Antigenic map showing the evolution of the Influenza A (H3N2) virus evolution from 1968 to 2002.
©Science.

Antigenic Cartography is the process of creating maps of antigenically variable pathogens (more details). In some cases, as in the image on the left, two-dimensional maps can be produced which reveal interesting information about the antigenic evolution of a pathogen.

Antigenic maps differ from genetic analyses in that they are based on data that reflect the antigenic properties of a pathogen (in this case as revealed by haemagglutination inhibition assay data). There is a close relationship between genetic and antigenic change for human influenza A(H3N2) virus, but genetic distance can be an unreliable predictor of antigenic distance. For example, a change in a single amino acid may cause a disproportionately large change in the binding properties of a virus strain. Antigenic maps can reveal large movements in the antigenic space that may be due to minimal amino acid changes. Antigenic cartography therefore offers the possibility of improved understanding of genetic and antigenic evolution.

Click here for published antigenic data.

A hands-on introduction to antigenic cartography and antibody landscapes

12 - 18 June 2019, Department of Zoology, University of Cambridge

This course will provide an introduction to antigenic cartography and the use of new tools and packages available for performing serological analysis using the R programming language, with no assumed previous programming or computer knowledge. We will first cover the theory and methods behind antigenic cartography as described in Smith et. al 2004*, before exploring how to make antigenic maps from your own data using available antigenic cartography software. Next, after a general introduction to the R programming language, we will shift focus to using simple R code to automate, customize, and visualise your own analyses. The course will conclude with an introduction to Antibody Landscapes as described in Fonville & Wilks et. al, 2014**, and how serological immunity can be modelled in terms of antigenic information to create and analyse profiles of individual and population immunity.

Although focused on applications for serological analysis, the course also aims to give a more general introduction to basic programming concepts and good practice, and by the end of the course you should be comfortable with use of the R language for practical data analysis, including the processes of importing, checking, plotting, analysing and exporting data.

The course will be spread over a total of 7 days, including 5 days of teaching and a 2 day weekend break in the middle to digest and practice the new concepts. The aim is to be as interactive as possible and you will be encouraged to work with each other and try hands-on analysis of your own data throughout. Sample data will be provided for practising. You will need to bring your own laptop running macOS or Linux, unfortunately the software is not yet compatible in Windows. There will be a small number of laptops for those without a Mac or Linux machine, on a first-come first-served basis.

If you would like to register for the course or have any questions, please use the text entry field below to send the message to the author. Please do not forget to write your name and contact details there.


*Smith, D. J., Lapedes, A. S., de Jong, J. C., Bestebroer, T. M., Rimmelzwaan, G. F., Osterhaus, A. D. M. E., & Fouchier, R. A. M. (2004). Mapping the antigenic and genetic evolution of influenza virus. Science, 305(5682), 371–376. http://doi.org/10.1126/science.1097211

**Fonville, J. M., Wilks, S. H., James, S. L., Fox, A., Ventresca, M., Aban, M., et al. (2014). Antibody landscapes after influenza virus infection or vaccination. Science, 346(6212), 996–1000.http://doi.org/10.1126/science.1256427

Last modified: 9 May 2019

Software

Please click here and then click on the Sign Up link on that page, if you would like to use alpha release of our web-based software for making and viewing antigenic maps. Note IE is not supported.

Click to get information about the source code of Acmacs - a library for making antigenic maps

Contact

The Antigenic Cartography Group at the University of Cambridge