Sep 28, 2015 the influenza a h1n1 virus causes seasonal epidemics that result in severe illnesses and deaths almost every year. A tale of three next generation sequencing platforms. Novel h1n2 influenza a viruses iavs in swine have been identified in chile cocirculating with pandemic h1n1 2009like ah1n1pdm09like viruses. Segments are only reported if the have a minimum size of 8 residues. A web database and bioinformatics analysis tool for gene families involved in antigenic variation and immune system evasion in pathogens. Mapping the antigenic and genetic evolution of influenza virus science 3055682. Sep 19, 20 however, it is difficult to visualise antigenic differences, especially when the number of viruses and sera are large. Researchers from the dengue antigenic cartography consortium, writing in todays edition of science, analysed 47 strains of dengue virus with 148. The emergence of the novel humaninfecting avian h7n9 virus in china has caused widespread concern. However, it is difficult to visualise antigenic differences, especially when the number of viruses and sera are large. Improving influenza vaccine virus selection world health. Antigenic shift, genetic alteration occurring in an infectious agent that causes a dramatic change in a protein called an antigen, which stimulates the production of antibodies by the immune systems of humans and other animals. 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.
Original antigenic sin refers to the propensity of the bodys immune system. Mapping the antigenic and genetic evolution of influenza. One grid in 2d map or one unit in 3d map corresponds to a twofold change in hi assay. Author summary influenza antigenic cartography is an analogy of geographic cartography, and it projects influenza antigens into a two or. To access a sequence from a database, enter the usa here. 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. Mapping antigenic variation in hiv1 envelope retrovirology. Antigenic cartography, a new computational method of quantifying antigenic distances between strains has been applied to human and equine in. Antigenic article about antigenic by the free dictionary. Although its utility was first established in both research and public health in the context of the influenza virus, the techniques of antigenic cartography have subsequently been applied to many other pathogens.
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. Each strain is coloured to represent the antigenic. For example, antigenic cartography studies demonstrated that h3n2 strains. Antigenic variation not only enables the pathogen to avoid the immune response in its current host, but also allows reinfection of. Jan 07, 2011 derek smith on antigenic cartography 7 january 2011 derek smith, professor of infectious disease informatics, university of cambridge, u. Mapping the evolution of pathogens who collaborating centre. May 23, 2016 because the sources of the viruses were known, the patterns of mutation could be mapped using antigenic cartography. Antigenic variations occured either when one variation occurs at a sialic acid receptorbinding site and another at an antigenic site or greater than or equal to2 variations occur at. Antigenic cartography is the product of collaboration between researchers in virology, immunology, computational biology, mathematics, and computer science. Antigenic definition of antigenic by medical dictionary. Antigenic peptides are determined using the method of kolaskar and tongaonkar 1990. Integrating influenza antigenic dynamics with molecular. Influenza viruses are classic examples of antigenically variable pathogens and have a seemingly endless capacity to evade the immune response.
It also occurs because the rna genome of influenza a viruses is in the form of eight segments, which during viral replication are susceptible to a type of genetic exchange known as genetic reassortment. Here, we extend previous approaches to antigenic cartography, and simultaneously characterize antigenic and. Antigenic cartography is the process of creating maps of antigenically variable pathogens. Antigenic shift occurs because influenza a viruses have a large animal reservoir, consisting primarily of wild aquatic birds e. 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. Antigenic definition of antigenic by the free dictionary. Antigenic cartography of h1n1 influenza viruses using sequence. Bcell epitope mapping for the design of vaccines and effective. It is measurable and need not be linear or of a ratelimited step or equation. We used this method to study quantitatively the antigenic evolution of influenza a h3n2 virus, revealing both similarities to, and important differences from, its genetic evolution. Although there was remarkable correspondence between antigenic and genetic evolution, significant differences were observed. Thus, infectious agents that have evolved through antigenic drift may cause potentially.
Antigenic characterization of novel h1 influenza a viruses. Antigenic determinant definition of antigenic determinant. 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. May 30, 2008 this guest post was written by terry jones, former antigenic cartographer and founder of fluidinfo. Cdv produces multisystemic disease in dogs and other terrestrial carnivores. The purchasing and successful trialling of a personal genome machine ion torrent by the. Migratio is a cartography and gis software that enables you to create thematic map. Antigenmap 3d presents an online, interactive, and robust 3d antigenic cartography construction and. Prediction, dynamics, and visualization of antigenic phenotypes of seasonal in. Antigenic cartography is a computational and mathematical tool for the analysis of binding assay data, providing a quantification and visualisationcalled antigenic mapsof antigenic data. 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. 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.
