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Timofeeva TA, Sadykova GK, Lomakina NF, Gambaryan AS, Rudneva IA, Timofeeva EB, Shilov AA, Boravleva EY, Zhuravleva MM, Ivanov PA, Ryazanova EL, Prilipov AG. The Effect of I155T, K156Q, K156E and N186K Mutations in Hemagglutinin on the Virulence and Reproduction of Influenza A/H5N1 Viruses. Mol Biol 2021; 54:861-869. [PMID: 33424035 PMCID: PMC7783499 DOI: 10.1134/s0026893320060126] [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: 05/06/2020] [Revised: 05/25/2020] [Accepted: 05/27/2020] [Indexed: 11/23/2022]
Abstract
The continued circulation of influenza A virus subtype H5 may cause the emergence of new potential pandemic virus variants, which can be transmitted from person to person. The occurrence of such variants is mainly related to mutations in hemagglutinin (HA). Previously we discovered mutations in H5N1 influenza virus hemagglutinin, which contributes to virus immune evasion. The purpose of this work was to study the role of these mutations in changing other, non-antigenic properties of the virus and the possibility of their maintenance in the viral population. Mutations were introduced into the HA gene of a recombinant H5N1 influenza A virus (VNH5N1-PR8/CDC-RG) using site-specific mutagenesis. The "variant" viruses were investigated and compared with respect to replication kinetics in chicken embryos, thermostability, reproductive activity at different temperatures (33, 37 and 40°C), and virulence for mice. Amino acid substitutions I155T, K156Q, K156E+V138A, N186K led to a decrease in thermal stability, replication activity of the mutant viruses in chicken embryos, and virulence for mice, although these effects differed between the variants. The K156Q and N186K mutations reduced viral reproduction at elevated temperature (40°C). The analysis of the frequency of these mutations in natural isolates of H5N1 influenza viruses indicated that the K156E/Q and N186K mutations have little chance to gain a foothold during evolution, in contrast to the I155T mutation, which is the most responsible for antigenic drift. The A138V and N186K mutations seem to be adaptive in mammalian viruses.
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Affiliation(s)
- T. A. Timofeeva
- Gamaleya National Research Center for Epidemiology and Microbiology, Ministry of Health of the Russian Federation, 123098 Moscow, Russia
| | - G. K. Sadykova
- Gamaleya National Research Center for Epidemiology and Microbiology, Ministry of Health of the Russian Federation, 123098 Moscow, Russia
| | - N. F. Lomakina
- Gamaleya National Research Center for Epidemiology and Microbiology, Ministry of Health of the Russian Federation, 123098 Moscow, Russia
| | - A. S. Gambaryan
- Chumakov Federal Scientific Center for Research and Development of Immune-and-Biological Products, Russian Academy of Sciences, 108819 Moscow, Russia
| | - I. A. Rudneva
- Gamaleya National Research Center for Epidemiology and Microbiology, Ministry of Health of the Russian Federation, 123098 Moscow, Russia
| | - E. B. Timofeeva
- Gamaleya National Research Center for Epidemiology and Microbiology, Ministry of Health of the Russian Federation, 123098 Moscow, Russia
| | - A. A. Shilov
- Gamaleya National Research Center for Epidemiology and Microbiology, Ministry of Health of the Russian Federation, 123098 Moscow, Russia
| | - E. Y. Boravleva
- Chumakov Federal Scientific Center for Research and Development of Immune-and-Biological Products, Russian Academy of Sciences, 108819 Moscow, Russia
| | - M. M. Zhuravleva
- Gamaleya National Research Center for Epidemiology and Microbiology, Ministry of Health of the Russian Federation, 123098 Moscow, Russia
| | - P. A. Ivanov
- Gamaleya National Research Center for Epidemiology and Microbiology, Ministry of Health of the Russian Federation, 123098 Moscow, Russia
| | - E. L. Ryazanova
- Gamaleya National Research Center for Epidemiology and Microbiology, Ministry of Health of the Russian Federation, 123098 Moscow, Russia
- Sechenov First Moscow State Medical University, Ministry of Health of the Russian Federation, 119991 Moscow, Russia
| | - A. G. Prilipov
- Gamaleya National Research Center for Epidemiology and Microbiology, Ministry of Health of the Russian Federation, 123098 Moscow, Russia
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2
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Musa WI, Sa'idu L, Bello M, Abdu PA. Co-inections of domestic and wild birds with avian influenza and Newcastle disease viruses: implications for control and genetic mutations. Vet Res Commun 2020; 44:159-166. [PMID: 33040313 DOI: 10.1007/s11259-020-09783-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2020] [Accepted: 10/02/2020] [Indexed: 01/20/2023]
Abstract
Co-infections of birds' upper respiratory tract by avian pathogens are common and cause increasing economic losses. This study determines co-infection status of avian influenza (AI) and Newcastle disease (ND) in birds in two Nigerian states with different highly pathogenic avian influenza (HPAI) records and where modified stamping out policy contained the virus for seven years after which the virus resurged with higher infectivity in 2015. A cross-sectional study sampling 910 apparently healthy domestic and 90 wild birds from wild habitats, commercial poultry farms, households and live bird markets (LBMs) was conducted. Cloacal and tracheal swabs were tested for AI H5 and ND viruses using conventional reverse transcriptase polymerase chain reaction (RT-PCR). Overall detection rates of 3% and 18% for AI and ND were obtained. There was an equivalence of 8.5% ND detection rate in poultry and wild birds in the two states. Co-infection (0.2%) of a local chicken from a live bird market (LBM) and crown crane (Balearica regulorum) from a household to AI H5 and ND viruses occurred, respectively. Exposure of birds to AI and ND was significantly detected in apparently healthy domestic and wild birds. The probability of these viruses exchanging genetic materials to resurge with increasing virulence is foreseen. Therefore, routine AI and ND control measures should incorporate virus surveillance and instituting appropriate preventive measures in domestic and wild birds held in households, commercial farms and LBMs.
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Affiliation(s)
- Waziri Ibrahim Musa
- Department of Veterinary Medicine, Ahmadu Bello University Zaria, Zaria, Nigeria.
| | - Lawal Sa'idu
- Veterinary Teaching Hospital, Ahmadu Bello University Zaria, Zaria, Nigeria
| | - Mohammed Bello
- Department of Veterinary Public Health and Preventive Medicine, A.B.U Zaria, Zaria, Nigeria
| | - Paul Ayuba Abdu
- Department of Veterinary Medicine, Ahmadu Bello University Zaria, Zaria, Nigeria
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3
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Han AX, Parker E, Scholer F, Maurer-Stroh S, Russell CA. Phylogenetic Clustering by Linear Integer Programming (PhyCLIP). Mol Biol Evol 2020; 36:1580-1595. [PMID: 30854550 PMCID: PMC6573476 DOI: 10.1093/molbev/msz053] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Subspecies nomenclature systems of pathogens are increasingly based on sequence data. The use of phylogenetics to identify and differentiate between clusters of genetically similar pathogens is particularly prevalent in virology from the nomenclature of human papillomaviruses to highly pathogenic avian influenza (HPAI) H5Nx viruses. These nomenclature systems rely on absolute genetic distance thresholds to define the maximum genetic divergence tolerated between viruses designated as closely related. However, the phylogenetic clustering methods used in these nomenclature systems are limited by the arbitrariness of setting intra and intercluster diversity thresholds. The lack of a consensus ground truth to define well-delineated, meaningful phylogenetic subpopulations amplifies the difficulties in identifying an informative distance threshold. Consequently, phylogenetic clustering often becomes an exploratory, ad hoc exercise. Phylogenetic Clustering by Linear Integer Programming (PhyCLIP) was developed to provide a statistically principled phylogenetic clustering framework that negates the need for an arbitrarily defined distance threshold. Using the pairwise patristic distance distributions of an input phylogeny, PhyCLIP parameterizes the intra and intercluster divergence limits as statistical bounds in an integer linear programming model which is subsequently optimized to cluster as many sequences as possible. When applied to the hemagglutinin phylogeny of HPAI H5Nx viruses, PhyCLIP was not only able to recapitulate the current WHO/OIE/FAO H5 nomenclature system but also further delineated informative higher resolution clusters that capture geographically distinct subpopulations of viruses. PhyCLIP is pathogen-agnostic and can be generalized to a wide variety of research questions concerning the identification of biologically informative clusters in pathogen phylogenies. PhyCLIP is freely available at http://github.com/alvinxhan/PhyCLIP, last accessed March 15, 2019.
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Affiliation(s)
- Alvin X Han
- Bioinformatics Institute, Agency for Science, Technology and Research (A*STAR), Singapore.,NUS Graduate School for Integrative Sciences and Engineering, National University of Singapore (NUS), Singapore.,Laboratory of Applied Evolutionary Biology, Department of Medical Microbiology, Academic Medical Centre, University of Amsterdam, Amsterdam, The Netherlands
| | - Edyth Parker
- Laboratory of Applied Evolutionary Biology, Department of Medical Microbiology, Academic Medical Centre, University of Amsterdam, Amsterdam, The Netherlands.,Department of Veterinary Medicine, University of Cambridge, Cambridge, United Kingdom
| | - Frits Scholer
- Department of Medical Microbiology, Academic Medical Centre, University of Amsterdam, Amsterdam, The Netherlands
| | - Sebastian Maurer-Stroh
- Bioinformatics Institute, Agency for Science, Technology and Research (A*STAR), Singapore.,NUS Graduate School for Integrative Sciences and Engineering, National University of Singapore (NUS), Singapore.,Department of Biological Sciences, National University of Singapore, Singapore
| | - Colin A Russell
- Laboratory of Applied Evolutionary Biology, Department of Medical Microbiology, Academic Medical Centre, University of Amsterdam, Amsterdam, The Netherlands
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Park YR, Lee YN, Lee DH, Baek YG, Si YJ, Meeduangchanh P, Theppangna W, Douangngeun B, Kye SJ, Lee MH, Park CK, Lee YJ. Genetic and pathogenic characteristics of clade 2.3.2.1c H5N1 highly pathogenic avian influenza viruses isolated from poultry outbreaks in Laos during 2015-2018. Transbound Emerg Dis 2019; 67:947-955. [PMID: 31769586 DOI: 10.1111/tbed.13430] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2019] [Revised: 10/25/2019] [Accepted: 11/18/2019] [Indexed: 12/17/2022]
Abstract
Since 2004, there have been multiple outbreaks of H5 highly pathogenic avian influenza (HPAI) viruses in Laos. Here, we isolated H5N1 HPAI viruses from poultry outbreaks in Laos during 2015-2018 and investigated their genetic characteristics and pathogenicity in chickens. Phylogenetic analysis revealed that the isolates belonged to clade 2.3.2.1c and that they differed from previous Laos viruses with respect to genetic composition. In particular, the isolates were divided into two genotypes, each of which had a different NS segments. The results of possible migration analysis suggested a high likelihood that the Laos isolates were introduced from neighbouring countries, particularly Vietnam. The recent Laos isolate, A/Duck/Laos/NL-1504599/2018, had an intravenous pathogenicity index score of 3.0 and showed a 50% chicken lethal dose of 102.5 EID50 /0.1 ml, indicating high pathogenicity. The isolated viruses exhibited no critical substitution in the markers associated with mammalian adaptation, but possess markers related to neuraminidase inhibitor resistance. These results emphasize the need for ongoing surveillance of circulating influenza virus in South-East Asia, including Laos, to better prepare for and mitigate global spread of H5 HPAI.
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Affiliation(s)
- Yu-Ri Park
- Avian Influenza Research Diagnostic Division, Animal and Plant Quarantine Agency, Gimcheon, Korea.,College of Veterinary Medicine, Animal Disease Intervention Center, Kyungpook National University, Daegu, Korea
| | - Yu-Na Lee
- Avian Influenza Research Diagnostic Division, Animal and Plant Quarantine Agency, Gimcheon, Korea
| | - Dong-Hun Lee
- Department of Pathobiology and Veterinary Science, University of Connecticut, Storrs, CT, USA
| | - Yoon-Gi Baek
- Avian Influenza Research Diagnostic Division, Animal and Plant Quarantine Agency, Gimcheon, Korea
| | - Young-Jae Si
- Avian Influenza Research Diagnostic Division, Animal and Plant Quarantine Agency, Gimcheon, Korea
| | | | | | | | - Soo-Jeong Kye
- Avian Influenza Research Diagnostic Division, Animal and Plant Quarantine Agency, Gimcheon, Korea
| | - Myoung-Heon Lee
- Avian Influenza Research Diagnostic Division, Animal and Plant Quarantine Agency, Gimcheon, Korea
| | - Choi-Kyu Park
- College of Veterinary Medicine, Animal Disease Intervention Center, Kyungpook National University, Daegu, Korea
| | - Youn-Jeong Lee
- Avian Influenza Research Diagnostic Division, Animal and Plant Quarantine Agency, Gimcheon, Korea
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5
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Chicken anemia virus in northern Vietnam: molecular characterization reveals multiple genotypes and evidence of recombination. Virus Genes 2019; 55:643-653. [PMID: 31290064 DOI: 10.1007/s11262-019-01686-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2019] [Accepted: 07/02/2019] [Indexed: 10/26/2022]
Abstract
Chicken anemia virus (CAV) has a ubiquitous and worldwide distribution in the chicken production industry. Our group previously reported a high seroprevalence of CAV in chickens from northern Vietnam. In the present study, tissue samples collected from a total of 330 broiler and breeder commercial chickens in eleven provinces of northern Vietnam were tested for CAV infection. All samples were collected from clinically suspected flocks and diseased birds. The CAV genome was detected in 157 out of 330 (47.58%) chicken samples by real-time PCR. The rate of CAV genome detection in young chickens at 2-3 weeks of age (61.43%), which had not been previously reported in Vietnam, was significantly higher than that in older chickens at 4-11 (44.83%) and 12-28 (35.71%) weeks of age. For nine representative CAV strains from broiler chickens, analysis of the entire protein-coding region of the viral genome was conducted. Phylogenetic analysis of the VP1 gene indicated that the CAVs circulating in northern Vietnam were divided into three distinct genotypes: II, III, and V. Only one of the nine Vietnamese CAV strains clustered with a vaccine strain (Del-Ros), whereas the other eight strains did not cluster with any vaccine strains. Among the three genotypes, genotype III was most widely found in northern Vietnam and this included three sub-genotypes (IIIa, IIIb, and IIIc). The Vietnamese CAV strains were closely related to the Chinese, Taiwanese, and USA strains. One strain was defined to be of genotype V, which is a newly reported CAV genotype. Moreover, recombination analysis suggests that this novel genotype V was generated by recombination between genotype II and sub-genotype IIIc.
