1
|
Croville G, Walch M, Sécula A, Lèbre L, Silva S, Filaire F, Guérin JL. An amplicon-based nanopore sequencing workflow for rapid tracking of avian influenza outbreaks, France, 2020-2022. Front Cell Infect Microbiol 2024; 14:1257586. [PMID: 38318163 PMCID: PMC10839014 DOI: 10.3389/fcimb.2024.1257586] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2023] [Accepted: 01/04/2024] [Indexed: 02/07/2024] Open
Abstract
During the recent avian influenza epizootics that occurred in France in 2020/21 and 2021/22, the virus was so contagiousness that it was impossible to control its spread between farms. The preventive slaughter of millions of birds consequently was the only solution available. In an effort to better understand the spread of avian influenza viruses (AIVs) in a rapid and innovative manner, we established an amplicon-based MinION sequencing workflow for the rapid genetic typing of circulating AIV strains. An amplicon-based MinION sequencing workflow based on a set of PCR primers targeting primarily the hemagglutinin gene but also the entire influenza virus genome was developed. Thirty field samples from H5 HPAIV outbreaks in France, including environmental samples, were sequenced using the MinION MK1C. A real-time alignment of the sequences with MinKNOW software allowed the sequencing run to be stopped as soon as enough data were generated. The consensus sequences were then generated and a phylogenetic analysis was conducted to establish links between the outbreaks. The whole sequence of the hemagglutinin gene was obtained for the 30 clinical samples of H5Nx HPAIV belonging to clade 2.3.4.4b. The consensus sequences comparison and the phylogenetic analysis demonstrated links between some outbreaks. While several studies have shown the advantages of MinION for avian influenza virus sequencing, this workflow has been applied exclusively to clinical field samples, without any amplification step on cell cultures or embryonated eggs. As this type of testing pipeline requires only a short amount of time to link outbreaks or demonstrate a new introduction, it could be applied to the real-time management of viral epizootics.
Collapse
|
2
|
Xiang H, Wen X, Wen Y, Zhang H, Cao S, Huang X, Wu R, Zhao Q. Development and application of a visual microarray for synchronously detecting H5N1, H7N9 and H9N2 avian influenza virus RNA. J Virol Methods 2021; 301:114371. [PMID: 34808230 DOI: 10.1016/j.jviromet.2021.114371] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2019] [Revised: 09/06/2021] [Accepted: 11/18/2021] [Indexed: 11/19/2022]
Abstract
The aim of this study was to develop a microarray assay for the simultaneous detection of the H5, H7, H9, N1, N9 and N2 genes of the avian influenza virus (AIV) using a Nanogold-streptavidin and silver-stain-enhanced nucleic acid dot-blot hybridisation system. The conserved sequences of H5 genes from H5N1, H7 genes from H7N9, H9 genes from H9N2, N9 genes from H7N9 and N2 genes from H9N2 AIV were cloned, together with that of N1 obtained commercially, and were used as templates for generating the probes using biotin-labeled primers, which targeted the conserved regions of H5, H7, H9, N1, N9 and N2 genes, respectively. The oligonucleotide probes were diluted using the spotting buffer and ddH2O, and each probe was then spotted to each specific position on the microarray. The PCR products including biotin-labeled lambda, NP, H5, H7, H9, N1, N9 and N2 were mixed, 200 μL of which was then added to the microarray chamber after denaturing. Following a hybridization incubation at 45℃ for 120 min, the microarray was then incubated with nanogold-streptavidin about 4 μg/mL for 30 min. After the supplementary of 200 μL of silver buffer A and silver buffer B in the chamber, the hybridization results were assessed by direct visualization in the dark at room temperature. The microarray assay was optimized and its specificity, sensitivity and stability were evaluated. The optimal conditions comprised a probe concentration of 50 μmol/L, a hybridization temperature of 45℃ and a hybridization time of 2 h. The optimal concentration of nanogold-streptavidin was 4 μg/mL and the optimal staining time was 7 min. The results of specificity evaluation showed that no cross-binding of the probes with each other and no cross-hybridization with Newcastle disease virus, infectious bronchitis virus and infectious laryngotracheitis virus was observed. The optimized microarray assay was significantly more sensitivity than the reverse-transcription PCR assay. The microarray was available after storing at less 90 d at 4 ℃. The optimized microarray assay was validated on clinical specimens and the results showed that it had over 95.6% correlation with reverse-transcription PCR method. Therefore, the microarray assay could be used for the high throughput detection of AIV infections due to H5N1, H7N9 and H9N2.
