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The SARS-CoV-2 pandemic lasted from March 2020 to May 2023 and claimed over seven million lives worldwide. The virus was not eliminated but instead is now considered an endemic pathogen with seasonal spikes. Vaccination and treatment options have reduced hospitalization and mortality, but protection is short lived and continued viral mutations increase risk of reinfection. Further investigation into long lasting vaccination and mechanisms behind SARS-CoV-2 evolution are essential in limiting current or future coronavirus outbreaks. Here we examine how the use of alternative coronavirus antigens, excluding the SARS-CoV-2 Spike protein, alters duration and cross-reactivity of protection. We found that SARS-CoV-2 Nucleocapsid protein limited viral dissemination and provides partial protection against infection. Additionally, vaccination with SARS-CoV Spike protein reduced viral titers upon subsequent SARS-CoV-2 challenge. Afterwards, we evaluated the effect of vaccination on viral evolution. Preexisting immunity did not influence acute viral diversity; however, there was increased viral diversity within the CNS, where we observed negative selection against the furin cleavage site (FCS). Deletion of the FCS altered viral entry and resulted in tissue specific attenuation of SARS-CoV-2. We also found evidence of positive selective pressure for the FCS within the lung, indicating there are compartment specific drivers for viral adaptations. Intrahost adaptations, such as the deletion of the FCS, could explain non-respiratory symptoms seen in COVID-19 and PASC patients. In addition, the compartment specific selective pressures on SARS-CoV-2 may be related to development of variants of concern (VOCs), especially in immunocompromised patients who experience prolonged infections. These finding indicates that alternative Coronavirus antigens, not just from SARS-CoV-2, should be evaluated in pan-coronavirus vaccine development. Furthermore, our data provides insight into the pathways driving long-COVID and generation of VOCs.