrens
- Institute of Diagnostic Virology, Friedrich-Loeffler-Institut, 17493 Greifswald-Insel Riems, Germany; (K.E.H.); (A.K.A.); (M.B.)
| | - Ahmed Ali
- Department of Poultry Diseases, Faculty of Veterinary Medicine, Beni-Suef University, Beni-Suef 62511, Egypt; (A.A.); (M.F.E.-K.)
| | - Magdy F. El-Kady
- Department of Poultry Diseases, Faculty of Veterinary Medicine, Beni-Suef University, Beni-Suef 62511, Egypt; (A.A.); (M.F.E.-K.)
| | - Hafez M. Hafez
- Institute of Poultry Diseases, Free University Berlin, 14163 Berlin, Germany;
| | | | - Martin Beer
- Institute of Diagnostic Virology, Friedrich-Loeffler-Institut, 17493 Greifswald-Insel Riems, Germany; (K.E.H.); (A.K.A.); (M.B.)
| | - Timm Harder
- Institute of Diagnostic Virology, Friedrich-Loeffler-Institut, 17493 Greifswald-Insel Riems, Germany; (K.E.H.); (A.K.A.); (M.B.)
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Ssematimba A, Malladi S, Bonney PJ, Flores-Figueroa C, Muñoz-Aguayo J, Halvorson DA, Cardona CJ. Quantifying the effect of swab pool size on the detection of influenza A viruses in broiler chickens and its implications for surveillance. BMC Vet Res 2018; 14:265. [PMID: 30176867 PMCID: PMC6122460 DOI: 10.1186/s12917-018-1602-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2017] [Accepted: 08/28/2018] [Indexed: 11/15/2022] Open
Abstract
BACKGROUND Timely diagnosis of influenza A virus infections is critical for outbreak control. Due to their rapidity and other logistical advantages, lateral flow immunoassays can support influenza A virus surveillance programs and here, their field performance was proactively assessed. The performance of real-time polymerase chain reaction and two lateral flow immunoassay kits (FluDETECT and VetScan) in detecting low pathogenicity influenza A virus in oropharyngeal swab samples from experimentally inoculated broiler chickens was evaluated and at a flock-level, different testing scenarios were analyzed. RESULTS For real-time polymerase chain reaction positive individual-swabs, FluDETECT respectively detected 37% and 58% for the H5 and H7 LPAIV compared to 28% and 42% for VetScan. The mean virus titer in H7 samples was higher than for H5 samples. For real-time polymerase chain reaction positive pooled swabs (containing one positive), detections by FluDETECT were significantly higher in the combined 5- and 6-swab samples compared to 11-swab samples. FluDETECT detected 58%, 55.1% and 44.9% for the H7 subtype and 28.3%, 34.0% and 24.6% for the H5 in pools of 5, 6 and 11 respectively. In our testing scenario analysis, at low flock-level LPAIV infection prevalence, testing pools of 11 detected slightly more infections while at higher prevalence, testing pools of 5 or 6 performed better. For highly pathogenic avian influenza virus, testing pools of 11 (versus 5 or 6) detected up to 5% more infections under the assumption of similar sensitivity across pools and detected less by 3% when its sensitivity was assumed to be lower. CONCLUSIONS Much as pooling a bigger number of swab samples increases the chances of having a positive swab included in the sample to be tested, this study's outcomes indicate that this practice may actually reduce the chances of detecting the virus since it may result into lowering the virus titer of the pooled sample. Further analysis on whether having more than one positive swab in a pooled sample would result in increased sensitivity for low pathogenicity avian influenza virus is needed.
