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Lu XM, Feng XY, Wu Y, Wen CB, Liu H, Zhang DX. Genetic characterization of a novel H5N6 subtype highly pathogenic avian influenza virus from goose in China. J Infect 2023; 87:e94-e95. [PMID: 37838253 DOI: 10.1016/j.jinf.2023.10.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2023] [Accepted: 10/10/2023] [Indexed: 10/16/2023]
Affiliation(s)
- Xi-Ming Lu
- School of Life Science and Engineering, Foshan University, Foshan 528225, China
| | - Xiang-Yan Feng
- School of Life Science and Engineering, Foshan University, Foshan 528225, China
| | - Yue Wu
- School of Life Science and Engineering, Foshan University, Foshan 528225, China
| | - Cheng-Bo Wen
- School of Life Science and Engineering, Foshan University, Foshan 528225, China
| | - Hao Liu
- School of Life Science and Engineering, Foshan University, Foshan 528225, China
| | - De-Xian Zhang
- School of Life Science and Engineering, Foshan University, Foshan 528225, China.
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2
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Yao XY, Lian CY, Lv ZH, Zhang XL, Shao JW. Emergence of a novel reassortant H5N6 subtype highly pathogenic avian influenza virus in farmed dogs in China. J Infect 2023; 87:e70-e72. [PMID: 37507094 DOI: 10.1016/j.jinf.2023.07.013] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2023] [Accepted: 07/22/2023] [Indexed: 07/30/2023]
Affiliation(s)
- Xin-Yan Yao
- School of Life Science and Engineering, Foshan University, Foshan 528225, China
| | - Chun-Yang Lian
- School of Life Science and Engineering, Foshan University, Foshan 528225, China
| | - Zhi-Hang Lv
- School of Life Science and Engineering, Foshan University, Foshan 528225, China
| | - Xue-Lian Zhang
- School of Life Science and Engineering, Foshan University, Foshan 528225, China
| | - Jian-Wei Shao
- School of Life Science and Engineering, Foshan University, Foshan 528225, China.
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3
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Yang XY, Gong QL, Li YJ, Ata EB, Hu MJ, Sun YY, Xue ZY, Yang YS, Sun XP, Shi CW, Yang GL, Huang HB, Jiang YL, Wang JZ, Cao X, Wang N, Zeng Y, Yang WT, Wang CF. The global prevalence of highly pathogenic avian influenza A (H5N8) infection in birds: A systematic review and meta-analysis. Microb Pathog 2023; 176:106001. [PMID: 36682670 DOI: 10.1016/j.micpath.2023.106001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2022] [Revised: 01/18/2023] [Accepted: 01/18/2023] [Indexed: 01/20/2023]
Abstract
The zoonotic pathogen avian influenza A H5N8 causes enormous economic losses in the poultry industry and poses a serious threat to the public health. Here, we report the first systematic review and meta-analysis of the worldwide prevalence of birds. We filtered 45 eligible articles from seven databases. A random-effects model was used to analyze the prevalence of H5N8 in birds. The pooled prevalence of H5N8 in birds was 1.6%. In the regions, Africa has the highest prevalence (8.0%). Based on the source, village (8.3%) was the highest. In the sample type, the highest prevalence was organs (79.7%). In seasons, the highest prevalence was autumn (28.1%). The largest prevalence in the sampling time was during 2019 or later (7.0%). Furthermore, geographical factors also were associated with the prevalence. Therefore, we recommend site-specific prevention and control tools for this strain in birds and enhance the surveillance to reduce the spread of H5N8.
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Affiliation(s)
- Xue-Yao Yang
- College of Veterinary Medicine, College of Animal Science and Technology, Jilin Provincial Engineering Research Center of Animal Probiotics, Key Laboratory of Animal Production and Product Quality Safety of Ministry of Education, Jilin Agricultural University, 2888 Xincheng Street, Changchun, 130118, China
| | - Qing-Long Gong
- College of Veterinary Medicine, College of Animal Science and Technology, Jilin Provincial Engineering Research Center of Animal Probiotics, Key Laboratory of Animal Production and Product Quality Safety of Ministry of Education, Jilin Agricultural University, 2888 Xincheng Street, Changchun, 130118, China
| | - Yan-Jin Li
- College of Veterinary Medicine, College of Animal Science and Technology, Jilin Provincial Engineering Research Center of Animal Probiotics, Key Laboratory of Animal Production and Product Quality Safety of Ministry of Education, Jilin Agricultural University, 2888 Xincheng Street, Changchun, 130118, China
| | - Emad Beshir Ata
- Parasitology and Animal Diseases Dep., Vet. Res. Institute, National Research Centre, 12622, Dokki, Cairo, Egypt
| | - Man-Jie Hu
- College of Veterinary Medicine, College of Animal Science and Technology, Jilin Provincial Engineering Research Center of Animal Probiotics, Key Laboratory of Animal Production and Product Quality Safety of Ministry of Education, Jilin Agricultural University, 2888 Xincheng Street, Changchun, 130118, China
| | - Yong-Yang Sun
- College of Veterinary Medicine, College of Animal Science and Technology, Jilin Provincial Engineering Research Center of Animal Probiotics, Key Laboratory of Animal Production and Product Quality Safety of Ministry of Education, Jilin Agricultural University, 2888 Xincheng Street, Changchun, 130118, China
| | - Zhi-Yang Xue
- College of Veterinary Medicine, College of Animal Science and Technology, Jilin Provincial Engineering Research Center of Animal Probiotics, Key Laboratory of Animal Production and Product Quality Safety of Ministry of Education, Jilin Agricultural University, 2888 Xincheng Street, Changchun, 130118, China
| | - Ying-Shi Yang
- College of Veterinary Medicine, College of Animal Science and Technology, Jilin Provincial Engineering Research Center of Animal Probiotics, Key Laboratory of Animal Production and Product Quality Safety of Ministry of Education, Jilin Agricultural University, 2888 Xincheng Street, Changchun, 130118, China
| | - Xue-Pan Sun
- College of Veterinary Medicine, College of Animal Science and Technology, Jilin Provincial Engineering Research Center of Animal Probiotics, Key Laboratory of Animal Production and Product Quality Safety of Ministry of Education, Jilin Agricultural University, 2888 Xincheng Street, Changchun, 130118, China
| | - Chun-Wei Shi
- College of Veterinary Medicine, College of Animal Science and Technology, Jilin Provincial Engineering Research Center of Animal Probiotics, Key Laboratory of Animal Production and Product Quality Safety of Ministry of Education, Jilin Agricultural University, 2888 Xincheng Street, Changchun, 130118, China
| | - Gui-Lian Yang
- College of Veterinary Medicine, College of Animal Science and Technology, Jilin Provincial Engineering Research Center of Animal Probiotics, Key Laboratory of Animal Production and Product Quality Safety of Ministry of Education, Jilin Agricultural University, 2888 Xincheng Street, Changchun, 130118, China
| | - Hai-Bin Huang
- College of Veterinary Medicine, College of Animal Science and Technology, Jilin Provincial Engineering Research Center of Animal Probiotics, Key Laboratory of Animal Production and Product Quality Safety of Ministry of Education, Jilin Agricultural University, 2888 Xincheng Street, Changchun, 130118, China
| | - Yan-Long Jiang
- College of Veterinary Medicine, College of Animal Science and Technology, Jilin Provincial Engineering Research Center of Animal Probiotics, Key Laboratory of Animal Production and Product Quality Safety of Ministry of Education, Jilin Agricultural University, 2888 Xincheng Street, Changchun, 130118, China
| | - Jian-Zhong Wang
- College of Veterinary Medicine, College of Animal Science and Technology, Jilin Provincial Engineering Research Center of Animal Probiotics, Key Laboratory of Animal Production and Product Quality Safety of Ministry of Education, Jilin Agricultural University, 2888 Xincheng Street, Changchun, 130118, China
| | - Xin Cao
- College of Veterinary Medicine, College of Animal Science and Technology, Jilin Provincial Engineering Research Center of Animal Probiotics, Key Laboratory of Animal Production and Product Quality Safety of Ministry of Education, Jilin Agricultural University, 2888 Xincheng Street, Changchun, 130118, China
| | - Nan Wang
- College of Veterinary Medicine, College of Animal Science and Technology, Jilin Provincial Engineering Research Center of Animal Probiotics, Key Laboratory of Animal Production and Product Quality Safety of Ministry of Education, Jilin Agricultural University, 2888 Xincheng Street, Changchun, 130118, China
| | - Yan Zeng
- College of Veterinary Medicine, College of Animal Science and Technology, Jilin Provincial Engineering Research Center of Animal Probiotics, Key Laboratory of Animal Production and Product Quality Safety of Ministry of Education, Jilin Agricultural University, 2888 Xincheng Street, Changchun, 130118, China
| | - Wen-Tao Yang
- College of Veterinary Medicine, College of Animal Science and Technology, Jilin Provincial Engineering Research Center of Animal Probiotics, Key Laboratory of Animal Production and Product Quality Safety of Ministry of Education, Jilin Agricultural University, 2888 Xincheng Street, Changchun, 130118, China.
| | - Chun-Feng Wang
- College of Veterinary Medicine, College of Animal Science and Technology, Jilin Provincial Engineering Research Center of Animal Probiotics, Key Laboratory of Animal Production and Product Quality Safety of Ministry of Education, Jilin Agricultural University, 2888 Xincheng Street, Changchun, 130118, China.
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4
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Wan L, Ma J, Yi J, Dong Y, Niu R, Su Y, Li Q, Dan Zhu, Chao J, Su S, Fan C, Wang L, Wan Y. CRISPR-empowered hybridization chain reaction amplification for an attomolar electrochemical sensor. Chem Commun (Camb) 2022; 58:8826-8829. [PMID: 35848536 DOI: 10.1039/d2cc01155g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Rapid pathogen screening holds the key against certain viral infections, especially in an overwhelming pandemic. Herein, a CRISPR-empowered electrochemical biosensor was designed for the ultrasensitive detection of the avian influenza A (H7N9) virus gene sequence. Combining the CRISPR/Cas system, a signal-amplification strategy and a high-conductivity sensing substrate, the developed biosensor showed an ultrawide dynamic range, an ultralow detection limit, and excellent selectivity for H7N9 detection, providing a potential sensing platform for the simple, fast, sensitive, and on-site detection of infectious diseases.
