Sequence variation in the influenza A virus nucleoprotein associated with escape from cytotoxic T lymphocytes

CD8+ cytotoxic T lymphocytes (CTLs) contribute to the control of viral infections by recognizing peptides of viral proteins presented by MHC class I molecules on infected cells. Some viruses have developed strategies to evade recognition by CTL. One of these strategies involves antigenic variation in CTL epitopes as described for viruses chronically infecting their host like EBV, HIV, HBV and HCV. Here we show three examples of variation in CTL epitopes in the influenza virus nucleoprotein (NP) associated with escape from CTL immunity. The first two involve a mutation at position 384 of the NP, which is the anchor residue of a HLA-B*2705-restricted epitope NP 383-391 (SRYWAIRTR) and the HLA-B*08-restricted epitope NP380-388 (ELRSRYWAI). It was shown that these mutations have arisen in the 1993/1994 season and that these mutant variants completely replaced the virus strains containing the wild-type epitopes. Furthermore, T cell recognition was completely abrogated by the R384G mutation. A third example of variation in an influenza virus CTL epitope was found in a newly identified HLA-B*3501-restricted CTL epitope. This immunodominant epitope exhibited extensive amino acid sequence variation and the variants emerged in a chronological order. Again CTL specific for older variants failed to recognize more recent strains of influenza A virus, indicating an escape from CTL immunity. Thus, in addition to the introduction of mutations in the surface glycoproteins like the hemagglutinin, allowing escape from antibody-mediated immunity, there is now evidence that influenza viruses can escape in a similar way from CTL-mediated immunity.

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