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Viau L, Azé J, Chen F, Pompidor P, Poncelet P, Raveneau V, Rodriguez N, Sallaberry A. Epid data explorer: A visualization tool for exploring and comparing spatio-temporal epidemiological data. Health Informatics J 2024; 30:14604582241279720. [PMID: 39224960 DOI: 10.1177/14604582241279720] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/04/2024]
Abstract
The analysis of large sets of spatio-temporal data is a fundamental challenge in epidemiological research. As the quantity and the complexity of such kind of data increases, automatic analysis approaches, such as statistics, data mining, machine learning, etc., can be used to extract useful information. While these approaches have proven effective, they require a priori knowledge of the information being sought, and some interesting insights into the data may be missed. To bridge this gap, information visualization offers a set of techniques for not only presenting known information, but also exploring data without having a hypothesis formulated beforehand. In this paper, we introduce Epid Data Explorer (EDE), a visualization tool that enables exploration of spatio-temporal epidemiological data. EDE allows easy comparisons of indicators and trends across different geographical areas and times. It facilitates this exploration through ready-to-use pre-loaded datasets as well as user-chosen datasets. The tool also provides a secure architecture for easily importing new datasets while ensuring confidentiality. In two use cases using data associated with the COVID-19 epidemic, we demonstrate the substantial impact of implemented lockdown measures on mobility and how EDE allows assessing correlations between the spread of COVID-19 and weather conditions.
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Affiliation(s)
| | - Jérôme Azé
- LIRMM, Université de Montpellier, CNRS, France
| | - Fati Chen
- LIRMM, Université de Montpellier, CNRS, France
| | | | | | | | | | - Arnaud Sallaberry
- LIRMM, Université de Montpellier, CNRS, France
- AMIS, Université Paul-Valéry Montpellier 3, France
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Di Lorenzo A, Mangone I, Colangeli P, Cioci D, Curini V, Vincifori G, Mercante MT, Di Pasquale A, Iannetti S. One health system supporting surveillance during COVID-19 epidemic in Abruzzo region, southern Italy. One Health 2023; 16:100471. [PMID: 36507072 PMCID: PMC9726647 DOI: 10.1016/j.onehlt.2022.100471] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2022] [Revised: 12/06/2022] [Accepted: 12/06/2022] [Indexed: 12/12/2022] Open
Abstract
The Istituti Zooprofilattici Sperimentali (IZSs) are public health institutes dealing with the aetiology and pathogenesis of infectious diseases of domestic and wild animals. During Coronavirus Disease 2019 epidemic, the Italian Ministry of Health appointed the IZSs to carry out diagnostic tests for the detection of SARS-CoV-2 in human samples. In particular, the IZS of Abruzzo and Molise (IZS-Teramo) was involved in the diagnosis of SARS-CoV-2 through testing nasopharyngeal swabs by Real Time RT-PCR. Activities and infrastructures were reorganised to the new priorities, in a "One Health" framework, based on interdisciplinary, laboratory promptness, accreditation of the test for the detection of the RNA of SARS-CoV-2 in human samples, and management of confidentiality of sensitive data. The laboratory information system - SILAB - was implemented with a One Health module for managing data of human origin, with tools for the automatic registration of information improving the quality of the data. Moreover, the "National Reference Centre for Whole Genome Sequencing of microbial pathogens - database and bioinformatics analysis" - GENPAT - formally established at the IZS-Teramo, developed bioinformatics workflows and IT dashboard with ad hoc surveillance tools to support the metagenomics-based SARS-CoV-2 surveillance, providing molecular sequencing analysis to quickly intercept the variants circulating in the area. This manuscript describes the One Health system developed by adapting and integrating both SILAB and GENPAT tools for supporting surveillance during COVID-19 epidemic in the Abruzzo region, southern Italy. The developed dashboard permits the health authorities to observe the SARS-CoV-2 spread in the region, and by combining spatio-temporal information with metagenomics provides early evidence for the identification of emerging space-time clusters of variants at the municipality level. The implementation of the One Health module was designed to be easily modelled and adapted for the management of other diseases and future hypothetical events of pandemic nature.
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Huang J, Li K, Xiao S, Hu J, Yin Y, Zhang J, Li S, Wang W, Hong J, Zhao Z, Chen X, Liu Y, Shi J, Hu F, Ran X, Ge Y, Jiang H, Liu Z, Ward MP, Zhang Z. Global epidemiology of animal influenza infections with explicit virus subtypes until 2016: A spatio-temporal descriptive analysis. One Health 2023. [DOI: 10.1016/j.onehlt.2023.100514] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/22/2023] Open
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Tiwari S, Dhakal T, Kim TS, Lee DH, Jang GS, Oh Y. Climate Change Influences the Spread of African Swine Fever Virus. Vet Sci 2022; 9:606. [PMID: 36356083 PMCID: PMC9698898 DOI: 10.3390/vetsci9110606] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2022] [Revised: 10/28/2022] [Accepted: 10/30/2022] [Indexed: 08/26/2023] Open
Abstract
Climate change is an inevitable and urgent issue in the current world. African swine fever virus (ASFV) is a re-emerging viral animal disease. This study investigates the quantitative association between climate change and the potential spread of ASFV to a global extent. ASFV in wild boar outbreak locations recorded from 1 January 2019 to 29 July 2022 were sampled and investigated using the ecological distribution tool, the Maxent model, with WorldClim bioclimatic data as the predictor variables. The future impacts of climate change on ASFV distribution based on the model were scoped with Representative Concentration Pathways (RCP 2.6, 4.5, 6.0, and 8.5) scenarios of Coupled Model Intercomparison Project 5 (CMIP5) bioclimatic data for 2050 and 2070. The results show that precipitation of the driest month (Bio14) was the highest contributor, and annual mean temperature (Bio1) was obtained as the highest permutation importance variable on the spread of ASFV. Based on the analyzed scenarios, we found that the future climate is favourable for ASFV disease; only quantitative ratios are different and directly associated with climate change. The current study could be a reference material for wildlife health management, climate change issues, and World Health Organization sustainability goal 13: climate action.
