Antigenic cartography of h1n1 influenza viruses using sequence. Mar 11, 2020 substitutions in all antigenic sites e153g in sa, q193h in sb, d168n in ca1, p7s in ca2, and f71l in cb were detected in antigenic variants from chh1a cluster, whereas only a single. However, a 2d cartography may not be sufficient to capture the antigenic relationship from highdimensional immunological data. With this pc software you will be able to download a wide variety of cartography from the internet and also analyse your routes. The global antigenic diversity of swine influenza a viruses core. This is the first antigenic map of the influenza ah3n2 virus from 1968 to 2003. Hi antigenic maps, developed with antisera from both hosts, revealed. Antigenic peptides are determined using the method of kolaskar and tongaonkar 1990. Hint is a valuable new antigenic analysis tool for vaccine strain selection. Antigenic cartography, a new computational method of quantifying antigenic distances between strains has been applied to human and equine in. Data availability complementary research materials and software. Antigenic and genetic evolution of contemporary swine h1. Here, we extend previous approaches to antigenic cartography, which seeks to place strains on an antigenic map, such that distances on this map best recapitulate titers observed across multiple hi assays. Antigenic characterization of novel h1 influenza a viruses in.
We applied the acmacs antigenic cartography algorithm adapted from to. It reports segments if they have a minimum size of 8 residues. This software has been specially designed for 4x4 lovers, bike tourists, excursionists and, in general, everyone who uses gps, likes to create and accomplish their own routes and then later on analyse. 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. Author summary immunity to human malaria parasites never fully protects against infection, even after a lifetime of exposure.
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. Antigenic cartography of h9 avian influenza virus and its. 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. Users may download and print one copy of any publication from the public.
Here, we extend previous approaches to antigenic cartography, and simultaneously characterize antigenic and genetic evolution by modeling the diffusion of antigenic phenotype over a. Author summary influenza antigenic cartography is an analogy of. This tool is able to produce results with an accuracy about 75 per cent. Finally, we constructed an antigenic cartography of all h3n2 viruses with hemagglutinin. Instead of sending their dataladen digital spreadsheets to cambridge, where the researchers cluster of 20 computer servers run the antigenic cartography software that makes the.
Antigenic cartography is the product of collaboration between researchers in virology, immunology, computational biology, mathematics, and computer science. 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. The pathogen evolution group conducts highly translational scientific research focussed on improving our understanding and ability to predict pathogen evolution in humans and other animals, provides support to the world health organization who influenza vaccine strain selection process, and develops and distributes free highquality software. Antigenic cartography is the process of creating maps of antigenically variable pathogens. 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. Mapping and gis applications range from free to costing tens of thousan. Antigenic definition of antigenic by the free dictionary. My slides from the talk are online having the flu is something of a generic. A robust antigenic cartography can facilitate influenza vaccine strain selection since the antigenic map can simplify data interpretation through intuitive antigenic map.
Jul 16, 2004 the antigenic evolution of influenza a h3n2 virus was quantified and visualized from its introduction into humans in 1968 to 2003. These viruses are specifically labeled as eleven clusters hk68, en72, vi75, tx77, bk79, si87, be89, and be92, wu95, sy97, and fu02. Cartography software free download cartography top 4 download. Cartography software free download cartography top 4. Apr 23, 2008 instead of sending their dataladen digital spreadsheets to cambridge, where the researchers cluster of 20 computer servers run the antigenic cartography software that makes the maps, researchers. Antigenic cartography is the process of creating maps of antigenically variable pathogens more details. Insights into the antigenic advancement of influenza ah3n2.
