14 results on '"Gilbert, Marius"'
Search Results
2. Combined Phylogeographic Analyses and Epidemiologic Contact Tracing to Characterize Atypically Pathogenic Avian Influenza (H3N1) Epidemic, Belgium, 2019.
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Van Borm, Steven, Boseret, Géraldine, Dellicour, Simon, Steensels, Mieke, Roupie, Virginie, Vandenbussche, Frank, Mathijs, Elisabeth, Vilain, Aline, Driesen, Michèle, Dispas, Marc, Delcloo, Andy W., Lemey, Philippe, Mertens, Ingeborg, Gilbert, Marius, Lambrecht, Bénédicte, and van den Berg, Thierry
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AVIAN influenza ,CONTACT tracing ,EPIDEMICS ,VIRAL genomes ,GENOMICS - Abstract
The high economic impact and zoonotic potential of avian influenza call for detailed investigations of dispersal dynamics of epidemics. We integrated phylogeographic and epidemiologic analyses to investigate the dynamics of a low pathogenicity avian influenza (H3N1) epidemic that occurred in Belgium during 2019. Virus genomes from 104 clinical samples originating from 85% of affected farms were sequenced. A spatially explicit phylogeographic analysis confirmed a dominating northeast to southwest dispersal direction and a long-distance dispersal event linked to direct live animal transportation between farms. Spatiotemporal clustering, transport, and social contacts strongly correlated with the phylogeographic pattern of the epidemic. We detected only a limited association between wind direction and direction of viral lineage dispersal. Our results highlight the multifactorial nature of avian influenza epidemics and illustrate the use of genomic analyses of virus dispersal to complement epidemiologic and environmental data, improve knowledge of avian influenza epidemiologic dynamics, and enhance control strategies. [ABSTRACT FROM AUTHOR]
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- 2023
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3. Wild waterfowl migration and domestic duck density shape the epidemiology of highly pathogenic H5N8 influenza in the Republic of Korea
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Hill, Sarah Catherine, Lee, Youn Jeong, Song, Byung Min, Kang, Hyun Mi, Lee, Eun Kyoung, Hanna, Amanda, Brown, Ian H., Gilbert, Marius, and Pybus, Oliver George
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Microbiology (medical) ,Genes, Viral ,ROK, Republic of Korea ,Avian influenza ,Microbiology ,Article ,Disease Outbreaks ,H5N8 ,Republic of Korea ,Genetics ,Animals ,Molecular Biology ,Phylogeny ,Poultry Diseases ,Ecology, Evolution, Behavior and Systematics ,Korea ,Ecology ,Sequence Analysis, DNA ,Sciences bio-médicales et agricoles ,Molecular Typing ,Phylogenetics ,Phylogeography ,Ducks ,Infectious Diseases ,Influenza A virus ,Influenza in Birds ,Animal Migration - Abstract
Highly pathogenic avian influenza (HPAI) viruses threaten human and animal health yet their emergence is poorly understood, partly because sampling of the HPAI Asian-origin H5N1 lineage immediately after its identification in 1996 was comparatively sparse. The discovery of a novel H5N8 virus in 2013 provides a new opportunity to investigate HPAI emergence in greater detail. Here we investigate the origin and transmission of H5N8 in the Republic of Korea, the second country to report the new strain. We reconstruct viral spread using phylogeographic methods and interpret the results in the context of ecological data on poultry density, overwintering wild bird numbers, and bird migration patterns. Our results indicate that wild waterfowl migration and domestic duck density were important to H5N8 epidemiology. Specifically, we infer that H5N8 entered the Republic of Korea via Jeonbuk province, then spread rapidly among western provinces where densities of overwintering waterfowl and domestic ducks are higher, yet rarely persisted in eastern regions. The common ancestor of H5N8 in the Republic of Korea was estimated to have arrived during the peak of inward migration of overwintering birds. Recent virus isolations likely represent re-introductions via bird migration from an as-yet unsampled reservoir. Based on the limited data from outside the Republic of Korea, our data suggest that H5N8 may have entered Europe at least twice, and Asia at least three times from this reservoir, most likely carried by wild migrating birds., SCOPUS: ar.j, info:eu-repo/semantics/published
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- 2015
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4. Effectiveness of Live Poultry Market Interventions on Human Infection with Avian Influenza A(H7N9) Virus, China.