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Suttie A, Karlsson EA, Deng YM, Hurt AC, Greenhill AR, Barr IG, Dussart P, Horwood PF. Avian influenza in the Greater Mekong Subregion, 2003-2018. INFECTION GENETICS AND EVOLUTION 2019; 74:103920. [PMID: 31201870 DOI: 10.1016/j.meegid.2019.103920] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/14/2019] [Revised: 05/20/2019] [Accepted: 06/11/2019] [Indexed: 12/15/2022]
Abstract
The persistent circulation of avian influenza viruses (AIVs) is an ongoing problem for many countries in South East Asia, causing large economic losses to both the agricultural and health sectors. This review analyses AIV diversity, evolution and the risk of AIV emergence in humans in countries of the Greater Mekong Subregion (GMS): Cambodia, Laos, Myanmar, Thailand and Vietnam (excluding China). The analysis was based on AIV sequencing data, serological studies, published journal articles and AIV outbreak reports available from January 2003 to December 2018. All countries of the GMS have suffered losses due repeated outbreaks of highly pathogenic (HP) H5N1 that has also caused human cases in all GMS countries. In Laos, Myanmar and Vietnam AIV outbreaks in domestic poultry have also been caused by clade 2.3.4.4 H5N6. A diverse range of low pathogenic AIVs (H1-H12) have been detected in poultry and wild bird species, though surveillance for and characterization of these subtypes is limited. Subtype H3, H4, H6 and H11 viruses have been detected over prolonged periods; whilst H1, H2, H7, H8, H10 and H12 viruses have only been detected transiently. H9 AIVs circulate endemically in Cambodia and Vietnam with seroprevalence data indicating human exposure to H9 AIVs in Cambodia, Thailand and Vietnam. As surveillance studies focus heavily on the detection of H5 AIVs in domestic poultry further research is needed to understand the true level of AIV diversity and the risk AIVs pose to humans in the GMS.
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Affiliation(s)
- Annika Suttie
- Virology Unit, Institute Pasteur in Cambodia, Phnom Penh, Cambodia; School of Applied and Biomedical Sciences, Federation University, Churchill, Australia; WHO Collaborating Centre for Reference and Research on Influenza, Victorian Infectious Diseases Reference Laboratory, Peter Doherty Institute for Infection and Immunity, Melbourne, VIC 3000, Australia
| | - Erik A Karlsson
- Virology Unit, Institute Pasteur in Cambodia, Phnom Penh, Cambodia
| | - Yi-Mo Deng
- WHO Collaborating Centre for Reference and Research on Influenza, Victorian Infectious Diseases Reference Laboratory, Peter Doherty Institute for Infection and Immunity, Melbourne, VIC 3000, Australia
| | - Aeron C Hurt
- WHO Collaborating Centre for Reference and Research on Influenza, Victorian Infectious Diseases Reference Laboratory, Peter Doherty Institute for Infection and Immunity, Melbourne, VIC 3000, Australia
| | - Andrew R Greenhill
- School of Applied and Biomedical Sciences, Federation University, Churchill, Australia
| | - Ian G Barr
- WHO Collaborating Centre for Reference and Research on Influenza, Victorian Infectious Diseases Reference Laboratory, Peter Doherty Institute for Infection and Immunity, Melbourne, VIC 3000, Australia
| | - Philippe Dussart
- Virology Unit, Institute Pasteur in Cambodia, Phnom Penh, Cambodia
| | - Paul F Horwood
- College of Public Health, Medical and Veterinary Sciences, James Cook University, Townsville, QLD 4811, Australia.
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7
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The PB2 Polymerase Host Adaptation Substitutions Prime Avian Indonesia Sub Clade 2.1 H5N1 Viruses for Infecting Humans. Viruses 2019; 11:v11030292. [PMID: 30909490 PMCID: PMC6480796 DOI: 10.3390/v11030292] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2019] [Revised: 03/21/2019] [Accepted: 03/22/2019] [Indexed: 12/27/2022] Open
Abstract
Significantly higher numbers of human infections with H5N1 virus have occurred in Indonesia and Egypt, compared with other affected areas, and it is speculated that there are specific viral factors for human infection with avian H5N1 viruses in these locations. We previously showed PB2-K526R is present in 80% of Indonesian H5N1 human isolates, which lack the more common PB2-E627K substitution. Testing the hypothesis that this mutation may prime avian H5N1 virus for human infection, we showed that: (1) K526R is rarely found in avian influenza viruses but was identified in H5N1 viruses 2–3 years after the virus emerged in Indonesia, coincident with the emergence of H5N1 human infections in Indonesia; (2) K526R is required for efficient replication of Indonesia H5N1 virus in mammalian cells in vitro and in vivo and reverse substitution to 526K in human isolates abolishes this ability; (3) Indonesian H5N1 virus, which contains K526R-PB2, is stable and does not further acquire E627K following replication in infected mice; and (4) virus containing K526R-PB2 shows no fitness deficit in avian species. These findings illustrate an important mechanism in which a host adaptive mutation that predisposes avian H5N1 virus towards infecting humans has arisen with the virus becoming prevalent in avian species prior to human infections occurring. A similar mechanism is observed in the Qinghai-lineage H5N1 viruses that have caused many human cases in Egypt; here, E627K predisposes towards human infections. Surveillance should focus on the detection of adaptation markers in avian strains that prime for human infection.
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Durr PA, Indriani R, Selleck P, Adjid ARM, Syafriati T, Ignjatovic J. Developing Farm-Level Post-vaccination Sero-Monitoring Systems for H5N1 Highly Pathogenic Avian Influenza in an Endemically Infected Country. Front Vet Sci 2019; 5:324. [PMID: 30671438 PMCID: PMC6331391 DOI: 10.3389/fvets.2018.00324] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2018] [Accepted: 12/03/2018] [Indexed: 11/13/2022] Open
Abstract
Whilst the serological responses of poultry following vaccination against highly pathogenic avian influenza H5N1 has been extensively investigated under laboratory conditions, there have been fewer studies conducted in the field. This applies particularly to the endemically infected countries routinely practicing vaccination, where the combination of multiple circulating clades and/or the use of vaccines with different seed strains makes the design and interpretation of field studies especially problematic. To address this for the particular situation of layer hens in the small to medium commercial sector in Indonesia, we developed a sampling regime before and after the vaccination given to point-of-lay pullets, and assessed serological response with a panel of test antigens. This confirmed that high titres were induced in those birds vaccinated with locally produced homologous H5N1 vaccines administered two or more times, but in flocks using imported heterologous H5N2 vaccines median titres were significantly lower, and unlikely to provide protection throughout the production cycle, without additional vaccination. Comparing the HI responses against the panel of antigens enabled the detection of the flock's exposure to different vaccine antigens, and made possible the detection of mislabelled vaccine seed strains. Furthermore, we show that test antigens need not be exactly matched to assess sero-protection in well vaccinated birds. Finally our study suggests that the POL vaccination serves as a useful reference point for following cohorts of layers throughout their production cycle, and thus enabling robust vaccination field effectiveness studies.
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Affiliation(s)
- Peter A. Durr
- CSIRO-Australian Animal Health Laboratory, Geelong, VIC, Australia
| | - Risa Indriani
- Indonesian Research Centre for Veterinary Sciences, Bogor, Indonesia
| | - Paul Selleck
- CSIRO-Australian Animal Health Laboratory, Geelong, VIC, Australia
| | - Abdul R. M. Adjid
- Indonesian Research Centre for Veterinary Sciences, Bogor, Indonesia
| | - Tatty Syafriati
- Indonesian Research Centre for Veterinary Sciences, Bogor, Indonesia
| | - Jagoda Ignjatovic
- Faculty of Veterinary Science, University of Melbourne, Melbourne, VIC, Australia
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9
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Mellor KC, Meyer A, Elkholly DA, Fournié G, Long PT, Inui K, Padungtod P, Gilbert M, Newman SH, Vergne T, Pfeiffer DU, Stevens KB. Comparative Epidemiology of Highly Pathogenic Avian Influenza Virus H5N1 and H5N6 in Vietnamese Live Bird Markets: Spatiotemporal Patterns of Distribution and Risk Factors. Front Vet Sci 2018; 5:51. [PMID: 29675418 PMCID: PMC5896172 DOI: 10.3389/fvets.2018.00051] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2017] [Accepted: 02/27/2018] [Indexed: 01/08/2023] Open
Abstract
Highly pathogenic avian influenza (HPAI) H5N1 virus has been circulating in Vietnam since 2003, whilst outbreaks of HPAI H5N6 virus are more recent, having only been reported since 2014. Although the spatial distribution of H5N1 outbreaks and risk factors for virus occurrence has been extensively studied, there have been no comparative studies for H5N6. Data collected through active surveillance of Vietnamese live bird markets (LBMs) between 2011 and 2015 were used to explore and compare the spatiotemporal distributions of H5N1- and H5N6-positive LBMs. Conditional autoregressive models were developed to quantify spatiotemporal associations between agroecological factors and the two HPAI strains using the same set of predictor variables. Unlike H5N1, which exhibited a strong north–south divide, with repeated occurrence in the extreme south of a cluster of high-risk provinces, H5N6 was homogeneously distributed throughout Vietnam. Similarly, different agroecological factors were associated with each strain. Sample collection in the months of January and February and higher average maximum temperature were associated with higher likelihood of H5N1-positive market-day status. The likelihood of market days being positive for H5N6 increased with decreased river density, and with successive Rounds of data collection. This study highlights marked differences in spatial patterns and risk factors for H5N1 and H5N6 in Vietnam, suggesting the need for tailored surveillance and control approaches.
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Affiliation(s)
- Kate C Mellor
- Veterinary Epidemiology, Economics and Public Health Group, Department of Pathobiology and Population Sciences, Royal Veterinary College, Hatfield, United Kingdom
| | - Anne Meyer
- Veterinary Epidemiology, Economics and Public Health Group, Department of Pathobiology and Population Sciences, Royal Veterinary College, Hatfield, United Kingdom
| | - Doaa A Elkholly
- Veterinary Epidemiology, Economics and Public Health Group, Department of Pathobiology and Population Sciences, Royal Veterinary College, Hatfield, United Kingdom
| | - Guillaume Fournié
- Veterinary Epidemiology, Economics and Public Health Group, Department of Pathobiology and Population Sciences, Royal Veterinary College, Hatfield, United Kingdom
| | - Pham T Long
- Department of Animal Health, Ministry of Agriculture and Rural Development, Hanoi, Vietnam
| | - Ken Inui
- Country Office for Vietnam, Food and Agriculture Organization of the United Nations, Hanoi, Vietnam
| | - Pawin Padungtod
- Country Office for Vietnam, Food and Agriculture Organization of the United Nations, Hanoi, Vietnam
| | - Marius Gilbert
- Spatial Epidemiology Laboratory, Université Libre de Bruxelles, Brussels, Belgium
| | - Scott H Newman
- Country Office for Vietnam, Food and Agriculture Organization of the United Nations, Hanoi, Vietnam.,Country Office for Ethiopia, Food and Agriculture Organization of the United Nations, Addis Ababa, Ethiopia
| | - Timothée Vergne
- Veterinary Epidemiology, Economics and Public Health Group, Department of Pathobiology and Population Sciences, Royal Veterinary College, Hatfield, United Kingdom.,Maladies Infectieuses et Vecteurs Ecologie, Génétique, Evolution et Contrôle (MIVEGEC), Institut de Recherche pour le Développement (IRD), Montpellier, France.,UMR 1225 INRA, ENVT Interactions Hôtes - Agents Pathogènes (IHAP), University of Toulouse, Toulouse, France
| | - Dirk U Pfeiffer
- Veterinary Epidemiology, Economics and Public Health Group, Department of Pathobiology and Population Sciences, Royal Veterinary College, Hatfield, United Kingdom.,College of Veterinary Medicine & Life Sciences, City University of Hong Kong, Kowloon, Hong Kong
| | - Kim B Stevens
- Veterinary Epidemiology, Economics and Public Health Group, Department of Pathobiology and Population Sciences, Royal Veterinary College, Hatfield, United Kingdom
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10
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Tarigan S, Wibowo MH, Indriani R, Sumarningsih S, Artanto S, Idris S, Durr PA, Asmara W, Ebrahimie E, Stevenson MA, Ignjatovic J. Field effectiveness of highly pathogenic avian influenza H5N1 vaccination in commercial layers in Indonesia. PLoS One 2018; 13:e0190947. [PMID: 29320563 PMCID: PMC5761929 DOI: 10.1371/journal.pone.0190947] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2017] [Accepted: 12/24/2017] [Indexed: 12/30/2022] Open
Abstract
Although vaccination of poultry for control of highly pathogenic avian influenza virus (HPAIV) H5N1 has been practiced during the last decade in several countries, its effectiveness under field conditions remains largely unquantified. Effective HPAI vaccination is however essential in preventing incursions, silent infections and generation of new H5N1 antigenic variants. The objective of this study was to asses the level and duration of vaccine induced immunity in commercial layers in Indonesia. Titres of H5N1 haemagglutination inhibition (HI) antibodies were followed in individual birds from sixteen flocks, age 18-68 week old (wo). The study revealed that H5N1 vaccination had highly variable outcome, including vaccination failures, and was largely ineffective in providing long lasting protective immunity. Flocks were vaccinated with seven different vaccines, administer at various times that could be grouped into three regimes: In regime A, flocks (n = 8) were vaccinated two or three times before 19 wo; in regime B (n = 2), two times before and once after 19 wo; and in regime C (n = 6) three to four times before and two to three times after 19 wo. HI titres in regime C birds were significantly higher during the entire observation period in comparison to titres of regime A or B birds, which also differed significantly from each other. The HI titres of individual birds in each flock differed significantly from birds in other flocks, indicating that the effectiveness of field vaccination was highly variable and farm related. Protective HI titres of >4log2, were present in the majority of flocks at 18 wo, declined thereafter at variable rate and only two regime C flocks had protective HI titres at 68 wo. Laboratory challenge with HPAIV H5N1 of birds from regime A and C flocks confirmed that protective immunity differed significantly between flocks vaccinated by these two regimes. The study revealed that effectiveness of the currently applied H5N1 vaccination could be improved and measures to achieve this are discussed.