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Affiliation(s)
- Shraddha Tiwari
- Department of Veterinary Pathology, College of Veterinary Medicine and Institute of Veterinary Science, Kangwon National University, Chuncheon 24341, Korea
| | - Thakur Dhakal
- Department of Life Science, Yeungnam University, Daegu 38541, Korea
| | - Tae-Su Kim
- Department of Life Science, Yeungnam University, Daegu 38541, Korea
| | - Do-Hun Lee
- National Institute of Ecology (NIE), Seocheon 33657, Korea
| | - Gab-Sue Jang
- Department of Life Science, Yeungnam University, Daegu 38541, Korea
| | - Yeonsu Oh
- Department of Veterinary Pathology, College of Veterinary Medicine and Institute of Veterinary Science, Kangwon National University, Chuncheon 24341, Korea
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Matthews C, Cotter PD, O’ Mahony J. MAP, Johne's disease and the microbiome; current knowledge and future considerations. Anim Microbiome 2021; 3:34. [PMID: 33962690 PMCID: PMC8105914 DOI: 10.1186/s42523-021-00089-1] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2020] [Accepted: 03/20/2021] [Indexed: 12/17/2022] Open
Abstract
Mycobacterium avium subsp. paratuberculosis is the causative agent of Johne's disease in ruminants. As an infectious disease that causes reduced milk yields, effects fertility and, eventually, the loss of the animal, it is a huge financial burden for associated industries. Efforts to control MAP infection and Johne's disease are complicated due to difficulties of diagnosis in the early stages of infection and challenges relating to the specificity and sensitivity of current testing methods. The methods that are available contribute to widely used test and cull strategies, vaccination programmes also in place in some countries. Next generation sequencing technologies have opened up new avenues for the discovery of novel biomarkers for disease prediction within MAP genomes and within ruminant microbiomes. Controlling Johne's disease in herds can lead to improved animal health and welfare, in turn leading to increased productivity. With current climate change bills, such as the European Green Deal, targeting livestock production systems for more sustainable practices, managing animal health is now more important than ever before. This review provides an overview of the current knowledge on genomics and detection of MAP as it pertains to Johne's disease.
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Affiliation(s)
- Chloe Matthews
- Cork Institute of Technology, Bishopstown, Co. Cork, Ireland
- Teagasc, Food Research Centre, Food Biosciences Department, Fermoy, Co. Cork, Ireland
| | - Paul D. Cotter
- Teagasc, Food Research Centre, Food Biosciences Department, Fermoy, Co. Cork, Ireland
- APC Microbiome Institute, University College Cork, Co. Cork, Ireland
| | - Jim O’ Mahony
- Cork Institute of Technology, Bishopstown, Co. Cork, Ireland
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Phadke S, Macherla S, Scheuermann RH. Database and Analytical Resources for Viral Research Community. ENCYCLOPEDIA OF VIROLOGY 2021. [PMCID: PMC7173540 DOI: 10.1016/b978-0-12-809633-8.20995-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Many public databases and analytical resources are available to facilitate virology research. The Virus Pathogen Database and Analysis Resource (ViPR, see “Relevant Websites section”) and Influenza Research Database (IRD, see “Relevant Websites section”) are comprehensive and highly curated repositories of genome and protein sequence records and annotations, protein structures, immune epitopes, and epidemiological and surveillance data about human and related viral pathogens. These data are acquired from public repositories, direct submissions and in-house bioinformatics analyses. The resources offer seamless integration of data, analytics and visualization, and are freely available without cost or restriction to facilitate diagnostics and therapeutics development for priority pathogens.
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Li X, Li X, Xu B. Phylogeography of Highly Pathogenic H5 Avian Influenza Viruses in China. Virol Sin 2020; 35:548-555. [DOI: 10.1007/s12250-020-00193-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2019] [Accepted: 12/17/2019] [Indexed: 12/09/2022] Open
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Dellicour S, Lemey P, Artois J, Lam TT, Fusaro A, Monne I, Cattoli G, Kuznetsov D, Xenarios I, Dauphin G, Kalpravidh W, Von Dobschuetz S, Claes F, Newman SH, Suchard MA, Baele G, Gilbert M. Incorporating heterogeneous sampling probabilities in continuous phylogeographic inference - Application to H5N1 spread in the Mekong region. Bioinformatics 2020; 36:2098-2104. [PMID: 31790143 DOI: 10.1093/bioinformatics/btz882] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2019] [Revised: 11/01/2019] [Accepted: 11/22/2019] [Indexed: 12/25/2022] Open
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.
