Highly conserved influenza A virus epitope sequences as candidates of H3N2 flu vaccine targets

This study focused on identifying the conserved epitopes in a single subtype A (H3N2)—as candidates for vaccine targets. We identified a total of 32 conserved epitopes in four viral proteins [22 HA, 4PB1, 3 NA, 3 NP]. Evaluation of conserved epitopes in coverage during 1968–2010 revealed that (1) 12 HA conserved epitopes were highly present in the circulating viruses; (2) the remaining 10 HA conserved epitopes appeared with lower percentage but a significantly increasing trend after 1989 [p < 0.001]; and (3) the conserved epitopes in NA, NP and PB1 are also highly frequent in wild-type viruses. These conserved epitopes also covered an extremely high percentage of the 16 vaccine strains during the 42 year period. The identification of highly conserved epitopes using our approach can also be applied to develop broad-spectrum vaccines.

► Sequence conservation of 7690 protein sequences of A/H3N2 viruses were analyzed.
► A total of 32 conserved epitopes were identified in four viral proteins.
► Conserved epitopes were highly present in circulating viruses during 1968–2010.
► Conserved epitopes showed high identities among flu vaccine strains during 42 years.
► Our results revealed the candidates of broad-spectrum epitope-based vaccine targets.