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Affiliation(s)
- Ling Wan
- State Key Laboratory of Organic Electronics and Information Displays & Jiangsu Key Laboratory for Biosensors, Institute of Advanced Materials (IAM), Nanjing University of Posts and Telecommunications, 9 Wenyuan Road, Nanjing 210023, China.
| | - Jianfeng Ma
- State Key Laboratory of Organic Electronics and Information Displays & Jiangsu Key Laboratory for Biosensors, Institute of Advanced Materials (IAM), Nanjing University of Posts and Telecommunications, 9 Wenyuan Road, Nanjing 210023, China.
| | - Jiasheng Yi
- State Key Laboratory of Organic Electronics and Information Displays & Jiangsu Key Laboratory for Biosensors, Institute of Advanced Materials (IAM), Nanjing University of Posts and Telecommunications, 9 Wenyuan Road, Nanjing 210023, China.
| | - Yan Dong
- State Key Laboratory of Organic Electronics and Information Displays & Jiangsu Key Laboratory for Biosensors, Institute of Advanced Materials (IAM), Nanjing University of Posts and Telecommunications, 9 Wenyuan Road, Nanjing 210023, China.
| | - Renjie Niu
- State Key Laboratory of Organic Electronics and Information Displays & Jiangsu Key Laboratory for Biosensors, Institute of Advanced Materials (IAM), Nanjing University of Posts and Telecommunications, 9 Wenyuan Road, Nanjing 210023, China.
| | - Yan Su
- School of Mechanical Engineering, Nanjing University of Science and Technology, Nanjing 210094, China.
| | - Qian Li
- School of Chemistry and Chemical Engineering, Frontiers Science Center for Transformative Molecules and National Center for Translational Medicine, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Dan Zhu
- State Key Laboratory of Organic Electronics and Information Displays & Jiangsu Key Laboratory for Biosensors, Institute of Advanced Materials (IAM), Nanjing University of Posts and Telecommunications, 9 Wenyuan Road, Nanjing 210023, China.
| | - Jie Chao
- State Key Laboratory of Organic Electronics and Information Displays & Jiangsu Key Laboratory for Biosensors, Institute of Advanced Materials (IAM), Nanjing University of Posts and Telecommunications, 9 Wenyuan Road, Nanjing 210023, China.
| | - Shao Su
- State Key Laboratory of Organic Electronics and Information Displays & Jiangsu Key Laboratory for Biosensors, Institute of Advanced Materials (IAM), Nanjing University of Posts and Telecommunications, 9 Wenyuan Road, Nanjing 210023, China.
| | - Chunhai Fan
- School of Chemistry and Chemical Engineering, Frontiers Science Center for Transformative Molecules and National Center for Translational Medicine, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Lianhui Wang
- State Key Laboratory of Organic Electronics and Information Displays & Jiangsu Key Laboratory for Biosensors, Institute of Advanced Materials (IAM), Nanjing University of Posts and Telecommunications, 9 Wenyuan Road, Nanjing 210023, China.
| | - Ying Wan
- School of Mechanical Engineering, Nanjing University of Science and Technology, Nanjing 210094, China.
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5
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Nishiyama K, Takahashi K, Fukuyama M, Kasuya M, Imai A, Usukura T, Maishi N, Maeki M, Ishida A, Tani H, Hida K, Shigemura K, Hibara A, Tokeshi M. Facile and rapid detection of SARS-CoV-2 antibody based on a noncompetitive fluorescence polarization immunoassay in human serum samples. Biosens Bioelectron 2021; 190:113414. [PMID: 34130087 PMCID: PMC8178067 DOI: 10.1016/j.bios.2021.113414] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2021] [Revised: 05/27/2021] [Accepted: 06/03/2021] [Indexed: 01/14/2023]
Abstract
Antibody detection methods for viral infections have received broad attention due to the COVID-19 pandemic. In addition, there remains an ever-increasing need to quantitatively evaluate the immune response to develop vaccines and treatments for COVID-19. Here, we report an analytical method for the rapid and quantitative detection of SARS-CoV-2 antibody in human serum by fluorescence polarization immunoassay (FPIA). A recombinant SARS-CoV-2 receptor binding domain (RBD) protein labeled with HiLyte Fluor 647 (F-RBD) was prepared and used for FPIA. When the anti-RBD antibody in human serum binds to F-RBD, the degree of polarization (P) increases by suppressing the rotational diffusion of F-RBD. The measurement procedure required only mixing a reagent containing F-RBD with serum sample and measuring the P value with a portable fluorescence polarization analyzer after 15 min incubation. We evaluated analytical performance of the developed FPIA system using 30 samples: 20 COVID-19 positive sera and 10 negative sera. The receiver operating characteristic curve drawn with the obtained results showed that this FPIA system had high accuracy for discriminating COVID-19 positive or negative serum (AUC = 0.965). The total measurement time was about 20 min, and the serum volume required for measurement was 0.25 μL. Therefore, we successfully developed the FPIA system that enables rapid and easy quantification of SARS-CoV-2 antibody. It is believed that our FPIA system will facilitate rapid on-site identification of infected persons and deepen understanding of the immune response to COVID-19.
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Affiliation(s)
- Keine Nishiyama
- Graduate School of Chemical Sciences and Engineering, Hokkaido University, Kita 13 Nishi 8, Kita-ku, Sapporo, 060-8628, Japan
| | - Kazuki Takahashi
- Graduate School of Chemical Sciences and Engineering, Hokkaido University, Kita 13 Nishi 8, Kita-ku, Sapporo, 060-8628, Japan
| | - Mao Fukuyama
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, Katahira 2-1-1, Aoba-ku, Sendai, 980-8577, Japan
| | - Motohiro Kasuya
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, Katahira 2-1-1, Aoba-ku, Sendai, 980-8577, Japan
| | - Ayuko Imai
- Tianma Japan, Ltd., Shin-Kawasaki Mitsui Building West Tower 28F 1-1-2, Kashimada, Saiwai-ku, Kawasaki, Kanagawa, 212-0058, Japan
| | - Takumi Usukura
- Tianma Japan, Ltd., Shin-Kawasaki Mitsui Building West Tower 28F 1-1-2, Kashimada, Saiwai-ku, Kawasaki, Kanagawa, 212-0058, Japan
| | - Nako Maishi
- Vascular Biology and Molecular Pathology, Graduate School of Dental Medicine, Hokkaido University, Kita 13 Nishi 7, Kita-ku, Sapporo, 060-8586, Japan
| | - Masatoshi Maeki
- Division of Applied Chemistry, Faculty of Engineering, Hokkaido University, Kita 13 Nishi 8, Kita-ku, Sapporo, 060-8628, Japan
| | - Akihiko Ishida
- Division of Applied Chemistry, Faculty of Engineering, Hokkaido University, Kita 13 Nishi 8, Kita-ku, Sapporo, 060-8628, Japan
| | - Hirofumi Tani
- Division of Applied Chemistry, Faculty of Engineering, Hokkaido University, Kita 13 Nishi 8, Kita-ku, Sapporo, 060-8628, Japan
| | - Kyoko Hida
- Vascular Biology and Molecular Pathology, Graduate School of Dental Medicine, Hokkaido University, Kita 13 Nishi 7, Kita-ku, Sapporo, 060-8586, Japan
| | - Koji Shigemura
- Tianma Japan, Ltd., Shin-Kawasaki Mitsui Building West Tower 28F 1-1-2, Kashimada, Saiwai-ku, Kawasaki, Kanagawa, 212-0058, Japan
| | - Akihide Hibara
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, Katahira 2-1-1, Aoba-ku, Sendai, 980-8577, Japan
| | - Manabu Tokeshi
- Division of Applied Chemistry, Faculty of Engineering, Hokkaido University, Kita 13 Nishi 8, Kita-ku, Sapporo, 060-8628, Japan; Innovative Research Centre for Preventive Medical Engineering, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, 464-8601, Japan; Institute of Innovation for Future Society, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, 464-8601, Japan.
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6
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Mirzaei SG, Shoushtari A, Nouri A. Development and Evaluation of Real-Time Reverse Transcription Polymerase Chain Reaction Test for Quantitative and Qualitative Recognition of H5 Subtype of Avian Influenza Viruses. ARCHIVES OF RAZI INSTITUTE 2020; 75:17-22. [PMID: 32291998 DOI: 10.22092/ari.2019.120821.1201] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 04/04/2020] [Accepted: 01/17/2019] [Indexed: 12/16/2022]
Abstract
Avian influenza viruses (AIV) affect a wide range of birds and mammals, cause severe economic damage to the poultry industry, and pose a serious threat to humans. Highly pathogenic avian influenza viruses (HPAI) H5N1 were first identified in Southeast Asia in 1996 and spread to four continents over the following years. The viruses have caused high mortality in chickens and various bird species and deadly infections in humans. Multiple conventional methods have been so far introduced for the detection and identification of avian influenza viruses. Traditional virus isolation methods are gold standard protocol in AI detection; nonetheless, virus isolation in embryonating chicken eggs (ECE) is not a rapid method for the detection of influenza viruses since it is time-consuming and labor-intensive. Furthermore, the isolation of highly pathogenic viruses, such as H5, needs BSL3 laboratories. Real-Time Reverse Transcription-Polymerase Chain Reaction (RRT-PCR) is a sensitive and specific method for the detection of influenza viruses. The application of these nucleic acid-based techniques has increased our ability to identify and perform influenza virus care programs, especially in surveillance programs. The current study aimed to detect H5 subtype of avian influenza (AI) virus using fast, specific, and sensitive TaqMan RRT-PCR. Notably, single step RRT-PCR was used to prevent possible laboratory contamination. The specificity of this test was evaluated using nucleic acid extracted from several poultry pathogenic microorganisms and negative clinical specimens from AI-uninfected birds. The sensitivity analysis of the RRT-PCR assay was performed using in vitro-transcribed RNA copy and 10-fold serial dilution of standard AI virus with specific titer. The results indicated the high sensitivity of this method and the lowest detectable dilution of this method based on RNA copies and 1:10 serial dilutions of the standard virus was 10 1.9 EID50 /100.
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Affiliation(s)
- S G Mirzaei
- Department of Poultry Diseases Research and Diagnosis, Razi Vaccine and Serum Research Institute, Agricultural Research, Education and Extension Organization (AREEO), Karaj, Iran.,Department of Poultry Diseases Research and Diagnosis, Razi Vaccine and Serum Research Institute, Agricultural Research, Education and Extension Organization (AREEO), Karaj, Iran
| | - A Shoushtari
- Department of Poultry Diseases Research and Diagnosis, Razi Vaccine and Serum Research Institute, Agricultural Research, Education and Extension Organization (AREEO), Karaj, Iran
| | - A Nouri
- Department of Poultry Diseases Research and Diagnosis, Razi Vaccine and Serum Research Institute, Agricultural Research, Education and Extension Organization (AREEO), Karaj, Iran
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Isolation and characterization of a novel H7N8 avian influenza virus from domestic ducks in Central China in 2017. Virus Genes 2019; 55:411-414. [PMID: 30895439 DOI: 10.1007/s11262-018-01630-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2018] [Accepted: 12/22/2018] [Indexed: 10/27/2022]
Abstract
In 2017, an H7N8 avian influenza virus (AIV) was isolated from a domestic duck from a farm in Central China. Sequences analysis showed that this strain received its genes from H7, H1, H2, H3, H5, and H6 AIVs of domestic poultry and wild birds in Asia. It exhibited low pathogenicity in chickens and mild pathogenicity in mice. These results suggest the importance of continued surveillance of the H7N8 virus to better understand the ecology and evolution of the AIVs in poultry and wild birds and the potential threat to human health.