This project aims at providing a desktop application for working with antigenic maps. Antigenic evolution was more punctuated than genetic evolution, and genetic change sometimes had a disproportionately large antigenic effect. Although there was remarkable correspondence between antigenic and genetic evolution, significant differences were observed. To do so, we borrow a technique used in the study of immune crossreactivity of influenza a viruses called antigenic cartography 24,25 that is used to annually update flu vaccines in order to cover the antigenic space of the circulating pathogen population. Hk2014like ferret sera for 20142017 ah3n2 isolates were modelled with the acmacs antigenic cartography application. Mapping the evolution of pathogens who collaborating centre. Empirical methods to determine influenza virus antigenic properties are timeconsuming and midthroughput and require live viruses. Download links are directly from our mirrors or publishers. However, antigenic cartography construction is not trivial due to the challenging features embedded in the immunological data, such as data incompleteness, high noises, and. Antigenic peptide prediction bioinformatics tools omicx. Our overall aim is to lay the foundation for inferring the subset of.
Antigenic evolution was more punctuated than genetic evolution, and genetic change sometimes had a disproportionately large. Predictions are based on a table that reflects the occurrence of amino acid residues in experimentally known segmental epitopes. 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. 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. Cai z, zhang t, wan xf 2010 a computational framework for influenza antigenic cartography. Integrating influenza antigenic dynamics with molecular. Antigenic characterization of novel h1 influenza a viruses. Global consortium rewrites the cartography of dengue virus. Predicting influenza antigenicity from hemagglutintin sequence data. In support of the hi cartographyderived data, polyplabased cartography also showed that these seven isolates were grouped in two antigenic clusters. Dengue antigenic cartography consortium who collaborating. Antigenic characterization of highly pathogenic avian influenza a. Prediction, dynamics, and visualization of antigenic.
The first antigenic map of the influenza ah3n2 virus from 1968 to 2003. Each strain is coloured to represent the antigenic. Smith during icaac boston 2010, as part of twiv 99. Drawing antigenic maps javascript mit 0 0 0 0 updated apr 28, 2020. 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. Software mapping and cartography software digitals the mapping software is designed for creationrevision of topographic and special maps, map publishing, urban cadastre and land management, solving special tasks. A new vaccine is required every year because influenza virus has the ability to undergo antigenic drift. 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. Top 4 download periodically updates software information of cartography full versions from the publishers, but some information may be slightly outofdate using warez version, crack, warez passwords, patches, serial numbers, registration codes, key generator, pirate key, keymaker or keygen for cartography license key is illegal. A web database and bioinformatics analysis tool for gene families involved in antigenic variation and immune system evasion in pathogens. By contrast, protection against severe disease occurs early in life in malariaendemic areas. Detection of antigenic variants of subtype h3 swine. The center for pathogen evolution antigenic cartography.
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. 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 cluster to which that strain belongs, while the antisera used in the hi assays are shown as uncoloured open shapes. Prediction, dynamics, and visualization of antigenic phenotypes of seasonal in. This paper deals with the antigenic evolution of influenza. Researchers from the dengue antigenic cartography consortium, writing in todays edition of science, analysed 47 strains of dengue virus with 148. This antigenic evolution requires frequent update of seasonal influenza vaccines. One grid in 2d map or one unit in 3d map corresponds to a twofold change in hi assay.
Antigenic characterization of h3 subtypes of avian influenza a. Compegps is an essential software to make the most of your gps. Wed like to understand how you use our websites in order to improve them. These include price, functionality, and whether you need high quality map data.
Repository for course materials for the antigenic cartography and antibody landscapes course 2019 r 6 2 0 0 updated jun 17, 2019. Maps point the way to fighting the flu virus scientific. Mapublisher cartography software seamlessly integrates more than fifty gis mapping tools into adobe illustrator to help you create beautiful maps. Both antiinfection and antidisease immunity depend on antibody responses to proteins expressed by the parasite on the red blood cell surface which cause pathology.
Software for the the detection of antigenic peptides. Antigenic cartography of immune responses to plasmodium. May 23, 2016 because the sources of the viruses were known, the patterns of mutation could be mapped using antigenic cartography. Antigenic peptide prediction is based on a table that underlines the occurrence of amino acid residues in experimentally known segmental epitopes. 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. 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. Antigenic cartography centre for pathogen evolution. This paper makes a clear methodological improvement on the original antigenic cartography technique. Antigenic variation not only enables the pathogen to avoid the immune response in its current host, but also allows reinfection 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. Geneotree is a gedcom files php viewer, full dynamic on the web. A computational framework for influenza antigenic cartography. Mapping the antigenic and genetic evolution of influenza.
