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Fu X, Wang Q, Ma B, Zhang B, Sun K, Yu X, Ye Z, Zhang M. Advances in Detection Techniques for the H5N1 Avian Influenza Virus. Int J Mol Sci 2023; 24:17157. [PMID: 38138987 PMCID: PMC10743243 DOI: 10.3390/ijms242417157] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2023] [Revised: 11/27/2023] [Accepted: 11/29/2023] [Indexed: 12/24/2023] Open
Abstract
Avian influenza is caused by avian influenza virus infection; the H5N1 avian influenza virus is a highly pathogenic subtype, affecting poultry and human health. Since the discovery of the highly pathogenic subtype of the H5N1 avian influenza virus, it has caused enormous losses to the poultry farming industry. It was recently found that the H5N1 avian influenza virus tends to spread among mammals. Therefore, early rapid detection methods are highly significant for effectively preventing the spread of H5N1. This paper discusses the detection technologies used in the detection of the H5N1 avian influenza virus, including serological detection technology, immunological detection technology, molecular biology detection technology, genetic detection technology, and biosensors. Comparisons of these detection technologies were analyzed, aiming to provide some recommendations for the detection of the H5N1 avian influenza virus.
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Affiliation(s)
| | | | | | | | | | | | | | - Mingzhou Zhang
- Zhejiang Provincial Key Laboratory of Biometrology and Inspection & Quarantine, College of Life Science, China Jiliang University, 258 Xueyuan Street, Xiasha Higher Education Zone, Hangzhou 310018, China; (X.F.); (Q.W.); (B.M.); (B.Z.); (K.S.); (X.Y.); (Z.Y.)
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Zhu M, Gong X, Hu Y, Ou W, Wan Y. Streptavidin-biotin-based directional double Nanobody sandwich ELISA for clinical rapid and sensitive detection of influenza H5N1. J Transl Med 2014; 12:352. [PMID: 25526777 PMCID: PMC4274719 DOI: 10.1186/s12967-014-0352-5] [Citation(s) in RCA: 57] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2014] [Accepted: 12/02/2014] [Indexed: 12/27/2022] Open
Abstract
BACKGROUND Influenza H5N1 is one subtype of the influenza A virus which can infect human bodies and lead to death. Timely diagnosis before its breakout is vital to the human health. The current clinical biochemical diagnosis for influenza virus are still flawed, and the diagnostic kits of H5N1 are mainly based on traditional monoclonal antibodies that hardly meet the requirements for clinical applications. Nanobody is a promising tool for diagnostics and treatment due to its smallest size, high specificity and stability. In this study, a novel Nanobody-based bioassay was developed for rapid, low-cost and sensitive detection of the influenza H5N1 virus. METHODS Nanobodies specific to H5N1 virus were selected from a VHH library by phage display technology. In this system, the biotinylated Nanobody was directionally captured by streptavidin coated on ELISA plate, which can specifically capture the H5N1 virus. Another Nanobody conjugated with HRP was used as a detector. A novel directional enzyme-linked immunosorbent assay for H5N1 using specific Nanobodies was established and compared to the conventional undirected ELISA assay. RESULTS We have successfully constructed a high quality phage display Nanobody library and isolated two Nanobodies against H5N1 with high affinity and specificity. These two Nanobodies were further used to prepare the biosensor detection system. This streptavidin-biotin-based directional double Nanobodies sandwich ELISA for H5N1 detection showed superiority over the commonly undirectional ELISA protocol. The linear range of detection for standards in this immunoassay was approximately 50-1000 ng/mL and the detection limit was 14.1 ng/mL. The average recoveries of H5N1 virus from human serum samples were in the range from 94.58% to 114.51%, with a coefficient of variation less than 6.5%. CONCLUSION Collectively, these results demonstrated that the proposed detection system is an alternative diagnostic tool that enables a rapid, inexpensive, sensitive and specific detection of the influenza virus.
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Affiliation(s)
- Min Zhu
- The Key Laboratory of Developmental Genes and Human Disease, Ministry of Education, Institute of Life Sciences, Southeast University, Nanjing, 210096, P.R. China.
| | - Xue Gong
- The Key Laboratory of Developmental Genes and Human Disease, Ministry of Education, Institute of Life Sciences, Southeast University, Nanjing, 210096, P.R. China.
| | - Yonghong Hu
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing, 210009, P.R. China.
| | - Weijun Ou
- Jiangsu Nanobody Engineering and Research Center, Nantong, 226010, P.R. China.
| | - Yakun Wan
- The Key Laboratory of Developmental Genes and Human Disease, Ministry of Education, Institute of Life Sciences, Southeast University, Nanjing, 210096, P.R. China. .,Jiangsu Nanobody Engineering and Research Center, Nantong, 226010, P.R. China.