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Affiliation(s)
- Amos Ssematimba
- Secure Food Systems Team, University of Minnesota, Veterinary and Biomedical Sciences, 301C Veterinary Science Building, 1971 Commonwealth Avenue, Saint Paul, MN 55108 USA
- Department of Mathematics, Faculty of Science, Gulu University, P.O. Box 166, Gulu, Uganda
| | - Sasidhar Malladi
- Secure Food Systems Team, University of Minnesota, Veterinary and Biomedical Sciences, 301C Veterinary Science Building, 1971 Commonwealth Avenue, Saint Paul, MN 55108 USA
| | - Peter J. Bonney
- Secure Food Systems Team, University of Minnesota, Veterinary and Biomedical Sciences, 301C Veterinary Science Building, 1971 Commonwealth Avenue, Saint Paul, MN 55108 USA
| | | | | | - David A. Halvorson
- Secure Food Systems Team, University of Minnesota, Veterinary and Biomedical Sciences, 301C Veterinary Science Building, 1971 Commonwealth Avenue, Saint Paul, MN 55108 USA
| | - Carol J. Cardona
- Secure Food Systems Team, University of Minnesota, Veterinary and Biomedical Sciences, 301C Veterinary Science Building, 1971 Commonwealth Avenue, Saint Paul, MN 55108 USA
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El Zowalaty ME, Bustin SA, Husseiny MI, Ashour HM. Avian influenza: virology, diagnosis and surveillance. Future Microbiol 2014; 8:1209-27. [PMID: 24020746 DOI: 10.2217/fmb.13.81] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Avian influenza virus (AIV) is the causative agent of a zoonotic disease that affects populations worldwide with often devastating economic and health consequences. Most AIV subtypes cause little or no disease in waterfowl, but outbreaks in poultry can be associated with high mortality. Although transmission of AIV to humans occurs rarely and is strain dependent, the virus has the ability to mutate or reassort into a form that triggers a life-threatening infection. The constant emergence of new influenza strains makes it particularly challenging to predict the behavior, spread, virulence or potential for human-to-human transmission. Because it is difficult to anticipate which viral strain or what location will initiate the next pandemic, it is difficult to prepare for that event. However, rigorous implementation of biosecurity, vaccination and education programs can minimize the threat of AIV. Global surveillance programs help record and identify newly evolving and potentially pandemic strains harbored by the reservoir host.
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Affiliation(s)
- Mohamed E El Zowalaty
- Postgraduate Medical Institute, Faculty of Health, Social Care & Education, Anglia Ruskin University, Chelmsford, Essex, UK
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4
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Nava GM, Merino R, Jarquin R, Ledesma N, Sanchez-Betancourt I, Lucio E, Martinez E, Escorcia M. A rapid test for avian influenza detects swine influenza virus. Vet Rec 2013; 173:424. [PMID: 24114732 DOI: 10.1136/vr.101527] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
Affiliation(s)
- G M Nava
- Facultad de Quimica, Universidad Autonoma de Queretaro, Queretaro, Mexico
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Grabowska I, Malecka K, Stachyra A, Góra-Sochacka A, Sirko A, Zagórski-Ostoja W, Radecka H, Radecki J. Single Electrode Genosensor for Simultaneous Determination of Sequences Encoding Hemagglutinin and Neuraminidase of Avian Influenza Virus Type H5N1. Anal Chem 2013; 85:10167-73. [DOI: 10.1021/ac401547h] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Iwona Grabowska
- Institute
of Animal Reproduction and Food Research, Polish Academy of Sciences, Tuwima 10, Olsztyn, Warmian-Masurian, 10-747 Poland
| | - Kamila Malecka
- Institute
of Animal Reproduction and Food Research, Polish Academy of Sciences, Tuwima 10, Olsztyn, Warmian-Masurian, 10-747 Poland
| | - Anna Stachyra
- Institute
of Biochemistry and Biophysics, Polish Academy of Sciences, Pawińskiego
5A, Warsaw, Masovian, 02-106 Poland
| | - Anna Góra-Sochacka
- Institute
of Biochemistry and Biophysics, Polish Academy of Sciences, Pawińskiego
5A, Warsaw, Masovian, 02-106 Poland
| | - Agnieszka Sirko
- Institute
of Biochemistry and Biophysics, Polish Academy of Sciences, Pawińskiego
5A, Warsaw, Masovian, 02-106 Poland
| | - Włodzimierz Zagórski-Ostoja
- Institute
of Biochemistry and Biophysics, Polish Academy of Sciences, Pawińskiego
5A, Warsaw, Masovian, 02-106 Poland
| | - Hanna Radecka
- Institute
of Animal Reproduction and Food Research, Polish Academy of Sciences, Tuwima 10, Olsztyn, Warmian-Masurian, 10-747 Poland
| | - Jerzy Radecki