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Torrontegi O, Alvarez V, Acevedo P, Gerrikagoitia X, Höfle U, Barral M. Long-term avian influenza virus epidemiology in a small Spanish wetland ecosystem is driven by the breeding Anseriformes community. Vet Res 2019; 50:4. [PMID: 30654831 PMCID: PMC6337815 DOI: 10.1186/s13567-019-0623-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2018] [Accepted: 11/20/2018] [Indexed: 11/12/2022] Open
Abstract
During 2007-2009 and 2012-2014, avian influenza virus (AIV) was studied in a wild avian community of a northern Spanish wetland using non-invasive sampling methods and host identification by COI barcoding. The aim of this longitudinal study was to evaluate AIV dynamics in a natural wetland ecosystem, taking into account both virological aspects and ecological traits of hosts. Global AIV prevalence decreased significantly during the second sampling period (0.3%) compared to the first (6.6%). Circulating subtype distributions were also different between periods, with a noteworthy H5 and H7 subtype richness during the first sampling period. Mallard Anas platyrhynchos was identified as the main AIV host, although not all positive samples could be ascribed to the host. We modelled AIV prevalence with regard to the avian host community composition and meteorological data from the wetland. Statistical analysis revealed seasonal differences in AIV detection, with higher prevalence during the breeding season compared to other phenological events. The model also shows that the lower AIV prevalence during the second study period was associated with a significant reduction of breeding Anseriformes in the wetland, revealing a long-term fluctuation of AIV prevalence driven by the breeding Anseriformes community. This longitudinal study on AIV epidemiology in a natural ecosystem reveals that although prevalence follows seasonal and annual patterns, long-term prevalence fluctuation is linked to the breeding community composition and size. These results are relevant to understanding the influence of host ecology on pathogen transmission for preventing and managing influenza emergence.
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Affiliation(s)
- Olalla Torrontegi
- Animal Health Department, NEIKER-Instituto Vasco de Investigación y Desarrollo Agrario, Parque tecnológico de Bizkaia P-812, 48160 Derio, Bizkaia Spain
| | - Vega Alvarez
- Animal Health Department, NEIKER-Instituto Vasco de Investigación y Desarrollo Agrario, Parque tecnológico de Bizkaia P-812, 48160 Derio, Bizkaia Spain
| | - Pelayo Acevedo
- Grupo SaBio, Instituto de Investigación en Recursos Cinegéticos, IREC (CSIC-UCLM-JCCM), Ronda de Toledo 12, 13071 Ciudad Real, Spain
| | - Xeider Gerrikagoitia
- Animal Health Department, NEIKER-Instituto Vasco de Investigación y Desarrollo Agrario, Parque tecnológico de Bizkaia P-812, 48160 Derio, Bizkaia Spain
| | - Ursula Höfle
- Grupo SaBio, Instituto de Investigación en Recursos Cinegéticos, IREC (CSIC-UCLM-JCCM), Ronda de Toledo 12, 13071 Ciudad Real, Spain
| | - Marta Barral
- Animal Health Department, NEIKER-Instituto Vasco de Investigación y Desarrollo Agrario, Parque tecnológico de Bizkaia P-812, 48160 Derio, Bizkaia Spain
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9
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Choi J, Seong TW, Jeun M, Lee KH. Field-Effect Biosensors for On-Site Detection: Recent Advances and Promising Targets. Adv Healthc Mater 2017; 6. [PMID: 28885777 DOI: 10.1002/adhm.201700796] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2017] [Revised: 07/24/2017] [Indexed: 12/21/2022]
Abstract
There is an explosive interest in the immediate and cost-effective analysis of field-collected biological samples, as many advanced biodetection tools are highly sensitive, yet immobile. On-site biosensors are portable and convenient sensors that provide detection results at the point of care. They are designed to secure precision in highly ionic and heterogeneous solutions with minimal hardware. Among various methods that are capable of such analysis, field-effect biosensors are promising candidates due to their unique sensitivity, manufacturing scalability, and integrability with computational circuitry. Recent developments in nanotechnological surface modification show promising results in sensing from blood, serum, and urine. This report gives a particular emphasis on the on-site efficacy of recently published field-effect biosensors, specifically, detection limits in physiological solutions, response times, and scalability. The survey of the properties and existing detection methods of four promising biotargets, exosomes, bacteria, viruses, and metabolites, aims at providing a roadmap for future field-effect and other on-site biosensors.
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Affiliation(s)
- Jaebin Choi
- Sensor System Research Center; Korea Institute of Science and Technology (KIST); 5 Hwarang-ro 14-gil Seongbuk-gu Seoul 02792 Republic of Korea
| | - Tae Wha Seong
- Center for Biomaterials; Biomedical Research Institute; Korea Institute of Science and Technology (KIST); 5 Hwarang-ro 14-gil Seongbuk-gu Seoul 02792 Republic of Korea
| | - Minhong Jeun
- Center for Biomaterials; Biomedical Research Institute; Korea Institute of Science and Technology (KIST); 5 Hwarang-ro 14-gil Seongbuk-gu Seoul 02792 Republic of Korea
| | - Kwan Hyi Lee
- Center for Biomaterials; Biomedical Research Institute; Korea Institute of Science and Technology (KIST); 5 Hwarang-ro 14-gil Seongbuk-gu Seoul 02792 Republic of Korea
- Department of Biomedical Engineering; Korea University of Science and Technology (UST); 5 Hwarang-ro 14-gil Seongbuk-gu Seoul 02792 Republic of Korea
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10
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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.
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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.
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11
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Naguib MM, Graaf A, Fortin A, Luttermann C, Wernery U, Amarin N, Hussein HA, Sultan H, Al Adhadh B, Hassan MK, Beer M, Monne I, Harder TC. Novel real-time PCR-based patho- and phylotyping of potentially zoonotic avian influenza A subtype H5 viruses at risk of incursion into Europe in 2017. ACTA ACUST UNITED AC 2017; 22:30435. [PMID: 28084214 PMCID: PMC5388100 DOI: 10.2807/1560-7917.es.2017.22.1.30435] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2016] [Accepted: 12/20/2016] [Indexed: 12/20/2022]
Abstract
Since November 2016, Europe witnesses another wave of incursion of highly pathogenic avian influenza (HPAI) A(H5) viruses of the Asian origin goose/Guangdong (gs/GD) lineage. Infections with H5 viruses of clade 2.3.4.4b affect wild bird and poultry populations. H5 viruses of clades 2.2, 2.3.1.2c and 2.3.4.4a were detected previously in Europe in 2006, 2010 and 2014. Clades 2.2.1.2 and 2.3.2.1.c are endemic in Egypt and Western Africa, respectively and have caused human fatalities. Evidence exists of their co-circulation in the Middle East. Subtype H5 viruses of low pathogenicity (LPAI) are endemic in migratory wild bird populations. They potentially mutate into highly pathogenic phenotypes following transmission into poultry holdings. However, to date only the gs/GD H5 lineage had an impact on human health. Rapid and specific diagnosis marks the cornerstone for control and eradication of HPAI virus incursions. We present the development and validation of five real-time RT-PCR assays (RT-qPCR) that allow sequencing-independent pathotype and clade-specific distinction of major gs/GD HPAI H5 virus clades and of Eurasian LPAI viruses currently circulating. Together with an influenza A virus-generic RT-qPCR, the assays significantly speed up time-to-diagnosis and reduce reaction times in a OneHealth approach of curbing the spread of gs/GD HPAI viruses.
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Affiliation(s)
- Mahmoud M Naguib
- Institute of Diagnostic Virology, Friedrich Loeffler Institute, Greifswald-Riems, Germany.,National Laboratory for Veterinary Quality Control on Poultry Production, Animal Health Research Institute, Giza, Egypt
| | - Annika Graaf
- Institute of Diagnostic Virology, Friedrich Loeffler Institute, Greifswald-Riems, Germany
| | - Andrea Fortin
- Istituto Zooprofilattico Sperimentale delle Venezie, Padua, Italy
| | - Christine Luttermann
- Institute of Immunology, Friedrich Loeffler Institute, Greifswald-Riems, Germany
| | - Ulrich Wernery
- Central Veterinary Research Laboratory (CVRL), Dubai, United Arab Emirates
| | - Nadim Amarin
- Boehringer Ingelheim, Dubai, United Arab Emirates
| | | | - Hesham Sultan
- Birds and Rabbits Medicine Department, Faculty of Veterinary Medicine, Sadat City University, Egypt
| | - Basem Al Adhadh
- Central Veterinary Laboratory, Ministry of Agriculture, Baghdad, Iraq
| | - Mohamed K Hassan
- National Laboratory for Veterinary Quality Control on Poultry Production, Animal Health Research Institute, Giza, Egypt
| | - Martin Beer
- Institute of Diagnostic Virology, Friedrich Loeffler Institute, Greifswald-Riems, Germany
| | - Isabella Monne
- Istituto Zooprofilattico Sperimentale delle Venezie, Padua, Italy
| | - Timm C Harder
- Institute of Diagnostic Virology, Friedrich Loeffler Institute, Greifswald-Riems, Germany
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12
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Riems influenza a typing array (RITA): An RT-qPCR-based low density array for subtyping avian and mammalian influenza a viruses. Sci Rep 2016; 6:27211. [PMID: 27256976 PMCID: PMC4891686 DOI: 10.1038/srep27211] [Citation(s) in RCA: 84] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2016] [Accepted: 05/17/2016] [Indexed: 12/03/2022] Open
Abstract
Rapid and sensitive diagnostic approaches are of the utmost importance for the detection of humans and animals infected by specific influenza virus subtype(s). Cascade-like diagnostics starting with the use of pan-influenza assays and subsequent subtyping devices are normally used. Here, we demonstrated a novel low density array combining 32 TaqMan® real-time RT-PCR systems in parallel for the specific detection of the haemagglutinin (HA) and neuraminidase (NA) subtypes of avian and porcine hosts. The sensitivity of the newly developed system was compared with that of the pan-influenza assay, and the specificity of all RT-qPCRs was examined using a broad panel of 404 different influenza A virus isolates representing 45 different subtypes. Furthermore, we analysed the performance of the RT-qPCR assays with diagnostic samples obtained from wild birds and swine. Due to the open format of the array, adaptations to detect newly emerging influenza A virus strains can easily be integrated. The RITA array represents a competitive, fast and sensitive subtyping tool that requires neither new machinery nor additional training of staff in a lab where RT-qPCR is already established.
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13
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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.
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Affiliation(s)
- Lih-Chiann Wang
- School of Veterinary Medicine, National Taiwan University, No 1, Sec 4, Roosevelt Rd, Taipei 10617, Taiwan
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14
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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.
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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.