Collapse
Affiliation(s)
- Hua Xiang
- College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, 611130, China; Sichuan Science-observation Experimental Station of Veterinary Drugs and Veterinary Diagnostic Technology, Ministry of Agriculture, Chengdu, 611130, China; College of Life Science and Technology, Southwest Minzu University, Chengdu, 610041, China.
| | - Xintian Wen
- College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, 611130, China.
| | - Yiping Wen
- College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, 611130, China.
| | - Huanrong Zhang
- College of Life Science and Technology, Southwest Minzu University, Chengdu, 610041, China.
| | - Sanjie Cao
- College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, 611130, China; Sichuan Science-observation Experimental Station of Veterinary Drugs and Veterinary Diagnostic Technology, Ministry of Agriculture, Chengdu, 611130, China.
| | - Xiaobo Huang
- College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, 611130, China; Sichuan Science-observation Experimental Station of Veterinary Drugs and Veterinary Diagnostic Technology, Ministry of Agriculture, Chengdu, 611130, China.
| | - Rui Wu
- College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, 611130, China; Sichuan Science-observation Experimental Station of Veterinary Drugs and Veterinary Diagnostic Technology, Ministry of Agriculture, Chengdu, 611130, China.
| | - Qin Zhao
- College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, 611130, China; Sichuan Science-observation Experimental Station of Veterinary Drugs and Veterinary Diagnostic Technology, Ministry of Agriculture, Chengdu, 611130, China.
| |
Collapse
|
3
|
Graaf A, Beer M, Harder T. Real-time reverse transcription PCR-based sequencing-independent pathotyping of Eurasian avian influenza A viruses of subtype H7. Virol J 2017; 14:137. [PMID: 28738896 PMCID: PMC5525275 DOI: 10.1186/s12985-017-0808-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2017] [Accepted: 07/14/2017] [Indexed: 12/22/2022] Open
Abstract
Low pathogenic avian influenza viruses (LPAIV) of the subtypes H5 and H7 are known to give rise to highly pathogenic (HP) phenotypes by spontaneous insertional mutations which convert a monobasic trypsin-sensitive endoproteolytical cleavage site (CS) within the hemagglutinin (HA) protein into a polybasic subtilisin-sensitive one. Sporadic outbreaks of notifiable LPAIV H7 infections are continuously recorded in Europe and in Asia, and some lineages showed zoonotic transmission. De novo generation of HPAIV H7 from LPAIV precursors has been reported several times over the past decade. Rapid differentiation between LP and HP H7 virus strains is required as a prerequisite to emplace appropriate control measures. Here, reverse transcription real-time PCR assays (RT-qPCR) were developed and evaluated that allow LP and HP pathotype identification and distinction by probe-assisted detection of the HACS. These new RT-qPCRs allow a sensitive and highly specific pathotype identification of Eurasian subtype H7 AIV in allantoic fluids as well as in diagnostic field samples. RT-qPCR assisted pathotyping presents a rapid and sensitive alternative to pathotyping by animal inoculation or nucleotide sequencing.