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Tsunetsugu-Yokota Y, Nishimura K, Misawa S, Kobayashi-Ishihara M, Takahashi H, Takayama I, Ohnishi K, Itamura S, Nguyen HLK, Le MTQ, Dang GT, Nguyen LT, Tashiro M, Kageyama T. Development of a sensitive novel diagnostic kit for the highly pathogenic avian influenza A (H5N1) virus. BMC Infect Dis 2014; 14:362. [PMID: 24992826 PMCID: PMC4227021 DOI: 10.1186/1471-2334-14-362] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2014] [Accepted: 06/30/2014] [Indexed: 11/19/2022] Open
Abstract
Background Sporadic emergence of the highly pathogenic avian influenza (HPAI) H5N1 virus infection in humans is a serious concern because of the potential for a pandemic. Conventional or quantitative RT-PCR is the standard laboratory test to detect viral influenza infections. However, this technology requires well-equipped laboratories and highly trained personnel. A rapid, sensitive, and specific alternative screening method is needed. Methods By a luminescence-linked enzyme immunoassay, we have developed a H5N1 HPAI virus detection kit using anti-H5 hemagglutinin monoclonal antibodies in combination with the detection of a universal NP antigen of the type A influenza virus. The process takes 15 minutes by use of the fully automated luminescence analyzer, POCube. Resutls We tested this H5/A kit using 19 clinical specimens from 13 patients stored in Vietnam who were infected with clade 1.1 or clade 2.3.4 H5N1 HPAI virus. Approximately 80% of clinical specimens were H5-positive using the POCube system, whereas only 10% of the H5-positive samples were detected as influenza A-positive by an immunochromatography-based rapid diagnostic kit. Conclusions This novel H5/A kit using POCube is served as a rapid and sensitive screening test for H5N1 HPAI virus infection in humans.
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Affiliation(s)
- Yasuko Tsunetsugu-Yokota
- Department of Immunology, National Institute of Infectious Diseases, Shinjuku Tokyo 162-8640, Japan.
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Tian M, Tian Y, Li Y, Lu H, Li X, Li C, Xue F, Jin N. Microarray multiplex assay for the simultaneous detection and discrimination of influenza a and influenza B viruses. Indian J Microbiol 2013; 54:211-7. [PMID: 25320424 DOI: 10.1007/s12088-013-0432-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2013] [Accepted: 10/13/2013] [Indexed: 10/26/2022] Open
Abstract
In this study, we present a microarray approach for the typing of influenza A and B viruses, and the subtyping of H1 and H3 subtypes. We designed four pairs of specific multiplex RT-PCR primers and eight specific oligonucleotide probes and prepared microarrays to identify the specific subtype of influenza virus. Through amplification and fluorescent marking of the multiplex RT-PCR products on the M gene of influenza A and B viruses and the HA gene of subtypes H1 and H3, the PCR products were hybridized with the microarray, and the results were analyzed using a microarray scanner. The results demonstrate that the chip developed by our research institute can detect influenza A and B viruses specifically and identify the subtypes H1 and H3 at a minimum concentration of 1 × 10(2) copies/μL of viral RNA. We tested 35 clinical samples and our results were identical to other fluorescent methods. The microarray approach developed in this study provides a reliable method for the monitoring and testing of seasonal influenza.
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Affiliation(s)
- Mingyao Tian
- College of Animal Science and Veterinary Medicine, Jilin University, Changchun, 130062 People's Republic of China ; Institute of Military Veterinary, Academy of Military Medical Sciences of PLA, Liuying West Road 666, Changchun, 130122 People's Republic of China
| | - Yufei Tian
- College of Animal Science and Veterinary Medicine, Jilin University, Changchun, 130062 People's Republic of China ; Institute of Military Veterinary, Academy of Military Medical Sciences of PLA, Liuying West Road 666, Changchun, 130122 People's Republic of China
| | - Yang Li
- Department of Respiration, The First Hospital of Jilin University, Changchun, 130021 People's Republic of China
| | - Huijun Lu
- Institute of Military Veterinary, Academy of Military Medical Sciences of PLA, Liuying West Road 666, Changchun, 130122 People's Republic of China
| | - Xiao Li
- Institute of Military Veterinary, Academy of Military Medical Sciences of PLA, Liuying West Road 666, Changchun, 130122 People's Republic of China
| | - Chang Li
- Institute of Military Veterinary, Academy of Military Medical Sciences of PLA, Liuying West Road 666, Changchun, 130122 People's Republic of China
| | - Fei Xue
- Institute of Military Veterinary, Academy of Military Medical Sciences of PLA, Liuying West Road 666, Changchun, 130122 People's Republic of China
| | - Ningyi Jin
- Institute of Military Veterinary, Academy of Military Medical Sciences of PLA, Liuying West Road 666, Changchun, 130122 People's Republic of China
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Sakurai A, Shibasaki F. Updated values for molecular diagnosis for highly pathogenic avian influenza virus. Viruses 2012; 4:1235-57. [PMID: 23012622 PMCID: PMC3446759 DOI: 10.3390/v4081235] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2012] [Revised: 07/31/2012] [Accepted: 08/03/2012] [Indexed: 01/31/2023] Open
Abstract
Highly pathogenic avian influenza (HPAI) viruses of the H5N1 strain pose a pandemic threat. H5N1 strain virus is extremely lethal and contagious for poultry. Even though mortality is 59% in infected humans, these viruses do not spread efficiently between humans. In 1997, an outbreak of H5N1 strain with human cases occurred in Hong Kong. This event highlighted the need for rapid identification and subtyping of influenza A viruses (IAV), not only to facilitate surveillance of the pandemic potential of avian IAV, but also to improve the control and treatment of infected patients. Molecular diagnosis has played a key role in the detection and typing of IAV in recent years, spurred by rapid advances in technologies for detection and characterization of viral RNAs and proteins. Such technologies, which include immunochromatography, quantitative real-time PCR, super high-speed real-time PCR, and isothermal DNA amplification, are expected to contribute to faster and easier diagnosis and typing of IAV.