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15
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Ye WW, Tsang MK, Liu X, Yang M, Hao J. Upconversion luminescence resonance energy transfer (LRET)-based biosensor for rapid and ultrasensitive detection of avian influenza virus H7 subtype. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2014; 10:2390-7. [PMID: 24599581 DOI: 10.1002/smll.201303766] [Citation(s) in RCA: 94] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/07/2013] [Revised: 01/09/2014] [Indexed: 05/20/2023]
Abstract
Avian influenza viruses (AIV) with good adaptation and various mutations have threatened both human and animals' health. The H7 subtypes have the potential to cause pandemic threats to human health due to the highly pathogenic characteristics. Therefore, it is quite urgent to develop a novel biosensor for rapid and sensitive detection of H7 subtypes. In this work, a biosensor based on luminescence resonance energy transfer (LRET) from BaGdF5:Yb/Er upconversion nanoparticles (UCNPs) to gold nanoparticles (AuNPs) has been developed for rapid and sensitive H7 subtypes detection. The amino modified capture oligonucleotide probes are covalently linked to poly(ethylenimine) (PEI) modified BaGdF5:Yb/Er UCNPs. The thiol modified oligonucleotides with H7 hemagglutinin gene sequence are conjugated to surfaces of AuNPs. The hybridization process between complementary strands of H7 Hemagglutinin gene and its probe brings the energy donor and acceptor into close proximity, leading to the quenching of fluorescence of UCNPs. A linear response is obtained ranging from 10 pm to 10 nm and the limit of detection (LOD) is around 7 pm with detection time around 2 hours. This biosensor is expected to be a valuable diagnostic tool for rapid and sensitive detection of AIV.
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MESH Headings
- Animals
- Biosensing Techniques/instrumentation
- Biosensing Techniques/methods
- Birds
- Fluorescence Resonance Energy Transfer/instrumentation
- Fluorescence Resonance Energy Transfer/methods
- Gold
- Hemagglutinin Glycoproteins, Influenza Virus/genetics
- Humans
- Influenza A Virus, H7N1 Subtype/genetics
- Influenza A Virus, H7N1 Subtype/isolation & purification
- Influenza A Virus, H7N2 Subtype/genetics
- Influenza A Virus, H7N2 Subtype/isolation & purification
- Influenza A Virus, H7N3 Subtype/genetics
- Influenza A Virus, H7N3 Subtype/isolation & purification
- Influenza A Virus, H7N7 Subtype/genetics
- Influenza A Virus, H7N7 Subtype/isolation & purification
- Influenza A Virus, H7N9 Subtype/genetics
- Influenza A Virus, H7N9 Subtype/isolation & purification
- Influenza A virus/classification
- Influenza A virus/genetics
- Influenza A virus/isolation & purification
- Influenza in Birds/diagnosis
- Influenza in Birds/virology
- Influenza, Human/diagnosis
- Influenza, Human/genetics
- Limit of Detection
- Luminescence
- Metal Nanoparticles/chemistry
- Sensitivity and Specificity
- Time Factors
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Affiliation(s)
- Wei Wei Ye
- Interdisciplinary Division of Biomedical Engineering, the Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong, P. R. China
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Kim YT, Jung JH, Choi YK, Seo TS. A packaged paper fluidic-based microdevice for detecting gene expression of influenza A virus. Biosens Bioelectron 2014; 61:485-90. [PMID: 24949821 DOI: 10.1016/j.bios.2014.06.006] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2014] [Revised: 05/21/2014] [Accepted: 06/01/2014] [Indexed: 11/27/2022]
Abstract
Pathotyping and subtyping of influenza A virus were performed with a packaged paper fluidic-based analytical microdevice (PFAM) after one-step reverse transcription-polymerase chain reaction (RT-PCR). The PFAM contains two test lines: one for detecting M gene to identify the influenza A virus and another for haemagglutinin subtyping to determine the viral strain among H1N1, H3N2, and H5N1. The M gene and the haemagglutinin gene (H1, H3, and H5 genes) were amplified by using the Digoxigenin and the Texas Red modified primers, respectively, in the multiplex RT-PCR. The amplicon products were loaded in the conjugate pad of the PFAM in which the streptavidin coated gold nanoparticles were linked with the biotin moieties that were incorporated in the middle of the DNA strands, and then captured by the anti-Digoxigenin and anti-Texas Red immobilized on the test lines. Influenza A H1N1, H3N2, and H5N1 could be identified with a limit of detection of 10(2) copies of RNA templates in 10 min. Pathotyping and subtyping of the clinical nasopharyngeal swab samples were also analyzed whose results were confirmed by real-time RT-PCR.
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Affiliation(s)
- Yong Tae Kim
- Department of Chemical and Biomolecular Engineering (BK21 Plus Program), Korea Advanced Institute of Science and Technology (KAIST), 291 Daehak-ro, Yuseong-gu, Daejeon 305-701, Republic of Korea
| | - Jae Hwan Jung
- Department of Chemical and Biomolecular Engineering (BK21 Plus Program), Korea Advanced Institute of Science and Technology (KAIST), 291 Daehak-ro, Yuseong-gu, Daejeon 305-701, Republic of Korea
| | - Young Ki Choi
- Department of Microbiology, College of Medicine and Medical Research Institute, Chungbuk National University, 12 Gaeshin-Dong, Heungduk-gu, Cheongju-si, Chungcheongbuk-do 361-763, Republic of Korea
| | - Tae Seok Seo
- Department of Chemical and Biomolecular Engineering (BK21 Plus Program), Korea Advanced Institute of Science and Technology (KAIST), 291 Daehak-ro, Yuseong-gu, Daejeon 305-701, Republic of Korea.
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17
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Elizalde M, Agüero M, Buitrago D, Yuste M, Arias ML, Muñoz MJ, Lelli D, Pérez-Ramírez E, Moreno-Martin AM, Fernández-Pinero J. Rapid molecular haemagglutinin subtyping of avian influenza isolates by specific real-time RT-PCR tests. J Virol Methods 2013; 196:71-81. [PMID: 24184949 DOI: 10.1016/j.jviromet.2013.10.031] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2013] [Revised: 10/14/2013] [Accepted: 10/18/2013] [Indexed: 10/26/2022]
Abstract
Sixteen haemagglutinin (HA) subtypes of avian influenza viruses (AIV) have been described to date. Rapid subtype identification of any AIV is of major interest because of the possible serious consequences for the poultry industry and even public health. Molecular techniques currently allow immediate accurate subtype characterisation prior to virus isolation. In this study, a set of fourteen specific real-time RT-PCR methods were developed and evaluated for AIV HA subtyping (H1-H4, H6-H8, H10-H16), H5 and H9 being excluded on the basis of the current validity of the European Union (EU) recommended specific assays. Specific primers and probes sets for each HA-subtype were designed to hybridise the largest isolates range within each single subtype, considering the Eurasian lineage as a major target. The robustness and general application of the 14 HA-subtype methods were verified by the analysis of 110 AIV isolates belonging to all 16 HA-subtypes, performed in different laboratories. The developed real-time RT-PCR assays proved to be highly specific and revealed suitable sensitivity, allowing direct HA-subtyping of clinical material. In summary, this study provides for the first time a panel of molecular tests using specific hydrolysis probes for rapid and complete AIV HA-subtype identification.
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Affiliation(s)
- Maia Elizalde
- Centro de Investigación en Sanidad Animal (CISA-INIA), Valdeolmos, 28130 Madrid, Spain
| | | | | | - María Yuste
- Centro de Investigación en Sanidad Animal (CISA-INIA), Valdeolmos, 28130 Madrid, Spain
| | - María Luisa Arias
- Centro de Investigación en Sanidad Animal (CISA-INIA), Valdeolmos, 28130 Madrid, Spain
| | - María Jesús Muñoz
- Centro de Investigación en Sanidad Animal (CISA-INIA), Valdeolmos, 28130 Madrid, Spain
| | - Davide Lelli
- Istituto Zooprofilattico Sperimentale della Lombardia e dell'Emilia Romagna (IZSLER), Via Bianchi 9, 25124 Brescia, Italy
| | - Elisa Pérez-Ramírez
- Centro de Investigación en Sanidad Animal (CISA-INIA), Valdeolmos, 28130 Madrid, Spain
| | - Ana María Moreno-Martin
- Istituto Zooprofilattico Sperimentale della Lombardia e dell'Emilia Romagna (IZSLER), Via Bianchi 9, 25124 Brescia, Italy
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18
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Truncation and sequence shuffling of segment 6 generate replication-competent neuraminidase-negative influenza H5N1 viruses. J Virol 2013; 87:13556-68. [PMID: 24109212 DOI: 10.1128/jvi.02244-13] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Abstract
Influenza viruses are highly genetically variable and escape from immunogenic pressure by antigenic changes in their surface proteins, referred to as "antigenic drift" and "antigenic shift." To assess the potential genetic plasticity under strong selection pressure, highly pathogenic avian influenza virus (HPAIV) of subtype H5N1 was passaged 50 times in embryonated chicken eggs in the presence of a neutralizing, polyclonal chicken serum. The resulting mutant acquired major alterations in the neuraminidase (NA)-encoding segment. Extensive deletions and rearrangements were detected, in contrast to only 12 amino acid substitutions within all other segments. Interestingly, this new neuraminidase segment resulted from complex sequence shuffling and insertion of a short fragment originating from the PA segment. Characterization of that novel variant revealed a loss of the neuraminidase protein and enzymatic activity, but its replication efficiency remained comparable to that of the wild type. Using reverse genetics, a recombinant virus consisting of the wild-type backbone and the shortened NA segment could be generated; however, generation of this recombinant virus required the polybasic hemagglutinin cleavage site. Two independent repetitions starting with egg passage 30 in the presence of alternative chicken-derived immune sera selected mutants with similar but different large deletions within the NA segment without any neuraminidase activity, indicating a general mechanism. In chicken, these virus variants were avirulent, even though the HPAIV polybasic hemagglutinin cleavage site was still present. Overall, the variants reported here are the first HPAIV H5N1 strains without a functional neuraminidase shown to grow efficiently without any helper factor. These novel HPAIV variants may facilitate future studies shedding light on the role of neuraminidase in virus replication and pathogenicity.
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19
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Dong J, Sakurai A, Nomura N, Park EY, Shibasaki F, Ueda H. Isolation of recombinant phage antibodies targeting the hemagglutinin cleavage site of highly pathogenic avian influenza virus. PLoS One 2013; 8:e61158. [PMID: 23577205 PMCID: PMC3618430 DOI: 10.1371/journal.pone.0061158] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2012] [Accepted: 03/06/2013] [Indexed: 11/18/2022] Open
Abstract
Highly pathogenic avian influenza (HPAI) H5N1 viruses, which have emerged in poultry and other wildlife worldwide, contain a characteristic multi-basic cleavage site (CS) in the hemagglutinin protein (HA). Because this arginine-rich CS is unique among influenza virus subtypes, antibodies against this site have the potential to specifically diagnose pathogenic H5N1. By immunizing mice with the CS peptide and screening a phage display library, we isolated four antibody Fab fragment clones that specifically bind the antigen peptide and several HPAI H5N1 HA proteins in different clades. The soluble Fab fragments expressed in Escherichia coli bound the CS peptide and the H5N1 HA protein with nanomolar affinity. In an immunofluorescence assay, these Fab fragments stained cells infected with HPAI H5N1 but not those infected with a less virulent strain. Lastly, all the Fab clones could detect the CS peptide and H5N1 HA protein by open sandwich ELISA. Thus, these recombinant Fab fragments will be useful novel reagents for the rapid and specific detection of HPAI H5N1 virus.