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Wei Wang, Artois, Jean, Xiling Wang, Kucharski, Adam J., Yao Pei, Xin Tong, Virlogeux, Victor, Peng Wu, Cowling, Benjamin J., Gilbert, Marius, Hongjie Yu, Wang, Wei, Wang, Xiling, Pei, Yao, Tong, Xin, Wu, Peng, and Yu, Hongjie
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AVIAN influenza prevention ,AVIAN influenza epidemiology ,INFLUENZA prevention ,INFLUENZA epidemiology ,RESEARCH ,INFLUENZA A virus ,POULTRY ,ANIMAL experimentation ,RESEARCH methodology ,MEDICAL cooperation ,EVALUATION research ,COMPARATIVE studies - Abstract
Various interventions for live poultry markets (LPMs) have emerged to control outbreaks of avian influenza A(H7N9) virus in mainland China since March 2013. We assessed the effectiveness of various LPM interventions in reducing transmission of H7N9 virus across 5 annual waves during 2013-2018, especially in the final wave. With the exception of waves 1 and 4, various LPM interventions reduced daily incidence rates significantly across waves. Four LPM interventions led to a mean reduction of 34%-98% in the daily number of infections in wave 5. Of these, permanent closure provided the most effective reduction in human infection with H7N9 virus, followed by long-period, short-period, and recursive closures in wave 5. The effectiveness of various LPM interventions changed with the type of intervention across epidemics. Permanent LPM closure should be considered to maintain sufficient effectiveness of interventions and prevent the recurrence of H7N9 epidemics. [ABSTRACT FROM AUTHOR]
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- 2020
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5. Incorporating heterogeneous sampling probabilities in continuous phylogeographic inference — Application to H5N1 spread in the Mekong region.
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Dellicour, Simon, Lemey, Philippe, Artois, Jean, Lam, Tommy T, Fusaro, Alice, Monne, Isabella, Cattoli, Giovanni, Kuznetsov, Dmitry, Xenarios, Ioannis, Dauphin, Gwenaelle, Kalpravidh, Wantanee, Dobschuetz, Sophie Von, Claes, Filip, Newman, Scott H, Suchard, Marc A, Baele, Guy, and Gilbert, Marius
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INFLUENZA A virus, H5N1 subtype ,AVIAN influenza ,PROBABILITY theory - Abstract
Motivation The potentially low precision associated with the geographic origin of sampled sequences represents an important limitation for spatially explicit (i.e. continuous) phylogeographic inference of fast-evolving pathogens such as RNA viruses. A substantial proportion of publicly available sequences is geo-referenced at broad spatial scale such as the administrative unit of origin, rather than more precise locations (e.g. geographic coordinates). Most frequently, such sequences are either discarded prior to continuous phylogeographic inference or arbitrarily assigned to the geographic coordinates of the centroid of their administrative area of origin for lack of a better alternative. Results We here implement and describe a new approach that allows to incorporate heterogeneous prior sampling probabilities over a geographic area. External data, such as outbreak locations, are used to specify these prior sampling probabilities over a collection of sub-polygons. We apply this new method to the analysis of highly pathogenic avian influenza H5N1 clade data in the Mekong region. Our method allows to properly include, in continuous phylogeographic analyses, H5N1 sequences that are only associated with large administrative areas of origin and assign them with more accurate locations. Finally, we use continuous phylogeographic reconstructions to analyse the dispersal dynamics of different H5N1 clades and investigate the impact of environmental factors on lineage dispersal velocities. Availability and implementation Our new method allowing heterogeneous sampling priors for continuous phylogeographic inference is implemented in the open-source multi-platform software package BEAST 1.10. Supplementary information Supplementary data are available at Bioinformatics online. [ABSTRACT FROM AUTHOR]
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- 2020
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6. Contrasting effects of host species and phylogenetic diversity on the occurrence of HPAI H5N1 in European wild birds.
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Huang, Zheng Y. X., Xu, Chi, van Langevelde, Frank, Ma, Yuying, Langendoen, Tom, Mundkur, Taej, Si, Yali, Tian, Huaiyu, Kraus, Robert H. S., Gilbert, Marius, Han, Guan‐Zhu, Ji, Xiang, Prins, Herbert H. T., de Boer, Willem F., and Dunn, Jenny
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H5N1 Influenza ,BIRDS ,SPECIES diversity ,WATER birds ,AVIAN influenza ,CONTRAST effect ,HOST specificity (Biology) - Abstract
Studies on the highly pathogenic avian influenza (HPAI) H5N1 suggest that wild bird migration may facilitate its long‐distance spread, yet the role of wild bird community composition in its transmission risk remains poorly understood. Furthermore, most studies on the diversity–disease relationship focused on host species diversity without considering hosts' phylogenetic relationships, which may lead to rejecting a species diversity effect when the community has host species that are only distantly related.Here, we explored the influence of waterbird community composition for determining HPAI H5N1 occurrence in wild birds in a continental‐scale study across Europe. In particular, we tested the diversity–disease relationship using both host species diversity and host phylogenetic diversity.Our results provide the first demonstration that host community composition—compared with previously identified environmental risk factors—can also effectively explain the spatial pattern of H5N1 occurrence in wild birds. We further show that communities with more higher risk host species and more closely related species have a higher risk of H5N1 outbreaks. Thus, both host species diversity and community phylogenetic structure, in addition to environmental factors, jointly influence H5N1 occurrence.Our work not only extends the current theory on the diversity–disease relationship, but also has important implications for future monitoring of H5N1 and other HPAI subtypes. [ABSTRACT FROM AUTHOR]
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- 2019
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7. The impact of surveillance and control on highly pathogenic avian influenza outbreaks in poultry in Dhaka division, Bangladesh.