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Affiliation(s)
- Akira Sakurai
- Department of Molecular Medical Research, Tokyo Metropolitan Institute of Medical Science, 2-1-6, Kamikitazawa, Setagaya-ku, Tokyo 156-8506, Japan.
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Applicability of a sensitive duplex real-time PCR assay for identifying B/Yamagata and B/Victoria lineages of influenza virus from clinical specimens. Appl Microbiol Biotechnol 2011; 93:797-805. [PMID: 22113559 DOI: 10.1007/s00253-011-3710-8] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2011] [Revised: 10/24/2011] [Accepted: 11/05/2011] [Indexed: 10/15/2022]
Abstract
Type B influenza virus is one of the major epidemic strains and responsible for considerable mortality and morbidity. Rapidly and accurately identifying different influenza B virus lineages, i.e., B/Yamagata (B/Y) and B/Victoria (B/V), is desirable during the flu season. However, the available rapid techniques lack sensitivity, and the usual methods for identifying influenza viruses require expansion of virus in tissue culture or embryonated hen's eggs. Thus, we developed several sets of primer pairs that were able to detect and distinguish B/Y and B/V in a single real-time PCR assay. Used in conjunction with two sets of specific primers that exhibited purine at 3' end of at least one primer targeting on HA gene of B/Y and B/V lineages allows us to accurately identify approximately 10(2) copies per microliter for B/Y and B/V with intra- and inter-assay coefficient of variation (CV) <4%. When it was used to test 17,765 throat swab specimens obtained in the 2006-2010 influenza surveillance season, this method was comparable to hemagglutination inhibition assay in detection, typing and subtyping of influenza viruses with 100% true-negative (specificity) and 100% true-positive (sensitivity). Taken together, this method provides sensitive and robust tool for routine diagnosis and on-time epidemiological examination for WHO decisions on vaccine composition.
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Molecular Detection of Respiratory Viruses. Mol Microbiol 2011. [DOI: 10.1128/9781555816834.ch39] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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Abstract
Influenza viruses continue to be a major cause of respiratory tract infection, resulting in substantial morbidity and mortality throughout the world. Accurate and rapid differential diagnosis of influenza virus infections, particularly associated with zoonotic infections, is important for public health actions, patient management, and treatment. Real-time PCR is widely considered the gold standard for molecular detection of influenza viruses owing to its high assay specificity, extreme detection sensitivity, and wide linear dynamic range. This protocol describes the use of a real-time RT-PCR assay for identification of influenza A and B viruses, detection of H5 subtype viruses, and an internal control, in a multiplexed, single-tube format. The inclusion of an internal bacteriophage control allows the efficiency of the extraction and amplification process to be monitored, so that false-negative results may be avoided. The primers and probe sets in this multiplex assay have been validated with a panel of influenza A viruses of different subtypes (including swine influenza viruses), and influenza B viruses, and specificity further confirmed with non-related respiratory viruses.
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Shisong F, Jianxiong L, Xiaowen C, Cunyou Z, Ting W, Xing L, Xin W, Chunli W, Renli Z, Jinquan C, Hong X, Muhua Y. Simultaneous detection of influenza virus type B and influenza A virus subtypes H1N1, H3N2, and H5N1 using multiplex real-time RT-PCR. Appl Microbiol Biotechnol 2011; 90:1463-70. [PMID: 21400097 DOI: 10.1007/s00253-011-3192-8] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2011] [Revised: 02/25/2011] [Accepted: 02/27/2011] [Indexed: 11/29/2022]
Abstract
Use of multiplex real-time reverse transcription polymerase chain reaction (RT-PCR) for the simultaneous detection of influenza type B virus and influenza A virus subtypes H5N1, H3N2, and H1N1 has been described. The method exhibited a high specificity and sensitivity of approximately 10(1)-10(2) copies per microliter or 10(-3)-10(-2) TCID50/L for each subtype, as well as a high reproducibility with coefficient of variation (CV) ranging from 0.27% to 4.20%. The assays can be performed commendably on various models of real-time PCR instruments; including ABI7500, ROCH 2.0, and Mx3005p. In an analysis of 436 clinical samples from patients during the year 2009, this detection method has successfully identified 261 positive samples, as compared to only 189 positive samples using the conventional cell culture systems, and at the same time further differentiated them as 35 type B, 21 subtype H1N1, and 205 subtype H3N2. The results indicate that the multiplex real-time RT-PCR method is a potential tool for rapid screening of influenza virus from a large pool of clinical samples during flu pandemics and facilitates early influenza virus identification in most public health laboratories around the world.