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Affiliation(s)
- Simon Dellicour
- Department of Microbiology, Immunology and Transplantation, Rega Institute, KU Leuven, 3000 Leuven, Belgium.,Spatial Epidemiology Lab (SpELL), Université Libre de Bruxelles, 1050 Bruxelles, Belgium
| | - Philippe Lemey
- Department of Microbiology, Immunology and Transplantation, Rega Institute, KU Leuven, 3000 Leuven, Belgium
| | - Jean Artois
- Spatial Epidemiology Lab (SpELL), Université Libre de Bruxelles, 1050 Bruxelles, Belgium
| | - Tommy T Lam
- State Key Laboratory of Emerging Infectious Diseases, School of Public Health, The University of Hong Kong, Hong Kong SAR, China
| | - Alice Fusaro
- Department of Comparative Biomedical Sciences, Istituto Zooprofilattico Sperimentale delle Venezie (IZSVe), Legnaro, Italy
| | - Isabella Monne
- Department of Comparative Biomedical Sciences, Istituto Zooprofilattico Sperimentale delle Venezie (IZSVe), Legnaro, Italy
| | - Giovanni Cattoli
- Department of Comparative Biomedical Sciences, Istituto Zooprofilattico Sperimentale delle Venezie (IZSVe), Legnaro, Italy.,Animal Production and Health Laboratory, Joint FAO/IAEA Division, 2444 Seibersdorf, Austria
| | | | - Ioannis Xenarios
- Center for Integrative Genomics, University of Lausanne, 1005 Lausanne, Switzerland
| | | | - Wantanee Kalpravidh
- Food and Agriculture Organization of the United Nations, Regional Office for Asia and the Pacific, Emergency Center of the Transboundary Animal Diseases, Bangkok 10200, Thailand
| | | | - Filip Claes
- Food and Agriculture Organization of the United Nations, Regional Office for Asia and the Pacific, Emergency Center of the Transboundary Animal Diseases, Bangkok 10200, Thailand
| | - Scott H Newman
- Food and Agriculture Organization of the United Nations, Regional Office for Africa, Accra, Ghana
| | - Marc A Suchard
- Department of Biomathematics, David Geffen School of Medicine, Los Angeles, CA, USA.,Department of Biostatistics, Fielding School of Public Health, Los Angeles, CA, USA.,Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, CA, USA
| | - Guy Baele
- Department of Microbiology, Immunology and Transplantation, Rega Institute, KU Leuven, 3000 Leuven, Belgium
| | - Marius Gilbert
- Spatial Epidemiology Lab (SpELL), Université Libre de Bruxelles, 1050 Bruxelles, Belgium
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Venkatesh D, Brouwer A, Goujgoulova G, Ellis R, Seekings J, Brown IH, Lewis NS. Regional Transmission and Reassortment of 2.3.4.4b Highly Pathogenic Avian Influenza (HPAI) Viruses in Bulgarian Poultry 2017/18. Viruses 2020; 12:v12060605. [PMID: 32492965 PMCID: PMC7354578 DOI: 10.3390/v12060605] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2020] [Revised: 05/26/2020] [Accepted: 05/28/2020] [Indexed: 11/20/2022] Open
Abstract
Between 2017 and 2018, several farms across Bulgaria reported outbreaks of H5 highly-pathogenic avian influenza (HPAI) viruses. In this study we used genomic and traditional epidemiological analyses to trace the origin and subsequent spread of these outbreaks within Bulgaria. Both methods indicate two separate incursions, one restricted to the northeastern region of Dobrich, and another largely restricted to Central and Eastern Bulgaria including places such as Plovdiv, Sliven and Stara Zagora, as well as one virus from the Western region of Vidin. Both outbreaks likely originate from different European 2.3.4.4b virus ancestors circulating in 2017. The viruses were likely introduced by wild birds or poultry trade links in 2017 and have continued to circulate, but due to lack of contemporaneous sampling and sequences from wild bird viruses in Bulgaria, the precise route and timing of introduction cannot be determined. Analysis of whole genomes indicates a complete lack of reassortment in all segments but the matrix protein gene (MP), which presents as multiple smaller clusters associated with different European 2.3.4.4b viruses. Ancestral reconstruction of host states of the hemagglutinin (HA) gene of viruses involved in the outbreaks suggests that transmission is driven by domestic ducks into galliform poultry. Thus, according to present evidence, we suggest the surveillance of domestic ducks as they are an epidemiologically relevant species for subclinical infection. Monitoring the spread due to movement between farms within regions and links to poultry production systems in European countries can help to predict and prevent future outbreaks. The 2.3.4.4b lineage which caused the largest recorded poultry epidemic in Europe continues to circulate, and the risk of further transmission by wild birds during migration remains.
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Affiliation(s)
- Divya Venkatesh
- Department of Pathobiology and Population Sciences, Royal Veterinary College, Hatfield, Hertfordshire AL9 7TA, UK;
- Correspondence:
| | - Adam Brouwer
- OIE/FAO/ International Reference Laboratory for avian influenza, swine influenza and Newcastle Disease, Animal and Plant Health Agency (APHA), Weybridge, Addlestone, Surrey KT15 3NB, UK; (A.B.); (J.S.); (I.H.B.)
| | - Gabriela Goujgoulova
- National Diagnostic Research Veterinary Medical Institute, 1231 Sofia, Bulgaria;
| | - Richard Ellis
- Surveillance and Laboratory Services Department, Animal and Plant Health Agency (APHA), Weybridge, Addlestone, Surrey KT15 3NB, UK;
| | - James Seekings
- OIE/FAO/ International Reference Laboratory for avian influenza, swine influenza and Newcastle Disease, Animal and Plant Health Agency (APHA), Weybridge, Addlestone, Surrey KT15 3NB, UK; (A.B.); (J.S.); (I.H.B.)
- Virology Department, Animal and Plant Health Agency (APHA), Weybridge, Addlestone, Surrey KT15 3NB, UK
| | - Ian H. Brown
- OIE/FAO/ International Reference Laboratory for avian influenza, swine influenza and Newcastle Disease, Animal and Plant Health Agency (APHA), Weybridge, Addlestone, Surrey KT15 3NB, UK; (A.B.); (J.S.); (I.H.B.)
| | - Nicola S. Lewis
- Department of Pathobiology and Population Sciences, Royal Veterinary College, Hatfield, Hertfordshire AL9 7TA, UK;
- OIE/FAO/ International Reference Laboratory for avian influenza, swine influenza and Newcastle Disease, Animal and Plant Health Agency (APHA), Weybridge, Addlestone, Surrey KT15 3NB, UK; (A.B.); (J.S.); (I.H.B.)