Collapse
Affiliation(s)
- Annika Graaf
- Friedrich Loeffler Institute, Institute of Diagnostic Virology, Südufer 10, Greifswald, 17493, Germany
| | - Martin Beer
- Friedrich Loeffler Institute, Institute of Diagnostic Virology, Südufer 10, Greifswald, 17493, Germany
| | - Timm Harder
- Friedrich Loeffler Institute, Institute of Diagnostic Virology, Südufer 10, Greifswald, 17493, Germany.
| |
Collapse
|
4
|
Sultankulova KT, Kozhabergenov NS, Strochkov VM, Burashev YD, Shorayeva KA, Chervyakova OV, Rametov NM, Sandybayev NT, Sansyzbay AR, Orynbayev MB. New oligonucleotide microarray for rapid diagnosis of avian viral diseases. Virol J 2017; 14:69. [PMID: 28381285 PMCID: PMC5382490 DOI: 10.1186/s12985-017-0738-0] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2017] [Accepted: 03/28/2017] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND We developed a new oligonucleotide microarray comprising 16 identical subarrays for simultaneous rapid detection of avian viruses: avian influenza virus (AIV), Newcastle disease virus (NDV), infection bronchitis virus (IBV), and infectious bursal disease virus (IBDV) in single- and mixed-virus infections. The objective of the study was to develop an oligonucleotide microarray for rapid diagnosis of avian diseases that would be used in the course of mass analysis for routine epidemiological surveillance owing to its ability to test one specimen for several infections. METHODS AND RESULTS The paper describes the technique for rapid and simultaneous diagnosis of avian diseases such as avian influenza, Newcastle disease, infectious bronchitis and infectious bursal disease with use of oligonucleotide microarray, conditions for hybridization of fluorescent-labelled viral cDNA on the microarray and its specificity tested with use of AIV, NDV, IBV, IBDV strains as well as biomaterials from poultry. Sensitivity and specificity of the developed microarray was evaluated with use of 122 specimens of biological material: 44 cloacal swabs from sick birds and 78 tissue specimens from dead wild and domestic birds, as well as with use of 15 AIV, NDV, IBV and IBDV strains, different in their origin, epidemiological and biological characteristics (RIBSP Microbial Collection). This microarray demonstrates high diagnostic sensitivity (99.16% within 95% CI limits 97.36-100%) and specificity (100%). Specificity of the developed technique was confirmed by direct sequencing of NP and M (AIV), VP2 (IBDV), S1 (IBV), NP (NDV) gene fragments. CONCLUSION Diagnostic effectiveness of the developed DNA microarray is 99.18% and therefore it can be used in mass survey for specific detection of AIV, NDV, IBV and IBDV circulating in the region in the course of epidemiological surveillance. Rather simple method for rapid diagnosis of avian viral diseases that several times shortens duration of assay versus classical diagnostic methods is proposed.
Collapse
Affiliation(s)
- Kulyaisan T Sultankulova
- Research Institute for Biological Safety Problems (RIBSP), Science Committee of RK ME&S, Gvardeiskiy, 080409, Republic of Kazakhstan.
| | - Nurlan S Kozhabergenov
- Research Institute for Biological Safety Problems (RIBSP), Science Committee of RK ME&S, Gvardeiskiy, 080409, Republic of Kazakhstan
| | - Vitaliy M Strochkov
- Research Institute for Biological Safety Problems (RIBSP), Science Committee of RK ME&S, Gvardeiskiy, 080409, Republic of Kazakhstan
| | - Yerbol D Burashev
- Research Institute for Biological Safety Problems (RIBSP), Science Committee of RK ME&S, Gvardeiskiy, 080409, Republic of Kazakhstan
| | - Kamshat A Shorayeva
- Research Institute for Biological Safety Problems (RIBSP), Science Committee of RK ME&S, Gvardeiskiy, 080409, Republic of Kazakhstan
| | - Olga V Chervyakova
- Research Institute for Biological Safety Problems (RIBSP), Science Committee of RK ME&S, Gvardeiskiy, 080409, Republic of Kazakhstan
| | - Nurkuisa M Rametov
- Research Institute for Biological Safety Problems (RIBSP), Science Committee of RK ME&S, Gvardeiskiy, 080409, Republic of Kazakhstan
| | - Nurlan T Sandybayev
- Research Institute for Biological Safety Problems (RIBSP), Science Committee of RK ME&S, Gvardeiskiy, 080409, Republic of Kazakhstan
| | - Abylay R Sansyzbay
