What epitopes does the human immune system recognize in swine flu?

This forum post contains a summary of our analysis of swine flu epitopes.The definite version (2.0) has been published in PNAS as an open access article, and is attached to this post here. Previous versions are attached to this post as well. The dataset is included as supplemental material on the PNAS website. Additional analyses can be found on the Biohealthbase website at http://www.biohealthbase.org/GSearch/home.do?decorator=Influenza

Abstract

A major concern about the ongoing swine-origin H1N1 influenza virus (S-OIV) outbreak is that the virus may be so different from seasonal H1N1 that little immune protection exists in the human population. In this study, we examined the molecular basis for pre-existing immunity against S-OIV, namely the recognition of viral immune epitopes by T cells or B cells/antibodies that have been previously primed by circulating influenza strains. Using data from the Immune Epitope Database, we found that only 31% (8/26) of B cell epitopes present in recently circulating H1N1 strains are conserved in the S-OIV, with only 17% (1/6) conserved in the hemagglutinin (HA) and neuraminidase (NA) surface proteins. In contrast, 69% (54/78) of the epitopes recognized by CD8⁺ T cells are completely invariant. We further demonstrate experimentally that some memory T cell immunity against S-OIV is present in the adult population and that such memory is of similar magnitude as the pre-existing memory against seasonal H1N1 influenza. Since protection from infection is antibody-mediated, a new vaccine based on the specific S-OIV HA and NA proteins is likely to be required to prevent infection. However, T cells are known to blunt disease severity. Therefore, the conservation of a large fraction of T cell epitopes suggests that the severity of an S-OIV infection, as far as it is determined by susceptibility of the virus to immune attack, would not differ much from seasonal flu. These results are consistent with reports about disease incidence, severity and mortality rates associated with human S-OIV.