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Bui CM, Adam DC, Njoto E, Scotch M, MacIntyre CR. Characterising routes of H5N1 and H7N9 spread in China using Bayesian phylogeographical analysis. Emerg Microbes Infect 2018; 7:184. [PMID: 30459301 PMCID: PMC6246557 DOI: 10.1038/s41426-018-0185-z] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2018] [Revised: 09/08/2018] [Accepted: 09/20/2018] [Indexed: 11/08/2022]
Abstract
Avian influenza H5N1 subtype has caused a global public health concern due to its high pathogenicity in poultry and high case fatality rates in humans. The recently emerged H7N9 is a growing pandemic risk due to its sustained high rates of human infections, and recently acquired high pathogenicity in poultry. Here, we used Bayesian phylogeography on 265 H5N1 and 371 H7N9 haemagglutinin sequences isolated from humans, animals and the environment, to identify and compare migration patterns and factors predictive of H5N1 and H7N9 diffusion rates in China. H7N9 diffusion dynamics and predictor contributions differ from H5N1. Key determinants of spatial diffusion included: proximity between locations (for H5N1 and H7N9), and lower rural population densities (H5N1 only). For H7N9, additional predictors included low avian influenza vaccination rates, low percentage of nature reserves and high humidity levels. For both H5N1 and H7N9, we found viral migration rates from Guangdong to Guangxi and Guangdong to Hunan were highly supported transmission routes (Bayes Factor > 30). We show fundamental differences in wide-scale transmission dynamics between H5N1 and H7N9. Importantly, this indicates that avian influenza initiatives designed to control H5N1 may not be sufficient for controlling the H7N9 epidemic. We suggest control and prevention activities to specifically target poultry transportation networks between Central, Pan-Pearl River Delta and South-West regions.
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Affiliation(s)
- Chau M Bui
- University of New South Wales (UNSW), Sydney, NSW, Australia.
| | - Dillon C Adam
- University of New South Wales (UNSW), Sydney, NSW, Australia
| | - Edwin Njoto
- University of New South Wales (UNSW), Sydney, NSW, Australia
| | - Matthew Scotch
- University of New South Wales (UNSW), Sydney, NSW, Australia
- Arizona State University (ASU), Tempe, AZ, USA
| | - C Raina MacIntyre
- University of New South Wales (UNSW), Sydney, NSW, Australia
- Arizona State University (ASU), Tempe, AZ, USA
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Hamid S, Arima Y, Dueger E, Konings F, Bell L, Lee CK, Luo D, Otsu S, Olowokure B, Li A. From H5N1 to HxNy: An epidemiologic overview of human infections with avian influenza in the Western Pacific Region, 2003-2017. Western Pac Surveill Response J 2018; 9:53-67. [PMID: 31832254 PMCID: PMC6902648 DOI: 10.3565/wpsar.2018.9.2.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
| | - Yuzo Arima
- National Institute of Infectious Diseases, Japan
| | - Erica Dueger
- WHO Regional Office for the Western Pacific
- Influenza Division, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | | | - Leila Bell
- WHO Regional Office for the Western Pacific
| | | | - Dapeng Luo
- WHO Country Office Lao People’s Democratic Republic
| | | | | | - Ailan Li
- WHO Regional Office for the Western Pacific
| | - WPRO Health Emergencies Programme Teama
- WHO Regional Office for the Western Pacific
- National Institute of Infectious Diseases, Japan
- WHO Country Office China
- WHO Country Office Lao People’s Democratic Republic
- WHO Country Office Viet Nam
- Influenza Division, Centers for Disease Control and Prevention, Atlanta, GA, USA
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Contalbrigo L, Borgo S, Pozza G, Marangon S. Data distribution in public veterinary service: health and safety challenges push for context-aware systems. BMC Vet Res 2017; 13:397. [PMID: 29273034 PMCID: PMC5741927 DOI: 10.1186/s12917-017-1320-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2017] [Accepted: 12/13/2017] [Indexed: 11/16/2022] Open
Abstract
Background Today’s globalised and interconnected world is characterized by intertwined and quickly evolving relationships between animals, humans and their environment and by an escalating number of accessible data for public health. The public veterinary services must exploit new modeling and decision strategies to face these changes. The organization and control of data flows have become crucial to effectively evaluate the evolution and safety concerns of a given situation in the territory. This paper discusses what is needed to develop modern strategies to optimize data distribution to the stakeholders. Main text If traditionally the system manager and knowledge engineer have been concerned with the increase of speed of data flow and the improvement of data quality, nowadays they need to worry about data overflow as well. To avoid this risk an information system should be capable of selecting the data which need to be shown to the human operator. In this perspective, two aspects need to be distinguished: data classification vs data distribution. Data classification is the problem of organizing data depending on what they refer to and on the way they are obtained; data distribution is the problem of selecting which data is accessible to which stakeholder. Data classification can be established and implemented via ontological analysis and formal logic but we claim that a context-based selection of data should be integrated in the data distribution application. Data distribution should provide these new features: (a) the organization of situation types distinguishing at least ordinary vs extraordinary scenarios (contextualization of scenarios); (b) the possibility to focus on the data that are really important in a given scenario (data contextualization by scenarios); and (c) the classification of which data is relevant to which stakeholder (data contextualization by users). Short conclusion Public veterinary services, to efficaciously and efficiently manage the information needed for today’s health and safety challenges, should contextualize and filter the continuous and growing flow of data by setting suitable frameworks to classify data, users’ roles and possible situations.