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. This image is a derivative work of the following images. These mutations typically produce antigens to which only part of a population may be immune. Antigenic specificity is the ability of the host cells to recognize an antigen specifically as a unique molecular entity and distinguish it from another with exquisite precision. Computational analysis of antigenic epitopes of avian. Global consortium rewrites the cartography of dengue virus. A new vaccine is required every year because influenza virus has the ability to undergo antigenic drift. Dengue antigenic cartography consortium who collaborating. Because the sources of the viruses were known, the patterns of mutation could be mapped using antigenic cartography. Antigenic cartography is the process of creating maps of antigenically variable pathogens more details. In some cases, as in the image on the left, twodimensional maps can be produced which reveal interesting information about the antigenic evolution of a pathogen. An examination of cartographic design is a cartographic classic by arthur h. Apr 23, 2008 maps point the way to fighting the flu virus.
Antigenic variation is a major method by which microbes evade the immune response, and persist in the body. Antigenic variations occured either when one variation occurs at a sialic acid receptorbinding site and another at an antigenic site or greater than or equal to2 variations occur at antigenic sites li et al. 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 evolution was more punctuated than genetic evolution, and genetic change sometimes had a disproportionately large antigenic effect. Why is it such a successful method of studying relationships between virus strains. This project aims at providing a desktop application for working with antigenic maps. The centre for pathogen evolution, department of zoology, university of cambridge, uk antigenic cartography. The influenza a h1n1 virus causes seasonal epidemics that result in severe illnesses and deaths almost every year. Influenza antigenic cartography is an analogy of geographic cartography, and it projects influenza antigens into a two or threedimensional map through which we can visualize and measure the antigenic distances between influenza antigens as we visualize and measure geographic distances between the cities in a geographic cartography. The influenza antigenic 2d a and 3d b cartography for h3n2 viruses from 1968 to 2003. This is the first antigenic map of the influenza ah3n2 virus from 1968 to 2003.
Antigenic mismatch between circulating strains and vaccine strains results in. Des wt allele, nci thesaurus a normal feature of responses to infectious agents that allows recognition of multiple antigenic targets, epitope spreading involves noncrossreactive epitopes, distinct from the. The viruses labeled with the cluster names hk68, en72, vi75, tx77, bk79, si87, be89, be92, wu95, sy97 and. Integrating influenza antigenic dynamics with molecular evolution. This map demonstrates that there is lack of antigenic drifts during the first wave of this pandemic influenza as all of these viruses are mixed altogether. However, evolution of the antigenicity of this virus is not well understood. Deep sequencing reveals potential antigenic variants at low. A molecule that is capable of binding to an antibody or to an antigen receptor on a t cell, especially one that induces an immune response. Genetic and antigenic mapping of ha and na indicate that na. Antigenic variation may be classified into two types, antigenic drift that results from a change in few amino acids and antigenic shift which is the outcome of acquiring new structural proteins. Find antigenic sites in proteins read the manual unshaded fields are optional and can safely be ignored. Cartographers of the infectious world medical xpress. Antigenic shift has been studied most extensively in influenza type a viruses, which experience this change about once every 10 years. This method is highly applicable to other important pathogens displaying antigenic diversity, such as fmd.
In some cases twodimensional maps can be produced which reveal interesting information about the antigenic evolution of a pathogen. Repository for course materials for the antigenic cartography and antibody landscapes course 2019 r 6 2 0 0 updated jun 17, 2019. The simplest form of an antigenic determinant, on a complex antigenic molecule, which can combine with antibody or t cell receptor. Antigenic cartography of h1n1 influenza viruses using.
