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Smith GJD, Naipospos TSP, Nguyen TD, de Jong MD, Vijaykrishna D, Usman TB, Hassan SS, Nguyen TV, Dao TV, Bui NA, Leung YHC, Cheung CL, Rayner JM, Zhang JX, Zhang LJ, Poon LLM, Li KS, Nguyen VC, Hien TT, Farrar J, Webster RG, Chen H, Peiris JSM, Guan Y. Evolution and adaptation of H5N1 influenza virus in avian and human hosts in Indonesia and Vietnam. Virology 2006; 350:258-68. [PMID: 16713612 DOI: 10.1016/j.virol.2006.03.048] [Citation(s) in RCA: 181] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2006] [Revised: 03/21/2006] [Accepted: 03/27/2006] [Indexed: 11/24/2022]
Abstract
Highly pathogenic avian influenza virus H5N1 is endemic in poultry in East and Southeast Asia with disease outbreaks recently spreading to parts of central Asia, Europe and Africa. Continued interspecies transmission to humans has been reported in Vietnam, Thailand, Cambodia, Indonesia and China, causing pandemic concern. Here, we genetically characterize 82 H5N1 viruses isolated from poultry throughout Indonesia and Vietnam and 11 human isolates from southern Vietnam together with sequence data available in public databases to address questions relevant to virus introduction, endemicity and evolution. Phylogenetic analysis shows that all viruses from Indonesia form a distinct sublineage of H5N1 genotype Z viruses suggesting this outbreak likely originated from a single introduction that spread throughout the country during the past two years. Continued virus activities in Indonesia were attributed to transmission via poultry movement within the country rather than through repeated introductions by bird migration. Within Indonesia and Vietnam, H5N1 viruses have evolved over time into geographically distinct groups within each country. Molecular analysis of the H5N1 genotype Z genome shows that only the M2 and PB1-F2 genes were under positive selection, suggesting that these genes might be involved in adaptation of this virus to new hosts following interspecies transmission. At the amino acid level 12 residues were under positive selection in those genotype Z viruses, in the HA and PB1-F2 proteins. Some of these residues were more frequently observed in human isolates than in avian isolates and are related to viral antigenicity and receptor binding. Our study provides insight into the ongoing evolution of H5N1 influenza viruses that are transmitting in diverse avian species and at the interface between avian and human hosts.
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Affiliation(s)
- G J D Smith
- State Key Laboratory of Emerging Infectious Diseases, Department of Microbiology, The University of Hong Kong, Faculty of Medicine Building, 21 Sassoon Road, Pokfulam, Hong Kong SAR, China
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Chen H, Smith GJD, Li KS, Wang J, Fan XH, Rayner JM, Vijaykrishna D, Zhang JX, Zhang LJ, Guo CT, Cheung CL, Xu KM, Duan L, Huang K, Qin K, Leung YHC, Wu WL, Lu HR, Chen Y, Xia NS, Naipospos TSP, Yuen KY, Hassan SS, Bahri S, Nguyen TD, Webster RG, Peiris JSM, Guan Y. Establishment of multiple sublineages of H5N1 influenza virus in Asia: implications for pandemic control. Proc Natl Acad Sci U S A 2006; 103:2845-50. [PMID: 16473931 PMCID: PMC1413830 DOI: 10.1073/pnas.0511120103] [Citation(s) in RCA: 453] [Impact Index Per Article: 25.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
Preparedness for a possible influenza pandemic caused by highly pathogenic avian influenza A subtype H5N1 has become a global priority. The spread of the virus to Europe and continued human infection in Southeast Asia have heightened pandemic concern. It remains unknown from where the pandemic strain may emerge; current attention is directed at Vietnam, Thailand, and, more recently, Indonesia and China. Here, we report that genetically and antigenically distinct sublineages of H5N1 virus have become established in poultry in different geographical regions of Southeast Asia, indicating the long-term endemicity of the virus, and the isolation of H5N1 virus from apparently healthy migratory birds in southern China. Our data show that H5N1 influenza virus, has continued to spread from its established source in southern China to other regions through transport of poultry and bird migration. The identification of regionally distinct sublineages contributes to the understanding of the mechanism for the perpetuation and spread of H5N1, providing information that is directly relevant to control of the source of infection in poultry. It points to the necessity of surveillance that is geographically broader than previously supposed and that includes H5N1 viruses of greater genetic and antigenic diversity.