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Affiliation(s)
- Simson Tarigan
- Indonesian Research Centre for Veterinary Science, Bogor, Indonesia
| | | | - Risa Indriani
- Indonesian Research Centre for Veterinary Science, Bogor, Indonesia
| | | | - Sidna Artanto
- Faculty of Veterinary Science, Universitas Gadjah Mada, Yogyakarta, Indonesia
| | - Syafrison Idris
- Directorate General of Livestock and Animal Health Services, Jakarta, Indonesia
| | - Peter A. Durr
- CSIRO Australian Animal Health Laboratory, Geelong, Victoria, Australia
| | - Widya Asmara
- Faculty of Veterinary Science, Universitas Gadjah Mada, Yogyakarta, Indonesia
| | - Esmaeil Ebrahimie
- School of Information Technology and Mathematical Sciences, Division of Information Technology, Engineering and the Environment, University of South Australia, Adelaide, South Australia, Australia
| | - Mark A. Stevenson
- School of Veterinary and Agricultural Sciences, University of Melbourne, Melbourne, Victoria, Australia
| | - Jagoda Ignjatovic
- School of Veterinary and Agricultural Sciences, University of Melbourne, Melbourne, Victoria, Australia
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11
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Abstract
Waterbirds are the main reservoir for low pathogenic avian influenza A viruses (LPAIV), from which occasional spillover to poultry occurs. When circulating among poultry, LPAIV may become highly pathogenic avian influenza A viruses (HPAIV). In recent years, the epidemiology of HPAIV viruses has changed drastically. HPAIV H5N1 are currently endemic among poultry in a number of countries. In addition, global spread of HPAIV H5Nx viruses has resulted in major outbreaks among wild birds and poultry worldwide. Using data collected during these outbreaks, the role of migratory birds as a vector became increasingly clear. Here we provide an overview of current data about various aspects of the changing role of wild birds in the epidemiology of avian influenza A viruses.
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12
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Waziri MI, Abdu PA, Sa'idu L, Bello M. Seroepidemiology and assessment of risk factors for the spread of avian influenza in birds in two Nigerian states. Vet Med Sci 2017; 3:227-238. [PMID: 29152316 PMCID: PMC5677776 DOI: 10.1002/vms3.73] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022] Open
Abstract
Despite modified stamping out eradication policy adopted in Nigeria, there was resurgence in 2015 of highly pathogenic avian influenza (HPAI) H5N1 with greater infectivity. A survey of the risk of spread of HPAI in two HPAI‐infected and ‐uninfected Nigerian states were studied. A cross‐sectional study to detect avian influenza (AI) H5 antibodies was conducted using haemagglutination inhibition (HI) test and enzyme‐linked immunosorbent assay (ELISA). A total of 950 birds’ sera were tested for AI H5 antibodies. Questionnaires were also administered to evaluate risks of AI spread in two states of Nigeria in 2013. AI H5 seroprevalence of 3% and 5% were obtained in Bauchi and Gombe states, respectively. Free flying and captive wild birds had 15% and 11% seroprevalence, respectively. Ninety‐two per cent AI awareness and 90% preparedness to report outbreaks of poultry diseases were recorded. Veterinary personnel, radio and television contributed 87% to HPAI awareness. Of the 10 risk categories evaluated, Gombe state had 3 moderate and 1 high risk of AI virus spread. Bauchi state recorded 5 moderate and 1 high risk of AI virus spread. Chi‐square analysis showed associations of altitude, temperature, rainfall and presence of live bird markets (LBMs) (P < 0.05) to AI seroprevalence. Odds ratio at 95% CI (1.313–6.333) indicated LBMs presence to be three times more likely to influence AI occurrence. HPAI H5N1 resurged in many states and occurred for the first time in Gombe state in 2015. Veterinary personnel, radio and television may be reliable in changing farmers’ attitudes to adopt good biosecurity practices.
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Affiliation(s)
| | - Paul A Abdu
- Department of Veterinary MedicineAhmadu Bello University ZariaZariaNigeria
| | - Lawal Sa'idu
- Veterinary Teaching HospitalDepartment of Veterinary Public Health and Preventive MedicineAhmadu Bello University ZariaZariaNigeria
| | - Mohammed Bello
- Department of Public Health and Preventive MedicineAhmadu Bello UniversityZariaNigeria
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13
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Peng Y, Li X, Zhou H, Wu A, Dong L, Zhang Y, Gao R, Bo H, Yang L, Wang D, Lin X, Jin M, Shu Y, Jiang T. Continual Antigenic Diversification in China Leads to Global Antigenic Complexity of Avian Influenza H5N1 Viruses. Sci Rep 2017; 7:43566. [PMID: 28262734 PMCID: PMC5337931 DOI: 10.1038/srep43566] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2016] [Accepted: 01/25/2017] [Indexed: 12/31/2022] Open
Abstract
The highly pathogenic avian influenza (HPAI) H5N1 virus poses a significant potential threat to human society due to its wide spread and rapid evolution. In this study, we present a comprehensive antigenic map for HPAI H5N1 viruses including 218 newly sequenced isolates from diverse regions of mainland China, by computationally separating almost all HPAI H5N1 viruses into 15 major antigenic clusters (ACs) based on their hemagglutinin sequences. Phylogenetic analysis showed that 12 of these 15 ACs originated in China in a divergent pattern. Further analysis of the dissemination of HPAI H5N1 virus in China identified that the virus's geographic expansion was co-incident with a significant divergence in antigenicity. Moreover, this antigenic diversification leads to global antigenic complexity, as typified by the recent HPAI H5N1 spread, showing extensive co-circulation and local persistence. This analysis has highlighted the challenge in H5N1 prevention and control that requires different planning strategies even inside China.
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Affiliation(s)
- Yousong Peng
- College of Biology, Human University, Changsha, 410082, China
- Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China
| | - Xiaodan Li
- National Institute for Viral Disease Control and Prevention, China CDC, Beijing, 100052, China
| | - Hongbo Zhou
- College of Animal Science & Medicine, Huazhong Agricultural University, Wuhan, 430070, China
| | - Aiping Wu
- Center of System Medicine, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100005, China
- Suzhou Institute of Systems Medicine, Suzhou, Jiangsu, 215123, China
| | - Libo Dong
- National Institute for Viral Disease Control and Prevention, China CDC, Beijing, 100052, China
| | - Ye Zhang
- National Institute for Viral Disease Control and Prevention, China CDC, Beijing, 100052, China
| | - Rongbao Gao
- National Institute for Viral Disease Control and Prevention, China CDC, Beijing, 100052, China
| | - Hong Bo
- National Institute for Viral Disease Control and Prevention, China CDC, Beijing, 100052, China
| | - Lei Yang
- National Institute for Viral Disease Control and Prevention, China CDC, Beijing, 100052, China
| | - Dayan Wang
- National Institute for Viral Disease Control and Prevention, China CDC, Beijing, 100052, China
| | - Xian Lin
- College of Animal Science & Medicine, Huazhong Agricultural University, Wuhan, 430070, China
| | - Meilin Jin
- College of Animal Science & Medicine, Huazhong Agricultural University, Wuhan, 430070, China
| | - Yuelong Shu
- National Institute for Viral Disease Control and Prevention, China CDC, Beijing, 100052, China
| | - Taijiao Jiang
- Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China
- Center of System Medicine, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100005, China
- Suzhou Institute of Systems Medicine, Suzhou, Jiangsu, 215123, China
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14
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Moriguchi S, Onuma M, Goka K. Spatial assessment of the potential risk of avian influenza A virus infection in three raptor species in Japan. J Vet Med Sci 2016; 78:1107-15. [PMID: 26972333 PMCID: PMC4976265 DOI: 10.1292/jvms.15-0551] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
Avian influenza A, a highly pathogenic avian influenza, is a lethal infection in certain
species of wild birds, including some endangered species. Raptors are susceptible to avian
influenza, and spatial risk assessment of such species may be valuable for conservation
planning. We used the maximum entropy approach to generate potential distribution models
of three raptor species from presence-only data for the mountain hawk-eagle
Nisaetus nipalensis, northern goshawk Accipiter
gentilis and peregrine falcon Falco peregrinus, surveyed
during the winter from 1996 to 2001. These potential distribution maps for raptors were
superimposed on avian influenza A risk maps of Japan, created from data on incidence of
the virus in wild birds throughout Japan from October 2010 to March 2011. The avian
influenza A risk map for the mountain hawk-eagle showed that most regions of Japan had a
low risk for avian influenza A. In contrast, the maps for the northern goshawk and
peregrine falcon showed that their high-risk areas were distributed on the plains along
the Sea of Japan and Pacific coast. We recommend enhanced surveillance for each raptor
species in high-risk areas and immediate establishment of inspection systems. At the same
time, ecological risk assessments that determine factors, such as the composition of prey
species, and differential sensitivity of avian influenza A virus between bird species
should provide multifaceted insights into the total risk assessment of endangered
species.
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Affiliation(s)
- Sachiko Moriguchi
- Invasive Alien Species Research Team, National Institute for Environmental Studies, 16-2 Onogawa, Tsukuba, Ibaraki 305-8506, Japan
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15
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Artois J, Newman SH, Dhingra MS, Chaiban C, Linard C, Cattoli G, Monne I, Fusaro A, Xenarios I, Engler R, Liechti R, Kuznetsov D, Pham TL, Nguyen T, Pham VD, Castellan D, Von Dobschuetz S, Claes F, Dauphin G, Inui K, Gilbert M. Clade-level Spatial Modelling of HPAI H5N1 Dynamics in the Mekong Region Reveals New Patterns and Associations with Agro-Ecological Factors. Sci Rep 2016; 6:30316. [PMID: 27453195 PMCID: PMC4958987 DOI: 10.1038/srep30316] [Citation(s) in RCA: 6] [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: 02/15/2016] [Accepted: 07/04/2016] [Indexed: 11/16/2022] Open
Abstract
The highly pathogenic avian influenza (HPAI) H5N1 virus has been circulating in Asia since 2003 and diversified into several genetic lineages, or clades. Although the spatial distribution of its outbreaks was extensively studied, differences in clades were never previously taken into account. We developed models to quantify associations over time and space between different HPAI H5N1 viruses from clade 1, 2.3.4 and 2.3.2 and agro-ecological factors. We found that the distribution of clades in the Mekong region from 2004 to 2013 was strongly regionalised, defining specific epidemiological zones, or epizones. Clade 1 became entrenched in the Mekong Delta and was not supplanted by newer clades, in association with a relatively higher presence of domestic ducks. In contrast, two new clades were introduced (2.3.4 and 2.3.2) in northern Viet Nam and were associated with higher chicken density and more intensive chicken production systems. We suggest that differences in poultry production systems in these different epizones may explain these associations, along with differences in introduction pressure from neighbouring countries. The different distribution patterns found at the clade level would not be otherwise apparent through analysis treating all outbreaks equally, which requires improved linking of disease outbreak records and genetic sequence data.
