Detection of antigenic variants of subtype h3 swine influenza. Antigenic patterns and evolution of the human influenza a. Empirical methods to determine influenza virus antigenic properties are timeconsuming and midthroughput and require live viruses. New antigenic cartography method for more effective flu. American association of avian pathologists annual meeting, st. Segments are only reported if the have a minimum size of 8 residues. To experience the full functionality of the epiflu database application it is recommended to use the following software programs. While standard cartography does not use sequence information, sequences have been used as priors for distances in a bayesian version of multidimensional scaling bedford et al. Thus each antigen is measured in relation to many antisera, and thus this redundancy allows. Unable to find the pdb entry atom 19 cd1 leu a 23 10.
The role of antigenic cartography in monitoring derek smith department of zoology, university of cambridge, uk department of virology, erasmus medical center, nl antigenic map influenza a h3n2 19682004 smith et alscience 305, 3776, 2004. The influenza a h1n1 virus causes seasonal epidemics that result in severe illnesses and deaths almost every year. Researchers from the dengue antigenic cartography consortium, writing in todays edition of science, analysed 47 strains of dengue virus with 148. Antigenic cartography therefore offers an improved understanding of genetic and antigenic evolution. Antigenic cartography is the process of creating maps of antigenically variable pathogens more details. Mapping the antigenic and genetic evolution of influenza virus. Antigenic peptides are determined using the method of kolaskar and tongaonkar 1990.
Employs a suite of software packages to analyze binding assay data with mds algorithms. I need recommendation about antigenic software or epitope. Mapping the antigenic and genetic evolution of influenza virus science 3055682. Prediction, dynamics, and visualization of antigenic. Antigenic cartography was then visualized using r v3. The viruses labeled with the cluster names hk68, en72, vi75, tx77, bk79, si87, be89, be92, wu95, sy97 and fu02 were adapted from smith et al. There is considerable diversity in both h1 and h3 influenza viruses circulating in swine due to the frequent introductions of viruses from humans and birds coupled with geographic segregation of global swine populations. Programs to import phylogenetic tree and draw it on a tree or signature page. The ease at which influenza virus sequence data can be used to estimate antigenic relationships between strains and the existence of databases containing sequence data for hundreds of thousands influenza strains make sequencebased antigenic distance estimates an attractive approach to researchers. Students may learn traditional surveying and drafting techniques along with advanced spatial tools, such as gis software, computer graphics and data from satellites, aerial photography.
An examination of cartographic design is a cartographic classic by arthur h. May 30, 2008 this guest post was written by terry jones, former antigenic cartographer and founder of fluidinfo. Global consortium rewrites the cartography of dengue virus. Mapping the evolution of pathogens who collaborating centre. Determination of efficacious vaccine seed strains for use against egyptian h5n1 highly pathogenic avian influenza viruses through antigenic cartography and in vivo challenge studies abstract. Antigenic mismatch between circulating strains and vaccine strains results in. The technique provides, for the first time, quantitative measurements and a visualisation of phenotypic differences among the objects of binding assays, such as viral strains.
Topics in cartography degree programs include quantitative methods, webbased cartography, remote sensing and laboratory courses in imageprocessing software. The program was parallelized using openmp and run on the. May 22, 2019 antigenic cartography was then visualized using r v3. American association of avian pathologists annual meeting, july 1114, 2009, seattle, washington. Dengue antigenic cartography consortium who collaborating. In some cases, as in the image on the left, twodimensional maps can be produced which reveal interesting information about the. Jan 07, 2011 derek smith on antigenic cartography 7 january 2011 derek smith, professor of infectious disease informatics, university of cambridge, u. However, antigenic cartography construction is not trivial due to the challenging features embedded in the immunological data, such as data incompleteness, high noises, and.
