We have produced a series of plant viruses that have epitopes from proteins of H1N1. The epitopes have different sizes but none are more than 40 aa. All of the epitopes have been added to the c-terminal of a plant virus protein, so they don't have their own start or stop codons, obviously. The problem is that our western blot with antibody against H1N1 cannot label anything on the membrane, maybe because it doesn't recognize the epitopes.
Computational analysis show that the epitopes must be outside the surface, however I don't think it would make a difference since we are doing wb.
We have not added any whole gene of H1N1 into our plasmid. Do you think it is more likely to be detected by the antibody if a bigger portion of the protein is present? Suggestions will be appreciated.