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Affiliation(s)
- Jean Artois
- Biological Control and Spatial Ecology, Université Libre de Bruxelles, Brussels, Belgium
| | - Scott H. Newman
- Emergency Center for Transboundary Animal Diseases (ECTAD), Food and Agriculture Organization of the United Nations, Hanoi, Viet Nam
| | - Madhur S. Dhingra
- Biological Control and Spatial Ecology, Université Libre de Bruxelles, Brussels, Belgium
- Department of Animal Husbandry & Dairying, Government of Haryana, India
| | - Celia Chaiban
- Biological Control and Spatial Ecology, Université Libre de Bruxelles, Brussels, Belgium
- Earth and Life Institute (ELI), Université catholique de Louvain (UCL), Louvain-la-Neuve, Belgium
| | - Catherine Linard
- Biological Control and Spatial Ecology, Université Libre de Bruxelles, Brussels, Belgium
- Department of Geography, Université de Namur, Namur, Belgium
| | - Giovanni Cattoli
- Joint FAO/IAEA Division of Nuclear Techniques in Food and Agriculture Department of Nuclear Sciences and Applications, International Atomic Energy Agency, Seibersdorf, Austria
| | - Isabella Monne
- Istituto Zooprofilattico Sperimentale delle Venezie, Legnaro (Padua), Italy
| | - Alice Fusaro
- Istituto Zooprofilattico Sperimentale delle Venezie, Legnaro (Padua), Italy
| | - Ioannis Xenarios
- Swiss-Prot & Vital-IT group, Swiss Institute of Bioinformatics (SIB), Lausanne, Switzerland
- Center for Integrative Genomics (CIG), University of Lausanne, Lausanne, Switzerland
| | - Robin Engler
- Swiss-Prot & Vital-IT group, Swiss Institute of Bioinformatics (SIB), Lausanne, Switzerland
| | - Robin Liechti
- Swiss-Prot & Vital-IT group, Swiss Institute of Bioinformatics (SIB), Lausanne, Switzerland
| | - Dmitri Kuznetsov
- Swiss-Prot & Vital-IT group, Swiss Institute of Bioinformatics (SIB), Lausanne, Switzerland
| | - Thanh Long Pham
- Department of Animal Health, Epidemiology Division, Ministry of Agriculture and Rural Development, Hanoi, Viet Nam
| | - Tung Nguyen
- Department of Animal Health, Epidemiology Division, Ministry of Agriculture and Rural Development, Hanoi, Viet Nam
| | - Van Dong Pham
- Department of Animal Health, Epidemiology Division, Ministry of Agriculture and Rural Development, Hanoi, Viet Nam
| | - David Castellan
- Emergency Center for Transboundary Animal Diseases (ECTAD), FAO Regional Office for Asia and the Pacific (FAO-RAP), Bangkok, Thailand
| | - Sophie Von Dobschuetz
- Animal Production and Health Division (AGAH), Food and Agriculture Organization of the United Nations (FAO), Rome, Italy
| | - Filip Claes
- Animal Production and Health Division (AGAH), Food and Agriculture Organization of the United Nations (FAO), Rome, Italy
| | - Gwenaëlle Dauphin
- Animal Production and Health Division (AGAH), Food and Agriculture Organization of the United Nations (FAO), Rome, Italy
| | - Ken Inui
- Emergency Center for Transboundary Animal Diseases (ECTAD), Food and Agriculture Organization of the United Nations, Hanoi, Viet Nam
| | - Marius Gilbert
- Biological Control and Spatial Ecology, Université Libre de Bruxelles, Brussels, Belgium
- Fonds National de la Recherche Scientifique, Brussels, Belgium
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16
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Lai S, Qin Y, Cowling BJ, Ren X, Wardrop NA, Gilbert M, Tsang TK, Wu P, Feng L, Jiang H, Peng Z, Zheng J, Liao Q, Li S, Horby PW, Farrar JJ, Gao GF, Tatem AJ, Yu H. Global epidemiology of avian influenza A H5N1 virus infection in humans, 1997-2015: a systematic review of individual case data. THE LANCET. INFECTIOUS DISEASES 2016; 16:e108-e118. [PMID: 27211899 PMCID: PMC4933299 DOI: 10.1016/s1473-3099(16)00153-5] [Citation(s) in RCA: 171] [Impact Index Per Article: 21.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/11/2015] [Revised: 01/30/2016] [Accepted: 03/08/2016] [Indexed: 12/13/2022]
Abstract
Avian influenza viruses A(H5N1) have caused a large number of typically severe human infections since the first human case was reported in 1997. However, there is a lack of comprehensive epidemiological analysis of global human cases of H5N1 from 1997-2015. Moreover, few studies have examined in detail the changing epidemiology of human H5N1 cases in Egypt, especially given the most recent outbreaks since November 2014 which have the highest number of cases ever reported globally over a similar period. Data on individual cases were collated from different sources using a systematic approach to describe the global epidemiology of 907 human H5N1 cases between May 1997 and April 2015. The number of affected countries rose between 2003 and 2008, with expansion from East and Southeast Asia, then to West Asia and Africa. Most cases (67.2%) occurred from December to March, and the overall case fatality risk was 53.5% (483/903) which varied across geographical regions. Although the incidence in Egypt has increased dramatically since November 2014, compared to the cases beforehand there were no significant differences in the fatality risk , history of exposure to poultry, history of human case contact, and time from onset to hospitalization in the recent cases.
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Affiliation(s)
- Shengjie Lai
- Division of Infectious Disease, Key Laboratory of Surveillance and Early-warning on Infectious Disease, Chinese Center for Disease Control and Prevention, Beijing, China; Department of Geography and Environment, University of Southampton, Southampton, UK; Flowminder Foundation, Stockholm, Sweden
| | - Ying Qin
- Division of Infectious Disease, Key Laboratory of Surveillance and Early-warning on Infectious Disease, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Benjamin J Cowling
- WHO Collaborating Centre for Infectious Disease Epidemiology and Control, School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong Special Administrative Region, China
| | - Xiang Ren
- Division of Infectious Disease, Key Laboratory of Surveillance and Early-warning on Infectious Disease, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Nicola A Wardrop
- Department of Geography and Environment, University of Southampton, Southampton, UK
| | - Marius Gilbert
- Biological Control and Spatial Ecology, Université Libre de Bruxelles, Brussels, Belgium; Fonds National de la Recherche Scientifique, Brussels, Belgium
| | - Tim K Tsang
- WHO Collaborating Centre for Infectious Disease Epidemiology and Control, School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong Special Administrative Region, China
| | - Peng Wu
- WHO Collaborating Centre for Infectious Disease Epidemiology and Control, School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong Special Administrative Region, China
| | - Luzhao Feng
- Division of Infectious Disease, Key Laboratory of Surveillance and Early-warning on Infectious Disease, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Hui Jiang
- Division of Infectious Disease, Key Laboratory of Surveillance and Early-warning on Infectious Disease, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Zhibin Peng
- Division of Infectious Disease, Key Laboratory of Surveillance and Early-warning on Infectious Disease, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Jiandong Zheng
- Division of Infectious Disease, Key Laboratory of Surveillance and Early-warning on Infectious Disease, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Qiaohong Liao
- Division of Infectious Disease, Key Laboratory of Surveillance and Early-warning on Infectious Disease, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Sa Li
- Division of Infectious Disease, Key Laboratory of Surveillance and Early-warning on Infectious Disease, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Peter W Horby
- Oxford University Clinical Research Unit, Wellcome Trust Major Overseas Programme, Ho Chi Minh City, Vietnam; Centre for Tropical Medicine, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, UK; Singapore Infectious Disease Initiative, Singapore
| | - Jeremy J Farrar
- Oxford University Clinical Research Unit, Wellcome Trust Major Overseas Programme, Ho Chi Minh City, Vietnam; Centre for Tropical Medicine, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, UK; Singapore Infectious Disease Initiative, Singapore; International Severe Acute Respiratory and Emerging Infection Consortium, Centre for Tropical Medicine, University of Oxford, Churchill Hospital, Oxford, UK
| | - George F Gao
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China; Chinese Center for Disease Control and Prevention, Beijing, China
| | - Andrew J Tatem
- Department of Geography and Environment, University of Southampton, Southampton, UK; Flowminder Foundation, Stockholm, Sweden; Fogarty International Center, National Institutes of Health, Bethesda, MD, USA
| | - Hongjie Yu
- Division of Infectious Disease, Key Laboratory of Surveillance and Early-warning on Infectious Disease, Chinese Center for Disease Control and Prevention, Beijing, China; School of Public Health, Fudan University, Key Laboratory of Public Health Safety, Ministry of Education, Shanghai, China.
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17
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Li X, Zhang Z, Yu A, Ho SYW, Carr MJ, Zheng W, Zhang Y, Zhu C, Lei F, Shi W. Global and local persistence of influenza A(H5N1) virus. Emerg Infect Dis 2016; 20:1287-95. [PMID: 25061965 PMCID: PMC4111173 DOI: 10.3201/eid2008.130910] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
An understanding of the global migration dynamics of highly pathogenic avian influenza A(H5N1) virus is helpful for surveillance and disease prevention. To characterize the migration network of this virus, we used genetic analysis, which supported a global persistence model in which each of 9 regions acts to some extent as a source. Siberia is the major hub for the dispersal of the virus. Southeast Asia and Africa are major sources of genetically and antigenically novel strains. We found evidence of local persistence of the virus in Southeast Asia and Africa, which is rare for human influenza A viruses. The differences in migration dynamics between avian and human influenza viruses might help with the design of region-specific surveillance efforts and the selection of vaccine candidates.
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Affiliation(s)
| | | | | | | | | | | | | | - Chaodong Zhu
- These authors contributed equally to this article
| | - Fumin Lei
- These authors contributed equally to this article
| | - Weifeng Shi
- These authors contributed equally to this article
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18
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Nguyen TH, Than VT, Thanh HD, Hung VK, Nguyen DT, Kim W. Intersubtype Reassortments of H5N1 Highly Pathogenic Avian Influenza Viruses Isolated from Quail. PLoS One 2016; 11:e0149608. [PMID: 26900963 PMCID: PMC4765837 DOI: 10.1371/journal.pone.0149608] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2015] [Accepted: 02/03/2016] [Indexed: 11/18/2022] Open
Abstract
H5N1 highly pathogenic avian influenza (HPAI) viruses are considered a threat to national animal industries, causing production losses and high mortality in domestic poultry. In recent years, quail has become a popular terrestrial poultry species raised for production of meat and eggs in Asia. In this study, to better understand the roles of quail in H5N1 viral evolution, two H5N1-positive samples, designated A/quail/Vietnam/CVVI-49/2010 (CVVI-49/2010) and A/quail/Vietnam/CVVI-50/2014 (CVVI-50/2014), were isolated from quail during H5N1 outbreaks in Vietnam, and their whole genome were analyzed. The phylogenetic analysis reveals new evolutionary variation in the worldwide H5N1 viruses. The quail HA genes were clustered into clades 1.1.1 (CVVI-49/2010) and clade 2.3.2.1c (CVVI-50/2014), which may have evolved from viruses circulating from chickens and/or ducks in Cambodia, mainland of China, Taiwan, Indonesia, and South Korea in recent years. Interestingly, the M2 gene of the CVVI-49/2010 strain contained amino acid substitutions at position 26L-I and 31S-N that are related to amantadine-resistance. In particular, the CVVI-50/2014 strain revealed evidence of multiple intersubtype reassortment events between virus clades 2.3.2.1c, 2.3.2.1b, and 2.3.2.1a. Data from this study supports the possible role of quail as an important intermediate host in avian influenza virus evolution. Therefore, additional surveillance is needed to monitor these HPAI viruses both serologically and virologically in quail.
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Affiliation(s)
- Tinh Huu Nguyen
- Department of Microbiology, Chung-Ang University College of Medicine, Seoul, South Korea
- Central Vietnam Veterinary Institute, Nha Trang, Vietnam
| | - Van Thai Than
- Department of Microbiology, Chung-Ang University College of Medicine, Seoul, South Korea
| | - Hien Dang Thanh
- Department of Microbiology, Chung-Ang University College of Medicine, Seoul, South Korea
- Central Vietnam Veterinary Institute, Nha Trang, Vietnam
| | - Vu-Khac Hung
- Central Vietnam Veterinary Institute, Nha Trang, Vietnam
| | - Duc Tan Nguyen
- Central Vietnam Veterinary Institute, Nha Trang, Vietnam
| | - Wonyong Kim
- Department of Microbiology, Chung-Ang University College of Medicine, Seoul, South Korea
- * E-mail:
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19
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Kirunda H, Kabi F, Muwereza N, Kabuuka T, Kerfua SD, Kasaija PD, Byarugaba DK, Wabwire-Mangen F. Seroprevalence and Risk Factors for Exposure of Free-Range Poultry to Avian Influenza Viruses in Important Bird Areas in Uganda. Avian Dis 2015; 59:64-70. [PMID: 26292536 DOI: 10.1637/10874-052714-reg] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
Avian influenza (AI) viruses cause disease in domestic and wild bird species. Although these viruses have been reported to occur in poultry in Uganda, risk factors for their introduction and spread were largely unknown. We investigated the seroprevalence and risk factors for exposure of free-range poultry to AI viruses in Important Bird Areas (IBAs) in the country. A structured questionnaire was administered to 664 respondents, and 1342 sera were collected from poultry. Sera were analyzed for antibody titers against AI using competitive ELISA. AI antibody prevalence was 7.6% (95% confidence interval [CI]: 6.2-9.0) in the Lake Victoria Basin, 8.4% (95% CI: 7.0-9.8) in the southwestern region, and none (0/432) in the Kyoga region. High proportions of risky practices were observed among respondent farmers. Significant predictors for exposure of poultry to AI viruses were the source of restocking poultry, method of disposal of inedible parts of slaughtered poultry, and waterfowl visits to a nearby body of water. In addition, visits by waterbirds to a nearby body of water during October-December were more associated with exposure to AI viruses (odds ratio = 3.6; 95% CI: 1.42-9.23) compared with January-March visits'. These results suggested the existence of several risk factors for exposure of free-range to AI viruses in IBAs in Uganda.
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20
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Abstract
The spatial spread of the highly pathogenic avian influenza virus H5N1 and its long-term persistence in Asia have resulted in avian influenza panzootics and enormous economic losses in the poultry sector. However, an understanding of the regional long-distance transmission and seasonal patterns of the virus is still lacking. In this study, we present a phylogeographic approach to reconstruct the viral migration network. We show that within each wild fowl migratory flyway, the timing of H5N1 outbreaks and viral migrations are closely associated, but little viral transmission was observed between the flyways. The bird migration network is shown to better reflect the observed viral gene sequence data than other networks and contributes to seasonal H5N1 epidemics in local regions and its large-scale transmission along flyways. These findings have potentially far-reaching consequences, improving our understanding of how bird migration drives the periodic reemergence of H5N1 in Asia.