- Research Institute for Biological Safety Problems (RIBSP), Science Committee of RK ME&S, Gvardeiskiy, 080409, Republic of Kazakhstan
| | - Mukhit B Orynbayev
- Research Institute for Biological Safety Problems (RIBSP), Science Committee of RK ME&S, Gvardeiskiy, 080409, Republic of Kazakhstan
| |
Collapse
|
5
|
Schelm S, Haase I, Fischer C, Fischer M. Development of a Multiplex Real-Time PCR for Determination of Apricot in Marzipan Using the Plexor System. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2017; 65:516-522. [PMID: 27943676 DOI: 10.1021/acs.jafc.6b04457] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Marzipan is a confectionary which is mostly offered in form of filled chocolate, pralines, or pure. According to the German guidelines for oil seeds only almonds, sugar and water are admitted ingredients of marzipan. A product very similar in taste is persipan which is used in the confectionary industry because of its stronger flavor. For persipan production almonds are replaced by debittered apricot or peach kernels. To guarantee high quality products for consumers, German raw paste producers have agreed a limit of apricot kernels in marzipan raw paste of 0.5%. Different DNA-based methods for quantitation of persipan contaminations in marzipan are already published. To increase the detection specificity compared to published intercalation dye-based assays, the present work demonstrate the utilization of a multiplex real-time PCR based on the Plexor technology. Thus, the present work enables the detection of at least 0.1% apricot DNA in almond DNA or less. By analyzing DNA mixtures, the theoretical limit of quantification of the duplex PCR for the quantitation of persipan raw paste DNA in marzipan raw paste DNA was determined as 0.05%.
Collapse
Affiliation(s)
- Stefanie Schelm
- Hamburg School of Food Science, Institute of Food Chemistry, University of Hamburg , Grindelallee 117, 20146 Hamburg, Germany
| | - Ilka Haase
- Hamburg School of Food Science, Institute of Food Chemistry, University of Hamburg , Grindelallee 117, 20146 Hamburg, Germany
| | - Christin Fischer
- Hamburg School of Food Science, Institute of Food Chemistry, University of Hamburg , Grindelallee 117, 20146 Hamburg, Germany
| | - Markus Fischer
- Hamburg School of Food Science, Institute of Food Chemistry, University of Hamburg , Grindelallee 117, 20146 Hamburg, Germany
| |
Collapse
|
6
|
Tahir M, Mehmood D, Sultan A, Saeed M, Khan A, Ansari F, Salman M, Majeed K. A modified strategy of multiplex RT-PCR for simultaneous detection of H5, H7, and H9 subtypes of avian influenza virus based on common forward oligo. J APPL POULTRY RES 2016. [DOI: 10.3382/japr/pfw014] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
|
7
|
Accurate Detection of Avian Respiratory Viruses by Use of Multiplex PCR-Based Luminex Suspension Microarray Assay. J Clin Microbiol 2016; 54:2716-2725. [PMID: 27558184 DOI: 10.1128/jcm.00610-16] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2016] [Accepted: 08/18/2016] [Indexed: 02/07/2023] Open
Abstract
A novel oligonucleotide suspension microarray (Luminex microsphere system) was developed for the rapid detection of avian respiratory viruses of major clinical importance. This test was optimized and validated with 70 clinical samples. The developed tool was accurate for high-throughput detection and differentiation of the most important avian respiratory viruses: avian influenza virus (AIV), Newcastle disease virus (NDV), infection bronchitis virus (IBV), and infectious laryngotracheitis virus (ILTV) in single- and mixed-virus infections. A multiplex reverse transcriptase PCR (RT-PCR), followed by a monoplex or a multiplex Luminex assays, were realized using a Luminex 200 analyzer instrument. The sensitivity, specificity, and reproducibility of the multiplex DNA suspension microarray system were evaluated. The results showed no significant differences in the median fluorescence intensity (MFI) value in monoplex and multiplex Luminex assays. The sensitivity and specificity proved to be completely concordant with monoplex real-time RT-PCR. We demonstrated that the multiplex DNA suspension microarray system is an accurate, high-throughput, and relatively simple method for the rapid detection of the main respiratory viruses of poultry.