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Affiliation(s)
- Jinhua Dong
- Graduate School of Science and Technology, Shizuoka University, Suruga-ku, Shizuoka, Japan
- Department of Chemistry and Biotechnology, The University of Tokyo, Bunkyo-ku, Tokyo, Japan
| | - Akira Sakurai
- Molecular Medicine Project, Department of Genome Medicine, Tokyo Metropolitan Institute of Medical Science, Setagaya-ku, Tokyo, Japan
| | - Namiko Nomura
- Molecular Medicine Project, Department of Genome Medicine, Tokyo Metropolitan Institute of Medical Science, Setagaya-ku, Tokyo, Japan
| | - Enoch Y. Park
- Graduate School of Science and Technology, Shizuoka University, Suruga-ku, Shizuoka, Japan
| | - Futoshi Shibasaki
- Molecular Medicine Project, Department of Genome Medicine, Tokyo Metropolitan Institute of Medical Science, Setagaya-ku, Tokyo, Japan
| | - Hiroshi Ueda
- Department of Chemistry and Biotechnology, The University of Tokyo, Bunkyo-ku, Tokyo, Japan
- * E-mail:
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20
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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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21
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Pérez LJ, Díaz de Arce H, Cilloni F, Salviato A, Marciano S, Perera C, Salomoni A, Beato M, Romero A, Capua I, Cattoli G. An SYBR Green-based real-time RT-PCR assay for the detection of H5 hemagglutinin subtype avian influenza virus. Mol Cell Probes 2012; 26:137-45. [DOI: 10.1016/j.mcp.2012.02.001] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2011] [Revised: 02/01/2012] [Accepted: 02/21/2012] [Indexed: 12/01/2022]
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22
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Qin ZF, Sun J, Lu TK, Zeng SL, Hua QY, Ling QY, Chen SK, Lv JQ, Zhang CH, Cheng B, Ruan ZX, Bi YZ, Giambrone JJ, Wu HZ. Subtyping animal influenza virus with general multiplex RT-PCR and Liquichip high throughput (GMPLex). Virol Sin 2012; 27:120-31. [PMID: 22492003 DOI: 10.1007/s12250-012-3232-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2011] [Accepted: 03/05/2012] [Indexed: 11/24/2022] Open
Abstract
This study developed a multiplex RT-PCR integrated with luminex technology to rapidly subtype simultaneously multiple influenza viruses. Primers and probes were designed to amplify NS and M genes of influenza A viruses HA gene of H1, H3, H5, H7, H9 subtypes, and NA gene of the N1 and N2 subtypes. Universal super primers were introduced to establish a multiplex RT-PCR (GM RT-PCR). It included three stages of RT-PCR amplification, and then the RT-PCR products were further tested by LiquiChip probe, combined to give an influenza virus (IV) rapid high throughput subtyping test, designated as GMPLex. The IV GMPLex rapid high throughput subtyping test presents the following features: high throughput, able to determine the subtypes of 9 target genes in H1, H3, H5, H7, H9, N1, and N2 subtypes of the influenza A virus at one time; rapid, completing the influenza subtyping within 6 hours; high specificity, ensured the specificity of the different subtypes by using two nested degenerate primers and one probe, no cross reaction occurring between the subtypes, no non-specific reactions with other pathogens and high sensitivity. When used separately to detect the product of single GM RT-PCR for single H5 or N1 gene, the GMPLex test showed a sensitivity of 10⁻⁵(= 280ELD₅₀) forboth tests and the Luminex qualitative ratio results were 3.08 and 3.12, respectively. When used to detect the product of GM RT-PCR for H5N1 strain at the same time, both showed a sensitivity of 10⁻⁴(=2800 ELD₅₀). The GMPLex rapid high throughput subtyping test can satisfy the needs of influenza rapid testing.
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Affiliation(s)
- Zhi-feng Qin
- Shenzhen Entry-Exit Inspection and Quarantine Bureau, Shenzhen 518010, China.
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23
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Mahony JB, Petrich A, Smieja M. Molecular diagnosis of respiratory virus infections. Crit Rev Clin Lab Sci 2012; 48:217-49. [PMID: 22185616 DOI: 10.3109/10408363.2011.640976] [Citation(s) in RCA: 134] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
The appearance of eight new respiratory viruses, including the SARS coronavirus in 2003 and swine-origin influenza A/H1N1 in 2009, in the human population in the past nine years has tested the ability of virology laboratories to develop diagnostic tests to identify these viruses. Nucleic acid based amplification tests (NATs) for respiratory viruses were first introduced two decades ago and today are utilized for the detection of both conventional and emerging viruses. These tests are more sensitive than other diagnostic approaches, including virus isolation in cell culture, shell vial culture (SVC), antigen detection by direct fluorescent antibody (DFA) staining, and rapid enzyme immunoassay (EIA), and now form the backbone of clinical virology laboratory testing around the world. NATs not only provide fast, accurate and sensitive detection of respiratory viruses in clinical specimens but also have increased our understanding of the epidemiology of both new emerging viruses such as the pandemic H1N1 influenza virus of 2009, and conventional viruses such as the common cold viruses, including rhinovirus and coronavirus. Multiplex polymerase chain reaction (PCR) assays introduced in the last five years detect up to 19 different viruses in a single test. Several multiplex PCR tests are now commercially available and tests are working their way into clinical laboratories. The final chapter in the evolution of respiratory virus diagnostics has been the addition of allelic discrimination and detection of single nucleotide polymorphisms associated with antiviral resistance. These assays are now being multiplexed with primary detection and subtyping assays, especially in the case of influenza virus. These resistance assays, together with viral load assays, will enable clinical laboratories to provide physicians with new and important information for optimal treatment of respiratory virus infections.
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Affiliation(s)
- James B Mahony
- M.G. DeGroote Institute for Infectious Disease Research, St. Joseph’s Healthcare, Hamilton, Canada.
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24
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SYBR green-based real-time reverse transcription-PCR for typing and subtyping of all hemagglutinin and neuraminidase genes of avian influenza viruses and comparison to standard serological subtyping tests. J Clin Microbiol 2011; 50:37-45. [PMID: 22031706 DOI: 10.1128/jcm.01195-11] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Continuing outbreaks of H5N1 highly pathogenic (HP) avian influenza virus (AIV) infections of wild birds and poultry worldwide emphasize the need for global surveillance of wild birds. To support the future surveillance activities, we developed a SYBR green-based, real-time reverse transcriptase PCR (rRT-PCR) for detecting nucleoprotein (NP) genes and subtyping 16 hemagglutinin (HA) and 9 neuraminidase (NA) genes simultaneously. Primers were improved by focusing on Eurasian or North American lineage genes; the number of mixed-base positions per primer was set to five or fewer, and the concentration of each primer set was optimized empirically. Also, 30 cycles of amplification of 1:10 dilutions of cDNAs from cultured viruses effectively reduced minor cross- or nonspecific reactions. Under these conditions, 346 HA and 345 NA genes of 349 AIVs were detected, with average sensitivities of NP, HA, and NA genes of 10(1.5), 10(2.3), and 10(3.1) 50% egg infective doses, respectively. Utility of rRT-PCR for subtyping AIVs was compared with that of current standard serological tests by using 104 recent migratory duck virus isolates. As a result, all HA genes and 99% of the NA genes were genetically subtyped, while only 45% of HA genes and 74% of NA genes were serologically subtyped. Additionally, direct subtyping of AIVs in fecal samples was possible by 40 cycles of amplification: approximately 70% of HA and NA genes of NP gene-positive samples were successfully subtyped. This validation study indicates that rRT-PCR with optimized primers and reaction conditions is a powerful tool for subtyping varied AIVs in clinical and cultured samples.
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Rapid PCR-based molecular pathotyping of H5 and H7 avian influenza viruses. J Clin Microbiol 2011; 49:3860-73. [PMID: 21900520 DOI: 10.1128/jcm.01179-11] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
While the majority of avian influenza virus (AIV) subtypes are classified as low-pathogenicity avian influenza viruses (LPAIV), the H5 and H7 subtypes have the ability to mutate to highly pathogenic avian influenza viruses (HPAIV) in poultry and therefore are the etiological agents of notifiable AIV (NAIV). It is of great importance to distinguish HPAIV from LPAIV variants during H5/H7 outbreaks and surveillance. To this end, a novel and fast strategy for the molecular pathotyping of H5/H7 AIVs is presented. The differentiation of the characteristic hemagglutinin (HA) protein cleavage sites (CSs) of HPAIVs and LPAIVs is achieved by a novel PCR method where the samples are interrogated for all existing CSs with a 484-plex primer mixture directly targeting the CS region. CSs characteristic for HP or LP H5/H7 viruses are distinguished in a seminested duplex real-time PCR format using plexor fluorogenic primers. Eighty-six laboratory isolates and 60 characterized NAIV-positive clinical specimens from poultry infected with H5/H7 both experimentally and in the field were successfully pathotyped in the validation. The method has the potential to substitute CS sequencing in the HA gene for the determination of the molecular pathotype, thereby providing a rapid means to acquire additional information concerning NAIV outbreaks, which may be critical to their management. The new assay may be extended to the LP/HP differentiation of previously unknown H5/H7 isolates. It may be considered for integration into surveillance and control programs in both domestic and wild bird populations.
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Mahony JB. Nucleic acid amplification-based diagnosis of respiratory virus infections. Expert Rev Anti Infect Ther 2011; 8:1273-92. [PMID: 21073292 DOI: 10.1586/eri.10.121] [Citation(s) in RCA: 69] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
The appearance of eight new respiratory viruses in the human population in the past 9 years, including two new pandemics (SARS coronavirus in 2003 and swine-origin influenza A/H1N1 in 2009), has tested the ability of virology laboratories to develop diagnostic tests to identify these viruses. Nucleic acid amplification tests (NATs) that first appeared two decades ago have been developed for both conventional and emerging viruses and now form the backbone of the clinical laboratory. NATs provide fast, accurate and sensitive detection of respiratory viruses and have significantly increased our understanding of the epidemiology of these viruses. Multiplex PCR assays have been introduced recently and several commercial tests are now available. The final chapter in the evolution of respiratory virus diagnostics will be the addition of allelic discrimination and detection of single nucleotide polymorphisms associated with antiviral resistance to multiplex assays. These resistance assays together with new viral load tests will enable clinical laboratories to provide physicians with important information for optimal treatment of patients.
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Affiliation(s)
- James B Mahony
- Regional Virology Laboratory, St. Joseph's Healthcare Hamilton, 50 Charlton Ave. East, Hamilton, ON, L8N 4A6, Canada.
