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Antigenic Cartography and Antibody Landscapes

A hands-on introduction to antigenic cartography and antibody landscapes
When Jun 12, 2019 10:00 AM to
Jun 18, 2019 05:00 PM
Where Department of Zoology
Contact Name
Contact Phone +44 (0)1223 334872
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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.

*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

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Software

Please click here 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.

Key Publications

Derek J. Smith, Alan S. Lapedes, et al, (2004). Mapping the Antigenic and Genetic Evolution of Influenza Virus Science 305(5682):371-376.

Colin A. Russell, Terry C. Jones, et al, (2008). The Global Circulation of Seasonal Influenza A (H3N2) Viruses Science 320(5874):340-346.

Björn F. Koel, David F. Burke, et al, (2013). Substitutions Near the Receptor Binding Site Determine Major Antigenic Change During Influenza Virus Evolution Science 342(6161):976-979.

J. M. Fonville, S. H. Wilks, et al, (2014). Antibody landscapes after influenza virus infection or vaccination Science 346(6212):996-1000

Colin A. Russell, Judith M. Fonville, et al, (2012). The Potential for Respiratory Droplet–Transmissible A/H5N1 Influenza Virus to Evolve in a Mammalian Host Science 336(6088):1541-1547