Collapse
|
8
|
Detection of influenza A virus from live-bird market poultry swab samples in China by a pan-IAV, one-step reverse-transcription FRET-PCR. Sci Rep 2016; 6:30015. [PMID: 27445010 PMCID: PMC4957103 DOI: 10.1038/srep30015] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2016] [Accepted: 06/27/2016] [Indexed: 12/21/2022] Open
Abstract
The persistent public health threat of animal to human transmission of influenza A virus (IAV) has stimulated interest in rapid and accurate detection of all IAV subtypes in clinical specimens of animal origin. In this study, a new set of primers and probes was designed for one-step pan-IAV reverse-transcription fluorescence resonance energy transfer (FRET)-PCR. The detection limit of one-step pan-IAV RT FRET-PCR was 10 copies of the matrix gene per reaction, and proved to be equivalent or superior to virus isolation in detecting nine IAV subtypes. Application of the pan-IAV RT FRET-PCR to oral-pharyngeal and cloacal swab specimens collected from healthy poultry in 34 live bird markets in 24 provinces of China revealed that 9.2% of the animals (169/1,839) or 6.3% of their oral-pharyngeal or cloacal swabs (233/3,678) were positive for IAV, and 56.8% of IAV-positive samples were of the H9N2 subtype. Paralleling detection of IAV in H9N2-infected SPF chickens and chickens from LBM showed that pan-IAV FRET-PCR had a higher detection limit than virus isolation in eggs while the results by FRET-PCR and virus isolation overall matched. It is expected that this strategy can be useful for facile surveillance for IAV in clinical samples from a variety of sources.
Collapse
|
9
|
Wang LC, Huang D, Chen HW. Simultaneous subtyping and pathotyping of avian influenza viruses in chickens in Taiwan using reverse transcription loop-mediated isothermal amplification and microarray. J Vet Med Sci 2016; 78:1223-8. [PMID: 27086860 PMCID: PMC5053921 DOI: 10.1292/jvms.15-0602] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023] Open
Abstract
The H6N1 avian influenza virus has circulated in Taiwan for more than 40 years. The sporadic activity of low pathogenic H5N2 virus has been noted since 2003, and highly pathogenic H5N2 avian influenza virus has been detected since 2008. Ressortant viruses between H6N1 and H5N2 viruses have become established and enzootic in chickens throughout Taiwan. Outbreaks caused by Novel highly pathogenic H5 avian influenza viruses whose HA genes were closely related to that of the H5N8 virus isolated from ducks in Korea in 2014 were isolated from outbreaks in Taiwan since early 2015. The avian influenza virus infection status is becoming much more complicated in chickens in Taiwan. This necessitates a rapid and simple approach to detect and differentiate the viruses that prevail. H6N1, H5N2 and novel H5 viruses were simultaneously subtyped and pathotyped in this study using reverse transcription loop-mediated isothermal amplification and microarray, with detection limits of 10°, 10(1) and 10° viral copy numbers, respectively. The microarray signals were read by the naked eye with no expensive equipment needed. The method developed in this study could greatly improve avian influenza virus surveillance efficiency.