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Kalthoff D, Giritch A, Geisler K, Bettmann U, Klimyuk V, Hehnen HR, Gleba Y, Beer M. Immunization with plant-expressed hemagglutinin protects chickens from lethal highly pathogenic avian influenza virus H5N1 challenge infection. J Virol 2010; 84:12002-10. [PMID: 20810729 PMCID: PMC2977904 DOI: 10.1128/jvi.00940-10] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2010] [Accepted: 08/19/2010] [Indexed: 01/06/2023] Open
Abstract
Highly pathogenic avian influenza (HPAI) is a striking disease in susceptible poultry, which leads to severe economic losses. Inactivated vaccines are the most widely used vaccines in avian influenza virus (AIV) vaccination programs. However, these vaccines interfere with the serological detection of wild-type AIV infections in immunized populations. The use of vaccines that allow differentiation between infected and vaccinated animals (DIVA strategy) would stop current stamping-out policies. Therefore, novel vaccination strategies are needed to allow improved protection of animals and humans against HPAI virus (HPAIV) infection. The presented study analyzed for the first time the immunogenic capacity of plant-expressed full-length hemagglutinin (rHA0) of HPAIV H5N1 in several vaccine formulations within the highly relevant host species chicken. We were able to express plant-expressed rHA0 at high levels and could show that, when administered with potent adjuvants, it is highly immunogenic and can fully protect chicken against lethal challenge infection. Real-time reverse transcription (RT)-PCR and serological tests demonstrated only marginally increased virus replication in animals vaccinated with plant-derived rHA0 compared to animals immunized with an inactivated reference vaccine. In addition, the use of plant-expressed rHA0 also allowed an easy serological differentiation of vaccinated from AIV-infected animals based on antibodies against the influenza virus NP protein.
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Affiliation(s)
- Donata Kalthoff
- Institute of Diagnostic Virology, Friedrich-Loeffler-Institut, Insel Riems, Germany, ICON Genetics GmbH, Halle, Germany, Bayer Animal Health GmbH, Monheim, Germany
| | - Anatoli Giritch
- Institute of Diagnostic Virology, Friedrich-Loeffler-Institut, Insel Riems, Germany, ICON Genetics GmbH, Halle, Germany, Bayer Animal Health GmbH, Monheim, Germany
| | - Katharina Geisler
- Institute of Diagnostic Virology, Friedrich-Loeffler-Institut, Insel Riems, Germany, ICON Genetics GmbH, Halle, Germany, Bayer Animal Health GmbH, Monheim, Germany
| | - Ulrike Bettmann
- Institute of Diagnostic Virology, Friedrich-Loeffler-Institut, Insel Riems, Germany, ICON Genetics GmbH, Halle, Germany, Bayer Animal Health GmbH, Monheim, Germany
| | - Victor Klimyuk
- Institute of Diagnostic Virology, Friedrich-Loeffler-Institut, Insel Riems, Germany, ICON Genetics GmbH, Halle, Germany, Bayer Animal Health GmbH, Monheim, Germany
| | - Hans-Robert Hehnen
- Institute of Diagnostic Virology, Friedrich-Loeffler-Institut, Insel Riems, Germany, ICON Genetics GmbH, Halle, Germany, Bayer Animal Health GmbH, Monheim, Germany
| | - Yuri Gleba
- Institute of Diagnostic Virology, Friedrich-Loeffler-Institut, Insel Riems, Germany, ICON Genetics GmbH, Halle, Germany, Bayer Animal Health GmbH, Monheim, Germany
| | - Martin Beer
- Institute of Diagnostic Virology, Friedrich-Loeffler-Institut, Insel Riems, Germany, ICON Genetics GmbH, Halle, Germany, Bayer Animal Health GmbH, Monheim, Germany
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Hoffmann B, Freuling CM, Wakeley PR, Rasmussen TB, Leech S, Fooks AR, Beer M, Müller T. Improved safety for molecular diagnosis of classical rabies viruses by use of a TaqMan real-time reverse transcription-PCR "double check" strategy. J Clin Microbiol 2010; 48:3970-8. [PMID: 20739489 PMCID: PMC3020878 DOI: 10.1128/jcm.00612-10] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2010] [Revised: 04/29/2010] [Accepted: 08/18/2010] [Indexed: 11/20/2022] Open
Abstract
To improve the diagnosis of classical rabies virus with molecular methods, a validated, ready-to-use, real-time reverse transcription-PCR (RT-PCR) assay was developed. In a first step, primers and 6-carboxyfluorescien-labeled TaqMan probes specific for rabies virus were selected from the consensus sequence of the nucleoprotein gene of 203 different rabies virus sequences derived from GenBank. The selected primer-probe combination was highly specific and sensitive. During validation using a sample set of rabies virus strains from the virus archives of the Friedrich-Loeffler-Institut (FLI; Germany), the Veterinary Laboratories Agency (VLA; United Kingdom), and the DTU National Veterinary Institute (Lindholm, Denmark), covering the global diversity of rabies virus lineages, it was shown that both the newly developed assay and a previously described one had some detection failures. This was overcome by a combined assay that detected all samples as positive. In addition, the introduction of labeled positive controls (LPC) increased the diagnostic safety of the single as well as the combined assay. Based on the newly developed, alternative assay for the detection of rabies virus and the application of LPCs, an improved diagnostic sensitivity and reliability can be ascertained for postmortem and intra vitam real-time RT-PCR analyses in rabies reference laboratories.
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Affiliation(s)
- B Hoffmann
- Institute of Diagnostic Virology, Südufer 10, 17493 Greifswald-Insel Riems, Germany.
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Breithaupt A, Kalthoff D, Dale J, Bairlein F, Beer M, Teifke JP. Neurotropism in blackcaps (Sylvia atricapilla) and red-billed queleas (Quelea quelea) after highly pathogenic avian influenza virus H5N1 infection. Vet Pathol 2010; 48:924-32. [PMID: 20974871 DOI: 10.1177/0300985810386467] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
The epidemiologic role of passerine birds in the spread of highly pathogenic avian influenza virus (HPAIV) remains controversial. However, confirmed natural infections with HPAIV in Passeriformes, their close contact to poultry and humans, and their role as a human food source indicate a need for increased research on passerines. To date, there are only a few studies on viral shedding and pathomorphologic changes in songbirds infected with HPAIV. To investigate susceptibility, clinical outcome, virus spread, and pathomorphology, the authors inoculated oculo-oronasally 22 red-billed queleas (Quelea quelea) and 11 blackcaps (Sylvia atricapilla) with A/Cygnus cygnus/Germany/R65/2006 (H5N1) using 2 different doses of either 10(4) EID50 (50% egg infective dose) or 10(6) EID50 per animal. They monitored all birds for clinical signs and oropharyngeal and cloacal virus shedding. They also performed immunohistochemistry and obtained molecular virologic data by real-time reverse transcription polymerase chain reaction in tissue samples. In contrast to blackcaps, where 100% of the infected individuals died, queleas were much less susceptible, with a mortality of 82% and 18%, depending on the doses applied. In both species, the virus was shed within 3 to 6 days postinfection, mainly via the respiratory tract. Viral antigen was detected in 100% of the succumbed birds, particularly in the central nervous system. In blackcaps, the heart, lungs, and pancreas were mainly infected. In contrast, the pancreas was predominantly affected in queleas, whereas the heart and the lower respiratory tract were of minor relevance. The authors hypothesize that neurotropism should be considered a main factor for the fatal course of disease in Passeriformes after infection with HPAIV.
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Affiliation(s)
- A Breithaupt
- Institute of Diagnostic Virology, Friedrich-Loeffler-Institut, Südufer 10, 17493 Greifswald-Insel Riems, Germany
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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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Broad detection of diverse H5 and H7 hemagglutinin genes of avian influenza viruses by real-time reverse transcription-PCR using primer and probe sets containing mixed bases. J Clin Microbiol 2010; 48:4275-8. [PMID: 20861344 DOI: 10.1128/jcm.01264-10] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Real-time reverse transcription-PCR (RT-PCR) was developed for broad detection of diverse H5 and H7 genes in Eurasian and American lineages of avian influenza viruses by using primer and probe sets containing mixed bases. Optimal use of the mixed bases enabled us to minimize sequence mismatches and to broaden the gene detection spectrum without decreasing sensitivity.
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Virulence determinants of avian H5N1 influenza A virus in mammalian and avian hosts: role of the C-terminal ESEV motif in the viral NS1 protein. J Virol 2010; 84:10708-18. [PMID: 20686040 DOI: 10.1128/jvi.00610-10] [Citation(s) in RCA: 68] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
We assessed the prediction that access of the viral NS1 protein to cellular PDZ domain protein networks enhances the virulence of highly pathogenic avian influenza A viruses. The NS1 proteins of most avian influenza viruses bear the C-terminal ligand sequence Glu-Ser-Glu-Val (ESEV) for PDZ domains present in multiple host proteins, whereas no such motif is found in the NS1 homologues of seasonal human virus strains. Previous analysis showed that a C-terminal ESEV motif increases viral virulence when introduced into the NS1 protein of mouse-adapted H1N1 influenza virus. To examine the role of the PDZ domain ligand motif in avian influenza virus virulence, we generated three recombinants, derived from the prototypic H5N1 influenza A/Vietnam/1203/04 virus, expressing NS1 proteins that either have the C-terminal ESEV motif or the human influenza virus RSKV consensus or bear a natural truncation of this motif, respectively. Cell biological analyses showed strong control of NS1 nuclear migration in infected mammalian and avian cells, with only minor differences between the three variants. The ESEV sequence attenuated viral replication on cultured human, murine, and duck cells but not on chicken fibroblasts. However, all three viruses caused highly lethal infections in mice and chickens, with little difference in viral titers in organs, mean lethal dose, or intravenous pathogenicity index. These findings demonstrate that a PDZ domain ligand sequence in NS1 contributes little to the virulence of H5N1 viruses in these hosts, and they indicate that this motif modulates viral replication in a strain- and host-dependent manner.
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Dovas CI, Papanastassopoulou M, Georgiadis MP, Chatzinasiou E, Maliogka VI, Georgiades GK. Detection and quantification of infectious avian influenza A (H5N1) virus in environmental water by using real-time reverse transcription-PCR. Appl Environ Microbiol 2010; 76:2165-74. [PMID: 20118369 PMCID: PMC2849232 DOI: 10.1128/aem.01929-09] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2009] [Accepted: 01/25/2010] [Indexed: 01/13/2023] Open
Abstract
Routes of avian influenza virus (AIV) dispersal among aquatic birds involve direct (bird-to-bird) and indirect (waterborne) transmission. The environmental persistence of H5N1 virus in natural water reservoirs can be assessed by isolation of virus in embryonated chicken eggs. Here we describe development and evaluation of a real-time quantitative reverse transcription (RT)-PCR (qRT-PCR) method for detection of H5N1 AIV in environmental water. This method is based on adsorption of virus particles to formalin-fixed erythrocytes, followed by qRT-PCR detection. The numbers of hemagglutinin RNA copies from H5N1 highly pathogenic AIV particles adsorbed to erythrocytes detected correlated highly with the infectious doses of the virus that were determined for three different types of artificially inoculated environmental water over a 17-day incubation period. The advantages of this method include detection and quantification of infectious H5N1 AIVs with a high level of sensitivity, a wide dynamic range, and reproducibility, as well as increased biosecurity. The lowest concentration of H5N1 virus that could be reproducibly detected was 0.91 50% egg infective dose per ml. In addition, a virus with high virion stability (Tobacco mosaic virus) was used as an internal control to accurately monitor the efficiency of RNA purification, cDNA synthesis, and PCR amplification for each individual sample. This detection system could be useful for rapid high-throughput monitoring for the presence of H5N1 AIVs in environmental water and in studies designed to explore the viability and epidemiology of these viruses in different waterfowl ecosystems. The proposed method may also be adapted for detection of other AIVs and for assessment of their prevalence and distribution in environmental reservoirs.