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Hill, Edward M., Tildesley, Michael J., Prosser, Diann J., Takekawa, John Y., Xiao, Xiangming, House, Thomas, Gilbert, Marius, Dhingra, Madhur S., Morzaria, Subhash, Kalpravidh, Wantanee, Osmani, Muzaffar G., Brum, Eric, Yamage, Mat, and Kalam, Md. A.
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ANIMAL health surveillance ,PREVENTIVE medicine ,PATHOGENIC viruses ,AVIAN influenza ,POULTRY diseases - Abstract
In Bangladesh, the poultry industry is an economically and socially important sector, but it is persistently threatened by the effects of H5N1 highly pathogenic avian influenza. Thus, identifying the optimal control policy in response to an emerging disease outbreak is a key challenge for policy-makers. To inform this aim, a common approach is to carry out simulation studies comparing plausible strategies, while accounting for known capacity restrictions. In this study we perform simulations of a previously developed H5N1 influenza transmission model framework, fitted to two separate historical outbreaks, to assess specific control objectives related to the burden or duration of H5N1 outbreaks among poultry farms in the Dhaka division of Bangladesh. In particular, we explore the optimal implementation of ring culling, ring vaccination and active surveillance measures when presuming disease transmission predominately occurs from premises-to-premises, versus a setting requiring the inclusion of external factors. Additionally, we determine the sensitivity of the management actions under consideration to differing levels of capacity constraints and outbreaks with disparate transmission dynamics. While we find that reactive culling and vaccination policies should pay close attention to these factors to ensure intervention targeting is optimised, across multiple settings the top performing control action amongst those under consideration were targeted proactive surveillance schemes. Our findings may advise the type of control measure, plus its intensity, that could potentially be applied in the event of a developing outbreak of H5N1 amongst originally H5N1 virus-free commercially-reared poultry in the Dhaka division of Bangladesh. [ABSTRACT FROM AUTHOR]
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- 2018
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8. Avian influenza A (H5N1) outbreaks in different poultry farm types in Egypt: the effect of vaccination, closing status and farm size.
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Artois, Jean, Ippoliti, Carla, Conte, Annamaria, Dhingra, Madhur S., Alfonso, Pastor, Tahawy, Abdelgawad El, Elbestawy, Ahmed, Ellakany, Hany F., and Gilbert, Marius
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AVIAN influenza A virus ,AVIAN influenza ,POULTRY farm management ,DISEASE outbreaks ,PUBLIC health - Abstract
Background: The Avian Influenza A (H5N1) virus is endemic in poultry in Egypt. The winter of 2014/2015 was particularly worrying as new clusters of HPAI A (H5N1) virus emerged, leading to an important number of AI A (H5N1) outbreaks in poultry farms and sporadic human cases. To date, few studies have investigated the distribution of HPAI A (H5N1) outbreaks in Egypt in relation to protective / risk factors at the farm level, a gap we intend to fill. The aim of the study was to analyse passive surveillance data that were based on observation of sudden and high mortality of poultry or drop in duck or chicken egg production, as a basis to better understand and discuss the risk of HPAI A (H5N1) presence at the farm level in large parts of the Nile Delta. Results: The probability of HPAI A (H5N1) presence was associated with several characteristics of the farms. Vaccination status, absence of windows/openings in the farm and the number of birds per cycle of production were found to be protective factors, whereas the presence of a duck farm with significant mortality or drop in egg production in the village was found to be a risk factor. Conclusions: Results demonstrate the key role of several prevention and biosecurity measures to reduce HPAI A (H5N1) virus circulation, which could promote better poultry farm biosecurity in Egypt. [ABSTRACT FROM AUTHOR]
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- 2018
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9. Dynamics of the 2004 avian influenza H5N1 outbreak in Thailand: The role of duck farming, sequential model fitting and control.