Up to 10 years ago, maps were made by professional cartographers, who had the time and the need to carefully plan where each map feature would be placed and consider the visual impact of the map. Sep 28, 2015 the influenza a h1n1 virus causes seasonal epidemics that result in severe illnesses and deaths almost every year. A task for theoretical cartography is to develop a typology of dynamic spatial phenomena and formulate principles and rules of. Antigenic cartography is the process of creating maps of antigenically variable pathogens. Antigenic maps are the fit of all binding assay data simultaneously. Swine influenza presents a substantial disease burden for pig populations worldwide and poses a potential pandemic threat to humans. Antigenic cartography of h1n1 influenza viruses using sequence. He has presented more than 100 posters and almost 150 oral presentations at prestigious venues all over the world. The mapping, says kawaoka, identifies clusters of viruses featuring novel mutations which, according to the new study, can effectively predict the molecular characteristics of the next seasonal influenza virus. One of the most important factors for selecting an effective vaccine strain is the antigenic match between the hemagglutinin protein of the vaccine and the strain circulating in the field. Antigenic cartography is the product of collaboration between researchers in virology, immunology, computational biology, mathematics, and computer science. Hibased antigenic cartography showed that the seven isolates were separated into two antigenic clusters. The global antigenic diversity of swine influenza a viruses. Analysis of h7 avian influenza viruses by antigenic cartography and correlation to protection by vaccination abstract.
The mapping software is designed for creationrevision of topographic and special maps, map publishing, urban cadastre and land management, solving special tasks. Concepts and applications for influenza antigenic cartography. This project aims at providing a desktop application for working with antigenic maps. At the oreilly etech conference in march i gave a talk describing antigenic cartography, a new method being used to visualize virus evolution and to aid in. The first antigenic map of the influenza ah3n2 virus from 1968 to 2003. They have pointers to a lot of cartographic software. Collaboration on h5 antigenic cartography preliminary antigenic map of h5 hemagglutinin in recognition of the rapid genetic and antigenic evolution of highly pathogenic avian influenza viruses of the h5 subtype, investigators from the university of cambridge, the university of wisconsin at madison, and erasmus medical center in rotterdam are. Antigenic cartography is a useful technique to visualize and minimize errors in immunological data by projecting antigens to 2d or 3d cartography.
Inference of genotypephenotype relationships in the. This guest post was written by terry jones, former antigenic cartographer and founder of fluidinfo. In an effective vaccination program, vaccine strain selection will be the most. A computational framework for influenza antigenic cartography. Apr 22, 2016 swine influenza presents a substantial disease burden for pig populations worldwide and poses a potential pandemic threat to humans. Antigenic cartography of h1n1 influenza viruses using. Antigenic maps of h1n1 virus strains reveal that strains cluster antigenically. A deep understanding of the antigenic patterns and evolution of human influenza.
Vaccination is frequently used as a control method for the h9 subtype of low pathogenicity avian influenza virus aiv, which is widespread in asia and the middle east. Field antisera from chickens and ducks vaccinated with commercial vaccines in vietnam were collected to test antibody titers. These include price, functionality, and whether you need high quality map data. Software for the the detection of antigenic peptides several methods based on various physiochemical properties of experimental determined epitopes flexibility, hydrophibility, accessibility have published for the prediction of antigenic determinants, of which the antigenic index and preditop are good examples. At the oreilly etech conference in march i gave a talk describing antigenic cartography, a new method being used to visualize virus evolution and to aid in the design of vaccines, in the context of influenza. Unable to find the pdb entry atom 18 cg leu a 23 10.
The tx77ba79 transition was not predicted with our method in this setting, as the weights of the corresponding branch were slightly. A combination of a multidimensional clustering algorithm and a visualization to allow influenza hemagluttinin inhibition assay distances between influenza strains to be viewed as twodimensional maps. A systematic study towards evolutionary and epidemiological. May 23, 2016 because the sources of the viruses were known, the patterns of mutation could be mapped using antigenic cartography. Mississippi state celebrates research success with annual. However, a 2d cartography may not be sufficient to capture the antigenic relationship from highdimensional immunological data. Sep 17, 2015 researchers from the dengue antigenic cartography consortium, writing in todays edition of science, analysed 47 strains of dengue virus with 148 samples taken from both humans and primates to see. Antigenic characterization of recent h5n1 highly pathogenic.