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Affiliation(s)
- C I Dovas
- Laboratory of Microbiology and Infectious Diseases, Faculty of Veterinary Medicine, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece.
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Chen L, Sheng Z, Zhang A, Guo X, Li J, Han H, Jin M. Quantum-dots-based fluoroimmunoassay for the rapid and sensitive detection of avian influenza virus subtype H5N1. LUMINESCENCE 2009; 25:419-23. [DOI: 10.1002/bio.1167] [Citation(s) in RCA: 61] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2009] [Revised: 05/25/2009] [Accepted: 06/20/2009] [Indexed: 11/09/2022]
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Newcastle disease: evolution of genotypes and the related diagnostic challenges. INFECTION GENETICS AND EVOLUTION 2009; 10:26-35. [PMID: 19800028 DOI: 10.1016/j.meegid.2009.09.012] [Citation(s) in RCA: 284] [Impact Index Per Article: 18.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/19/2009] [Revised: 09/22/2009] [Accepted: 09/22/2009] [Indexed: 11/20/2022]
Abstract
Since the discovery of Newcastle disease virus (NDV) in 1926, nine genotypes of class I viruses and ten of class II have been identified, representing a diverse and continually evolving group of viruses. The emergence of new virulent genotypes from global epizootics and the year-to-year changes observed in the genomic sequence of NDV of low and high virulence implies that distinct genotypes of NDV are simultaneously evolving at different geographic locations across the globe. This vast genomic diversity may be favored by the large variety of avian species susceptible to NDV infection and by the availability of highly mobile wild bird reservoirs. The genomic diversity of NDV increases the possibility of diagnostic failures, resulting in unidentified infections. Constant epidemiological surveillance and pro-active characterization of circulating strains are needed to ensure that the immunological and PCR reagents are effective in identifying NDV circulating worldwide. For example, in the United States, the widely used real-time reverse transcription polymerase chain reaction (RRT-PCR) matrix gene assay for the identification of NDV often fails to detect low virulence APMV-1 from waterfowl, while the RRT-PCR fusion gene assay, used to identify virulent isolates, often fails to detect certain virulent NDV genotypes. A new matrix-polymerase multiplex test that detects most of the viruses currently circulating worldwide and a modified fusion test for the identification of virulent pigeon viruses circulating in the U.S. and Europe have recently been developed. For newly isolated viruses with unknown sequences, recently developed random priming sequencing methods need to be incorporated into the diagnostic arsenal. In addition, the current system of classifying NDV into genotypes or lineages is inadequate. Here, we review the molecular epidemiology and recent diagnostic problems related to viral evolution of NDV and explain why a new system, based on objective criteria, is needed to categorize genotypes.
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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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Slomka MJ, Pavlidis T, Coward VJ, Voermans J, Koch G, Hanna A, Banks J, Brown IH. Validated RealTime reverse transcriptase PCR methods for the diagnosis and pathotyping of Eurasian H7 avian influenza viruses. Influenza Other Respir Viruses 2009; 3:151-64. [PMID: 19627372 PMCID: PMC4634683 DOI: 10.1111/j.1750-2659.2009.00083.x] [Citation(s) in RCA: 92] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
Abstract
BACKGROUND Avian influenza (AI) caused by H7 AI viruses (AIVs) of both low pathogenicity (LP) and high pathogenicity (HP) are notifiable poultry diseases. OBJECTIVES Design and validate two RealTime reverse transcriptase polymerase chain reactions (RRT PCRs) for Eurasian H7 AIV detection and pathotyping. METHODS The H7 RRT PCRs amplified within the (i) HA2 and (ii) cleavage site CS regions of the haemagglutinin gene. Both were validated against 65 H7 AIVs, 57 non-H7 AIVs and 259 poultry swabs in comparison to M gene (AI generic) RRT PCR and virus isolation (VI). An additional 38 swabs and 20 tissue specimens extended validation against M gene RRT PCR. RESULTS Both H7 RRT PCRs amplified all 61 Eurasian lineage H7 AIVs and none of 57 non-H7 AIVs. A total of 297 poultry swabs were used to determine diagnostic sensitivity and specificity relative to M gene RRT PCR, sensitivity was 95.4% and 64.6% for the HA2 and CS RRT PCRs respectively, and specificity 97.9% and 99.6% respectively. The H7 HA2 RRT PCR was more sensitive than VI. This was emphasized by analysis of 37 swabs from turkeys infected experimentally with HPAI H7N1 virus sampled at 24 hours post-inoculation and LPAI H7N1 chicken infections sampled at 40-64 hours. Although less sensitive, usefulness of the H7 CS RRT PCR was confirmed by the correct molecular pathotyping for all 61 Eurasian lineage H7 AIVs tested. CONCLUSIONS The high sensitivity of H7 HA2 RRT PCR confirms its suitability for use in poultry surveillance and disease diagnosis. H7 CS RRT PCR provides an opportunity for rapid pathotyping of H7 AIVs.
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Affiliation(s)
- Marek J Slomka
- Avian Virology Workgroup, Virology Department, Veterinary Laboratories Agency (VLA Weybridge), Addlestone, Surrey, UK.
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Chances and limitations of wild bird monitoring for the avian influenza virus H5N1--detection of pathogens highly mobile in time and space. PLoS One 2009; 4:e6639. [PMID: 19680560 PMCID: PMC2722081 DOI: 10.1371/journal.pone.0006639] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2008] [Accepted: 07/13/2009] [Indexed: 11/19/2022] Open
Abstract
Highly pathogenic influenza virus (HPAIV) H5N1 proved to be remarkably mobile in migratory bird populations where it has led to extensive outbreaks for which the true number of affected birds usually cannot be determined. For the evaluation of avian influenza monitoring and HPAIV early warning systems, we propose a time-series analysis that includes the estimation of confidence intervals for (i) the prevalence in outbreak situations or (ii) in the apparent absence of disease in time intervals for specified regional units. For the German outbreak regions in 2006 and 2007, the upper 95% confidence limit allowed the detection of prevalences below 1% only for certain time intervals. Although more than 25,000 birds were sampled in Germany per year, the upper 95% confidence limit did not fall below 5% in the outbreak regions for most of the time. The proposed analysis can be used to monitor water bodies and high risk areas, also as part of an early-warning system. Chances for an improved targeting of the monitoring system as part of a risk-based approach are discussed with the perspective of reducing sample sizes.
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Harder TC, Teuffert J, Starick E, Gethmann J, Grund C, Fereidouni S, Durban M, Bogner KH, Neubauer-Juric A, Repper R, Hlinak A, Engelhardt A, Nöckler A, Smietanka K, Minta Z, Kramer M, Globig A, Mettenleiter TC, Conraths FJ, Beer M. Highly pathogenic avian influenza virus (H5N1) in frozen duck carcasses, Germany, 2007. Emerg Infect Dis 2009; 15:272-9. [PMID: 19193272 PMCID: PMC2657628 DOI: 10.3201/eid1502.080949] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Article summary line: Phylogenetic and epidemiologic evidence shows incursion of HPAIV into the food chain. We conducted phylogenetic and epidemiologic analyses to determine sources of outbreaks of highly pathogenic avian influenza virus (HPAIV), subtype H5N1, in poultry holdings in 2007 in Germany, and a suspected incursion of HPAIV into the food chain through contaminated deep-frozen duck carcasses. In summer 2007, HPAIV (H5N1) outbreaks in 3 poultry holdings in Germany were temporally, spatially, and phylogenetically linked to outbreaks in wild aquatic birds. Detection of HPAIV (H5N1) in frozen duck carcass samples of retained slaughter batches of 1 farm indicated that silent infection had occurred for some time before the incidental detection. Phylogenetic analysis established a direct epidemiologic link between HPAIV isolated from duck meat and strains isolated from 3 further outbreaks in December 2007 in backyard chickens that had access to uncooked offal from commercial deep-frozen duck carcasses. Measures that will prevent such undetected introduction of HPAIV (H5N1) into the food chain are urgently required.
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Gall A, Hoffmann B, Harder T, Grund C, Ehricht R, Beer M. Rapid haemagglutinin subtyping and pathotyping of avian influenza viruses by a DNA microarray. J Virol Methods 2009; 160:200-5. [PMID: 19447139 DOI: 10.1016/j.jviromet.2009.05.004] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2009] [Revised: 05/03/2009] [Accepted: 05/07/2009] [Indexed: 11/17/2022]
Abstract
Rapid and reliable methods are fundamental for the comprehensive characterization of emerging and evolving avian influenza viruses. Although microarrays provide new possibilities with their parallel approach, their use in diagnostic laboratories is still limited due to economical and practical factors. An easy-to-use, low-cost microarray-based assay for haemagglutinin subtyping and pathotyping of avian influenza viruses and specific detection of highly pathogenic H5N1/Asia clade 2.2 is described as a novel diagnostic tool. The ArrayTube platform is user-friendly, inexpensive and allows processing of many samples. The sensitivity of the assay developed was comparable to real-time RT-PCR, and the simultaneous detection of different subtypes was possible. Validation with 90 influenza A virus isolates representing all 16 haemagglutinin subtypes and 44 field samples (cloacal swabs from wild and domestic birds) demonstrated the feasibility of the system for sensitive and specific characterization of AIV. Facilitating haemagglutinin subtyping and pathotyping for the majority of influenza A-positive cloacal swabs within 24h, the new assay enables detailed AIV diagnosis even in less well-equipped laboratories.