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21
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Wei K, Chen Y, Lin Y, Pan Y. Genetic dynamic analysis of the influenza A H5N1 NS1 gene in China. PLoS One 2014; 9:e101384. [PMID: 25003973 PMCID: PMC4086889 DOI: 10.1371/journal.pone.0101384] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2014] [Accepted: 06/06/2014] [Indexed: 12/03/2022] Open
Abstract
The direct precursors of the A/Goose/Guangdong/1/1996 (GS/GD) virus lineage and its reassortants have been established geographically and ecologically. To investigate the variation and evolutionary dynamics of H5N1 viruses, whole-genome viral sequences (n = 164) were retrieved from the NCBI Influenza Virus Resource. Here, we present phylogenetic evidence for intrasubtype reassortments among H5N1 viruses isolated from China during 1996–2012. On the basis of phylogenetic analysis, we identified four major groups and further classified the reassortant viruses into three subgroups. Putative mosaic structures were mostly found in the viral ribonucleoprotein (vRNP) complexes and 91.0% (10/11) mosaics were obtained from terrestrial birds. Sequence variability and selection pressure analyses revealed that both surface glycoproteins (HA and NA) and nonstructural protein 1 (NS1) have higher dN/dS ratio and variability than other internal proteins. Furthermore, we detected 47 positively selected sites in genomic segments with the exception of PB2 and M1 genes. Hemagglutinin (HA) and neuraminidase (NA) are considered highly variable due to host immune pressure, however, it is not known what drives NS1 variability. Therefore, we performed a thorough analysis of the genetic variation and selective pressure of NS1 protein (462 available NS1 sequences). We found that most of positively selected sites and variable amino acids were located in the C-terminal effector domain (ED) of NS1. In addition, we focused on the NS1–RNA and NS1–protein interactions that were involved in viral replication mechanisms and host immune response. Transcriptomic analysis of H5N1-infected monkey lungs showed that certain PI3K-related genes were up-regulated.
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Affiliation(s)
- Kaifa Wei
- School of Biological Sciences and Biotechnology, Minnan Normal University, Zhangzhou, China
- * E-mail: (KW); (YP)
| | - Yanhui Chen
- School of Life Sciences, Tsinghua University, Beijing, China
| | - Yina Lin
- School of Biological Sciences and Biotechnology, Minnan Normal University, Zhangzhou, China
| | - Yutian Pan
- The Engineering Technological Center of Mushroom Industry, Minnan Normal University, Zhangzhou, China
- * E-mail: (KW); (YP)
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22
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Daniels P, Wiyono A, Sawitri E, Poermadjaja B, Sims LD. H5N1 highly pathogenic avian influenza in Indonesia: retrospective considerations. Curr Top Microbiol Immunol 2014; 365:171-84. [PMID: 22956392 DOI: 10.1007/82_2012_265] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/20/2023]
Abstract
Indonesia is one of the five countries where highly pathogenic avian influenza viruses of the H5N1 subtype (H5N1 HPAI) remain endemic in poultry. Importantly, it is one of the countries where the virus causes human infections. WHO data indicate that as of 2 May 2012, 189 human cases of Influenza A (H5N1) had been reported in Indonesia, with 157 human deaths. These human cases included a small number in which limited human-to-human transmission could have occurred. Hence, there remains a critical need in Indonesia for a more effective One Health approach to the control and prevention of this disease in people and in poultry. This chapter explores a number of aspects of the evolution of this disease in Indonesia, the virus that causes it and the control and preventive measures introduced, focusing on the successes and shortcomings of veterinary and One Health approaches. Indonesia provides many examples of situations where this latter approach has been successful, and others where further work is needed to maximize the benefits from coordinated responses to this disease leading to effective management of the risk to human health.
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Affiliation(s)
- Peter Daniels
- Australian Animal Health Laboratory, CSIRO Animal, Food and Health Sciences, PMB 24, Geelong, 3220, Australia,
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Sonnberg S, Webby RJ, Webster RG. Natural history of highly pathogenic avian influenza H5N1. Virus Res 2013; 178:63-77. [PMID: 23735535 PMCID: PMC3787969 DOI: 10.1016/j.virusres.2013.05.009] [Citation(s) in RCA: 99] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2012] [Revised: 05/03/2013] [Accepted: 05/20/2013] [Indexed: 12/27/2022]
Abstract
The ecology of highly pathogenic avian influenza (HPAI) H5N1 has significantly changed from sporadic outbreaks in terrestrial poultry to persistent circulation in terrestrial and aquatic poultry and potentially in wild waterfowl. A novel genotype of HPAI H5N1 arose in 1996 in Southern China and through ongoing mutation, reassortment, and natural selection, has diverged into distinct lineages and expanded into multiple reservoir hosts. The evolution of Goose/Guangdong-lineage highly pathogenic H5N1 viruses is ongoing: while stable interactions exist with some reservoir hosts, these viruses are continuing to evolve and adapt to others, and pose an un-calculable risk to sporadic hosts, including humans.
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Affiliation(s)
- Stephanie Sonnberg
- Department of Infectious Diseases St. Jude Children's Research Hospital 262 Danny Thomas Drive MS 330, Memphis, TN, 38103 USA
| | - Richard J. Webby
- Department of Infectious Diseases St. Jude Children's Research Hospital 262 Danny Thomas Drive MS 330, Memphis, TN, 38103 USA
| | - Robert G. Webster
- corresponding author, Department of Infectious Diseases St. Jude Children's Research Hospital 262 Danny Thomas Drive MS 330, Memphis, TN, 38103 USA Tel +1 901 595 3400 Fax +1 901 595 8559
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Guan Y, Smith GJ. The emergence and diversification of panzootic H5N1 influenza viruses. Virus Res 2013; 178:35-43. [PMID: 23735533 PMCID: PMC4017639 DOI: 10.1016/j.virusres.2013.05.012] [Citation(s) in RCA: 73] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2012] [Revised: 04/23/2013] [Accepted: 05/20/2013] [Indexed: 02/05/2023]
Abstract
The Asian highly pathogenic avian influenza H5N1 virus was first detected in the goose population of Guangdong, China in 1996. The viruses in this lineage are unique in their ecological success, demonstrating an extremely broad host range and becoming established in poultry over much of Asia and in Africa. H5N1 viruses have also diverged into multiple clades and subclades that generally do not cross neutralize, which has greatly confounded control measures in poultry and pre-pandemic vaccine strain selection. Although H5N1 viruses currently cannot transmit efficiently between mammals they exhibit high mortality in humans and recent experimental studies have shown that it is possible to generate an H5N1 virus that is transmissible in mammals. In addition to causing unprecedented economic losses, the long-term presence of the H5N1 virus in poultry and its frequent introductions to humans continue to pose a significant pandemic threat. Here we provide a summary of the genesis, molecular epidemiology and evolution of this H5N1 lineage, particularly the factors that have contributed to the continued diversification and ecological success of H5N1 viruses, with particular reference to the poultry production systems they have emerged from.
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Affiliation(s)
- Yi Guan
- State Key Laboratory of Emerging Infectious Diseases and Center of Influenza Research, The University of Hong Kong, Hong Kong SAR, China
- International Institution of Infection and Immunity, Shantou University Medical College, Shantou, China
| | - Gavin J.D. Smith
- Duke-NUS Graduate Medical School, 8 College Road, Singapore 169857
- Duke Global Health Institute, Duke University, Box 90519, Durham, North Carolina 27708
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Fuller TL, Gilbert M, Martin V, Cappelle J, Hosseini P, Njabo KY, Abdel Aziz S, Xiao X, Daszak P, Smith TB. Predicting hotspots for influenza virus reassortment. Emerg Infect Dis 2013; 19:581-8. [PMID: 23628436 PMCID: PMC3647410 DOI: 10.3201/eid1904.120903] [Citation(s) in RCA: 59] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
TOC summary: Reassortment is most likely to occur in eastern China, central China, or the Nile Delta in Egypt. The 1957 and 1968 influenza pandemics, each of which killed ≈1 million persons, arose through reassortment events. Influenza virus in humans and domestic animals could reassort and cause another pandemic. To identify geographic areas where agricultural production systems are conducive to reassortment, we fitted multivariate regression models to surveillance data on influenza A virus subtype H5N1 among poultry in China and Egypt and subtype H3N2 among humans. We then applied the models across Asia and Egypt to predict where subtype H3N2 from humans and subtype H5N1 from birds overlap; this overlap serves as a proxy for co-infection and in vivo reassortment. For Asia, we refined the prioritization by identifying areas that also have high swine density. Potential geographic foci of reassortment include the northern plains of India, coastal and central provinces of China, the western Korean Peninsula and southwestern Japan in Asia, and the Nile Delta in Egypt.
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Affiliation(s)
- Trevon L Fuller
- Institute of the Environment and Sustainability, University of California, Los Angeles, California 90095-1496, USA.
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Liu Q, Liu DY, Yang ZQ. Characteristics of human infection with avian influenza viruses and development of new antiviral agents. Acta Pharmacol Sin 2013; 34:1257-69. [PMID: 24096642 PMCID: PMC3791557 DOI: 10.1038/aps.2013.121] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2013] [Accepted: 08/01/2013] [Indexed: 12/21/2022] Open
Abstract
Since 1997, several epizootic avian influenza viruses (AIVs) have been transmitted to humans, causing diseases and even deaths. The recent emergence of severe human infections with AIV (H7N9) in China has raised concerns about efficient interpersonal viral transmission, polygenic traits in viral pathogenicity and the management of newly emerging strains. The symptoms associated with viral infection are different in various AI strains: H5N1 and newly emerged H7N9 induce severe pneumonia and related complications in patients, while some H7 and H9 subtypes cause only conjunctivitis or mild respiratory symptoms. The virulence and tissue tropism of viruses as well as the host responses contribute to the pathogenesis of human AIV infection. Several preventive and therapeutic approaches have been proposed to combat AIV infection, including antiviral drugs such as M2 inhibitors, neuraminidase inhibitors, RNA polymerase inhibitors, attachment inhibitors and signal-transduction inhibitors etc. In this article, we summarize the recent progress in researches on the epidemiology, clinical features, pathogenicity determinants, and available or potential antivirals of AIV.
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Affiliation(s)
- Qiang Liu
- State Key Laboratory of Virology/Institute of Medical Virology, School of Medicine, Wuhan University, Wuhan 430071, China
- The First College of Clinical Medical Science, China Three Gorges University/Yichang Central People's Hospital, Yichang 443000, China
| | - Dong-ying Liu
- State Key Laboratory of Virology/Institute of Medical Virology, School of Medicine, Wuhan University, Wuhan 430071, China
- Department of Microbiology, School of Medicine, Wuhan University, Wuhan 430071, China
| | - Zhan-qiu Yang
- State Key Laboratory of Virology/Institute of Medical Virology, School of Medicine, Wuhan University, Wuhan 430071, China
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Carrel M, Emch M. Genetics: A New Landscape for Medical Geography. ANNALS OF THE ASSOCIATION OF AMERICAN GEOGRAPHERS. ASSOCIATION OF AMERICAN GEOGRAPHERS 2013; 103:1452-1467. [PMID: 24558292 PMCID: PMC3928082 DOI: 10.1080/00045608.2013.784102] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
The emergence and re-emergence of human pathogens resistant to medical treatment will present a challenge to the international public health community in the coming decades. Geography is uniquely positioned to examine the progressive evolution of pathogens across space and through time, and to link molecular change to interactions between population and environmental drivers. Landscape as an organizing principle for the integration of natural and cultural forces has a long history in geography, and, more specifically, in medical geography. Here, we explore the role of landscape in medical geography, the emergent field of landscape genetics, and the great potential that exists in the combination of these two disciplines. We argue that landscape genetics can enhance medical geographic studies of local-level disease environments with quantitative tests of how human-environment interactions influence pathogenic characteristics. In turn, such analyses can expand theories of disease diffusion to the molecular scale and distinguish the important factors in ecologies of disease that drive genetic change of pathogens.
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Affiliation(s)
| | - Michael Emch
- Department of Geography, University of North Carolina-Chapel Hill
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Ratanakorn P, Wiratsudakul A, Wiriyarat W, Eiamampai K, Farmer AH, Webster RG, Chaichoune K, Suwanpakdee S, Pothieng D, Puthavathana P. Satellite tracking on the flyways of brown-headed gulls and their potential role in the spread of highly pathogenic avian influenza H5N1 virus. PLoS One 2012; 7:e49939. [PMID: 23209623 PMCID: PMC3509151 DOI: 10.1371/journal.pone.0049939] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2012] [Accepted: 10/18/2012] [Indexed: 11/18/2022] Open
Abstract
Brown-headed gulls (Larus brunnicephalus), winter visitors of Thailand, were tracked by satellite telemetry during 2008-2011 for investigating their roles in the highly pathogenic avian influenza (HPAI) H5N1 virus spread. Eight gulls negative for influenza virus infection were marked with solar-powered satellite platform transmitters at Bang Poo study site in Samut Prakarn province, Thailand; their movements were monitored by the Argos satellite tracking system, and locations were mapped. Five gulls completed their migratory cycles, which spanned 7 countries (China, Bangladesh, India, Myanmar, Thailand, Cambodia, and Vietnam) affected by the HPAI H5N1 virus. Gulls migrated from their breeding grounds in China to stay overwinter in Thailand and Cambodia; while Bangladesh, India, Myanmar, and Vietnam were the places of stopovers during migration. Gulls traveled an average distance of about 2400 km between Thailand and China and spent 1-2 weeks on migration. Although AI surveillance among gulls was conducted at the study site, no AI virus was isolated and no H5N1 viral genome or specific antibody was detected in the 75 gulls tested, but 6.6% of blood samples were positive for pan-influenza A antibody. No AI outbreaks were reported in areas along flyways of gulls in Thailand during the study period. Distance and duration of migration, tolerability of the captive gulls to survive the HPAI H5N1 virus challenge and days at viral shedding after the virus challenging suggested that the Brown-headed gull could be a potential species for AI spread, especially among Southeast Asian countries, the epicenter of H5N1 AI outbreak.