- Institute
of Animal Reproduction and Food Research, Polish Academy of Sciences, Tuwima 10, Olsztyn, Warmian-Masurian, 10-747 Poland
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Malecka K, Grabowska I, Radecki J, Stachyra A, Góra-Sochacka A, Sirko A, Radecka H. Electrochemical Detection of Avian Influenza Virus Genotype Using Amino-ssDNA Probe Modified Gold Electrodes. ELECTROANAL 2013. [DOI: 10.1002/elan.201300113] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
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7
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Zhang RQ, Liu SL, Zhao W, Zhang WP, Yu X, Li Y, Li AJ, Pang DW, Zhang ZL. A Simple Point-of-Care Microfluidic Immunomagnetic Fluorescence Assay for Pathogens. Anal Chem 2013; 85:2645-51. [DOI: 10.1021/ac302903p] [Citation(s) in RCA: 68] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Affiliation(s)
- Rui-Qiao Zhang
- Key Laboratory of Analytical
Chemistry for Biology and Medicine (Ministry of Education), College
of Chemistry and Molecular Sciences, State Key Laboratory of Virology, Wuhan University, Wuhan, 430072, People’s Republic
of China
- Wuhan Institute
of Biotechnology,
Wuhan, 430075, People’s Republic of China
| | - Shu-Lin Liu
- Key Laboratory of Analytical
Chemistry for Biology and Medicine (Ministry of Education), College
of Chemistry and Molecular Sciences, State Key Laboratory of Virology, Wuhan University, Wuhan, 430072, People’s Republic
of China
| | - Wei Zhao
- Key Laboratory of Analytical
Chemistry for Biology and Medicine (Ministry of Education), College
of Chemistry and Molecular Sciences, State Key Laboratory of Virology, Wuhan University, Wuhan, 430072, People’s Republic
of China
| | - Wan-Po Zhang
- College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, 430070, People’s
Republic of China
| | - Xu Yu
- Key Laboratory of Analytical
Chemistry for Biology and Medicine (Ministry of Education), College
of Chemistry and Molecular Sciences, State Key Laboratory of Virology, Wuhan University, Wuhan, 430072, People’s Republic
of China
| | - Yong Li
- Key Laboratory of Analytical
Chemistry for Biology and Medicine (Ministry of Education), College
of Chemistry and Molecular Sciences, State Key Laboratory of Virology, Wuhan University, Wuhan, 430072, People’s Republic
of China
| | - An-Jun Li
- Key Laboratory of Analytical
Chemistry for Biology and Medicine (Ministry of Education), College
of Chemistry and Molecular Sciences, State Key Laboratory of Virology, Wuhan University, Wuhan, 430072, People’s Republic
of China
| | - Dai-Wen Pang
- Key Laboratory of Analytical
Chemistry for Biology and Medicine (Ministry of Education), College
of Chemistry and Molecular Sciences, State Key Laboratory of Virology, Wuhan University, Wuhan, 430072, People’s Republic
of China
- Wuhan Institute
of Biotechnology,
Wuhan, 430075, People’s Republic of China
| | - Zhi-Ling Zhang
- Key Laboratory of Analytical
Chemistry for Biology and Medicine (Ministry of Education), College
of Chemistry and Molecular Sciences, State Key Laboratory of Virology, Wuhan University, Wuhan, 430072, People’s Republic
of China
- Wuhan Institute
of Biotechnology,
Wuhan, 430075, People’s Republic of China
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O’Connor TP, Lawrence J, Andersen P, Leathers V, Workman E. Immunoassay Applications in Veterinary Diagnostics. THE IMMUNOASSAY HANDBOOK 2013. [PMCID: PMC7151925 DOI: 10.1016/b978-0-08-097037-0.00053-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
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Slomka MJ, To TL, Tong HH, Coward VJ, Mawhinney IC, Banks J, Brown IH. Evaluation of lateral flow devices for identification of infected poultry by testing swab and feather specimens during H5N1 highly pathogenic avian influenza outbreaks in Vietnam. Influenza Other Respir Viruses 2011; 6:318-27. [PMID: 22151025 PMCID: PMC5779812 DOI: 10.1111/j.1750-2659.2011.00317.x] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
Abstract
