Most of the recent viral outbreaks were caused by highly mutating RNA and single stranded DNA viruses. The availability of safe and effective rapid response vaccines early on in an epidemic situation, along with good vaccine delivery systems, is critical for pandemic response plans. Additionally, immunodominance patterns in the host response to epitopes in vaccine antigens can complicate immune responses to vaccines. In this thesis, using porcine circovirus type 2 (PCV2) as a model, we have focused on changing viral immunodominance patterns to rationally improve vaccine efficacy. We hypothesized that rational alteration of the immunodominant decoy epitope would remove nonprotective antibody response and improve the overall quality of neutralizing antibodies. As hypothesized, the antibody response to the target immunodominant epitopes were abrogated in the vaccinated pigs, and they were protected upon with the challenge of a heterologous strain PCV2d. To ensure the safety of the rationally restructured PCV2 vaccine, we have developed novel strategy to ensure suicidal replication of the vaccine virus in vivo. We hypothesized that recoding serine and leucine codons of the PCV2 capsid gene will increase the probability of accumulating stop mutations during viral replication. As expected, immunized pigs with the suicidal vaccine, protected them against PCV2d heterologous challenge. Furthermore, subjecting the suicidal vaccine construct to in vitro immune pressure with sub-neutralizing serum, resulted in an accumulation of stop mutations and abortive replication. Finally, using porcine epidemic diarrhea virus (PEDV) as a model, we have developed an effective oral delivery system for a rapid response vaccine. Treatment of PEDV with heat to denature the capsid, followed by RNase to fragment the RNA genome, resulted in a minimally replicative vaccine which was highly effective in weanling piglets. Here, we determined treatment conditions to either completely inactivate or rapidly attenuate PEDV. To improve oral delivery of the vaccine to sows, biodegradable niosome formulation composed of edible lipid, cholesterol, and charge stabilizer was optimized. The antigen loading capacity of the niosome was over 80% with minimal cellular cytotoxicity. In summary, the methods described in this thesis have addressed three major gaps in vaccinology and have broad applicability in the field.