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Affiliation(s)
- Parntep Ratanakorn
- Faculty of Veterinary Science, Mahidol University, Nakhon Pathom, Thailand
| | | | | | - Krairat Eiamampai
- Department of National Park, Wildlife and Plant Conservation, Ministry of Natural Resource and Environment, Bangkok, Thailand
| | - Adrian H. Farmer
- Wild Ecological Solutions, Fort Collins, Colorado, United States of America
| | - Robert G. Webster
- Division of Virology, Department of Infectious Diseases, St. Jude Children Research Hospital, Memphis, Tennessee, United States of America
| | | | - Sarin Suwanpakdee
- Faculty of Veterinary Science, Mahidol University, Nakhon Pathom, Thailand
| | - Duangrat Pothieng
- Department of National Park, Wildlife and Plant Conservation, Ministry of Natural Resource and Environment, Bangkok, Thailand
| | - Pilaipan Puthavathana
- Department of Microbiology, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
- * E-mail:
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Increased substitution rate in H5N1 avian influenza viruses during mass vaccination of poultry. ACTA ACUST UNITED AC 2012. [DOI: 10.1007/s11434-012-5215-y] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
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Carrel MA, Emch M, Nguyen T, Todd Jobe R, Wan XF. Population-environment drivers of H5N1 avian influenza molecular change in Vietnam. Health Place 2012; 18:1122-31. [PMID: 22652510 DOI: 10.1016/j.healthplace.2012.04.009] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/16/2011] [Revised: 04/16/2012] [Accepted: 04/19/2012] [Indexed: 11/26/2022]
Abstract
This study identifies population and environment drivers of genetic change in H5N1 avian influenza viruses (AIV) in Vietnam using a landscape genetics approach. While prior work has examined how combinations of local-level environmental variables influence H5N1 occurrence, this research expands the analysis to the complex genetic characteristics of H5N1 viruses. A dataset of 125 highly pathogenic H5N1 AIV isolated in Vietnam from 2003 to 2007 is used to explore which population and environment variables are correlated with increased genetic change among viruses. Results from non-parametric multidimensional scaling and regression analyses indicate that variables relating to both the environmental and social ecology of humans and birds in Vietnam interact to affect the genetic character of viruses. These findings suggest that it is a combination of suitable environments for species mixing, the presence of high numbers of potential hosts, and in particular the temporal characteristics of viral occurrence, that drive genetic change among H5N1 AIV in Vietnam.
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Affiliation(s)
- Margaret A Carrel
- Department of Geography, University of Iowa, Iowa City, IA 52242, USA.
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The ecology and age structure of a highly pathogenic avian influenza virus outbreak in wild mute swans. Parasitology 2012; 139:1914-23. [DOI: 10.1017/s0031182012000261] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
SUMMARYThe first UK epizootic of highly pathogenic (HP) H5N1 influenza in wild birds occurred in 2008, in a population of mute swans that had been the subject of ornithological study for decades. Here we use an innovative combination of ornithological, phylogenetic and immunological approaches to investigate the ecology and age structure of HP H5N1 in nature. We screened samples from swans and waterbirds using PCR and sequenced HP H5N1-positive samples. The outbreak's origin was investigated by linking bird count data with a molecular clock analysis of sampled virus sequences. We used ringing records to reconstruct the age-structure of outbreak mortality, and we estimated the age distribution of prior exposure to avian influenza. Outbreak mortality was low and all HP H5N1-positive mute swans in the affected population were <3 years old. Only the youngest age classes contained an appreciable number of individuals with no detectable antibody responses to viral nucleoprotein. Phylogenetic analysis indicated that the outbreak strain circulated locally for ∼1 month before detection and arrived when the immigration rate of migrant waterbirds was highest. Our data are consistent with the hypothesis that HP H5N1 epizootics in wild swans exhibit limited mortality due to immune protection arising from previous exposure. Our study population may represent a valuable resource for investigating the natural ecology and epidemiology of avian influenza.
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Trevennec K, Chevalier V, Grosbois V, Garcia JM, Thu HH, Berthouly-Salazar C, Peiris JSM, Roger F. Looking for avian influenza in remote areas. A case study in Northern Vietnam. Acta Trop 2011; 120:160-6. [PMID: 21840292 DOI: 10.1016/j.actatropica.2011.07.010] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2011] [Revised: 07/26/2011] [Accepted: 07/30/2011] [Indexed: 11/29/2022]
Abstract
Epidemiological surveys of avian influenza infections rarely focus on backyard poultry systems in remote locations because areas with low levels of poultry production are considered to have little influence on the emergence, re-emergence, persistence or spread of avian influenza viruses. In addition, routine disease investigations in remote areas often are neglected due to the lower availability and relatively high cost of veterinary services there. A bank of avian sera collected in 2005 from ethnic minority households in Ha Giang province (Northern Vietnam), located on the Chinese border, was analysed to estimate the seroprevalence of avian influenza virus (AIV) during a H5N1 epidemic and to identify potential risk factors for infection. The results suggest that the chicken population had been exposed to AIV with a seroprevalence rate of 7.2% [1.45; 10.5]. The H5 and H9 subtypes were identified with a seroprevalence of 3.25% [2.39; 4.11] and 1.12% [0.61; 1.63], respectively. The number of inhabitants in a village and the distance to the main national road were the most influential risk factors of AIV infection, and high-risk clusters were located along the road leading to China. These two results suggest a virus spread through commercial poultry exchanges and a possible introduction of AIV from southern China. Remote areas and small-scale farms may play an under-estimated role in the spread and persistence of AIV.
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Affiliation(s)
- K Trevennec
- French Agricultural Research Center for International Development (CIRAD), Animal and Integrated Risk Management Research Unit, Baillarguet Campus, Montpellier Cedex 5, France.
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Wibawa H, Henning J, Wong F, Selleck P, Junaidi A, Bingham J, Daniels P, Meers J. A molecular and antigenic survey of H5N1 highly pathogenic avian influenza virus isolates from smallholder duck farms in Central Java, Indonesia during 2007-2008. Virol J 2011; 8:425. [PMID: 21896207 PMCID: PMC3179459 DOI: 10.1186/1743-422x-8-425] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2011] [Accepted: 09/07/2011] [Indexed: 12/29/2022] Open
Abstract
Background Indonesia is one of the countries most severely affected by H5N1 highly pathogenic avian influenza (HPAI) virus in terms of poultry and human health. However, there is little information on the diversity of H5N1 viruses circulating in backyard farms, where chickens and ducks often intermingle. In this study, H5N1 virus infection occurring in 96 smallholder duck farms in central Java, Indonesia from 2007-2008 was investigated and the molecular and antigenic characteristics of H5N1 viruses isolated from these farms were analysed. Results All 84 characterised viruses belonged to H5N1 clade 2.1 with three virus sublineages being identified: clade 2.1.1 (1), clade 2.1.3 (80), and IDN/6/05-like viruses (3) that did not belong to any of the present clades. All three clades were found in ducks, while only clade 2.1.3 was isolated from chickens. There were no significant amino acid mutations of the hemagglutinin (HA) and neuraminidase (NA) sites of the viruses, including the receptor binding, glycosylation, antigenic and catalytic sites and NA inhibitor targets. All the viruses had polybasic amino acids at the HA cleavage site. No evidence of major antigenic variants was detected. Based on the HA gene, identical virus variants could be found on different farms across the study sites and multiple genetic variants could be isolated from HPAI outbreaks simultaneously or at different time points from single farms. HPAI virus was isolated from both ducks and chickens; however, the proportion of surviving duck cases was considerably higher than in chickens. Conclusions The 2.1.3 clade was the most common lineage found in this study. All the viruses had sequence characteristic of HPAI, but negligible variations in other recognized amino acids at the HA and NA proteins which determine virus phenotypes. Multiple genetic variants appeared to be circulating simultaneously within poultry communities. The high proportion of live duck cases compared to chickens over the study period suggests that ducks are more likely to survive infection and they may better suit the role of long-term maintenance host for H5N1. As some viruses were isolated from dead birds, there was no clear correlation between genetic variations and pathogenicity of these viruses.
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Affiliation(s)
- Hendra Wibawa
- CSIRO-Australian Animal Health Laboratory, Geelong, Victoria, Australia.
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Is H9N2 avian influenza virus a pandemic potential? CANADIAN JOURNAL OF INFECTIOUS DISEASES & MEDICAL MICROBIOLOGY 2011; 20:e35-6. [PMID: 20514156 DOI: 10.1155/2009/578179] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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Zhang J, Lei F. Analysis of human infectious avian influenza virus: hemagglutinin genetic characteristics in Asia and Africa from 2004 to 2009. Integr Zool 2011; 5:264-71. [PMID: 21392344 DOI: 10.1111/j.1749-4877.2010.00212.x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
In the present study, we used nucleotide and protein sequences of avian influenza virus H5N1, which were obtained in Asia and Africa, analyzed HA proteins using ClustalX1.83 and MEGA4.0, and built a genetic evolutionary tree of HA nucleotides. The analysis revealed that the receptor specificity amino acid of A/HK/213/2003, A/Turkey/65596/2006 and etc mutated into QNG, which could bind with á-2, 3 galactose and á-2, 6 galactose. A mutation might thus take place and lead to an outbreak of human infections of avian influenza virus. The mutations of HA protein amino acids from 2004 to 2009 coincided with human infections provided by the World Health Organization, indicating a "low-high-highest-high-low" pattern. We also found out that virus strains in Asia are from different origins: strains from Southeast Asia and East Asia are of the same origin, whereas those from West Asia, South Asia and Africa descend from one ancestor. The composition of the phylogenetic tree and mutations of key site amino acids in HA proteins reflected the fact that the majority of strains are regional and long term, and virus diffusions exist between China, Laos, Malaysia, Indonesia, Azerbaijan, Turkey and Iraq. We would advise that pertinent vaccines be developed and due attention be paid to the spread of viruses between neighboring countries and the dangers of virus mutation and evolution.
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Affiliation(s)
- Jirong Zhang
- Ningxia Medical University Basic Medical Science School, Yinchuan, China
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Zilberman D, Otte J, Roland-Holst D, Pfeiffer D. Epidemiology of Highly Pathogenic Avian Influenza Virus Strain Type H5N1. HEALTH AND ANIMAL AGRICULTURE IN DEVELOPING COUNTRIES 2011; 36. [PMCID: PMC7122524 DOI: 10.1007/978-1-4419-7077-0_10] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
Highly pathogenic avian influenza (HPAI) is a severe disease of poultry. It is highly transmissible with a flock mortality rate approaching 100% in vulnerable species (Capua et al. 2007a). Due to the potentially disastrous impact the disease can have on affected poultry sectors, HPAI has received huge attention and is classified as a notifiable disease by the World Organisation for Animal Health (OIE).
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Affiliation(s)
- David Zilberman
- College of Natural Resources, Dept. Agricultural & Resource Economics, University of California, Berkeley, Giannini Hall 206, Berkeley, 94720-3310 California USA
| | - Joachim Otte
- Food and Agriculture Organization of the, Viale delle Terme di Caracalla, Rome, 00100 Italy
| | - David Roland-Holst
- , Department of Agricultural and Resource, University of California, Giannini Hall 207, Berkeley, 94720-3310 USA
| | - Dirk Pfeiffer
- , Veterinary Clinical Sciences, The Royal Veterinary College, Hawkshead Lane, Hatfield, AL9 7TA United Kingdom
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Giles BM, Ross TM. A computationally optimized broadly reactive antigen (COBRA) based H5N1 VLP vaccine elicits broadly reactive antibodies in mice and ferrets. Vaccine 2011; 29:3043-54. [PMID: 21320540 DOI: 10.1016/j.vaccine.2011.01.100] [Citation(s) in RCA: 135] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2010] [Revised: 01/25/2011] [Accepted: 01/29/2011] [Indexed: 12/11/2022]
Abstract
Pandemic outbreaks of influenza are caused by the emergence of a pathogenic and transmissible virus to which the human population is immunologically naïve. Recent outbreaks of highly pathogenic avian influenza (HPAI) of the H5N1 subtype are of particular concern because of the high mortality rate (60% case fatality rate) and novel subtype. In order to develop a vaccine that elicits broadly reactive antibody responses against emerging H5N1 isolates, we utilized a novel antigen design technique termed computationally optimized broadly reactive antigen (COBRA). The COBRA HA sequence was based upon HA amino acid sequences from clade 2 H5N1 human infections and the expressed protein retained the ability to bind the receptor, as well as mediate particle fusion. Non-infectious recombinant VLP vaccines using the COBRA HA were purified from a mammalian expression system. Mice and ferrets vaccinated with COBRA HA H5N1 VLPs had protective levels of HAI antibodies to a representative isolates from each subclade of clade 2. Furthermore, VLP vaccinated animals were completely protected from a lethal challenge of the clade 2.2 H5N1 virus A/Whooper Swan/Mongolia/244/2005. This is the first report describing the use of COBRA-based antigen design. The COBRA HA H5N1 VLP vaccine elicited broadly reactive antibodies and is an effective influenza vaccine against HPAI virus.
