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PEDS Advance Access originally published online on July 3, 2009
Protein Engineering Design and Selection 2009 22(9):543-546; doi:10.1093/protein/gzp027
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© 2009 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

This article appears in the following Protein Engineering issue: Computational Methods Special Issue [View the issue table of contents]

The epitope regions of H1-subtype influenza A, with application to vaccine efficacy

Michael W. Deem1,2,3 and Keyao Pan1

1Departments of Bioengineering and 2Physics and Astronomy, Rice University, 6100 Main Street, MS 142, Houston, TX 77005-1892, USA

3 To whom correspondence should be addressed. E-mail: mwdeem{at}rice.edu

The recent emergence of H1N1 (swine flu) illustrates the ability of the influenza virus to create antigens new to the human immune system, even within a given hemagglutinin and neuraminidase subtype. This new H1N1 strain is sufficiently distinct, for example, from the A/Brisbane/59/2007 (H1N1)-like virus strain of influenza in the 2008/09 Northern hemisphere vaccine that protection is not expected to be substantial. The human immune system responds primarily to the five epitope regions of the hemagglutinin protein. By determining the fraction of amino acids that differ between a vaccine strain and a viral challenge strain in the dominant epitope regions, a measure of antigenic distance that correlates with epidemiological studies of H3 influenza A vaccine efficacy in humans with R2 = 0.81 is derived. This measure of antigenic distance is called pepitope. The relation between vaccine efficacy and pepitope is given by E = 0.47 – 2.47 x pepitope. We here identify the epitope regions of H1 hemagglutinin, so that vaccine efficacy may be reliably estimated for H1N1 influenza A.

Keywords: antibody/epitopes/influenza A/swine flu

Received May 28, 2009; revised May 28, 2009; accepted June 3, 2009.


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