A foundational paper in science in 2004 by smith et al introduced antigenic cartography, the technique used to monitor antigenic drift and select the influenza vaccine. Antigenic cartography showed that the largest antigenic distance among the 37 avian iavs is about four units, and. New antigenic cartography method for more effective flu. 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. Segments are only reported if the have a minimum size of 8 residues. Author summary 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. We then downloaded the ha1 protein sequences of length 329 for the 253. Geosystem mapping and cartography software digitals. Antigenic cartography is a useful technique to visualize and minimize errors in immunological data by projecting antigens to 2d or 3d cartography. Antigenic cartography is a computational and mathematical tool for the analysis of binding assay data, providing a quantification and visualisationcalled antigenic mapsof antigenic data. Feb 04, 2014 this paper deals with the antigenic evolution of influenza. 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.
Import industrystandard gis data formats and make crisp, clean maps with all attributes and georeferencing intact using the adobe illustrator design environment. An antigen is usually a foreign substance, such as a toxin or a component of a virus. Antigenmap 3d presents an online, interactive, and robust 3d antigenic cartography construction and. 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. Why is it such a successful method of studying relationships between virus strains. Antigenic cartography therefore offers an improved understanding of genetic and antigenic evolution. 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. Posted on 201031 201031 author admin categories miscellaneous tags antigenic cartography, antigenmap, antigenmap 3d, construction. Insights into the antigenic advancement of influenza ah3n2 nature.
In some cases, as in the image above, twodimensional maps can be produced which reveal interesting information about the antigenic evolution of a pathogen. The influenza antigenic 2d a and 3d b cartography for h3n2 viruses from 1968 to 2003. Antigenic map showing the evolution of the influenza a h3n2 virus evolution from 1968 to 2002. The efficacy of current influenza vaccines requires a close antigenic match between circulating and vaccine strains. Using antigenic cartography, a technique developed to probe the forces underlying the antigenic evolution of influenza viruses, we are testing for. In some cases twodimensional maps can be produced which reveal interesting information about the antigenic evolution of a pathogen. The antigenic evolution of influenza a h3n2 virus was quantified and visualized from its introduction into humans in 1968 to 2003. The scale of antigenic cartography is based on the antigenic distances from hi tables, e. Thus, influenza antigenic cartography can be utilized to identify. Software mapping and cartography software digitals. 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.
Pdf antigenic cartography is a useful technique to visualize and minimize errors in immunological data by. 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. This method is highly applicable to other important pathogens displaying antigenic diversity, such as fmd. Genetic evolution of swine h1 influenza viruses currently circulating in the u. Antigenic characterization of recent h5n1 highly pathogenic. Because the sources of the viruses were known, the patterns of mutation could be mapped using antigenic cartography. 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. Antigenic mismatch between circulating strains and vaccine strains results in. The mapping software is designed for creationrevision of topographic and special maps, map publishing, urban cadastre and land management, solving special tasks. Mar 22, 2016 humans mount an antibodymediated immune response against influenza viruses that can be recalled.
Antigenic cartography of h1n1 influenza viruses using. There are several factors that should be considered when looking for custom map design tools. Mapping the antigenic and genetic evolution of influenza virus. The centre for pathogen evolution, department of zoology, university of cambridge, uk antigenic cartography. Using sequence data to infer the antigenicity of influenza. 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. As such, timely identification of emerging influenza virus antigenic variants is central to the success of influenza vaccination programs. Nevertheless, individuals can suffer from recurrent influenza infections as viruses can change their antigenic properties by altering their surface glycoproteins. Derek smith on antigenic cartography virology blog. Sign up link on that page if you would like to use alpha release of our webbased software for making and viewing antigenic maps.