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Affiliation(s)
- Laura Contalbrigo
- Istituto Zooprofilattico Sperimentale delle Venezie, Viale Dell'Università 10, 35020, Legnaro, (PD), Italy.
| | - Stefano Borgo
- Laboratory for Applied Ontology, ISTC-CNR, Via alla Cascata, 56/C, 38123, Trento, Italy
| | - Giandomenico Pozza
- Istituto Zooprofilattico Sperimentale delle Venezie, Viale Dell'Università 10, 35020, Legnaro, (PD), Italy
| | - Stefano Marangon
- Istituto Zooprofilattico Sperimentale delle Venezie, Viale Dell'Università 10, 35020, Legnaro, (PD), Italy
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Artois J, Lai S, Feng L, Jiang H, Zhou H, Li X, Dhingra MS, Linard C, Nicolas G, Xiao X, Robinson TP, Yu H, Gilbert M. H7N9 and H5N1 avian influenza suitability models for China: accounting for new poultry and live-poultry markets distribution data. STOCHASTIC ENVIRONMENTAL RESEARCH AND RISK ASSESSMENT : RESEARCH JOURNAL 2017; 31:393-402. [PMID: 28298880 PMCID: PMC5329093 DOI: 10.1007/s00477-016-1362-z] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
In the last two decades, two important avian influenza viruses infecting humans emerged in China, the highly pathogenic avian influenza (HPAI) H5N1 virus in the late nineties, and the low pathogenic avian influenza (LPAI) H7N9 virus in 2013. China is home to the largest population of chickens (4.83 billion) and ducks (0.694 billion), representing, respectively 23.1 and 58.6% of the 2013 world stock, with a significant part of poultry sold through live-poultry markets potentially contributing to the spread of avian influenza viruses. Previous models have looked at factors associated with HPAI H5N1 in poultry and LPAI H7N9 in markets. However, these have not been studied and compared with a consistent set of predictor variables. Significant progress was recently made in the collection of poultry census and live-poultry market data, which are key potential factors in the distribution of both diseases. Here we compiled and reprocessed a new set of poultry census data and used these to analyse HPAI H5N1 and LPAI H7N9 distributions with boosted regression trees models. We found a limited impact of the improved poultry layers compared to models based on previous poultry census data, and a positive and previously unreported association between HPAI H5N1 outbreaks and the density of live-poultry markets. In addition, the models fitted for the HPAI H5N1 and LPAI H7N9 viruses predict a high risk of disease presence for the area around Shanghai and Hong Kong. The main difference in prediction between the two viruses concerned the suitability of HPAI H5N1 in north-China around the Yellow sea (outlined with Tianjin, Beijing, and Shenyang city) where LPAI H7N9 has not spread intensely.
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Affiliation(s)
- Jean Artois
- Spatial Epidemiology Lab. (SpELL), Université Libre de Bruxelles, Brussels, Belgium
| | - Shengjie Lai
- Division of Infectious Disease, Key Laboratory of Surveillance and Early-warning on Infectious Disease, Chinese Center for Disease Control and Prevention, 155 Changbai Road, Changping District, Beijing, 102206 China
- WorldPop, Department of Geography and Environment, University of Southampton, Southampton, SO17 1BJ UK
- Key Laboratory of Public Health Safety, Ministry of Education, School of Public Health, Fudan University, Shanghai, 200032 China
| | - Luzhao Feng
- Division of Infectious Disease, Key Laboratory of Surveillance and Early-warning on Infectious Disease, Chinese Center for Disease Control and Prevention, 155 Changbai Road, Changping District, Beijing, 102206 China
| | - Hui Jiang
- Division of Infectious Disease, Key Laboratory of Surveillance and Early-warning on Infectious Disease, Chinese Center for Disease Control and Prevention, 155 Changbai Road, Changping District, Beijing, 102206 China
| | - Hang Zhou
- Division of Infectious Disease, Key Laboratory of Surveillance and Early-warning on Infectious Disease, Chinese Center for Disease Control and Prevention, 155 Changbai Road, Changping District, Beijing, 102206 China
| | - Xiangping Li
- Institute of Biodiversity Science, Fudan University, Shanghai, 200433 China
| | - Madhur S. Dhingra
- Spatial Epidemiology Lab. (SpELL), Université Libre de Bruxelles, Brussels, Belgium
- Department of Animal Husbandry & Dairying, Government of Haryana, Pashudhan Bhawan, Bays No. 9-12, Sector -2, Panchkula, Haryana 134109 India
| | - Catherine Linard
- Spatial Epidemiology Lab. (SpELL), Université Libre de Bruxelles, Brussels, Belgium
- Department of Geography, Université de Namur, Namur, Belgium
| | - Gaëlle Nicolas
- Spatial Epidemiology Lab. (SpELL), Université Libre de Bruxelles, Brussels, Belgium
| | - Xiangming Xiao
- Department of Microbiology and Plant Biology, Center for Spatial AnalysisUniversity of Oklahoma, 101 David L. Boren Blvd, Norman, OK 73019 USA
| | - Timothy P. Robinson
- Livestock Systems and Environment (LSE), International Livestock Research Institute (ILRI), Nairobi, Kenya
| | - Hongjie Yu
- Key Laboratory of Public Health Safety, Ministry of Education, School of Public Health, Fudan University, Shanghai, 200032 China
| | - Marius Gilbert
- Spatial Epidemiology Lab. (SpELL), Université Libre de Bruxelles, Brussels, Belgium
- Fonds National de la Recherche Scientifique, Brussels, Belgium
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14
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Dhingra MS, Artois J, Robinson TP, Linard C, Chaiban C, Xenarios I, Engler R, Liechti R, Kuznetsov D, Xiao X, Dobschuetz SV, Claes F, Newman SH, Dauphin G, Gilbert M. Global mapping of highly pathogenic avian influenza H5N1 and H5Nx clade 2.3.4.4 viruses with spatial cross-validation. eLife 2016; 5. [PMID: 27885988 PMCID: PMC5161450 DOI: 10.7554/elife.19571] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2016] [Accepted: 11/14/2016] [Indexed: 01/09/2023] Open
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.