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Retkute, Renata, Jewell, Chris P., Van Boeckel, Thomas P., Zhang, Geli, Xiao, Xiangming, Thanapongtharm, Weerapong, Keeling, Matt, Gilbert, Marius, and Tildesley, Michael J.
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AVIAN influenza , *DUCK farming , *ZOONOSES , *PREVENTIVE medicine , *INFECTIOUS disease transmission - Abstract
Abstract The Highly Pathogenic Avian Influenza (HPAI) subtype H5N1 virus persists in many countries and has been circulating in poultry, wild birds. In addition, the virus has emerged in other species and frequent zoonotic spillover events indicate that there remains a significant risk to human health. It is crucial to understand the dynamics of the disease in the poultry industry to develop a more comprehensive knowledge of the risks of transmission and to establish a better distribution of resources when implementing control. In this paper, we develop a set of mathematical models that simulate the spread of HPAI H5N1 in the poultry industry in Thailand, utilising data from the 2004 epidemic. The model that incorporates the intensity of duck farming when assessing transmision risk provides the best fit to the spatiotemporal characteristics of the observed outbreak, implying that intensive duck farming drives transmission of HPAI in Thailand. We also extend our models using a sequential model fitting approach to explore the ability of the models to be used in "real time" during novel disease outbreaks. We conclude that, whilst predictions of epidemic size are estimated poorly in the early stages of disease outbreaks, the model can infer the preferred control policy that should be deployed to minimise the impact of the disease. [ABSTRACT FROM AUTHOR]
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- 2018
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10. Global mapping of highly pathogenic avian influenza H5N1 and H5Nx clade 2.3.4.4 viruses with spatial cross- validation.
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Dhingra, Madhur S., Artois, Jean, Robinson, Timothy P., Linard, Catherine, Chaiban, Celia, Xenarios, Ioannis, Engler, Robin, Liechti, Robin, Kuznetsov, Dmitri, Xiangming Xiao, Von Dobschuetz, Sophie, Claes, Filip, Newman, Scott H., Dauphin, Gwenaëlle, and Gilbert, Marius
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AVIAN influenza , *INFLUENZA viruses , *DISEASE mapping , *HOST-virus relationships , *VIRUS diseases in poultry - Abstract
Global disease suitability models are essential tools to inform surveillance systems and enable early detection. We present the first global suitability model of highly pathogenic avian influenza (HPAI) H5N1 and demonstrate that reliable predictions can be obtained at global scale. Best predictions are obtained using spatial predictor variables describing host distributions, rather than land use or eco-climatic spatial predictor variables, with a strong association with domestic duck and extensively raised chicken densities. Our results also support a more systematic use of spatial cross-validation in large-scale disease suitability modelling compared to standard random cross-validation that can lead to unreliable measure of extrapolation accuracy. A global suitability model of the H5 clade 2.3.4.4 viruses, a group of viruses that recently spread extensively in Asia and the US, shows in comparison a lower spatial extrapolation capacity than the HPAI H5N1 models, with a stronger association with intensively raised chicken densities and anthropogenic factors. [ABSTRACT FROM AUTHOR]
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- 2016
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11. The dawn of Structural One Health: A new science tracking disease emergence along circuits of capital.
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Wallace, Robert G., Bergmann, Luke, Kock, Richard, Gilbert, Marius, Hogerwerf, Lenny, Wallace, Rodrick, and Holmberg, Mollie
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AVIAN influenza prevention , *ANIMALS , *WORLD health - Abstract
The One Health approach integrates health investigations across the tree of life, including, but not limited to, wildlife, livestock, crops, and humans. It redresses an epistemological alienation at the heart of much modern population health, which has long segregated studies by species. Up to this point, however, One Health research has also omitted addressing fundamental structural causes underlying collapsing health ecologies. In this critical review we unpack the relationship between One Health science and its political economy, particularly the conceptual and methodological trajectories by which it fails to incorporate social determinants of epizootic spillover. We also introduce a Structural One Health that addresses the research gap. The new science, open to incorporating developments across the social sciences, addresses foundational processes underlying multispecies health, including the place-specific deep-time histories, cultural infrastructure, and economic geographies driving disease emergence. We introduce an ongoing project on avian influenza to illustrate Structural One Health's scope and ambition. For the first time researchers are quantifying the relationships among transnational circuits of capital, associated shifts in agroecological landscapes, and the genetic evolution and spatial spread of a xenospecific pathogen. [ABSTRACT FROM AUTHOR]