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Affiliation(s)
- Fang Shisong
- Shenzhen Centre for Disease Control and Prevention, Shenzhen, China
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Moore C, Telles JN, Corden S, Gao RB, Vernet G, Van Aarle P, Shu YL. Development and validation of a commercial real-time NASBA assay for the rapid confirmation of influenza A H5N1 virus in clinical samples. J Virol Methods 2010; 170:173-6. [DOI: 10.1016/j.jviromet.2010.09.014] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2010] [Revised: 08/05/2010] [Accepted: 09/13/2010] [Indexed: 11/16/2022]
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Zhao J, Tang S, Storhoff J, Marla S, Bao YP, Wang X, Wong EY, Ragupathy V, Ye Z, Hewlett IK. Multiplexed, rapid detection of H5N1 using a PCR-free nanoparticle-based genomic microarray assay. BMC Biotechnol 2010; 10:74. [PMID: 20942949 PMCID: PMC2964543 DOI: 10.1186/1472-6750-10-74] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2010] [Accepted: 10/13/2010] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND For more than a decade there has been increasing interest in the use of nanotechnology and microarray platforms for diagnostic applications. In this report, we describe a rapid and simple gold nanoparticle (NP)-based genomic microarray assay for specific identification of avian influenza virus H5N1 and its discrimination from other major influenza A virus strains (H1N1, H3N2). RESULTS Capture and intermediate oligonucleotides were designed based on the consensus sequences of the matrix (M) gene of H1N1, H3N2 and H5N1 viruses, and sequences specific for the hemaglutinin (HA) and neuraminidase (NA) genes of the H5N1 virus. Viral RNA was detected within 2.5 hours using capture-target-intermediate oligonucleotide hybridization and gold NP-mediated silver staining in the absence of RNA fragmentation, target amplification, and enzymatic reactions. The lower limit of detection (LOD) of the assay was less than 100 fM for purified PCR fragments and 103 TCID50 units for H5N1 viral RNA. CONCLUSIONS The NP-based microarray assay was able to detect and distinguish H5N1 sequences from those of major influenza A viruses (H1N1, H3N2). The new method described here may be useful for simultaneous detection and subtyping of major influenza A viruses.
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Affiliation(s)
- Jiangqin Zhao
- Lab of Molecular Virology, Center for Biologics Evaluation and Research, Food and Drug Administration, Bethesda, MD 20892, USA.
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Abstract
Molecular-based techniques for detecting influenza viruses have become an integral component of human and animal surveillance programs in the last two decades. The recent pandemic of the swine-origin influenza A virus (H1N1) and the continuing circulation of highly pathogenic avian influenza A virus (H5N1) further stress the need for rapid and accurate identification and subtyping of influenza viruses for surveillance, outbreak management, diagnosis and treatment. There has been remarkable progress on the detection and molecular characterization of influenza virus infections in clinical, mammalian, domestic poultry and wild bird samples in recent years. The application of these techniques, including reverse transcriptase-PCR, real-time PCR, microarrays and other nucleic acid sequencing-based amplifications, have greatly enhanced the capability for surveillance and characterization of influenza viruses.
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Affiliation(s)
- Ruixue Wang
- Viral Pathogenesis and Evolution Section, Laboratory of Infectious Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Jeffery K Taubenberger
- Viral Pathogenesis and Evolution Section, Laboratory of Infectious Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
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Thanh TT, Pawestri HA, Ngoc NM, Hien VM, Syahrial H, Trung NV, van Doorn RH, Wertheim HFL, Chau NVV, Ha do Q, Farrar JJ, Hien TT, Sedyaningsih ER, de Jong MD. A real-time RT-PCR for detection of clade 1 and 2 H5N1 influenza A virus using locked nucleic acid (LNA) TaqMan probes. Virol J 2010; 7:46. [PMID: 20170549 PMCID: PMC2838857 DOI: 10.1186/1743-422x-7-46] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2009] [Accepted: 02/22/2010] [Indexed: 01/28/2023] Open
Abstract
BACKGROUND The emergence and co-circulation of two different clades (clade 1 and 2) of H5N1 influenza viruses in Vietnam necessitates the availability of a diagnostic assay that can detect both variants. RESULTS We developed a single real-time RT-PCR assay for detection of both clades of H5N1 viruses, directly from clinical specimens, using locked nucleic acid TaqMan probes. Primers and probe used in this assay were designed based on a highly conserved region in the HA gene of H5N1 viruses. The analytical sensitivity of the assay was < 0.5 PFU and 10-100 ssDNA plasmid copies. A total of 106 clinical samples (58 from patients infected with clade 1, 2.1 or 2.3 H5N1 viruses and 48 from uninfected or seasonal influenza A virus-infected individuals) were tested by the assay. The assay showed 97% concordance with initial diagnostics for H5 influenza virus infection with a specificity of 100%. CONCLUSIONS This assay is a useful tool for diagnosis of H5N1 virus infections in regions where different genetic clades are co-circulating.
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Affiliation(s)
- Tran Tan Thanh
- Oxford University Clinical Research Unit, Hospital for Tropical Diseases, 190 Ben Ham Tu, Dist 05, Ho Chi Minh City, Viet Nam.
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Wu W, Tang YW. Emerging molecular assays for detection and characterization of respiratory viruses. Clin Lab Med 2010; 29:673-93. [PMID: 19892228 PMCID: PMC7130760 DOI: 10.1016/j.cll.2009.07.005] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/31/2022]
Abstract
This article describes several emerging molecular assays that have potential applications in the diagnosis and monitoring of respiratory viral infections. These techniques include direct nucleic acid detection by quantum dots, loop-mediated isothermal amplification, multiplex ligation-dependent probe amplification, amplification using arbitrary primers, target-enriched multiplexing amplification, pyrosequencing, padlock probes, solid and suspension microarrays, and mass spectrometry. Several of these systems already are commercially available to provide multiplex amplification and high-throughput detection and identification of a panel of respiratory viral pathogens. Further validation and implementation of such emerging molecular assays in routine clinical virology services will enhance the rapid diagnosis of respiratory viral infections and improve patient care.