BACKGROUND Evaluation of two commercial lateral flow devices (LFDs) for avian influenza (AI) detection in H5N1 highly pathogenic AI infected poultry in Vietnam. OBJECTIVES Determine sensitivity and specificity of the LFDs relative to a validated highly sensitive H5 RRT PCR. METHODS Swabs (cloacal and tracheal) and feathers were collected from 46 chickens and 48 ducks (282 clinical specimens) and tested by both LFDs and H5 RRT PCR. A subset of 59 chicken and 34 duck specimens was also tested by virus isolation (VI), the 'gold standard'. RESULTS Twenty-six chickens and 15 ducks were shown to be infected by at least one RRT PCR positive clinical specimen per bird. Bird-level sensitivity for the Anigen LFD was 84·6% for chickens and 53·3% for ducks, and for the Quickvue LFD 65·4% for chickens and 33·3% for ducks. Comparison of the three clinical specimens revealed that chicken feathers were the most sensitive with 84% and 56% sensitivities for Anigen and Quickvue respectively. All 21 RRT PCR positive swabs from ducks were negative by both LFDs. However, duck feather testing gave sensitivities of 53·3% and 33·3% for Anigen and Quickvue respectively. Specificity was 100% for both LFDs in all investigations. CONCLUSIONS Although LFDs were less sensitive than AI RRT PCR and VI, high titre viral shedding in H5N1 highly pathogenic avian influenza (HPAI) infected and diseased chickens is sufficient for a proportion of birds to be identified as AI infected by LFDs. Feathers were the optimal specimen for LFD testing in such diseased HPAI scenarios, particularly for ducks where swab testing by LFDs failed to identify any infected birds. However, specimens should be forwarded to the laboratory for confirmation by more sensitive diagnostic techniques.
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Affiliation(s)
- Marek J Slomka
- Avian Virology Workgroup, OIE, FAO and EU Reference Laboratory for Avian Influenza, Animal Health and Veterinary Laboratories Agency (AHVLA Weybridge), Addlestone, Surrey, UK.
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10
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Liu X, Cheng Z, Fan H, Ai S, Han R. Electrochemical detection of avian influenza virus H5N1 gene sequence using a DNA aptamer immobilized onto a hybrid nanomaterial-modified electrode. Electrochim Acta 2011. [DOI: 10.1016/j.electacta.2011.05.055] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
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11
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Quality standards are needed for reporting of test accuracy studies for animal diseases. Prev Vet Med 2010; 97:136-43. [DOI: 10.1016/j.prevetmed.2010.09.009] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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12
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Soliman M, Selim A, Coward VJ, Hassan MK, Aly MM, Banks J, Slomka MJ. Evaluation of two commercial lateral flow devices (LFDs) used for flockside testing of H5N1 highly-pathogenic avian influenza infections in backyard gallinaceous poultry in Egypt. J Mol Genet Med 2010; 4:247-51. [PMID: 21139668 PMCID: PMC2981883 DOI: 10.4172/1747-0862.1000043] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2010] [Revised: 09/29/2010] [Accepted: 09/30/2010] [Indexed: 11/09/2022] Open
Abstract
Quickvue and Anigen lateral flow devices (LFDs) were evaluated for detection of H5N1 highly pathogenic avian influenza (HPAI) infections in Egyptian poultry. Sixty five chickens and two turkeys were sampled in eight flocks where H5N1 HPAI infection was suspected. Swabs (tracheal and cloacal) and feathers were collected from each bird for flockside testing by the two LFDs. The same clinical specimens were transported for laboratory testing by M gene RRT PCR where a positive result by this “gold standard” test for one or both swabs from a given bird indicated infection at the bird level, showing 57 birds (including 15 carcassess) to be truly AI infected. Among these 57, similar bird-level LFD testing of swabs showed 43 and 44 to be AI infected by Quickvue and Anigen LFDs, respectively. Nine birds were AI negative by M gene RRT PCR and both LFDs, and one was M gene RRT PCR negative but positive by both LFDs, suggesting one false positive LFD result. Sensitivities of the LFDs relative to M gene RRT PCR were 77.2% for Anigen and 75.4% for Quickvue tests, with 90.0% specificity for both. By including feathers with swabs for LFD testing, the number of LFD positives among 57 infected birds increased by four to 48 by Anigen and 47 by Quickvue, increasing the sensitivity of the LFDs to 84.2% and 82.5% for Anigen and Quickvue, respectively. Although LFD sensitivity cannot compare to the high sensitivity displayed by validated AI RRT PCRs, they may be utilised for flockside testing of birds infected with HPAI at the peak of viral shedding, when birds are displaying advanced clinical signs or sampled as fresh carcasses. Swabs are classic field specimens collected from outbreaks, but inclusion of feathers from birds infected with H5N1 HPAI increased LFD sensitivity. However, the LFD false positive observation emphasises the importance of returning samples for confirmatory laboratory testing.