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Affiliation(s)
- Madhur S Dhingra
- Spatial Epidemiology Lab, Université Libre de Bruxelles, Brussels, Belgium.,Department of Animal Husbandry and Dairying, Government of Haryana, Panchkula, India
| | - Jean Artois
- Spatial Epidemiology Lab, Université Libre de Bruxelles, Brussels, Belgium
| | - Timothy P Robinson
- Livestock Systems and Environment, International Livestock Research Institute, Nairobi, Kenya
| | - Catherine Linard
- Spatial Epidemiology Lab, Université Libre de Bruxelles, Brussels, Belgium.,Department of Geography, Université de Namur, Namur, Belgium
| | - Celia Chaiban
- Spatial Epidemiology Lab, Université Libre de Bruxelles, Brussels, Belgium
| | - Ioannis Xenarios
- Swiss-Prot and Vital-IT group, Swiss Institute of Bioinformatics, Lausanne, Switzerland.,Center for Integrative Genomics, University of Lausanne, Lausanne, Switzerland
| | - Robin Engler
- Swiss-Prot and Vital-IT group, Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Robin Liechti
- Swiss-Prot and Vital-IT group, Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Dmitri Kuznetsov
- Swiss-Prot and Vital-IT group, Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Xiangming Xiao
- Department of Microbiology and Plant Biology, University of Oklahoma, Norman, United States.,Center for Spatial Analysis, University of Oklahoma, Norman, United States.,Institute of Biodiversity Science, Fudan University, Shanghai, China
| | - Sophie Von Dobschuetz
- Animal Production and Health Division, Food and Agriculture Organization of the United Nations, Rome, Italy
| | - Filip Claes
- Emergency Center for Transboundary Animal Diseases, FAO Regional Office for Asia and the Pacific, Bangkok, Thailand
| | - Scott H Newman
- Emergency Center for Transboundary Animal Diseases, Food and Agriculture Organization of the United Nations, Hanoi, Vietnam
| | - Gwenaëlle Dauphin
- Animal Production and Health Division, Food and Agriculture Organization of the United Nations, Rome, Italy
| | - Marius Gilbert
- Spatial Epidemiology Lab, Université Libre de Bruxelles, Brussels, Belgium.,Fonds National de la Recherche Scientifique, Brussels, Belgium
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15
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Zhang Y, Aevermann BD, Anderson TK, Burke DF, Dauphin G, Gu Z, He S, Kumar S, Larsen CN, Lee AJ, Li X, Macken C, Mahaffey C, Pickett BE, Reardon B, Smith T, Stewart L, Suloway C, Sun G, Tong L, Vincent AL, Walters B, Zaremba S, Zhao H, Zhou L, Zmasek C, Klem EB, Scheuermann RH. Influenza Research Database: An integrated bioinformatics resource for influenza virus research. Nucleic Acids Res 2016; 45:D466-D474. [PMID: 27679478 PMCID: PMC5210613 DOI: 10.1093/nar/gkw857] [Citation(s) in RCA: 233] [Impact Index Per Article: 29.1] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2016] [Revised: 09/12/2016] [Accepted: 09/16/2016] [Indexed: 12/26/2022] Open
Abstract
The Influenza Research Database (IRD) is a U.S. National Institute of Allergy and Infectious Diseases (NIAID)-sponsored Bioinformatics Resource Center dedicated to providing bioinformatics support for influenza virus research. IRD facilitates the research and development of vaccines, diagnostics and therapeutics against influenza virus by providing a comprehensive collection of influenza-related data integrated from various sources, a growing suite of analysis and visualization tools for data mining and hypothesis generation, personal workbench spaces for data storage and sharing, and active user community support. Here, we describe the recent improvements in IRD including the use of cloud and high performance computing resources, analysis and visualization of user-provided sequence data with associated metadata, predictions of novel variant proteins, annotations of phenotype-associated sequence markers and their predicted phenotypic effects, hemagglutinin (HA) clade classifications, an automated tool for HA subtype numbering conversion, linkouts to disease event data and the addition of host factor and antiviral drug components. All data and tools are freely available without restriction from the IRD website at https://www.fludb.org.