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Affiliation(s)
- H. Chen
- Joint Influenza Research Centre (Shantou University Medical College and Hong Kong University), Shantou University Medical College, Shantou, Guangdong 515031, China
- State Key Laboratory of Emerging Infectious Diseases, Department of Microbiology, University of Hong Kong, Faculty of Medicine Building, 21 Sassoon Road, Pokfulam, Hong Kong SAR, China
| | - G. J. D. Smith
- Joint Influenza Research Centre (Shantou University Medical College and Hong Kong University), Shantou University Medical College, Shantou, Guangdong 515031, China
- State Key Laboratory of Emerging Infectious Diseases, Department of Microbiology, University of Hong Kong, Faculty of Medicine Building, 21 Sassoon Road, Pokfulam, Hong Kong SAR, China
| | - K. S. Li
- Joint Influenza Research Centre (Shantou University Medical College and Hong Kong University), Shantou University Medical College, Shantou, Guangdong 515031, China
| | - J. Wang
- Joint Influenza Research Centre (Shantou University Medical College and Hong Kong University), Shantou University Medical College, Shantou, Guangdong 515031, China
| | - X. H. Fan
- State Key Laboratory of Emerging Infectious Diseases, Department of Microbiology, University of Hong Kong, Faculty of Medicine Building, 21 Sassoon Road, Pokfulam, Hong Kong SAR, China
| | - J. M. Rayner
- Joint Influenza Research Centre (Shantou University Medical College and Hong Kong University), Shantou University Medical College, Shantou, Guangdong 515031, China
- State Key Laboratory of Emerging Infectious Diseases, Department of Microbiology, University of Hong Kong, Faculty of Medicine Building, 21 Sassoon Road, Pokfulam, Hong Kong SAR, China
| | - D. Vijaykrishna
- Joint Influenza Research Centre (Shantou University Medical College and Hong Kong University), Shantou University Medical College, Shantou, Guangdong 515031, China
- State Key Laboratory of Emerging Infectious Diseases, Department of Microbiology, University of Hong Kong, Faculty of Medicine Building, 21 Sassoon Road, Pokfulam, Hong Kong SAR, China
| | - J. X. Zhang
- Joint Influenza Research Centre (Shantou University Medical College and Hong Kong University), Shantou University Medical College, Shantou, Guangdong 515031, China
- State Key Laboratory of Emerging Infectious Diseases, Department of Microbiology, University of Hong Kong, Faculty of Medicine Building, 21 Sassoon Road, Pokfulam, Hong Kong SAR, China
| | - L. J. Zhang
- Joint Influenza Research Centre (Shantou University Medical College and Hong Kong University), Shantou University Medical College, Shantou, Guangdong 515031, China
- State Key Laboratory of Emerging Infectious Diseases, Department of Microbiology, University of Hong Kong, Faculty of Medicine Building, 21 Sassoon Road, Pokfulam, Hong Kong SAR, China
| | - C. T. Guo
- State Key Laboratory of Emerging Infectious Diseases, Department of Microbiology, University of Hong Kong, Faculty of Medicine Building, 21 Sassoon Road, Pokfulam, Hong Kong SAR, China
| | - C. L. Cheung
- Joint Influenza Research Centre (Shantou University Medical College and Hong Kong University), Shantou University Medical College, Shantou, Guangdong 515031, China
- State Key Laboratory of Emerging Infectious Diseases, Department of Microbiology, University of Hong Kong, Faculty of Medicine Building, 21 Sassoon Road, Pokfulam, Hong Kong SAR, China
| | - K. M. Xu
- Joint Influenza Research Centre (Shantou University Medical College and Hong Kong University), Shantou University Medical College, Shantou, Guangdong 515031, China
- State Key Laboratory of Emerging Infectious Diseases, Department of Microbiology, University of Hong Kong, Faculty of Medicine Building, 21 Sassoon Road, Pokfulam, Hong Kong SAR, China