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Affiliation(s)
- Brendan M Giles
- Center for Vaccine Research, University of Pittsburgh, Pittsburgh, PA 15261, USA
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Pfeiffer DU, Otte MJ, Roland-Holst D, Inui K, Nguyen T, Zilberman D. Implications of global and regional patterns of highly pathogenic avian influenza virus H5N1 clades for risk management. Vet J 2011; 190:309-16. [PMID: 21288747 DOI: 10.1016/j.tvjl.2010.12.022] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2010] [Revised: 11/07/2010] [Accepted: 12/19/2010] [Indexed: 01/05/2023]
Abstract
This paper analyses the publicly available data on the distribution and evolution of highly pathogenic avian influenza virus (HPAIV) H5N1 clades, whilst acknowledging the biases resulting from the non-random selection of isolates for gene sequencing. The data indicate molecular heterogeneity in the global distribution of HPAIV H5N1, in particular in different parts of East and Southeast Asia. Analysis of the temporal pattern of haemagglutinin clade data shows a progression from clade 0 (the 'dominant' clade between 1996 and 2002) to clade 1 (2003-2005) and then to clade 2.3.4 (2005 onwards). This process continuously produces variants, depending on the frequency of virus multiplication in the host population, which is influenced by geographical variation in poultry density, poultry production systems and also HPAI risk management measures such as vaccination. Increased multilateral collaboration needs to focus on developing enhanced disease surveillance and control targeted at evolutionary 'hotspots'.
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Affiliation(s)
- Dirk U Pfeiffer
- Veterinary Epidemiology & Public Health Group, Royal Veterinary College, Hawkshead Lane, North Mymms, Hatfield, Hertfordshire AL9 7TA, UK.
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Liang L, Xu B, Chen Y, Liu Y, Cao W, Fang L, Feng L, Goodchild MF, Gong P. Combining spatial-temporal and phylogenetic analysis approaches for improved understanding on global H5N1 transmission. PLoS One 2010; 5:e13575. [PMID: 21042591 PMCID: PMC2962646 DOI: 10.1371/journal.pone.0013575] [Citation(s) in RCA: 74] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2010] [Accepted: 09/30/2010] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND Since late 2003, the highly pathogenic influenza A H5N1 had initiated several outbreak waves that swept across the Eurasia and Africa continents. Getting prepared for reassortment or mutation of H5N1 viruses has become a global priority. Although the spreading mechanism of H5N1 has been studied from different perspectives, its main transmission agents and spread route problems remain unsolved. METHODOLOGY/PRINCIPAL FINDINGS Based on a compilation of the time and location of global H5N1 outbreaks from November 2003 to December 2006, we report an interdisciplinary effort that combines the geospatial informatics approach with a bioinformatics approach to form an improved understanding on the transmission mechanisms of H5N1 virus. Through a spherical coordinate based analysis, which is not conventionally done in geographical analyses, we reveal obvious spatial and temporal clusters of global H5N1 cases on different scales, which we consider to be associated with two different transmission modes of H5N1 viruses. Then through an interdisciplinary study of both geographic and phylogenetic analysis, we obtain a H5N1 spreading route map. Our results provide insight on competing hypotheses as to which avian hosts are responsible for the spread of H5N1. CONCLUSIONS/SIGNIFICANCE We found that although South China and Southeast Asia may be the virus pool of avian flu, East Siberia may be the source of the H5N1 epidemic. The concentration of migratory birds from different places increases the possibility of gene mutation. Special attention should be paid to East Siberia, Middle Siberia and South China for improved surveillance of H5N1 viruses and monitoring of migratory birds.
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Affiliation(s)
- Lu Liang
- State Key Laboratory of Remote Sensing Science, Jointly Sponsored by
Institute of Remote Sensing Applications, Chinese Academy of Sciences, Beijing
Normal University, Beijing, China
- Center for Earth System Science, Tsinghua University, Beijing,
China
| | - Bing Xu
- Department of Geography, University of Utah, Salt Lake City, Utah, United
States of America
- Department of Environmental Science and Engineering, Tsinghua University,
Beijing, China
| | - Yanlei Chen
- Department of Environmental Science, Policy and Management, University of
California, Berkeley, California, United States America
| | - Yang Liu
- Computational and Molecular Population Genetics, Institute of Ecology and
Evolution, University of Bern, Bern, Switzerland
| | - Wuchun Cao
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of
Microbiology and Epidemiology, Beijing, China
| | - Liqun Fang
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of
Microbiology and Epidemiology, Beijing, China
| | - Limin Feng
- Key Laboratory for Biodiversity Science and Ecological Engineering,
Ministry of Education, College of Life Science, Beijing Normal University,
Beijing, China
| | - Michael F. Goodchild
- Department of Geography, University of California Santa Barbara, Santa
Barbara, California, United States of America
| | - Peng Gong
- State Key Laboratory of Remote Sensing Science, Jointly Sponsored by
Institute of Remote Sensing Applications, Chinese Academy of Sciences, Beijing
Normal University, Beijing, China
- Center for Earth System Science, Tsinghua University, Beijing,
China
- Department of Environmental Science, Policy and Management, University of
California, Berkeley, California, United States America
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Abstract
Although influenza A viruses of avian origin have long been responsible for influenza pandemics, including the "Spanish flu" pandemic of 1918, human infections caused by avian subtypes of influenza A virus, most notably H5N1, have emerged since the 1990s (H5N1 in 1997; H9N2 in 1999; and H7N7 in 2003). The wide geographic distribution of influenza A H5N1 in avian species, and the number and severity of human infections are unprecedented. Together with the ongoing genetic evolution of this virus, these features make influenza A H5N1 a likely candidate for a future influenza pandemic. This article discusses the epidemiology, pathogenesis, and diagnosis of human infections caused by influenza A H5N1 virus.
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Ferreira HL, Lambrecht B, van Borm S, Torrieri-Dramard L, Klatzmann D, Bellier B, van den Berg T. Identification of a dominant epitope in the hemagglutinin of an Asian highly pathogenic avian influenza H5N1 clade 1 virus by selection of escape mutants. Avian Dis 2010; 54:565-71. [PMID: 20521695 DOI: 10.1637/8750-033009-resnote.1] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
H5N1 avian influenza virus has caused widespread infection in poultry and wild birds, and has the potential to emerge as a pandemic threat to humans. The hemagglutinin (HA) is a glycoprotein on the surface of the virus envelope. Understanding its antigenic structure is essential for designing novel vaccines that can inhibit virus infection. The aim of this study was to map the amino acid substitutions that resulted in resistance to neutralization by monoclonal antibodies (MAbs) of the highly pathogenic A/crested eagle/Belgium/01/2004 (H5N1), a clade 1 virus. Two hybridomas specific to H5N1 clade 1 viruses were selected by enzyme-linked immunosorbent assay, virus neutralization test, and immunofluorescence assay. Escape mutant populations resisting neutralization by those MAbs (8C5 and 5A1) were then selected, and sequencing of these mutants allowed the prediction of the HA protein structure by molecular homology. We could detect an amino acid change in our escape mutants at position K189E corresponding to antigenic site 2 of H5 HA1 and site B of H3 HA1. Interestingly, 336 out of 350 available HA sequences from H5N1 clade 1 and clade 2.3 viruses had Lys (K) at position 189 in the HA1, whereas HA sequences analyzed from dade 2.1 and 2.2 viruses had Arg (R). This residue also interacts with the receptor-binding site, and it is thus important for the evolution of H5N1 viruses. An additional substitution K29E in HA2 subunit was also observed and identified with the use of NetChop software as a loss of a proteasomal cleavage site, which seems to be an advantage for H5N1 viruses.
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Affiliation(s)
- Helena Lage Ferreira
- Avian Virology and Immunology, CODA-CERVA-VAR, Groeselenberg 99, B-1180 Uccle, Brussels, Belgium.
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Davis CT, Balish AL, O'Neill E, Nguyen CV, Cox NJ, Xiyan X, Klimov A, Nguyen T, Donis RO. Detection and characterization of clade 7 high pathogenicity avian influenza H5N1 viruses in chickens seized at ports of entry and live poultry markets in Vietnam. Avian Dis 2010; 54:307-12. [PMID: 20521651 DOI: 10.1637/8801-040109-resnote.1] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
High pathogenicity avian influenza H5N1 has become an endemic poultry disease in several Asian countries, including Vietnam. Recently, dade 7 H5N1 viruses of the Eurasian lineage were isolated from chickens seized at ports of entry in Lang Son Province, Vietnam. Extensive nucleotide and amino acid divergence across the hemagglutinin (HA) protein gene of these isolates in comparison to previously described clade 7 viruses was identified. Clade 7 viruses are antigenically distinct from contemporary strains of H5N1 known to circulate in Vietnamese poultry (clade 1 and clade 2.3.4). Subsequent surveillance of sick poultry in live poultry markets in Hai Duong Province identified additional clade 7 isolates with HA genes very similar to the group B virus cluster detected previously at the Lang Son Province border. Antigenic analysis of the isolates from the live bird markets revealed significant cross-reactivity only between those clade 7 viruses belonging to the same subgroups. To meet pandemic response preparedness objectives, we have developed a reassortant virus from A/chicken/Vietnam/NCVD-016/2008, which could be used as a new prepandemic vaccine candidate for veterinary or human vaccination, should the need arise. Findings from these studies indicate that viruses with clade 7 HA have continued to evolve in Southeast Asian poultry, leading to significant antigenic drift relative to other H5N1 viruses currently circulating in Vietnam.
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Affiliation(s)
- C Todd Davis
- Influenza Division, Centers for Disease Control and Prevention, Atlanta, GA 30333, USA
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Abstract
AbstractAvian influenza (AI) virus is one of the most important diseases of the poultry industry around the world. The virus has a broad host range in birds and mammals, although the natural reservoir is wild birds where it typically causes an asymptomatic to mild infection. The virus in poultry can cause a range of clinical diseases and is defined either as low pathogenic AI (LPAI) or highly pathogenic AI (HPAI) depending on the type of disease it causes in chickens. Viruses that replicate primarily on mucosal surfaces and cause mild disease with low mortality are termed LPAI. Viruses that replicate on mucosal surfaces and systemically and cause severe disease with a mortality rate of 75% or greater in experimentally infected chickens are referred to as HPAI. A virus that is highly pathogenic in chickens may infect but result in a completely different disease and replication pattern in other host species. Outbreaks of HPAI have been relatively uncommon around the world in the last 50 years and have had limited spread within a country or region with one major exception, Asian lineage H5N1 that was first identified in 1996. This lineage of virus has spread to over 60 countries and has become endemic in poultry in at least four countries. AI virus also represents a public health threat, with some infected humans having severe disease and with a high case fatality rate. AI remains a difficult disease to control because of the highly infectious nature of the virus and the interface of domestic and wild animals. A better understanding of the disease and its transmission is important for control.
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Huang K, Bahl J, Fan XH, Vijaykrishna D, Cheung CL, Webby RJ, Webster RG, Chen H, Smith GJD, Peiris JSM, Guan Y. Establishment of an H6N2 influenza virus lineage in domestic ducks in southern China. J Virol 2010; 84:6978-86. [PMID: 20463062 PMCID: PMC2898240 DOI: 10.1128/jvi.00256-10] [Citation(s) in RCA: 75] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2010] [Accepted: 04/30/2010] [Indexed: 11/20/2022] Open
Abstract
Multiple reassortment events between different subtypes of endemic avian influenza viruses have increased the genomic diversity of influenza viruses circulating in poultry in southern China. Gene exchange from the natural gene pool to poultry has contributed to this increase in genetic diversity. However, the role of domestic ducks as an interface between the natural gene pool and terrestrial poultry in the influenza virus ecosystem has not been fully characterized. Here we phylogenetically and antigenically analyzed 170 H6 viruses isolated from domestic ducks from 2000 to 2005 in southern China, which contains the largest population of domestic ducks in the world. Three distinct hemagglutinin lineages were identified. Group I contained the majority of isolates with a single internal gene complex and was endemic in domestic ducks in Guangdong from the late 1990s onward. Group II was derived from reassortment events in which the surface genes of group I viruses were replaced with novel H6 and N2 genes. Group III represented H6 viruses that undergo frequent reassortment with multiple virus subtypes from the natural gene pool. Surprisingly, H6 viruses endemic in domestic ducks and terrestrial poultry seldom reassort, but gene exchanges between viruses from domestic ducks and migratory ducks occurred throughout the surveillance period. These findings suggest that domestic ducks in southern China mediate the interaction of viruses between different gene pools and facilitate the generation of novel influenza virus variants circulating in poultry.