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Affiliation(s)
- Yun Zhang
- J. Craig Venter Institute, La Jolla, CA 92037, USA
| | | | - Tavis K Anderson
- Virus and Prion Research Unit, National Animal Disease Center, USDA-ARS, Ames, IA 50010, USA
| | - David F Burke
- Department of Zoology, University of Cambridge, Cambridge, CB2 3EJ, UK
| | - Gwenaelle Dauphin
- Animal Health Service, Food and Agriculture Organization of the United Nations, Rome 00153, Italy
| | - Zhiping Gu
- Northrop Grumman Health Solutions, Rockville, MD 20850, USA
| | - Sherry He
- Northrop Grumman Health Solutions, Rockville, MD 20850, USA
| | - Sanjeev Kumar
- Northrop Grumman Health Solutions, Rockville, MD 20850, USA
| | | | | | - Xiaomei Li
- Northrop Grumman Health Solutions, Rockville, MD 20850, USA
| | - Catherine Macken
- Bioinformatics Institute, University of Auckland, Auckland 1010, New Zealand
| | - Colin Mahaffey
- Northrop Grumman Health Solutions, Rockville, MD 20850, USA
| | | | | | - Thomas Smith
- Northrop Grumman Health Solutions, Rockville, MD 20850, USA
| | - Lucy Stewart
- J. Craig Venter Institute, La Jolla, CA 92037, USA
| | | | - Guangyu Sun
- Vecna Technologies, Greenbelt, MD 20770, USA
| | - Lei Tong
- Northrop Grumman Health Solutions, Rockville, MD 20850, USA
| | - Amy L Vincent
- Virus and Prion Research Unit, National Animal Disease Center, USDA-ARS, Ames, IA 50010, USA
| | - Bryan Walters
- Northrop Grumman Health Solutions, Rockville, MD 20850, USA
| | - Sam Zaremba
- Northrop Grumman Health Solutions, Rockville, MD 20850, USA
| | - Hongtao Zhao
- Northrop Grumman Health Solutions, Rockville, MD 20850, USA
| | - Liwei Zhou
- Northrop Grumman Health Solutions, Rockville, MD 20850, USA
| | | | - Edward B Klem
- Northrop Grumman Health Solutions, Rockville, MD 20850, USA
| | - Richard H Scheuermann
- J. Craig Venter Institute, La Jolla, CA 92037, USA .,Department of Pathology, University of California, San Diego, CA 92093, USA.,Division of Vaccine Discovery, La Jolla Institute for Allergy and Immunology, La Jolla, CA 92037, USA
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16
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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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17
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Naguib MM, Abdelwhab EM, Harder TC. Evolutionary features of influenza A/H5N1 virus populations in Egypt: poultry and human health implications. Arch Virol 2016; 161:1963-7. [DOI: 10.1007/s00705-016-2849-0] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2016] [Accepted: 03/28/2016] [Indexed: 01/29/2023]
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18
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Muellner P, Stärk KDC, Dufour S, Zadoks RN. ‘Next-Generation’ Surveillance: An Epidemiologists’ Perspective on the Use of Molecular Information in Food Safety and Animal Health Decision-Making. Zoonoses Public Health 2015; 63:351-7. [DOI: 10.1111/zph.12230] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2015] [Indexed: 01/01/2023]
Affiliation(s)
- P. Muellner
- Epi-interactive; Miramar Wellington New Zealand
- Epi-interactive; Eppingen Germany
| | - K. D. C. Stärk
- Royal Veterinary College; North Mymms UK
- SAFOSO AG; Bern Switzerland
| | - S. Dufour
- Faculté de médecine vétérinaire; Université de Montréal; St-Hyacinthe QC Canada
- Canadian Bovine Mastitis Research Network; St-Hyacinthe QC Canada
| | - R. N. Zadoks
- Institute for Biodiversity, Animal Health and Comparative Medicine; College of Medical, Veterinary and Life Sciences; University of Glasgow; Glasgow UK
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19
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Hill AA, Dewé T, Kosmider R, Von Dobschuetz S, Munoz O, Hanna A, Fusaro A, De Nardi M, Howard W, Stevens K, Kelly L, Havelaar A, Stärk K. Modelling the species jump: towards assessing the risk of human infection from novel avian influenzas. ROYAL SOCIETY OPEN SCIENCE 2015; 2:150173. [PMID: 26473042 PMCID: PMC4593676 DOI: 10.1098/rsos.150173] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/27/2015] [Accepted: 08/12/2015] [Indexed: 05/06/2023]
Abstract
The scientific understanding of the driving factors behind zoonotic and pandemic influenzas is hampered by complex interactions between viruses, animal hosts and humans. This complexity makes identifying influenza viruses of high zoonotic or pandemic risk, before they emerge from animal populations, extremely difficult and uncertain. As a first step towards assessing zoonotic risk of influenza, we demonstrate a risk assessment framework to assess the relative likelihood of influenza A viruses, circulating in animal populations, making the species jump into humans. The intention is that such a risk assessment framework could assist decision-makers to compare multiple influenza viruses for zoonotic potential and hence to develop appropriate strain-specific control measures. It also provides a first step towards showing proof of principle for an eventual pandemic risk model. We show that the spatial and temporal epidemiology is as important in assessing the risk of an influenza A species jump as understanding the innate molecular capability of the virus. We also demonstrate data deficiencies that need to be addressed in order to consistently combine both epidemiological and molecular virology data into a risk assessment framework.