A robust antigenic cartography can facilitate influenza vaccine strain selection since the antigenic map can simplify data interpretation through intuitive antigenic map. Download links are directly from our mirrors or publishers website, cartography torrent files or shared files from free file sharing and free upload services, including rapidshare, megaupload, yousendit, letitbit, dropsend, mediamax, hellshare, hotfile, fileserve, leapfile, myotherdrive or mediafire, are not allowed. This guest post was written by terry jones, former antigenic cartographer and founder of fluidinfo 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. The first antigenic map of the influenza ah3n2 virus from 1968 to 2003. 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. Antigenic cartography therefore offers an improved understanding of genetic and antigenic evolution. Antigenic cartography is a powerful method that allows for the calculation of antigenic distances between influenza viruses or sera and their positioning on a map, by quantifying raw data from.
The broad scope of the book appeals to all those working in the field of infectious disease, immunology of infection, pathogenesis, molecular biology and also to evolutionary biologists. Drawing antigenic maps javascript mit 0 0 0 0 updated apr 28, 2020. Antigenic map showing the evolution of the influenza a h3n2 virus evolution from 1968 to 2002. 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. Concepts and applications for influenza antigenic cartography. Although its utility was first established in both research and public health in the context of the influenza virus, the techniques of antigenic cartography have subsequently been applied to many other. Antigenic mismatch between circulating strains and vaccine strains results in significantly. These maps are made with data that provide information on the antigenic properties of the pathogen. My slides from the talk are online having the flu is something of a generic. This is the first antigenic map of the influenza a h3n2 virus from 1968 to 2003. Docking programs are assuming that the structure of the antigenantibody complex is representing the lowest free energy state accessible to the system 63.
Thus, influenza antigenic cartography can be utilized to identify influenza antigenic variants, and it is useful for influenza vaccine strain selection. Antigenic cartography is a useful technique to visualize and minimize errors in immunological data by projecting antigens to 2d or 3d cartography. Cartography freeware free cartography download top 4. New antigenic cartography method for more effective flu. 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. Antigen specificity is due primarily to the sidechain conformations of the antigen. A computational framework for influenza antigenic cartography. Figure 2c is an antigenic cartography generated using a hi dataset with 2009 h1n1 influenza viruses spanning from april of 2009 to june of 2009. The antigenic evolution of influenza a h3n2 virus was quantified and visualized from its introduction into humans in 1968 to 2003. Antigenic variation or antigenic alteration refers to the mechanism by which an infectious agent such as a protozoan, bacterium or virus alters the proteins or carbohydrates on its surface and thus avoids a host immune response.
The ease at which influenza virus sequence data can be used to estimate antigenic relationships between strains and the existence of. 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. In some cases, as in the image above, twodimensional maps can be produced which reveal interesting information about the antigenic evolution of a pathogen. Here, we extend previous approaches to antigenic cartography, and simultaneously characterize antigenic and genetic evolution by modeling the diffusion of antigenic phenotype over a shared virus phylogeny.
Using antigenic cartography, a technique developed to probe the forces underlying the antigenic evolution of influenza viruses, we are testing for. 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. Cartography software free download cartography top 4. Influenza virus can rapidly change its antigenicity, via mutation in the hemagglutinin ha protein, to evade host immunity. Here, we extend previous approaches to antigenic cartography, which seeks to place strains on an. In some cases, as in the image above, twodimensional maps can be produced which reveal interesting information about the antigenic evolution of a pathogen this is the first antigenic map of the influenza ah3n2 virus from 1968 to 2003. Software for the the detection of antigenic peptides. You can draw choropleths, diagrams and put labels on each polygon.
Antigenic patterns and evolution of the human influenza a. Borrowing from developments in antigenic cartography in influenza, i present a statistical model to map viruses and sera into antigenic space, and apply it to data from five published studies of hiv1 neutralisation. 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. Canine distemper virus cdv is an rna virus of the genus morbillivirus within the family paramyxoviridae. Use of antigenic cartography in vaccine seed strain selection. Maps point the way to fighting the flu virus scientific. With the development of modified live vaccines in the 1950s and 1960s, the disease, with a few exceptions, has been successfully controlled. Easy to use, make your maps in few clicks, making it a true power tool. A deep understanding of the antigenic patterns and evolution of human influenza. Predictions are based on a table that reflects the occurrence of amino acid residues in experimentally known segmental epitopes. An antigen is usually a foreign substance, such as a toxin or a component of a virus. Here, we inferred the antigenic epitopes of the ha protein from all h7 viruses, based on. 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 drift, random genetic mutation of an infectious agent resulting in minor changes in proteins called antigens, which stimulate the production of antibodies by the immune systems of humans and animals.
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