The influenza virus PB1-F2 protein is a novel protein previously shown to be involved in induction of cell death. Here we characterize the expression and the function of the protein within the context of influenza viral infection in tissue culture and a mouse model. We show that the C-terminal region of the protein can be expressed from a downstream initiation codon and is capable of interaction with the full-length protein. Using this knowledge, we generated influenza viruses knocked out for the expression of PB1-F2 protein and its downstream truncation products. Knocking out the PB1-F2 protein had no effect on viral replication in tissue culture but diminished virus pathogenicity and mortality in mice. The viruses replicated to similar levels in mouse lungs by day 3 postinfection, suggesting that the knockout did not impair viral replication. However, while the PB1-F2 knockout viruses were cleared after day 5, the wild-type viruses were detectable in mouse lungs until day 7, implying that expression of PB1-F2 resulted in delayed clearance of the viruses by the host immune system. Based on our findings and on the fact that the PB1 genomic segment was always newly introduced into some pandemic influenza viruses of the last century, we speculate that the PB1-F2 protein plays an important role in pathogenesis of influenza virus infection and may be an important contributor to pathogenicity of pandemic influenza viruses.In the course of a systematic search for influenza virus antigenic peptides presented by major histocompatibility complex class I on the surface of infected cells, a cytotoxic T lymphocyte (CTL) peptide that did not correspond to any of the known standard viral open reading frames was identified (4). Further screening of the influenza virus genome revealed that the peptide corresponded to residues 62 to 70 of an 87-amino-acidlong protein encoded by an alternate reading frame within the PB1 gene (4). The translation of the novel protein starts from nucleotide position 120 in the PB1 genomic segment and is believed to be initiated by ribosomal scanning (4, 13). In view of the fact that the protein is expressed from a second open reading frame (ϩ1) of the PB1 gene, it was named PB1-F2 (4).Further work showed that PB1-F2 is a relatively short-lived protein which is maximally expressed about 5 hours postinfection (4). The protein localizes to both inner and outer mitochondrial membranes, resulting in alteration of mitochondrial morphology, dissipation of mitochondrial membrane potential, and cell death. Knocking out the PB1-F2 open reading frame attenuated the ability of the A/Puerto Rico/8/34 virus to induce apoptosis in immune cells (4). Subsequently, the basic amphipathic helix in the C-terminal region of the PB1-F2 protein was shown to be responsible for its inner mitochondrial membrane targeting (9, 26) and peptides derived from the C-terminal domain were shown to have a cytotoxic effect and to induce formation of nonspecific pores in synthetic bilayer membranes (2).We further recently showed that P...