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Affiliation(s)
- A. A. Hill
- Royal Veterinary College, London, UK
- Animal and Plant Health Agency, New Haw, Surrey, UK
- Author for correspondence: A. A. Hill e-mail:
| | - T. Dewé
- Animal and Plant Health Agency, New Haw, Surrey, UK
| | - R. Kosmider
- Animal and Plant Health Agency, New Haw, Surrey, UK
| | - S. Von Dobschuetz
- Royal Veterinary College, London, UK
- Food and Agriculture Organization of the United Nations, Rome, Italy
| | - O. Munoz
- Instituto Zooprofilattico Sperimentale delle Venizie, Padua, Italy
| | - A. Hanna
- Animal and Plant Health Agency, New Haw, Surrey, UK
| | - A. Fusaro
- Instituto Zooprofilattico Sperimentale delle Venizie, Padua, Italy
| | - M. De Nardi
- Instituto Zooprofilattico Sperimentale delle Venizie, Padua, Italy
| | - W. Howard
- Animal and Plant Health Agency, New Haw, Surrey, UK
| | | | - L. Kelly
- Animal and Plant Health Agency, New Haw, Surrey, UK
| | | | - K. Stärk
- Royal Veterinary College, London, UK
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20
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Surveillance at the molecular level: Developing an integrated network for detecting variation in avian influenza viruses in Indonesia. Prev Vet Med 2015; 120:96-105. [DOI: 10.1016/j.prevetmed.2015.02.015] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2014] [Revised: 02/13/2015] [Accepted: 02/16/2015] [Indexed: 11/23/2022]
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21
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Nolte N, Kurzawa N, Eils R, Herrmann C. MapMyFlu: visualizing spatio-temporal relationships between related influenza sequences. Nucleic Acids Res 2015; 43:W547-51. [PMID: 25940623 PMCID: PMC4489300 DOI: 10.1093/nar/gkv417] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2015] [Accepted: 04/18/2015] [Indexed: 11/13/2022] Open
Abstract
Understanding the molecular dynamics of viral spreading is crucial for anticipating the epidemiological implications of disease outbreaks. In the case of influenza, reassortments or point mutations affect the adaption to new hosts or resistance to anti-viral drugs and can determine whether a new strain will result in a pandemic infection or a less severe progression. To this end, tools integrating molecular information with epidemiological parameters are important to understand how molecular characteristics reflect in the infection dynamics. We present a new web tool, MapMyFlu, which allows to spatially and temporally display influenza viruses related to a query sequence on a Google Map based on BLAST results against the NCBI Influenza Database. Temporal and geographical trends appear clearly and may help in reconstructing the evolutionary history of a particular sequence. The tool is accessible through a web server, hence without the need for local installation. The website has an intuitive design and provides an easy-to-use service, and is available at http://mapmyflu.ipmb.uni-heidelberg.de
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Affiliation(s)
- Nicholas Nolte
- Institute of Pharmacy and Molecular Biotechnology, and Bioquant Center, University of Heidelberg, Im Neuenheimer Feld 267, Heidelberg 69120, Germany Division of Theoretical Bioinformatics, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 580, Heidelberg 69120, Germany
| | - Nils Kurzawa
- Institute of Pharmacy and Molecular Biotechnology, and Bioquant Center, University of Heidelberg, Im Neuenheimer Feld 267, Heidelberg 69120, Germany Division of Theoretical Bioinformatics, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 580, Heidelberg 69120, Germany
| | - Roland Eils
- Institute of Pharmacy and Molecular Biotechnology, and Bioquant Center, University of Heidelberg, Im Neuenheimer Feld 267, Heidelberg 69120, Germany Division of Theoretical Bioinformatics, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 580, Heidelberg 69120, Germany
| | - Carl Herrmann
- Institute of Pharmacy and Molecular Biotechnology, and Bioquant Center, University of Heidelberg, Im Neuenheimer Feld 267, Heidelberg 69120, Germany Division of Theoretical Bioinformatics, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 580, Heidelberg 69120, Germany
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22
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Stevens KB, Pfeiffer DU. Sources of spatial animal and human health data: Casting the net wide to deal more effectively with increasingly complex disease problems. Spat Spatiotemporal Epidemiol 2015; 13:15-29. [PMID: 26046634 PMCID: PMC7102771 DOI: 10.1016/j.sste.2015.04.003] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/02/2015] [Accepted: 04/28/2015] [Indexed: 12/29/2022]
Abstract
During the last 30years it has become commonplace for epidemiological studies to collect locational attributes of disease data. Although this advancement was driven largely by the introduction of handheld global positioning systems (GPS), and more recently, smartphones and tablets with built-in GPS, the collection of georeferenced disease data has moved beyond the use of handheld GPS devices and there now exist numerous sources of crowdsourced georeferenced disease data such as that available from georeferencing of Google search queries or Twitter messages. In addition, cartography has moved beyond the realm of professionals to crowdsourced mapping projects that play a crucial role in disease control and surveillance of outbreaks such as the 2014 West Africa Ebola epidemic. This paper provides a comprehensive review of a range of innovative sources of spatial animal and human health data including data warehouses, mHealth, Google Earth, volunteered geographic information and mining of internet-based big data sources such as Google and Twitter. We discuss the advantages, limitations and applications of each, and highlight studies where they have been used effectively.
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Affiliation(s)
- Kim B Stevens
- Veterinary Epidemiology, Economics and Public Health Group, Dept. of Production & Population Health, Royal Veterinary College, London, United Kingdom.
| | - Dirk U Pfeiffer
- Veterinary Epidemiology, Economics and Public Health Group, Dept. of Production & Population Health, Royal Veterinary College, London, United Kingdom.
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23
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Donis RO. Antigenic analyses of highly pathogenic avian influenza a viruses. Curr Top Microbiol Immunol 2014; 385:403-40. [PMID: 25190014 DOI: 10.1007/82_2014_422] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/08/2022]
Abstract
In response to the ongoing threat to animal and human health posed by HPAI endemic in poultry, Asia (H5N1) and North America (H7N3) have revived efforts to reduce pandemic risk by disease control at the source and improved pandemic vaccines. Discovery of conserved neutralization epitopes in the HA, which mediate broad protection within and across HA subtypes have changed the paradigm of "broadly reactive" or "universal" vaccine design. Development of such vaccines would benefit from comparative antigenic analysis of viruses with increasing divergence within (and between) HA subtypes. A review of recent work to define the antigenic properties of HPAI viruses revealed data generated through an array of experimental approaches. This information has supported diagnostics and vaccine development for animal and human health. Further harmonization of analytical methods is needed to determine the antigenic relationships among multiple lineages of rapidly evolving HPAI viruses.
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Affiliation(s)
- Ruben O Donis
- Influenza Division, Centers for Disease Control and Prevention, 1600 Clifton Road NE Mailstop A20, Atlanta, GA, 30333, USA,
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