Collapse
Affiliation(s)
- Lih-Chiann Wang
- School of Veterinary Medicine, National Taiwan University, No 1, Sec 4, Roosevelt Rd, Taipei 10617, Taiwan
| | | | | |
Collapse
|
10
|
Granberg F, Karlsson OE, Leijon M, Liu L, Belák S. Molecular approaches to recognize relevant and emerging infectious diseases in animals. Methods Mol Biol 2015; 1247:109-24. [PMID: 25399090 PMCID: PMC7123086 DOI: 10.1007/978-1-4939-2004-4_7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/31/2023]
Abstract
Since the introduction of the first molecular tests, there has been a continuous effort to develop new and improved assays for rapid and efficient detection of infectious agents. This has been motivated by a need for improved sensitivity as well as results that can be easily communicated. The experiences and knowledge gained at the World Organisation for Animal Health (OIE) Collaborating Centre for Biotechnology-based Diagnosis of Infectious Diseases in Veterinary Medicine, Uppsala, Sweden, will here be used to provide an overview of the different molecular approaches that can be used to diagnose and identify relevant and emerging infectious diseases in animals.
Collapse
Affiliation(s)
- Fredrik Granberg
- OIE Collaborating Centre for the Biotechnology-Based Diagnosis of Infectious Diseases in Veterinary Medicine, Swedish University of Agricultural Sciences (SLU), Uppsala, Sweden,
| | | | | | | | | |
Collapse
|
11
|
Khaliq Z, Leijon M, Belák S, Komorowski J. A complete map of potential pathogenicity markers of avian influenza virus subtype H5 predicted from 11 expressed proteins. BMC Microbiol 2015; 15:128. [PMID: 26112351 PMCID: PMC4482282 DOI: 10.1186/s12866-015-0465-x] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2015] [Accepted: 06/12/2015] [Indexed: 01/18/2023] Open
Abstract
Background Polybasic cleavage sites of the hemagglutinin (HA) proteins are considered to be the most important determinants indicating virulence of the avian influenza viruses (AIV). However, evidence is accumulating that these sites alone are not sufficient to establish high pathogenicity. There need to exist other sites located on the HA protein outside the cleavage site or on the other proteins expressed by AIV that contribute to the pathogenicity. Results We employed rule-based computational modeling to construct a map, with high statistical significance, of amino acid (AA) residues associated to pathogenicity in 11 proteins of the H5 type viruses. We found potential markers of pathogenicity in all of the 11 proteins expressed by the H5 type of AIV. AA mutations S-43HA1-D, D-83HA1-A in HA; S-269-D, E-41-H in NA; S-48-N, K-212-N in NS1; V-166-A in M1; G-14-E in M2; K-77-R, S-377-N in NP; and Q-48-P in PB1-F2 were identified as having a potential to shift the pathogenicity from low to high. Our results suggest that the low pathogenicity is common to most of the subtypes of the H5 AIV while the high pathogenicity is specific to each subtype. The models were developed using public data and validated on new, unseen sequences. Conclusions Our models explicitly define a viral genetic background required for the virus to be highly pathogenic and thus confirm the hypothesis of the presence of pathogenicity markers beyond the cleavage site. Electronic supplementary material The online version of this article (doi:10.1186/s12866-015-0465-x) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Zeeshan Khaliq
- Department of Cell and Molecular Biology, Computational and Systems Biology, Science for Life Laboratory, Uppsala University, SE-751 24, Uppsala, Sweden.
| | - Mikael Leijon
- Department of Virology, Parasitology and Immunobiology (VIP), National Veterinary Institute (SVA), Uppsala, Sweden. .,OIE Collaborating Centre for the Biotechnology-based Diagnosis of Infectious Diseases in Veterinary Medicine, Ulls väg 2B and 26, SE-756 89, Uppsala, Sweden.
| | - Sándor Belák
- OIE Collaborating Centre for the Biotechnology-based Diagnosis of Infectious Diseases in Veterinary Medicine, Ulls väg 2B and 26, SE-756 89, Uppsala, Sweden. .,Department of Biomedical Sciences and Veterinary Public Health (BVF), Swedish University of Agricultural Sciences (SLU), Uppsala, Sweden.
| | - Jan Komorowski
- Department of Cell and Molecular Biology, Computational and Systems Biology, Science for Life Laboratory, Uppsala University, SE-751 24, Uppsala, Sweden. .,Institute of Computer Science, Polish Academy of Sciences, 01-248, Warszawa, Poland.