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Affiliation(s)
- Wenjuan Wu
- Department of Pathology, Vanderbilt University Medical Center, Nashville, TN, USA
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Deyde VM, Gubareva LV. Influenza genome analysis using pyrosequencing method: current applications for a moving target. Expert Rev Mol Diagn 2009; 9:493-509. [PMID: 19580433 DOI: 10.1586/erm.09.21] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Pyrosequencing is a high-throughput non-gel-based DNA sequencing method that was introduced in the late 1990s. It employs a DNA sequencing-by-synthesis approach based on real-time measurement of pyrophosphate released from incorporation of dNTPs. A cascade of enzymatic reactions proportionally converts the pyrophosphate to a light signal recorded in a form of peaks, known as pyrograms. Routinely, a 45-60-nucleotide sequence is obtained per reaction. Recent improvements introduced in the assay chemistry have extended the read to approximately 100 nucleotides. Since its advent, pyrosequencing has been applied in the fields of microbiology, molecular biology and pharmacogenomics. The pyrosequencing approach was first applied to analysis of influenza genome in 2005, when it played a critical role in the timely detection of an unprecedented rise in resistance to the adamantane class of anti-influenza drugs. More recently, pyrosequencing was successfully applied for monitoring the emergence and spread of influenza A (H1N1) virus resistance to oseltamivir, a newer anti-influenza drug. The present report summarizes known applications of the pyrosequencing approach for influenza genome analysis with an emphasis on drug-resistance detection.
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Affiliation(s)
- Varough M Deyde
- Virus Surveillance and Diagnosis Branch, Influenza Division, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Mail Stop G-16, 1600 Clifton Road, Atlanta, GA 30333, USA
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Development of Real Time RT-PCR Assays for Detection of Type A Influenza Virus and for Subtyping of Avian H5 and H7 Hemagglutinin Subtypes. Mol Biotechnol 2009; 44:41-50. [DOI: 10.1007/s12033-009-9211-7] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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Jones S, Evans K, McElwaine-Johnn H, Sharpe M, Oxford J, Lambkin-Williams R, Mant T, Nolan A, Zambon M, Ellis J, Beadle J, Loudon PT. DNA vaccination protects against an influenza challenge in a double-blind randomised placebo-controlled phase 1b clinical trial. Vaccine 2009; 27:2506-12. [DOI: 10.1016/j.vaccine.2009.02.061] [Citation(s) in RCA: 95] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2008] [Revised: 02/10/2009] [Accepted: 02/18/2009] [Indexed: 12/20/2022]
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Universal detection and identification of avian influenza virus by use of resequencing microarrays. J Clin Microbiol 2009; 47:988-93. [PMID: 19279171 DOI: 10.1128/jcm.01346-08] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Zoonotic microbes have historically been, and continue to emerge as, threats to human health. The recent outbreaks of highly pathogenic avian influenza virus in bird populations and the appearance of some human infections have increased the concern of a possible new influenza pandemic, which highlights the need for broad-spectrum detection methods for rapidly identifying the spread or outbreak of all variants of avian influenza virus. In this study, we demonstrate that high-density resequencing pathogen microarrays (RPM) can be such a tool. The results from 37 influenza virus isolates show that the RPM platform is an effective means for detecting and subtyping influenza virus, while simultaneously providing sequence information for strain resolution, pathogenicity, and drug resistance without additional analysis. This study establishes that the RPM platform is a broad-spectrum pathogen detection and surveillance tool for monitoring the circulation of prevalent influenza viruses in the poultry industry and in wild birds or incidental exposures and infections in humans.
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Mosleh N, Dadras H, Mohammadi A. Molecular quantitation of H9N2 avian influenza virus in various organs of broiler chickens using TaqMan real time PCR. J Mol Genet Med 2009; 3:152-7. [PMID: 19565023 PMCID: PMC2702075 DOI: 10.4172/1747-0862.1000027] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2008] [Revised: 12/07/2008] [Accepted: 12/10/2008] [Indexed: 11/09/2022] Open
Abstract
During the past decade, H9N2 low pathogenic avian influenza virus (LPAI) has caused considerable economic loss due to decreased production, increased mortality and the cost of vaccination in Iranian poultry industry. Because of widespread occurrence of this disease and the virus potential to mutate to highly-pathogenic (HP) form and transmission to humans, it is, therefore, imperative to understand the pathogenesis and properties of these viruses. In this study, a two step TaqMan real time PCR assay was performed for the quantitation of A/chicken/Iran/772/1998(H(9)N(2)) virus in various organs of broiler chickens at different days post inoculation (DPI). Forty 5-week-old commercial broiler chickens were inoculated with the virus. Five chickens were randomly selected on days 1, 3, 6 and 9 PI. Their trachea, lungs, spleen, kidneys, pancreas, blood and faeces were collected for virus detection. A PCR test was performed and the positive samples were used for quantitative real time PCR assay. The result of RT-PCR assay showed the presence of the virus in trachea (40%, 33%), lungs (20%, 66.6%) and spleen (20%, 50%) of infected chickens on days 3 and 6 PI, respectively. The virus was also detected in the kidneys of inoculated chickens on 3 (40%), 6 (60%) and 9 (100%) DPI. In faecal samples the virus was only detected on day 6 PI (83.3%). The molecular quantitation of AIV showed that the AIV titre in the trachea, lungs and spleen of chickens at 3 DPI is lower than the AIV titre at 6 DPI in these organs. The highest titre was observed in the faeces. The AIV titre in all organs of the birds which died at 6 DPI was higher than those of the same organs in the other experimental birds.