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- 2015
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12. Pathogens and parasites, species unlike others: The spatial distribution of avian influenzas in poultry
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Artois, Jean, Gilbert, Marius, Vereecken, Nicolas, Mardulyn, Patrick, Saegerman, Claude, and Morand, Serge
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Systèmes d'information géographique ,Aviculture ,Ecologie ,spatial epidemiology ,HPAI A (H5N1) ,avian influenza ,Epidémiologie ,Biologie spatiale ,Virologie générale ,species distribution models ,LPAI A (H7N9) - Abstract
What explains the geographic distribution of pathogens? Better understanding and characterising disease patterns will help scientists to identify areas likely to host future epidemics and epizootics and to prioritise surveillance and intervention. However, the use of disease surveillance data to assess the risk of transmission and generate risk maps raises conceptual and methodological issues. Indeed, pathogens and more particularly viruses aren't ”species” like others that live in the open environment and must be studied with methods and concepts of their own. Avian influenza (AI), a disease caused by a virus infecting bird populations, has been selected to study these issues. AI has a major economic impact on the poultry industry in many countries, raises concerns of livelihood in low and middle-income countries, and represents a major concern for human health. The aim of this PhD thesis was to improve the knowledge on the spatial epidemiology of AI in different settings and conditions (i). For this, recent epizootics caused by the subtypes A (H5N1) and A (H7N9) were selected as case studies. First, highly pathogenic subtypes of the A (H5N1) virus have been studied in poultry farms (ducks and chickens) at different spatial scales: at the continental scale and the regional scale in the Mekong (Cambodia, Laos, Vietnam, Thailand) and the Nile Delta in Egypt. All these cases occurred between 2003, the date on which the virus starts to spread outside China, and 2015; the HPAI A (H5N1) subtypes are still reported today in many countries. Human infections caused by the A (H7N9) virus in China from March 2013 to 2017 were also studied. Studied different AI subtypes at different spatial scales within different host species also allowed to develop a conceptual model of AI transmission and to discuss the issue of the transferability of results in epidemiology (ii). Lastly, this PhD thesis leads to a discussion about the transfer of methods and concepts from ecology to spatial epidemiology, with a particular emphasis on their possible limitations (iii)., Doctorat en Sciences agronomiques et ingénierie biologique, info:eu-repo/semantics/nonPublished
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- 2019
13. Global epidemiology of avian influenza A H5N1 virus infection in humans, 1997-2015: a systematic review of individual case data.
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Lai, Shengjie, Qin, Ying, Cowling, Benjamin J, Ren, Xiang, Wardrop, Nicola A, Gilbert, Marius, Tsang, Tim K, Wu, Peng, Feng, Luzhao, Jiang, Hui, Peng, Zhibin, Zheng, Jiandong, Liao, Qiaohong, Li, Sa, Horby, Peter W, Farrar, Jeremy J, Gao, George F, Tatem, Andrew J, and Yu, Hongjie
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H5N1 Influenza , *EPIDEMIOLOGY , *SYSTEMATIC reviews , *EPIDEMICS , *HOSPITAL admission & discharge , *AVIAN influenza , *AVIAN influenza epidemiology , *INFLUENZA epidemiology , *ANIMAL experimentation , *POULTRY , *RESEARCH funding , *WORLD health , *DISEASE incidence , *INFLUENZA A virus, H5N1 subtype , *INFECTIOUS disease transmission - Abstract
Avian influenza A H5N1 viruses have caused many, typically severe, human infections since the first human case was reported in 1997. However, no comprehensive epidemiological analysis of global human cases of H5N1 from 1997 to 2015 exists. Moreover, few studies have examined in detail the changing epidemiology of human H5N1 cases in Egypt, especially given the outbreaks since November, 2014, which have the highest number of cases ever reported worldwide in a similar period. Data on individual patients 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 483 (53·5%) of 903 cases which varied across geographical regions. Although the incidence in Egypt has increased dramatically since November, 2014, compared with the cases beforehand, there were no significant differences in the fatality risk, history of exposure to poultry, history of patient contact, and time from onset to hospital admission in the recent cases. [ABSTRACT FROM AUTHOR]
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- 2016
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14. Corrigendum to “Zero-inflated models for identifying disease risk factors when case detection is imperfect: Application to highly pathogenic avian influenza H5N1 in Thailand” [Prev. Vet. Med. 114 (2014) 28–36].
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Vergne, Timothée, Paul, Mathilde C., Chaengprachak, Wanida, Durand, Benoit, Gilbert, Marius, Dufour, Barbara, Roger, François, Kasemsuwan, Suwicha, and Grosbois, Vladimir
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PUBLISHED errata , *AVIAN influenza , *ZERO-inflated probability distribution , *H5N1 Influenza , *ANIMAL health - Published
- 2015
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