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Affiliation(s)
- Mohammed Soliman
- National Laboratory for Veterinary Quality Control on Poultry Production, Animal Health Research Institute, Ministry of Agriculture, PO Box 264, Nadi Elseid Street, Dokki, Giza, Egypt
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13
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Marché S, van den Berg T. Evaluation of rapid antigen detection kits for the diagnosis of highly pathogenic avian influenza H5N1 infection. Avian Dis 2010; 54:650-4. [PMID: 20521709 DOI: 10.1637/8779-040109-resnote.1] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
Early detection of highly pathogenic (HP) strains of avian influenza, especially the HP H5N1, is important in terms of controlling and minimizing the spread of the virus. Several rapid antigen detection kits that are able to detect influenza A viruses in less than 1 hr are commercially available, but only a few of them have been evaluated. In this study, four commercially available rapid tests for veterinary usage and two tests for human usage were evaluated and compared. The evaluation of the detection limits of the different tests established with serial dilution of HP H5N1 indicated that most of them have a detection limit of about 10(5) to 10(6) 50% tissue culture infectious dose/ml. None of the tests was able to detect virus in oral and cloacal swabs 24 hr post-experimental infection of specific-pathogen-free chickens with HP H5N1. However, 48 hr postinfection, almost all of the rapid tests were able to detect infected birds (dead or alive). Moreover, organs were also successful samples for detection of H5N1 with the rapid tests. Unexpectedly, the specificity was not very high for some tests. However, in general in this study, the tests for veterinary usage showed better sensitivity. To conclude, these tests offer good indicative value in the event of an outbreak, but as a result of their low sensitivity and some aspecific reactions, test results always need to be confirmed by other methods.
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Affiliation(s)
- Sylvie Marché
- Avian Virology & Immunology Unit, Veterinary and Agrochemical Research Centre, Groeselenberg, 99 B-1180 Brussels, Belgium.
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14
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Development of microsphere-based multiplex branched DNA assay for detection and differentiation of avian influenza virus strains. J Clin Microbiol 2010; 48:2575-7. [PMID: 20484609 DOI: 10.1128/jcm.01979-09] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
We developed and evaluated a multiplex branched DNA assay for the detection and subtyping of avian influenza (AI) virus strains. The assay successfully detected all 94 AI virus strains of 15 different hemagglutinin (HA) subtypes tested while simultaneously differentiating 24 North American H5, 11 Eurasian H5, and 11 H7 strains. Our study demonstrates for the first time that a branched DNA method can detect targets that show a great amount of sequence variation.
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Abstract
Analytical methods accounting for imperfect detection are often used to facilitate reliable inference in population and community ecology. We contend that similar approaches are needed in disease ecology because these complicated systems are inherently difficult to observe without error. For example, wildlife disease studies often designate individuals, populations, or spatial units to states (e.g., susceptible, infected, post-infected), but the uncertainty associated with these state assignments remains largely ignored or unaccounted for. We demonstrate how recent developments incorporating observation error through repeated sampling extend quite naturally to hierarchical spatial models of disease effects, prevalence, and dynamics in natural systems. A highly pathogenic strain of avian influenza virus in migratory waterfowl and a pathogenic fungus recently implicated in the global loss of amphibian biodiversity are used as motivating examples. Both show that relatively simple modifications to study designs can greatly improve our understanding of complex spatio-temporal disease dynamics by rigorously accounting for uncertainty at each level of the hierarchy.