The influenza antigenic 2d a and 3d b cartography for h3n2 viruses from 1968 to 2003. There are several factors that should be considered when looking for custom map design tools. Import industrystandard gis data formats and make crisp, clean maps with all attributes and georeferencing intact using the adobe illustrator design environment. The general approach of software cartography, as illustrated in figure 1, is as. The book was based on robinsons doctoral research which investigated the relationship between science and art in cartography and the resultant refinement of graphic techniques in mapmaking to present dynamic geographic information.
Antigenic cartography of h9 avian influenza virus and its. In particular, the use of antigenic cartography, which explores the pattern of pairwise hemagglutinin inhibition hi distances, has suggested that antigenic drift is punctuated with major jumps. The dengue antigenic cartography consortium is an international collaboration of leading dengue researchers to systematically characterise antigenic variation among a large sample of dengue viruses. Infectious disease modeling methods as tools for informing. Provides unlimited possibilities for creatingeditingrevising of digital maps. Maps point the way to fighting the flu virus scientific. The global circulation of seasonal influenza a h3n2 viruses science 3205874. In some cases, as in the image above, twodimensional maps can be produced which reveal interesting information about the antigenic evolution of a pathogen. Geosystem mapping and cartography software digitals. Mapublisher cartography software seamlessly integrates more than fifty gis mapping tools into adobe illustrator to help you create beautiful maps.
Using sequence data to infer the antigenicity of influenza virus. Antigenic cartography is a useful technique to visualize and. The goal of this study was to evaluate for the first time the antigenic characteristics of an extensive and representative collection of recent egyptian h5n1 hpai viruses by the antigenic cartography and principal component analysis pca and to assess the antigenic differences of clade 2. Cartography predates the invention of geographic information system gis by thousands of years. This is the first antigenic map of the influenza ah3n2 virus from 1968 to 2003. Thus, influenza antigenic cartography can be utilized to identify.
Geological survey the usgs covers many topics in geology, mapping, and water resources. We present two variations of software cartography, an of. As such, timely identification of emerging influenza virus antigenic variants is central to the success of influenza vaccination programs. The cartographers guild is a forum created by and for map makers and aficionados, a place where every aspect of cartography can be admired, examined, learned, and discussed. Antigenic map showing the evolution of the influenza a h3n2 virus evolution from 1968 to 2002.
Please click here and then click on the sign up link on that page, if you would like to use alpha release of our webbased. Apr 23, 2008 maps point the way to fighting the flu virus. Derek smith on antigenic cartography 7 january 2011 derek smith, professor of infectious disease informatics, university of cambridge, u. In some cases twodimensional maps can be produced which reveal interesting information about the antigenic evolution of a pathogen. The results from polypla indicated that the titers for these seven testing isolates ranged from 1. The centre for pathogen evolution, department of zoology, university of cambridge, uk antigenic cartography. A robust antigenic cartography can facilitate influenza vaccine strain selection since the antigenic map can simplify data interpretation through intuitive antigenic map. The efficacy of current influenza vaccines requires a close antigenic match between circulating and vaccine strains.
Antigenic cartography, a new computational method of quantifying antigenic distances between strains has been applied to human and equine in. Using antigenic cartography, a technique developed to probe the forces underlying the antigenic evolution of influenza viruses, we are testing for. Supports 3dinput from dps delta and external formats. Because the sources of the viruses were known, the patterns of mutation could be mapped using antigenic cartography. Pdf antigenic cartography is a useful technique to visualize and. Predictions are based on a table that reflects the occurrence of amino acid residues in experimentally known segmental epitopes. The jpl cartographic applications group is involved with many projects involving digital cartography, geographic information systems, digital elevation models, terrain analysis and remote sensing. Each strain is coloured to represent the antigenic cluster to which that strain belongs, while the antisera used in the hi assays are shown as uncoloured open shapes. Department of zoology, university of cambridge, uk antigenic cartography.
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