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Affiliation(s)
- Najmeh Mosleh
- Group of Veterinary Medicine, Yasouj Branch, Islamic Azad University (IAU), Yasouj, presently postgraduate student of Avian Medicine, School of Veterinary Medicine, Shiraz University, Shiraz, Iran
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Wang W, Ren P, Mardi S, Hou L, Tsai C, Chan KH, Cheng P, Sheng J, Buchy P, Sun B, Toyoda T, Lim W, Peiris JSM, Zhou P, Deubel V. design of multiplexed detection assays for identification of avian influenza a virus subtypes pathogenic to humans by SmartCycler real-time reverse transcription-PCR. J Clin Microbiol 2009; 47:86-92. [PMID: 18971359 PMCID: PMC2620859 DOI: 10.1128/jcm.01090-08] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2008] [Revised: 08/13/2008] [Accepted: 10/13/2008] [Indexed: 11/20/2022] Open
Abstract
Influenza A virus (IAV) epidemics are the result of human-to-human or poultry-to-human transmission. Tracking seasonal outbreaks of IAV and other avian influenza virus (AIV) subtypes that can infect humans, aquatic and migratory birds, poultry, and pigs is essential for epidemiological surveillance and outbreak alerts. In this study, we performed four real-time reverse transcription-PCR (rRT-PCR) assays for identification of the IAV M and hemagglutinin (HA) genes from six known AIVs infecting pigs, birds, and humans. IAV M1 gene-positive samples tested by single-step rRT-PCR and a fluorogenic Sybr green I detection system were further processed for H5 subtype identification by using two-primer-set multiplex and Sybr green I rRT-PCR assays. H5 subtype-negative samples were then tested with either a TaqMan assay for subtypes H1 and H3 or a TaqMan assay for subtypes H2, H7, and H9 and a beacon multiplex rRT-PCR identification assay. The four-tube strategy was able to detect 10 RNA copies of the HA genes of subtypes H1, H2, H3, H5, and H7 and 100 RNA copies of the HA gene of subtype H9. At least six H5 clades of H5N1 viruses isolated in Southeast Asia and China were detected by that test. Using rRT-PCR assays for the M1 and HA genes in 202 nasopharyngeal swab specimens from children with acute respiratory infections, we identified a total of 39 samples positive for the IAV M1 gene and subtypes H1 and H3. When performed with a portable SmartCycler instrument, the assays offer an efficient, flexible, and reliable platform for investigations of IAV and AIV in remote hospitals and in the field.
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Affiliation(s)
- Wei Wang
- Chinese Academy of Sciences, Institut Pasteur of Shanghai, Shanghai Institute of Biological Sciences, 411 Hefei Road, 200025 Shanghai, People's Republic of China
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22
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Chen HY, Li XK, Cui BA, Wei ZY, Li XS, Wang YB, Zhao L, Wang ZY. A TaqMan-based real-time polymerase chain reaction for the detection of porcine parvovirus. J Virol Methods 2008; 156:84-8. [PMID: 19041671 DOI: 10.1016/j.jviromet.2008.10.029] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2008] [Revised: 10/07/2008] [Accepted: 10/21/2008] [Indexed: 11/26/2022]
Abstract
A real-time polymerase chain reaction (PCR) using a TaqMan probe was developed to detect porcine parvovirus (PPV). Real-time PCR was optimized to quantify PPV using a detection system (Rotor Gene 2000 detector) and a dual-labeled fluorogenic probe. The gene-specific labeled fluorogenic probe for the VP2 gene of PPV was used to detect PPV. Quantitation of PPV was accomplished by a standard curve plotting cycle threshold values (Ct) against each dilution of standard plasmids. When the specificity of the assay using specific PPV primers was evaluated by testing the PPV standard strain and other viruses, no cross-reactions were detected with non-PPV reference viruses. The detection limit of real-time PCR for PPV was 2.08log10 genome copy equivalent (gce). In this study, a real-time PCR assay was performed on 80 clinical samples and compared with a conventional PCR assay. In 48 of 80 samples, PPV DNA was detected by the conventional PCR assay. All samples positive for PPV DNA by the conventional PCR assay were also positive by the real-time PCR assay, and 12 of 32 samples that tested negative for PPV DNA by the conventional method tested positive by the real-time PCR assay. Using the real-time PCR assay, the number of samples in which PPV was detected increased by 15%. Therefore, it is considered to be a useful tool for the detection of PPV.