| |
Collapse
|
12
|
Wang LC, Huang D, Cheng MC, Lee SH, Wang CH. H5 avian influenza virus pathotyping using oligonucleotide microarray. J Virol Methods 2015; 220:39-42. [PMID: 25896189 DOI: 10.1016/j.jviromet.2015.04.006] [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: 11/12/2014] [Revised: 04/02/2015] [Accepted: 04/07/2015] [Indexed: 12/09/2022]
Abstract
The H5 avian influenza virus subtype has huge impact on the poultry industry. Rapid diagnosis and accurate identification of the highly pathogenic avian influenza virus and low-pathogenicity avian influenza virus is essential, especially during H5 outbreaks and surveillance. To this end, a novel and rapid strategy for H5 virus molecular pathotyping is presented. The specific hemagglutinin gene of the H5 virus and the basic amino acid number of the motif at the hemagglutinin precursor protein cleavage site were detected using oligonucleotide microarray. Highly pathogenic and low-pathogenicity avian influenza viruses in Taiwan were differentiated using 13 microarray probes with the naked eye. The detection limit reached 3.4 viral RNA copies, 1000 times more sensitive than reverse transcription polymerase chain reaction. Thus, the oligonucleotide microarray would provide an alternative H5 pathogenicity determination using the naked eye for laboratories lacking facilities.
Collapse
Affiliation(s)
- Lih-Chiann Wang
- School of Veterinary Medicine, National Taiwan University, No. 1, Sec. 4, Roosevelt Road, Taipei 10617, Taiwan.
| | - Dean Huang
- School of Veterinary Medicine, National Taiwan University, No. 1, Sec. 4, Roosevelt Road, Taipei 10617, Taiwan.
| | - Ming-Chu Cheng
- Animal Health Research Institute, Council of Agriculture, Taipei, Taiwan.
| | - Shu-Hwae Lee
- Animal Health Research Institute, Council of Agriculture, Taipei, Taiwan.
| | - Ching-Ho Wang
- School of Veterinary Medicine, National Taiwan University, No. 1, Sec. 4, Roosevelt Road, Taipei 10617, Taiwan.
| |
Collapse
|
13
|
Kalthoff D, Bogs J, Harder T, Grund C, Pohlmann A, Beer M, Hoffmann B. Nucleic acid-based detection of influenza A virus subtypes H7 and N9 with a special emphasis on the avian H7N9 virus. ACTA ACUST UNITED AC 2014; 19. [PMID: 24650867 DOI: 10.2807/1560-7917.es2014.19.10.20731] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
In 2013, a novel influenza A virus of subtype H7N9 was transmitted from avian sources to humans in China, causing severe illness and substantial mortality. Rapid and sensitive diagnostic approaches are the basis of epidemiological studies and of utmost importance for the detection of infected humans and animals. We developed various quantitative reverse transcriptase PCR (RT-qPCR) assays for (i) the generic detection of the haemagglutinin (HA) gene of H7 viruses or the neuraminidase (NA) gene of N9 viruses, and (ii) the specific detection of HA and NA of the novel avian H7N9/2013 virus. The sensitivity of the newly developed assays was compared with previously published PCRs, and the specificity of all RT-qPCRs was examined using a panel of 42 different H7 and 16 different N9 isolates. Furthermore, we analysed the performance of the RT-qPCR assays with dilution series and diagnostic samples obtained from animal experiments. Our study provides a comprehensive set of RT-qPCR assays for the reliable detection of the novel avian H7N9 virus, with high sensitivity and improved and tailored specificity values compared with published assays. Finally, we also present data about the robustness of a duplex assay for the simultaneous detection of HA and NA of the avian influenza H7N9/2013 virus.