| | - L. Duan
- Joint Influenza Research Centre (Shantou University Medical College and Hong Kong University), Shantou University Medical College, Shantou, Guangdong 515031, China
- State Key Laboratory of Emerging Infectious Diseases, Department of Microbiology, University of Hong Kong, Faculty of Medicine Building, 21 Sassoon Road, Pokfulam, Hong Kong SAR, China
| | - K. Huang
- State Key Laboratory of Emerging Infectious Diseases, Department of Microbiology, University of Hong Kong, Faculty of Medicine Building, 21 Sassoon Road, Pokfulam, Hong Kong SAR, China
| | - K. Qin
- Joint Influenza Research Centre (Shantou University Medical College and Hong Kong University), Shantou University Medical College, Shantou, Guangdong 515031, China
- State Key Laboratory of Emerging Infectious Diseases, Department of Microbiology, University of Hong Kong, Faculty of Medicine Building, 21 Sassoon Road, Pokfulam, Hong Kong SAR, China
| | - Y. H. C. Leung
- State Key Laboratory of Emerging Infectious Diseases, Department of Microbiology, University of Hong Kong, Faculty of Medicine Building, 21 Sassoon Road, Pokfulam, Hong Kong SAR, China
| | - W. L. Wu
- Joint Influenza Research Centre (Shantou University Medical College and Hong Kong University), Shantou University Medical College, Shantou, Guangdong 515031, China
- State Key Laboratory of Emerging Infectious Diseases, Department of Microbiology, University of Hong Kong, Faculty of Medicine Building, 21 Sassoon Road, Pokfulam, Hong Kong SAR, China
| | - H. R. Lu
- State Key Laboratory of Emerging Infectious Diseases, Department of Microbiology, University of Hong Kong, Faculty of Medicine Building, 21 Sassoon Road, Pokfulam, Hong Kong SAR, China
| | - Y. Chen
- Research Center for Medical Molecular Virology of Fujian Province, Xiamen University, Xiamen, Fujian 361005, China
| | - N. S. Xia
- Research Center for Medical Molecular Virology of Fujian Province, Xiamen University, Xiamen, Fujian 361005, China
| | - T. S. P. Naipospos
- Ministry of Agriculture and Animal Health, Government of Indonesia, Pasar Minggu, Jakarta Selatan 12550, Indonesia
| | - K. Y. Yuen
- State Key Laboratory of Emerging Infectious Diseases, Department of Microbiology, University of Hong Kong, Faculty of Medicine Building, 21 Sassoon Road, Pokfulam, Hong Kong SAR, China
| | - S. S. Hassan
- Veterinary Research Institute, 31 400 Ipoh, Malaysia
| | - S. Bahri
- Ministry of Agriculture and Animal Health, Government of Indonesia, Pasar Minggu, Jakarta Selatan 12550, Indonesia
| | - T. D. Nguyen
- **National Institute of Veterinary Research, Dong Da, Hanoi, Vietnam; and
| | - R. G. Webster
- State Key Laboratory of Emerging Infectious Diseases, Department of Microbiology, University of Hong Kong, Faculty of Medicine Building, 21 Sassoon Road, Pokfulam, Hong Kong SAR, China
- **National Institute of Veterinary Research, Dong Da, Hanoi, Vietnam; and
- To whom correspondence may be addressed. E-mail:
or
| | - J. S. M. Peiris
- Joint Influenza Research Centre (Shantou University Medical College and Hong Kong University), Shantou University Medical College, Shantou, Guangdong 515031, China
- State Key Laboratory of Emerging Infectious Diseases, Department of Microbiology, University of Hong Kong, Faculty of Medicine Building, 21 Sassoon Road, Pokfulam, Hong Kong SAR, China
| | - Y. Guan
- Joint Influenza Research Centre (Shantou University Medical College and Hong Kong University), Shantou University Medical College, Shantou, Guangdong 515031, China
- State Key Laboratory of Emerging Infectious Diseases, Department of Microbiology, University of Hong Kong, Faculty of Medicine Building, 21 Sassoon Road, Pokfulam, Hong Kong SAR, China
- To whom correspondence may be addressed. E-mail:
or
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