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Affiliation(s)
- Hong-Ying Chen
- College of Animal Husbandry and Veterinary, Henan Agricultural University, Zhengzhou 450002, China
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23
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Abstract
SUMMARY Clinical laboratories historically diagnose seven or eight respiratory virus infections using a combination of techniques including enzyme immunoassay, direct fluorescent antibody staining, cell culture, and nucleic acid amplification tests. With the discovery of six new respiratory viruses since 2000, laboratories are faced with the challenge of detecting up to 19 different viruses that cause acute respiratory disease of both the upper and lower respiratory tracts. The application of nucleic acid amplification technology, particularly multiplex PCR coupled with fluidic or fixed microarrays, provides an important new approach for the detection of multiple respiratory viruses in a single test. These multiplex amplification tests provide a sensitive and comprehensive approach for the diagnosis of respiratory tract infections in individual hospitalized patients and the identification of the etiological agent in outbreaks of respiratory tract infection in the community. This review describes the molecular methods used to detect respiratory viruses and discusses the contribution that molecular testing, especially multiplex PCR, has made to our ability to detect respiratory viruses and to increase our understanding of the roles of various viral agents in acute respiratory disease.
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Pasick J. Advances in the molecular based techniques for the diagnosis and characterization of avian influenza virus infections. Transbound Emerg Dis 2008; 55:329-38. [PMID: 18786072 DOI: 10.1111/j.1865-1682.2008.01047.x] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
There have been remarkable advances in the molecular diagnosis and characterization of avian influenza virus infections in domestic poultry and free-living birds in the past two decades. Rapid pathotyping became possible with the recognition that the amino acid sequence of the connecting peptide of the haemagglutinin precursor, HA(0), is a major virulence determinant for H5 and H7 subtype viruses. This in turn resulted in nucleic acid sequencing as a relatively routine method for identifying highly pathogenic avian influenza virus isolates. Subsequent development of diagnostic methods based on reverse transcription-polymerase chain reaction (RT-PCR), real-time RT-PCR, nucleic acid sequence-based amplification and loop-mediated isothermal amplification has made the rapid detection of group A influenza and H5 and H7 subtype viruses possible. Further development of these assay platforms has enabled the specific detection of H5N1 Eurasian subtype viruses and the inference of their HA(0) cleavage sites. Identification of additional virulence determinants of influenza A viruses for birds and mammals will allow the emerging area of microarray technology to further extend our understanding of their ecology, epidemiology and pathogenesis.
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Affiliation(s)
- J Pasick
- Canadian Food Inspection Agency, National Centre for Foreign Animal Disease, Winnipeg, MB, Canada.
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Saijo M, Morikawa S, Kurane I. Real-time quantitative polymerase chain reaction for virus infection diagnostics. ACTA ACUST UNITED AC 2008; 2:1155-71. [DOI: 10.1517/17530059.2.10.1155] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
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Lemmon GH, Gardner SN. Predicting the sensitivity and specificity of published real-time PCR assays. Ann Clin Microbiol Antimicrob 2008; 7:18. [PMID: 18817537 PMCID: PMC2566554 DOI: 10.1186/1476-0711-7-18] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2008] [Accepted: 09/25/2008] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND In recent years real-time PCR has become a leading technique for nucleic acid detection and quantification. These assays have the potential to greatly enhance efficiency in the clinical laboratory. Choice of primer and probe sequences is critical for accurate diagnosis in the clinic, yet current primer/probe signature design strategies are limited, and signature evaluation methods are lacking. METHODS We assessed the quality of a signature by predicting the number of true positive, false positive and false negative hits against all available public sequence data. We found real-time PCR signatures described in recent literature and used a BLAST search based approach to collect all hits to the primer-probe combinations that should be amplified by real-time PCR chemistry. We then compared our hits with the sequences in the NCBI taxonomy tree that the signature was designed to detect. RESULTS We found that many published signatures have high specificity (almost no false positives) but low sensitivity (high false negative rate). Where high sensitivity is needed, we offer a revised methodology for signature design which may designate that multiple signatures are required to detect all sequenced strains. We use this methodology to produce new signatures that are predicted to have higher sensitivity and specificity. CONCLUSION We show that current methods for real-time PCR assay design have unacceptably low sensitivities for most clinical applications. Additionally, as new sequence data becomes available, old assays must be reassessed and redesigned. A standard protocol for both generating and assessing the quality of these assays is therefore of great value. Real-time PCR has the capacity to greatly improve clinical diagnostics. The improved assay design and evaluation methods presented herein will expedite adoption of this technique in the clinical lab.
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Affiliation(s)
- Gordon H Lemmon
- Center for Structural Biology, Vanderbilt University, 465 21st Ave. South, BIOSCI/MRB III suite 5140, Nashville, TN 37240, USA.
