Flu vaccines come in either a shot or nasal spray formula. They cause antibodies to develop in the body that help protect against infection, and it takes about two weeks for the vaccination to start working. There are three common flu viruses: influenza B, influenza A (H1N1), and influenza A (H3N2). Each year, one flu virus of each kind is used to make flu vaccines. Yet, as stated before this newer strain isn't really protected by the current vaccine.