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Affiliation(s)
- K. Huang
- International Institute of Infection and Immunity, Shantou University Medical College, Shantou 515031, Guangdong, China, State Key Laboratory of Emerging Infectious Diseases and Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, 21 Sassoon Road, Pok Fu Lam, Hong Kong SAR, China, Division of Virology, Department of Infectious Diseases, St. Jude Children's Research Hospital, 332 North Lauderdale Street, Memphis, Tennessee 38105-2794
| | - J. Bahl
- International Institute of Infection and Immunity, Shantou University Medical College, Shantou 515031, Guangdong, China, State Key Laboratory of Emerging Infectious Diseases and Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, 21 Sassoon Road, Pok Fu Lam, Hong Kong SAR, China, Division of Virology, Department of Infectious Diseases, St. Jude Children's Research Hospital, 332 North Lauderdale Street, Memphis, Tennessee 38105-2794
| | - X. H. Fan
- International Institute of Infection and Immunity, Shantou University Medical College, Shantou 515031, Guangdong, China, State Key Laboratory of Emerging Infectious Diseases and Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, 21 Sassoon Road, Pok Fu Lam, Hong Kong SAR, China, Division of Virology, Department of Infectious Diseases, St. Jude Children's Research Hospital, 332 North Lauderdale Street, Memphis, Tennessee 38105-2794
| | - D. Vijaykrishna
- International Institute of Infection and Immunity, Shantou University Medical College, Shantou 515031, Guangdong, China, State Key Laboratory of Emerging Infectious Diseases and Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, 21 Sassoon Road, Pok Fu Lam, Hong Kong SAR, China, Division of Virology, Department of Infectious Diseases, St. Jude Children's Research Hospital, 332 North Lauderdale Street, Memphis, Tennessee 38105-2794
| | - C. L. Cheung
- International Institute of Infection and Immunity, Shantou University Medical College, Shantou 515031, Guangdong, China, State Key Laboratory of Emerging Infectious Diseases and Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, 21 Sassoon Road, Pok Fu Lam, Hong Kong SAR, China, Division of Virology, Department of Infectious Diseases, St. Jude Children's Research Hospital, 332 North Lauderdale Street, Memphis, Tennessee 38105-2794
| | - R. J. Webby
- International Institute of Infection and Immunity, Shantou University Medical College, Shantou 515031, Guangdong, China, State Key Laboratory of Emerging Infectious Diseases and Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, 21 Sassoon Road, Pok Fu Lam, Hong Kong SAR, China, Division of Virology, Department of Infectious Diseases, St. Jude Children's Research Hospital, 332 North Lauderdale Street, Memphis, Tennessee 38105-2794
| | - R. G. Webster
- International Institute of Infection and Immunity, Shantou University Medical College, Shantou 515031, Guangdong, China, State Key Laboratory of Emerging Infectious Diseases and Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, 21 Sassoon Road, Pok Fu Lam, Hong Kong SAR, China, Division of Virology, Department of Infectious Diseases, St. Jude Children's Research Hospital, 332 North Lauderdale Street, Memphis, Tennessee 38105-2794
| | - H. Chen
- International Institute of Infection and Immunity, Shantou University Medical College, Shantou 515031, Guangdong, China, State Key Laboratory of Emerging Infectious Diseases and Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, 21 Sassoon Road, Pok Fu Lam, Hong Kong SAR, China, Division of Virology, Department of Infectious Diseases, St. Jude Children's Research Hospital, 332 North Lauderdale Street, Memphis, Tennessee 38105-2794
| | - Gavin J. D. Smith
- International Institute of Infection and Immunity, Shantou University Medical College, Shantou 515031, Guangdong, China, State Key Laboratory of Emerging Infectious Diseases and Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, 21 Sassoon Road, Pok Fu Lam, Hong Kong SAR, China, Division of Virology, Department of Infectious Diseases, St. Jude Children's Research Hospital, 332 North Lauderdale Street, Memphis, Tennessee 38105-2794
| | - J. S. M. Peiris
- International Institute of Infection and Immunity, Shantou University Medical College, Shantou 515031, Guangdong, China, State Key Laboratory of Emerging Infectious Diseases and Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, 21 Sassoon Road, Pok Fu Lam, Hong Kong SAR, China, Division of Virology, Department of Infectious Diseases, St. Jude Children's Research Hospital, 332 North Lauderdale Street, Memphis, Tennessee 38105-2794
| | - Y. Guan
- International Institute of Infection and Immunity, Shantou University Medical College, Shantou 515031, Guangdong, China, State Key Laboratory of Emerging Infectious Diseases and Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, 21 Sassoon Road, Pok Fu Lam, Hong Kong SAR, China, Division of Virology, Department of Infectious Diseases, St. Jude Children's Research Hospital, 332 North Lauderdale Street, Memphis, Tennessee 38105-2794
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Sánchez-Vizcaíno F, Perez A, Lainez M, Sánchez-Vizcaíno JM. A quantitative assessment of the risk for highly pathogenic avian influenza introduction into Spain via legal trade of live poultry. RISK ANALYSIS : AN OFFICIAL PUBLICATION OF THE SOCIETY FOR RISK ANALYSIS 2010; 30:798-807. [PMID: 20136740 DOI: 10.1111/j.1539-6924.2009.01351.x] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
Highly pathogenic avian influenza (HPAI) is considered one of the most important diseases of poultry. During the last 9 years, HPAI epidemics have been reported in Asia, the Americas, Africa, and in 18 countries of the European Union (EU). For that reason, it is possible that the risk for HPAI virus (HPAIV) introduction into Spain may have recently increased. Because of the EU free-trade policy and because legal trade of live poultry was considered an important route for HPAI spread in certain regions of the world, there are fears that Spain may become HPAIV-infected as a consequence of the legal introduction of live poultry. However, no quantitative assessment of the risk for HPAIV introduction into Spain or into any other EU member state via the trade of poultry has been published in the peer-reviewed literature. This article presents the results of the first quantitative assessment of the risk for HPAIV introduction into a free country via legal trade of live poultry, along with estimates of the geographical variation of the risk and of the relative contribution of exporting countries and susceptible poultry species to the risk. The annual mean risk for HPAI introduction into Spain was estimated to be as low as 1.36 x 10(-3), suggesting that under prevailing conditions, introduction of HPAIV into Spain through the trade of live poultry is unlikely to occur. Moreover, these results support the hypothesis that legal trade of live poultry does not impose a significant risk for the spread of HPAI into EU member states.
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Affiliation(s)
- Fernando Sánchez-Vizcaíno
- Centro de Tecnología Animal, Instituto Valenciano de Investigaciones Agrarias, Segorbe, Castellón, Spain.
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Soares Magalhães RJ, Ortiz-Pelaez A, Thi KLL, Dinh QH, Otte J, Pfeiffer DU. Associations between attributes of live poultry trade and HPAI H5N1 outbreaks: a descriptive and network analysis study in northern Vietnam. BMC Vet Res 2010; 6:10. [PMID: 20175881 PMCID: PMC2837645 DOI: 10.1186/1746-6148-6-10] [Citation(s) in RCA: 54] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2009] [Accepted: 02/22/2010] [Indexed: 11/10/2022] Open
Abstract
Background The structure of contact between individuals plays an important role in the incursion and spread of contagious diseases in both human and animal populations. In the case of avian influenza, the movement of live birds is a well known risk factor for the geographic dissemination of the virus among poultry flocks. Live bird markets (LBM's) contribute to the epidemiology of avian influenza due to their demographic characteristics and the presence of HPAI H5N1 virus lineages. The relationship between poultry producers and live poultry traders (LPT's) that operate in LBM's has not been adequately documented in HPAI H5N1-affected SE Asian countries. The aims of this study were to document and study the flow of live poultry in a poultry trade network in northern Vietnam, and explore its potential role in the risk for HPAI H5N1 during 2003 to 2006. Results Our results indicate that LPT's trading for less than a year and operating at retail markets are more likely to source poultry from flocks located in communes with a past history of HPAI H5N1 outbreaks during 2003 to 2006 than LPT's trading longer than a year and operating at wholesale markets. The results of the network analysis indicate that LPT's tend to link communes of similar infection status. Conclusions Our study provides evidence which can be used for informing policies aimed at encouraging more biosecure practices of LPT's operating at authorised LBM's. The results suggest that LPT's play a role in HPAI H5N1 transmission and may contribute to perpetuating HPAI H5N1 virus circulation amongst certain groups of communes. The impact of current disease prevention and control interventions could be enhanced by disseminating information about outbreak risk and the implementation of a formal data recording scheme at LBM's for all incoming and outgoing LPT's.
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Affiliation(s)
- Ricardo J Soares Magalhães
- Royal Veterinary College, Veterinary Epidemiology & Public Health Group, Dpt Veterinary Clinical Sciences, Hawkshead Lane, North Mymms, Hatfield, Herts AL9 7TA, UK.
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Hovmöller R, Alexandrov B, Hardman J, Janies D. Tracking the geographical spread of avian influenza (H5N1) with multiple phylogenetic trees. Cladistics 2010; 26:1-13. [DOI: 10.1111/j.1096-0031.2009.00297.x] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022] Open
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Spatiotemporal structure of molecular evolution of H5N1 highly pathogenic avian influenza viruses in Vietnam. PLoS One 2010; 5:e8631. [PMID: 20072619 PMCID: PMC2799669 DOI: 10.1371/journal.pone.0008631] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2009] [Accepted: 12/03/2009] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND Vietnam is one of the countries most affected by outbreaks of H5N1 highly pathogenic avian influenza viruses. First identified in Vietnam in poultry in 2001 and in humans in 2004, the virus has since caused 111 cases and 56 deaths in humans. In 2003/2004 H5N1 outbreaks, nearly the entire poultry population of Vietnam was culled. Our earlier study (Wan et al., 2008, PLoS ONE, 3(10): e3462) demonstrated that there have been at least six independent H5N1 introductions into Vietnam and there were nine newly emerged reassortants from 2001 to 2007 in Vietnam. H5N1 viruses in Vietnam cluster distinctly around Hanoi and Ho Chi Minh City. However, the nature of the relationship between genetic divergence and geographic patterns is still unclear. METHODOLOGY/PRINCIPAL FINDINGS In this study, we hypothesized that genetic distances between H5N1 viruses in Vietnam are correlated with geographic distances, as the result of distinct population and environment patterns along Vietnam's long north to south longitudinal extent. Based on this hypothesis, we combined spatial statistical methods with genetic analytic techniques and explicitly used geographic space to explore genetic evolution of H5N1 highly pathogenic avian influenza viruses at the sub-national scale in Vietnam. Our dataset consisted of 125 influenza viruses (with whole genome sets) isolated in Vietnam from 2003 to 2007. Our results document the significant effect of space and time on genetic evolution and the rise of two regional centers of genetic mixing by 2007. These findings give insight into processes underlying viral evolution and suggest that genetic differentiation is associated with the distance between concentrations of human and poultry populations around Hanoi and Ho Chi Minh City. CONCLUSIONS/SIGNIFICANCE The results show that genetic evolution of H5N1 viruses in Vietnamese domestic poultry is highly correlated with the location and spread of those viruses in geographic space. This correlation varies by scale, time, and gene, though a classic isolation by distance pattern is observed. This study is the first to characterize the geographic structure of influenza viral evolution at the sub-national scale in Vietnam and can shed light on how H5N1 HPAIVs evolve in certain geographic settings.
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Ma Y, Feng Y, Liu D, Gao GF. Avian influenza virus, Streptococcus suis serotype 2, severe acute respiratory syndrome-coronavirus and beyond: molecular epidemiology, ecology and the situation in China. Philos Trans R Soc Lond B Biol Sci 2009; 364:2725-37. [PMID: 19687041 PMCID: PMC2865088 DOI: 10.1098/rstb.2009.0093] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
The outbreak and spread of severe acute respiratory syndrome-associated coronavirus and the subsequent identification of its animal origin study have heightened the world's awareness of animal-borne or zoonotic pathogens. In addition to SARS, the highly pathogenic avian influenza virus (AIV), H5N1, and the lower pathogenicity H9N2 AIV have expanded their host ranges to infect human beings and other mammalian species as well as birds. Even the ‘well-known’ reservoir animals for influenza virus, migratory birds, became victims of the highly pathogenic H5N1 virus. Not only the viruses, but bacteria can also expand their host range: a new disease, streptococcal toxic shock syndrome, caused by human Streptococcus suis serotype 2 infection, has been observed in China with 52 human fatalities in two separate outbreaks (1998 and 2005, respectively). Additionally, enterohaemorrhagic Escherichia coli O157:H7 infection has increased worldwide with severe disease. Several outbreaks and sporadic isolations of this pathogen in China have made it an important target for disease control. A new highly pathogenic variant of porcine reproductive and respiratory syndrome virus (PRRSV) has been isolated in both China and Vietnam recently; although PRRSV is not a zoonotic human pathogen, its severe outbreaks have implications for food safety. All of these pathogens occur in Southeast Asia, including China, with severe consequences; therefore, we discuss the issues in this article by addressing the situation of the zoonotic threat in China.
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Affiliation(s)
- Ying Ma
- CAS Key Laboratory of Pathogenic Microbiology and Immunology (CASPMI), Institute of Microbiology, Chinese Academy of Sciences (CAS), Beijing 100101, The People's Republic of China
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50
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Neumann G, Chen H, Gao GF, Shu Y, Kawaoka Y. H5N1 influenza viruses: outbreaks and biological properties. Cell Res 2009; 20:51-61. [PMID: 19884910 DOI: 10.1038/cr.2009.124] [Citation(s) in RCA: 153] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
All known subtypes of influenza A viruses are maintained in wild waterfowl, the natural reservoir of these viruses. Influenza A viruses are isolated from a variety of animal species with varying morbidity and mortality rates. More importantly, influenza A viruses cause respiratory disease in humans with potentially fatal outcome. Local or global outbreaks in humans are typically characterized by excess hospitalizations and deaths. In 1997, highly pathogenic avian influenza viruses of the H5N1 subtype emerged in Hong Kong that transmitted to humans, resulting in the first documented cases of human death by avian influenza virus infection. A new outbreak started in July 2003 in poultry in Vietnam, Indonesia, and Thailand, and highly pathogenic avian H5N1 influenza viruses have since spread throughout Asia and into Europe and Africa. These viruses continue to infect humans with a high mortality rate and cause worldwide concern of a looming pandemic. Moreover, H5N1 virus outbreaks have had devastating effects on the poultry industries throughout Asia. Since H5N1 virus outbreaks appear to originate from Southern China, we here examine H5N1 influenza viruses in China, with an emphasis on their biological properties.
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Affiliation(s)
- Gabriele Neumann
- Department of Pathological Sciences, School of Veterinary Medicine, University of Wisconsin-Madison, Madison, WI 53711, USA
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