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Affiliation(s)
- Astrid Gall
- Institute of Diagnostic Virology, Friedrich-Loeffler-Institut, Greifswald - Insel Riems, Germany
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41
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Hoffmann B, Beer M, Reid SM, Mertens P, Oura CAL, van Rijn PA, Slomka MJ, Banks J, Brown IH, Alexander DJ, King DP. A review of RT-PCR technologies used in veterinary virology and disease control: sensitive and specific diagnosis of five livestock diseases notifiable to the World Organisation for Animal Health. Vet Microbiol 2009; 139:1-23. [PMID: 19497689 DOI: 10.1016/j.vetmic.2009.04.034] [Citation(s) in RCA: 124] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2008] [Revised: 04/15/2009] [Accepted: 04/28/2009] [Indexed: 12/31/2022]
Abstract
Real-time, reverse transcription polymerase chain reaction (rRT-PCR) has become one of the most widely used methods in the field of molecular diagnostics and research. The potential of this format to provide sensitive, specific and swift detection and quantification of viral RNAs has made it an indispensable tool for state-of-the-art diagnostics of important human and animal viral pathogens. Integration of these assays into automated liquid handling platforms for nucleic acid extraction increases the rate and standardisation of sample throughput and decreases the potential for cross-contamination. The reliability of these assays can be further enhanced by using internal controls to validate test results. Based on these advantageous characteristics, numerous robust rRT-PCRs systems have been developed and validated for important epizootic diseases of livestock. Here, we review the rRT-PCR assays that have been developed for the detection of five RNA viruses that cause diseases that are notifiable to the World Organisation for Animal Health (OIE), namely: foot-and-mouth disease, classical swine fever, bluetongue disease, avian influenza and Newcastle disease. The performance of these tests for viral diagnostics and disease control and prospects for improved strategies in the future are discussed.
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Affiliation(s)
- Bernd Hoffmann
- Institute of Diagnostic Virology, Friedrich-Loeffler-Institut, Greifswald-Insel Riems, Germany
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Globig A, Staubach C, Beer M, Köppen U, Fiedler W, Nieburg M, Wilking H, Starick E, Teifke JP, Werner O, Unger F, Grund C, Wolf C, Roost H, Feldhusen F, Conraths FJ, Mettenleiter TC, Harder TC. Epidemiological and Ornithological Aspects of Outbreaks of Highly Pathogenic Avian Influenza Virus H5N1 of Asian Lineage in Wild Birds in Germany, 2006 and 2007. Transbound Emerg Dis 2009; 56:57-72. [DOI: 10.1111/j.1865-1682.2008.01061.x] [Citation(s) in RCA: 74] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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43
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Pozo F, Casas I, Ruiz G, Falcón A, Pérez-Breña P. [Application of molecular methods in the diagnosis and epidemiological study of viral respiratory infections]. Enferm Infecc Microbiol Clin 2009; 26 Suppl 9:15-25. [PMID: 19195443 PMCID: PMC7130302 DOI: 10.1016/s0213-005x(08)76537-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Hasta la fecha se han identificado más de 200 virus pertenecientes a 6 familias taxonómicas diferentes asociados con la infección del tracto respiratorio humano. La utilización generalizada de métodos moleculares en los laboratorios de microbiología clínica no sólo ha aportado grandes ventajas al diagnóstico de estas infecciones, sino también está permitiendo profundizar en el conocimiento de la enfermedad y el comportamiento epidemiológico de los virus causantes. Esta tecnología incrementa de manera notable el rendimiento de detección de virus en las muestras respiratorias, debido a su elevada sensibilidad en comparación con las técnicas clásicas y a la posibilidad de identificar virus no cultivables o de crecimiento fastidioso en las líneas celulares habituales, lo que permite realizar el diagnóstico etiológico con mayor rapidez. Sin embargo, también comporta algunos inconvenientes, como son detectar virus que se encuentran colonizando la mucosa respiratoria de personas asintomáticas, o en secreciones de pacientes que ya se han recuperado de una infección pasada, a consecuencia de excreción prolongada de éstos. La secuenciación de los productos obtenidos en la reacción de amplificación genómica permite caracterizar de forma adicional los virus detectados mediante su genotipado, realizar estudios de epidemiología molecular e identificar resistencias a determinados antivirales, por citar sólo algunos ejemplos.
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Affiliation(s)
- Francisco Pozo
- Laboratorio de Gripe y Virus Respiratorios, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Majadahonda, Madrid, España.
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Chang CM, Lebarbenchon C, Gauthier-Clerc M, Le Bohec C, Beaune D, Le Maho Y, van der Werf S. Molecular surveillance for avian influenza A virus in king penguins ( Aptenodytes patagonicus). Polar Biol 2009; 32:663. [PMID: 32214634 PMCID: PMC7087602 DOI: 10.1007/s00300-009-0587-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2008] [Revised: 01/16/2009] [Accepted: 01/19/2009] [Indexed: 10/27/2022]
Abstract
An investigation of the presence of influenza A virus has been conducted in king penguins (Aptenodytes patagonicus) at the Possession Island in the Crozet Archipelago, Antarctica, using a rapid molecular diagnostic method based on real-time polymerase chain reaction. No evidence of outbreak or positive viral infection of influenza A virus was found in this study. We however recommend the implementation of long-term surveillance in seabird populations of polar ecosystems to detect the potential introduction of exotic strains and potential existence of a local epidemiological cycle for avian influenza viruses.
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Affiliation(s)
- Chung-Ming Chang
- 1Unité de Génétique Moléculaire des Virus Respiratoires, URA3015 CNRS, EA302 Université Paris-Diderot Paris 7, Institut Pasteur, 25 rue du Dr Roux, 75724 Paris Cedex 15, France.,2Génétique et Évolution des Maladies Infectieuses, UMR 2724, IRD, 911 avenue Agropolis, BP 64501, 34394 Montpellier Cedex 5, France.,5Department of Medical Biotechnology and Laboratory Science, Research Center for Emerging Viral Infections, Chang Gung University, 259 Wen-Hwa 1st Road, Kwei-Shan, Tao-Yuan, 333 Taiwan
| | - Camille Lebarbenchon
- 1Unité de Génétique Moléculaire des Virus Respiratoires, URA3015 CNRS, EA302 Université Paris-Diderot Paris 7, Institut Pasteur, 25 rue du Dr Roux, 75724 Paris Cedex 15, France.,2Génétique et Évolution des Maladies Infectieuses, UMR 2724, IRD, 911 avenue Agropolis, BP 64501, 34394 Montpellier Cedex 5, France.,3Centre de Recherche de la Tour du Valat, Le Sambuc, 13200 Arles, France
| | | | - Céline Le Bohec
- 4Département d'Écologie, Physiologie et Éthologie, Institut Pluridisciplinaire Hubert Curien, UMR 7178, 23 rue Becquerel, 67087 Strasbourg Cedex 02, France
| | - David Beaune
- 4Département d'Écologie, Physiologie et Éthologie, Institut Pluridisciplinaire Hubert Curien, UMR 7178, 23 rue Becquerel, 67087 Strasbourg Cedex 02, France
| | - Yvon Le Maho
- 4Département d'Écologie, Physiologie et Éthologie, Institut Pluridisciplinaire Hubert Curien, UMR 7178, 23 rue Becquerel, 67087 Strasbourg Cedex 02, France
| | - Sylvie van der Werf
- 1Unité de Génétique Moléculaire des Virus Respiratoires, URA3015 CNRS, EA302 Université Paris-Diderot Paris 7, Institut Pasteur, 25 rue du Dr Roux, 75724 Paris Cedex 15, France
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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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Yacoub A, Kiss I, Zohari S, Hakhverdyan M, Czifra G, Mohamed N, Gyarmati P, Blomberg J, Belák S. The rapid molecular subtyping and pathotyping of avian influenza viruses. J Virol Methods 2008; 156:157-61. [PMID: 19026689 DOI: 10.1016/j.jviromet.2008.10.019] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2008] [Revised: 10/03/2008] [Accepted: 10/13/2008] [Indexed: 10/21/2022]
Abstract
Highly conserved nucleotide stretches flanking the cleavage site of the haemagglutinin (HA) gene of influenza type A viruses were utilised for generating PCR amplicons from a broad range of avian influenza viruses (AIV) in a one-step real-time SYBR Green RT-PCR assay. The nucleotide sequencing of the amplified PCR products simultaneously reveals both the HA subtype and the pathotype of the AIV isolates, as we demonstrated in case of H5 subtype viruses. The specificity of the assay was confirmed by investigating 66 strains of AIV and nine heterologous pathogens, including influenza B, C and various avian pathogenic viruses. This assay enables a general HA subtype identification and pathotype determination of AIV isolates providing a useful alternative tool for avian influenza diagnosis.
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Affiliation(s)
- A Yacoub
- The National Veterinary Institute and The Swedish University of Agricultural Sciences, OIE Collaborating Centre for the Biotechnology-Based Diagnosis of Infectious Diseases in Veterinary Medicine, Ulls väg 2B, SE 751 89 Uppsala, Sweden.
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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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Fereidouni SR, Harder TC, Starick E. Rapid pathotyping of recent H5N1 highly pathogenic avian influenza viruses and of H5 viruses with low pathogenicity by RT-PCR and restriction enzyme cleavage pattern (RECP). J Virol Methods 2008; 154:14-9. [PMID: 18851993 DOI: 10.1016/j.jviromet.2008.09.011] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2008] [Revised: 09/04/2008] [Accepted: 09/15/2008] [Indexed: 11/18/2022]
Abstract
Rapid and accurate diagnosis of avian influenza virus infections of poultry and humans comprises detection, subtyping, and, in case of subtypes H5 and H7, pathotyping of such viruses. Reliable methods for pathotyping of H5 avian influenza viruses (AIV) are based on determination of the intravenous pathogenicity index (IVPI) in specific pathogen free (SPF) chickens and on characterization of the hemagglutinin (HA) gene cleavage site by sequencing. The number of basic amino acids (arginine and lysine) at the cleavage site is an important indicator of pathogenicity. In this paper, a new rapid method for pathotyping of H5 subtype avian influenza viruses is described which is based on RT-PCR and restriction enzyme cleavage pattern (RECP) assay using the MboII restriction enzyme. Validation of the method using 28 H5 subtype reference isolates from different animal species revealed good performance characteristics regarding sensitivity and specificity, especially when targeting recent highly pathogenic AIV (HPAIV) of subtype H5N1 and Asian origin. In addition, RECP results were validated by testing 47 field samples from different sources and by sequencing of their RT-PCR products. This approach for H5 AIV pathotyping proved to be fast, reliable, and comparatively sensitive and is suitable especially for laboratories lacking sequencing or in vivo pathotyping facilities.
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Affiliation(s)
- Sasan R Fereidouni
- Institute of Diagnostic Virology, Friedrich-Loeffler-Institute (FLI), Südufer 10, 17493 Greifswald, Insel Riems, Germany.
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49
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Kalthoff D, Breithaupt A, Teifke JP, Globig A, Harder T, Mettenleiter TC, Beer M. Highly pathogenic avian influenza virus (H5N1) in experimentally infected adult mute swans. Emerg Infect Dis 2008; 14:1267-70. [PMID: 18680652 PMCID: PMC2600380 DOI: 10.3201/eid1408.080078] [Citation(s) in RCA: 68] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
Adult, healthy mute swans were experimentally infected with highly pathogenic avian influenza virus A/Cygnus cygnus/Germany/R65/2006 subtype H5N1. Immunologically naive birds died, whereas animals with preexisting, naturally acquired avian influenza virus–specific antibodies became infected asymptomatically and shed virus. Adult mute swans are highly susceptible, excrete virus, and can be clinically protected by preexposure immunity.
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Affiliation(s)
- Donata Kalthoff
- Friedrich-Loeffler-Institut, Greifswald-Insel Riems, Germany
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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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