Collapse
Affiliation(s)
- D Kalthoff
- Friedrich-Loeffler-Institute, Institute of Diagnostic Virology, Greifswald-Insel Riems, Germany
| | | | | | | | | | | | | |
Collapse
|
14
|
Pinette MM, Rodriguez-Lecompte JC, Pasick J, Ojkic D, Leith M, Suderman M, Berhane Y. Development of a duplex Fluorescent Microsphere Immunoassay (FMIA) for the detection of antibody responses to influenza A and newcastle disease viruses. J Immunol Methods 2014; 405:167-77. [DOI: 10.1016/j.jim.2014.02.004] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2013] [Revised: 02/05/2014] [Accepted: 02/06/2014] [Indexed: 11/26/2022]
|
15
|
Leijon M, Belák S. Review of a new molecular virus pathotyping method in the context of bioterrorism. Biosecur Bioterror 2013; 11 Suppl 1:S241-6. [PMID: 23971812 DOI: 10.1089/bsp.2012.0087] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
Avian influenza virus (AIV) and Newcastle disease virus (NDV) infect various avian species including domestic poultry. Clinical manifestations vary from subclinical or mild to severe multiorgan systemic disease with a near 100% mortality rate. Severe disease is caused by highly virulent specific virus strains, termed highly pathogenic AIV and velogenic NDV. Recent controversial influenza H5 adaptation studies in ferrets have highlighted the importance of preparedness against AIV as a bioterrorism agent. Furthermore, NDV also has zoonotic potential, although symptoms in humans are mild and self-limiting for naturally occurring viruses. Thus, both of these viruses pose a direct biothreat to domestic poultry but also indirectly to humans via zoonotic transmission. For diagnosis and rapid containment of disease, it is crucial to differentiate highly pathogenic AIVs and NDVs from frequently occurring low pathogenic variants. Recently, we developed a novel strategy for pathotyping of AIV and NDV that we review here. The method should be ideal for rapid testing and surveillance in food safety, for wild bird monitoring, and for combating acts of bioterrorism.
Collapse
Affiliation(s)
- Mikael Leijon
- Mikael Leijon, PhD, is Associate Professor and head of the group for molecular characterization and bioinformatics, Division of Virology, Immunobiology and Parasitology (VIP), and Sándor Belák, DVM, PhD, DSc, is a Professor, both at the National Veterinary Institute , Uppsala, Sweden . Dr. Belák is also Director of the Collaborative Center of the World Organization for Animal Health (OIE) for the Biotechnology-based Diagnosis of Infectious Diseases in Veterinary Medicine
| | | |
Collapse
|
16
|
Development of a novel real-time PCR-based strategy for simple and rapid molecular pathotyping of Newcastle disease virus. Arch Virol 2012; 157:833-44. [PMID: 22302287 DOI: 10.1007/s00705-012-1231-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2011] [Accepted: 12/12/2011] [Indexed: 02/01/2023]
Abstract
A novel real-time PCR strategy was applied to simultaneously detect and to discriminate low-pathogenic lentogenic and virulent meso/velogenic Newcastle disease virus (NDV). The pathotyping is achieved by a three-step semi-nested PCR. A pre-amplification of the cleavage site (CS) region of the F gene is followed by a two-level duplex real-time PCR directly targeting the CS, combining detection and pathotyping in a single tube. A wide range of NDV isolates spanning all genotypes were successfully detected and pathotyped. Clinical samples from outbreaks in Sweden in 2010 that were positive by the novel PCR method were also successfully pathotyped. The method is time-saving, reduces labour and costs and provides opportunities for rapid diagnosis at remote locations and in the field. Since the same strategy was also recently applied to avian influenza virus pathotyping, it shows promise of finding broad utility in diagnostics of infectious diseases caused by different RNA viruses in various hosts.
Collapse
|
17
|
Vlasakova M, Jackova A, Leskova V, Vilcek S. Development of a Plexor real-time PCR assay for the detection of porcine circovirus type 2. J Virol Methods 2012; 179:311-5. [DOI: 10.1016/j.jviromet.2011.11.014] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2011] [Revised: 11/04/2011] [Accepted: 11/14/2011] [Indexed: 11/16/2022]
|