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Choi KM, Lee SJ, Choi JH, Park TJ, Park JW, Shin WH, Kang JK. Facile fabrication of networked patterns and their superior application to realize the virus immobilized networked pattern circuit. Chem Commun (Camb) 2010; 46:8609-11. [DOI: 10.1039/c0cc03323e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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17
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Label-free electrochemical detection of Avian Influenza Virus genotype utilizing multi-walled carbon nanotubes–cobalt phthalocyanine–PAMAM nanocomposite modified glassy carbon electrode. Electrochem commun 2009. [DOI: 10.1016/j.elecom.2009.05.055] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
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18
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Ellis TM, Dyrting KC, Wong CW, Chadwick B, Chan C, Chiang M, Li C, Li P, Smith GJD, Guan Y, Malik Peiris JS. Analysis of H5N1 avian influenza infections from wild bird surveillance in Hong Kong from January 2006 to October 2007. Avian Pathol 2009; 38:107-19. [PMID: 19322709 DOI: 10.1080/03079450902751855] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
Intensive surveillance of dead wild birds for H5N1 avian influenza infection is conducted in Hong Kong. Between January 2006 and October 2007 pooled cloacal and tracheal swabs from 17692 dead wild birds (from 16 different orders including 82 genera) were tested and 33 H5N1 highly pathogenic avian influenza viruses were isolated. No H5N1 infection has occurred in poultry farms since January 2003, or in live poultry markets in Hong Kong since November 2003 until a recent detection of H5N1 virus by surveillance of live poultry markets in June 2008. The gross and histopathology in the various H5N1-infected avian species is described, along with the performance of the virus isolation and polymerase chain reaction (PCR) tests used. This evaluation also included determination of virus titres and detection limits for the H5 haemagglutinin gene (H5)and matrix gene real-time reverse-transcription PCR tests in cloacal and tracheal swabs from 12 wild birds. The viruses isolated belonged to Clades 2.3.2 and 2.3.4, and within Clade 2.3.4 some clustering was evident based on H5 haemagglutinin gene haemagglutinating sequencing. There were no differences in the pathology findings between these subgroupings and the various diagnostic tests gave similar results for these viruses, except for a loss in sensitivity of the H5 real-time reverse-transcription PCR for several viruses in one cluster from birds submitted in February 2007. The use of multiple test methods was important in maintaining the diagnostic sensitivity for detecting avian influenza viruses with high genetic variability.
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Affiliation(s)
- Trevor M Ellis
- Tai Lung Veterinary Laboratory, Agriculture Fisheries and Conservation Department, Lin Tong Mei, Sheung Shui, New Territories, Hong Kong, SAR, China.
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Efficient capture of infectious H5 avian influenza virus utilizing magnetic beads coated with anionic polymer. Biochem Biophys Res Commun 2008; 377:85-8. [DOI: 10.1016/j.bbrc.2008.09.083] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2008] [Accepted: 09/17/2008] [Indexed: 11/16/2022]
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20
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Chen Y, Xu F, Fan X, Luo H, Ge S, Zheng Q, Xia N, Chen H, Guan Y, Zhang J. Evaluation of a rapid test for detection of H5N1 avian influenza virus. J Virol Methods 2008; 154:213-5. [DOI: 10.1016/j.jviromet.2008.08.013] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2008] [Revised: 08/14/2008] [Accepted: 08/20/2008] [Indexed: 11/29/2022]
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Zarkov IS. Use of a commercial immunoassay for rapid detection of influenza A antigen in ducks. Vet Rec 2008; 163:661-2. [DOI: 10.1136/vr.163.22.661] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
Affiliation(s)
- I. S. Zarkov
- Department of Microbiology, Infectious and Parasitic Diseases; Faculty of Veterinary Medicine; Thracian University; 6000 Stara Zagora Bulgaria
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Yamamoto Y, Nakamura K, Okamatsu M, Miyazaki A, Yamada M, Mase M. Detecting avian influenza virus (H5N1) in domestic duck feathers. Emerg Infect Dis 2008. [PMID: 18826847 PMCID: PMC2609858 DOI: 10.3201/1410.080415] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
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Yamamoto Y, Nakamura K, Okamatsu M, Miyazaki A, Yamada M, Mase M. Detecting avian influenza virus (H5N1) in domestic duck feathers. Emerg Infect Dis 2008; 14:1671-2. [PMID: 18826847 DOI: 10.3201/eid1410.080415] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
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Loth L, Prijono WB, Wibawa H, Usman TB. Evaluation of two avian influenza type A rapid antigen tests under Indonesian field conditions. J Vet Diagn Invest 2008; 20:642-4. [PMID: 18776101 DOI: 10.1177/104063870802000519] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
The current study evaluated the test characteristics of 2 commercially available rapid antigen tests for highly pathogenic avian influenza. Diagnostic specimens were collected from free-ranging village chickens in Indonesia. A total of 174 healthy, sick, and dead birds were included in the study. The relative diagnostic test sensitivity and the relative diagnostic test specificity were calculated by using real-time reverse transcription polymerase chain reaction (RT-PCR) as the confirmatory diagnosis. The AnigenR Rapid AIV Ag test had a relative diagnostic sensitivity of 0.69 (95% confidence interval [CI]: 0.56-0.80) and a relative diagnostic specificity of 0.98 (95% CI: 0.93-0.99). The Flu Detect(TM) Antigen Capture test strip had a relative diagnostic sensitivity of 0.71 (95% CI: 0.58-0.82) and a relative diagnostic specificity of 0.98 (95% CI: 0.93-0.99). These tests are a valuable tool for the Indonesian avian influenza control program by reliably and quickly detecting Influenza A virus from oropharyngeal swabs from sick or dying chickens.
