PB1-F2 gene in influenza a viruses of different hemagglutinin subtype.

The second ORF frame (+1) of PB1 polymerase gene of Influenza A virus (IAV) encodes the PB1-F2 protein. The length of PB1-F2 encoded by the A/Puerto Rico/8/34 (H1N1) (PR8) virus is 87 aa. The analysis of nucleotide sequences of PB1 gene of 626 IAV isolates available in GenBank and Influenza Sequence Database revealed that this gene has mostly the capacity to encode a putative protein of 90 aa. The predicted extra three amino acids in the 90-aa PB1-F2 are to a great extent conservative. Some IAV isolates, particularly human, avian and swine with hemagglutinin (HA) of H1 subtype can potentially encode a C-terminally truncated PB1-F2 of various lengths. The C-terminally truncated PB1-F2 in H1 isolates is lacking the region responsible for mitochondrial targeting and apoptosis. About 50% of avian isolates of H9 subtype possess an ORF for truncated PB1-F2. Eighteen aa, 10 at the N-terminus and 8 at the C terminus are strictly conservative in all 148 human isolates.