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Development and validation of a one-step real-time PCR assay for simultaneous detection of subtype H5, H7, and H9 avian influenza viruses. J Clin Microbiol 2008; 46:1769-73. [PMID: 18367569 DOI: 10.1128/jcm.02204-07] [Citation(s) in RCA: 117] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Among the different hemagglutinin (HA) subtypes of avian influenza (AI) viruses, H5, H7, and H9 are of major interest because of the serious consequences for the poultry industry and the increasing frequency of direct transmission of these viruses to humans. The availability of new tools to rapidly detect and subtype the influenza viruses can enable the immediate application of measures to prevent the widespread transmission of the infection. In this study, a novel one-step real-time reverse transcription-PCR (RRT-PCR) was developed to detect simultaneously the H5, H7, and H9 subtypes of AI viruses from clinical samples of avian origin. The sensitivity of the RRT-PCR assay was determined by using in vitro-transcribed RNA and 10-fold serial dilutions of titrated AI viruses. High sensitivity levels were obtained, with limits of detection ranging from 10(1) to 10(3) RNA copies and from 10(1) 50% egg infectious dose (EID(50))/100 microl to 10(2.74) EID(50)/100 microl with titrated viruses. Excellent results were achieved in the intra- and interassay variability tests. The comparison of the results with those obtained from the analysis of 725 avian samples by means of the reference method (virus isolation [VI]) showed a high level of agreement. To date, this is the first real-time PCR protocol available for the simultaneous detection of AI viruses belonging to subtypes H5, H7, and H9, and the results obtained indicate that this method is suitable as a routine laboratory test for the rapid detection and differentiation of the three most-important AI virus subtypes in samples of avian origin.
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28
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Rapid differentiation of influenza A virus subtypes and genetic screening for virus variants by high-resolution melting analysis. J Clin Microbiol 2008; 46:1090-7. [PMID: 18174299 DOI: 10.1128/jcm.02015-07] [Citation(s) in RCA: 64] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
We assessed the use of high-resolution melting (HRM) analysis for the rapid identification of influenza A virus subtypes and the detection of newly emerging virus variants. The viral matrix gene was amplified by LightCycler real-time reverse transcription-PCR (RT-PCR) in the presence of the LCGreen I fluorescent dye. Upon optimization of the assay conditions, all the major influenza A virus subtypes, including H1N1, H3N2, H5N1, H7N3, and H9N2, were amplifiable by this method and had a PCR product length of 179 bp. Real-time RT-PCR of in vitro-transcribed H3N2 RNA revealed a standard curve for quantification with a linear range (correlation coefficient = 0.9935) across at least 8 log units of RNA concentrations and a detection limit of 10(3) copies of viral RNA. We performed HRM analysis of the PCR products with the HR-1 instrument and used the melting profiles as molecular fingerprints for virus subtyping. The virus subtypes were identified from the high-resolution derivative plot obtained by heteroduplex formation between the PCR products of the viral isolates tested and those of the reference viral isolates. The melting profiles were consistent with minimal interassay variability. Hence, an HRM database and a working protocol were established for the identification of these five influenza A virus subtypes. When this protocol was used to test 21 clinical influenza A virus isolates, the results were comparable to those obtained by RT-PCR with hemagglutinin-specific primer sets. Sequence variants of the clinical isolates (n = 4) were also revealed by our HRM analytical scheme. This assay requires no multiplexing or hybridization probes and provides a new approach for influenza A virus subtyping and genetic screening of virus variants in a clinical virology laboratory.
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Curran MD, Ellis JS, Wreghitt TG, Zambon MC. Establishment of a UK National Influenza H5 Laboratory Network. J Med Microbiol 2007; 56:1263-1267. [PMID: 17893159 DOI: 10.1099/jmm.0.47336-0] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Avian (H5N1) influenza continues to pose a significant threat to human health, although it remains a zoonotic infection. Sensitive and robust surveillance measures are required to detect any evidence that the virus has acquired the ability to transmit between humans and emerge as the next pandemic strain. An integral part of the pandemic planning response in the UK was the creation in 2005 of the UK National H5 Laboratory Network, capable of rapidly and accurately identifying potential human H5N1 infections in all regions of the UK, and the Republic of Ireland. This review details the challenges that designing molecular detection methods for a rapidly evolving virus present, and the strategic decisions and choices required to ensure successful establishment of a functional national laboratory network, providing round the clock testing for H5N1. Laboratory partnerships have delivered improved real-time one-step multiplex PCR methodologies to ensure streamlined testing capable of not only detecting H5 but also a differential diagnosis of seasonal influenza A/B. A range of fully validated real-time PCR H5 confirmatory assays have been developed to run in parallel with a universal first-screening assay. Regular proficiency panels together with weekly surveillance runs, intermittent on-call testing for suspect cases of avian flu in returning travellers, and several outbreaks of avian influenza outbreaks in poultry that have occurred since 2005 in the UK have fully tested the network and the current diagnostic strategies for avian influenza. The network has clearly demonstrated its capability of delivering a confirmed H5N1 diagnosis within 3-4 h of receipt of a sample, an essential prerequisite for administration of the appropriate antiviral therapy, effective clinical management, disease containment and implementation of infection control measures. A functional network is an important means of enhancing laboratory capability and building diagnostic capacity for a newly emerging pandemic of influenza, and is an essential part of pandemic preparedness.
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Affiliation(s)
- Martin D Curran
- Health Protection Agency, East of England, Clinical Microbiology and Public Health Laboratory, Addenbrooke's Hospital, Hills Road, Cambridge CB2 2QW, UK
| | - Joanna S Ellis
- Respiratory Virus Unit, Health Protection Agency, Colindale, London NW9 5HT, UK
| | - Tim G Wreghitt
- Health Protection Agency, East of England, Clinical Microbiology and Public Health Laboratory, Addenbrooke's Hospital, Hills Road, Cambridge CB2 2QW, UK
| | - Maria C Zambon
- Respiratory Virus Unit, Health Protection Agency, Colindale, London NW9 5HT, UK
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