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Affiliation(s)
- Leo Loth
- Food and Agricultural Organization of the United Nations, Jakarta, Indonesia.
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Kandun IN, Tresnaningsih E, Purba WH, Lee V, Samaan G, Harun S, Soni E, Septiawati C, Setiawati T, Sariwati E, Wandra T. Factors associated with case fatality of human H5N1 virus infections in Indonesia: a case series. Lancet 2008; 372:744-9. [PMID: 18706688 DOI: 10.1016/s0140-6736(08)61125-3] [Citation(s) in RCA: 114] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
BACKGROUND Indonesia has had the most human cases of highly pathogenic avian influenza A (H5N1) and one of the highest case-fatality rates worldwide. We described the factors associated with H5N1 case-fatality in Indonesia. METHODS Between June, 2005, and February, 2008, there were 127 confirmed H5N1 infections. Investigation teams were deployed to investigate and manage each confirmed case; they obtained epidemiological and clinical data from case-investigation reports when possible and through interviews with patients, family members, and key individuals. FINDINGS Of the 127 patients with confirmed H5N1 infections, 103 (81%) died. Median time to hospitalisation was 6 days (range 1-16). Of the 122 hospitalised patients for whom data were available, 121 (99%) had fever, 107 (88%) cough, and 103 (84%) dyspnoea on reaching hospital. However, for the first 2 days after onset, most had non-specific symptoms; only 31 had both fever and cough, and nine had fever and dyspnoea. Median time from onset to oseltamivir treatment was 7 days (range 0-21 days); treatment started within 2 days for one patient who survived, four (36.4%) of 11 receiving treatment within 2-4 days survived, six (37.5%) of 16 receiving treatment within 5-6 days survived, and ten (18.5%) of 44 receiving treatment at 7 days or later survived (p=0.03). Initiation of treatment within 2 days was associated with significantly lower mortality than was initiation at 5-6 days or later than 7 days (p<0.0001). Mortality was lower in clustered than unclustered cases (odds ratio 33.3, 95% CI 3.13-273). Treatment started at a median of 5 days (range 0-13 days) from onset in secondary cases in clusters compared with 8 days (range 4-16) for primary cases (p=0.04). INTERPRETATION Development of better diagnostic methods and improved case management might improve identification of patients with H5N1 influenza, which could decrease mortality by allowing for earlier treatment with oseltamivir.
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Affiliation(s)
- I Nyoman Kandun
- Directorate General of Disease Control and Environmental Health, Ministry of Health, Jakarta, Indonesia
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MANZOOR R, SAKODA Y, SAKABE S, MOCHIZUKI T, NAMBA Y, TSUDA Y, KIDA H. Development of a Pen-Site Test Kit for the Rapid Diagnosis of H7 Highly Pathogenic Avian Influenza. J Vet Med Sci 2008; 70:557-62. [DOI: 10.1292/jvms.70.557] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Affiliation(s)
- Rashid MANZOOR
- Laboratory of Microbiology, Department of Disease Control, Graduate School of Veterinary Medicine, Hokkaido University
| | - Yoshihiro SAKODA
- Laboratory of Microbiology, Department of Disease Control, Graduate School of Veterinary Medicine, Hokkaido University
| | - Saori SAKABE
- Laboratory of Microbiology, Department of Disease Control, Graduate School of Veterinary Medicine, Hokkaido University
| | | | | | - Yoshimi TSUDA
- Laboratory of Microbiology, Department of Disease Control, Graduate School of Veterinary Medicine, Hokkaido University
| | - Hiroshi KIDA
- Laboratory of Microbiology, Department of Disease Control, Graduate School of Veterinary Medicine, Hokkaido University
- Research Center for Zoonosis Control, Hokkaido University
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